bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-genome sequencing across 449 samples spanning 47 ethnolinguistic groups provides insights into genetic diversity in Nigeria
Authors: Joshi Esha , Biddanda Arjun , Popoola Jumi , Yakubu Aminu , Osakwe Oluyemisi , Attipoe Delali ,   54gene Team, NCD-GHS Consortium, Dogbo Estelle , Salako Babatunde , Nash Oyekanmi , Salako Omolola , Oyedele Olubukunola , Eze-Echesi Golibe , Fatumo Segun , Ene-Obong Abasi , O’Dushlaine Colm 
Published: December 2022

SummaryAfrican populations have been drastically underrepresented in genomics research and failure to capture the genetic diversity across the numerous ethnolinguistic groups (ELGs) found in the continent has hindered the equity of precision medicine initiatives globally. Here, we describe the whole-genome sequencing of 449 Nigerian individuals across 47 unique self-reported ELGs. Population structure analysis reveals genetic differentiation amongst our ELGs, consistent with previous findings. From the 36 million SNPs and INDELs discovered in our dataset, we provide a high-level catalog of both novel and medically-relevant variation present across the ELGs. These results emphasize the value of this resource for genomics research, with added granularity by representing multiple ELGs from Nigeria. Our results also underscore the potential of using these cohorts with larger sample sizes to improve our understanding of human ancestry and health in Africa.
It takes neurons to understand neurons: Digital twins of visual cortex synthesize neural metamers
Authors: Cobos Erick , Muhammad Taliah , Fahey Paul G. , Ding Zhiwei , Ding Zhuokun , Reimer Jacob , Sinz Fabian H. , Tolias Andreas S. 
Published: December 2022

ABSTRACTMetamers, images that are perceived as equal, are a useful tool to study representations of natural images in biological and artificial vision systems. We synthesized metamers for the mouse visual system by inverting a deep encoding model to find an image that matched the observed neural activity to the original presented image. When testing the resulting images in physiological experiments we found that they most closely reproduced the neural activity of the original image when compared to other decoding methods, even when tested in a different animal whose neural activity was not used to produce the metamer. This demonstrates that deep encoding models do capture general characteristic properties of biological visual systems and can be used to define a meaningful perceptual loss for the visual system.
The benefits and perils of import in small cattle breeding programs
Authors: Obšteter J. , Jenko J. , Pocrnic I. , Gorjanc G. 
Published: December 2022

ABSTRACTSmall breeding programs are limited in achieving competitive genetic gain and prone to high rates of inbreeding. Thus, they often import genetic material to increase genetic gain and to limit the loss of genetic variability. However, the benefit of import depends on the strength of genotype by environment interaction. It also also diminishes the relevance of domestic selection and the use of domestic breeding animals. Introduction of genomic selection has potentially execerbated this issue, but is also opening the potential for smaller breeding program.The aim of this paper was to determine when and to what extent do small breeding programs benefit from import. We simulated two cattle breeding programs differing in selection parameters representing a large foreign and a small domestic breeding program that differ in the initial genetic mean and annual genetic gain. We evaluated a control scenario without the use of foreign sires in the domestic breeding program and 20 scenarios that varied the percentage of domestic dams mated with foreign sires, the genetic correlation between the breeding programs (0.8 or 0.9), and the time of implementing genomic selection in the domestic compared to the foreign breeding program (concurrently or with a 10-year delay). We compared the scenarios based on the genetic gain and genic standard deviation. Finally, we partitioned breeding values and genetic trends of the scenarios to quantify the contribution of domestic selection and import to the domestic genetic gain.The simulation revealed that when both breeding programs implemented genomic selection simultaneously, the use of foreign sires increased domestic genetic gain only when genetic correlation was 0.9. In contrast, when the domestic breeding program implemented genomic selection with a 10-year delay, genetic correlation of 0.8 sufficed for a positive impact of import. In that scenario, domestic genetic gain increased with the increasing use of foreign sires but with a diminishing return. The partitioning analysis revealed that the contribution of import expectedly increased with the increased use of foreign sires. However, the increase did not depend on the genetic correlation and was not proportional to the increase in domestic genetic gain. This means that a small breeding program could be overly relying on import with diminishing returns for the genetic gain and marginal benefit for the genetic variability.The benefit of import depends on an interplay of genetic correlation, extent of using foreign sires, and a breeding scheme. It is therefore crucial that small breeding programs assess the possible benefits of import beyond domestic selection. The benefit of import should be weighted against the perils of decreased use of domestic sires and decreased contribution and value of domestic selection.
A mechanistic model towards ecological inclusion for a better plant growth understanding
Authors: Nasti Lucia , Del Dottore Emanuela , Tedone Fabio , Palladino Michele , Mazzolai Barbara , Marcati Pierangelo 
Published: December 2022

AbstractPlants growth is a complex and delicate balance among different factors involving environmental and physiological conditions. In this context, we propose a mechanistic model that considers the main internal processes of plant growth and reproduces a wide range of plant behaviors observed experimentally. In particular, we describe the model plant ofArabidopsis thalianain a realistic environment with a day-and-night cycle, which considers different inputs as light, water, phosphorus, nitrogen, starch and sucrose. In addition, we propose a new function that describes the affinity between the plant and a specific nutrient, and a novel feedback signal to model how plants have the remarkable capacity to distribute resources among their organs. The result is an efficient tool applicable in ecological and agricultural studies, which can estimate several parameters, simulate several soil conditions and analyze how limiting or toxic resources can affect the plant development. We improve our understanding of plant adaptive strategies, reproducing results in line with experiments.
Microscale geometrical features in the plant leaf epidermis confer enhanced resistance to mechanical failure
Authors: Bidhendi Amir J. , Lampron Olivier , Gosselin Frédérick P. , Geitmann Anja 
Published: December 2022

AbstractIn many plant species, epidermal tissues of leaves and petals feature irregular wavy cell geometries forming jigsaw puzzle patterns. At the origin of plant tissues are simple polyhedral progenitor cells that divide and grow into a kaleidoscopic array of morphologies that underpin plant organ functionality. The wide prevalence and great diversity of the wavy cell shape in the plant kingdom point to the significance of this trait and its tunability by environmental pressures. Despite multiple attempts to explain the advent of this complex cell geometry by evolutionary relevant functionality, our understanding of this peculiar tissue patterning preserved through evolution remains lacking. Here, by combining microscopic and macroscopic fracture experiments with computational fracture mechanics, we show that wavy epidermal cells toughen the plants’ protective skin. Based on a multi-scale approach, we demonstrate that, biological and synthetic materials alike can be toughened through an energy-efficient patterning process. Our data reveal a ubiquitous and tunable structural-mechanical mechanism employed in the macro-scale design of plants to protect them from the detrimental effects of surface fissures and to enable and guide the direction of beneficial fractures. We expect these data to inform selective plant breeding for traits enhancing plant survival under changing environmental conditions. From a materials engineering perspective, this work exemplifies that plants hold sophisticated design principles to inspire human-made materials.
Does it pay to pay? A comparison of the benefits of open-access publishing across various sub-fields in Biology
Authors: Clark Amanda D. , Myers Tanner C. , Steury Todd D. , Krzton Ali , Yanes Julio A. , Barber Angela , Barry Jacqueline L. , Barua Subarna , Eaton Katherine M. , Gosavi Devadatta , Nance Rebecca L. , Pervaiz Zahida H. , Ugochukwu Chidozie G. , Hartman Patricia , Stevison Laurie S. 
Published: December 2022

AbstractAuthors are often faced with the decision of whether to maximize impact or minimize costs when publishing the results of their research. For example, to potentially improve impact via increased accessibility, many subscription-based journals now offer the option of paying a fee to publish open access (i.e., hybrid journals), but this solution excludes authors who lack the capacity to pay to make their research accessible. Here, we tested if paying to publish open access in a subscriptionbased journal benefited authors by conferring more citations relative to closed access articles. We identified 146,415 articles published in 152 hybrid journals in the field of biology from 2013-2018 to compare the number of citations between various types of open access and closed access articles. In a simple generalized linear model analysis of our full dataset, we found that publishing open access in hybrid journals that offer the option confers an average citation advantage to authors of 17.8 citations compared to closed access articles in similar journals. After taking into account the number of authors, journal impact, year of publication, and subject area, we still found that open access generated significantly more citations than closed access (p< 0.0001). However, results were complex, with exact differences in citation rates among access types impacted by these other variables. This citation advantage based on access type was even similar when comparing open and closed access articles published in the same issue of a journal (p< 0.0001). However, by examining articles where the authors paid an article processing charge, we found that cost itself was not predictive of citation rates (p= 0.14). Based on our findings of access type and other model parameters, we suggest that, in most cases, paying for access does confer a citation advantage. For authors with limited budgets, we recommend pursuing open access alternatives that do not require paying a fee as they still yielded more citations than closed access. For authors who are considering where to submit their next article, we offer additional suggestions on how to balance exposure via citations with publishing costs.
A Tri-light Warning System for Hospitalized COVID-19 Patients: Credibility-based Risk Stratification under Data Shift
Authors: Xu Chuanjun , Xu Qinmei , Liu Li , Zhou Mu , Xing Zijian , Zhou Zhen , Zhou Changsheng , Li Xiao , Wang Rong , Wu Yanjun , Wang Jiangtao , Zhang Longjiang , Zhan Xianghao , Gevaert Olivier , Lu Guangming 
Published: December 2022

AbstractOBJECTIVETo develop a tri-light warning system for the early warning of novel coronavirus pneumonia (COVID-19) and stratification of patients.MATERIALS AND METHODSThe system extracts radiomic features from CT images and integrates clinical record information to output a prediction probability and credibility of each prediction. It classifies patients in the general ward into red (high risk), yellow (uncertain risk), and green (low risk) labels. The system was tested using a multi-center cohort of 8,721 patients.RESULTSThe system demonstrated reliability and performance validation under data distribution shifts, and was applicable to both the original strain and variant strains of COVID-19.DISCUSSIONThe tri-light warning system has the potential to improve patient stratification performance and identify epidemiological risks early, thus allowing for timely treatment and optimization of medical resource allocation.CONCLUSIONThe tri-light warning system based on conformal prediction is a reliable and effective method for the early warning and stratification of COVID-19 patients.
Antibiotic Treatment Duration for Bacterial Infections - A Systematic Review and Critical Appraisal
Authors: Mo Yin , Tan Wei Cong , Cooper Ben S. 
Published: December 2022

SummaryReducing antibiotic treatment duration is a key stewardship intervention to mitigate antimicrobial resistance (AMR). We performed a systematic review of antibiotic duration randomised controlled trials for treatment or prevention of bacterial infections in humans, appraised their methodologies and identified gaps in evidence. All randomised trials indexed in MEDLINE and EMBASE up to October 2022 which compared different treatment durations were included. We found 296 trials, of which 85% showed equivalence or non-inferiority. The majority (73%) considered treatment for respiratory tract infections, genitourinary infections, and post-surgical prophylaxis. Few trials studied severe infections, such as bloodstream infections and ventilator-associated pneumonia. Trial designs shifted from superiority (74%, 178/242 before 2016) to non-inferiority (74%, 40/54 after 2016). 94% of the trials that defined a per- protocol population reported non-adherence, which may increase the probability of concluding non-inferiority. Only 9 trials collected data to demonstrate the effect of antibiotic duration on AMR colonisation.RegistrationPROSPERO 2021 CRD42021276209FundingNational Research Foundation Singapore Central Gap Fund; National Medical Research Council, Singapore; Medical Research Council, UK
Evaluating the Significance of Atypical and Malignant Breast Lesions Arising in Fibroadenoma of the Breast
Authors: Sham Sunder , Morrar Doaa , Al-Refai Reham , Bandari Ahmed , Garajayev Azar , Hajiyeva Sabina 
Published: December 2022

AbstractContextWhile fibroadenomas (FAs) are the most common benign neoplasm of the breast, little data exists about the clinical characteristics and prognostic value of FAs found to be directly associated with atypical and malignant lesions.ObjectiveCases of FA of the breast were reviewed to establish the exact clinical significance of these lesions involved by atypia and malignancy.DesignAll FA cases diagnosed on core needle biopsy (CNB) between 2013 and 2022 were screened to identify atypical and malignant lesions {(atypical lobular hyperplasia (ALH), lobular carcinoma in situ (LCIS), atypical ductal hyperplasia (ADH), flat epithelial atypia (FEA), ductal carcinoma in situ(DCIS), invasive ductal carcinoma (IDC), and invasive lobular carcinoma (ILC)} arising in FA. The relationship between CNB and excisional findings for each case was reviewed.ResultsA total of 1500 cases of FA diagnosed on CNB were identified. Among these, 23 cases showed atypical and/or malignant lesions within FA. The median age at diagnosis was 53 years. Of those 23 cases, five were LCIS, one was LCIS+ILC, one was LCIS+ALH, one DCIS+IDC, one was LCIS+DCIS, three were ADH, seven were ALH, and four were DCIS. For LCIS, the excision showed LCIS (2/5), LCIS + ALH (1/5), LCIS + DCIS (1/5), LCIS + DCIS + ALH (1/5). For DCIS, excisions showed Invasive carcinoma with mixed ductal and lobular features (1/4), LCIS + DCIS (1/4), LCIS + DCIS + IDC [classic and pleomorphic type] (1/4), no residual carcinoma (1/4). For ALH, excision showed ALH (2/7), no residual ALH (2/7), ALH+IDP (Intraductal Papilloma) (2/7), LCIS (1/7). For ADH, DCIS (1/3), and benign findings (2/3). For LCIS+ILC and DCIS+IDC, the excisional findings were the same. For LCIS+ ALH, the excisional findings showed benign findings with the radial scar (1/1).ConclusionThere is a low percentage of FA harboring atypia or carcinoma. Due to the high upgrade rate following excision, complete excision of these lesions may guide recommended method of clinical management
The fast diffusion of NKCC1 along the axon is driven by glutamatergic activity
Authors: Côme Etienne , Pol Erwan , Merlaud Zaha , Gouhier Juliette , Russeau Marion , Marques Xavier , Scotto-Lomassese Sophie , Moutkine Imane , Lévi Sabine 
Published: December 2022

SummaryNKCC1 and KCC2 transporters regulate neuronal chloride homeostasis and thus synaptic inhibition. KCC2 activity is tuned by diffusion-capture in an activity-dependent manner. The mechanisms controlling NKCC1 in neurons are unknown. We found using super-resolution imaging that NKCC1 like KCC2 form nanodomains in the somato-dendritic membrane at extrasynaptic sites and at the periphery of excitatory and inhibitory synapses. NKCC1 nanoclusters are half the size and density in molecules than KCC2 clusters. This is accompanied by a higher mobility of NKCC1 compared to KCC2 in the dendritic membrane, suggesting a weaker NKCC1 anchoring to the cytoskeleton. In contrast, NKCC1, but not KCC2, is confined to endocytic zones, which would explain its controlled surface expression and the fact that endocytic zones would provide a reservoir from which NKCC1 could be released into the membrane. Finally, we show an increased confinement of NKCC1 in axons but not in dendrites upon glutamatergic activity blockade, indicating a selective mechanism of regulation in the axon. We propose that a rapid regulation of NKCC1 by lateral diffusion in the axon would control presynaptic glutamate release and the firing of action potentials.
Salmonellainfection induces the reorganisation of follicular dendritic cell networks concomitant with the failure to generate germinal centres
Authors: Marcial-Juárez Edith , Perez-Toledo Marisol , Nayar Saba , Pipi Elena , Alshayea Areej , Persaud Ruby , Jossi Sian E. , Lamerton Rachel , Barone Francesca , Henderson Ian R. , Cunningham Adam F. 
Published: December 2022

SummaryGerminal centres (GCs) are sites where plasma and memory B cells form to generate high-affinity, Ig class switched antibodies. Specialised stromal cells called follicular dendritic cells (FDCs) are essential for GC formation. During systemicSalmonellaTyphimurium (STm) infection GCs are absent, whereas extensive extrafollicular switched antibody responses are maintained. The mechanisms that underpin the absence of GC formation are incompletely understood. Here, we show that STm-induces a reversible disruption of niches within the splenic microenvironment, including the T and B cell compartments and the marginal zone. Alongside to these effects post-infection, mature FDC networks are strikingly absent, whereas immature FDC precursors, including marginal sinus pre-FDCs (MadCAM-1+) and perivascular Pre-FDCs (PDGFRβ+) are enriched. As normal FDC networks re-establish, extensive GCs become detectable throughout the spleen. Therefore, the reorganisation of FDC networks and the loss of GC responses are key, parallel features of systemic STm infections.Graphical abstract
The Geographical Gap in Leading Medical Journals - a Computational Audit
Authors: Brück Oscar 
Published: December 2022

ABSTRACTBackgroundAuditing geographical representation in medical publishing could help to mitigate possible national and regional disparities.MethodsUsing the Web of Science indexing database, we collected bibliometric data of original research articles published between 2010-2019 inThe New England Journal of Medicine, Nature Medicine, Journal of the American Medical Association, The BMJ, andThe Lancet. We studied the corresponding authors’ geolocation in regard to publication and citation count, their temporal evolution, and the journals’ and citing organizations’ nationality.ResultsWe identified 10,558 articles. Based on the nationality of the corresponding authors’ institutes, only 32 countries published more than 10 publications in 10 years equaling to 98.9% of all publications. English-speaking countries USA (48.2%), UK (15.9%), Canada (5.3%), and Australia (3.2%) were most represented, but with a declining trend in recent years. Normalized to their accumulated citations, 9/32 countries were associated with ≥10% publication excess, of which USA (n=1,174 publications) and UK (n=410) accounted for 85.7%. Similar findings were replicated at the municipal level where all top 10 most productive cities were located in USA (n=7), UK (n=2), or Canada (n=1), and 21 out of 25 most productive cities published more articles than predicted based on their accumulated citations. Finally, we discovered that both journals published, and researchers cited more commonly research conducted in the same country.DiscussionThe audit revealed Anglocentric dominance, domestic preference occurring in both journals and citation selection, and increased geographical representation in recent years in medical publishing.
Identifying and preventing fraudulent responses in online public health surveys: Lessons learned during the COVID-19 pandemic
Authors: Wang June , Calderon Gabriela , Hager Erin R. , Edwards Lorece V. , Berry Andrea A. , Liu Yisi , Dinh Janny , Summers Amber C. , Connor Katherine A. , Collins Megan E. , Pritchett Laura , Marshall Beth R. , Johnson Sara B. 
Published: December 2022

AbstractWeb-based survey data collection has become increasingly popular, and limitations on in-person data collection during the COVID-19 pandemic have fueled this growth. However, the anonymity of the online environment increases the risk of fraud, which pose major risks to data integrity. As part of a study of COVID-19 and the return to in-person school, we implemented a web-based survey of parents in Maryland, USA, between December 2021 and July 2022. Recruitment relied, in part, on social media advertisements. Despite implementing many existing best practices, the survey was challenged by sophisticated fraudsters. In this paper, we describe efforts to identify and prevent fraudulent online survey responses and provide specific, actionable recommendations for identifying and preventing online survey fraud. Some strategies can be deployed within the web-based data collection platform such as Internet Protocol address logging to identify duplicate responses and comparison of client-side and server-side time stamps to identify responses that may have been completed by respondents outside of the survey’s target geography. Additional approaches include the use of a 2-stage survey design, repeated within-survey and cross-survey validation questions, the addition of “speed bump” questions to thwart careless or computerized responders, and the use of optional open-ended survey responses to identify irrelevant responses. We describe best practices for ongoing survey data review and verification, including algorithms to simplify aspects of this review.