Phase-contrast magnetic resonance (PC-MR) is widely used in patients with idiopathic normal pressure hydrocephalus (iNPH), but its role in predicting prognosis remains controversial. To evaluate the effectiveness of preoperative PC-MR CSF flow measurement in predicting the clinical response to shunt surgery in patients with iNPH.Forty-six patients with definite iNPH were included between January 2018 and January 2022. PC-MR was used to evaluate CSF peak velocity (PV), average velocity, aqueductal stroke volume (ASV), net ASV, and net flow. The modified Rankin Scale (mRS), iNPH grading scale (iNPHGS), Mini-Mental State Examination (MMSE), and Timed 3-m Up and Go Test (TUG) were used for clinical assessment. The primary endpoint was the improvement in the mRS score 1 year after surgery, and the secondary endpoints were the iNPHGS, MMSE, and TUG scores at 1 year. Differences between shunt improvement and non-improvement groups, based on the clinical outcomes, were compared using the Mann-Whitney U-test, logistic regression models, and receiver operating characteristic curves. Correlations between CSF flow parameters and the baseline clinical outcomes were assessed using Spearman's correlation coefficient.No CSF parameters significantly differed between shunt improvement and non-improvement groups based on mRS and secondary outcomes. And all CSF parameters showed significant overlap in both shunt improvement and non-improvement groups based on mRS and secondary outcomes. Significant correlations between the mRS and iNPHGS scores, and PV, ASV, and net ASV were observed.While some preoperative PC-MR CSF flow parameters reflected the symptom severity of iNPH to a certain extent, they alone might not be ideal markers of shunt responsiveness. Idiopathic normal pressure hydrocephalus (iNPH) is an increasingly recognized treatable disease among older adults and is characterized by a triad of gait impairment, cognitive disturbances, and urinary incontinence, as well as the presence of normal cerebrospinal fluid (CSF) pressure on lumbar puncture , 2. SympCSF tap tests have been widely used to predict shunt responses in clinical practice. Meanwhile, the infusion test, as one of the useful diagnosis procedure for iNPH, have been also used to predict shunt responses in some clinical centers , 7. HoweTherefore, in this study, we used consistent MR scanning equipment and PC-MR scanning methods, collected multiple PC-MR CSF parameters, and focused on definite iNPH patients. The purpose of this study was to investigate whether PC-MR measurements of CSF parameters could be used as predictive markers of shunt outcomes in iNPH patients.The original cohort consisted of 61 consecutive iNPH patients who had undergone PC-MR within 1 week before diagnostic lumbar CSF puncture and received a shunt at the authors' hospital between January 2018 and January 2022. The inclusion criteria were as follows: 1) meeting the diagnostic criteria of the iNPH guidelines  meeting , age ≥60Based on both the iNPH guidelines and previous studies , 2, 14, Shunt improvement was defined as an improvement of 1 or more grades on the mRS, ≥1 point on the iNPHGS, and ≥3 points on the MMSE; and a decrease of >10% on the TUG. The primary endpoint was an improvement of ≥1 point (favorable outcome) on the mRS at 12 months after shunt placement. The secondary outcome measures were the iNPHGS, MMSE, and TUG findings.All patients underwent PC-MRI examinations using the same scanning sequence. To reduce heterogeneities in baseline aqueductal flow in PC-MR as much as possible, the scans of all patients with iNPH were performed at night (8–10 pm) . All imaQuantitative analysis of CSF flow parameters was performed using the flow quantification software provided with the MR scanner. The region of interest was manually defined along the outer border of the aqueduct by the unified opinions of three neuroradiologists with more than 15 years of experience in brain MRI interpretation to reduce the difference in measurement . CSF floThe net ASV was calculated by subtracting the PC-MRI-derived volumetric estimate of retrograde aqueductal flow from that of antegrade flow during one cardiac cycle , 19. Nett-test was used to identify significant differences among normally distributed data between the improvement and non-improvement groups, such as age. Similarly, the Mann-Whitney and chi-square tests (when appropriate) were used to test for differences in CSF flow parameters between shunt responders and non-responders. Associations between outcome and CSF flow parameters were assessed using logistic regression models, with results presented as odds ratios with 95% confidence intervals (CIs) in a forest plot. Receiver operating characteristic curves (ROCs) were used to evaluate the predictive effectiveness of the CSF flow parameters on the results. Correlations between the CSF flow parameters from PC-MR and clinical assessment parameters were determined using the Spearman correlation coefficient. Statistical significance was accepted at the level of 0.05 (two-tailed).All statistical analyses were performed using the SPSS version 24 . The Shapiro-Wilk test of normality was used to determine the distribution of variables. A The preoperative demographic characteristics, preoperative clinical characteristics, and PC-MR CSF flow results of the iNPH patients are summarized in One year after surgery, 28 patients showed improved mRS scores and iNPHGS scores. Twenty-five (74%) patients showed improvement on the MMSE by at least three levels (definitive improvement in cognition). Twenty-eight (61%) of the 46 patients tested exhibited a >10% decrease in the TUG, and 10 (45%) showed improved continence.Patients with iNPH were divided into shunt improvement and non-improvement groups, based on the preoperative and postoperative mRS scores, and their PC-MR CSF parameters and preoperative clinical characteristics were compared . We did Subsequently, we divided iNPH patients into shunt improvement and non-improvement groups based on the secondary outcome measures  before and after shunt surgery, and compared their PC-MR CSF parameters . Similarp > 0.05). Under the primary result, the AUCs of the PC-MR CSF parameters were 0.58  for peak velocity, 0.54  for average velocity, 0.62  for ASV, 0.56  for net ASV and 0.52  for net flow, respectively  was comparable to that in previous studies , 22. AftIn addition to ASV, net ASV, which was used to diagnose iNPH, is another frequently noted PC-MR parameter. However, measurements of the net ASV are associated with technical difficulties similar to those of ASV , 17. TheIn addition to PC-MR parameter measurements, which easily vary, intraventricular CSF flow measurements in iNPH patients also show substantial variations. Jaeger et al. found that substantial variations in the mean wave amplitudes of iNPH patients over the course of several hours of intracranial pressure (ICP) monitoring are common, demonstrating that intracranial pulsatility is not stable, but rather a highly fluctuating phenomenon . These vMoreover, CSF flow itself undergoes dynamic changes, which increases the variability of PC-MR parameters over time, casting further doubt over the value of this method as a prognostic marker. Therefore, we believe that it is difficult to determine the prognosis of iNPH patients post-shunting using only aqueductal CSF parameters in PC-MR. Accordingly, our results question the clinical utility of PC-MR parameters, both with respect to its ability to diagnose iNPH and its value in predicting a clinically favorable shunt response.Furthermore, we found negative correlations between some PC-MR parameters and clinical symptoms, where the more severe the symptoms of iNPH, the lower the PC-MR CSF dynamics. Previous studies found that patients with iNPH have more severe symptoms with a longer duration , and thaOur study has some limitations. Although the number of iNPH patients in our study was relatively larger than that in previous PC-MR studies , 13, theIn conclusion, there were no significant differences in any PC-MR CSF parameters between iNPH patients with and without improvement after shunting. In addition, some PC-MR parameters were associated with symptom severity. Based on these findings, while PC-MR CSF flow parameters may reasonably reflect the severity of iNPH symptoms, used alone, they are not ideal markers for predicting shunt responsiveness in iNPH.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 studies involving human participants were reviewed and approved by Shenzhen Second People's Hospital Bioethics Committee . The patients/participants provided their written informed consent to participate in this study.W-JH performed the experiments, analyzed the data, and wrote the original draft of the manuscript. X-jZ and Q-ZX performed the experiments, analyzed the data, and revised the manuscript. XZ contributed to the experiments. Q-ZX contributed to the data analysis. J-kC contributed to the experiment design and manuscript revision. JX designed the project, supervised the experiments, and drafted and revised the manuscript. All authors read and approved the final manuscript.This work was supported in part by the National Natural Science Foundation of China (Grant No. 82171913) and the Project of Shenzhen International Cooperation Foundation (GJHZ20180926165402083).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.


Poultry is currently the most efficient animal productive system and could contribute to fulfilling the need for protein in order to supply the increasing human population. However, intensive selection of broilers makes them more susceptible to several welfare concerns. Moreover, in order to improve animal welfare, alternative housing systems, such as free-range and organic systems, are becoming increasingly popular. These changes in the modern poultry industry, in combination with restrictions on antibiotics, have led to the need for poultry with higher disease resistance. Naturally occurring antibodies (NAbs), which are major components of innate immunity, have been previously detected in chicken sera. These studies showed that NAbs are heritable and that high levels of NAbs are associated with survival and highly specific antibody responses against pathogens. Therefore, we investigated the circulating levels of IgM and IgY NAbs against selected antigens  as potential biomarkers of poultry welfare and productivity in fast-growth (Ross 308) and slow-growth (Sasso) broilers raised in conventional and free-range systems, respectively, under 3-year industrial-scale production. Overall, we demonstrated significant differences in IgM NAb levels during the final breeding step between the two commercial genotypes, highlighting NAbs as potential biomarkers to be exploited in the poultry industry.n = 555) raised in conventional and free-range systems, respectively, through the use of the specificity, isotypes and levels of circulating NAbs. The possible beneficial effect of oregano-based dietary supplementation was also evaluated. To this end, serum IgM and IgY NAbs against self- (actin and DNA) and non-self- antigens (trinitrophenol and lipopolysaccharide) were measured by ELISA and further correlated with genotype, season and performance. Significantly higher levels of IgM NAbs against all antigens were found in slow-growth compared to fast-growth broilers. IgM NAb levels were also significantly increased in dietarily supplemented slow-growth broilers versus those consuming standard feed. Moreover, significantly elevated levels of anti-DNA IgY NAbs were found in fast-growth compared to slow-growth broilers, whereas the opposite was observed for anti-LPS IgY NAbs. Multivariate linear regression analysis confirmed multiple interactions between NAb levels, genotype, season and performance. Overall, serum NAbs have proven to be valuable innovative immunotools in the poultry industry, efficiently differentiating fast-growing versus slow-growing broilers, and dietary supplementation of plant extracts can enhance natural immunity.Naturally occurring antibodies (NAbs), which are major components of innate immunity, exist in circulation under healthy conditions without prior antigenic stimulation and are able to recognize both self- and non-self-constituents. The present study aimed at identifying potential immunological differences between commercial fast- and slow-growth broilers ( Poultry is currently the most rapidly growing animal productive system and could contribute to fulfilling the need for protein in order to supply the steadily increasing human population. Since the mid-twentieth century, an intensive selection production process has been carried out, resulting in more efficient chickens in terms of feed conversion and rapid growth, making them an effective system for high-quality protein production. However, this intensive selection of broilers has made them more susceptible to several welfare concerns . Under cChanges in the modern poultry industry, in combination with the recent developments in restricted preventive medicine, have led to the need for poultry with higher disease resistance ,2. ThereNaturally occurring antibodies (NAbs), which are important players in both innate and acquired immunity, belong to M, G, A and E immunoglobulin classes and are defined as germline encoded antibodies found in every vertebrate species tested, existing in circulation under healthy conditions without prior known exogenous antigenic stimulation . NAbs arTherefore, we investigated circulating IgM and IgY NAb levels as potential biomarkers of poultry welfare and productivity in two commercial genotypes (Ross 308 and Sasso) raised in either conventional or alternative (free-range) systems under 3-year industrial-scale production. The effect of domestic plant extracts (oregano derivatives) as diet supplements on the immune status of free-range poultry was also studied. For the evaluation of NAb specificity, we focused on the IgM and IgY NAbs, as IgM is the major immunoglobulin class of NAbs in serum, and it biological roles have been mainly attributed to its function and characteristics, such as polyreactivity. IgY NAbs also occur in vivo and can serve as an index of an organism’s immunological history. For the evaluation of NAb levels, common and conserved self-antigens such as actin and native DNA, as well as non-self-antigens such as lipopolysaccharide (LPS) and trinitrophenol (TNP), were chosen. Cytoskeletal proteins  are frequent targets of NAbs and are thought to perform homeostatic roles within the immune response , while DTherefore, with the proposed protocol, we aimed to identify potential differences in the levels and specificity of NAbs by using informative antigenic targets of self- and non-self-constituents that could be further utilized to discriminate fast-growing Ross 308 chicks raised in conventional systems from slow-growing Sasso chicks raised in free-range systems during the final stage of farm breeding.2; FR and FRp groups, 13 birds/m2 indoors and 1 bird/m2 in forage paddock) and raised under the same conditions  with free access to feed and water. Birds were placed in commercial poultry farms on the same date, which were fully equipped with automatic ventilation, heating, lighting and feeding systems. Water and feed were offered to all birds ad libitum, and the lighting program and microenvironmental conditions  were automatically regulated in all houses according to the recommendations of the breeding company [This study was set up to investigate three study groups under industrial-scale meat production : fast-growth broilers  raised in conventional systems constituted the C group, slow-growth broilers  raised in free-range systems constituted the FR group and slow-growth broilers  raised in free-range systems with 5% domestic oregano derivatives incorporated into their feed constituted the FRp group. Oregano derivatives (oregano oil) were purchased by local farmers in the agricultural area of Ioannina, Epirus and used as premixed (with food) dietary supplements. Broilers of different genotypes were allocated to different facilities , feed conversion ratio (FCR) and European Production Efficiency Factor (EPEF) were calculated cumulatively at the end of the farm breeding. Feed intake (FI) and body weight gain (BWG) were monitored per growing period. FCR and EPEF were calculated cumulatively for the whole breeding period according to the Equations (1) and (2). Final values of performance parameters are shown in Escherichia coli (L2880) were purchased from Sigma Aldrich . The hapten trinitrophenol (TNP) was used in ELISA coupled to a carrier molecule, namely bovine serum albumin (BSA), and TNP25-BSA conjugate was prepared as previously described [Actin (A3653) from bovine muscle, deoxyribonucleic acid sodium salt (native DNA) from calf thymus (D1501) and lipopolysaccharide (LPS) from escribed . High biThe d’Agostino–Pearson omnibus normality test was used to assess the normality of the data distribution. For comparison of two independent groups the Mann–Whitney U test was used. The non-parametric Friedman test was used to detect differences between groups.In addition, principal component analysis (PCA) was used. PCA is a dimensionality reduction method used to identify potential correlations and to reduce the dimensionality of datasets . The new coordinates of the datasets in the dimensionality-reduced space denote the “scores”, while the “loadings” correspond to the correlations between the original variables and the new dimensions (components). Loading values close to +1 or −1 indicate that a variable strongly influences the component, while estimates close to zero indicate that the variable has a weak or no influence on the component. The input data were centered, and singular value decomposition was applied. Biplots were created to show the scores and loadings in a single plot.Moreover, to study the correlation among NAb levels, European Production Efficiency Factor (EPEF), genotype and season, we applied two similar multivariate linear regression models with two-way interactions. In the first model, we specified NAb levels as the dependent variable and genotype and season as independent factors, with EPEF as the independent continuous variable. In the second model, we specified EPEF as the dependent variable and genotype and season as independent factors, with NAb levels as independent continuous variables.p-value (p) was less than the significance level. Statistical analysis was performed, and graphs were made in GraphPad Prism version 9.0.0 .In all cases, the significance level was set at 5%, the tests were two-sided and a result was considered significant if the estimated n = 210) and C  groups are shown in p < 0.0001). Similarly, for non-self/foreign antigens, the FR group exhibited 1.5- and 2.4-fold higher levels for TNP and LPS, respectively (p < 0.0001).Levels of circulating IgM NAbs for the FR . A non-significant 1.1-fold difference in levels was observed for actin, while no differences were observed for TNP. Interestingly, levels of NAb against DNA were significantly lower by about 0.6 fold for the FR group in comparison to the C group (p < 0.0001).Similarly, levels of circulating IgY NAbs for the C and FR groups are shown in n = 210) and FR  groups are shown in p < 0.001) for the winter, summer and autumn seasons but not for spring. Moreover, for the C group, IgM NAb levels reached a peak in spring for all antigens, as also observed for IgY NAb levels. On the other hand, levels of IgY NAbs against actin, TNP and LPS had an obvious decline in spring for the FR group, reaching lower levels than those of the C group in the same period. IgY NAb levels against DNA were significantly higher in the C group in all seasons (p < 0.0001). Furthermore, DNA and IgY NAb levels exhibited significant differences between the FR and C groups for winter, spring and autumn but not for summer.An attempt was also made to assess the impact of seasons on NAb levels and, consequently, on how innate immunity levels are shaped. Levels of circulating IgM and IgY NAbs for the C , they were negatively correlated with EPEF in summer in the case of slow-growth poultry (p < 0.05). On the other hand, levels of IgY NAbs against all tested antigens were positively correlated with EPEF, independent of season and genotype (p < 0.05). Specifically, levels of IgY NAbs against TNP were found to be positively correlated with the free-range genotype (p < 0.05). Additionally, a positive correlation between anti-LPS IgY NAb levels in summer (p < 0.05) and autumn (p < 0.01) was found, but with a negative correlation with slow-growth EPEF for the same periods .In order to further investigate how genotype, season and growth performance  may collp < 0.0001). This model also indicated a positive correlation between EPEF, the fast-growth genotype, season (summer and autumn) and levels of anti-LPS IgM NAbs (p < 0.05). IgY NAb levels strongly influenced EPEF, and more specifically, anti-actin NAbs negatively affected EPEF in spring (p < 0.05), whereas levels of anti-DNA, anti-TNP and anti-LPS NAbs negatively affected EPEF in autumn (p < 0.05).Subsequently, we reversed the question, asking whether the levels of NAbs against the four antigens collectively, together with genotype and season, may correlate with EPEF. Hence, we performed another multivariate linear regression analysis for each antibody isotype independently and defined the EPEF as the dependent variable and the other parameters as the independent variables. Parameter estimates and significance are shown in One of the most critical performance parameters is the mortality rate, which is greatly dependent on the immune status of the poultry. Therefore, we investigated its association with the specificity and levels of NAbs. For that reason, principal component analysis was performed for each antibody isotype independently in order to classify predictor variables according to emergent interrelationship patterns among all NAb specificities and mortality rate. Specifically, five variables were used per PCA analysis : anti-LPS, anti-actin, anti-DNA and anti-TNP NAbs, along with mortality rate. The assumption of independent sampling was met. The assumptions of normality, linear relationships between pairs of variables and the variables being correlated at a moderate level were checked. Two components were rotated based on the criterion of eigenvalues over 1 (Keiser rule) and the scree plot. n = 135) and FR  groups are shown in p < 0.0001) and DNA (p = 0.0002), respectively. Similarly, for non-self/foreign antigens, the FRp group exhibited 1.3-fold higher levels for TNP (p < 0.0001). No significant differences were found between the FR and FRp groups for IgY NAbs against the four tested antigens.Levels of circulating IgM and IgY NAbs for the FRp  compared to fast-growth (Ross 308) chickens. Additionally, multivariate regression and principal component analysis showed a negative correlation between IgM NAb levels and mortality in free-range broilers. As the beneficial roles of NAbs have been primarily attributed to secreted IgM, our results indicate the significant supremacy of slow-growth over fast-growth broilers, in line with the notion that resistant genotypes are more efficient in free-range systems, where there is a higher incidence of pathogenic and environmental exposure. Indeed, many efforts have been made by researchers to identify and reproduce resistant genotypes in the poultry industry, as well as in other meat-based industries ,43. On tp < 0.05), probably reflecting the higher incidence of bacterial pathogenic infection during the summer period. As mentioned above, IgG (IgY for chickens) autoprofiles could represent an ‘antibody fingerprinting’ of each individual based on immune stimulators to which the individual has been exposed. This is in line with the fact that birds spend more time outdoors when weather conditions are mild; therefore, the time frame of exposure increases. Nevertheless, EPEF was found to be strongly associated with the levels of IgY NAbs against all tested antigens, highlighting the fact that active antibody class switching and/or enhancement in the production of IgY NAbs upon stressors is crucial for the productivity of broilers.In terms of performance, slow-growth broilers exhibited a higher cumulative mortality, lower body weight and higher feed conversion ratio (FCR), which led to a lower European Production Efficiency Factor (EPEF). Far from actual numbers, the higher cumulative mortality in broilers raised in free-range conditions could be attributed to their longevity, as they face a higher incidence of disease prior to environmental exposure outdoors, which usually leads to the loss of more birds than in conventional rearing systems. Our regression analysis confirmed significant changes in levels of IgM and IgY anti-LPS NAbs for slow-growth broilers, especially during spring-to-autumn periods. Interestingly, levels of IgM NAbs against LPS in slow-growth poultry were negatively correlated with EPEF in summer (Overall, the increased NAb levels observed in free-range broilers in this study and their association with performance, highlight their potential use as informative biomarkers that could be further utilized in the poultry industry. Similarly to our work, the significance of NAbs in animal welfare and survival has been introduced in other animals in the production sector, such as bovine, cows, calves, pigs and laying hens. ,51,52,53Accordingly, in the poultry industry and, more precisely, in free-range poultry, the particularities of specific management conditions still need to be often re-evaluated, as the high worldwide demand for healthier and safer meat products has been rising steadily for years and is projected to continue ,45,46,47This study was carried out under 3-year industrial-scale production of commercial Ross 308 and Sasso genotype broilers for the evaluation of different rearing systems, with significant conclusions drawn. Overall, serum natural antibodies were proven to be valuable immunotools in the poultry industry, as particularly IgM NAbs against the selected panel antigens are able to differentiate between these two genotypes in terms of their immunological status. Additionally, it was shown that natural immune strengthening could be achieved by dietary supplementation with domestic plant extracts.


In Germany, multimodal psychosomatic inpatient treatment can be initiated for patients with substantial mental disorders  and comorbid physical disease. However, studies investigating changes in psychological and functional treatment outcomes, and predictors of long-term treatment effects in patients undergoing psychosomatic inpatient treatment are needed.This cohort study analyzed 160 patients aged ≥18 who were treated on an integrated psychosomatic inpatient unit at the University of Göttingen Medical Center. Its aim was to analyze changes in psychological and functional outcomes, and to identify predictors of long-term improvements in health-related quality of life (HRQoL) in patients with comorbid mental and physical illness who were undergoing integrated inpatient psychosomatic treatment. Assessments were completed at admission, discharge, and 12- or 24-month follow-up. Outcomes included physical complaints [Giessen Subjective Complaints List (GBB-24)], psychological symptoms [Brief Symptom Inventory (BSI)], and HRQoL [European Quality of Life Questionnaire (EQ-5D)].d = −0.83, p < 0.001), physical symptom burden , and HRQoL  from admission to discharge, and significant, small- to medium-sized greater improvements in all psychological outcomes from admission to follow-up . Furthermore, better improvement in HRQoL during hospitalization  was associated with higher HRQoL at follow-up. Finally, intake of antidepressant at discharge was associated with impaired HRQoL at follow-up .One-hundred sixty inpatients were included . There were significant, medium- to large-sized improvements in psychological symptoms (BSI-Global Severity Index; There were significant short- and long-term improvements in psychological symptoms, physical complaints, and HRQoL after treatment on an integrated psychosomatic inpatient unit in patients with mental disorders and a comorbid physical disease. Among individuals with chronic physical diseases, mental disorders are highly prevalent –4 and arOne potential treatment option for more severely ill patients with mental disorders  and comorbid physical illness is multimodal care in an inpatient psychosomatic medicine setting –23. InpaIn addition, physical diseases  with pronounced psychological components are treated. A meta-analysis of randomized controlled trials (RCTs) evaluating these types of psychotherapy-focused hospital treatments  found thN = 1829) found age not be associated with changes in psychological outcomes at admission, discharge, and 1-year follow-up (N = 298) of standardized five-week multimodal cognitive-behavioral therapy (CBT) demonstrated that women with depressive disorders and chronic pain syndromes benefit significantly more than men from the program (N = 2481) investigating a treatment effects of CBT in patients with minor or major depression after myocardial infarction  the multimodal, inpatient psychosomatic treatment would lead to significant improvements in psychological and functional outcomes at discharge and 12- or 24-month follow-up compared to admission. Furthermore, we expected that (2) female sex, higher age, and the presence of comorbid cardiovascular disease would moderate these effects; and that (3) both sociodemographic and treatment-related variables  would be associated with HRQoL in this population.The primary aim of this single-center cohort study was to assess changes in psychological and functional outcomes from admission to discharge and 12- or 24-month follow-up in patients with mental disorders and a comorbid physical disease undergoing an integrated, inpatient psychosomatic treatment program. The secondary aims were to investigate whether (i) age, sex, and the presence of comorbid cardiovascular disease act as moderators of changes in treatment outcomes; and whether (ii) there are influencing factors on HRQoL at follow-up in patients with indication for an inpatient psychosomatic care with a comorbid physical disease. Ethical approval for this study protocol was obtained from the Ethics Committee of the University of Göttingen Medical Center (#1/10/11) on January 31, 2012.In total, 160 patients aged 18 years or older who were treated on the multimodal inpatient psychosomatic unit of the Department of Psychosomatic Medicine and Psychotherapy located in the Heart Center of the University Medical Center in Göttingen, Germany, between February 2010 and January 2012 were included. The inclusion criteria were as follows: (a) completed inpatient treatment for at least three weeks; (b) age 18 years or more; and (c) sufficient cognitive skills and ability to speak, read and understand German; The exclusion criteria were severe cognitive impairment, communicative difficulties , or inability to provide informed consent.Data at baseline and discharge were obtained during routine diagnostics and quality assurance and were extracted from participant records retrospectively. They included detailed medical history data obtained during hospitalization, as well as a set of psychological and functional questionnaires completed upon admission and before discharge. For the prospective follow-up assessment at 12- or 24-month post-discharge , informed consent was obtained from all participants after providing detailed study information. Follow-up data were prospectively collected by mailing the study participants a set of the same questionnaires that had been used during hospitalization and a number of tailored items related to events and treatments that occurred after initial hospital discharge.The inpatient psychosomatic unit is run by the Department of Psychosomatic Medicine and Psychotherapy in collaboration with the Department of Cardiology of the University Medical Center Göttingen, Germany, and focuses on treating patients with mental disorders and comorbid cardiovascular or other physical diseases. The unit is integrated into the Göttingen Heart Center and has a treatment capacity for 18 inpatients.Admission is electively planned after a detailed outpatient interview. The minimum age for admission is 18 years. A maximum age is not defined, but the patients should be physically and psychologically able to participate as much as possible in the treatment setting. Furthermore, common admission criteria for an inpatient stay are the simultaneous occurrence of a mental disorder , and a physical disease  or severe functional somatic symptoms attributed to a putative underlying medical illness.2 to severe obesity).The treatment concept of the inpatient unit is based on a bio-psycho-social model . The fouParticipants’ health records were reviewed to obtain sociodemographic and clinical data, including primary admission diagnoses and healthcare utilization. Psychological and functional outcomes were assessed using valid and reliable questionnaires –34.The Giessen Subjective Complaints List (GBB-24) is a 24-item questionnaire for the assessment of physical complaints. For each item there are possible answers from 0 = “not at all” up to 4 = “very much” . The indThe Brief Symptom Inventory (BSI)  assessesThe EQ-5D  is a short instrument, consisting of 5 items, which is used to record health-related quality of life (HRQoL). The 5 items represent the dimensions of mobility, self-care, usual activities, pain/physical complaints and fear/depression , 35. IndSelf-efficacy was assessed using a short form of the General Self-Efficacy Scale (GSE-6) . In the Clinical and psychological data are shown as means (M) and standard deviations (SD) of continuous variables or frequencies and percentages of categorical variables. To analyze relationships between physical and psychological variables at all three timepoints and the comorbid physical disorders, Mann-Whitney U tests were performed. To assess differences between the individuals who did or did not complete all three measurements, we performed one-way analyses of variance (ANOVAs) for continuous variables and Fisher’s exact tests for categorical variables.d  or in the form of the partial eta square (η2): Concretely, η2 ≥ 0.01 assumes a small effect, η2 ≥ 0.06 a medium effect, and η2 ≥ 0.14 a large effect  in order to test the influence of the between-subject factor on the temporal development of the individual psychometric findings.To test influencing factors on the change in psychological and functional outcomes over the course of time between admission and discharge, multi-factorial ANOVA with repeated measurements were used. The time of assessment (discharge vs. admission) was defined as the intra-subject factor, and the influencing variable to be analyzed was the between-subject factor. Significant between-subject effects and within-subject contrasts were examined for their effect size using the η2. To compare mean scores in psychological and functional variables between patients with and without intake of antidepressants, a paired t-test was performed.Finally, we used Spearman’s correlation analysis to examine bivariate relationships between HRQoL at follow-up and HRQoL at admission and discharge, as well as intake of antidepressants at discharge, referral for outpatient psychotherapy post-discharge, and self-efficacy at admission and discharge. Afterward, a multi-factorial ANOVA with repeated measurements was performed to analyze factors associated with change in HRQoL over the course of time between follow-up and admission. The time of assessment (follow-up vs. admission) was defined as the intra-subject factor, and the influencing variable to be analyzed was the between-subject factor. Significant between-subject effects and within-subject contrasts were examined for their effect size using ηp value of <0.05 was considered statistically significant.All analyses were performed using SPSS software, version 27 . A U tests, there were no associations between the comorbid physical diseases and the physical or psychological outcomes at any of the three timepoints.We identified 245 eligible patients who underwent inpatient psychosomatic treatment between February 2010 and January 2012. Of these, 160 patients  completed both the admission and discharge questionnaires and were enrolled in the study. Of these, 92 patients  completed the 12- or 24-month follow-up questionnaires . The cliN = 68) were comparable to completers of all measurements in all variables at follow-up (N = 92), aside from having lower age , and higher psychological distress .Patients lost from discharge to follow-up  and physical complaints , and significant medium-sized improvements in HRQoL , from admission to discharge in patients undergoing integrated inpatient psychosomatic treatment. The adjusted general linear models , physical symptoms , and HRQoL  compared to admission. Between discharge and follow-up there was only a small and non-significant increase in psychological symptoms and only minimal decrease in HRQoL. Physical symptoms increased again at follow-up compared to discharge  but remained significantly lower than on admission. Changes in physical and psychological symptoms as well as HRQoL, were unrelated to the timing of follow-up assessment at 12 vs. 24 months.At follow-up , patientp < 0.001) and discharge , and a significant negative association between EQ-5D-3L at follow-up and intake of antidepressant at discharge . There were no significant associations between HRQoL at 12- or 24-month follow-up with referral of outpatient psychotherapy after discharge , self-efficacy at admission , or self-efficacy at discharge . In multi-factorial ANOVA with repeated measurements, improvement in HRQoL during hospitalization  was associated with better HRQoL at follow-up. Furthermore, intake of antidepressant at discharge was associated with impaired HRQoL at follow-up ; there was no significant effect of follow-up assessment performed at 12 vs. 24 months on HRQoL at follow-up  as well as symptom burden (p = 0.02) at admission but not at discharge  compared with patients without a treatment with antidepressant. The HRQoL was only insignificantly worse in patients receiving antidepressants at admission and discharge while a significant difference emerged during follow-up , and HRQoL (EQ-5D) in patients with mental disorders and physical comorbidity treated on an integrated inpatient psychosomatic unit in an academic Heart Center. These improvements were independent of age and sex and for most variables also of cardiovascular comorbidity. Small- to medium-sized improvements in all outcomes were still found at 12- or 24-month follow-up compared to admission. Better improvement of HRQoL during hospitalization was associated with substantially higher HRQoL at follow-up. Continued psychotherapy after discharge or self-efficacy at admission or discharge did not show significant associations with HRQoL at 12- or 24-month follow-up, while antidepressant medication at discharge was independently associated with poorer HRQoL at follow-up.Inpatient psychosomatic treatment provides a protective environment with a variety of therapeutic interventions , and can focus specifically on patients with a comorbid physical disease  . A meta-However, the present study did not compare the changes in mental health outcomes between integrated inpatient psychosomatic treatment with multimodal components  to an active comparator  in patients with physical comorbidities. Future studies are necessary to provide more information on the following aspects in patients with mental health disorder and a comorbid physical disease: (a) effective duration of inpatient treatment ; (b) effectiveness of the treatment domains; and (c) cost-effectiveness of integrated multimodal inpatient units with specialized care of physical comorbidities  compared to general psychosomatic/psychiatric units. Given the trend of sub-specialization in medicine, it might be of clinical importance that psychosomatic (and psychiatric) inpatient units focus on prevalent physical comorbidities in patients with mental health disorders with further expertise in areas such as psycho-cardiology, psycho-diabetology, or psycho-oncology. However, better scientific evidence is necessary to implement more sub-specialized inpatients units not only in the German health system but also worldwide.N = 93) comparing an integrated concept of psycho-cardiac rehabilitation vs. monodisciplinary cardiac or psychosomatic rehabilitation showed that cardiac patients benefit more from an integrated psycho-cardiac treatment concept  who are typically older than those studies in the previous meta-analysis . This is concept . In line concept .Finally, in the present study, intake of antidepressants at discharge was independently associated with poorer HRQoL at follow-up. There might be several explanations for this finding. First, patients on antidepressants showed higher symptom burden and psychological stress at admission compared with patients without intake of antidepressants. Therefore, higher initial symptom severity of major depressive disorder (MDD) may have been a reason for antidepressant prescription, which would suggest that it is the initial severity of depression rather that the medication itself that impaired follow-up HRQoL scores in patients taking antidepressants. However, our model controlled for baseline HRQoL, making such inverse causation less likely. Previous studies in patients with MDD undergoing inpatient treatment or day hospital treatment , 41 showIn summary, this cohort study provides further scientific support for significant improvement in patient-reported outcomes after integrated psychosomatic inpatient care and for factors influencing long-term improvements in HRQoL in patients with mental disorder and a concomitant physical disease . The strengths of our study are the longitudinal approach with various psychological and functional outcomes at three time points. However, our study has several limitations. Firstly, this is a single-center cohort study without randomization or an active comparator. Secondly, we excluded 68 patients, as they did not complete all the study assessments. Finally, the German system with established departments for psychosomatic medicine and psychotherapy with inpatient treatments of 4–6 weeks duration and more represents a unique treatment system worldwide which impedes generalizability of our results to other health care systems.Multimodal, integrated inpatient psychosomatic treatment was associated with significant medium- to large-sized improvements in physical and psychological symptoms, and HRQoL in inpatients with mental disorders and a comorbid physical disease. These results indicate that integrative patient-centered care concepts  are useful for treatment of patient with somatic-mental comorbidity. Finally, improvement in HRQoL from admission to discharge seems to remain mostly stable over 1–2 years. Large, randomized-controlled, multi-center clinical trials investigating the effectiveness of integrated, specialized  psychosomatic inpatient treatments compared to an active comparator are needed to confirm their impact on psychological, functional, and medical outcomes. Furthermore, cost-effectiveness analyses should be provided. However, for the multimorbid patients treated on the unit studied here, inpatient treatment is often the last resort after unsuccessful outpatient therapies. Both, ethical considerations and clear patient preferences for an established and probably effective treatment make randomized trials hard to conduct in this setting, as long as no equally attractive treatment of proven efficacy can be offered as a comparator.msadlonova@mgh.harvard.edu.The dataset generated and/or analyzed for the present article is not available for sharing as the informed consent form did not include information about data sharing policy. Requests to access the datasets should be directed to MS, Ethical approval for this study protocol was obtained from the Ethics Committee of the University of Göttingen Medical Center (#1/10/11) on January 31, 2012. The patients/participants provided their written informed consent to participate in this study.MS and CH-L: conceptualization, methodology, statistical analyzes, and writing—original draft. JKL and CK: conceptualization, investigation, project administration, and data curation. JKL, CK, CC, DB, and CH-L: writing—review and editing. CC and CH-L: supervision. MS: data curation and writing—review and editing. All authors have read and agreed to the published version of the manuscript.


The symbiont-associated (SA) environmental package is a new extension to the minimum information about any (x) sequence (MIxS) standards, established by the Parasite Microbiome Project (PMP) consortium, in collaboration with the Genomics Standard Consortium. The SA was built upon the host-associated MIxS standard, but reflects the nestedness of symbiont-associated microbiota within and across host-symbiont-microbe interactions. This package is designed to facilitate the collection and reporting of a broad range of metadata information that apply to symbionts such as life history traits, association with one or multiple host organisms, or the nature of host-symbiont interactions along the mutualism-parasitism continuum. To better reflect the inherent nestedness of all biological systems, we present a novel feature that allows users to co-localize samples, to nest a package within another package, and to identify replicates. Adoption of the MIxS-SA and of the new terms will facilitate reports of complex sampling design from a myriad of environments. With the realization that eukaryotic organisms can harbor rich microbial communities, came also the view that these smaller partners may in fact play important roles in mediating host-symbiont associations, thus adding a further layer to this complex set of nested interactions, -microbe –8. As th-microbe , which w-microbe , it reflhttps://gensc.org) has developed and maintains a suite of minimal information metadata standards for describing sequence metadata (checklists) for genome (MIGS), metagenome (MIMS), marker gene sequences (MIMARKS), simple amplified genome (MISAG), metagenome-assembled genome (MIMAG), virus genomes (MIUViG) and environmental packages for describing habitat-specific contextual data of the sampling environment [https://gensc.org/mixs/).Collecting relevant metadata (data describing data) is now widely recognized as critical to contextualize samples and increase their reusability and reproducibility –11. The ironment , 12, 13,ironment , https:/https://www.hmpdacc.org/), Earth Microbiome Project (https://earthmicrobiome.org/), Microbiology of the Built Environment , microbiome bioinformatics platforms  and are now required upon manuscript submission. A primary advantage of the MIxS standards is the collation of large aggregates of associated metadata that can be harnessed to uncover, and eventually comprehend, patterns of microbial diversity and ecology.The MIxS standards are used broadly across the microbiome research communities. These standards have been integrated into large scale microbiome projects , commensal , or parasitic  . In the https://github.com/GenomicsStandardsConsortium/mixs).Here, we present the selected list of metadata descriptors for symbiont-associated microbiota studies, including a subset of mandatory (M) terms that underpin metadata compliance  and “type of symbiosis”  are discrete but complementary items. While “host dependence” aims to provide a general characterization of the known type of host dependence for the symbiotic organism , “type of symbiosis” was specifically designed to further characterize the type of biological interaction established between the symbiotic organism and its respective host at the moment the biological sample was taken . As a result, the MIxS-SA package features mandatory and conditionally mandatory, and optional features that enable flexibility according to the knowledge of the study system at the time of sampling. Two examples of MIxS-SA-compliant metadata are provided in Supplementary information era spp. .Fig. 1Exhttps://gensc.org/mixs/), here we introduce three additional new terms: one is shared by several relevant MIxS environmental packages, and the two others will feature within the core MIxS package. The new term “observed host symbionts” provides a more comprehensive descriptor for the subject organism associations with smaller symbionts and it has been added to the host-associated, human-associated, plant-associated, human-vaginal, human-skin, human-oral and human-gut packages. The term “biotic relationship” has been added to the core package as a conditional descriptor of the relationship between the subject organism and other larger host organism(s). Finally, it appears necessary to include in the MIxS core a new term that takes into account the nested feature of most associations found in nature, such as host-symbiont-microorganism, in which multiple packages are necessary to describe the samples of the study . The proposed term “relationship to other samples” indicates the direct relationship between two samples from the same Bioproject, that are described in different environmental package(s). This proposed feature, still under development, will allow for integrated analyses of the microbiota of symbiotic organisms and their direct environment, even in the context of co-infections . This feature will also benefit other studies by providing ecologically-relevant contextual information . In conclusion, it is our hope that the MIxS-SA, together with the new terms, will enable researchers to better conduct integrated analyses of multi-level biological systems with the ultimate goal of better understanding the role of microbes associated with symbionts.While identical terms are often used in several of the 17 environmental packages currently available (Table S1Table S3


Zeugodacus cucurbitae (Coquillett), Bactrocera dorsalis (Hendel), and Ceratitis capitata (Wiedemann) are important pests of fruit and vegetable crops and are difficult to control because of their rapid reproduction rate and egg production. To investigate the key genes regulating reproduction in three fruit fly species, we selected genomic information of three fruit fly species, screened specific genes and single-copy homolog genes, and performed KEGG and GO enrichment analysis on specific genes and single-copy homolog genes of the strong positive select (SP); the results showed that Z. cucurbitae (Coquillett), B. dorsalis (Hendel), and C. capitata (Wiedemann) had seven, 11, and one Vitellogenin-related genes, respectively; Z. cucurbitae (Coquillett) had 84 specific genes enriched in immune system-related pathways; B. dorsalis (Hendel) had 1,121 specific genes enriched in signaling pathways related to cell growth and differentiation; C. capitata (Wiedemann) had 42 specific genes enriched in the degradation and metabolism pathways of exogenous organisms; Z. cucurbitae (Coquillett) may have a stronger immune system; B. dorsalis (Hendel) has a faster developmental and reproductive rate; and C. capitata (Wiedemann) has a higher detoxification capacity. Only one SP single-copy homolog gene  is enriched in the fatty acid metabolic pathway in both Z. cucurbitae (Coquillett) and B. dorsalis (Hendel) as well as in Z. cucurbitae (Coquillett) and C. capitata (Wiedemann). This study provides a molecular basis for studying the reproductive mechanisms of three fruit fly species and provides a scientific basis for developing effective control strategies for fruit flies. Zeugodacus cucurbitae (Coquillett), Bactrocera dorsalis (Hendel), and Ceratitis capitata (Wiedemann) are important quarantine pest fruit flies that are widely distributed in the tropical, subtropical, and temperate regions, and Z. cucurbitae (Coquillett) originated in India and mainly affects plants of the Cucurbitaceae and can parasitize more than 125 species of plants  originated in Southeast Asia and affects more than 450 species of fruits and vegetables (C. capitata (Wiedemann) originated in the western region of sub-Saharan Africa and affects more than 260 species of fruits and vegetables, including Solanaceae (Fruit flies (Diptera: Tephritidae) have a large number of species, with about 500 genera and 4,500 species known worldwide, of which about 1,500 species may be associated with various fruits and more than 250 species are of economic importance . Zeugodaf plants ; B. dorsgetables ; C. capilanaceae . There alanaceae . A compaLactobacillus plantarum from different sources revealed that L. plantarum of animal intestinal origin had better amino acid transport capacity and L. plantarum strains attached to plant surfaces had better carbohydrate utilization capacity , B. dorsalis (Hendel), and C. capitata (Wiedemann) were comparatively analyzed to further investigate the mechanisms of regulating reproduction in the Vg-related genes of the three species and to provide new ideas for the control of the three fruit fly species.Vitellogenin (Vg) is a large-molecule lipoprotein of the phospho-glycine class. After synthesis in the fat body, Vg is secreted into the hemolymph, where it is normally taken up by the developing oocyte as the main nutrient in the egg, but in the absence of food, increased feeding pressure, failure to find an egg-laying site, or the lack of males to mate with, egg absorption occurs, and Vg in the egg is degraded and released into the hemolymph as a nutrient to maintain individual development. The primary function of Vg is to be a source of energy for egg production and development of insects, including amino acids, carbohydrates, fats, phosphates, vitamins, and sulfates . In receZ. cucurbitae (Coquillett), B. dorsalis (Hendel), and C. capitata (Wiedemann) was obtained from the National Center for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov/).Basic genome information for Z. cucurbitae (Coquillett), B. dorsalis (Hendel), and C. capitata (Wiedemann) were used to identify homologous genes using blastp in combination with OrthoMCL. After obtaining homologous and specific gene families, the number of genes contained in each gene family (the number of gene family copies) was counted in each of the three fruit fly species, and the gene families specific to the three fruit fly species were identified and subjected to functional annotation, KEGG enrichment analysis, and GO enrichment analysis. The gene families corresponding to homologous genes in the three fruit fly species were classified into two gene sets, single-copy homologous genes, and multi-copy homologous genes, and the Ka/Ks values of single-copy homologous genes were calculated, and the single-copy homologous genes were classified into the strong positive select (SP), weak positive select (WP), and negative select (NG) genes according to the Ka/Ks values, and KEGG enrichment analysis and GO enrichment analysis were performed on the SP single-copy homolog genes.The genomic data of p-value of this hypothesis test is calculated as follows:Within an organism, different genes coordinate their biology with each other, and pathway-based analysis helps to further understand the biological functions of genes. KEGG is the main public database on pathways. The pathway significant enrichment analysis uses the KEGG pathway as the unit and applies a hypergeometric test to identify pathways that are significantly enriched in species-specific genes when compared to the entire genome. The p-value. The Q-value of a particular hypothesis test is the minimum of the FDR, and the hypothesis test can be considered significant under these FDR. Enrichment by pathway significance identifies the most important biochemical metabolic pathways and signal transduction pathways involved in specific genes.where N is the number of genes with pathway annotation in all unigenes, n is the number of specifically expressed genes in N, M is the number of genes annotated with a specific pathway in all unigenes, and m is the number of specific genes expressed with a specific pathway annotation. After correction for multiple testing, pathways with Q-value ≤ 0.05 were selected as those significantly enriched in specific genes. The q-value and FDR are similar, both being a correction for the Gene Ontology (GO) is an international standardized gene function classification system that provides a dynamically updated set of controlled vocabulary to comprehensively describe the properties of genes and gene products in an organism. GO has a total of three ontologies, which describe the molecular function of a gene, the cellular component, and the biological process involved. Each term corresponds to an attribute.http://www.geneontology.org/) and counts the number of genes per term to obtain a list of genes with a particular GO function and a count of the number of genes. A hypergeometric test was then applied to identify GO entries that were significantly enriched in differentially expressed genes compared to the whole genomic background, and the p-value of this hypothesis test was calculated as follows:GO function significant enrichment analysis provides GO function entries that are significantly enriched in specific genes after comparison with reference genes and screens which biological functions are significantly associated with specific genes. This analysis first maps all specific genes to each term of the Gene Ontology database , and then the Ka ratio between each single-copy homologous gene was calculated based on the nucleic acid sequence corresponding to the protein sequence. The Ka, Ks, and Ka/Ks values between homologous genes were calculated using the KaKs_Calculator Toolbox (version 2.0).In genetics, Ka/Ks or dN/dS indicates the ratio between the rate of non-synonymous substitutions (Ka) and the rate of synonymous substitutions (Ks). This ratio can determine whether there is a selective pressure acting on this protein-coding gene. It is generally accepted that synonymous mutations are not subjected to natural selection, whereas non-synonymous mutations are subjected to the action of natural selection. In evolutionary analysis, it is of interest to know the rate at which synonymous and non-synonymous mutations occur. The following parameters are commonly used: the frequency of synonymous mutations (Ks), the frequency of non-synonymous mutations (Ka), and the ratio of the rate of non-synonymous mutations to the rate of synonymous mutations (Ka/Ks). Single-copy homologous gene protein sequences from different species or subspecies were subjected to multiple sequence alignment by using muscle (The basic information of the genomic data of the three fruit fly species is shown in Z cucurbitae (Coquillett) and B. dorsalis (Hendel), 37,415 and 10,547 homologous genes and gene families in Z cucurbitae (Coquillett) and C. capitata (Wiedemann), and 61 and 24 homologous genes and gene families in B. dorsalis (Hendel) and C. capitata (Wiedemann). Z cucurbitae (Coquillett) had 2,754 specific genes and 1,881 gene families, B. dorsalis (Hendel) had 19701 specific genes and 19701 gene families, and C. capitata (Wiedemann) had 3,160 specific genes and 2,718 gene families.For the genomes of the three fruit fly species, blastp was used in conjunction with OrthoMCL to identify homologous genes among the three species. The sequences were matched two by two, and pairs with an E-value less than 1e-5 and a coverage of more than 30% were considered homologous genes in the Blast comparison. OrthoMCL was used to assign homologous genes to the same family. As shown in Z cucurbitae (Coquillett), B. dorsalis (Hendel), and C. capitata (Wiedemann) were annotated to the KEGG database for comparison, and their specific gene KEGG enrichment analysis bubble maps were obtained to identify the pathways that were significantly enriched in specific genes. The highest gene abundance in Z. cucurbitae (Coquillett) was found for the Toll and Imd signaling pathway with about 50 genes, followed by MicroRNAs in cancer and influenza A, all three with Q values less than 0.0005. Among all metabolic pathways in Z. cucurbitae (Coquillett), the largest enrichment factor was neomycin, kanamycin, and gentamicin biosynthesis with an enrichment factor of about 0.7, followed by hematopoietic cell lineage, with an enrichment factor of about 0.46  with human papillomavirus infection, enriched with 331 genes, followed by the MAPK signaling pathway—fly MAPK and viral carcinogenesis. Among all metabolic pathways in B. dorsalis (Hendel), the largest enrichment factor is the TGF-beta signaling pathway with an enrichment factor of about 1, followed by oocyte meiosis and the Hippo signaling pathway—fly (C. capitata (Wiedemann) were found for protein digestion and absorption (39 genes), followed by viral carcinogenesis and the Toll and Imd signaling pathway. Among all metabolic pathways in C. capitata (Wiedemann), the largest enrichment factor is circadian rhythm—fly with an enrichment factor of about 0.42, followed by ECM-receptor interaction with an enrichment factor of about 0.34 (The unigenes of out 0.46 . The highway—fly . The higout 0.34 .Z. cucurbitae (Coquillett), B. dorsalis (Hendel), and C. capitata (Wiedemann) are shown in Z. cucurbitae (Coquillett) was enriched most in the broad category of cellular components in the pathways of membranes, cells, and cellular components. B. dorsalis (Hendel) and C. capitata (Wiedemann) were most enriched in the cellular component major category for cellular, cellular component, and organelle pathways, and in the molecular function major category, all three species were more catalytically active and binding enriched for genes.The results of GO enrichment analysis for genes specific to Z. cucurbitae (Coquillett) and B. dorsalis (Hendel) have 508 homologous unigene pairs (Z. cucurbitae (Coquillett) and C. capitata (Wiedemann) have 519 homologous unigene pairs  and C. capitata (Wiedemann) have 517 homologous unigene pairs with Ka/Ks ratios less than 1  and B. dorsalis (Hendel), and the enriched pathways were fatty acid degradation, fatty acid metabolism, and lipid metabolism (Z. cucurbitae (Coquillett) and C. capitata (Wiedemann) were similar to those of Z. cucurbitae (Coquillett) and B. dorsalis (Hendel) (Z. cucurbitae (Coquillett) and B. dorsalis (Hendel), genes were enriched in the GO:0044699-single-organism process. Among the molecular functional categories, genes are enriched in GO: 0005488-binding, GO:0003824-catalytic activity, and GO:0005198-structural molecule activity, while the cellular components are enriched in GO:0005623-cell, GO:0044464-cell part, and GO:0043226-organelle (Z. cucurbitae (Coquillett) and C. capitata (Wiedemann), genes are enriched in the GO:0008152-metabolic process and GO:0044699-single-organism process; in the molecular function category, genes are enriched in GO:0005488-binding and GO:0003824-catalytic activity; and the cellular component is enriched in GO:0005623-cell, GO:0044464-cell part, and GO:0032991-macromolecular complex  and C. capitata (Wiedemann), genes are enriched in the GO:0008152-metabolic process and GO:0044699-single-organism process; in the molecular function category, genes are enriched in GO:0005488-binding and GO:0003824-catalytic activity; and in the cellular component, genes are enriched in GO:0005623-cell and GO:0044464-cell part  . GO enrirganelle . In the  complex . In the ell part .Z. cucurbitae (Coquillett), 7 are associated with Vg genes, 5 are associated with Vg-1 genes and 2 with Vg-3 genes. B. dorsalis (Hendel) had 11 Vg-related specific genes, with four associated with Vg-1 genes, one associated with Vg-2 genes, one associated with Vg-3 genes, and five associated with other Vg genes. C. capitata (Wiedemann) had only 1 Vg-1 gene-related specific gene  had significantly more number and variety of Vg-related genes than Z. cucurbitae (Coquillett) and C. capitata (Wiedemann), indicating that B. dorsalis (Hendel) can provide more energy for the reproduction of offspring, giving it characteristics such as faster reproduction and larger egg production. Among the genes specific to B. dorsalis (Hendel), there are 3 Vg-A2, 1 Vg-like, and 1 Vg-6 genes, and studies have shown that Vg-A2 and Vg-like are precursors of Vg , B. dorsalis (Hendel), and C. capitata (Wiedemann) were comparatively analyzed, and the GO and KEGG enrichment analyses were performed for genes specific to the three fruit fly species. Among the first 20 pathways of KEGG enrichment in Z. cucurbitae (Coquillett), pathways related to the immune system such as the Toll and Imd signaling pathway and natural killer cell-mediated cytotoxicity appeared, and the most enriched pathway was the Toll and Imd signaling pathway, suggesting that Z. cucurbitae (Coquillett) may have a strong immune functions. In B. dorsalis (Hendel), the MAPK signaling pathway-fly and the Wnt signaling pathway, which are related to cell growth and differentiation, are more frequent, suggesting that B. dorsalis (Hendel) may have a faster developmental and reproductive rate. In the KEGG enrichment of genes specific to C. capitata (Wiedemann), the pathways associated with human diseases such as chronic myeloid leukemia and hepatocellular carcinoma were the most frequent, followed by drug metabolism-cytochrome P450 and the metabolism of xenobiotics by cytochrome P450. P450 is an important component of a multi-functional oxidase system that functions as both an oxidase and a monooxygenase, which not only catalyzes the biosynthesis and degradation of endogenous substances to maintain the normal function of the organism but also plays a detoxifying and activating role against exogenous substances  (C. capitata (Wiedemann) has a higher detoxification capacity.In this study, the genomes of stances) , indicatACC gene expression decreases egg production and reproduction in Aedes aegypti  , fatty acid synthase (FAS), elongase of very long-chain fatty acids (ELO), desaturase , and fatty coenzyme A reductase  . Interfe aegypti , deletios  , and RNAit flies . FAR is it flies , and fat


Here, we describe recent updates to the ENA’s submission and retrieval services as well as focused efforts to improve connectivity, reusability, and interoperability of ENA data and metadata.The European Nucleotide Archive (ENA;  It is a freely accessible and global platform for managing nucleotide sequence data and offers a comprehensive set of data submission, discovery and dissemination services.The European Nucleotide Archive  , a long-ENA content is global, representing the interests of scientists in all parts of the world with over 92% of the world's countries represented in the user-base.In 2022, we have continued to develop new data types as the world of sequencing and bioinformatics progresses; focused on improving data linking to further data connectivity and traceability; and endeavoured to build better recognition for users’ data sharing efforts.The ENA provides services for the submission and retrieval of sequence data including but not limited to: the Webin submissions portal, the Webin command line client and the Webin REST API; the ENA browser and web services for data display, search and discovery; the support helpdesk with associated training and user documentation. Table In the past 12 months, the ENA has supported 2721 submission accounts, both individual submitters and large-scale brokers, from over 80 different countries. This spans over 11 million individual submissions and 8036 studies, including over 4.1 million samples, 2.6 million runs and 3.1 million assemblies with an average of 31 unique submitters a day and an average of 24 129 daily submissions.https://www.ebi.ac.uk/ena/submit/webin), Webin REST for programmatic submissions (https://www.ebi.ac.uk/ena/submit/drop-box), Webin-CLI for command-line submissions (https://github.com/enasequence/webin-cli/releases), and also Webin-CLI REST currently for SARS-CoV-2 programmatic submissions (https://www.ebi.ac.uk/ena/submit/webin-cli). For programmatic submitters, Webin also provides reporting (https://www.ebi.ac.uk/ena/submit/report) and authentication (https://www.ebi.ac.uk/ena/submit/webin/auth) services.Data are submitted to the ENA using the Webin submission service introduced >20 years ago. Webin supports both small-scale and high-throughput submitters, and includes the Webin Portal for interactive submissions (https://www.ebi.ac.uk/ena/submit/webin-v2) which provides both synchronous and asynchronous submission endpoints. The asynchronous endpoint supports larger submissions and better load balancing in case of high submission loads. This new API also supports the submission of multiple XMLs of different data types together  in the HTTP POST request body, rather than only a single object type using HTTP POST multipart/form-data. This can assist users to streamline their submissions of a whole study and its components into a single submission. In the future, we also plan to introduce JSON support alongside the existing XML support. We encourage programmatic submitters to transition to these new endpoints. Further information about the new Webin REST service is available from: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/programmatic-v2.html.In the last year, we have introduced a new version of the Webin REST programmatic submission service . This aims to bring together pathogenic data resources not only from the ENA but also from other EMBL-EBI resources, and provide rapid access to available data for new outbreaks. The new Pathogen Portal also includes the Infectious Diseases Cohort Browser (https://www.ebi.ac.uk/ena/pathogens/v2/cohorts), supported by ReCODiD (https://recodid.eu/).We have released a new and improved version of our Pathogen Portal (https://github.com/enasequence/ena-ftp-downloader/).We have made several improvements to the ena-file-downloader command line tool including support for downloading private data from ENA data hubs to share pre-publication data between registered users in pathogen data hubs . We have also improved access to genome assemblies by providing a single route to retrieve all sequences of a genome assembly in one go, both through the browser and programmatically via the API (e.g. https://www.ebi.ac.uk/ena/browser/api/embl/GCA_000001215.4?download=true&gzip=true).We have expanded the ENA Advanced Search API to include several new metadata fields, including the retrieval of primary publications information from sequence flat files (https://www.ebi.ac.uk/ena/browser/xref).Other improvements include adding new links to the ENA cross-reference service between ENA data and BacDive Metadatabase as well as Gene Expression Omnibus  system will be familiar to many as a method for claiming publications, grants and other types of contributions against an ID unique to each individual. ENA studies (projects) can now be claimed against a user's ORCID ID, in the same way that publications can. This is implemented through the EBI Search search interface: https://www.ebi.ac.uk/ebisearch/orcidclaimdocumentation.ebi.To improve the visibility of the contributions researchers and data providers make to open data, the ENA has developed features that allow its users to get recognition for datasets. The ORCID (https://www.ebi.ac.uk/ena/browser/about/citing-ena), in order to provide recognition and credit for the open sharing of sequence data. Additionally, the ENA has brought in support for generating Digital Object Identifiers (DOIs) specifically for SARS-CoV-2 projects. In these circumstances, a DOI is issued for ENA records through an associated BioStudies record created on behalf of the submitter, that collects all relevant ENA projects (https://www.ebi.ac.uk/biostudies/about). However, DOIs are not routinely issued for ENA or BioStudies records, so to request a DOI for a SARS-CoV-2 dataset, users must contact the SARS-CoV-2 helpdesk through virus-dataflow@ebi.ac.uk.The ENA is well established as an open access repository for sequence data. We continue to request that all authors refer to ENA records in publications using accession numbers issued directly by the ENA (see https://www.insdc.org/submitting-standards/feature-table/). However, this metadata is not always complete, or may be ambiguous, preventing the direct linking of sequence data to their biological origin. We have developed a publicly accessible open-source tool, the ENA Source Attribute Helper API, to help users validate and construct these source attributes (https://www.ebi.ac.uk/ena/sah/api/)  . This fiah/api/) , a HorizThere are plans to integrate this API into submission services with development of a User Interface underway at the time of writing.In the last year, the ENA has continued our ongoing work to normalise sample data management into the central EMBL-EBI service, BioSamples .As part of this, EBI BioSamples now supports Webin authentication. This allows submitters to register samples in EBI BioSamples using their Webin credentials and to then use these samples in ENA submissions while they remain in pre-publication private state. Once data in the ENA becomes public, the associated BioSamples will become automatically public. In our presentation services, we now display the BioSamples record in the ENA browser and the BioSamples accession (SAME- format accession) is considered the primary accession. These improvements are part of our roadmap to deepen the integration between EBI BioSamples and move away from samples registered specifically in the ENA, which will allow the use of common BioSample records in cross-omics studies.As well as the above technical changes, the ENA has adopted the BioSamples standard model for defining relationships between samples to model ‘derived from’ hierarchies of samples and ‘composed of’ groupings of samples. Although it was previously possible to include these relationships in the ENA sample metadata when provided, this now propagates a ‘relationship’ link within the BioSamples service allowing easier navigation between related samples. Further to this, within the BioSamples service, when a relationship exists, metadata are automatically copied down from ‘parent’ to ‘child’ providing display of common metadata. There are plans to also integrate this copy-down display into the ENA Browser in future, which will further simplify use of this relationship model going forwards.https://www.ebi.ac.uk/biosamples/samples/SAMEA12928721), which will then be directly linked to the restricted access metadata and data. This provides better connectivity of the data in the two archives and enables users to trace a pathogen record back to the origin material.This model has already been used extensively within metagenome assemblies to provide links back from a submitted Metagenome-Assembled Genome or a binned assembly, to its source environmental sample. The availability of the sample in BioSamples will make these links more accessible. The model has also been used to link tissue-level samples to specimens in biodiversity initiatives, for example, so tissue-specific transcriptomic RNA-seq data can be linked to a specimen-level genome assembly. More recently, in light of the COVID-19 pandemic, it is being used to create links between pathogen data and associated patient data in restricted access archives such as the European Genome-Phenome Archive (EGA) . For patThe ENA has expanded its brokering network over recent years to a total of 60 brokers, consisting of sequencing facilities, national infrastructure and research institutes. Brokers are specialist ENA users who can submit data and metadata to the ENA on behalf of other people and institutes. Broker facilities drive good metadata compliance and can provide local or domain specific data and metadata management, which in turn enriches, standardises, and further validates the metadata and data in public archives.During the COVID-19 pandemic, we found that in many cases a central national brokering facility provided the most efficient means of data management at the required scale. This is particularly exemplified through the success of our first national broker of SARS-CoV-2 data, the COVID-19 Genomics UK Consortium (COG-UK), who since early 2020 have brokered the highest volume of COVID data to date (2 600 430 raw reads and 2 176 970 assembled sequences).Since then, this has grown to seven national brokers who have set up long-term SARS-CoV-2 data streams to the ENA, including the Robert Koch Institute (RKI) in Germany, the Irish Consortium for Sequencing Covid, and the Swiss Institute for Bioinformatics (SIB). Many of these organisations liaise with their national public health institutes as part of their setup. In terms of submissions, RKI are the second biggest contributors of assembled sequences to the ENA, totalling 503 645 sequences, while Irish and Swiss groups brokered the second highest volume of raw reads after COG-UK, totalling 76 095 and 57 827 reads, respectively.https://www.ebi.ac.uk/ena/submit/webin-cli) to facilitate high-volume assembly data sharing, and the GISAID to ENA sample conversion script (https://github.com/enasequence/ena-content-dataflow/tree/master/scripts/gisaid_to_ena) together with the advised ‘GISAID Accession ID’ sample attribute, to enhance the access of data already submitted to GISAID.Some brokers also utilise some of our dedicated SARS-CoV-2 submission tools, such as the Webin-CLI Rest API . Submission and update of genome assemblies to the ENA currently requires representation of both sequence and annotation with each new version. To make the submission and updating of genome annotation more accessible to users, the ENA is developing a new system to decouple the annotation from the sequence. As part of this, we recognise that many modern annotation tools output tab-delimited formats such as GFF3, and plan to support submission of annotation to the ENA in the GFF3 format. A submittable GFF3 format specification is being developed in collaboration with the Ensembl . Content is distributed under the EMBL-EBI Terms of Use available at (https://www.ebi.ac.uk/about/terms-of-use).ENA services are freely available at (


In the lead up to World Patient Safety Day on 17 September 2022, WHO is emphasizing the global burden of medication harm. The elderly population is one of the most at-risk groups of medication harm, especially those taking multiple medications. High rates of medication-related harm are also seen in surgical care, intensive care and emergency medicine.“Medicines are powerful tools for protecting health. But medicines that are wrongly prescribed, taken incorrectly or are of poor quality, can cause serious harm,” said Dr Tedros Adhanom Ghebreyesus, WHO Director-General. “Nobody should be harmed while seeking care.”Unsafe medication practices and medication errors are one of the main causes of injury and avoidable harm in health-care systems across the world. The global cost associated with medication errors has been estimated at US$42 billion annually. Medication errors happen due to systemic issues and/or human factors such as fatigue, poor environmental conditions or staff shortages which affect prescribing, transcribing, dispensing, administration and monitoring practices. These errors can result in severe harm, disability and even death.World Patient Safety Day aims to increase understanding among and engagement of the public and encourage countries to promote safety in health care. This year has a particular focus on medication safety with the slogan ‘Medication Without Harm’. The campaign will also see the consolidation of the ongoing WHO Global Patient Safety Challenge: Medication Without Harm, with the aim of reducing avoidable medication-related harm globally.WHO is advocating for urgent improvement in strategies to reduce medication-related harm in key risk areas. Furthermore, it is working with partners to develop a set of medication safety technical resources, including a policy brief and medication safety solutions such as medication safety for look-alike sound-alike (LASA) medicines. LASA medicines may look or sound similar to each other, either by their generic name, or brand name. They might have similar packaging, similar-sounding names, or similar spellings.Flaws in the systems for prescription are a big contributor to medication-related harm, alongside human error. Evidence has shown that more than half of all medication harm occurs at the stage when medicines are prescribed and when they are being taken by patients due to inadequate monitoring. The highest risk category for medication-related harm is antibiotics, but medicines such as sedatives, anti-inflammatories and heart and blood pressure medication also pose significant risks.WHO is calling on stakeholders to continue efforts to reduce medication-related harm, develop strategies and structures to improve medication safety at local, national, regional and global levels, and make a pledge to adopt the Medication Without Harm Challenge.https://www.who.int/news/item/16-09-2022-who-calls-for-urgent-action-by-countries-for-achieving-medication-without-harmAvailable from:


The immune system is vital for survival in humans. It is responsible for the body's defense against infectious organisms, external pathogens and other invaders, while the immune response is regulated precisely, to prevent extensive damage to the body. However, this system sometimes malfunctions, misinterpreting the body's own tissues as foreign and produce antibodies or active immune cells to target and attack particular cells or tissues, resulting in autoimmune disease.The kidneys contribute to immune homeostasis, while several key components of the immune response have been implicated in the progression of renal diseases. Although several mechanisms of immune dysregulation leading to renal disease is broad, the pathways leading to injury are similar. Loss of immune homeostasis in renal disease results in perpetual immune cell recruitment and worsening damage to the kidney. At the same time, uncoordinated attempts at tissue repair, after immune-mediated disease or non-immune mediated injury, result in fibrosis of structures important for renal function, leading eventually to kidney failure.Immune Regulation in Kidney Diseases: Importance, Mechanism and Translation (https://www.frontiersin.org/research-topics/10976/immune-regulation-in-kidney-diseases-importance-mechanism-and-translation). There are 12 papers in this issue, with 11 original research and one case report. Renal acute and chronic injury, kidney transplantation, infection, and immunological modulation are all included in this field.We were able to collect Volume II of Chen et al. used poly (I:C) to produce anti-inflammatory MSCs that had better benefits in maintaining renal function, reducing tissue damage, and reducing systemic inflammation in IR. They discovered that anti-inflammatory MSCs had the powerful anti-inflammatory properties mentioned above injury. In previous study, Yan et al. discovered that SHP-1 deficiency exacerbates renal IR injury in a prior investigation .In kidney transplantation, ischemia reperfusion (IR) injury is a preventable process and is linked to delayed graft function, rejection, and long-term allograft survival. In terms of innate immunity activation, inflammation and stress play a significant role in IR injury. Positive immunological responses, on the other hand, might lead to negative immune system activation. Mesenchymal stem cells (MSCs) have a strong and distinct immunosuppressive effect. They can be split into two types: pro-inflammatory phenotype and anti-inflammatory phenotype . Wu et al. In obese individuals, lipotoxicity in the kidneys contribute to renal cell injury and death. In obesity-related kidney disease, local renin-angiotensin system (RAS) activation may play a role. The cargo miR- 6869-5p in plasma extracellular vehicles (EVs) produced RAS activation and renal tubular injury, according to Liu et al. As a result, plasma miR-6869-5p in obesity-related kidney illness, obese-EVs could be a therapeutic target for local RAS activation. It is critical to select an appropriate experimental model for renal IR injury. Human pluripotent stem cells (hPSCs)-derived kidney organoids operate as a model of different types of kidney cells in vitro and eliminate potential confounders in vivo. Zhang et al. used human kidney organoids to create LPS-induced kidney damage models. These findings laid a solid foundation for kidney damage research.Two important pathophysiological processes in kidney IR injury are inflammation and cell death. Calpains, a Ca2+-dependent cysteine protease family, are important in the pathophysiology of renal disorders. Calpeptin, a calpain inhibitor, reduced AIM2 inflammasome activation and raised Klotho protein expression, protecting renal function in an IR damage model, according to Wang et al. used multivariate logistic regression analysis and external validation to retrospectively examine clinical and laboratory variables associated with a higher risk of BK virus activation from 195 renal transplant recipients. In kidney transplant recipients, the innovative predictive nomogram accurately predicted BK virus activation. Severe pneumonia is a life-threatening complication that occurs after a kidney transplant and results in long-term immunosuppression. However, only a few immune-related markers are employed to determine the severity of pneumonia. Myeloid-derived suppressor cells (MDSCs) are an important immune regulatory cell that is induced during infection and has a significant immunosuppressive capacity. The relationship between MDSCs and pneumonia in kidney transplant recipients was investigated by Peng et al. They discovered that G-MDSCs were linked to the severity of pneumonia and may thus be used to measure pneumonia severity as an indicator of immunological function. Despite tremendous improvements in immunosuppression, the long-term result of juvenile kidney transplantation remains unsatisfactory. The 10-year graft survival rate is only about 60%. Donor-derived cell-free DNA (ddcfDNA) has emerged as a possible biomarker for graft damage and rejection detection. The dynamic features of ddcfDNA after juvenile kidney transplantation were revealed by Nie et al. We included an omics study on acute rejection in this issue. Using RNA sequencing, Wang et al. identified the peripheral blood mononuclear cells (PBMCs) of patients with acute renal allograft rejection. This issue also includes a case report in addition to the original clinical and fundamental studies mentioned above. Zhao et al. were the first to report a successful ABO-incompatible deceased donor kidney transplantation (ABOi DDKT) in a newborn. No pre- or post-transplantation antibody removal treatment was performed, since the recipient's anti-iso-hemagglutinin-A Ig- M/G antibody titers were both low (1:2) before transplantation and have remained at low levels or undetectable to date .Immunosuppression therapy is unavoidable in kidney transplant recipients. Because all immunosuppressive medicines are not specific to allografts, the immune system is typically inhibited. As a result, infection following transplantation is a common but difficult problem. In kidney transplant recipients, opportunistic infections like the BK virus are common. Gohda et al. examined the association between baseline TNFR levels, early febuxostat-induced TNFR changes, and future eGFR reduction in chronic kidney disease (CKD) patients without diabetes. C4d is a diagnostic marker for antibody-mediated rejection in kidney transplantation; however, Yang et al. found that the amount and pattern of renal C4d distribution differed between lupus nephritis (LN) and IgA nephropathy (IgAN) patients. They concluded that the presence of C4d in renal tissue acted as an independent predictor of relapse for LN patients and disease progression for IgAN patients .In diabetic patients, the levels of circulating tumor necrosis factor receptor (TNFR) 1 and 2 can predict decline in estimated glomerular filtration rate (eGFR). Finally, all of the manuscripts discussed immune modulation in acute, chronic, and kidney transplantation. We believe that this study area will lead to new insights into immune modulation in renal disease. All authors, reviewers, and editors who contributed are greatly appreciated. We believe readers enjoy this special issue.CY and BY wrote the editorial. Both authors approved the submitted version.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.