bluuebunny/crossref_metadata_2025_split huggingface dataset:
National genomic surveillance integrating standardized quantitative susceptibility testing clarifies antimicrobial resistance in Enterobacterales
Authors: Kayama Shizuo , Yahara Koji , Sugawara Yo , Kawakami Sayoko , Kondo Kohei , Zuo Hui , Kutsuno Shoko , Kitamura Norikazu , Hirabayashi Aki , Kajihara Toshiki , Kurosu Hitomi , Yu Liansheng , Suzuki Masato , Hisatsune Junzo , Sugai Motoyuki 
Published: December 2023

AbstractAntimicrobial resistance is a global health concern; Enterobacterales resistant to third-generation cephalosporins (3GCs) and carbapenems are of the highest priority. Here, we conducted genome sequencing and standardized quantitative antimicrobial susceptibility testing of 4,195 isolates of Escherichia coli and Klebsiella pneumoniae resistant to 3GCs and Enterobacterales with reduced meropenem susceptibility collected across Japan. Our analyses provided a complete classification of 3GC resistance mechanisms. Analyses with complete reference plasmids revealed that among the blaCTX-M extended-spectrum β-lactamase genes, blaCTX-M-8 was typically encoded in highly similar plasmids. The two major AmpC β-lactamase genes were blaCMY-2 and blaDHA-1. Long-read sequencing of representative plasmids revealed that approximately 60% and 40% of blaCMY-2 and blaDHA-1 were encoded by such plasmids, respectively. Our analyses identified strains positive for carbapenemase genes but phenotypically susceptible to carbapenems and undetectable by standard antimicrobial susceptibility testing. Systematic long-read sequencing enabled reconstruction of 183 complete plasmid sequences encoding three major carbapenemase genes and elucidation of their geographical distribution stratified by replicon types and species carrying the plasmids and potential plasmid transfer events. Overall, we provide a blueprint for a national genomic surveillance study that integrates standardized quantitative antimicrobial susceptibility testing and characterizes resistance determinants.
Collaborative and privacy-preserving retired battery sorting for profitable direct recycling via federated machine learning
Authors: Tao Shengyu , Liu Haizhou , Sun Chongbo , Ji Haocheng , Ji Guanjun , Han Zhiyuan , Gao Runhua , Ma Jun , Ma Ruifei , Chen Yuou , Fu Shiyi , Wang Yu , Sun Yaojie , Rong Yu , Zhang Xuan , Zhou Guangmin , Sun Hongbin 
Published: December 2023

AbstractUnsorted retired batteries with varied cathode materials hinder the adoption of direct recycling due to their cathode-specific nature. The surge in retired batteries necessitates precise sorting for effective direct recycling, but challenges arise from varying operational histories, diverse manufacturers, and data privacy concerns of recycling collaborators (data owners). Here we show, from a unique dataset of 130 lithium-ion batteries spanning 5 cathode materials and 7 manufacturers, a federated machine learning approach can classify these retired batteries without relying on past operational data, safeguarding the data privacy of recycling collaborators. By utilizing the features extracted from the end-of-life charge-discharge cycle, our model exhibits 1% and 3% cathode sorting errors under homogeneous and heterogeneous battery recycling settings respectively, attributed to our innovative Wasserstein-distance voting strategy. Economically, the proposed method underscores the value of precise battery sorting for a prosperous and sustainable recycling industry. This study heralds a new paradigm of using privacy-sensitive data from diverse sources, facilitating collaborative and privacy-respecting decision-making for distributed systems.
Metabolic tagging of extracellular vesicles and development of enhanced extracellular vesicle based cancer vaccines
Authors: Bhatta Rimsha , Han Joonsu , Liu Yusheng , Bo Yang , Lee David , Zhou Jiadiao , Wang Yueji , Nelson Erik Russell , Chen Qian , Zhang Xiaojia Shelly , Hassaneen Wael , Wang Hua 
Published: December 2023

AbstractAs key mediators of cellular communication, extracellular vesicles (EVs) have been actively explored for diagnostic and therapeutic applications. However, effective methods to functionalize EVs and modulate the interaction between EVs and recipient cells are still lacking. Here we report a facile and universal metabolic tagging technology that can install unique chemical tags (e.g., azido groups) onto EVs. The surface chemical tags enable conjugation of molecules via efficient click chemistry, for the tracking and targeted modulation of EVs. In the context of tumor EV vaccines, we show that the conjugation of toll-like receptor 9 agonists onto EVs enables timely activation of dendritic cells and generation of superior antitumor CD8+ T cell response. These lead to 80% tumor-free survival against E.G7 lymphoma and 33% tumor-free survival against B16F10 melanoma. Our study yields a universal technology to generate chemically tagged EVs from parent cells, modulate EV-cell interactions, and develop potent EV vaccines.
Population fraction of Parkinson’s disease attributable to preventable risk factors
Authors: Payami Haydeh , Cohen Gwendolyn , Murchison Charles F. , Sampson Timothy R. , Standaert David G. , Wallen Zachary D. 
Published: December 2023

AbstractParkinson’s disease is the fastest-growing neurologic disease with seemingly no means of prevention. Intrinsic risk factors (age, sex, and genetics) are inescapable, but environmental factors are not. We identified repeated blows to the head in sports/combat as a potential new risk factor. 23% of PD cases in females were attributable to pesticide/herbicide exposure, and 30% of PD in males were attributable to pesticides/herbicides, military-related chemical exposures, and repeated blows to the head, and therefore could have potentially been prevented.
Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda
Authors: Monod Mélodie , Brizzi Andrea , Galiwango Ronald M. , Ssekubugu Robert , Chen Yu , Xi Xiaoyue , Kankaka Edward Nelson , Ssempijja Victor , Abeler-Dörner Lucie , Akullian Adam , Blenkinsop Alexandra , Bonsall David , Chang Larry W. , Dan Shozen , Fraser Christophe , Golubchik Tanya , Gray Ronald H. , Hall Matthew , Jackson Jade C. , Kigozi Godfrey , Laeyendecker Oliver , Mills Lisa A. , Quinn Thomas C. , Reynolds Steven J. , Santelli John , Sewankambo Nelson K. , Spencer Simon E. F. , Ssekasanvu Joseph , Thomson Laura , Wawer Maria J. , Serwadda David , Godfrey-Faussett Peter , Kagaayi Joseph , Grabowski M. Kate , Ratmann Oliver ,   Rakai Health Sciences Program,   PANGEA-HIV consortium
Published: December 2023

AbstractHIV incidence in eastern and southern Africa has historically been concentrated among girls and women aged 15–24 years. As new cases decline with HIV interventions, population-level infection dynamics may shift by age and gender. Here, we integrated population-based surveillance of 38,749 participants in the Rakai Community Cohort Study and longitudinal deep-sequence viral phylogenetics to assess how HIV incidence and population groups driving transmission have changed from 2003 to 2018 in Uganda. We observed 1,117 individuals in the incidence cohort and 1,978 individuals in the transmission cohort. HIV viral suppression increased more rapidly in women than men, however incidence declined more slowly in women than men. We found that age-specific transmission flows shifted: whereas HIV transmission to girls and women (aged 15–24 years) from older men declined by about one-third, transmission to women (aged 25–34 years) from men that were 0–6 years older increased by half in 2003 to 2018. Based on changes in transmission flows, we estimated that closing the gender gap in viral suppression could have reduced HIV incidence in women by half in 2018. This study suggests that HIV programmes to increase HIV suppression in men are critical to reduce incidence in women, close gender gaps in infection burden and improve men’s health in Africa.
Hypoblast from human pluripotent stem cells regulates epiblast development
Authors: Okubo Takumi , Rivron Nicolas , Kabata Mio , Masaki Hideki , Kishimoto Keiko , Semi Katsunori , Nakajima-Koyama May , Kunitomi Haruko , Kaswandy Belinda , Sato Hideyuki , Nakauchi Hiromitsu , Woltjen Knut , Saitou Mitinori , Sasaki Erika , Yamamoto Takuya , Takashima Yasuhiro 
Published: December 2023

AbstractRecently, several studies using cultures of human embryos together with single-cell RNA-seq analyses have revealed differences between humans and mice, necessitating the study of human embryos1–8. Despite the importance of human embryology, ethical and legal restrictions have limited post-implantation-stage studies. Thus, recent efforts have focused on developing in vitro self-organizing models using human stem cells9–17. Here, we report genetic and non-genetic approaches to generate authentic hypoblast cells (naive hPSC-derived hypoblast-like cells (nHyCs))—known to give rise to one of the two extraembryonic tissues essential for embryonic development—from naive human pluripotent stem cells (hPSCs). Our nHyCs spontaneously assemble with naive hPSCs to form a three-dimensional bilaminar structure (bilaminoids) with a pro-amniotic-like cavity. In the presence of additional naive hPSC-derived analogues of the second extraembryonic tissue, the trophectoderm, the efficiency of bilaminoid formation increases from 20% to 40%, and the epiblast within the bilaminoids continues to develop in response to trophectoderm-secreted IL-6. Furthermore, we show that bilaminoids robustly recapitulate the patterning of the anterior–posterior axis and the formation of cells reflecting the pregastrula stage, the emergence of which can be shaped by genetically manipulating the DKK1/OTX2 hypoblast-like domain. We have therefore successfully modelled and identified the mechanisms by which the two extraembryonic tissues efficiently guide the stage-specific growth and progression of the epiblast as it establishes the post-implantation landmarks of human embryogenesis.
Chronic disease outcome metadata from German observational studies – public availability and FAIR principles
Authors: Schwedhelm Carolina , Nimptsch Katharina , Ahrens Wolfgang , Hasselhorn Hans Martin , Jöckel Karl-Heinz , Katzke Verena , Kluttig Alexander , Linkohr Birgit , Mikolajczyk Rafael , Nöthlings Ute , Perrar Ines , Peters Annette , Schmidt Carsten O. , Schmidt Börge , Schulze Matthias B. , Stang Andreas , Zeeb Hajo , Pischon Tobias 
Published: December 2023

AbstractMetadata from epidemiological studies, including chronic disease outcome metadata (CDOM), are important to be findable to allow interpretability and reusability. We propose a comprehensive metadata schema and used it to assess public availability and findability of CDOM from German population-based observational studies participating in the consortium National Research Data Infrastructure for Personal Health Data (NFDI4Health). Additionally, principal investigators from the included studies completed a checklist evaluating consistency with FAIR principles (Findability, Accessibility, Interoperability, Reusability) within their studies. Overall, six of sixteen studies had complete publicly available CDOM. The most frequent CDOM source was scientific publications and the most frequently missing metadata were availability of codes of the International Classification of Diseases, Tenth Revision (ICD-10). Principal investigators’ main perceived barriers for consistency with FAIR principles were limited human and financial resources. Our results reveal that CDOM from German population-based studies have incomplete availability and limited findability. There is a need to make CDOM publicly available in searchable platforms or metadata catalogues to improve their FAIRness, which requires human and financial resources.
Quantitative biodistribution of nanoparticles in plants with lanthanide complexes
Authors: Hou H. , Xu Z. , Takeda Y. S. , Powers M. , Yang Y. , Hershberger K. , Hanscom Hailey , Svenson S. , Simhadri R. K. , Vegas A. J. 
Published: December 2023

AbstractThe inefficient distribution of fertilizers, nutrients, and pesticides on crops is a major challenge in modern agriculture that leads to reduced productivity and environmental pollution. Nanoformulation of agrochemicals is an attractive approach to enable the selective delivery of agents into specific plant organs, their release in those tissues, and improve their efficiency. Already commercialized nanofertilizers utilize the physiochemical properties of metal nanoparticles such as size, charge, and the metal core to overcome biological barriers in plants to reach their target sites. Despite their wide application in human diseases, lipid nanoparticles are rarely used in agricultural applications and a systematic screening approach to identifying efficacious formulations has not been reported. Here, we developed a quantitative metal-encoded platform to determine the biodistribution of different lipid nanoparticles in plant tissues. In this platform lanthanide metal complexes were encapsulated into four types of lipid nanoparticles. Our approach was able to successfully quantify payload accumulation for all the lipid formulations across the roots, stem, and leaf of the plant. Lanthanide levels were 20- to 57-fold higher in the leaf and 100- to 10,000-fold higher in the stem for the nanoparticle encapsulated lanthanide complexes compared to the unencapsulated, free lanthanide complex. This system will facilitate the discovery of nanoparticles as delivery carriers for agrochemicals and plant tissue-targeting products.
Cumulative trauma load and timing of trauma prior to military deployment differentially influences inhibitory control processing across deployment
Authors: Miller Lisa N. , Forbes David , McFarlane Alexander C. , Lawrence-Wood Ellie , Simmons Julian G. , Felmingham Kim 
Published: December 2023

AbstractMilitary personnel experience high trauma load that can change brain circuitry leading to impaired inhibitory control and posttraumatic stress disorder (PTSD). Inhibitory control processing may be particularly vulnerable to developmental and interpersonal trauma. This study examines the differential role of cumulative pre-deployment trauma and timing of trauma on inhibitory control using the Go/NoGo paradigm in a military population. The Go/NoGo paradigm was administered to 166 predominately male army combat personnel at pre- and post-deployment. Linear mixed models analyze cumulative trauma, trauma onset, and post-deployment PTSD symptoms on NoGo-N2 and NoGo-P3 amplitude and latency across deployment. Here we report, NoGo-N2 amplitude increases and NoGo-P3 amplitude and latency decreases in those with high prior interpersonal trauma across deployment. Increases in NoGo-P3 amplitude following adolescent-onset trauma and NoGo-P3 latency following childhood-onset and adolescent-onset trauma are seen across deployment. Arousal symptoms positively correlated with conflict monitoring. Our findings support the cumulative trauma load and sensitive period of trauma exposure models for inhibitory control processing in a military population. High cumulative interpersonal trauma impacts conflict monitoring and response suppression and increases PTSD symptoms whereas developmental trauma differentially impacts response suppression. This research highlights the need for tailored strategies for strengthening inhibitory control, and that consider timing and type of trauma in military personnel.
Surgical drain has no benefits in hemiarthroplasty for femoral neck fractures in elderly patients
Authors: Lee Seung-Hun , Kwak Dae-Kyung , Yoo Je-Hyun 
Published: December 2023

AbstractFemoral neck fracture is a common osteoporotic fracture in elderly patients and is effectively managed with arthroplasty. However, the benefits and risks of a surgical drain after arthroplasty in these patients are still debatable. Hence, we conducted this study to investigate the necessity of a surgical drain after hemiarthroplasty in elderly patients with femoral neck fracture. This study enrolled elderly patients (aged ≥ 70 years) who underwent cementless bipolar hemiarthroplasty for femoral neck fracture between April 2016 and December 2021. The patients were divided into two groups; the control group (199 patients) with a surgical drain after surgery performed between April 2016 and June 2020 and the study group (134 patients) with no surgical drain between July 2020 and December 2021. The demographics, perioperative data, and postoperative complications were compared between the two groups. Estimated blood loss, perioperative transfusion volume and rate, and length of hospital stay were significantly lower in the study group than in the control group (p < 0.001, p < 0.001, p = 0.008, and p < 0.001, respectively). Although there were no significant intergroup differences in the length of intensive care unit stay and in-hospital, 1-month, and 1-year mortalities, the incidence of postoperative medical complications was significantly lower in the study group than the control group (p = 0.001). A surgical drain may be unnecessary after hemiarthroplasty in elderly patients with femoral neck fracture considering less blood loss and transfusion, lower incidence of postoperative medical complications, and shorter hospital stay in the study group with no surgical drain.
Deep learning-enabled breast cancer endocrine response determination from H&E staining based on ESR1 signaling activity
Authors: Ng Chun Wai , Wong Kwong-Kwok 
Published: December 2023

AbstractEstrogen receptor (ER) positivity by immunohistochemistry has long been a main selection criterium for breast cancer patients to be treated with endocrine therapy. However, ER positivity might not directly correlate with activated ER signaling activity, which is a better predictor for endocrine therapy responsiveness. In this study, we investigated if a deep learning method using whole-slide H&E-stained images could predict ER signaling activity. First, ER signaling activity score was determined using RNAseq data available from each of the 1082 breast cancer samples in the TCGA Pan-Cancer dataset based on the Hallmark Estrogen Response Early gene set from the Molecular Signature Database (MSigDB). Then the processed H&E-stained images and ER signaling activity scores from a training cohort were fed into ResNet101 with three additional fully connected layers to generate a predicted ER activity score. The trained models were subsequently applied to an independent testing cohort. The result demonstrated that ER + /HER2- breast cancer patients with a higher predicted ER activity score had longer progression-free survival (p = 0.0368) than those with lower predicted ER activity score. In conclusion, a convolutional deep neural network can predict prognosis and endocrine therapy response in breast cancer patients based on whole-slide H&E-stained images. The trained models were found to robustly predict the prognosis of ER + /HER2- patients. This information is valuable for patient management, as it does not require RNA-seq or microarray data analyses. Thus, these models can reduce the cost of the diagnosis workflow if such information is required.
Therapeutic interventions and the length of hospital stay for pediatric patients with COVID-19: a multicenter cohort study
Authors: Ishihara Tadashi , Tagami Takashi , Hirayama Atsushi , Nakamura Yuki , Sueyoshi Koichiro , Okamoto Ken , Tanaka Hiroshi 
Published: December 2023

AbstractThe evidence for pediatric patients with COVID-19 was very limited, which was attributed to the small number of the cases as well as the rare incidence of severe pneumonia in this population. This retrospective cohort study aimed to identify the characteristics of pediatric patients with COVID-19 in the early period of the pandemic by analyzing Diagnosis Procedure Combination (DPC) data in Japan. This retrospective cohort analysis of Japanese multicenter research on COVID-19 using DPC data compared the outcomes and costs of treatment for pediatric patients with COVID-19. Of 4700 patients with COVID-19, 186 pediatric patients were included in this study. Among the included pediatric patients, 17 received therapeutic drugs specifically for COVID-19, while the remaining 169 pediatric patients received only symptomatic therapy. There were no significant differences in the length of hospital stay (9 vs. 8 days, p = 0.96), and medical cost (97,585 vs. 73,291 JPY) for the intervention and control groups, respectively by multiple regression analysis. This is the first epidemiological study to use DPC data to summarize the pathophysiology of pediatric patients in the early period of COVID-19 pandemic. There was no significant difference in length of hospital stay or medical cost by intervention.
Detection of safety helmet and mask wearing using improved YOLOv5s
Authors: Li Shuangyuan , Lv Yanchang , Liu Xiangyang , Li Mengfan 
Published: December 2023

AbstractWith the advancement of society, ensuring the safety of personnel involved in municipal construction projects, particularly in the context of pandemic control measures, has become a matter of utmost importance. This paper introduces a security measure for municipal engineering, combining deep learning with object detection technology. It proposes a lightweight artificial intelligence (AI) detection method capable of simultaneously identifying individuals wearing masks and safety helmets. The method primarily incorporates the ShuffleNetv2 feature extraction mechanism within the framework of the YOLOv5s network to reduce computational overhead. Additionally, it employs the ECA attention mechanism and optimized loss functions to generate feature maps with more comprehensive information, thereby enhancing the precision of target detection. Experimental results indicate that this algorithm improves the mean average precision (mAP) value by 4.3%. Furthermore, it reduces parameter and computational loads by 54.8% and 53.8%, respectively, effectively striking a balance between lightweight operation and precision. This study serves as a valuable reference for research pertaining to lightweight target detection in the realm of municipal construction safety measures.
Clean assembly of van der Waals heterostructures using silicon nitride membranes
Authors: Wang Wendong , Clark Nicholas , Hamer Matthew , Carl Amy , Tovari Endre , Sullivan-Allsop Sam , Tillotson Evan , Gao Yunze , de Latour Hugo , Selles Francisco , Howarth James , Castanon Eli G. , Zhou Mingwei , Bai Haoyu , Li Xiao , Weston Astrid , Watanabe Kenji , Taniguchi Takashi , Mattevi Cecilia , Bointon Thomas H. , Wiper Paul V. , Strudwick Andrew J. , Ponomarenko Leonid A. , Kretinin Andrey V. , Haigh Sarah J. , Summerfield Alex , Gorbachev Roman 
Published: December 2023

AbstractVan der Waals heterostructures are fabricated by layer-by-layer assembly of individual two-dimensional materials and can be used to create a wide range of electronic devices. However, current assembly techniques typically use polymeric supports, which limit the cleanliness—and thus the electronic performance—of such devices. Here, we report a polymer-free technique for assembling van der Waals heterostructures using flexible silicon nitride membranes. Eliminating the polymeric supports allows the heterostructures to be fabricated in harsher environmental conditions (incompatible with a polymer) such as at temperatures of up to 600 °C, in organic solvents and in ultra-high vacuum. The resulting heterostructures have high-quality interfaces without interlayer contamination and exhibit strong electronic and optoelectronic behaviour. We use the technique to assemble twisted-graphene heterostructures in ultra-high vacuum, resulting in a tenfold improvement in moiré superlattice homogeneity compared to conventional transfer techniques.