Miracle-dz/UniFAR-FTUs huggingface dataset:
CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drug-binding and dynamics, protein–lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.
A vacuum-actuated soft robot inspired by Drosophila larvae to study kinetics of crawling behaviour

Peristalsis, a motion generated by the propagation of muscular contraction along the body axis, is one of the most common locomotion patterns in limbless animals. While the kinematics of peristalsis has been examined intensively, its kinetics remains unclear, partially due to the lack of suitable physical models to simulate the locomotion patterns and inner drive in soft-bodied animals. Inspired by a soft-bodied animal, Drosophila larvae, we propose a vacuum-actuated soft robot mimicking its crawling behaviour. The soft structure, made of hyperelastic silicone rubber, was designed to imitate the larval segmental hydrostatic structure. Referring to a numerical simulation by the finite element method, the dynamical change in the vacuum pressure in each segment was controlled accordingly, and the soft robots could exhibit peristaltic locomotion. The soft robots successfully reproduced two previous experimental phenomena on fly larvae: 1. Crawling speed in backward crawling is slower than in forward crawling. 2. Elongation of either the segmental contraction duration or intersegmental phase delay makes peristaltic crawling slow. Furthermore, our experimental results provided a novel prediction for the role of the contraction force in controlling the speed of peristaltic locomotion. These observations indicate that soft robots could serve to examine the kinetics of crawling behaviour in soft-bodied animals.
Recruiting controls from an online panel for a case–control study enabled a timely and reliable foodborne Salmonella outbreak investigation, Germany 2021

Abstract We explored the feasibility, suitability, and reliability of using controls recruited among members of a non-probabilistic online panel (‘panel controls’) in a case–control study (CCS) to investigate a Salmonella Braenderup outbreak in Germany. For comparison, another control group was recruited via random digit dialling (‘classical controls’). Panel members received questionnaires by email; classical controls were interviewed by phone. Both control groups were frequency-matched to cases by age and sex; the classical controls also by federal state. Cases and controls were queried mainly about fruit consumption since melons were the suspected infection vehicle. We calculated adjusted odds ratios (aOR) and 95% confidence intervals (CIs) using single-variable and multivariable logistic regression. The study included 32 cases, 81 panel controls and 110 classical controls. Analyses identified melons, particularly Galia melons, as the most likely infection vehicle using either control group (panel controls – aOR 12, CI 2.7–66; classical controls – aOR 55, CI 8–1100). Recruitment of panel versus classical controls required substantially less person-time (8 vs. 111 hours) and was about 10 times less expensive. We recommend this timely and reliable control recruitment method when investigating diffuse foodborne outbreaks with CCS.
Associations between hair cortisol and blood pressure: a systematic review and meta-analysis

Objective: Stress is widely considered to be a risk factor for high blood pressure (BP), but evidence on the associations between biomarkers of chronic stress and BP is inconsistent. This systematic review and meta-analysis assessed the current state of the science on relationships between measures of cortisol concentration reflecting chronic stress exposure [hair cortisol concentration (HCC), nail cortisol concentration)] and BP. Methods: PubMed, Cumulative Index to Nursing and Allied Health Literature, Web of Science, Cochrane Library, and Embase were searched. Random effects models were used to assess the pooled effect size. Exploratory moderation analysis was performed. Results: Out of 34 014 identified, 16 articles met eligibility criteria and were included in the review, while 14 were included in the meta-analysis. No articles were reported on the association between nail cortisol concentration and BP. Small, positive associations were observed between HCC and SBP [r = 0.19 (95% confidence interval (CI): 0.08–0.29)] and HCC and DBP [r = 0.13 (95% CI: 0.04–0.22)]. Cortisol analysis method was identified as a significant moderator of the association between HCC and DBP. HCC was largely, positively associated with hypertension status [odds ratio = 3.23 (95% CI: 2.55–4.09), P < 0.001]. Conclusions: Current evidence suggests that higher HCC may be associated with elevated BP and a potential risk factor for hypertension. However, results should be interpreted with caution because HCC can be affected by hair color, hair care products, and analytic methods. Given the limitations of studies included in this review, further research is needed.
Prolonged grief disorder: A bibliometric analysis

Abstract Prolonged Grief Disorder (PGD) has become a subject of increased interest among both researchers and practitioners, owing both to its recent inclusion in the DSM-5-TR and the growing evidence of widespread complications of bereavement in the context of the COVID-19 pandemic. From a set of 467 studies obtained from the Scopus database during the period 2009 to 2022, the present research provides bibliographic data on the most influential authors on the subject, most relevant journals based on the number of documents published, a keyword analysis of the focus of this work, and an overall characterization of the scientific literature on PGD. The Biblioshiny application along with VOSviewer software was used for the analysis and visual depiction of the results. Both the scientific and applied implications of this analysis are discussed.
Association of genetically-predicted placental gene expression with adult blood pressure traits

Objective: Blood pressure is a complex, polygenic trait, and the need to identify prehypertensive risks and new gene targets for blood pressure control therapies or prevention continues. We hypothesize a developmental origins model of blood pressure traits through the life course where the placenta is a conduit mediating genomic and nongenomic transmission of disease risk. Genetic control of placental gene expression has recently been described through expression quantitative trait loci (eQTL) studies which have identified associations with childhood phenotypes. Methods: We conducted a transcriptome-wide gene expression analysis estimating the predicted gene expression of placental tissue in adult individuals with genome-wide association study (GWAS) blood pressure summary statistics. We constructed predicted expression models of 15 154 genes from reference placenta eQTL data and investigated whether genetically-predicted gene expression in placental tissue is associated with blood pressure traits using published GWAS summary statistics. Functional annotation of significant genes was generated using FUMA. Results: We identified 18, 9, and 21 genes where predicted expression in placenta was significantly associated with systolic blood pressure (SBP), diastolic blood pressure (DBP), and pulse pressure (PP), respectively. There were 14 gene-tissue associations (13 unique genes) significant only in placenta. Conclusions: In this meta-analysis using S-PrediXcan and GWAS summary statistics, the predicted expression in placenta of 48 genes was statistically significantly associated with blood pressure traits. Notable findings included the association of FGFR1 expression with increased SBP and PP. This evidence of gene expression variation in placenta preceding the onset of adult blood pressure phenotypes is an example of extreme preclinical biological changes which may benefit from intervention.
Development and Validation of a Prediction Model for Future Estimated Glomerular Filtration Rate in People With Type 2 Diabetes and Chronic Kidney Disease

Key Points Question Can routinely available data from primary care visits be used to develop and externally validate a prediction model that reliably predicts estimated glomerular filtration rate (eGFR) for upcoming follow-up visits? Findings In this prognostic study involving 4637 adults with type 2 diabetes and chronic kidney disease, a prediction model including 13 routinely collected baseline variables based on data from 3 prospective multinational cohort studies was developed and externally validated. The model was robust, well calibrated, and capable of predicting decreases in eGFR up to 5 years after baseline. Meaning These findings suggest that the prediction model, which is publicly available in a web-based application, may be used to improve prediction of individual eGFR trajectories and kidney function decline.
Exaptation of Inactivated Host Enzymes for Structural Roles in Orthopoxviruses and Novel Folds of Virus Proteins Revealed by Protein Structure Modeling

Protein structures are more strongly conserved in evolution than are amino acid sequences. Comparative structural analysis is particularly important for inferring the origins of viral proteins that typically evolve at high rates. ABSTRACT Viruses with large, double-stranded DNA genomes captured the majority of their genes from their hosts at different stages of evolution. The origins of many virus genes are readily detected through significant sequence similarity with cellular homologs. In particular, this is the case for virus enzymes, such as DNA and RNA polymerases or nucleotide kinases, that retain their catalytic activity after capture by an ancestral virus. However, a large fraction of virus genes have no readily detectable cellular homologs, meaning that their origins remain enigmatic. We explored the potential origins of such proteins that are encoded in the genomes of orthopoxviruses, a thoroughly studied virus genus that includes major human pathogens. To this end, we used AlphaFold2 to predict the structures of all 214 proteins that are encoded by orthopoxviruses. Among the proteins of unknown provenance, structure prediction yielded clear indications of origin for 14 of them and validated several inferences that were previously made via sequence analysis. A notable emerging trend is the exaptation of enzymes from cellular organisms for nonenzymatic, structural roles in virus reproduction that is accompanied by the disruption of catalytic sites and by an overall drastic divergence that precludes homology detection at the sequence level. Among the 16 orthopoxvirus proteins that were found to be inactivated enzyme derivatives are the poxvirus replication processivity factor A20, which is an inactivated NAD-dependent DNA ligase; the major core protein A3, which is an inactivated deubiquitinase; F11, which is an inactivated prolyl hydroxylase; and more similar cases. For nearly one-third of the orthopoxvirus virion proteins, no significantly similar structures were identified, suggesting exaptation with subsequent major structural rearrangement that yielded unique protein folds. IMPORTANCE Protein structures are more strongly conserved in evolution than are amino acid sequences. Comparative structural analysis is particularly important for inferring the origins of viral proteins that typically evolve at high rates. We used a powerful protein structure modeling method, namely, AlphaFold2, to model the structures of all orthopoxvirus proteins and compared them to all available protein structures. Multiple cases of recruitment of host enzymes for structural roles in viruses, accompanied by the disruption of catalytic sites, were discovered. However, many viral proteins appear to have evolved unique structural folds.
Molecular characterization and comparative genomic analysis of Acinetobacter baumannii isolated from the community and the hospital: an epidemiological study in Segamat, Malaysia

Acinetobacter baumannii is a common cause of multidrug-resistant (MDR) nosocomial infections around the world. However, little is known about the persistence and dynamics of A. baumannii in a healthy community. This study investigated the role of the community as a prospective reservoir for A. baumannii and explored possible links between hospital and community isolates. A total of 12 independent A. baumannii strains were isolated from human faecal samples from the community in Segamat, Malaysia, in 2018 and 2019. Another 15 were obtained in 2020 from patients at the co-located tertiary public hospital. The antimicrobial resistance profile and biofilm formation ability were analysed, and the relatedness of community and hospital isolates was determined using whole-genome sequencing (WGS). Antibiotic profile analysis revealed that 12 out of 15 hospital isolates were MDR, but none of the community isolates were MDR. However, phylogenetic analysis based on single-nucleotide polymorphisms (SNPs) and a pangenome analysis of core genes showed clustering between four community and two hospital strains. Such clustering of strains from two different settings based on their genomes suggests that these strains could persist in both. WGS revealed 41 potential resistance genes on average in the hospital strains, but fewer (n=32) were detected in the community strains. In contrast, 68 virulence genes were commonly seen in strains from both sources. This study highlights the possible transmission threat to public health posed by virulent A. baumannii present in the gut of asymptomatic individuals in the community.
Expanding the boundaries of previously obtained informed consent in research: Views from participants in the Personalised Risk‐based Mammascreening study

Understanding participants' concerns and information needs regarding broadened consent is crucial to ensure transparency and participant autonomy. Our study qualitatively examined these issues in women participating in the Personalized RISk‐based MAmmascreening study (PRISMA). The original PRISMA informed consent was project‐specific (i.e., breast cancer research), limiting the scope of secondary research. We explored participants' needs for broadened consent to preserve informed decision‐making while maximising the potential re‐use of data.
Image Fusion Based on Finite Ridgelet Transform

Finite ridgelet transform(FRIT) is applied to image fusion,the character of original images is effectively extracted,and more important information is preserved.The fusion method based on FRIT needs two steps.Firstly,the original images are decomposed using finite ridgelet transform,then the coefficients are fused with the fusion regular in the different frequency bands,and finally the fused coefficients are reconstructed to obtain fusion results.Multi-focus images are taken as experimental data,subjective and objective standard are used to evaluate the results,and the comparison with results based on wavelet transform shows that this method gets much better fusion results tan wavelet.And image fusion algorithm based on FRIT is effective and feasible.
Migration background and COVID-19 related intensive care unit admission and mortality in the Netherlands: A cohort study

Background Since the beginning of the SARS-CoV-2 pandemic, studies have been reporting inconsistently on migration background as a risk factor for COVID-19 outcomes. The aim of this study was to evaluate the association between migration background and clinical outcomes with COVID-19 in the Netherlands. Methods This cohort study included 2,229 adult COVID-19 patients admitted in two Dutch hospitals between February 27, 2020 and March 31, 2021. Odds ratios (ORs) for hospital admission, intensive care unit (ICU) admission and mortality with 95% confidence intervals (CIs) were calculated for non-Western (Moroccan, Turkish, Surinamese or other) persons as compared with Western persons in the general population of the province of Utrecht (the Netherlands) as source population. Furthermore, among hospitalized patients, Hazard ratios (HRs) with 95% CIs for in-hospital mortality and intensive care unit (ICU) admission were calculated using Cox proportional hazard analyses. Hazard ratios were adjusted for age, sex, body mass index, hypertension, Charlson Comorbidity Index, chronic corticosteroid use before admission, income, education and population density to investigate explanatory variables. Results Of the 2,229 subjects, 1,707 were of Western origin and 522 were of non-Western origin. There were 313 in-hospital deaths and 503 ICU admissions. As compared with persons with a Western origin in the general population of the province of Utrecht, the ORs for non-Western persons was 1.8 (95% CI 1.7–2.0) for hospitalization, 2.1 (95% CI 1.7–2.5) for ICU admission and 1.3 (95% CI 1.0–1.7) for mortality. Among hospitalized patients, HR for ICU admission was 1.1 (95% CI 0.9–1.4) and 0.9 (95% CI 0.7–1.3) for mortality for non-Western hospitalized persons as compared with hospitalized patients of Western origin after adjustment. Conclusion Non-Western persons, including Moroccan, Turkish and Surinamese subjects, had increased risks of hospital admission, ICU admission and COVID-19 related death on a population level. Among hospitalized COVID-19 patients, no association was found between migration background and ICU admission or mortality.
Validation of the 2022 American College of Rheumatology/EULAR classification criteria for Takayasu arteritis.

OBJECTIVES The present study validates the 2022 American College of Rheumatology (ACR)/European Alliance of Associations for Rheumatology (EULAR) classification criteria for Takayasu's arteritis (TAK) compared with 1990 ACR TAK classification criteria. METHODS The fulfillment of 2022 ACR/EULAR and 1990 ACR TAK criteria from four referral centers was assessed for TAK compared with extracranial giant cell arteritis (EC-GCA) and other controls. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), likelihood ratio of a positive test (LR+) or negative test (LR-), and area under receiver operating characteristics curve (AUC) were calculated. RESULTS Among 504 TAK (404 females) and 222 controls (151 females, 144 EC-GCA), the 2022 ACR/EULAR criteria had better sensitivity (95.83% vs 82.94%) and NPV but poorer specificity (63.51% vs 90.54%), PPV, LR+, LR-, and AUC at the pre-determined cut-offs than 1990 ACR criteria. The 2022 ACR/EULAR criteria had greater specificity (76.06% vs 57.62%) and AUC (0.845 vs 0.771) with similar sensitivity (93% vs 96.53%) in males than in females. The 2022 ACR/EULAR criteria performed similarly with only EC-GCA as controls (sensitivity 95.83%, specificity 60.42%, AUC 0.781). Sensitivity remained similar, whereas specificity was higher for 40-60 vs < 40 years. Cut-offs ≥6 (sensitivity 91.87%, specificity 82.88%) and ≥7 (sensitivity 86.71%, specificity 86.49%), or removing the point for female sex (sensitivity 92.64%, specificity 81.08%) greatly improved balance between sensitivity and specificity. CONCLUSION The poor specificity of the 2022 ACR/EULAR TAK criteria in real-life settings was improved by increasing the cut-off to 6 or 7 or removing the point for female sex.
Brinjal leaf diseases detection based on discrete Shearlet transform and Deep Convolutional Neural Network

Different diseases are observed in vegetables, fruits, cereals, and commercial crops by farmers and agricultural experts. Nonetheless, this evaluation process is time-consuming, and initial symptoms are primarily visible at microscopic levels, limiting the possibility of an accurate diagnosis. This paper proposes an innovative method for identifying and classifying infected brinjal leaves using Deep Convolutional Neural Networks (DCNN) and Radial Basis Feed Forward Neural Networks (RBFNN). We collected 1100 images of brinjal leaf disease that were caused by five different species (Pseudomonas solanacearum, Cercospora solani, Alternaria melongenea, Pythium aphanidermatum, and Tobacco Mosaic Virus) and 400 images of healthy leaves from India’s agricultural form. First, the original plant leaf is preprocessed by a Gaussian filter to reduce the noise and improve the quality of the image through image enhancement. A segmentation method based on expectation and maximization (EM) is then utilized to segment the leaf’s-diseased regions. Next, the discrete Shearlet transform is used to extract the main features of the images such as texture, color, and structure, which are then merged to produce vectors. Lastly, DCNN and RBFNN are used to classify brinjal leaves based on their disease types. The DCNN achieved a mean accuracy of 93.30% (with fusion) and 76.70% (without fusion) compared to the RBFNN (82%—without fusion, 87%—with fusion) in classifying leaf diseases.
Woronin body hitchhiking on early endosomes is dispensable for septal localization in Aspergillus nidulans

The proper functioning of organelles depends on their intracellular localization, mediated by motor protein–dependent transport on cytoskeletal tracks. Rather than directly associating with a motor protein, peroxisomes move by hitchhiking on motile early endosomes in the filamentous fungus Aspergillus nidulans. However, the physiological role of peroxisome hitchhiking is unclear. Peroxisome hitchhiking requires the protein PxdA, which is conserved within the fungal subphylum Pezizomycotina but absent from other fungal clades. Woronin bodies are specialized peroxisomes that are also unique to the Pezizomycotina. In these fungi, multinucleate hyphal segments are separated by incomplete cell walls called septa that possess a central pore enabling cytoplasmic exchange. Upon damage to a hyphal segment, Woronin bodies plug septal pores to prevent widespread leakage. Here, we tested whether peroxisome hitchhiking is important for Woronin body motility, distribution, and function in A. nidulans. We show that Woronin body proteins are present within all motile peroxisomes and hitchhike on PxdA-labeled early endosomes during bidirectional, long-distance movements. Loss of peroxisome hitchhiking significantly affected Woronin body distribution and motility in the cytoplasm, but Woronin body hitchhiking is ultimately dispensable for septal localization and plugging.