bluuebunny/crossref_metadata_2025 huggingface dataset:
Phospholipids are imported into mitochondria by VDAC, a dimeric beta barrel scramblase
Authors: Jahn Helene , Bartoš Ladislav , Dearden Grace I. , Dittman Jeremy S. , Holthuis Joost C. M. , Vácha Robert , Menon Anant K.
Published: December 2023

Mitochondria are double-membrane-bounded organelles that depend critically on phospholipids supplied by the endoplasmic reticulum. These lipids must cross the outer membrane to support mitochondrial function, but how they do this is unclear. We identify the Voltage Dependent Anion Channel (VDAC), an abundant outer membrane protein, as a scramblase-type lipid transporter that catalyzes lipid entry. On reconstitution into membrane vesicles, dimers of human VDAC1 and VDAC2 catalyze rapid transbilayer translocation of phospholipids by a mechanism that is unrelated to their channel activity. Coarse-grained molecular dynamics simulations of VDAC1 reveal that lipid scrambling occurs at a specific dimer interface where polar residues induce large water defects and bilayer thinning. The rate of phospholipid import into yeast mitochondria is an order of magnitude lower in the absence of VDAC homologs, indicating that VDACs provide the main pathway for lipid entry. Thus, VDAC isoforms, members of a superfamily of beta barrel proteins, moonlight as a class of phospholipid scramblases - distinct from alpha-helical scramblase proteins - that act to import lipids into mitochondria.
Human and mouse neutrophils share core transcriptional programs in both homeostatic and inflamed contexts
Authors: Hackert Nicolaj S. , Radtke Felix A. , Exner Tarik , Lorenz Hanns-Martin , Müller-Tidow Carsten , Nigrovic Peter A. , Wabnitz Guido , Grieshaber-Bouyer Ricardo
Published: December 2023

Neutrophils are frequently studied in mouse models, but the extent to which findings translate to humans remains poorly defined. In an integrative analysis of 11 mouse and 13 human datasets, we find a strong correlation of neutrophil gene expression across species. In inflammation, neutrophils display substantial transcriptional diversity but share a core inflammation program. This program includes genes encoding IL-1 family members, CD14, IL-4R, CD69, and PD-L1. Chromatin accessibility of core inflammation genes increases in blood compared to bone marrow and further in tissue. Transcription factor enrichment analysis implicates members of the NF-κB family and AP-1 complex as important drivers, and HoxB8 neutrophils with JunB knockout show a reduced expression of core inflammation genes in resting and activated cells. In independent single-cell validation data, neutrophil activation by type I or type II interferon, G-CSF, and E. coli leads to upregulation in core inflammation genes. In COVID-19 patients, higher expression of core inflammation genes in neutrophils is associated with more severe disease. In vitro treatment with GM-CSF, LPS, and type II interferon induces surface protein upregulation of core inflammation members. Together, we demonstrate transcriptional conservation in neutrophils in homeostasis and identify a core inflammation program shared across heterogeneous inflammatory conditions.
Structural plasticity for neuromorphic networks with electropolymerized dendritic PEDOT connections
Authors: Janzakova Kamila , Balafrej Ismael , Kumar Ankush , Garg Nikhil , Scholaert Corentin , Rouat Jean , Drouin Dominique , Coffinier Yannick , Pecqueur Sébastien , Alibart Fabien
Published: December 2023

Neural networks are powerful tools for solving complex problems, but finding the right network topology for a given task remains an open question. Biology uses neurogenesis and structural plasticity to solve this problem. Advanced neural network algorithms are mostly relying on synaptic plasticity and learning. The main limitation in reconciling these two approaches is the lack of a viable hardware solution that could reproduce the bottom-up development of biological neural networks. Here, we show how the dendritic growth of PEDOT:PSS-based fibers through AC electropolymerization can implement structural plasticity during network development. We find that this strategy follows Hebbian principles and is able to define topologies that leverage better computing performances with sparse synaptic connectivity for solving non-trivial tasks. This approach is validated in software simulation, and offers up to 61% better network sparsity on classification and 50% in signal reconstruction tasks.
The separation pin distinguishes the pro– and anti–recombinogenic functions of Saccharomyces cerevisiae Srs2
Authors: Meir Aviv , Raina Vivek B. , Rivera Carly E. , Marie Léa , Symington Lorraine S. , Greene Eric C.
Published: December 2023

Srs2 is an Sf1a helicase that helps maintain genome stability in Saccharomyces cerevisiae through its ability to regulate homologous recombination. Srs2 downregulates HR by stripping Rad51 from single–stranded DNA, and Srs2 is also thought to promote synthesis–dependent strand annealing by unwinding D–loops. However, it has not been possible to evaluate the relative contributions of these two distinct activities to any aspect of recombination. Here, we used a structure–based approach to design an Srs2 separation–of–function mutant that can dismantle Rad51–ssDNA filaments but is incapable of disrupting D–loops, allowing us to assess the relative contributions of these pro– and anti–recombinogenic functions. We show that this separation–of–function mutant phenocopies wild–type SRS2 in vivo, suggesting that the ability of Srs2 to remove Rad51 from ssDNA is its primary role during HR.
Structures of human prostaglandin F2α receptor reveal the mechanism of ligand and G protein selectivity
Authors: Lv Xiuqing , Gao Kaixuan , Nie Jia , Zhang Xin , Zhang Shuhao , Ren Yinhang , Sun Xiaoou , Li Qi , Huang Jingrui , Liu Lijuan , Zhang Xiaowen , Zhang Weishe , Liu Xiangyu
Published: December 2023

Prostaglandins and their receptors regulate various physiological processes. Carboprost, an analog of prostaglandin F2α and an agonist for the prostaglandin F2-alpha receptor (FP receptor), is clinically used to treat postpartum hemorrhage (PPH). However, off-target activation of closely related receptors such as the prostaglandin E receptor subtype EP3 (EP3 receptor) by carboprost results in side effects and limits the clinical application. Meanwhile, the FP receptor selective agonist latanoprost is not suitable to treat PPH due to its poor solubility and fast clearance. Here, we present two cryo-EM structures of the FP receptor bound to carboprost and latanoprost-FA (the free acid form of latanoprost) at 2.7 Å and 3.2 Å resolution, respectively. The structures reveal the molecular mechanism of FP receptor selectivity for both endogenous prostaglandins and clinical drugs, as well as the molecular mechanism of G protein coupling preference by the prostaglandin receptors. The structural information may guide the development of better prostaglandin drugs.
Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex
Authors: Markert Jonathan W. , Vos Seychelle M. , Farnung Lucas
Published: December 2023

Acetylation of histones is a key post-translational modification that guides gene expression regulation. In yeast, the class I histone deacetylase containing Rpd3S complex plays a critical role in the suppression of spurious transcription by removing histone acetylation from actively transcribed genes. The S. cerevisiae Rpd3S complex has five subunits (Rpd3, Sin3, Rco1, Eaf3, and Ume1) but its subunit stoichiometry and how the complex engages nucleosomes to achieve substrate specificity remains elusive. Here we report the cryo-EM structure of the complete Rpd3S complex bound to a nucleosome. Sin3 and two copies of subunits Rco1 and Eaf3 encircle the deacetylase subunit Rpd3 and coordinate the positioning of Ume1. The Rpd3S complex binds both trimethylated H3 tails at position lysine 36 and makes multiple additional contacts with the nucleosomal DNA and the H2A–H2B acidic patch. Direct regulation via the Sin3 subunit coordinates binding of the acetylated histone substrate to achieve substrate specificity.
Contractile ring mechanosensation and its anillin-dependent tuning during early embryogenesis
Authors: Hsu Christina Rou , Sangha Gaganpreet , Fan Wayne , Zheng Joey , Sugioka Kenji
Published: December 2023

Cytokinesis plays crucial roles in morphogenesis. Previous studies have examined how tissue mechanics influences the position and closure direction of the contractile ring. However, the mechanisms by which the ring senses tissue mechanics remain largely elusive. Here, we show the mechanism of contractile ring mechanosensation and its tuning during asymmetric ring closure of Caenorhabditis elegans embryos. Integrative analysis of ring closure and cell cortex dynamics revealed that mechanical suppression of the ring-directed cortical flow is associated with asymmetric ring closure. Consistently, artificial obstruction of ring-directed cortical flow induces asymmetric ring closure in otherwise symmetrically dividing cells. Anillin is vital for mechanosensation. Our genetic analysis suggests that the positive feedback loop among ring-directed cortical flow, myosin enrichment, and ring constriction constitutes a mechanosensitive pathway driving asymmetric ring closure. These findings and developed tools should advance the 4D mechanobiology of cytokinesis in more complex tissues.
Multi-ancestry study of the genetics of problematic alcohol use in over 1 million individuals
Authors: Zhou Hang , Kember Rachel L. , Deak Joseph D. , Xu Heng , Toikumo Sylvanus , Yuan Kai , Lind Penelope A. , Farajzadeh Leila , Wang Lu , Hatoum Alexander S. , Johnson Jessica , Lee Hyunjoon , Mallard Travis T. , Xu Jiayi , Johnston Keira J. A. , Johnson Emma C. , Nielsen Trine Tollerup , Galimberti Marco , Dao Cecilia , Levey Daniel F. , Overstreet Cassie , Byrne Enda M. , Gillespie Nathan A. , Gordon Scott , Hickie Ian B. , Whitfield John B. , Xu Ke , Zhao Hongyu , Huckins Laura M. , Davis Lea K. , Sanchez-Roige Sandra , Madden Pamela A. F. , Heath Andrew C. , Medland Sarah E. , Martin Nicholas G. , Ge Tian , Smoller Jordan W. , Hougaard David M. , Børglum Anders D. , Demontis Ditte , Krystal John H. , Gaziano J. Michael , Edenberg Howard J. , Agrawal Arpana ,   Million Veteran Program, Zhao Hongyu , Justice Amy C. , Stein Murray B. , Kranzler Henry R. , Gelernter Joel
Published: December 2023

Problematic alcohol use (PAU), a trait that combines alcohol use disorder and alcohol-related problems assessed with a questionnaire, is a leading cause of death and morbidity worldwide. Here we conducted a large cross-ancestry meta-analysis of PAU in 1,079,947 individuals (European, N = 903,147; African, N = 122,571; Latin American, N = 38,962; East Asian, N = 13,551; and South Asian, N = 1,716 ancestries). We observed a high degree of cross-ancestral similarity in the genetic architecture of PAU and identified 110 independent risk variants in within- and cross-ancestry analyses. Cross-ancestry fine mapping improved the identification of likely causal variants. Prioritizing genes through gene expression and chromatin interaction in brain tissues identified multiple genes associated with PAU. We identified existing medications for potential pharmacological studies by a computational drug repurposing analysis. Cross-ancestry polygenic risk scores showed better performance of association in independent samples than single-ancestry polygenic risk scores. Genetic correlations between PAU and other traits were observed in multiple ancestries, with other substance use traits having the highest correlations. This study advances our knowledge of the genetic etiology of PAU, and these findings may bring possible clinical applicability of genetics insights—together with neuroscience, biology and data science—closer.
Fatty acid profiling and oxidative stability of biscuits available in the market of the city of Ludhiana, India
Authors: Kaur Prabhjot , Choudhary Monika , Sharma Sanjula
Published: December 2023

India has occupied third position in biscuit manufacturing with an average production of 1.95 million tonnes. The major ingredients in biscuit manufacturing are refined wheat flour, sugar and fat. Fat to be used must be chosen carefully as it affects quality of final product in terms of fatty acid composition and oxidative stability. Therefore, the present work was planned to study fatty acid profile of highly consumed baked products of biscuit family such as biscuits and cookies available in market. The study was carried out to do fatty acid profiling of a range of highly consumed baked products of biscuit family as a primary objective and also, to determine oxidative stability of these products by analysing peroxide value and free fatty acid content. The most commonly consumed packaged and unpackaged bakery products were selected and were bought from the local market of Ludhiana city on the basis of a survey conducted on 200 subjects. The selected products were analysed for fatty acid composition and oxidative stability using standard methods. Fatty acid profiling of 22 bakery products of biscuit family was done. Palmitic acid was the most abundant among all fatty acids in packaged and unpackaged samples. Peroxide value of all the products even after storage period of three months was found below the permissible limits (< 10 meq/kg). Free fatty acids value of all the products also did not cross acceptable level of 0.5 percent. Out of total selected eight brands, six were national and two were international. Amount of palmitic acid was higher in the products belonging to local brands.
Exploring the therapeutic potential of sodium deoxycholate tailored deformable-emulsomes of etodolac for effective management of arthritis
Authors: Sharma Gajanand , Mahajan Akanksha , Thakur Kanika , Kaur Gurjeet , Goni Vijay G. , Kumar Muniramiah Vinod , Barnwal Ravi Pratap , Singh Gurpal , Singh Bhupinder , Katare O. P.
Published: December 2023

The current piece of research intends to evaluate the potential of combining etodolac with deformable-emulsomes, a flexible vesicular system, as a promising strategy for the topical therapy of arthritis. The developed carrier system featured nanometric dimensions (102 nm), an improved zeta potential (− 5.05 mV), sustained drug release (31.33%), and enhanced drug deposition (33.13%) of DE-gel vis-à-vis conventional system (10.34% and 14.71%). The amount of permeation of the developed nano formulation across skin layers was demonstrated through CLSM and dermatokinetics studies. The safety profile of deformable-emulsomes has been investigated through in vitro HaCaT cell culture studies and skin compliance studies. The efficacy of the DE-gel formulation was sevenfold higher in case of Xylene induced ear edema model and 2.2-folds in CFA induced arthritis model than that of group treated with conventional gel (p < 0.01). The main technological rationale lies in the use of phospholipid and sodium deoxycholate-based nanoscale flexible lipoidal vesicles, which effectively encapsulate drug molecules within their interiors. This encapsulation enhances the molecular interactions and facilitates the transportation of the drug molecule effectively to the target-site. Hence, these findings offer robust scientific evidence to support additional investigation into the potential utility of flexible vesicular systems as a promising drug delivery alternative for molecules of this nature.
Acute kidney injury interacts with VKORC1 genotype on initiative warfarin dose among heart surgery recipients: a real-world research
Authors: Xiong Liang , Yu Feng , Ge Weihong , Xu Hang
Published: December 2023

Patients who receive heart valve surgery need anticoagulation prophylaxis to reduce the risk of thrombosis. Warfarin often is a choice but its dosage varies due to gene and clinical factors. We aim to study, among them, if there is an interaction between acute kidney injury and two gene polymorphisms from this study. We extracted data of heart valve surgery recipients from the electronic health record (EHR) system of a medical center. The primary outcome is about the average daily dose of warfarin, measured as an additive interaction effect (INTadd) between acute kidney injury (AKI) and warfarin-related gene polymorphisms. The confounders, including age, sex, body surface area (BSA), comorbidities (i.e., atrial fibrillation [AF], hypertension [HTN], congestive heart failure [CHF]), serum albumin level, warfarin-relevant gene polymorphism (i.e., CYP2C9, VKORC1), prosthetic valve type (i.e., metal, bio), and warfarin history were controlled via a multivariate-linear regression model. The study included 200 patients, among whom 108 (54.00%) are female. Further, the mean age is 54.45 years, 31 (15.50%) have CHF, and 40 (20.00%) patients were prescribed concomitant amiodarone, which potentially overlays with the warfarin prophylaxis period. During the follow-up, AKI occurred in 30 (15.00%) patients. VKORC1 mutation (1639G>A) occurred in 25 (12.50%) patients and CYPC29 *2 or *3 mutations presented in 20 patients (10.00%). We found a significant additive interaction effect between AKI and VKORC1 (− 1.17, 95% CI − 1.82 to − 0.53, p = 0.0004). This result suggests it is probable that there is an interaction between acute kidney injury and the VKORC1 polymorphism for the warfarin dose during the initial period of anticoagulation prophylaxis.
Increase of nesting habitat suitability for green turtles in a warming Mediterranean Sea
Authors: Mancino Chiara , Hochscheid Sandra , Maiorano Luigi
Published: December 2023

Climate change is reshaping global ecosystems at an unprecedented rate, with major impacts on biodiversity. Therefore, understanding how organisms can withstand change is key to identify priority conservation objectives. Marine ectotherms are being extremely impacted because their biology and phenology are directly related to temperature. Among these species, sea turtles are particularly problematic because they roam over both marine and terrestrial habitats throughout their life cycles. Focusing on green turtles (Chelonia mydas) in the Mediterranean Sea, we investigated the future potential changes of nesting grounds through time, assuming that marine turtles would shift their nesting locations. We modeled the current distribution of nesting grounds including both terrestrial and marine variables, and we projected the potential nesting distribution across the Mediterranean basin under alternative future greenhouse gas emission scenario (2000–2100). Our models show an increase in nesting probability in the western Mediterranean Sea, irrespective of the climate scenario we consider. Contrary to what is found in most global change studies, the worse the climate change scenario, the more suitable areas for green turtles will potentially increase. The most important predictors were anthropogenic variables, which negatively affect nesting probability, and sea surface temperature, positively linked to nesting probability, up to a maximum of 24–25 °C. The importance of the western Mediterranean beaches as potential nesting areas for sea turtles in the near future clearly call for a proactive conservation and management effort, focusing on monitoring actions (to document the potential range expansion) and threat detection.
Improving nonalcoholic fatty liver disease classification performance with latent diffusion models
Authors: Hardy Romain , Klepich Joe , Mitchell Ryan , Hall Steve , Villareal Jericho , Ilin Cornelia
Published: December 2023

Integrating deep learning with clinical expertise holds great potential for addressing healthcare challenges and empowering medical professionals with improved diagnostic tools. However, the need for annotated medical images is often an obstacle to leveraging the full power of machine learning models. Our research demonstrates that by combining synthetic images, generated using diffusion models, with real images, we can enhance nonalcoholic fatty liver disease (NAFLD) classification performance even in low-data regime settings. We evaluate the quality of the synthetic images by comparing two metrics: Inception Score (IS) and Fréchet Inception Distance (FID), computed on diffusion- and generative adversarial network (GAN)-generated images. Our results show superior performance for the diffusion-generated images, with a maximum IS score of 1.90 compared to 1.67 for GANs, and a minimum FID score of 69.45 compared to 100.05 for GANs. Utilizing a partially frozen CNN backbone (EfficientNet v1), our synthetic augmentation method achieves a maximum image-level ROC AUC of 0.904 on a NAFLD prediction task.
Improvement in the skill of CMIP6 decadal hindcasts for extreme rainfall events over the Indian summer monsoon region
Authors: Konda Gopinadh , Chowdary Jasti S. , Gnanaseelan C. , Parekh Anant
Published: December 2023

Decadal climate predictions have been widely used to predict the near-term climate information relevant for decision-making at multi-year timescales. In the present study, we evaluate the quality of the Coupled Model Intercomparison Project phase-6 (CMIP6) Decadal Climate Prediction Project (DCPP) hindcasts in capturing the extreme rainfall events (EREs) over the monsoon core region during Indian summer monsoon season (June–September) up to lead years 1–10. For the first time, in this study, we have used quantile mapping approach to downscale and bias correct the DCPP CMIP6 simulation/hindcast rainfall for the better representation of EREs. Detailed analysis suggests that the models in general strongly underestimate the rainfall variability over the summer monsoon region. However, after the downscaling and bias correction, the representation of rainfall variability and intensity improved multifold. The bias-corrected decadal hindcasts in fact show ~ 80% improvement in capturing the frequency, intensity, and spatial distribution of rainfall associated with the EREs. Present study brought out a downscaled DCPP product, with potential prediction skill for EREs over India. It is important to highlight that the models predict an increase in the small and medium-area EREs as compared to the large-area EREs over the monsoon core region for the decade 2019–2028.
Medication delivery errors in outpatients with percutaneous endoscopic gastrostomy: effect on tube feeding replacement
Authors: García González David , Martín-Suárez Ana , Salvador Sánchez Juan José , Sánchez Serrano Jesús Ángel , Calvo M. Victoria
Published: December 2023

Patients with enteral access usually receive oral drugs via feeding tubes and correct drug administration remains a challenge. The aim of this study was to identify common medication delivery errors (MDEs) in outpatients with percutaneous endoscopic gastrostomy (PEG) and evaluate their association with the need for tube replacement due to deterioration or clogging. A 2-year retrospective study that comprised adult outpatients with a placed/replaced PEG tube and whose electronic medical record included home medication was carried out. Treatment with medication that should not be crushed and administered through an enteral feeding tube was considered an MDE. We included 269 patients and 213 MDEs (20% of oral prescriptions) were detected in 159. Ninety-two percent of the medications associated with MDEs could be substituted by appropriate formulations. Tube replacement due to obstruction was needed in 85 patients. MDEs were associated with increased risk for tube replacement (OR 2.17; 95% CI 1.10–4.27). Omeprazole enteric-coated capsules were associated with the greatest risk (OR 2.24; 95% CI 1.01–4.93). PEG outpatients are highly exposed to MDEs, leading to a significant increase in the odds of tube replacement, mainly when treated with omeprazole. The use of appropriate alternative therapies would prevent unnecessary adverse events.
Evaluation of a decellularized bronchial patch transplant in a porcine model
Authors: Taniguchi Daisuke , Kamata Satoshi , Rostami Sara , Tuin Stephen , Marin-Araujo Alba , Guthrie Kelly , Petersen Thomas , Waddell Thomas K. , Karoubi Golnaz , Keshavjee Shaf , Haykal Siba
Published: December 2023

Biological scaffolds for airway reconstruction are an important clinical need and have been extensively investigated experimentally and clinically, but without uniform success. In this study, we evaluated the use of a decellularized bronchus graft for airway reconstruction. Decellularized left bronchi were procured from decellularized porcine lungs and utilized as grafts for airway patch transplantation. A tracheal window was created and the decellularized bronchus was transplanted into the defect in a porcine model. Animals were euthanized at 7 days, 1 month, and 2 months post-operatively. Histological analysis, immunohistochemistry, scanning electron microscopy, and strength tests were conducted in order to evaluate epithelialization, inflammation, and physical strength of the graft. All pigs recovered from general anesthesia and survived without airway obstruction until the planned euthanasia timepoint. Histological and electron microscopy analyses revealed that the decellularized bronchus graft was well integrated with native tissue and covered by an epithelial layer at 1 month. Immunostaining of the decellularized bronchus graft was positive for CD31 and no difference was observed with immune markers (CD3, CD11b, myeloperoxidase) at two months. Although not significant, tensile strength was decreased after one month, but recovered by two months. Decellularized bronchial grafts show promising results for airway patch reconstruction in a porcine model. Revascularization and re-epithelialization were observed and the immunological reaction was comparable with the autografts. This approach is clinically relevant and could potentially be utilized for future applications for tracheal replacement.
Genomic surveillance of SARS-CoV-2 reveals highest severity and mortality of delta over other variants: evidence from Cameroon
Authors: Fokam Joseph , Essomba Rene Ghislain , Njouom Richard , Okomo Marie-Claire A. , Eyangoh Sara , Godwe Celestin , Tegomoh Bryan , Otshudiema John O. , Nwobegahay Julius , Ndip Lucy , Akenji Blaise , Takou Desire , Moctar Mohamed M. M. , Mbah Cleophas Kahtita , Ndze Valantine Ngum , Maidadi-Foudi Martin , Kouanfack Charles , Tonmeu Sandrine , Ngono Dorine , Nkengasong John , Ndembi Nicaise , Bissek Anne-Cecile Z. K. , Mouangue Christian , Ndongo Chanceline B. , Epée Emilienne , Mandeng Nadia , Kamso Belinga Sandrine , Ayouba Ahidjo , Fernandez Nicolas , Tongo Marcel , Colizzi Vittorio , Halle-Ekane Gregory-Edie , Perno Carlo-Federico , Ndjolo Alexis , Ndongmo Clement B. , Shang Judith , Esso Linda , de-Tulio Oliviera , Diagne Moussa Moise , Boum Yap , Mballa Georges A. E. , Njock Louis R. ,   Genomic Surveillance Study Group, Mba Serge Alain Sadeuh , Ngoupou Paul-Alain Tagnoukam , Henri Moumbeket Yifomnjou , Eyoum Bertrand , Beloumou Grace , Ngaba Guy Pascal , Medi Christiane , Nyatte Lydie , Sanders Melissa , Amougou Marie , Bille Loko , Buyohnwenda Kizito Atehambe , Ngomtcho Claudine , Mouliom Abas , Njuwa Fai Karl Gwei , Ateba Gisele Nke , Nka Alex , Dimite Laura , Dir Adama N. , Eboumbou Carole
Published: December 2023

While the SARS-CoV-2 dynamic has been described globally, there is a lack of data from Sub-Saharan Africa. We herein report the dynamics of SARS-CoV-2 lineages from March 2020 to March 2022 in Cameroon. Of the 760 whole-genome sequences successfully generated by the national genomic surveillance network, 74% were viral sub-lineages of origin and non-variants of concern, 15% Delta, 6% Omicron, 3% Alpha and 2% Beta variants. The pandemic was driven by SARS-CoV-2 lineages of origin in wave 1 (16 weeks, 2.3% CFR), the Alpha and Beta variants in wave 2 (21 weeks, 1.6% CFR), Delta variants in wave 3 (11 weeks, 2.0% CFR), and omicron variants in wave 4 (8 weeks, 0.73% CFR), with a declining trend over time (p = 0.01208). Even though SARS-CoV-2 heterogeneity did not seemingly contribute to the breadth of transmission, the viral lineages of origin and especially the Delta variants appeared as drivers of COVID-19 severity in Cameroon.
Emergence of a mutual-growth mechanism in networks evolved by social preference based on indirect utility
Authors: Lee Jong-Hyeok , Ogawa Ken-ichiro
Published: December 2023

Preferential attachment is an important mechanism in the structural evolution of complex networks. However, though resources on a network propagate and have an effect beyond a direct relationship, growth by preferential attachment based on indirectly propagated resources has not been systematically investigated. Here, we propose a mathematical model of an evolving network in which preference is proportional to a utility function reflecting direct utility from directly connected nodes and indirect utility from indirectly connected nodes beyond the directly connected nodes. Our analysis showed that preferential attachment involving indirect utility forms a converged and hierarchical structure, thereby significantly increasing the indirect utility across the entire network. Further, we found that the structures are formed by mutual growth between adjacent nodes, which promotes a scaling exponent of 1.5 between the number of indirect and direct links. Lastly, by examining several real networks, we found evidence of mutual growth, especially in social networks. Our findings demonstrate a growth mechanism emerging in evolving networks with preference for indirect utility, and provide a foundation for systematically investigating the role of preference for indirect utility in the structural and functional evolution of large-scale social networks.
Angular surface plasmon resonance-based sensor with a silver nanocomposite layer for effective water pollution detection
Authors: Sayed Fatma A. , Elsayed Hussein A. , Al-Dossari M. , Eissa M. F. , Mehaney Ahmed , Aly Arafa H.
Published: December 2023

For sensing various samples of polluted water and various sodium chloride concentrations using an angular surface plasmon resonance (ASPR), we have introduced a conventional structure and a hybrid heterostructure in the current research. The suggested structures are composed of silver metal, dielectric layers, silver nanocomposite, and a sensing medium. The reflectance spectra of all structures in the visible region were obtained through the utilization of the transfer matrix method by using the angular interrogation method depending on the Kretschmann configuration. Through our findings, five substrate parameters have been optimized to attain the utmost level of sensitivity across all structures: the thickness of Ag-metal, the type and thickness of dielectric materials, the host material type and the volume fraction of nanoparticles for the nanocomposite layer. In this regard, the suggested sensor provides excellent performance with a sensitivity of 448.1°$$/\text{RIU}$$

/
RIU

, signal-to-noise ratio of 0.787, sensor resolution of 0.284°, and figure of merit of 78.766 RIU−1. Therefore, we believe that the introduced design of our ASPR sensor presents a good candidate for an accurate and efficient detection of low concentrations of contaminated water and sodium chloride as well.
Prediction of learning curves of wired and wireless intraoral scanners
Authors: Koo Boncheol , Son Keunbada , Lee Ji-Min , Kim So-Yeun , Jin Myoung-Uk , Lee Kyu-Bok
Published: December 2023

This clinical study aimed to predict the learning curve of wireless and wired intraoral scanners (IOSs) and to compare the reduction patterns of working time. Overall, 14 participants were enrolled in the study. The intraoral scanning procedure was repeated four times, each using wireless and wired IOSs (i700; MEDIT). The work time from the first to the 600th iterations was predicted using the Wright model. Regarding statistical analysis, the Mann–Whitney U-test was performed for comparison between wireless and wired IOSs and between groups with and without an IOS usage experience, and the Friedman test was performed to evaluate the time reduction (α = 0.05). There was a significant difference between wireless and wired IOSs in the first (P = 0.008) and the third (P = 0.035) iterations. Moreover, the time for 600 iterations was statistically significantly different between wireless and wired IOSs (P < 0.05); however, there was no significant difference after the sixth iteration (e.g., seventh iteration: P = 0.062). In wireless IOS, no significant difference was found between participants with and without an IOS usage experience after the 34th iteration (P = 0.053). The difference in the learning effect between wireless and wired IOSs can be overcome by initial learning; however, an IOS usage experience can affect the learning time of wireless IOSs.
Pericentromeric recombination suppression and the ‘large X effect’ in plants
Authors: Wong Edgar L. Y. , Filatov Dmitry A.
Published: December 2023

X chromosome was reported to be a major contributor to isolation between closely related species—the ‘large X’ effect (LXE). The causes of LXE are not clear, but the leading theory is that it is caused by recessive species incompatibilities exposed in the phenotype due to the hemizygosity of X-linked genes in the heterogametic sex. However, the LXE was also reported in species with relatively recently evolved sex chromosomes where Y chromosome is not completely degenerate and X-linked genes are not hemizygous, such as the plantSilene latifolia. Recent genome sequencing and detailed genetic mapping in this species revealed a massive (> 330 Mb) non- or rarely-recombining pericentromeric region on the X chromosome (Xpr) that comprises ~ 90% of the chromosome and over 13% of the entire genome. If any of the Xpr genes are involved in species incompatibilities, this would oppose interspecific gene flow for other genes tightly linked in the Xpr. Here we test the hypothesis that the previously reported LXE inS. latifoliais caused by the lack of recombination on most of the X chromosome. Based on genome-wide analysis of DNA polymorphism and gene expression inS. latifoliaand its close cross-compatible relativeS. dioica, we report that the rarely-recombining regions represent a significant barrier for interspecific gene flow. We found little evidence for any additional factors contributing to the LXE, suggesting that extensive pericentromeric recombination suppression on the X-chromosome is the major if not the only cause of the LXE inS. latifoliaandS. dioica.
Better individual-level risk models can improve the targeting and life-saving potential of early-mortality interventions
Authors: Hazlett Chad , Ramos Antonio P. , Smith Stephen
Published: December 2023

Infant mortality remains high and uneven in much of sub-Saharan Africa. Even low-cost, highly effective therapies can only save lives in proportion to how successfully they can be targeted to those children who, absent the treatment, would have died. This places great value on maximizing the accuracy of any targeting or means-testing algorithm. Yet, the interventions that countries deploy in hopes of reducing mortality are often targeted based on simple models of wealth or income or a few additional variables. Examining 22 countries in sub-Saharan Africa, we illustrate the use of flexible (machine learning) risk models employing up to 25 generally available pre-birth variables from the Demographic and Health Surveys. Using these models, we construct risk scores such that the 10 percent of the population at highest risk account for 15-30 percent of infant mortality, depending on the country. Successful targeting in these models turned on several variables other than wealth, while models that employ only wealth data perform little or no better than chance. Consequently, employing such data and models to predict high-risk births in the countries studied flexibly could substantially improve the targeting and thus the life-saving potential of existing interventions.
Popper’s conjecture with angular slits and twisted light
Authors: Gounden Neelan , Epstein Jenna , Ornelas Pedro , Beck Geoff , Nape Isaac , Forbes Andrew
Published: December 2023

Uncertainty relations are core to both classical and quantum physics, and lend themselves to tests across many degrees of freedom, with structured light emerging as a vibrant tool to harness these degrees of freedom. Here, we test Popper’s conjecture by replacing the traditional spatial and momentum states with angular position and orbital angular momentum (OAM) states of photons, showing that the OAM spectrum for an entangled photon passing through a virtual slit differs from that of a photon passing through a physical slit. To achieve this, we produce two OAM entangled photons, one of which is sent to a slit encoded as a digital hologram, thereby localising its angular position, all the while measuring the OAM of the other. We show that the measured OAM spectrum is limited to that of the initial SPDC photons, independent of the OAM encoded into the slit, consistent with Popper’s viewpoint. Our approach allows us to overcome prior limitations imposed by physical slits and linear momentum, and offers a versatile toolbox for further probes of quantum systems.
An improved deep reinforcement learning routing technique for collision-free VANET
Authors: Upadhyay Pratima , Marriboina Venkatadri , Goyal Samta Jain , Kumar Sunil , El-Kenawy El-Sayed M. , Ibrahim Abdelhameed , Alhussan Amel Ali , Khafaga Doaa Sami
Published: December 2023

Vehicular Adhoc Networks (VANETs) is an emerging field that employs a wireless local area network (WLAN) characterized by an ad-hoc topology. Vehicular Ad Hoc Networks (VANETs) comprise diverse entities that are integrated to establish effective communication among themselves and with other associated services. Vehicular Ad Hoc Networks (VANETs) commonly encounter a range of obstacles, such as routing complexities and excessive control overhead. Nevertheless, the majority of these attempts were unsuccessful in delivering an integrated approach to address the challenges related to both routing and minimizing control overheads. The present study introduces an Improved Deep Reinforcement Learning (IDRL) approach for routing, with the aim of reducing the augmented control overhead. The IDRL routing technique that has been proposed aims to optimize the routing path while simultaneously reducing the convergence time in the context of dynamic vehicle density. The IDRL effectively monitors, analyzes, and predicts routing behavior by leveraging transmission capacity and vehicle data. As a result, the reduction of transmission delay is achieved by utilizing adjacent vehicles for the transportation of packets through Vehicle-to-Infrastructure (V2I) communication. The simulation outcomes were executed to assess the resilience and scalability of the model in delivering efficient routing and mitigating the amplified overheads concurrently. The method under consideration demonstrates a high level of efficacy in transmitting messages that are safeguarded through the utilization of vehicle-to-infrastructure (V2I) communication. The simulation results indicate that the IDRL routing approach, as proposed, presents a decrease in latency, an increase in packet delivery ratio, and an improvement in data reliability in comparison to other routing techniques currently available.
Hydrothermal synthesis of hierarchical microstructure tungsten oxide/carbon nanocomposite for supercapacitor application
Authors: Alonzo Shanna Marie M. , Bentley John , Desai Salil , Bastakoti Bishnu Prasad
Published: December 2023

A hierarchical nanocomposite of carbon microspheres decorated with tungsten oxide (WO3) nanocrystals resulted from the hydrothermal treatment of a precursor solution containing glucose and tungstic acid. The dehydration of glucose molecules formed oligosaccharides, which consequently carbonized, turning into carbon microspheres. The carbon microspheres then acted as a spherical nucleus onto which WO3 nanocrystals grew via heterogeneous nucleation. The reaction product showed a phase junction of orthorhombic and monoclinic WO3, which transitioned to mix-phase of tetragonal and monoclinic WO3 after a subsequent heat treatment at 600 °C in an inert condition. The electrochemical tests showed that incorporating WO3 onto the carbon (WO3/C) resulted in a three-fold increase in the specific capacitance compared to WO3 alone and a high coulombic and energy efficiencies of 98.2% and 92.8%, respectively. The nanocomposite exhibited supercapacitance with both Faradaic and non-Faradaic charge storage mechanisms. Electrochemical impedance spectroscopy showed a lower charge transfer resistance for the composite at Rct = 11.7Ω.
Metagenomics reveals effects of fluctuating water conditions on functional pathways in plant litter microbial community
Authors: Likar Matevž , Grašič Mateja , Stres Blaž , Regvar Marjana , Gaberščik Alenka
Published: December 2023

Climate change modifies environmental conditions, resulting in altered precipitation patterns, moisture availability and nutrient distribution for microbial communities. Changes in water availability are projected to affect a range of ecological processes, including the decomposition of plant litter and carbon cycling. However, a detailed understanding of microbial stress response to drought/flooding is missing. In this study, an intermittent lake is taken up as a model for changes in water availability and how they affect the functional pathways in microbial communities of the decomposing Phragmites australis litter. The results show that most enriched functions in both habitats belonged to the classes of Carbohydrates and Clustering-based subsystems (terms with unknown function) from SEED subsystems classification. We confirmed that changes in water availability resulted in altered functional makeup of microbial communities. Our results indicate that microbial communities under more frequent water stress (due to fluctuating conditions) could sustain an additional metabolic cost due to the production or uptake of compatible solutes to maintain cellular osmotic balance. Nevertheless, although prolonged submergence seemed to have a negative impact on several functional traits in the fungal community, the decomposition rate was not affected.
Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin
Authors: Li Kangjing , Li Yaxin , Nakamura Fumihiko
Published: December 2023

The contact inhibition of proliferation (CIP) denotes the cell density-dependent inhibition of growth, and the loss of CIP represents a hallmark of cancer. However, the mechanism by which CIP regulates gene expression remains poorly understood. Chromatin is a highly complex structure consisting of DNA, histones, and trans-acting factors (TAFs). The binding of TAF proteins to specific chromosomal loci regulates gene expression. Therefore, profiling chromatin is crucial for gaining insight into the gene expression mechanism of CIP. In this study, using modified proteomics of TAFs bound to DNA, we identified a protein that shuttles between the nucleus and cytosol in a cell density-dependent manner. We identified TIPARP, PTGES3, CBFB, and SMAD4 as cell density-dependent nucleocytoplasmic shuttling proteins. In low-density cells, these proteins predominantly reside in the nucleus; however, upon reaching high density, they relocate to the cytosol. Given their established roles in gene regulation, our findings propose their involvement as CIP-dependent TAFs. We also identified and characterized potential open chromatin regions sensitive to changes in cell density. These findings provide insights into the modulation of chromatin structure by CIP.
The effect of the colour red in 20 years of Olympic taekwondo
Authors: Apollaro Gennaro , Falcó Coral , Morales-Sánchez Verónica , Hernández-Mendo Antonio
Published: December 2023

The objectives of this study were (1) to analyse the relationship between the colour of the protectors and the outcome of 895 matches in the six Olympic Games in which taekwondo has been included, and (2) to analyse the effect of confounding factors through the different degrees of asymmetry between contestants. Data were recorded on the colour of each athlete’s protectors, the scoring system, the sex of the athlete, the weight category, the round of competition, the winner of the match, the method of victory and the points scored by each athlete. Among the main results, a relationship emerged between male athletes wearing red and winning the match (p = 0.034) under the manual scoring system. There were relationships between female athletes wearing blue and winning the match in the quarterfinal (p = 0.014) and last 16 rounds (p = 0.021) using the manual and electronic scoring systems respectively. In female athletes, relationships emerged between wearing blue and winning the match with small (p = 0.008) and medium (p = 0.047) asymmetry under the manual system and with large (p = 0.036) asymmetry under the electronic system. The electronic system had a positive impact on the fairness of Olympic competition. Red tends to gain in importance as the asymmetry between the two athletes decreases, but not enough to give a competitive advantage. The results for Olympic competition held in the now concluded era of the manual system confirmed the presence of the colour effect as a result of psychological factors attributable to referees and judges.
An integrated reservoir operation framework for enhanced water resources planning
Authors: Dash Sonam Sandeep , Sahoo Bhabagrahi , Raghuwanshi Narendra Singh
Published: December 2023

Climate change induced spatiotemporal variation in global water availability modifies the proposed design criteria of water infrastructure structures like dams and reservoirs. Although reservoir operation is treated as a potential adaptation option, obsolescence of existing operation rules in the climate change scenarios could cause devastating situation through faulty water management practices. Presently onboard simulation–optimization based reservoir operation schemes fail to capture the uncertainty involved in the climate change scenario. Hence, there is a need to identify the limiting application scenario of the existing reservoir operation rule, and subsequently, revise the operation framework to address the future supply–demand uncertainty adequately. This research develops an integrated Soil and Water Assessment Tool (SWAT) (hydrologic), HEC-ResSim (hydraulic), and genetic algorithm (GA) (optimization) based adaptive reservoir operation framework, which is competent enough in accounting the future supply–demand uncertainty. Incorporation of the newly proposed environmental flow assessment approach in the reservoir operation would assist the decision makers in guiding the reservoir release for maintaining the water quality and sustenance of the downstream aquatic species. Certainly, corresponding to the existing operation rules under both the baseline and future climate change scenarios of RCP 4.5 and 8.5, the developed SWAT-HEC-ResSim-GA based reservoir operation scheme could improve the performance of the Kangsabati reservoir with the time and volume reliability estimates of 0.631 and 0.736, respectively. Conclusively, the developed approach in this study could be the best feasible alternative for hydrologic characterization in complex reservoir catchment-command regions with the option for enhanced reservoir planning in global catchment-command regions.