SARS-CoV-2 infection causes most cases of severe illness and fatality in older age groups. Over 92% of the Chinese population aged ≥12 years has been fully vaccinated against COVID-19 . At the end of October 2021, the vaccination programme has been extended to children aged 3–11 years. Here, we aim to assess whether, in this vaccination landscape, the importation of Delta variant infections could shift COVID-19 burden from adults to children. We developed an age-structured susceptible-infectious-removed model of SARS-CoV-2 transmission to simulate epidemics triggered by the importation of Delta variant infections and project the age-specific incidence of SARS-CoV-2 infections, cases, hospitalizations, intensive care unit admissions, and deaths. In the context of the vaccination programme targeting individuals aged ≥12 years, and in the absence of non-pharmaceutical interventions, the importation of Delta variant infections could have led to widespread transmission and substantial disease burden in mainland China, even with vaccination coverage as high as 89% across the eligible age groups. Extending the vaccination roll-out to include children aged 3–11 years (as it was the case since the end of October 2021) is estimated to dramatically decrease the burden of symptomatic infections and hospitalizations within this age group , but would have a low impact on protecting infants. Our findings highlight the importance of including children among the target population and the need to strengthen vaccination efforts by increasing vaccine effectiveness. The coronavirus disease 2019 (COVID-19) pandemic is still raging worldwide. The highly contagious Delta variant (B.1.617.2) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was the dominant strain across the world from June 2021 to November–December 2021 . ,20. 5,20e R< 2.4 are needed, in combination with the vaccination programme, to reduce the yearly COVID-19 death toll to a level similar to that of seasonal influenza [e R< 4.0 in combination with the vaccination programme is estimated to be sufficient to decrease the annual number of deaths to less than 89,000 .We leveraged the developed model to explore the impact of implementing different levels of NPIs on the COVID-19 burden while the “adults + adolescents + children” vaccination strategy is in place and considering different levels of VE against infection. When VE against infection is set at 51.8% (baseline scenario), stringent NPIs capable of maintaining the net reproduction number nfluenza   . No estiAnother feature able to shape the epidemiology of COVID-19 is the contact pattern of the population. In the baseline analysis, we used pre-pandemic mixing patterns to represent a situation close to the objective of returning to a pre-COVID-19 pandemic lifestyle   imported seed infections. The obtained disease burden is consistent with those obtained in the baseline analysis across age groups and vaccination strategies .Our modelling study indicates that, under a vaccination programme targeting individuals aged ≥12 years, symptomatic SARS-CoV-2 infections and hospitalization would shift towards children and young adolescents in a new COVID-19 wave caused by the Delta variant. These modelling results obtained for China are backed up by empirical evidence from other countries, where an upsurge of COVID-19 cases and hospitalizations among children and adolescents has been reported since the summer of 2021 ,11,44. EThe numbers depicted by the model are partially due to the relatively low effectiveness against Delta variant infection of the vaccines in use in China (51.8%) as of March 2022. Model simulations show that, in the absence of NPIs, even when 93% of the population aged ≥12 years is fully vaccinated, the importation of Delta variant infections could lead to a new COVID-19 wave and substantial health burden. In particular, the estimated number of deaths over six months was 2.4 per 1000 individuals as compared, for instance, with 0.36 deaths per 1000 individuals in the first epidemic wave in Wuhan in early 2020 .To return to normal (ie no NPIs), the combination of high vaccine coverage, including children and adolescents, and a highly efficacious vaccine that prevents infection appear to be key to reducing COVID-19 burden to levels closer to those of seasonal influenza. To reach this target, in addition to extending vaccination to children aged 3–11 years, as implemented in China since the end of October 2021, our modelling results suggest that vaccine efficacy against the infection would need to be increased to >88%, slightly higher than the estimated effectiveness of two doses of mRNA-1273 (Moderna) vaccine against Delta variant infection  . China iAlthough the inactivated vaccines in use in China as of March 2022 show a relatively low effectiveness against mild and moderate disease caused by Delta variant infection ,18,20, tWe conducted a set of sensitivity analyses to evaluate the impact of the uncertainty surrounding the estimates of COVID-19 epidemiological parameters. These sensitivity analyses show that the main results are essentially unaltered when we assume: (1) homogeneous susceptibility to infection across all age groups, (2) the mixing patterns estimated in Shanghai right after the end of the lockdown in March 2020 , (3) a lMoreover, our findings should be interpreted by considering the following limitations. First, we assumed that vaccine protection lasted longer than the time of our simulations (six months). However, recent studies have shown that the effectiveness of inactivated vaccines declines to a low level at six months after the second vaccine dose . Second,This study focuses on the estimation of COVID-19 burden and its potential age-shift towards younger ages in case of a widespread epidemic caused by the Delta variant in mainland China. As of March 2022, although no longer dominant, Delta is still circulating in countries neighbouring China and have caused local outbreaks in China – see for instance the outbreak in Hohhot, Inner Mongolia that started on 15 February 2022 and caused more than 450 cases . TogetheIn sum, although vaccination is key to dramatically reducing severe outcomes of SARS-CoV-2 infections and the overall burden of the COVID-19 pandemic, in the absence of NPIs, the importation of Delta variant infections could lead to widespread transmission and substantial disease burden in mainland China, even with vaccination coverage as high as 89% of those aged ≥12 years (VE = 51.8% in preventing the infection). Moreover, vaccination programmes targeting individuals aged ≥12 years only can potentially shift the COVID-19 burden towards younger ages. Extending vaccination to children aged 3–11 years would mitigate the disease burden within this age group, but would not be enough to suppress transmission. Our findings highlight the importance of maintaining a certain degree of NPIs  to prevent excessive COVID-19 burden in the case of a nationwide epidemic. Moreover, our results show the need to strengthen vaccination efforts by simultaneously extending the target age groups of the vaccination campaign and increasing vaccine protection via booster vaccination or through the administration of more efficacious vaccines. In particular, the development of new highly efficacious vaccines should be a point of emphasis for China as well as for the rest of the world.Click here for additional data file.


The leave-one-out cross-validation and area under the receiver operating characteristic curve were used to compare different models. The left–right-averaged, normalized volumes of the 25 nuclei of the thalamus and the zone variance of the thalamus demonstrated equal and excellent performance as classifier features for binary organization between AGU patients and healthy controls. Our findings show that texture-based features of susceptibility-weighted images and thalamic volumes can differentiate AGU patients from healthy controls with a very low error rate.Magnetic resonance (MR) imaging data can be used to develop computer-assisted diagnostic tools for neurodegenerative diseases such as aspartylglucosaminuria (AGU) and other lysosomal storage disorders. MR images contain features that are suitable for the classification and differentiation of affected individuals from healthy persons. Here, comparisons were made between MRI features extracted from different types of magnetic resonance images. Random forest classifiers were trained to classify AGU patients ( Aspartylglucosaminuria  is a rare lysosomal storage disorder caused by the deficiency of aspartylglucosaminidase (AGA), a hydrolase involved in lysosomal degradation of N-glycosylated proteins . A prAlthough no approved therapies for AGU are available, preclinical research in gene therapy and pharmacological chaperones has been carried out in recent years ,4. ThereAGA gene or the presence of aspartylglucosamine in a urine oligosaccharide screening, which is followed by genetic confirmation. The latter is the most common way of diagnosing AGU in Finland, and diagnosis based on MRI findings is rare. However, a brain MRI may have already been performed for many patients due to developmental delay or other indications before confirmation of an AGU diagnosis by genetic testing. As thalamic changes typical for AGU are also observed in young AGU patients [AGU is normally diagnosed by either a direct genetic analysis of the patients ,6,7,8, pThe accumulation of paramagnetic compounds in the thalamic nuclei of AGU patients was previously identified based on a decreased signal intensity in filtered-phase susceptibility-weighted (SWI) MR images . FurtherAGU is also known to have a diminishing effect on the volume of the thalamus . Tokola Previous findings on applying machine-learning principles to medical images of individuals affected with lysosomal storage diseases are scarce. Sharma et al.  used a mIn total, the data of 46 unique subjects were used for the analyses in this study. The dataset consisted of 22 patients with an AGU diagnosis and 24 healthy volunteers as controls. The susceptibility-weighted images used in this study were acquired using a 3T MAGNETOM Skyra  scanner. The imaging parameters of the SWI sequence were a TR of 27 ms, TE of 20 ms, flip angle of 15°, slice thickness of 2.0 mm, and in-plane resolution of 0.86 × 0.86 mm, with a matrix size of 256 × 232. Some of these images were previously used in Sairanen et al. [The T1- and T2-weighted images were acquired using a 3T MAGNETOM Skyra . T2 axial series  and T1 3D-MPRAGE series  were acquired. This material was previously used by Tokola et al. [https://surfer.nmr.mgh.harvard.edu/) (accessed on 7 September 2022) cortical reconstruction process recon-all [P, the th element of the matrix is the number of connected voxels of the gray level intensity, i, and the size, j [ZV) is then calculated by:P is the normalized gray level size zone matrix defined as sN is the number of discreet zone sizes in the image, gN is the number of discreet intensity values in the image, and For each subject, the T1-weighted anatomical images were preprocessed and volumetrically segmented using the FreeSurfer j  . DefaultThe caudate nucleus segmentation output by the recon-all FreeSurfer pipeline was used to extract the caudate nuclei of each subject from the T2-weighted MR images. The average intensity value was calculated after eroding the mask, which was performed to avoid including high-intensity cerebrospinal fluid signals from the borders due to a partial volume effect and possible inaccuracies in the segmentation and registration processes. For each subject, the average intensity of the caudate nuclei was then divided by the average intensity of the thalamus, extracted from the T2-weighted images with an eroded binary mask. This calculation of caudate–thalamus mean intensity ratios yielded another feature matrix used for the classification.To test and compare the robustness of the extracted features for the classification between healthy controls and AGU patients, the MATLAB  random forest classifier function TreeBagger was used to grow bootstrap-aggregated decision trees. The decision trees were grown using five separate feature matrices: one containing 25 left–right-averaged, normalized nucleic volumes of the thalami; a second containing total normalized thalamic volumes estimated by the thalamus segmentation tool; a third containing the whole normalized thalamic volumes estimated by the recon-all pipeline; a fourth containing the zone variances of the thalami from SWI; and a fifth containing the caudate–thalamus mean intensity ratios from the T2-weighted images. Due to the limited available data, the classifiers were evaluated using a leave-one-out cross-validation technique . Decisioy-axis than the intensity ratio of the x-axis. AGU patients  and controls  exhibited a statistically significant difference in the caudate–thalamus intensity ratio in the T2-weighted images with p < 0.001, using an alpha level of 0.05. The random forest classifier resulted in an AUC = 0.8008 when using the settings described in Caudate–thalamus intensity ratios in T2-weighted images were calculated as previously described and plotted against the nucleic volume sum and age. To investigate the effects of age on the caudate-thalamus intensity ratio classifier feature, the intensity ratio was plotted against the subject’s age. To compare and visually evaluate the performance of the three volume-based classifiers, receiving operating characteristics (ROC) curves were calculated and plotted. x-axis) and the zone variance (y-axis). The data points of the control group are more spread out, whereas the data points of the AGU patients are clustered closer together. The two subject groups are almost completely spatially separated at both the x- and y-axes, suggesting the robustness of the zone variance parameter in the classification.To visually inspect and compare the grouping of the data points, the zone variances and the sum of thalamic nucleic volumes were plotted as a scatter plot. x-axis) and the zone variance parameter. The differences in zone variance in the two subject groups were not due to the age of the subjects. The zone variances of AGU patients and healthy controls did not correlate with age at the significance level of 0.05.The effect of age on the zone variance classifier feature was further investigated. The robustness of the volumetric features calculated from T1-weighted images, the zone variance calculated from susceptibility-weighted images, and the caudate–thalamus intensity ratio in T2-weighted images were evaluated for binary classification between patients with AGU diagnosis and healthy controls using a random forest classifier and leave-one-out cross-validation. The areas under the receiver operating characteristic curves, accuracies, sensitivities, and specificities were used to compare the performance of the classifiers based on different features. Regarding the three normalized thalamic-volume-based classifiers shown in With an AUC of 0.9922 for Model 4, the radiomics feature zone variance of the gray level size zone matrix calculated from the SWI, was a near-perfect classifier feature for binary classification between diagnosed patients and healthy controls. Even though iron accumulation in the thalamic nuclei was shown to strongly correlate and increase with age and disease progression in AGU , the zonPotential limitations of our study are the low number of probands and patients used for training purposes. These limitations are due to the disease’s rareness and the differences in the MR images, which depend on the type of scanner used to obtain the images. Therefore, attention should be paid to the MRI scanner type and the technical specifications of the scanner when susceptibility-weighted images are analyzed, as compounds that distort the local magnetic field appear either as hypo- or hyperintensities, depending on the manufacturer. Future studies with MR images of AGU patients obtained with different scanner types but classified with our dataset will be useful to see if an improved training dataset will be required to classify images obtained using other scanners. However, regardless of the scanner manufacturer, the accumulated magnetic field distorting compounds are visible in SWI.Our study demonstrates that even in a rare systemic disease such as AGU, machine-learning-based analyses can differentiate previously diagnosed AGU patients from healthy controls when models are trained with simple volume and texture features calculated from various types of magnetic resonance images. In this study, our previous MRI findings of thalamic abnormalities were confirmed. Furthermore, these thalamic signal intensity and volumetric abnormalities could distinguish AGU patients from controls. We could also dissect which abnormalities in the patient images were the most effective ones for classification. The thalamus thus plays an important role in lysosomal storage diseases. Computer-aided analyses are useful, especially in diagnosing rare systemic diseases seldom seen by radiologists. Larger data sets would be beneficial in creating improved machine-learning models with a lower risk of over-fitting.


Opioid drugs are extremely potent synthetic analytes, and their abuse is common around the world. Hence, a rapid and point-of-need device is necessary to assess the presence of this compound in body fluid so that a timely countermeasure can be provided to the exposed individuals. Herein, we present an attractive microneedle sensing platform for the detection of the opioid drug fentanyl in real serum samples using an electrochemical detection method. The device contained an array of pyramidal microneedle structures that were integrated with platinum (Pt) and silver (Ag) wires, each with a microcavity opening. The working sensor was modified by graphene ink and subsequently with 4 (3-Butyl-1-imidazolio)-1-butanesulfonate) ionic liquid. The microneedle sensor showed direct oxidation of fentanyl in liquid samples with a detection limit of 27.8 μM by employing a highly sensitive square-wave voltammetry technique. The resulting microneedle-based sensing platform displayed an interference-free fentanyl detection in diluted serum without conceding its sensitivity, stability, and response time. The obtained results revealed that the microneedle sensor holds considerable promise for point-of-need fentanyl detection and opens additional opportunities for detecting substances of abuse in emergencies. Fentanyl is a prevailing synthetic opioid (schedule II) drug that is analogous to morphine but almost 100 times more potent . NewbornSmall-scale devices with micro and nanoscale features are the inevitable future of sensor technology ,8. TheseThe fabrication of microneedles plays a vital role in the performance of the small-scale biosensing device. Hollow needles provide an ideal platform for transdermal biosensing and drug delivery . MicroneE-Shell 200 is characterized by low water absorption (0.12%) and a high glass transition temperature of 109 C; flexural- and tensile-strength values of 57.8 and 108 GPa, respectively, for this material have been described ,20. In aIn this work, we present the applicability of a 3D-printed microneedle array to detect fentanyl in serum and demonstrate a novel sensing platform for screening opioids in real biofluid. Microneedles have recently earned enormous interest owing to their capability to continuously examine a wide scale of clinically significant analytes. Several important analytes and biomarkers have recently been detected using different microneedle sensing methods. A hollow microneedle platform is explored for fentanyl detection, which was prepared by 3D printing E-Shell 200 material. Subsequently, platinum, silver, and graphene ink were inserted into the hollow microneedle junctions. Graphite ink is used extensively for the construction of biosensors due to the low background current and the capability for surface regeneration . GraphenFentanyl was mixed in 1.0 mg/mL of methanol; graphene ink was used to modify the working-electrode surface. Other chemicals  were all purchased from Sigma-Aldrich . The bovine plasma in the Na-Citrate (filtered) sample was procured from Lampire Biological Laboratories . All of the solvents and other chemicals used in this study were of analytical grade and were used without any further processing.Computer-aided design drawings were used to fabricate the microneedle structure ,2. This The electrochemical operation for fentanyl detection was conducted using a polymeric microneedle platform that had three electrodes: platinum as a counter electrode, silver as a reference electrode, and graphene-ink-modified platinum wire as a working electrode. The SWV studies were performed on a microneedle platform using 0.1 M PBS solution at 7.4 pH at room temperature by swiping the electrode potential (vs. Ag) between 0 and +0.9 V. The fentanyl stock solutions were prepared in methanol and were diluted in PBS solution using the successive dilution method and were used for electrochemical analysis. Before testing the microneedles, the sensor platform was cleaned with ethanol and distilled water and subsequently air dried. Safety note: Fentanyl is a very powerful synthetic and potentially lethal opioid even at extremely low levels as 0.25 mg according to the Drug Enforcement Administration (DEA) [on (DEA) . AdditioThe direct voltammetric detection of fentanyl was conducted on a working sensor modified by graphene ink and subsequently with 4 (3-butyl-1-imidazolio)-1-butanesulfonate) ionic liquid. The ionic liquid plays an important role in increasing the conductivity and also acts as a strong electron-shuttling agent. The graphene-modified microneedle working electrode involves an oxidative dealkylation of the piperidine tertiary amine and nor-fentanyl structure, which exhibits a unique single peak at +0.55 V upon rhythmic scans reflecting the two-electron oxidation of the fentanyl tertiary amine groups. The obtained baseline-subtracted calibration plot confirms the linearity of this anodic current response with the fentanyl dosage over the tested range. Although previous fentanyl sensors have been described as reported using screen-printed electrodes ,16, glovThe electron-transfer characteristics and the earlier-reported carbon-chain conductivity were observed with microneedle electrodes using a 1 mM ferro/ferricyanide solution. The obtained CV peak showed a good response with the redox probe; therefore, we conducted the tests with fentanyl solution. 2 = 0.99 (n = 3), a sensitivity of 0.069 µA/µM, and an LOD (limit of detection) of 29.2 µM.To further extend the applicability of the developed microneedle for fentanyl detection, the sensor was examined in real serum samples by the dosing method wherein varying fentanyl concentrations between 20–100 μM (in 20 μM increments) were spiked in the serum sample and tested on the microneedle sensor. Several sensors have been employed to identify the concentration of fentanyl in liquid samples such as saliva and blood; however, this is the first report of fentanyl diagnostics using a microneedle sensor in serum. The serum samples were commercially procured and directly used for electrochemical testing. The raw serum samples were spiked with fentanyl and tested; however, the level of fentanyl was not detected on the microneedle sensors; therefore, the serum samples were diluted to five times and again tested after spiking with fentanyl. In the diluted samples of serum, the oxidation peak of fentanyl could be detected. As presented in Such unique analytical performance indicates an encouraging perspective on fentanyl detection using microneedles, and could potentially serve as a point-of-need detection for first responders and soldiers in opioid detection. The fentanyl oxidation peak is slightly shifted with the increase in analyte concentration due to the accumulation of the oxidation product on the surface, and possibly due to surface fouling. It is important to mention that the reaction takes place in a small surface area. This phenomenon will certainly affect the analysis when considering real samples with equipment that is optimized for use outside the laboratory. Future efforts will involve utilizing a printed circuit board and integrating the microneedle biosensor for a digitalized output in which the the increase in current value will be displayed.The selectivity of the sensor is important for distinguishing the analyte of interest in the presence of other similar co-existing molecules. Interferents such as uric acid, caffeine, ascorbic acid, acetaminophen, and theophylline were tested along with fentanyl as their presence in biofluid is possible. Ideally, a sensitive and reliable sensor should be able to differentiate the target analyte from interfering agents. This work presented the development of a microneedle platform for the minimally invasive detection of fentanyl in serum. The microneedle sensor array was able to distinguish between different fentanyl concentrations, which enables the potential application of this technology to medical diagnosis. Additionally, the new microneedle-sensor-array platform showed an attractive analytical response in the tested serum samples with high sensitivity, selectivity, and stability. The dynamic range of fentanyl detection was observed between 20–160 μM, with an LOD of 27.8 µM. This platform has the potential for use by first responders, clinicians, and on-site soldiers for rapid detection of fentanyl.


Mosaicing imaging was performed after fibre characterisation by translating the needle probe to enlarge the field-of-view in real-time. The developed ultrathin PA endomicroscopy probe is promising for guiding minimally invasive surgery by providing functional, molecular and microstructural information of tissue in real-time.Photoacoustic (PA) endoscopy has shown significant potential for clinical diagnosis and surgical guidance. Multimode fibres (MMFs) are becoming increasingly attractive for the development of miniature endoscopy probes owing to their ultrathin size, low cost and diffraction-limited spatial resolution enabled by wavefront shaping. However, current MMF-based PA endomicroscopy probes are either limited by a bulky ultrasound detector or a low imaging speed that hindered their usability. In this work, we report the development of a highly miniaturised and high-speed PA endomicroscopy probe that is integrated within the cannula of a 20 gauge medical needle. This probe comprises a MMF for delivering the PA excitation light and a single-mode optical fibre with a plano-concave microresonator for ultrasound detection. Wavefront shaping with a digital micromirror device enabled rapid raster-scanning of a focused light spot at the distal end of the MMF for tissue interrogation. High-resolution PA imaging of mouse red blood cells covering an area 100  As such, photoacoustic endoscopy (PAE) has attracted significant interest for in situ diagnosis of tissue. In the last decade, various photoacoustic endoscopy (PAE) probes have been developed for intravascular and gastrointestinal tract imaging [et al. developed several forward-viewing PAE probes based on the PA tomography principle. In a recent study [ex vivo were visualised down to a depth larger than 1 mm with a spatial resolution of several tens of micrometres [Optical endoscopy is commonly used for the diagnosis of diseases inside human body. However, conventional endoscopes using white-light-illumination only provide morphological information of superficial tissues and thus, biopsy is usually needed to extract small pieces of tissues from suspicious regions for definitive histopathological analysis. This process is time-consuming, cost-ineffective, and may remove functional tissue and miss abnormalities due to sampling errors. Various advanced endoscopy modalities have been investigated to provide tissue characterisation  biopsy’ . Endosco biopsy’ . In cont biopsy’ . As a hy biopsy’ –7. Furth imaging . Althoug imaging ,13. Earl imaging –16. The nt study , a bichrRecently, in order to scan a focused spot over a target located at the distal end of a fibre, MMFs were studied as an alternative to fibre bundles by focusing laser light through the fibres via wavefront shaping ,18. LighIn this work, we developed a miniature forward-viewing PA endomicroscopy probe integrated within the cannula of a medical needle for guiding minimally invasive procedures. This needle probe comprises a MMF for PA excitation laser delivery and a highly-sensitive fibre-optic microresonator sensor for ultrasound detection. As wavefront shaping employs a high-speed DMD, the imaging speed was improved by more than two orders of magnitude as compared to that with a LC-SLM.2.2.1A schematic diagram of the imaging system is shown in PA signals (ultrasound waves) were detected by a fibre-optic ultrasound sensor based on a plano-concave microresonator at the tip of a single-mode fibre. The microresonator comprised a dome-shaped epoxy spacer sandwiched by two dichroic mirrors, which was interrogated by a wavelength-tuneable continuous wave laser . The incident ultrasound waves deform the epoxy spacer leading to changes in the optical reflectivity of the microresonator ,25. An oiameter) ,25.Synchronisation of the DMD patterns display, laser-firing, and data acquisition was controlled by a waveform generator  and a custom MATLAB program. Both the MMF and the fibre-optic ultrasound sensor were integrated within the cannula of a spinal needle (20 gauge), which was affixed on a 3D translation stage. The needle tip  was inse2.2Since laser transmission through a MMF is scrambled due to modal dispersion , a charaThe expression of the transmission constant that connects the us study . Then, b2.3After MMF characterisation, the imaging samples were placed in front of the MMF tip at the focal plane, and the excitation light was focused and raster-scanned over the samples by displaying optimal patterns on the DMD. PAM images were displayed as maximum intensity projections (MIPs) after signal denoising with a 20 MHz low-pass filter. Two metrics, the enhancement factor (EF) and the size of the focus, were used to characterise the focusing performance. The former largely determines the signal-to-noise ratio and the latter determines the lateral resolution of the imaging system. The EF was defined as the ration between the maximum light intensity in the focusing position and the average light intensity in the background. Accordingly, the power ratio was calculated as the fraction of total output light energy distributed in the focal area. The size of the focus was defined as the full-width-at-half-maximum (FWHM) value of the intensity profile across the centre of the focus.The lateral resolution was measured by imaging a 1951 USAF Resolution Test Targets . PA images over a  regions , the latTwo methods of obtaining depth information in 3D-PA endomicroscopy imaging were compared: acoustic sectioning and optical sectioning. With acoustic sectioning, depth information was derived by converting the time-resolved PA signals into depth-resolved signals based on the known speed of sound of the acoustic coupling medium (1485 m/s), while optical sectioning was achieved by focusing and raster-scanning of the excitation laser at different distances from the distal tip of the MMF. Phantoms comprising carbon fibres were used for 3D imaging with a raster-scanning step of 1 2.4To evaluate the potential of the needle probe for imaging biological samples, PA imaging was performed on a mouse blood smear on a coverslip. Mouse blood was obtained from culled mice. The procedures involving mice were ethically reviewed and carried out in accordance with the Animals (Scientific Procedures) Act 1986 (ASPA) UK Home Office regulations governing animal experimentation. After MMF characterisation, the sample was placed in front of the MMF tip with a distance of Video mosaicing was employed to enlarge the FOV of the probe. With mosaicing, MIP PA images were acquired in real-time during the horizontal translation of the needle probe, whilst adjacent images were registered and stitched according to the their common features at the overlapped margins. A fast registration algorithm that performs optimised cross-correlations using discrete Fourier transformations  was used3.3.1The light focus was characterised as the point spread function of the endomicroscopy imaging system. Two examples of light foci at the central and peripheral positions are shown in 1.3 μm . In addiThe waveform of a PA signal generated from a carbon fibre and received by the fibre-optic microresonator ultrasound sensor is shown in The results of the lateral resolution measurement are shown in 0.5 μm . The latectively , which wVisualization 1 and Visualization 2. With acoustic sectioning, a MIP image is shown in The results of the axial resolution measurement are shown in d signal . 3D imag3.2Visualization 3. At the centre of the MMF tip, the total energy at the optical focus  smear sample . As showVisualization 4, and the last frame of the mosaicing video is shown in Mosaicing was implemented by translating the endomicroscopy probe over a mouse blood smear sample and stitching frames in real-time. An example of real-time mosaicing is shown in 4.In this work, we developed a highly miniaturised, high-speed, forward-reviewing, PA endomicroscopy probe integrated within the cannula of a 20 gauge medical needle for guiding minimally invasive procedures. This probe is based on light focusing through a MMF assisted by high-speed wavefront shaping using a DMD and a fibre-optic plano-concave microresonantor ultrasound sensor for signal detection. The fibre-optic ultrasound sensor is well suited to the development of such an ultrathin probe as this miniature sensor provides a high acoustic sensitivity, broad frequency bandwidth, and a near omni-directional response. In comparison, to match the fibre sensor sensitivity, a piezoelectric transducer would have to be made so large that it would be highly directional, which represents fundamental limitations for miniaturisation.The high-speed imaging capability was enabled by using a high-speed DMD for wavefront shaping. The MMF was characterised with a RVITM-based approach . It tookin vivo applications. Recent studies have shown that further increasing the frequency bandwidth of the ultrasound sensor can achieve even higher axial resolution than that with optical sectioning [Volumetric PA imaging was realised by both acoustic sectioning and optical sectioning. With acoustic sectioning, the axial resolution depends on the frequency bandwidth of the ultrasound sensor. For example, with the current ultrasound sensor, the axial resolution was measured as around 50 ctioning ,35,36.Although the optical fluence at the light foci (1.7 n OR-PAM ,35,37–39standard . Advancestandard . Howeverstandard ,43.Focusing light though a MMF by wavefront shaping usually requires a stationary fibre during imaging. However, as reported by Flaes et al. in 2018 , graded-us study . Here wiin vivo animal model, which is promising to provide complementary contrast to PA imaging. These imaging modalities could also be combined with PA endomicroscopy by sharing the same MMF for light delivery to provide complementary information of tissue. In the future, multispectral excitation could be implemented to provide functional information of tissue such as blood oxygen saturation.This work focused on the development of PA endomicroscopy, however, the developed high-speed wavefront shaping technology can be used for other endoscopic imaging modalities such as fluorescence microscopy ,45,46, R5.in situ for guiding minimally invasive procedures such as tumour biopsy.In summary, we developed a highly miniaturised, high-speed, forward-reviewing, optical-resolution PA endomicroscopy probe based on a MMF and a highly sensitive fibre-optic microresonator ultrasound sensor. High-fidelity 3D images of mouse red blood cells were acquired at an unprecedented speed. This needle probe thus holds the potential for providing 3D micro-structural, functional and molecular information of tissue at sub-celluar spatial resolution


The first COVID-19 vaccine outside a clinical trial setting was administered on Dec 8, 2020. To ensure global vaccine equity, vaccine targets were set by the COVID-19 Vaccines Global Access (COVAX) Facility and WHO. However, due to vaccine shortfalls, these targets were not achieved by the end of 2021. We aimed to quantify the global impact of the first year of COVID-19 vaccination programmes.A mathematical model of COVID-19 transmission and vaccination was separately fit to reported COVID-19 mortality and all-cause excess mortality in 185 countries and territories. The impact of COVID-19 vaccination programmes was determined by estimating the additional lives lost if no vaccines had been distributed. We also estimated the additional deaths that would have been averted had the vaccination coverage targets of 20% set by COVAX and 40% set by WHO been achieved by the end of 2021.Based on official reported COVID-19 deaths, we estimated that vaccinations prevented 14·4 million  deaths from COVID-19 in 185 countries and territories between Dec 8, 2020, and Dec 8, 2021. This estimate rose to 19·8 million (95% Crl 19·1–20·4) deaths from COVID-19 averted when we used excess deaths as an estimate of the true extent of the pandemic, representing a global reduction of 63% in total deaths (19·8 million of 31·4 million) during the first year of COVID-19 vaccination. In COVAX Advance Market Commitment countries, we estimated that 41% of excess mortality (7·4 million [95% Crl 6·8–7·7] of 17·9 million deaths) was averted. In low-income countries, we estimated that an additional 45% (95% CrI 42–49) of deaths could have been averted had the 20% vaccination coverage target set by COVAX been met by each country, and that an additional 111% (105–118) of deaths could have been averted had the 40% target set by WHO been met by each country by the end of 2021.COVID-19 vaccination has substantially altered the course of the pandemic, saving tens of millions of lives globally. However, inadequate access to vaccines in low-income countries has limited the impact in these settings, reinforcing the need for global vaccine equity and coverage.Schmidt Science Fellowship in partnership with the Rhodes Trust; WHO; UK Medical Research Council; Gavi, the Vaccine Alliance; Bill & Melinda Gates Foundation; National Institute for Health Research; and Community Jameel. The first COVID-19 vaccine was delivered outside of a clinical trial setting on Dec 8, 2020.Understanding the global impact of vaccination on the course of the COVID-19 pandemic is challenging given the heterogeneous access to vaccines coupled with different levels of transmission and ongoing non-pharmaceutical interventions across countries. In the early months of 2021, the impact of vaccination would have been minimal because of the delay in developing the infrastructure for a widespread vaccination campaign, the need for a delayed two-dose regimen in some jurisdictions to ensure maximum protection,Evidence before this studyWe searched PubMed up to April 26, 2022, without any date limits or language restrictions, using the search terms “vaccin* AND impact AND (death* OR live*) AND  AND (COVID-19 OR SARS-CoV-2)”. We found eight published studies that estimated the impact of COVID-19 vaccination, including deaths averted from vaccination. None of the studies considered the global impact of COVID-19 vaccination, focusing instead on specific regions . Furthermore, the study focusing on the WHO European region only quantified the direct impact of vaccination and did not estimate the indirect effects .Added value of this studyThis mathematical modelling study advances previous work both in terms of scale (number of regions modelled) and in terms of quantifying both the direct and indirect impact of COVID-19 vaccination globally. We estimated the impact of vaccination up to Dec 8, 2021, by fitting COVID-19 transmission models to both reported deaths and excess mortality during the pandemic as a proxy for deaths due to COVID-19. This study is, to the best of our knowledge, the first to use excess mortality estimates in this way, allowing for the impact of COVID-19 vaccination to be estimated more accurately in countries with weaker surveillance systems.Implications of all the available evidenceThe results highlight the substantial impact that vaccination has had on the trajectory of the COVID-19 pandemic. They also illustrate the broader impact of COVID-19 vaccination in terms of allowing countries with high vaccine coverage to relax interventions. Furthermore, the findings highlight the importance of equitable access to vaccines, particularly in low-income regions, where substantially more lives could have been saved if the vaccination targets set out by the COVID-19 Vaccines Global Access (COVAX) Facility (20% coverage in COVAX Advance Market Commitment countries by the end of 2021) and WHO (40% coverage in each country by the end of 2021) had been reached.To reduce inequality, a fair allocation mechanism for COVID-19 vaccines was developed through the COVID-19 Vaccines Global Access (COVAX) facility, with a key target of achieving 20% vaccine coverage for the countries covered by its Advance Market Commitment (AMC) through COVAX-secured doses by the end of 2021.The Economist uses a range of socioeconomic and epidemiological data to infer excess mortality.Quantifying the impact of vaccination is further challenged by the incomplete picture of the COVID-19 pandemic that is obtained from reported deaths. In many countries, vital registration systems are incomplete and therefore only a fraction of deaths are routinely reported. However, even in countries with complete vital registration systems, it is difficult to accurately define the cause of death in individuals who present with multiple morbidities. Excess all-cause mortality (the difference between the observed and expected number of deaths in non-pandemic years) has therefore been used to quantify the impact of the COVID-19 pandemic.We aimed to quantify the global impact of the first year of COVID-19 vaccination and estimate the number of deaths from COVID-19 averted in 185 countries and territories, both from the direct protection of vaccinated individuals and from the indirect protection of all individuals living in vaccinated environments due to the reduction in risk of infection. Additionally, we aimed to quantify the impact that a more equitable global vaccination campaign, meeting the vaccination targets set by COVAX of 20% vaccination coverage of the eligible population by the end of 2021, could have had in COVAX AMC countries. We also aimed to quantify the impact of achieving the WHO target of 40% coverage by the end of 2021 in all countries.Rt, denoting the mean number of secondary infections in the absence of both infection-induced and vaccine-derived immunity. By fitting directly to mortality, we indirectly captured the impact that non-pharmaceutical interventions have had over the course of the COVID-19 pandemic.For this mathematical modelling study, we used a previously published COVID-19 transmission modelWHO dashboard. We assumed a vaccination strategy that first targets those most at risk  and then iteratively distributes vaccines in descending age order. Vaccination was assumed to confer protection against SARS-CoV-2 infection and the development of severe disease requiring hospital admission,Rt trend. We fit the model to COVID-19 mortality in a Bayesian framework using a Metropolis-Hastings Markov Chain Monte Carlo-based sampling scheme. We used the resulting fit to estimate the time-varying reproductive number, Rt, and its associated uncertainty.Vaccination rates for first and second doses in each country were taken from Our World in DataComplete details of the model, vaccination, variants, and model fitting are given in the The Economist.Johns Hopkins University COVID-19 Data Repository ; and the observed scenario in which vaccines were delivered at the rates reported. The third scenario generated an estimate of the trajectory of the epidemic for our fitted model and hence closely matched reported COVID-19 or excess deaths or estimated excess deaths in each country. We calculated the deaths averted as a result of vaccination by subtracting the estimated COVID-19 deaths from the simulation with vaccines included (the observed scenario) from the estimated COVID-19 deaths under the first counterfactual scenario. This process is illustrated in the Rt trends for further non-pharmaceutical interventions, changes in mobility, or development of variants that probably would have occurred differently in the absence of vaccination. To explore the impact of key model parameters on estimates of deaths averted, we did additional sensitivity analyses. These included characterising the effects of the assumed relationship between the infection fatality ratio (IFR) and age .World Population Prospects 2019,All analyses were done with R software (version 4.1.3), with all data, code, packages, and versions used available online at GitHub. This analysis covered 185 countries and territories with a population greater than 90 000 as reported in The sponsors of the study had no role in study design, data collection, data analysis, data interpretation, or writing of the report.Based on our model fit to officially reported COVID-19 deaths, we estimated that 18·1 million  deaths due to COVID-19 would have occurred without vaccinations worldwide during the first year of the COVID-19 vaccination programme . Of these, we estimated that vaccination prevented 14·4 million (95% CrI 13·7–15·9) deaths due to COVID-19, representing a global reduction of 79% of deaths (14·4 million of 18·1 million) during the first year of COVID-19 vaccination . These eUsing our model fit to predicted and reported excess mortality , we estiUsing our model fit to excess mortality, we estimated that most deaths averted were due to the high levels of individual-level direct protection conferred by vaccination, with 79% (15·5 million of 19·8 million) of deaths averted through direct protection . VaccineOverall, estimated deaths averted per capita were highest in high-income countries, reflecting the earlier and wider roll-out of vaccination campaigns . We estiRt trends. When viewed across income strata, a linear log–log relationship was observed between per-capita deaths averted and vaccines administered  deaths due to COVID-19 would have occurred without vaccinations during the first year of COVID-19 vaccination. We estimated that vaccinations averted 7·4 million (95% Crl 6·8–7·7) deaths, 41% (7·4 million of 17·9 million) of the deaths that would have occurred in COVAX AMC countries. Notably, the shortfall of the COVAX target in several regions was estimated to have resulted in an additional 156 900 (95% CrI 147 800–165 400) deaths . AlthougWe found that 96 countries and administrative regions were below the WHO target of 40% vaccination coverage by the end of 2021. Had this target been met, we estimated that 599 300 (95% CrI 577 700–622 400) additional deaths would have been averted . The majOur vaccine impact estimates were dependent on the assumed level of immune escape shown by the delta variant and the assumed relationship between age and the IFR. In the scenario in which the epidemic wave caused by the delta variant was comparable to previous waves and neither reached herd immunity nor resulted in health-system capacity being breached, our estimates of vaccine impact were unchanged regardless of the assumed level of immune evasion associated with the delta variant . HoweverThe high individual-level protection against severe disease and mortality due to COVID-19, as well as the population-level benefit afforded by mild protection against SARS-CoV-2 infection (before the emergence of the omicron [B.1.1.529] variant), conferred by vaccination, has fundamentally altered the course of the COVID-19 pandemic. Directly measuring the impact of vaccination programmes on COVID-19 mortality is not possible as the counterfactual  cannot be observed. Mathematical models are a valuable tool for quantifying the impact of vaccination campaigns on epidemic dynamics.In low-income countries, particularly countries that did not reach the 20% targets set out by COVAX, vaccine impact was substantially lower, with vaccine impact estimated to have been almost doubled if the targets had been reached. If the 40% target, per country, from WHO had been met, we estimated a further increase in deaths averted, mainly focused in lower-middle-income countries and low-income countries. A limitation of our assessment of the COVAX and WHO targets is the timeframe of our analysis, as these targets were set to be reached by the end of 2021, whereas our modelling endpoint was Dec 8, 2021, to align with 1 year since the start of public vaccination. Hence, some countries might have moved closer to achieving the targets, or achieved them, by the end of the year. However, any recent vaccination drives would have had consequently negligible impact given the delay in developing protection and insufficient impact on COVID-19 dynamics.Deriving estimates of vaccine impact is heavily dependent on the counterfactual scenario chosen. In our counterfactual, we assumed the same time-varying levels of SARS-CoV-2 transmission as estimated in our model fits. Consequently, the largest impact was observed in countries that delivered the most vaccinations to date and simultaneously relaxed interventions, allowing SARS-CoV-2 transmission to increase. However, several countries with slower vaccination roll-out as well as countries adopting a zero-COVID strategy maintained stronger interventions to suppress transmission and thus observed smaller impacts of their vaccination programmes as a result. As these countries start to reopen, we predict that vaccine impact estimates would increase in line with increasing levels of SARS-CoV-2 transmission.Under-ascertainment of COVID-19 mortality is a known issue that has hindered our understanding of the pandemic.In our effort to provide impact estimates globally, we introduced various assumptions into our model. We were hindered by the global disparities in SARS-CoV-2 genomic surveillance and the absence of detailed vaccination data for the majority of countries. Consequently, key model inputs had to be created from working assumptions on which vaccines were delivered, how they were delivered, and when new variants of concern spread worldwide. We also assumed that the relationship between age and IFR was the same for each country. These assumptions would have affected our estimates of deaths averted, with sensitivity analyses showing that higher overall IFRs will increase the number of deaths that could be averted by vaccination. Our impact estimates were also limited by the inherent uncertainty in model-based estimates of excess mortality.More broadly, our estimates should be considered in light of the considerable uncertainty inherent in estimating vaccine impact. Uncertainty in the true death toll of the pandemic, the circulating variants of concern and their immunological phenotypes, and the vaccines themselves administered in many countries vastly complicate efforts to derive accurate estimates of the impact of COVID-19 vaccines. However, the results of this analysis still provide a comprehensive and thorough assessment of the impact of COVID-19 vaccination, revealing the substantial impact that vaccines have had and the millions of lives that are likely to have been saved during the first year of vaccination. Despite this, more lives could have been saved if vaccines had been distributed more rapidly to many parts of the world and if vaccine uptake could have been strengthened worldwide. Reaching vaccination coverage targets and improving vaccine coverage globally is dependent on multiple factors and not solely dependent on improving vaccine donations.GitHub repository (version 1.0.1) or the Zenodo open repository. All estimates of deaths averted from vaccination are available in the All data, codes, and supplementary tables used and generated by this study are available in a ACG has received personal consultancy fees from HSBC, GlaxoSmithKline, and WHO related to COVID-19 epidemiology and from The Global Fund to Fight AIDS, Tuberculosis and Malaria for work unrelated to COVID-19. ACG is a non-remunerated member of scientific advisory boards for Moderna and the Coalition for Epidemic Preparedness. ABH and PW have received personal consultancy related to COVID-19 work from WHO. All other authors declare no competing interests.


The impact of the coronavirus disease 2019 (COVID-19) outbreak on out-of-hospital cardiac arrest (OHCA) has been of interest worldwide. However, evidence from low-resource emergency medical service systems is limited. This study investigated the effects of the COVID-19 outbreak on the prehospital management and outcomes of OHCA in Thailand.This multicentered, retrospective, observational study compared the management and outcomes of OHCA for 2 periods: pre-COVID-19 (January–September 2019) and during the outbreak (January–September 2020). Study data were obtained from the Thai OHCA Network Registry. The primary outcome was survival rate to hospital discharge. Data of other OHCA outcomes and prehospital care during the two periods were also compared.P < 0.001). There were also significant decreases in prehospital intubation  and prehospital drug administration  during the COVID-19 outbreak.The study enrolled 691 patients: 341 (49.3%) in the pre-COVID-19 period and 350 (50.7%) in the COVID-19 period. There was a significant decrease in the survival rate to discharge during the COVID-19 outbreak . However, there were no significant differences between the 2 groups in terms of their rates of sustained return of spontaneous circulation  or their survival to intensive care unit/ward admission . The first-responder response interval was significantly longer during the COVID-19 outbreak (median [interquartile range] 5.3 [3.2–9.3] min vs 10 [6–14] min; There was a significant decrease in the rate of survival to hospital discharge of patients with OHCA during the COVID-19 outbreak in Thailand. Maintaining the first responder response quality and encouraging prehospital advanced airway insertion might improve the survival rate during the COVID-19 outbreak. Since 2020, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide and resulted in the coronavirus disease 2019 (COVID-19) outbreak –5. The hResearch revealed the impact of the COVID-19 outbreak during 2020 on the chain of survival of OHCA relative to the normal situation . StudiesThis retrospective observational study drew upon data for the years 2019 and 2020 from the Thai OHCA Network Registry. The Registry was established under the auspices of the Thai Resuscitation Council in 2018. The Registry aims to promote the use of cardiac arrest data to improve the outcomes of OHCA in the community. During the study period, 3 hospitals participated in the network. Two of the hospitals are in Bangkok, the capital city of Thailand. One is located in a predominantly suburban area, whereas the other is in a commercial urban area of Bangkok. The third hospital is in the city of Chiang Mai in northern region of Thailand. Before the current study started, its protocol was approved by the respective institutional review board of each of the 3 participating hospitals.The EMS system at each participating site, as detailed in Table In the event of an OHCA response, the dispatch center would simultaneously deploy a BLS team as the first responder and an ALS team to the scene. In addition, the dispatcher would initially provide dispatcher-assisted CPR to bystanders. The BLS team provided chest compression and bag-valve-mask ventilation using a reservoir system connected to an oxygen tank and applied an automatic external defibrillator. When the ALS team arrived, it provided high-quality CPR, manual defibrillation for shockable rhythms, vascular access, advanced airway insertion, and CPR drug administration. All participating sites applied the same universal termination of resuscitation criteria to withhold resuscitation. The characteristics of the EMS systems of the participating sites were described in a previous study .During the COVID-19 outbreak in 2020, the participating sites changed their prehospital OHCA management protocols, as did other countries. Specifically, the EMS and ED providers were required to don appropriate PPE. Two participating sites allowed their providers to perform endotracheal intubations at the scene as the ALS team included a physician. One site recommended that EMS providers avoid advanced airway insertion during the COVID outbreak. In the ED, providers performed early endotracheal intubation using video laryngoscopes. They were also encouraged to use mechanical CPR devices to reduce the number of resuscitation providers.https://webapps2.duke-nus.edu.sg/eparos/index.jsp). Study investigators reviewed the quality of the data before exporting them for analysis.The participating hospitals developed the OHCA Network Registry using variables and definitions from the Pan-Asian Resuscitation Outcome Study . The RegThe study included adults (age ≥ 18 years) with non-traumatic OHCA. EMS utilized patients, defined as OHCA patients who received prehospital resuscitation by EMS providers, and OHCA patients who were privately transported to the hospital were both eligible in this study. Patients who had Do Not Resuscitate orders were excluded. Eligible participants were assigned to a pre-COVID-19 group (patients experiencing OHCA January–September 2019) and a COVID-19 group (patients experiencing OHCA January–September 2020). A “public location” was defined as health care facilities, public and commercial buildings, nursing homes, streets and highways, industrial places, transportation centers, and recreation places. “First responder” was the BLS team dispatched by an emergency call center but not transporting the patient. “Prehospital advanced airway” included endotracheal intubation and supraglottic airway devices (SGA), that is, laryngeal mask airways) and laryngeal tubes. Lastly, “sustained ROSC” was defined as the return of pulse for more than 20 consecutive minutes.The primary objective of this study was to compare the survival-to-discharge rates of the pre-COVID-19 and COVID-19 groups. The secondary outcomes were all other OHCA outcomes, such as sustained ROSC at ED and survival to intensive care units (ICU) or wards admission. The study also compared the prehospital management performance of the 2 groups: bystander CPR, EMS response interval, first-responder response interval, prehospital intubation, and prehospital drug administration.U test. We illustrated the prehospital intubation and drug administration rates of both study groups and the incidence of COVID-19 by month in a run chart. The OHCA outcomes were analyzed using multiple logistic regression adjusted for age, initial cardiac arrest rhythm, bystander CPR, and witnessed status. The study also analyzed the OHCA outcomes of the shockable-first-rhythm subgroup. The results of the analyses are presented as odds ratios (ORs) and 95% confidence intervals (CIs). Probability (P) values of < 0.05 were considered statistically significant. PASW Statistics for Windows, version 18.0  was used for all data analyses.Based on previous data of the registry, approximately 7% of the patients with OHCA would survive to hospital discharge in the pre-COVID-19 period, while 2.2% survived to hospital discharge during the COVID-19 outbreak. Using a type I error of 5% and a power of 80%, a minimum sample size of 339 participants per group was required. Descriptive analyses of demographic data, clinical characteristics, prehospital management, post-resuscitation care, and patient outcomes were performed in all eligible OHCA patients and also in the EMS utilized subgroup. The categorical variables of the 2 groups were compared using a chi-square test or Fisher’s exact test. The prehospital interval was presented as the median and interquartile range and compared using the Mann–Whitney The data flow of the research is illustrated in Fig. P = 0.025).Table A comparison of the prehospital interventions of the groups is presented in Table Table This multicentered study used data from the Thai OHCA Network Registry to determine the impact of the COVID-19 outbreak on OHCA management and outcomes. Hyperlipidemia was more prevalent among the COVID-19 outbreak group. The investigation revealed that the first-responder response interval for patients with OHCA in the participating areas was significantly longer during the COVID-19 outbreak than in the pre-COVID-19 period. In contrast, the EMS response intervals for the 2 periods were the same. The outbreak did not significantly affect the bystander CPR rate. However, the COVID-19 group had significantly lower rates for first responder dispatch, prehospital advanced airway insertion, prehospital CPR drug administration, and survival to hospital discharge.Hyperlipidemia is one of the well-established cardiovascular risk factors. There was no study reporting the difference proportion of cardiac arrest patients with hyperlipidemia during the COVID-19 outbreak. In addition, there were no differences in other cardiovascular risk factors such as diabetes and hypertension in our study. Further studies are required to investigate the cause and association between hyperlipidemia and OHCA patients during the COVID-19 outbreak.A shortage of PPE and the use of a volunteer-based first-responder system had severe effects: a decreased first-responder dispatch rate and a longer response interval. Without adequate PPE and charity subsidies for volunteer BLS ambulances during the economic depression, BLS teams were reluctant or even refused to accept missions with risks of COVID-19 infection, especially cases of OHCA in which aerosol-generating procedures were inevitable. This was a direct consequence of our particular low-resource EMS system.However, the EMS response interval was unchanged. The hospital-based ALS teams were made up of medical personnel who worked in the ED during their shift and were prepared for EMS missions. Interestingly, no change in the EMS response interval contradicts studies in Singapore, Taiwan, and 5 Western countries. Their EMS response intervals increased regardless of the EMS system in use , 25, 26.The COVID-19 outbreak did not significantly affect the rate of bystander CPR in the study. We speculate that this was partly because most of the OHCA cases during the lockdown occurred at home, where family members willingly performed CPR. A meta-analysis in 2021 that gathered data primarily from developed countries identified a slight but significant increase in the bystander CPR rate during the outbreak period (44.1% vs 46.2%) . In addiThe study found that the prehospital intubation rate decreased during the COVID-19 outbreak. One of the 3 study sites launched a protocol requiring EMS personnel to swiftly transport patients to the ED and avoid prehospital advanced airway insertion. Other personnel with full PPE protection would then handle intubation, endotracheal tubes could be inserted in a controlled environment, and well-equipped airway devices such as video laryngoscopes were on hand. Moreover, rather than intubating patients with OHCA and presumed COVID-19 themselves, the EMS personnel at all 3 study sites would have found it less threatening to transport them to the ED where other personnel would manage the patient.In contrast, the rate of advanced airway placement in other countries, especially supraglottic airway devices, increased significantly , 28. A sIt is still unclear why the rate of prehospital CPR drug administration decreased during the COVID-19 outbreak period. No change was made to the protocol for administering CPR drugs by any of the 3 study sites. Data on prehospital drug administration have rarely been reported in the literature. A study from Korea did not demonstrate a change in prehospital epinephrine administration . We assuAs in other parts of the world , our stuTo improve the survival chances of patients with OHCA during the COVID-19 outbreak, we recommend supplying both first-responder and hospital EMS teams with adequate supplies of PPE and resuscitation equipment. Surge capacity must also be developed and maintained to handle mild cases of COVID-19, thereby sparing first responders for actual emergency patients. Additionally, in the face of limited resources, EMS providers must consider comprehensively to determine whether resuscitation efforts should be limited.This study has several limitations. Firstly, there were missing data, as expected with any retrospective observational study. Survival outcomes and important variables were sometimes not able to be obtained when patients were transported to hospitals that did not participate in the registry. Differences in the pre-COVID-19 and COVID-19 periods should be interpreted with caution, depending on the magnitude of missing data for each variable. In addition, time to prehospital defibrillation, as one of the core process measures, was not presented in the study due to uncertainty of data. This could be a potential confounder to survival outcomes. Secondly, each study site had slightly different EMS systems and OHCA protocols. These differences might have contributed to the heterogeneity of the outcomes. Moreover, only 3 sites were participating in the Thai OHCA Network Registry during the study period. All were tertiary academic hospitals that would have more resources than nonacademic hospitals. Therefore, this study might have underestimated the deleterious effects of the COVID-19 outbreak on national outcomes. Lastly, despite being categorized in the low-resource setting, Thailand is among the upper-middle-income countries. There might be great differences in EMS resources, EMS performance, and survival outcomes between Thailand and other lower income countries.In conclusion, there was a significant decrease in the survival rate to hospital discharge of out-of-hospital cardiac arrest patients during the COVID-19 outbreak compared to the pre-COVID-19 period in Thailand. This decline may represent the outcomes of low-resource EMS systems.


The concept of precision medicine is based on the identification of hallmarks of cancer to exploit them as drug targets. The basic idea was that in this way the therapeutic modalities will be more effective and the side effects will be less. Since the majority of these novel modalities are not specific for a cancer-related biological process or a cancer-specific (mutant) target protein, it is not a surprise that we had to learn new type of side effects, because these therapeutics also affect physiological or pathological processes. Even more, in cases of some of these novel therapies we were able to discover new molecular mechanisms of physiological and pathological processes. Identification of the on-target side effects of targeted drugs can help to prevent the development of them or better manage the patients when emerge during cancer therapy. Precision medicine emerged on the basis of genetic characterization of various cancers, establishing molecular classifications paving the way for the development of various target therapies. Major aim was to design more tumor-specific therapies to spare normal tissues. Today the majority of precision medicine drugs are not specific for mutant targets of the cancer cells since they are active on wild type targets as well, opening the way for the development of the so-called on-target side effects. Although, some of the novel targeted drugs are selective for mutant targets, they can affect wild type ones as well. This is especially true for angiogenesis inhibitors, bone metastasis inhibitors or the new immune checkpoint inhibitors. Herein we summarize the on-target side effects of the target therapies and the underlying pathological or molecular mechanisms behind them, since recognition of those mechanisms can prevent side effect development or can help to manage of them.3  . This drDevelopment of bone metastasis of various cancers has a common pathomechanism: cooperative interaction of cancer cells with the bone microenvironment as well as with osteoblasts and more importantly osteoclasts . Cancer Both bisphosphonates and anti-RANKL antibodies induce therapy resistant osteonecrosis , 13. TheUse of aminobisphosphonates can result in the development of another type of side-effect: fever and acute phase reaction. Caused by activation of macrophages and release of inflammatory cytokines. On the other hand, in case of anti-RANKL antibody therapies infections may emerge due to the fact that these antibodies accumulate in lymph nodes as well, where their inhibitory effect on macrophages may result in the inhibition of acute inflammatory responses , 10. TodDiscovery of immune checkpoints revolutionized the way we think about immune regulation. In case of adaptive immunity the regulatory phase seems to be equally important as compared to stimulatory phase, since that ensures the development of immune tolerance. This process is regulated by immune checkpoints, PD1, TIGIT, TIM-3, CD-200R1, BTLA, VISTA, LAG-3 and CTLA-4 expressed by activated T cells while their ligands are expressed mostly by dendritic cells and T cells, but some of them can be expressed by peripheral non-immune cells as well . The role of CTLA-4 is to block antigen presentation by inhibiting the activation of CD28 and preventing IL-2 production. CTLA-4 is also expressed by Treg cells maintaining long lasting immunotolerance. Expression of PD1 is relatively broader, since beside T cells, it is expressed by B cells, NK cells and macrophages . KnockinAdministration of Ipilimumab (anti-CTLA-4 antibody) to cancer patients induces dose dependently immune-related adverse events (irAE), at higher doses the frequency of grade >3 events is 37% while at lower doses 18%, developing after 2–3 months of therapy. The most frequent irAE is colitis, but dermatitis, hepatitis, endocrinopathies  are also prevalent. Interestingly, at lower rate myasthenia gravis, uveitis, ganglionopathies or even autoimmune thrombocytopenia can also occur (The serious irAE incidence of anti-PD1 therapies is lower as compared to anti-CTLA-4 (grade >3irAE <10%), but unfortunately they can occur later, can be long lasting, and more difficult to treat. Forms of these autoimmune diseases are similar to anti-CTLA-4 therapy, except arthritis and pneumonitis , 20.The irAE incidence of these therapies is lower as compared to anti-PD1, since this type of treatment does not affect the PDL2/PD1 axis and for example the incidence of pneumonitis is half as compared to anti-PD1 therapies , 22, 23.Although the anti-tumor efficacy of this combination immunotherapy is much higher, it also increase the incidence rate of irAE which are also more serious as compared to monotherapies. The most frequent forms are colitis, dermatitis, endocrinopathies and hepatitis , 25. In This is one of the most frequent irAE in case of checkpoint inhibitor therapies and occurs as lichenoid or spongiotic form. Extreme forms are involve more than 30% of the body surface. The autoimmune inflammation takes place at the interface of the epidermis-dermis and involves the accessory organs of the dermis (hair bulb and sweat glands). The incidence of cutaneous inflammations in psoriatic patients is more frequent but the treatment also activate the original disease. Frequently the autoimmune inflammation also involves mucosal surfaces as well , 27, 28.This inflammation type is also very frequent in immune checkpoint inhibitor therapies, especially in case of anti-CTLA-4 antibody administration. It appears as ulcerative colitis with epithelial damage and crypt abscess infiltrated by mixed immune cells (leukocytes and lymphocytes). The severity of the inflammation must be determined from colonic biopsy specimen. In case of the predominant ulcerations, massive anti-inflammatory treatment can be necessary. The key factor behind this induced autoimmune disease is the depletion of the mucosal Treg cells, which is more prevalent in patients with CTLA-4 polymorphism (Y60C). Interestingly, the pathomechanism of the anti-PD1/PDL1 antibody treatment induced enteritis is different, since all inflammatory cells overexpress PD1. Furthermore, the composition of the patient’s microbiome is also an important factor, since the incidence of colitis is higher in those patients where their microbiome is lacking bacteria which are poliamine transport- or B vitamin biosynthesis negatives , 27, 28.Autoimmune disease of the lung as irAE is the characteristics of the anti-PD1/PDL1 therapies and is more frequent in the COPD patients. The pathological spectrum is broad from ARDS and interstitial pneumonitis to sarcoidosis-like forms. Among fatal irAE pneumonitis is the leading cause, therefore early diagnosis is very important. Beside COPD other predisposing factors are smoking, and previous chemo- or radiotherapy. The bronchioalveolar lavage used to be lymphocyte-rich where the physiological ratio of CD4/CD8 is changed significantly , 27, 28 Hypophysitis is a novel autoimmune disease specific for immune checkpoint inhibitor therapies, especially of the anti-CTLA-4 one. This is an acute inflammation of the anterior lobe of the hypophysis which may lead to compression of the chiasma opticum. Peripheral consequences of the hypophysitis can be adrenal gland insufficiency, thyroid dysfunction or gonadal insufficiencies. In this autoimmune complication one can detect circulating autoantibodies against TSH-, FSH- or ACTH-producing cells. It is also important that the TSH- and prolactin-producing cells spontaneously express CTLA-4. It is also important, that the inflammation takes place in form of type-II hypersensitivity reaction. It is also interesting that in case of anti-PD1/PDL1 therapies there is another target organ which the thyroid. These therapies initially inducing hyperfunction which later turn into hypothyreosis , 27, 28.Administration of immuncheckpoint inhibitors, especially in combination, frequently results in hepatitis diagnosed by increased (>3x) transaminase levels, when biopsy is indicated. Histopathologically it is characterized by panlobular inflammation which is accompanied by focal or confluent hepatocyte necrosis. It can appear as lobular granulomatous inflammation, when histiocytes accumulate around lipid vacuoles and fibrin , 27, 28.This is a rare form of irAE in case of immunecheckpoint inhibitor therapies but among fatal cases it is relatively more frequent. Histologically myocarditis is characterized by an inflammatory exudate rich in T cells, but lacking immuncomplex deposition. In a small proportion of treated patients myositis may also occur, which can lead to myasthenia gravis and necrosis of muscles. Histologically, there is a peri- and endomysial mixed inflammatory exudate of T-, B-cells and macrophages, however, anti-AchR or myositis-autoantibodies are missing , 27, 28.Administration of checkpoint inhibitors may induce autoimmune reactions in the CNS in form of aseptic meningitis or encephalitis. Since the symptoms can be indispensable from CNS metastasis the diagnosis is very important based on the examination of the liquor or serum since in this irAE autoantibodies can be detected against NMDA receptor, contactin-associated protein-2 or Hu protein. Autoimmune inflammation can also be induced in the peripheral nerves affecting the neuromuscular junction or the nerves itself leading to demyelinization , 27, 28.Since immuncheckpoint inhibitors are not cancer-specific or selective treatments, they enhance the activity of the entire adaptive immune system resulting in the above mentioned autoimmune adverse events. That was the reason, why it was proposed that the autoimmune adverse events can be used as positive predictive marker for anti-cancer efficacies of these therapies. Such studies mostly done in case of melanoma, which demonstrated that emergence of early immunological adverse events (after 12 weeks) significantly associated with overall survival and it has an independent predictive power , 30. A mIdentification of the molecular subclass of breast cancer, the HER-2 amplified form, initiated a revolutionary change in the treatment of this cancer, originally using anti-HER-2 antibodies, later complementing it with small molecular TK inhibitors . HoweverAs mentioned before, the risk of cardial side effects is higher when anti-HER-2 therapies are combined with antracyclin chemotherapy of breast cancer. One of the main cause of the cardiotoxicity of antracyclins is the fact that this drug rapidly accumulate in the nuclei of cardiomyocytes (since this is a DNA-binding molecule) of the well-perfused heart after i.v. administration . AntracyEGF is the most important regeneratory ligand of the skin epithelia, but it is also involved in maintenance of the integrity of the epidermis and the function of the accessory glands. EGF acts through the EGFR1 receptor, which is therefore constitutively expressed by the epithelial cells . Anti-EGBRAF mutant tumors  can be treated by BRAF inhibitors . AlthougBRAF inhibitors designed as mutant-selective small molecular inhibitors but they have an inhibitory effect on the wild type protein as well. In normal cells BRAF inhibitors induce the activation of the MAPK pathway, due to the induced homo-or heterodimer formation of wild type C-RAF or BRAF. Today BRAF inhibitors are used frequently in combination with MEK inhibitors, in that case of this paradoxical MAPK activation is less frequent. It is interesting, that in RAS mutant premalignant lesions this MAPK activation finalizes the carcinogenic process . As a reAdvent of target therapy started with the development of ABL inhibitors for BCR-ABL fusion positive CML. The original first generation but even the later generation ABL inhibitors are still “dirty” drugs in a sense that they inhibit other kinases especially KIT. Since KIT is the master regulator of the bone marrow progenitor cells, the administration of these non-specific ABL inhibitors results in myelosupression , 42. FurMultikinase inhibitors are now widely used in several cancer types and most of them has VEGFR2 and or PDGFR inhibitory activity. Accordingly, the typical side effects of the angiogenesis inhibitors, such as bleeding and thromboembolism can be considered on-target side effects.It is a novel class of multikinase inhibitors, the ALK inhibitors which are most effective in ALK-fusion positive lung adenocarcinoma. ALK inhibitors also have significant side effects such as pneumonitis, neurological-, cardiological-, gastrointestinal-, and urogenital toxicities but none of them was shown to be considered as on-target ones .However, this cannot be applied to the new TRK inhibitors which are registered in TRK-fusion positive malignancies. TRK inhibitors have three targets, TRK-A, TRK-B and TRK-C which differ in ligands and functions. NGF is the ligand of TRK-A, BDNF and neurtrophin-4 are ligands for TRK-B while neurotrophin-3 is the ligand of TRK-C. These receptors are key regulators of the development of the nervous system. Since TRK-inhibitors are registered as tumor-agnostic therapies, it is important to consider that the development of the nervous system is ongoing in children till age two, therefore in case of TRK-fusion positive pediatric tumors the unique side effect profiles of those inhibitors must be considered. On the other hand, TRK inhibitor administration in adults can also lead to neurological toxicities and uniquely pain after cessation of therapy . This siThe PI3K/AKT/mammalian target of rapamycin (PI3K/AKT/mTOR) signaling pathway plays a key role in many cellular function. The inhibitors of this signaling pathway could be divided into five subgroups, as follows: panPI3K inhibitors, dual PI3K/mTOR inhibitors, PI3K isoform-specific inhibitors, AKT inhibitors, and mTOR inhibitors. The pathomechanism of the side effects are not completely clear in all instances, but as mTOR inhibitors are immunosuppressors, such an effect must always be considered in cancer patients. Inhibition of the different PI3K isoforms could cause different side effects, but some of them should be considered as class-effect of these drugs . Most ofThe PI3K/AKT/mTOR signaling pathway is one of the key effector of the insulin receptor (IR) and insulin receptor substrate proteins (IRS), and therefore it is an important regulator of the effect of insulin. The PI3K/AKT/mTOR axis regulate many targets, such as glycogen synthase kinase 3β (GSK3β) and the forkhead box protein O1 (FoxO1). These effectors increase the glycogen synthesis, and inhibit the gluconeogenesis, therefore lower the blood glucose level. It is not a surprise accordingly, that hyperglycemia is one of the more frequent adverse effect of PI3K/AKT/mTOR inhibitor treatment. The hyperglycemia, induced by PI3K inhibitors is isoform specific, mainly experienced during a PI3Kα specific treatment . HyperglHyperlipidemia is also a frequent side effect of mTOR inhibition therapy. The mTOR pathway is an important regulator of the lipid metabolism. The mTOR kinases form large protein complexes, the mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2). The activated complexes enhance the accumulation of triglycerides, promote adipogenesis and lipogenesis, and inhibit catabolic processes, such as lipolysis and β-oxidation , 47, 48..Most mTOR inhibitor treatment induce pneumonitis . The patThe mTOR targeted treatments frequently cause a wide range of dermatological and mucosal side effects, such as rash, acne-like lesions and mucositis. The pathomechanism of the dermatological side effects of mTOR targeted therapy is related to the inhibition of EGFR, similarly to EGFR target therapies , 46.The PI3K plays a key role in the survival of hepatocytes, therefore the inhibition of PI3K induces apoptosis and liver injury. Hepatotoxicity is frequently associated with PI3K inhibitor treatment, especially with pan-PI3K and PI3Kδ inhibitor therapy. The hepatotoxicity associated with pan-PI3K inhibitors is usually mild, while the hepatotoxicity induced by the PI3Kδ inhibitor idelalisib, is frequent and severe. Autoimmunity is the possible underlying patomechanism, since the liver biopsy of patient suffering idelalisib induced hepatitis shows activated T cell infiltration and treatment with steroids is usually effective .


Benchmarking results on both simulated and real datasets demonstrate that metaMIC outperforms existing tools when identifying misassembled contigs. Furthermore, metaMIC is able to localize the misassembly breakpoints, and the correction of misassemblies by splitting at misassembly breakpoints can improve downstream scaffolding and binning results.Evaluating the quality of metagenomic assemblies is important for constructing reliable metagenome-assembled genomes and downstream analyses. Here, we present metaMIC (The online version contains supplementary material available at 10.1186/s13059-022-02810-y. Constructing reliable metagenome-assembled genomes (MAGs) is of great importance for understanding microbial communities and downstream functional analysis, such as taxonomic annotations and reconstruction of metabolic processes –4. MAGs reference-based and reference-free approaches. Reference-based methods evaluate the de novo assemblies by aligning them against corresponding reference genomes. For example, MetaQUAST  will be regarded as an error k-mer, and a base is regarded as an error base if an error k-mer covers that base. For a given contig, metaMIC will count the number of error bases across the contig and divide it by the contig length. The proportion of error bases within a given region from a contig will be calculated in the same way.A In summary, the above these four types of features will be extracted for the whole contig (contig-based features) or a window of 100bp (window-based features). The contig-based features will be used to train a random forest to identify misassembled contigs, while the window-based features will be used as input of isolate forests to recognize the error regions containing breakpoints.S(c) representing the likelihood that the contig c is misassembled will be output by metaMIC.With the above contig-based features, metaMIC trains a random forest  with choWe split the data into two parts, and 2/3 of the data was used as the training set (20 metagenomes) for optimizing the parameters and 1/3 of the data used as the test set (10 metagenomes) for evaluating the learned models, where the test set will not be seen or used during the training process. The random forest model was trained on a training dataset, whereas the ground truth misassembly label of contigs provided by metaQUAST is used as a target for training the model. We performed 10-fold cross-validations on the training set to select the optimal hyperparameters for the random forest classifier. In more detail, given 20 metagenomes as the training set, we randomly pick 2 of them for validation while the rest 18 metagenomes for training. This procedure will be repeated for 100 times to make sure the robustness of the model trained. To handle the imbalance problem existing between the positive and negative samples, we will perform down-sampling to obtain the same number of correct contigs as that of the misassembled contigs, where there are fewer misassembled contigs as positive samples. Specifically, a subset of negative samples will be randomly selected from the whole negative training set during the down-sampling procedure and the size of the negative subset is the same as the positive training set. This down-sampling will be repeated for 10 times, and a classifier will be trained based on the positive training set and a selected negative subset each time. Thus, an ensemble classifier will be obtained with the average result of the 10 trained classifiers as output, and the ensemble classifier will be used as the final classifier.We used the AUPRC, corresponding to the area under the precision-recall curve, to evaluate the performance of the trained classifier, and the parameters leading to the highest AUPRC during the cross-validation procedure will be used as the optimal hyperparameters  are corrected, leading to the precision of 70~80%. Moreover, metaMIC only corrects contigs that can be split into fragments no shorter than 1000bp in order to avoid generating too short sequences.F1 score . Contigs are assembled with MEGAHIT, IDBA_UD, or metaSPAdes [The training datasets used for training metaMIC contains 30 bacterial metagenomes which were generated in the same way as DeepMAsED . In moreribution . AbundantaSPAdes  to generTo evaluate the performance of different tools, another six simulated and four real datasets are used to see the performance of metaMIC and other competing tools in identifying misassemblies. The simulated virome dataset were generated in the same way as the method used to generate the training dataset. It contains 10 replicate virome metagenomes simulated based on the 10,140 complete viral genomes obtained from NCBI RefSeq collection , where eBacillus cereus ATCC 10987 (B. cereus), Mycobacterium abscessus 6G-0125-R (M. abscessus), Rhodobacter sphaeroides 2.4.1 (R. sphaeroides), and Vibrio cholerae CP1032 (V. cholerae), are used to see the performance of metaMIC on isolate genomes. All the trimmed Illumina paired-end reads can be downloaded from http://ccb.jhu.edu/gage_b/genomeAssemblies/index.html. The contigs used in our experiments are assembled by Velvet [http://bioinf.spbau.ru/en/content/spades-30-gage-b-data-sets. These contigs are further scaffolded with BESST [Four real datasets from GAGE-B project , includiy Velvet , and allth BESST  and Scafth BESST . The acck-mer). When applying ALE to identify misassembled contigs, we aggregated the four ALE sub-scores into a contig score similar to Kuhring et al. [F1 score.We compare metaMIC against two popular approaches, i.e., ALE and DeepMAsED, for identifying misassembled contigs in metagenomic datasets. ALE calculates likelihood scores for each individual position in the contig based on the likelihood of observed reads generated from a given assembly, and the score consists of four sub-scores . The total number of nucleotides from the bin not covered by the representative genome corresponds to the false positives (FP), and the number of nucleotides in the representative genome not covered by any contigs from that bin represents the false negatives (FN). Then the completeness, contamination, and For the real metagenomics data sets where the ground truth genomes are inaccessible, we employ CheckM  to estimPRJNA507739) are used to validate the metaMIC predictions on short-read assemblies. Short-read sequencing approaches are based on Illumina NextSeq 500 sequencing technology, and long-read sequencing is performed on the Sequel systems via PacBio’s single molecule real-time (SMRT) sequencing technology. In total, the sample contains approximately 143 million short reads and 600,000 long reads. The Illumina short reads are assembled into contigs with MEGAHIT while the long-read assemblies are generated with PacBio reads by using metaFlye [A combined rumen fluid and solid sample sequenced with both short- and long-read DNA sequencing technologies (SRA BioProject numbers metaFlye . Then thAdditional file 1: Fig. S1-S29.Additional file 2: Table S1-S13.Additional file 3. Review history.