Derangements to the functioning of calcium-regulating organs have been associated with type 2 diabetes mellitus (T2DM), a condition preceded by pre-diabetes. Type 2 diabetes has shown to promote renal calcium wastage, intestinal calcium malabsorption and increased bone resorption. However, the changes to the functioning of calcium-regulating organs in pre-diabetes are not known. Subsequently, the effects of diet-induced pre-diabetes on the functioning of calcium-regulating organs in a rat model for pre-diabetes was investigated in this study. Male Sprague Dawley rats were separated into two groups : non-pre-diabetic (NPD) group and a diet-induced pre-diabetic (DIPD) group for 20 weeks. After the experimental period, postprandial glucose and HOMA-IR were analysed in addition to plasma and urinary calcium concentrations. Gene expressions of intestinal vitamin D (VDR), intestinal calbindin-D9k, renal 1-alpha hydroxylase and renal transient receptor potential vanilloid 5 (TRPV5) expressions in addition to plasma osteocalcin and urinary deoxypyridinoline concentrations were analysed at week 20. The results demonstrated significantly increased concentrations of postprandial glucose, HOMA-IR and urinary calcium in addition to unchanged plasma calcium levels in the DIPD group by comparison to NPD. Renal TRPV5, renal 1-alpha hydroxylase, intestinal VDR and intestinal calbindin-D9k expressions were increased in the DIPD group by comparison to NPD. Furthermore, plasma osteocalcin levels were increased and urine deoxypyridinoline levels were decreased in the DIPD group by comparison to NPD. These observations may suggest that calcium-regulating organs compensate for the changes to calcium homeostasis by inducing increased renal calcium reabsorption, increased intestinal calcium absorption and decreased bone resorption followed by increased bone formation. Urban lifestyle and the chronic consumption of diets which contain high fat and carbohydrate content has shown to promote the development of type 2 diabetes mellitus (T2DM), a condition which is preceded by pre-diabetes . Pre-diaFluxes of calcium between the small intestine, bone and kidney are controlled by parathyroid hormone (PTH), calcitonin and calcitriol . CalciumPrevious studies in our laboratory developed a high fat high carbohydrate (HFHC) diet-induced pre-diabetic animal model which mimics the human condition of pre-diabetes , 10. Sevad libitum. An experimental acclimatization interval of one week was carried out, whereby the rats were fed standard rat chow  and tap water, prior to the induction of pre-diabetes  were bred and housed at the University of KwaZulu-Natal’s Biomedical Research Unit (BRU). The protocol for animal experimentation and conditions were followed according to the Animal Research Ethics Committee of the University of KwaZulu-Natal (ETHICS#: AREC/00003627/2021). Procedures involving animals care were conducted in conformity with the institutional guidelines for animal care of the University of KwaZulu-Natal. The animals were maintained under standard conditions of a constant room temperature (22± 2°C), carbon dioxide content (<5000 p.m.), relative humidity (55± 5°C) and illumination . The noise levels in the room were maintained below 65 decibels and the animals had access to rat chow and water diabetes .The primary outcome was evaluation of intestinal calcium transport, renal calcium transport and bone turnover. The secondary outcome was evaluation of body calcium status, glucose tolerance and insulin resistance. Intestinal calcium transport was measured by evaluating intestinal VDR and intestinal calbindinD9k expression. Renal calcium transport was measured by evaluating renal TRPV5 and renal 1-alpha hydroxylase expression. Bone turnover was measured by evaluating plasma osteocalcin and urine deoxypyridinoline levels. Body calcium status was measured by evaluating plasma calcium and urine calcium levels. Glucose tolerance and insulin resistance was measured by evaluating OGTT, plasma insulin and HOMA-IR.The rats were randomly assigned following simple randomisation procedures (computerised random numbers) to 1 of 2 two groups  and fed their respective diets for an experimental period of 20 weeks. Six rats per group were the minimum amount of animals needed to achieve statistical significance according to the resource method equation . ExperimThis study comprised of two groups, namely a diet-induced pre-diabetic (DIPD) group and non-pre-diabetic (NPD) group . The animals that consumed the standard rat chow for 20 weeks and did not have pre-diabetes were regarded as the NPD group, whereas the animals that consumed the HFHC diet for the same number of weeks and diagnosed with pre-diabetes, were regarded as the DIPD group. Baseline OGTT and HOMA-IR could not be performed due to analysis being limited to changes in glycaemic parameters at week 20 after dietary intervention, in addition blood samples were not obtained at baseline.At week 20, an OGTT was conducted following glucose loading, to determine the glucose tolerance response of animals subjected to the chronic ingestion of the HFHC diet. The OGT responses were monitored in the animals according to a well-established protocol , 10, 15.via a gas anaesthetic chamber . While the rats are unconscious, blood was collected by cardiac puncture and then injected into individual pre-cooled heparinized containers. The blood was centrifuged  at 4°C, 503 g for 15 minutes. Plasma was separated from blood and stored at -70°C in a Bio Ultra freezer  until biochemical analysis as previously described by At the end of the experimental period, all animals were housed individually in Makrolon polycarbonate metabolic cages  for a 24-hour urine collection period. After the 24-hours, urine samples from all animals were collected and stored in a Bio Ultra freezer  at -80°C, thereafter the animals were anaesthetized with Isofor 100 mg/kg)  Ltd, Roodeport, South Africa) for 3 minutes 0 mg/kg (The homeostatic model assessment (HOMA) was used to measure insulin resistance from fasting blood glucose and insulin levels . The HOMPlasma calcium, urinary calcium and creatinine concentrations were measured with an autoanalyzer . The plasma insulin, plasma osteocalcin and urinary deoxypyridinoline concentrations were measured using separate specific ELISA kits according to the manufacturer’s instructions .® 2-Step RT-qPCR System as a cDNA synthesis kit  as described by the manufacturer.The harvested kidney and small intestine tissue was subjected to RNA extraction using a ReliaPrep tissue Miniprep system . The purity and concentration of RNA was determined by Nanodrop 2000 . A purity ratio (A260/A280) of 1.7-2.1 was considered acceptable for conversion to cDNA. Synthesis of cDNAs was performed by reverse transcription reactions with 2 μg of total RNA using GoTaq-ΔΔCt relative quantication method.The ROCHE light cycler SYBR Green I master mix was used for amplication according to the manufacturer’s instructions on the ROCHE light cycler system. The primer sequences  used in this study can be found in All data was expressed as mean ± S.E.M. Statistical comparisons were performed with Graph Pad InStat Software  using the student t test. A value of p < 0.05 was considered statistically significant.The OGTT and Area under curve (AUC) were analysed in the non-pre-diabetic (NPD) group and diet-induced pre-diabetic (DIPD) group after the experimental period . The results Figure 1The HOMA-IR values were calculated from the fasting plasma glucose and insulin concentrations after the experimental period . The results Table 2 Plasma and urinary calcium concentrations were analysed in the non-pre-diabetic (NPD) group and diet-induced pre-diabetic (DIPD) group after the experimental period . The results Figure 2Plasma osteocalcin and urine deoxypyridinoline concentrations were analysed in the non-pre-diabetic (NPD) group and diet-induced pre-diabetic (DIPD) group after the experimental period . The results Figure 3Renal Transient receptor potential cation channel subfamily V5 (TRPV5) gene expression was analysed in the non-pre-diabetic (NPD) group and diet-induced pre-diabetic (DIPD) group after the experimental period . The results Figure 4Intestinal vitamin D receptor (VDR) gene expression was analysed in the non-pre-diabetic (NPD) group and diet-induced pre-diabetic (DIPD) group after the experimental period . The results Figure 5Several studies have shown that the functioning of calcium-regulating organs are disturbed in T2DM , 19. HowPre-diabetes is characterised as a combination of impaired glucose tolerance (IGT) and impaired fasting glucose (IFG) which can be attributed to moderate insulin resistance in insulin-dependent tissues . Blood gCalcium plays a crucial role in various physiological processes and plasma calcium levels are kept within a narrow range through the interplay of calcium-regulating organs . CalciumThe kidneys contribute to calcium homeostasis by adjusting the reabsorption and excretion of filtered calcium . DisturbRenal-1 alpha hydroxylase is mainly expressed in the proximal convoluted tubules and is the key enzyme involved in the synthesis of calcitriol . DisturbIntestinal calcium absorption is a crucial physiological process for maintaining calcium homeostasis . The smaBone regulates plasma calcium levels by releasing calcium through a process known as bone resorption and storing calcium through a process known as bone formation . Bone foThe findings elucidated in this study may have the potential to provide an understanding into the physiological processes that occur in calcium-regulating organs during pre-diabetes. From a clinical perspective, pre-diabetes is asymptomatic and many people progress towards the development of T2DM due to being unaware. The findings of this study will not only add to academic knowledge but may serve as a novel marker in the identification of pre-diabetes. This study targets some of the complications and disrupted processes involved in T2DM. Furthermore, these findings may provide an early insight into the pathogenesis involved in the associated complications of T2DM. A future prospective would be to use these findings as insights to understand the possible changes that may occur to pre-diabetic humans.It is evident that during the pre-diabetic state there are changes to the functioning of calcium-regulating organs which compensate for disturbances to plasma calcium levels. This was made evident by increased urinary calcium levels along with increased expressions of renal TRPV5, renal 1-alpha hydroxylase, intestinal VDR and intestinal calbindinD9k. In addition, there was increased plasma osteocalcin and decreased urinary deoxypyridinoline concentrations along with unchanged plasma calcium in the pre-diabetic state. The normocalcaemia present in the pre-diabetic state may have been conserved due to increased renal calcium reabsorption, increased renal vitamin D activation, increased intestinal calcium absorption and increased bone formation followed by decreased bone resorption.Taken together, calcium-regulating organs compensate for renal calcium wastage and are aimed at maintaining normocalcaemia in HFHC diet-induced pre-diabetes. The effects associated with pre-diabetes on calcium-regulating organs are directed towards promoting increased renal calcium reabsorption, increased renal vitamin D activation, increased intestinal calcium absorption and decreased bone resorption followed by increased bone formation. This was evidenced by increased expression of renal calcium transport markers and intestinal calcium transport markers in addition to increased osteocalcin and decreased deoxypyridinoline levels. Collectively, these observations may suggest that calcium-regulating organs compensate for the changes to calcium homeostasis in the pre-diabetic state.A limitation of the study was the lack of blinding during the diet intervention stage and the lack of baseline measurement for hepatic and muscle insulin resistance marker (OGTT and HOMA-IR). A second limitation to this study is that it only focuses on mRNA expression and not proteins.In future, a further insight into the mechanisms in which bone turnover by-products participate in glucose homeostasis in the pre-diabetic state should be investigated.The original contributions presented in the study are included in the article/This animal study was reviewed and approved by the Animal Research Ethics Committee (AREC) of the University of KwaZulu-Natal, Durban, South Africa (AREC/00003627/2021).KN contributed to the study design, conducted the experiments, collected, analysed and interpreted data as well as being involved in writing the manuscript. PN and AK was involved in the conceptualization of the study, study design and editing of the manuscript as well as provide funding. All authors have read the manuscript and approved its submission.This study was funded by the UKZN College of Health Science and the National Research Foundation under the grant number (UID130598).The co-author AK of this manuscript is the editor of the Frontiers Journal Thieme (Pre-diabetes and endocrine function)The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.


Psychiatric readmissions cause a burden on the healthcare system, incur a monetary cost and cause additional distress to acutely unwell patients. This project explores the use of the free-text of electronic patient records to predict inpatients in psychiatric hospitals at risk of readmission using predictive models generated by machine learning.Free-text was extracted from the electronic patient records of patients admitted to hospitals in Birmingham and Solihull Mental Health Foundation Trust (BSMHFT) during the five years 2015–2019 inclusive. The anonymised records were obtained via the CRIS  database. A total of 17208 records were extracted.The free-text entered by clinicians during an admission was extracted and processed using techniques of natural language processing to generate input vectors suitable to be used with machine learning algorithms. tf-idf (term frequency-inverse document frequency) vectors were used.A selection of algorithms were used to train predictive models. Two-thirds of the records were used as training data with the remainder as test data. Baseline model performance was assessed and then best-performing candidates underwent hyperparameter optimisation using five-fold cross-validation to improve performance. Bayesian optimisation was used to automate hyperparameter tuning during cross-validation. Hyperparameters were optimised on the log loss function. As the dataset was imbalanced with negative instances outnumbering positive instances to a significant degree, various techniques such as random undersampling of negative instances in the training data were used to deal with class imbalance throughout this process. Following cross-validation, the best-performing models underwent performance analysis.Models were used to make predictions on the test data. Performance was assessed using F1-measures, precision-recall curves and the average precision metric . These metrics were chosen due to their suitability in assessing models trained on imbalanced datasets.The best F1 score obtained was 0.233 using a Random Forest model trained using unigram tf-idf vectors of 500 token dimension.The best average precision obtained was 0.157 using a Support Vector Machine trained using unigram tf-idf vectors of 2000 token dimension.Both the above results required the use of random oversampling of positive instances to improve performance on the imbalanced dataset.The performance indicates that the models generated are unlikely to have significant practical utility. Nevertheless, this exploratory project has produced a processed dataset with knowledge about its characteristics. This could be used for the further development of models using more complex techniques such as language modelling using neural networks.


Pandemic Electronic Benefits Transfer (P-EBT) benefits were intended for families of school children who lost access to free or reduced-price school meals (FRPMs) during the COVID-19 pandemic-related school closures. In high-poverty communities, all students from schools participating in the Community Eligibility Provision (CEP) were automatically eligible for P-EBT benefits; in non-CEP schools, only students already participating in FRPMs—for which their parents submitted an individual application—were eligible for P-EBT benefits. Using publicly available data from 105 K-12 public schools located in 4 sizeable low-income New Jersey (NJ) cities, this study investigated the association between school CEP participation status and the reach of P-EBT benefits for eligible students. A generalized linear model with a logit link, a binomial family, and robust standard errors was used. Across all levels of FRPM eligibility based on students’ household income, as expected, almost all students from CEP schools received P-EBT benefits; significantly fewer received P-EBT benefits if they attended non-CEP schools, even when they were eligible for FRPMs. Our findings show that without changes to the qualification process for CEP, large numbers of eligible children will not receive the intended health benefits of federal meals programs or similar emergency relief initiatives. Expanding CEP eligibility and simplifying the process through which schools qualify would likely improve the uptake of federal meals programs and emergency interventions, and more effectively achieve their intent. Prior to the COVID-19 pandemic, 30 million school-age children participated in the USDA’s National School Lunch Program (NSLP) and over 14 million participated in the School Breakfast Program (SBP) every day . To encoCOVID-19 restrictions compelled immediate federal action to address the challenges of providing meals to students in the face of extended school closures. For instance, the US Congress approved the provision of the Pandemic Electronic Benefits Transfer (P-EBT) program, which allowed state agencies to provide financial assistance for food purchases to households that had lost access to FRPMs for their children because of school closures . All stuWe examined the distribution of P-EBT benefits during the first 6 months of the COVID-19 pandemic using data from all public schools located in 4 large NJ cities  with predominantly lower-income populations  . De-idenCEP participation status (SY 2019–2020) for all public schools in the study cities was obtained using Open Public Records Act requests from the New Jersey Department of Education.The school-level characteristics were obtained from the Common Core of Data for SY 2019–2020 from the National Center for Education Statistics (NCES). The main variables of interest from the NCES data were total school enrollment and total number of students eligible for FRPMs. These two variables were used to calculate the proportion of students eligible for FRPMs. Other variables drawn from the NCES were the race/ethnicity of enrolled students and the school level .margins post-estimation command returned the predicted proportion of students enrolled who received P-EBT benefits by school CEP status at different levels of FRPM eligibility. This study was deemed to be exempt by the Arizona State University and Rutgers Institutional Review Boards as it was entirely based on aggregate-level, de-identified, publicly available data.The analyses were limited to 105 public schools that had complete information on CEP participation status and P-EBT distribution and were conducted using Stata 17. To model the proportion of students who received P-EBT benefits, a generalized multivariable linear model with a logit link, a binomial family, and robust standard errors  was usedLess than half (44%) of the schools in the sample participated in CEP , despiteAt the onset of the pandemic, a lack of access to school meals likely contributed to a rapid increase in food insecurity among families with children ,8. The pThe recently introduced Child Nutrition Reauthorization bill—the Healthy Meals, Healthy Kids act—includes a provision for summer EBT cards to ensure families have access to resources aimed at providing nutritious meals for children when schools are closed during the summer. However, the process of qualifying for benefits replicates the experience of P-EBT distribution; as a result, unless efforts are made to increase CEP participation among eligible schools, a significant number of children from low-income families will miss out on benefits that can improve their nutrition and wellbeing simply because their CEP-eligible school did not participate in CEP.One limitation of the current study was that it was based on a sample of New Jersey public schools located in predominantly lower-income areas; therefore, the findings may differ in other contexts or states. Additionally, while we had data on the receipt of P-EBT benefits, we did not have information on how families actually utilized these benefits.Expanding CEP eligibility and simplifying the process through which schools qualify would likely improve the uptake of federal meals programs and emergency interventions that rely on school meals eligibility criteria.


Ultrafast high-brightness X-ray pulses have proven invaluable for a broad range of research. Such pulses are typically generated via synchrotron emission from relativistic electron bunches using large-scale facilities. Recently, significantly more compact X-ray sources based on laser-wakefield accelerated (LWFA) electron beams have been demonstrated. In particular, laser-driven sources, where the radiation is generated by transverse oscillations of electrons within the plasma accelerator structure  can generate highly-brilliant ultrashort X-ray pulses using a comparably simple setup. Here, we experimentally demonstrate a method to markedly enhance the parameters of LWFA-driven betatron X-ray emission in a proof-of-principle experiment. We show a significant increase in the number of generated photons by specifically manipulating the amplitude of the betatron oscillations by using our novel Transverse Oscillating Bubble Enhanced Betatron Radiation scheme. We realize this through an orchestrated evolution of the temporal laser pulse shape and the accelerating plasma structure. This leads to controlled off-axis injection of electrons that perform large-amplitude collective transverse betatron oscillations, resulting in increased radiation emission. Our concept holds the promise for a method to optimize the X-ray parameters for specific applications, such as time-resolved investigations with spatial and temporal atomic resolution or advanced high-resolution imaging modalities, and the generation of X-ray beams with even higher peak and average brightness. In particular, transverse (betatron) oscillations of electrons during acceleration in these plasma structures can generate ultrashort high-brightness X-ray pulses via synchrotron emission  from a millimeter-scale interaction length3. Laser-driven betatron sources have matured to an extent suitable for use in applications in many research fields8. Their high brilliance enables advanced imaging methods and due to the ultrashort X-ray pulse duration and the intrinsic synchronization to the driving laser, these sources are ideal tools to investigate ultrafast dynamics10. The comparably compact footprint and simple setup of these sources allows variable experimental geometries, including the potential for multiple time-synchronized X-ray pulses, at different wavelengths and at different incident angles for multi-probe diagnostics or single-shot tomography. This holds the promise of widespread availability for applications in diverse fields ranging from medical imaging and structural biology to chemistry, physics and materials science.Relativistic electron bunches can generate tunable high-brightness X-ray pulses via synchrotron emission. The generation of electron beams with relativistic energies typically requires kilometer-scale facilities. Recently, significantly more compact X-ray sources have been demonstrated using laser-wakefield accelerated (LWFA) electron beams11. Subtle laser characteristics, such as a pulse front tilt were used to enhance the X-ray radiation12, manipulate the polarization13 and spectrum14. An increase in photon flux has been shown by using lasers with a high pulse energy17. A higher conversion efficiency has been demonstrated by using clustered gas targets18 and the transverse deflection of the injected and accelerated electron beam through transversally offsetting the accelerating plasma structure by laser-electron-beam interactions19 or a modulated gas density profile21.However, routine operation of these sources requires control over the source parameters, improvements in reproducibility and an increased laser-to-X-ray conversion efficiency. The latter is of particular importance for a potential reduction in the peak power of the driver laser, allowing for future sources with higher average flux at higher repetition-rate. Experiments have demonstrated that the X-ray spectrum can be enhanced through the direct interaction of the driver laser with the accelerating electrons22. The injection is controlled through a density downramp following the first peak, leading to a copious amount of electrons that are transversely injected with a longitudinally-correlated phase. As a result, the injected electrons perform coherent betatron oscillations similar to those in a permanent-magnet wiggler during a density depression and in a second density peak. The density depression between the peaks and the density upramp of the second peak results in a nearly constant kinetic energy of the oscillating electrons (see section Particle in Cell (PIC) Simulations), leading to an increased X-ray brightness. While for certain combinations of plasma densities and laser intensities, transverse injection due to laser evolution also occurs in flat-top gas jets as was shown in simulations23, our tailored plasma density profile enables control over these processes. Furthermore, it extends the length over which betatron radiation is emitted due to an increased laser depletion length of the lower integrated plasma density compared to a flat-top profile.Here we experimentally demonstrate a method to significantly enhance the radiation characteristics by manipulating the amplitude of the betatron oscillation during the electron injection process in a proof-of-principle experiment. Our approach is based on the evolution of the laser pulse into a highly asymmetric temporal shape see Fig. a. This, 21 or near the gas jet exit19. This enables the control of multiple degrees of freedom and the potential for additional significant enhancement through emission from many more betatron oscillation periods, further increasing the X-ray brightness and laser-to-X-ray conversion efficiency. We demonstrate that the X-ray properties can be modified through the manipulation of the betatron oscillation amplitudes by varying the plasma density profile.We were able to significantly enhance the generated number of X-ray photons when compared directly to targets with a flat-top density profile under identical laser conditions. In our concept, the coherent oscillations are initiated close to the gas jet entrance, unlike other methods where increased betatron oscillation amplitudes are achieved by manipulating the already injected and accelerated electron beam well into the gas jet24 perform transverse betatron oscillations during acceleration due to off-axis injection and a linear transverse restoring force26. The transverse acceleration causes betatron synchrotron emission into a narrow forward cone. The wiggler-like spectrum is characterized by the critical photon energy, which is given by27h and the speed of light c. In the bubble regime, the electron deflection parameter K is given bye the electron charge, m the electron mass and Electrons in LWFAs operating in the self-injection “bubble” regimeWe compare the betatron emission from different plasma density profiles, including an approximately 7-mm-long double-peaked “M”-shaped profile .We have performed two-dimensional PIC simulations with EPOCH31. This field distribution causes a transverse asymmetry in the bubble shape . Due to the increase in the bubble phase velocity, only a small fraction of electrons at the head slowly loose energy as they are propagating in a decelerating phase, while a large fraction of electrons are accelerated and gain energies similar to that of the bunch front. This leads to high-brightness X-ray betatron emission from electrons that perform coherent large-amplitude betatron oscillations with almost constant kinetic energy over a long propagation distance in the radiator section. Eventually, the laser pulse is nearly fully depleted and a bubble is driven by the injected electron bunch. The generated radiation for this density profile is significantly enhanced compared to flat-top gas jets. Both, the experimentally observed X-ray and electron beam properties agree well with the simulated kinematics of this process.The simulations of the M-jet  show a significant laser pulse evolution during the first density peak resulting in complex dynamics of the bubble boundary. This leads to electron injection with specific initial conditions, in particular a large longitudinally-correlated transverse momentum. As a result, the injected electrons perform collective large-amplitude betatron oscillations during the subsequent propagation Fig. . In the ape Fig. b22. The ane Fig. . Due to ane Fig. k22,23. TWe have also simulated the comparison between the different jet density profiles. The charge in an area near the laser propagation axis  Simulations, where the laser self-evolves during the first density peak into a highly asymmetric longitudinal shape. During the downramp of the first jet, electrons are transversally injected and X-rays are mostly generated throughout the density depression and the second density peak. Some of the injected charge is likely lost during the interaction. The M-jet combines the features of the other jets, namely the transverse injection of the 4 mm jet with the long emission length of the 6 mm jet for X-ray generation that is enhanced by the large betatron oscillation amplitude and by the density profile that allows X-ray emission over an extended length. While in the experiment it was not possible to measure the effect of only one of the density peaks, the 4 mm jet (at lower density) shows a qualitatively similar behavior to that of only the first density peak. These dynamics are consistent with simulations  generation regime that enables significant enhancement of laser-driven betatron radiation. In particular, we observe the generation of significantly more X-ray photons compared to standard targets using the same laser parameters. The X-ray source parameters are enhanced through manipulating the amplitude of the transverse betatron oscillations by using a laser pulse with a highly asymmetric temporal shape that has a nearly step-like rise. This leads to off-axis electron injection and coherent betatron oscillations, similar to those in a permanent-magnet wiggler. The source can be decomposed into three sections: (i) laser pulse shaping, (ii) electron injection and (iii) radiation generation. We demonstrate that this can be realized using a tailored plasma density profile. While longitudinally tailored density profiles have been used to improve the electron beam quality37 to extend distance over which radiation is emitted. Conversely, the plasma profile can also be optimized to generate beams with higher average brilliance using lasers with lower peak power, operating at higher repetition rates.The method can be extended to readily optimize the X-ray properties for specific applications. The plasma density profile enables control of multiple X-ray properties, including photon energy, number of generated photons and spectral intensity. The method also has the potential to adjust source properties, such as source size, beam divergence and likely pulse duration to the requirements of the specific application. Our concept has the potential for even further enhancement and control of the X-ray parameters and conversion efficiency. We expect that the X-ray beams can be scaled to higher peak brilliance through modifications in the plasma profile, by a higher-power driver laser or by using laser-generated electron bunches as driversThe control and enhancement of X-ray parameters is of particular importance for the development of future variable and tunable compact, high-repetition rate X-ray sources that can be readily used in applications.28E the photon energy and F is the modified Bessel function of the second kind. The amplitudes 38 to determine the confidence intervals via a statistical approach.The X-ray spectrum is diagnosed by the transmission through a filter array consisting of Mylar, Al, V, Ti, Co, Fe, Zn, Cu, Zr, Mo, Pd, Ag, Sn and an Andor iKon-L SO X-ray CCD. The camera is shielded by a thin Al foil to minimize any optical background contamination. A Pb filter is used to determine any background. The filters were placed 1.9 m from the source and 0.75 m from the detector. The beamline filters and the quantum efficiency of the detector limited the spectral observation range to 2.7–30 keV . The X-ray spectrum was deduced from least-square fitting of the transmitted signal through each filter, taking into account the transmission through additional beamline filters and the quantum efficiency of the detector (for detailed description see below). To account for the broad electron energy spread and the changing energy of the emitting electrons during the acceleration process, the spectral intensity was constrained to a sum of synchrotron spectra given by38 and to determine asymmetric point-wise confidence bands. Specifically, for each photon energy value we find the 1-sigma distribution around our best fitting model, which is indicated as confidence bands in Fig. We extract the X-ray spectra from the measured absorption filter transmission using a forward-propagation fitting method. To this end we first process the camera images using a despeckling algorithm to eliminate hot pixels, reduce the measured constant background given by the Pb filter transmission and perform a background gradient normalization using the direct beam in-between filters to account for beam nonuniformities. Experimental measurements for each absorption filter material are extracted by averaging the transmitted signal over the corresponding detector regions taken close to beam center. Standard deviations within these regions, prior to image processing, are used for measurement uncertainty estimates with appropriate scaling to account for image correction. The X-ray spectra are extracted via a Forward-Fitting Monte Carlo (MC) method. As input spectra, we assume a model constrained to a sum of synchrotron spectra given by Eq. . We use entclass1pt{minimaSupplementary Information 1.Supplementary Information 2.


Lung cancer classification and treatment has been revolutionized by improving our understanding of driver mutations and the introduction of tumor microenvironment (TME)-associated immune checkpoint inhibitors. Despite the significant improvement of lung cancer patient survival in response to either oncogene-targeted therapy or anticancer immunotherapy, many patients show initial or acquired resistance to these new therapies. Recent advances in genome sequencing reveal that specific driver mutations favor the development of an immunosuppressive TME phenotype, which may result in unfavorable outcomes in lung cancer patients receiving immunotherapies. Clinical studies with follow-up after immunotherapy, assessing oncogenic driver mutations and the TME immune profile, not only reveal the underlying potential molecular mechanisms in the resistant lung cancer patients but also hold the key to better treatment choices and the future of personalized medicine. In this review, we discuss the crosstalk between cancer cell genomic features and the TME to reveal the impact of genetic alterations on the TME phenotype. We also provide insights into the regulatory role of cellular TME components in defining the genetic landscape of cancer cells during tumor development. However, during the last three decades, we have witnessed a significant decline in lung cancer mortality that can be attributed to (i) the reduction of smoking, (ii) the promising developments in early diagnosis and (iii) new therapeutic modalities , EGFR, anaplastic lymphoma kinase (ALK), TP53 and liver kinase B1 (LKB1) as the most commonly mutated genes  caused by genetically transformed cancer cells, which by their unlimited proliferation properties, fuel local and systemic cancer development and progression . Subsequed genes . In numeed genes .However, the cancer-cell-based classification of any given tumor is too simplistic to explain or predict tumor behavior and its clinical response to treatment. A tumor is not just composed of genetically transformed cancer cells, but also contains multiple other types such as immune, stromal, and endothelial cells. This creates a unique environment, in which oxygen supply, availability of metabolites and pH are subject to tremendous fluctuations . Importareg) cells, and (ii) anti-tumorigenic immune effector cells, such as anti-tumor M1-macrophages, cytotoxic CD8+ T cells and natural killer (NK) cells  cells . The relK) cells . AlthougK) cells . TherefoFrom the genetic point of view, the TME is a heterogeneous niche that contains a mixture of differentially mutated cancer cells, which give rise to the distinct cancer cell populations (clones) with their unique genomic landscapes . DarwiniInteractions between organisms (i.e. cells) can be viewed as a game with multiple players and evolutionary game theory has been used to investigate the consequences of their interactions. According to the evolutionary game theory, the fitness of the selected cancer cell clones within the dynamic, complex and heterogeneous TME is not only associated with the individual cancer cell benefit but also essentially depends on the crosstalk of clones with other clones and cellular components of the TME .By applying the crosstalk scenario, we can advance the successive clonal evolution model of Peter Nowell, which did not fully consider the association of the non-genetic variability of immune / stroma cells and the potential functional crosstalk between clones and TME components . A tumorDuring the clonal evolution of the initial cancer cells, some of the daughter cells acquire stepwise additional somatic mutations. The sequential, subclonal selection not only favors cells with better autonomous proliferation capacities, but also selects cancer cells with the ability to transform the normal into a tumor microenvironment by reprogramming residential stroma or immune cells as well as newly recruited immune cells . NormallOne argument supporting this concept is the observation that tumor doubling times (around 60–200 days) is orders of magnitude slower than cancer cell doubling times (around 1–2 days). This argues for a suppressive function of the NME and as a result the majority of cancer cells usually die before they can divide and establish a tumor mass .One of the key clinical observations in support of the relation between the genomic landscape of lung cancer cells and the TME is the association with tumor mutational burden (TMB), defined as the number of non-synonymous somatic mutations per megabase of tumor DNA, and the outcomes in patients treated with immunotherapy . RecogniKRAS and TP53, are characterized by a high TMB and numerous somatic mutations, which are associated with increased tumor immunogenicity  foster the idea that the cancer cell genomic landscape and the TME phenotype interact with each other.KRAS mutations are the most frequent oncogenic driver mutations in human lung cancer cells –17-producing T helper (Th)17 cells and CD4+FoxP3+ Treg cells has been found  and tumor suppressor genes  and how they relate to alterations in the TME. er cells . Until ver cells . KRAS muer cells . Specifien found . This raKRAS is a small GTPase and an activator of MAPK pathways . It has As NF-κB-binding sites are found in the enhancers and promoters of numerous immunoregulatory genes , it is nreg cells while the CD8+ T-cell responses increases  to induce the phosphorylation of the transcription factor signal transducer and activator of transcription 3 (STAT3) which is found in immune components such as macrophages of the TME  are under complex control of ‘master cytokines’ such as IL-1α or IL-1β, which can induce the transcriptional and post-transcriptional expression of all of these factors simultaneously through a network of signaling pathways and transcription factors (including the NF-κB system) in multiple normal as well as cancer cells from both mice or humans . The IL-reg numbers and activities whereas in IL-1RA-deficient mice enhanced accumulation and activity of myeloid-derived suppressor cells were found, both resulting in suppressed antitumor immunity. In mice lacking IL-17, the study showed reduced tumor progression along with improved T cell function. These data provided evidence for a critical and unique role of IL-1 in upregulating cytokines (e.g. IL-17) and in determining the balance between inflammation and antitumor immunity in specific tumor microenvironments such as in the lung  cells and supported antitumor immunity by activated CD8+ lymphocytes expressing IFNγ, TNFα, and granzyme B. These T cells infiltrated tumors and induced their regression. Treating mice first with anti-IL-1β antibodies followed by anti-PD-1 antibodies completely abrogated tumor progression. These data define microenvironmental IL-1β as a master cytokine in tumor progression whose suppression also facilitates successful therapeutic checkpoint inhibition  trial . The CANA recent follow-up study examined circulating tumor DNA (ctDNA) and nine soluble inflammatory biomarkers  in blood samples from CANTOS patients. Catalogue of Somatic Mutations in Cancer (COSMIC) database ctDNA mutations were detected in 65% (46/71) of the CANTOS patients with lung cancer but none of the mutations commonly found in lung cancer were enriched (or depleted) following canakinumab treatment. Further, median time to lung cancer diagnosis was shorter in patients with  versus without  detectable COSMIC ctDNA mutations at baseline (p=0.011). High baseline levels of CRP and IL-6 trended toward shorter median time to lung cancer diagnosis, suggesting that IL-1β-inducible CRP and IL-6, similar to ctDNA at baseline, correlate positively with a more rapid progression to lung cancer diagnosis . These rIn conclusion, the results from CANTOS as well as the findings from pre-clinical studies clearly point to an important role of the IL-1 system, autocrine or paracrine cytokine loops, and the downstream cytokine / chemokine networks for lung tumor development and progression .EGFR is also one of the most commonly mutated genes in lung cancer. EGFR is a trans-membrane glycoprotein with an extracellular ligand binding domain for epidermal growth factor, a transmembrane domain, and an intracellular tyrosine kinase domain that regulates epithelial tissue maintenance and growth  and reduced shrinking properties of the tumor in response to immune cell activation -mediated prometastatic secretory vesicle biogenesis in the Golgi, resulting in the autocrine activation of a PLAU receptor/STAT3/PAQR11 feedforward signaling loop that triggers an immunosuppressive TME rich in effector/memory CD8+ T cells and M1 macrophages (TP53 loss induces Golgi reassembly and stacking protein 55 kD (G55)-dependent secretion that promotes angiogenesis and CD8+ T cell exhaustion  and AMPK-related family members  synthesis as a critical substrate for DNA methylation. Upregulation of SAM leads to increased DNA methylation in lung cancer cells with KRAS/LKB1 co-mutations  score to predict the probability for a patient’s MHC I variants to bind to a peptide sequence containing the relevant residues which can be recognized by matching immune cells. In their model, low PHBR scores demonstrate a high likelihood of residue presentation . Interes+ T cells, happens upon the accumulation of antigen/neoantigen within cancer cells. This immune infiltration creates a selection barrier for tumors by eliminating the clones with high antigen/neoantigen load. However, cancer cell subclones with HLA LOH may be positively selected based on their evasion capability from CD8+ T cell recognition  in the HLA locus, the gene which encodes MHC I molecules, is associated with a high neoantigen burden, APOBEC-mediated mutagenesis and significantly elevated PD-L1-positive immune cells compared to tumors without any HLA LOH, suggesting that HLA LOH can be considered as an immune escape mechanism . The autognition .Altogether, the development of the mutational landscape of cancer cells in the early stage of tumor development is tightly interconnected with the immune components of the TME. Although the immune component of TME can recognize and eliminate the clones with high antigen/neoantigen load, they eventually co-determine the genomic landscape of tumor by paving the way for the fitter clones with less immunogenic mutations (lower PHBR scores) or antigen presentation defects (high HLA LOH), which supports evasion from the immune response .As outlined above, there is ample evidence to suggest that cytokine networks govern immune evasion and foster the development of immunosuppressive T cells and TAMs within the TME . HoweverWith respect to the TME, it is important to consider the local concentrations of cytokines at time of diagnosis (and biopsy) and how they may change over time (during therapy). Many cytokines have natural antagonists and the ratios of agonists to antagonists will determine the TME phenotype. For example, the IL-1 family of cytokines (IL-1F) comprises seven proinflammatory receptor agonists  and four anti-inflammatory or antagonistic members  . Most cyTowards this goal, we propose that it will be instrumental to determine the (epi)genetic profile of individual cells in the TME by combinatorial high-resolution approaches to map cell states and understand the regulatory diversity at the single cell and molecular levels . While t+ tumor-infiltrating lymphocytes (TILs), to identify CCR5 and CXCL13 as T cell-intrinsic markers of ICI sensitivity  or adapted liquid chromatography mass spectrometry set ups (LC-MS/MS) . With reIn conclusion, the combined application of NGS and proteomics methods will allow to (i) deconvolute the main cellular sources of the altered cytokine milieu and (ii) quantify the entire spectrum of mediators that drive TME phenotypes as a prerequisite for much more precise targeted therapies.EGFR mutations and anaplastic lymphoma kinase (ALK) rearrangements and second, TME-based biomarkers including immune checkpoint molecules , for the treatment of adult and pediatric patients with unresectable or metastatic tumor with TMB-H ≥10 (mut/Mb) and solid tumors . A recend method  which neEGFR mutation showed an unfavorable response to PD-L1/PD-1 inhibitors compared to those with wild-type EGFR, which could be related to the low TMB of EGFR-mutant tumor and an immunosuppressive TME , significantly improved the disease-free survival among patients with stage IB to IIIA EGFR mutation–positive NSCLC (Although the development of lung cancer therapy from cytotoxic chemotherapies to genetic- and immune checkpoint-based strategies has shifted lung cancer therapy toward precision medicine, the study of the crosstalk between genomic landscape and TME immune phenotype offers new possibilities for more advanced personalized treatments. For example, arcinoma . Interesenformin . Moreovell death . Therefove NSCLC . Althougve NSCLC . In contve NSCLC . This hi+ T cells, dendritic cells, and a reduction of the pro-tumor M2-macrophage population in EGFR-driven lung tumor mouse models. However, most of these anti-tumor effects gradually diminished with the continuation of treatment while the main immunosuppressive cell type, MDSCs, was consistently becoming more dominant during tumor development under treatment (Further, EGFR-TKIs can also induce a rapid and temporary increase of cytotoxic CD8reatment . Combinireatment , may theKRAS patients have a large population of pro-tumor M2-macrophages that support the formation of the immunosuppressive TME phenotype (Another strategy, which has promising effects in lung tumor reduction, is the reprogramming of pro-tumor to anti-tumor macrophages . Chemothhenotype , whereashenotype . TherefoOver the last decades, the conceptual picture of a tumor has shifted from a solid mass of tumor cells to a complex and dynamic micro-organ where genetically altered cancer cells are embedded into an interactive tumor microenvironment containing numerous non-transformed immune and stromal cell types. This conceptual shift introduces the mutational landscape of the cancer cells and the cellular architecture and phenotype of the TME as the two major determinants of tumor initiation, progression and metastasis. Based on the accumulated and emerging evidence, we propose that the fate of individual tumor subclones depends on how well the cancer cell’s genetic profile and the TME phenotype harmonize. While cancer cells require genomic instability to bring forth strong oncogenic drivers that enable aggressive proliferation, the neoantigens, generated in this process, render the cells vulnerable to immune attack. A balance between these opposing forces is required for optimal tumor growth and results from a mutual crosstalk in which the genetic alterations of the cancer cells induce immunosuppressive signals that shape a tumor-supportive TME, while the TME immune components edit the genetic profile of the tumor cells by depleting highly immunogenic subclones until a balance between the two processes is achieved.In light of the key roles of cancer cell mutations and the TME phenotype during tumor evolution, integrating these two aspects for lung tumor stratification is expected to help anticipate primary and acquired therapy resistance, the key remaining obstacles to a long-term survival benefit under treatment with targeted and immunotherapy regimens. The main and immediate challenge for the integration of genetic landscape and TME phenotype is the heterogeneity of tumor tissues, which calls for spatially resolved single-cell analysis techniques. To address the TME phenotype and its heterogeneity, highly multiplexed imaging technologies and computational tools have been developed that can quantitatively and at single-cell resolution reveal the spatial distribution of tumor, immune and stromal cell components, their interactions and activity states in distinct tumor niches. While the mutational landscape is still primarily profiled by next generation sequencing of bulk tumor tissue, recent advances with single-cell genomics raise hope that tumor mutational status and TME phenotype can soon be better integrated in one framework for a refined classification of lung tumors that better informs clinical decision making for the benefit of long-term survival.


Here, we evaluated conditions that would support long-term in-vitro maintenance of undifferentiated spermatogonia from a goat breed that is endemic to Kenyan livestock production. Single-cell suspensions enriched for undifferentiated spermatogonia from pre-pubertal bucks were seeded on laminin-coated tissue culture plates and maintained in a commercial media based on serum-free composition. The serum-free media was conditioned on goat fetal fibroblasts and supplemented with a growth factor cocktail that included glial cell line-derived neurotrophic factor (GDNF), leukemia inhibitory factor (LIF), stromal cell-derived factor (SDF), and fibroblast growth factor (FGF) before use. Over 45 days, the primary cultures developed a cluster morphology indicative of in-vitro grown undifferentiated spermatogonia from other species and expressed the germ cell marker VASA, as well as the previously defined spermatogonial marker such as promyelocytic leukemia zinc finger (PLZF). Taken together, these findings provide a methodology for isolating the SSC containing undifferentiated spermatogonial population from goat testes and long-term maintenance in defined culture conditions.The undifferentiated spermatogonial population in mammalian testes contains a spermatogonial stem cell (SSC) population that can regenerate continual spermatogenesis following transplantation. This capacity has the potential to be exploited as a surrogate sires breeding tool to achieve widespread dissemination of desirable genetics in livestock production. Because SSCs are relatively rare in testicular tissue, the ability to expand a population  Spermatozoa are male gametes derived from undifferentiated spermatogonia through a series of cellular divisions (mitotic and meiotic) and morphological transformations collectively referred to as spermatogenesis. The process begins shortly before puberty and is continuous throughout a male's life and this continuity is dependent on the continuous self-renewal of a subset of the undifferentiated spermatogonia population that continues as spermatogonial stem cells (SSCs) . The SSCin vitro is important to provide sufficient numbers for transplant into a host of surrogate recipient males. For mice, conditions that support long-term maintenance and exponential expansion of SSCs in vitro have been devised  represent a major constraint to the improvement of performance in smallholder livestock systems  and mode devised –14. Undeand pigs –17.in vitro requires recreation of the cognate microenvironment or niche, which the cells reside in vivo . All the animal procedures were carried out using 10 pre-pubertal male goats of which five were 3 months old and the other five were 5 months old. The procedures adhered strictly to the approved guidelines of the Institutional Animal Care and Use Committee at the International Livestock Research Institute in Kenya (IACUC Ref. No: 2018-15) and the University of Nairobi (Ref.: FVM BAUEC/2019/243). The testicular tissue was obtained following the orchiectomy of the goats. Semi-open orchiectomy of the goats was done following the routine aseptic procedure . ScrotalA two-step cell isolation process by Oatley et al.  with minThe cell suspension was overlaid on a continuous 30% Percoll gradient and subjected to centrifugation (600 g at 4°C for 8 min) for separation based on cellular density. The cell suspension was seeded on gelatin-coated six well cell culture plates for differential plating , 23. Then = 5). The head, viscera, and gonads were removed. The tissues were minced and digested with an enzyme solution of 0.25% trypsin, 0.5 mM EDTA, and DNase I (1 mg/ml) in PBS to generate a single-cell suspension. The cells were plated in T75 culture flasks in 10% FBS/Dulbecco's Modified Eagle Medium (DMEM). The cells were mitotically inactivated by treatment with mitomycin C (20 μg/ml) for 3–4 h, followed by multiple washing in PBS. These cells were then used for conditioning of serum-free medium that was used for the culture of SSC.Goat fetuses aged 30–45 days of gestation were collected after the slaughter of pregnant dams . The medium was supplemented with human forms of growth factors: human glial cell line-derived neurotrophic factor (hGDNF) , human fibroblast growth factor 2 (hFGF2) , human leukemia inhibiting factor (hLIF) , and human stromal-derived factor 1 (hSDF-1) . The cells at a concentration of 0.02 × 10e medium  were seed Oatley . The celTesticular isolate and cultured cells adhered on poly-L-lysine-coated slides and SSC was localized using PLZF marker as described  with minPieces of goat testicular tissue were sectioned and fixed in 10% formalin overnight. The tissue was then dehydrated, embedded in paraffin, sectioned at a thickness of 7 μm, and then adhered to glass slides. The sections were deparaffinized in xylene and rehydrated with a descending series of gradient ethanol and water incubations. Antigen retrieval was done by boiling the slides in sodium citrate buffer (pH 6.0) for 20 min in a water bath at 95°C. Non-specific binding sites were blocked through overnight incubation in 10% normal goat serum/1% BSA in 0.2% Triton X-100 in PBS at 4°C. On the next day, slides were washed in PBS and incubated overnight with the primary antibody at 4°C [1:100 DDX/VASA polyclonal antibody (bs-3597R) and 1:100 PLZF antibody (sc-28319)]. The following day, sections are washed in PBS and then incubated with the secondary antibody for 2 h at room temperature (dilution factor 1:500). Afterward, the tissue was washed in PBS and then a glass coverslip was mounted on the tissue section using the aqueous DAPI-containing medium. Slides were observed under fluorescent microscopy.PLZF, B-cell CLL/lymphoma 6 member B (BCL6B), and Ubiquitin carboxyl-terminal hydrolase isozyme L1 (UCHL1) genes in multiparameter-selected SSC and cultured SSC colonies. The glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene was used as an internal reference gene in the qPCR. The primer sequences used in the reactions were documented for goat SSC gene expression (Quantitative PCR (qPCR) was performed as described previously . Total Rpression   cells were isolated per 200 mg of testicular tissue and ~70% of the population was determined to be PLZF + spermatogonia  after 1 month of culture of goat germ cell clumps. The results revealed the expression of these genes . qPCR waOver the years, livestock genetic improvement has been through a selection of elite sires for breeding. Male germplasm has played a vital role in genetic improvement. For example, over the years, tropical regions have benefited from the importation of top bull semen for artificial insemination in dairy cattle. This is primarily aimed at improving production traits, fertility, longevity, and disease resistance in subsequent generations. It suffices that artificial insemination has revolutionized the dairy industries of developing countries. Kenya is an example where milk production has dramatically increased over the years. Additionally, this has led to the availability of purebred dairy cattle as replacement heifers to apply superior genetics. Comparatively, the small ruminant's production system has lagged in fully exploiting the genetic potential. This is more apparent in indigenous goats with limited application of reproductive technologies. There is potential through reproductive technologies to facilitate the dissemination of superior germplasm. Thus, the opportunity to reap the benefits of genetic gains has not been fully tapped. Transplantation of SSCs from elite bucks into the locally adapted bucks would provide an alternative breeding method for disseminating genetically superior semen within these existing infrastructural limited breeding systems, especially in sub-Saharan Africa.NANOS2 gene, which is responsible for germ cell layer survival and development. These gene-edited surrogate sires exhibited complete donor-derived spermatogenesis with normal semen levels . Laminin base coating has previously been utilized in the feeder-free culture of SSC and successfully established feeder-free bovine SSC  at 37°C in a 5% COvine SSC . This isIn the current study, primary cultures of SSC were obtained by isolating testicular cells from pre-pubertal goats 3–6 months of age; at this age, the majority of gonocytes have transformed into undifferentiated type A spermatogonia. During the pre-pubertal period, the undifferentiated spermatogonia are mitotically active with regenerative capacity, which is a hallmark of SSCs , 33. ThuWe believe that this is the first report of serum-free, feeder culture of goat SSCs and culture of SSCs in African livestock breeds in Africa. The conditions established here can be used to develop robust long-term cultures of goat SSCs enabling an improved rate of genetic gain in goats. With the continued food insecurity due to the increase in the human population, efficient and effective breeding technologies are needed to match the demand for animal products. This necessitates the exploitation of advanced technologies such as surrogate sires breeding technology, where SSCs are utilized in transplantation.This will be highly applicable in arid and semi-arid areas where huge numbers of goats are kept by pastoralist communities and the infrastructure to support other reproductive technologies is not sustainably available. The current technology will be applicable through the initial introduction of surrogate sires as rotational breeding bucks to community goat flocks for the propagation of desirable genetics through natural mating within the existing infrastructure. The male offsprings born from rotational surrogate sire mating will continue the natural propagation of the desirable genetics within the flocks without the need for additional or improved infrastructure. Kenya has research centers such as the International Livestock Research Institute, universities, and other livestock research institutes that have the capacity to produce surrogate sires and distribute them to goat farmers for improved productivity.The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author/s.The animal study was reviewed and approved by Institutional Animal Care and Use Committee at International Livestock Research Institute in Kenya (IACUC Ref. No: 2018-15) University of Nairobi (Ref.: FVM BAUEC/2019/243).NN: carried out the research activities and manuscript writing. SK: manuscript review and editing. JO: played a great role in transfer of technology from Washington state university to ILRI, manuscript review and editing. MJO: training of the ILRI team on the isolation and cell culture of undifferentiated spermatogonia. TC: reproductive platform and project supervision. CM: research technician for the cell culture lab activities-asssited in cell culture. MO: research technician for molecular activities-assisted in castartions and PCR works. AK and JN-M: manuscript review. All authors contributed to the article and approved the submitted version.https://livestock.cgiar.org/) and the Centre for Tropical Livestock Genetics and Health (Grant Number: OPP01127286).This study was funded by the CGIAR Research Program on Livestock (The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.


Modern neurosurgical treatment of brain tumors involves maximal safe resection of tumorous tissue whilst preserving adjacent normal neurovascular anatomy in order to minimize the risk of neurological injury to the patient . A surgiFurther pioneering work published in 1916 by Dr. Dandy and his then senior neurosurgery resident, Dr. George J. Heuer, reported the localization of brain tumors in one hundred consecutive patients using x-ray roentgenography . This wa131iodine to differentiate tumor tissue from normal brain under ultraviolet (UV) light by Dr. George Eugene Moore in 1947 at the University of Minnesota was one of the first reports of exploiting the inherent leakiness of the blood-brain barrier (BBB) around brain tumors to allow for the extravasation of a radioactive fluorophore to enhance visualization of brain tumors. This landmark discovery paved the way for the introduction of radioactive nucleotides such as 18fluorodeoxyglucose for use with computed tomography (CT) and positron emission tomography (PET) to localize metabolically active tumor cells in the brain. However, it was the advent of nuclear magnetic resonance (NMR) by Professors Felix Block from Stanford University and Edward Purcell from Harvard, for which they were awarded the Nobel Prize in Physics in 1952, that led to the introduction of magnetic resonance imaging (MRI) scanners, which has since revolutionized our ability to visualize with stunning resolution the neurovascular anatomy of the brain and spinal cord. Since then, adaptations such as functional MRI (fMRI) (The use of intravenous fluorescein tagged with radioactive I (fMRI)  and diffI (fMRI)  have allI (fMRI) .Incorporating different image-guided technologies into the operative neurosurgical workflow varies depending on the modality that is used. Many neurosurgical centers now have access to portable neuronavigation systems such as the Medtronic StealthStation™  that occupy minimal footprint in the operating room and can overlay high resolution CT or MRI imaging with fMRI or DTI images to allow for fixed 3D mapping of intracranial lesions for presurgical planning Despite the improvements in preoperative imaging planning workflow, the surgeon is often times limited in their ability to differentiate tumor tissue from adjacent normal neuroanatomy under direct white light microscopy. This is particularly challenging during resection of infiltrative tumors such as high-grade gliomas, the most common and aggressive primary brain tumor in adults. To overcome this limitation, fluorescence-guided surgery (FGS) using tumor-targeting fluorophores have steadily been introduced into the neurosurgeon’s armamentarium . The FDASuccessful outcomes in neurosurgical oncology is increasingly being defined by the EoR to achieve a gross total resection (GTR) or maximal safe cytoreduction . SeveralStudies comparing across image-guided surgical modalities demonstrated that iMRI was superior over both 5-ALA FGS and conventional neuronavigation approaches in obtaining GTRs and led to prolonged survival . A recenhttps://www.soc-neuro-onc.org/WEB/WEB/Event_Content/Intraoperative_Visualization_and_the_Connectome.aspx).One caveat that must be taken into consideration when interpreting the results of the aforementioned network meta-analysis is that the majority of studies using 5-ALA to maximize EoR were in patients with HGGs that were located in the supratentorial space  . These ain vivo can improve specificity of delivery, although the effectiveness of receptor targeting of NPs in solid tumors has been recently questioned . We have provided a tabular summary of these NP formulations, specific targeting ligands and sequences, along with potential applications for use in neurosurgical oncology for ease of reference for our readers  that have been developed for potential CNS applications typically have a maximal diameter of ∼100 nm to facilitate trafficking across the tight junctions of the BBB. We previously developed a liposomal NP of ∼100 nm in diameter that was functionalized with a fluorophore and transferrin to enable transferrin receptor-mediated transcytosis across the BBB to deliver dual combination therapies to glioma brain tumors in mice . Other r readers .in vivo during surgery and track cellular biodistribution and treatment response throughout the course of adjuvant therapy, can allow for time and cost savings while adopting a personalized medicine approach to improve outcomes —highly specialized and modular nanoscale filamentous protein particles that can be genetically tuned for programmable assembly, chemically modified for surface functionalization of imaging, chemical, or antigenic moieties, for delivery ; Image-gdelivery ; And higdelivery . In thisLeiurus quinquestriatus scorpion  to enable SWIR imaging of ovarian tumors and lymph nodes in a mouse model of ovarian cancer . We hyposcorpion . CTX pepscorpion . To achiin vivo SWIR imaging . Results demonstrated IR1050-CTX-M13 ϕ or SWCNT-CTX-M13 ϕ signal localized to the right posterior frontal lobe region corresponding to the site of GBM22 tumor induction . Background uptake of IR1050-CTX-M13 or SWCNT-CTX-M13 phage was observed in the occipital bony protruberance of the mice . To further confirm the uptake of CTX-M13 ϕ at the site of GBM22 brain tumors, we removed the brains from the skulls of GBM22 mice and performed ex vivo SWIR imaging. Ex vivo SWIR imaging demonstrated focused IR1050-CTX-M13 or SWCNT-CTX-M13 signal at the site of GBM22 tumors . The elimination of signal from the bony region corresponding to the occipital bone during ex vivo SWIR imaging confirmed the nonspecific uptake of IR1050-CTX-M13 ϕ and SWCNT-CTX-M13 ϕ by the occipital bone  and the specificity of the CTX-M13 ϕ to detect GBM22 cells in the brain . Taken together, our preliminary data confirms the modular nature of M13 ϕ to be functionalized and conjugated for use in glioma tumor detection using SWIR imaging with the potential for further development as a theranostic nanomaterial for the treatment of gliomas.Brightfield images of the heads of GBM22 mice show their skulls outlined in red, their occipital boney prominence outlined in green, and the site of intracranial GBM22 tumor induction in the right posterior frontal lobe, outlined in black Filamentous bacteriophage are highly stable and scalable nanoscale materials that have been characterized for their inert effects as a nano-carrier for the delivery of a range of vaccine-based therapies in humans . Like otTNF), demonstrated tumor killing when systemically delivered over 3 consecutive doses in an intracranial orthotopic xenograft mouse model of U87MG human glioma (Herpes simplex virus thymidine kinase (RGD4C-AAVP-HSVtk) in U87MG mice followed by treatment with gangciclovir as suicide gene therapy. Both the RGD4C-AAVP-TNF and RGDC4C-AAVP-HSVtk constructs achieved the intended cytotoxic and theranostic effects, respectively, demonstrating the potential for using M13 ϕ as a theranostic for the treatment of human gliomas and potentially other brain tumors (Ex vivo SWIR images), and our previously published studies using NIR II conjugated-M13 ϕ expressing tumor-targeting peptides to detect ovarian cancer tumors during real-time surgical resection in a mouse model of ovarian cancer (A recent study using a hybrid vector expressing an adeno-associated virus and a single-stranded M13 phage (AAVP) displaying a double-cyclic RGD4C motif ligand  with the gene sequence for the cytotoxic protein tumor necrosis factor (RGD4C-AAVP-n glioma . The samn tumors . Our pren cancer , furthern cancer .in vitro, in vivo, and ex vivo, demonstrated that delivery of nanoliposomes to the tumor site did not correlate with EGFR expression in the three different glioma cell lines that were tested, underrepresenting the image-derived molecular specificity by up to 94.2% (The potential for tumor-targeting nanoscale materials to be used in the detection and treatment of a wide range of brain tumors can offer patients a personalized treatment path. In particular, the recent 2021 reclassification of CNS tumors into further molecular subtypes based on genetic modifiers and/or diagnostic molecular pathological features , has uncto 94.2% . This suIn conclusion, the increasing use of fluorescence image-guided tumor resection within the neurosurgical community opens an avenue for the introduction of innovative theranostic nanoplatforms that could further assist the tumor surgeon in achieving intraoperative detection and maximal EoR. Whilst future comparative studies are needed to definitively assess the ability of FGS to achieve better patient outcomes compared to the less costly, non-fluorescence-based navigated resection techniques, the potential for theranostics to be applied in a more personalized fashion may lead to breakthroughs in treating complex and heterogeneous brain tumors such as gliomas in order to achieve better survival outcomes afforded by current standard of care treatment regimens, which have largely remained unchanged over the past several decades.


The Connecting European SARS-CoV-2 Cohorts to Increase Common and Effective Response to SARS-CoV-2 Pandemic (ORCHESTRA) consortium, led by University of Verona , brings together key European academic experts and research institutions in infectious diseases, data management and High Performance Computing (HPC) from 26 organizations (extending to 37 partners) from 15 countries. The project aims to create a new pan-European cohort built on existing and new large-scale population cohorts in European and non-European countries to significantly impact on the responsiveness to SARS-CoV-2. The integration and analysis of the very heterogeneous characteristics of SARS-CoV-2 data coming from many different sources such as EHR, retrospective and prospective patient registries, and related ‘omics’ data  can benefit of data analytics enabled by HPC, where both high compute performance and fast storage capabilities are immensely important. During the first year of the project, a dedicated HPC cloud infrastructure have been designed and partially deployed to fulfill the functional requirements for data management ensuring healthcare data confidentiality/privacy, integrity and security in compliance with the European GDPR regulations. The result is an infrastructure for Data Management composed by three main layers: National Data Providers; National Hubs , to centralize data at national level and to support data storage, sharing and analysis on data ingested from the National Data Providers; ORCHESTRA Data Portal: the pan-European portal for sharing aggregated data and results. Currently data collection is on going; at the end of the project, clinical centers are expected to have enrolled more than 10.000 patients with about 50.000 samples for the prospective studies.• The SARS-CoV-2 crisis made evident the need to manage and analyse very heterogeneous health data coming from many different resources across different countries.• The HPC cloud infrastructure released for the Orchestra project can act as a model to manage future public health threats.


R2 > 0.92, RMSE < 0.06 N) and 8 PLS components with geometry-only . Changes in the superior neck and distal cortex were most important during single-leg stance while the superior neck, medial head, and lateral trochanter were most important during a sideways fall. Local changes in femoral neck and head geometry could differentiate the exercise groups from the control group. Exercise interventions may target BMD changes in the superior neck, inferior neck, and greater trochanter for improved femoral neck strength in single-leg stance and sideways fall.Physical exercise induces spatially heterogeneous adaptation in bone. However, it remains unclear where the changes in BMD and geometry have the greatest impact on femoral neck strength. The aim of this study was to determine the principal BMD-and-geometry changes induced by exercise that have the greatest effect on femoral neck strength. Pre- and post-exercise 3D-DXA images of the proximal femur were collected of male participants from the LIFTMOR-M exercise intervention trial. Meshes with element-by-element correspondence were generated by morphing a template mesh to each bone to calculate changes in BMD and geometry. Finite element (FE) models predicted femoral neck strength changes under single-leg stance and sideways fall load. Partial least squares regression (PLSR) models were developed with BMD-only, geometry-only, and BMD-and-geometry changes to determine the principal modes that explained the greatest variation in neck strength changes. The PLSR models explained over 90% of the strength variation with 3 PLS components using BMD-only ( Osteoporotic hip fractures are a considerable cause of morbidity and mortality  distribution from planar DXA images , a machine-based isometric axial compression group , and a control group of sex- and age-matched participants from the same community (67 ± 6 years) (n = 25). The HiRIT programme consisted of multi-joint, compound movement, high-intensity progressive resistance training, and high-impact jumping exercises. The IAC programme incorporated self-initiated near-maximal 5-s isometric contractions performed for the chest press, leg press, core pull, and vertical lift exercises using the bioDensity™ system. The trial protocol has been published describing the exercise interventions and control group activities  were obtained of the non-dominant proximal femur from male participants with osteoporosis and osteopenia (67 ± 7 years) in the LIFTMOR-M 8-month semi-randomised controlled exercise intervention trial  calibrated to equivalent BMC levels were obtained from the DXA scans with 3D-SHAPER software . The software delivers a 3D volume of images of the proximal femur from a planar DXA image using a 3D statistical shape and appearance model (SSAM) of the proximal femur built from a database of 111 Caucasian individuals (56 ± 12 years) with no signs of skeletal disease other than osteoporosis. Femur models generated from the 3D-DXA images produced by the software have shown a 0.93 mm mean point-surface distance to corresponding femurs generated from quantitative computed tomography (QCT) and a correlation coefficient = 0.95 for vBMD measurements . Secondly, non-rigid registration modelled as a sum of Gaussian Radial Basis Functions (G-RBF) with 10 iterations elastically deformed the template surface mesh to match the geometry of the target surface mesh. Following registration of the template surface mesh, a custom FE solution was then implemented in which the displacements at the nodes on the surface of the template volume mesh were imposed to equal those calculated while registering the surface meshes . This algorithm delivered morphed volume meshes with node numbering and connectivity correspondence.Iterative closest point (ICP) based registration was used to morph the template surface mesh over the geometry of each bone. First, the template surface mesh was rigidly registered to the target bone surface by aligning the principal axes of inertia of the template and the target surface. The registration was then optimised with a rigid ICP algorithm so that rotation, translation, and scaling of the template vertices were iteratively calculated as solutions to a weighted least squares minimisation problem by Singular Value Decomposition (SVD). The algorithm converged when the root mean squared error (RMSE) between the previous and current template vertices dropped below a threshold value (< 103) at corresponding elements between the pre- and post-exercise volume meshes.The bone density was mapped to the morphed template volume mesh from the 3D-DXA image. To achieve this, the bone density distribution in the image was integrated over each element volume using Gaussian quadrature to deliver the density distribution in the mesh. Changes in geometry were expressed as the pre- and post-exercise changes in x, y, and z coordinates (mm) of corresponding nodes in the morphed volume meshes to represent each bone instance in the dataset. BMD changes were expressed as the change in BMD (g/cm3) in the images to elastic modulus (MPa)  axis was applied to simulate a static single-leg stance  and the asymmetric elastic limit values of bone in compression  and tension (εLIM = 7000 µε)  (100 N) over the maximum RF (RFmax):Femoral neck strength was calculated for each loading configuration using a principal strain criterion  and root mean square error (RMSE) using tenfold cross-validation.Partial least squares regression (PLSR) was applied on the changes in proximal femur geometry, BMD distribution, and femoral neck strength with all participants. The analysis delivers a series of BMD-and-geometry change maps ranked according to the amount of variation in strength changes explained. PLSR models were developed with: (1) combined geometry and BMD, (2) geometry-only, and (3) BMD-only. All variables were standardised before applying the PLSR by calculating their z-score. The PLSR was solved with the SIMPLS algorithm . The compactness of the PLSR model was determined by how many PLS components were required to explain over 90% of the variation in strength changes where fewer components indicated a stronger relationship to strength. The error in the PLSR model was determined with the coefficient of determination (The relative importance of the geometry-and-BMD variable to the PLSR model was assessed using the Variable Importance in Projection (VIP) scores, which estimate the relative contribution of the BMD or geometry change at each point in the femur used in the PLSR model. The VIP scores are calculated as a weighted sum of the squared correlations between the PLS components , it was followed by unpaired t-tests with a Bonferroni adjustment for multiple comparisons.The effect of exercise on femoral neck strength was assessed by comparing changes in vBMD in the control group to corresponding changes in the HiRIT and the IAC group using a one-way ANOVA. The same test was then repeated for the per cent changes in predicted femoral neck strength and PLS component scores. Where the F value for a given parameter was found to be statistically significant  and over 95% of the variation with 4 PLS components  . The first PLS component accounted for 24% of the variability in each loading condition. The combined BMD-and-geometry models were closer to the BMD-only models, explaining 90% of the bone strength variation in both single-leg stance and sideways fall with 5 PLS components each . The first PLS component explained a level of variation in strength closer to the geometry-only model, with 43% variation explained in single-leg stance strength and 38% in sideways fall, whereas over 90% of the total variation was explained with 5 modes, which was more like the BMD-only model  were found in the cortex distal to the femoral neck for the first mode of variation. The second mode displayed focal changes (± 0.06 g/cm3) in the distal cortex, superior and inferior neck cortex, and the medial femoral head. The third mode showed the largest BMD changes (± 0.05 g/cm3) in the distal cortex and superior femoral head, while BMD changes in the superior neck were slightly larger for the sideways fall load case as compared to the single-leg stance load case  nor in strength changes either for single-leg stance  and sideways fall  as determined by one-way ANOVA (Table Comparing vBMD and strength changes in the HiRIT group, the IAC group, and the controls, there were no statistically significant differences between groups for vBMD changes (The aim of the current study was to determine the principal modes of variation of BMD-and-geometry changes with the greatest effect on femoral neck strength in participants who underwent an established exercise treatment. We found similar variations of BMD changes in the cortical, superior neck, and femoral head explained most of the variation in strength for single-leg stance and sideways fall. Nevertheless, the relative importance of different regional changes was loading-specific, with the superior neck and distal cortex being most important during single-leg stance while the superior neck, medial head, and lateral trochanter were most important during sideways fall. The present results can inform the design of exercise programmes on the principal target locations to enhance the strength of the proximal femur during single-leg stance and sideways fall loading.The principal modes of BMD-and-geometry variation explained, either separately or conjointly, more than 90% of the variation in femoral neck strength across the participants and their response to exercise. These results thereby indicated the interdependence between BMD and geometry in determining strength. Yet, the BMD-only model was more compact than both the geometry-only and the BMD-and-geometry models supporting the notion of a dominant effect of BMD on proximal femur strength over that of geometry (Cheng et al. The current study found that BMD changes had a greater contribution to the changes in strength with over 90% of the variation explained with 3 PLS components in accordance with previous investigations indicating low BMD as the strongest risk factor for fracture (Roberts et al. The strength of our study lies in the comprehensive analysis technique SSAM with FE simulations to estimate femoral neck strength in combination with use of PLSR models. However, there are limitations that warrant acknowledgement. Firstly, the 3D-DXA technology used in this study provided volumetric BMD distribution in each participant reconstructed from planar DXA images at two time points thereby enabling the present study into the relationship between geometry, BMD, and strength in the participants. The relatively low repeatability of the technology should be taken into consideration when applied on a participant-by-participant base (O'Rourke et al. In conclusion, the current study determined the principal BMD-and-geometry changes induced by exercise that explained most of the variation in femoral neck strength. Changes to BMD in the superior neck, inferior neck, and greater trochanter primarily explained the variation in neck strength changes seen in the group of middle-aged and older men with osteopenia and osteoporosis in single-leg stance and sideways fall loading. Local changes in femoral neck and head geometry could differentiate the exercise groups from the control group, but not in predicted strength changes. Exercise interventions may target BMD changes in the superior neck, inferior neck, and greater trochanter for improved femoral neck strength in single-leg stance and sideways fall.


The COVID-19 social lockdown imposed important limitation to non-emergency health care services in Italy, between March and May 2020, with many difficulties in the mental health assistance of those chronic conditions needing a continuative therapeutic support.Our study aimed to describe how therapeutic activities have been carried on by remote services in two Adolescent Psychiatric Day Hospital Units (Rome and Turin) and the outcome of these assistance interventions in youths with subacute psychopathology.The patient cohort includes 162 adolescents  DH outpatients presenting a complete clinical and neuropsychiatric assessment before the lockdown. During the several phases of COVID-19 quarantine all patients were monitored and supported by telemedicine interventions. All data were recorded and standardized every 15 days: symptom severity was rated by global severity (CGI-S) and stress level by self-reported measures of stress (IES-R).Among patients, CGI score remained stable, IES-R score declined over time: higher IES-R score was significantly associated with female gender and but no differences was observed related with the primary diagnosis. 5 patients presented a clinical acute state needing a hospitalization. The rate of hospitalization was not significantly different compared with the rate observed in the same period of 2019.In youth with psychopathological conditions, remote assistance for psychiatric cares resulted effective and it was associated with a clinical stability with decreasing stress levels.No significant relationships.


Introduction: MicroRNAs have a significant role in the regulation of the transcriptome. Several miRNAs have been proposed as potential biomarkers in different malignancies. However, contradictory results have been reported on the capability of miRNA biomarkers in cancer detection. The human biological clock involves molecular mechanisms that regulate several genes over time. Therefore, the sampling time becomes one of the significant factors in gene expression studies.Method: In the present study, we have tried to find miRNAs with minimum fluctuation in expression levels at different time points that could be more accurate candidates as diagnostic biomarkers. The small RNA-seq raw data of ten healthy individuals across nine-time points were analyzed to identify miRNAs with stable expression.Results: We have found five oscillation patterns. The stable miRNAs were investigated in 779 small-RNA-seq datasets of eleven cancer types. All miRNAs with the highest differential expression were selected for further analysis. The selected miRNAs were explored for functional pathways. The predominantly enriched pathways were miRNA in cancer and the P53-signaling pathway. Finally, we have found seven miRNAs, including miR-142-3p, miR-199a-5p, miR-223-5p, let-7d-5p, miR-148b-3p, miR-340-5p, and miR-421. These miRNAs showed minimum fluctuation in healthy blood and were dysregulated in the blood of eleven cancer types. Conclusion: We have found a signature of seven stable miRNAs which dysregulate in several cancer types and may serve as potential pan-cancer biomarkers. The discovery of microRNAs (miRNA) as the new player of the transcriptome has changed the field of molecular biology. miRNAs are single-stranded small non-coding RNAs composed of 18–22 nucleotides . The binmiRNAs have been found in various biological samples, including peripheral blood, which is readily obtainable in significant amounts . Studiesn = 90) were obtained from the study of (We conducted a detailed search in the Gene Expression Omnibus (GEO) database to find appropriate small RNA sequencing raw data, using the keywords “small-RNA seq”, “whole blood derived”, and “blood-derived cancer” resulting in 779 patient raw data sets from 11 cancer types . Our inpstudy of , includistudy of .b is constant (b = 1.4826)  for a single miRNA of each time point of healthy samples compared to the overall mean expression:This study was conducted in two steps . At firs 1.4826)  and Xn iTo specify whether the miRNA was diverted throughout the timepoints, thresholds were defined as where x stands for each miRNA in all time points:In the second step, miRNAs with MAD <0.2 and fold changes out of the threshold range (outlier) compared to cancer datasets and their specific control samples were selected for further analysis. COSINOR analysis was used to confirm the absence of oscillation in selected miRNAs.Small RNA-seq data analysis was performed on the GALAXY platform . The quaTimeClust software  was usedwww.graphpad.com) to specify clustering in healthy versus cancer samples.Principal component analysis (PCA) was performed using GraphPad Prism version 9.0.0  curves and the area under curve (AUC).The Deseq2-normalized read counts of all overlapping differentially expressed miRNAs(DEMs) were used to assess the sensitivity and specificity of each DEM to evaluate its detection capability in cancer datasets The sensitivity and specificity of all miRNAs as a prognostic signature for prediction were evaluated by AUC of the receiver operation characteristic with R program software using the Combiroc package .MIENTURNET  was usedThe MiRNET platform was used to explore the miRNA target genes and the miRNA-gene interaction network . Moreovewww.graphpad.com.The expression of candidate miRNAs was explored in three different studies. Array express and TCGA datasets was assessed and samples obtained from whole blood of patients with different types of cancer with no treatment was selected. Three different study were explored and analyzed. miRNA expression level from whole blood of patients detected by lung cancer and nasopharyngeal cancer including 1052 healthy individuals and 1438 cancer patients were assessed . The meaThe common miRNAs through nine time points were analyzed to find the miRNAs with minimum oscillation patterns. One hundred ninety-five miRNAs were found that were expressed in all time points . Five diTo evaluate the potential dysregulation regarding miRNAs in cluster C , we explp-value <0.05) and dysregulation level of the 37 candidate miRNAs were checked in all types of cancer by ranking miRNAs according to their distance from the threshold window. The top seven DEMs were selected based on their distance from the threshold (outliers) [2], including miR-142-3p, miR-199a-5p, and miR-223-5p showed the most significant distance to the cutoff border. Seven miRNAs with significantly distinct fold change in comparison to cancer datasets and study-specific controls and also distance from the threshold window in more than 80% of cancers were selected as top dysregulated miRNAs.Finally, the presence  with the first principal component (PC1) and second principal component (PC2) for seven miRNAs. The PC1 showed 54%, and PC2 showed a 17%  varianceMoreover, we conducted a literature review to compare the reported miRNAs in other cancer studies with the present candidate miRNAs result . The mosp-value <0.05  and 1971 nodes (target genes) . SeveralThe KEGG pathway enrichment and gene ontology analysis on 26 best-fitted target genes were performed using the ShinyGO tool. GO analysis in biological process term (BP) demonstrated that the target genes were associated with nucleobase-containing compound metabolite process and regulation of gene expression . In addiThe expression of candidate miRNAs was explored in total seven studies Including three studies from different cancer types obtained from whole blood. The expression intensity of candidate miRNAs in the whole blood  of canceThe molecular mechanisms that control a range of genes across time are part of the human biological clock, which influences many molecular processes . The regThe blood miRNAs in healthy controls showed different oscillation patterns. We have found a cluster of 37 miRNAs with the most stable behavior across all time points. It can be assumed that a change in the expression of these miRNAs may indicate an abnormal or pathological event . TherefoThe critical question is how changes in the expression of miRNAs in the blood may be associated with cancer in other tissues. A standard answer to this question is that the leakage of miRNAs from cancerous tissues into the blood changes the level of these molecules in the blood of cancer patients . HoweverIn a contradictory hypothesis  , it can In summary, we have found a pan-cancer signature of seven miRNAs that may have the potential for cancer detection. Also, this approach could be used as a survey for identifying biomarkers for other pathological conditions. However, further investigation is needed to validate our results and examine the miRNA’s pan-cancer role.


Childhood maltreatment (CM) is one of the best described environmental risk factors for developing any psychiatric disorder, while it also confers increased odds for obesity, cardiometabolic disorders and all-cause mortality. Inflammation has been suggested to mediate the widespread clinical effects of CM. Previously, Ligthart et al. (2016) identified a polyepigenetic signature of circulating CRP levels, a measure of chronic low-grade inflammation, that has been reliably associated with a wide array of complex disorders. The study of this biomarker could dilucidate the mechanistic relationship between CM and psychiatric outcomes.Thus, CRP-associated epigenetic modifications were explored regarding proximal exposure to CM.Genomic DNA was extracted from peripheral blood mononuclear cells of 157 children and adolescents (7 to 17 years old). Exposure to CM was assessed following the TASSCV criteria. Genome-wide DNA methylation was assessed by means of the EPIC array. Fifty-two out of the 58 original CRP-associated CpG sites surpassed quality control and were included in the analysis. Age, sex, psychopathological status and cell type proportions were included as covariates.DNA methylation at 12 out of 52 CpG sites (23%) was significantly associated with exposure to CM (p < .05); 8 of these associations survived correction for multiple testing (q < .05).This is the first study to date to explore the relationship between childhood maltreatment and an epigenetic signature of chronic low-grade inflammation. Our findings underscore the presence of immune dysregulation early after exposure to CM; further studies are needed to assess the long-term clinical implications of this signature in psychiatric patients.No significant relationships.


Streptococcus gallolyticus (SG) – among other bacterial infections – is associated with colorectal malignancy and adenoma. It is reported that patients with SG bacteraemia have a concomitant colorectal tumour in 25–80% of cases. We present a case of a patient with complications of this septicaemia associated with a rectal adenocarcinoma, as an example of this important radiological and clinical correlation.Teaching Point: Always screen for primary colorectal malignancy in a patient with malignancy-associated bacterial infection. Haemocultures were taken and analysed over the following days.An 81-year-old male patient was admitted to the hospital with fever and weight loss. Lab results showed merely signs of inflammation with elevated C-reactive protein (CRP) (96 mg/L) and white blood cell count  bacteraemia. Based on the observations on the MRI, the radiologists told the referral physician that screening colorectal malignancy would be mandatory. Positron Emission Tomography-Computed Tomography (PET-CT) was performed to locate the source of infection and screen for malignancy. A focus of F-18 fluorodeoxyglucose-uptake (FDG-uptake) was seen in the rectal wall , suggestMRI of the rectum  confirmeStreptococcus gallolyticus (SG) is part of the group of Streptococcus bovis pathogens and was previously known as S. bovis biotype I . SG has Although the pathophysiology of SG is not fully understood yet, it is hypothesised that the carcinoma is the entry site of the pathogens to the bloodstream . Many ofThis correlation could explain recurrent episodes of SG bacteraemia sensitive to appropriate antibiotic therapy, as in our case. After rectal surgery, no recurrent bacteremia was reported.This case demonstrates that knowledge of the association of S. bovis/S. gallolyticus with (colo)rectal malignancy contributes to the early detection of malignant lesions and therefore possible improved patient outcome. Additional diagnostic examinations  are recommended to exclude concomitant colorectal malignancy.