bluuebunny/crossref_metadata_2025_split huggingface dataset:
Noise Reduction and Localization Accuracy in a Mobile Magnetoencephalography System
Authors: Bardouille Timothy , Smith Vanessa , Vajda Elias , Leslie Carson Drake , Holmes Niall 
Published: March 2024

AbstractMagnetoencephalography (MEG) non-invasively provides important information about human brain electrophysiology. The growing use of optically pumped magnetometers (OPM) for MEG, as opposed to fixed arrays of cryogenic sensors, has opened the door for innovation in system design and use cases. For example, cryogenic MEG systems are housed in large shielded rooms to provide sufficient space for the system dewar. Here, we investigate the performance of OPM recordings inside of a cylindrical shield with a 1×2 m2footprint. The efficacy of shielding was measured in terms of field attenuation and isotropy, and the value of post hoc noise reduction algorithms was also investigated. Localization accuracy was quantified for 104 OPM sensors mounted on a fixed helmet array based on simulations and recordings from a bespoke current dipole phantom. Passive shielding attenuated direct current (DC) and power line (60 Hz) fields by approximately 60 dB, and all other frequencies by 80-90 dB. Post hoc noise reduction provided an additional 5-15 dB attenuation. Substantial field anisotropy remained in the volume encompassing the sensor array. The consistency of the anisotropy over months suggests that a field nulling solution could be readily applied. A current dipole phantom generating source activity at an appropriate magnitude for the human brain generated field fluctuations on the order of 0.5-1 pT. Phantom signals were localized with 3 mm localization accuracy and no significant bias in localization was observed, which is in line with performance for cryogenic and OPM MEG systems. This validation of the performance of a small footprint MEG system opens the door for lower cost MEG installations in terms of raw materials and facility space, as well as mobile imaging systems (e.g., truck-based). Such implementations are relevant for global adoption of MEG outside of highly resourced research and clinical institutions.
PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns
Authors: Zhuang Haotian , Ji Zhicheng 
Published: March 2024

ABSTRACTModeling temporal and spatial gene expression patterns in large-scale single-cell and spatial transcriptomics data is a computationally intensive task. We present PreTSA, a method that offers computational efficiency in modeling these patterns and is applicable to single-cell and spatial transcriptomics data comprising millions of cells. PreTSA consistently matches the results of state-of-the-art methods while significantly reducing computational time. PreTSA provides a unique solution for studying gene expression patterns in extremely large datasets.
Unveiling the genetic blueprint of a desert scorpion: A chromosome-level genome ofHadrurus arizonensisprovides the first reference for Parvorder Iurida
Authors: Bryant Meridia Jane , Coello Asher M. , Glendening Adam M. , Hilliman Samuel A. , Jara Carolina Fernanda , Pring Samuel S. , Rivera Aviel Rodriguez , Santiago Membreño Jennifer , Nigro Lisa , Pauloski Nicole , Graham Matthew R. , King Teisha , Jockusch Elizabeth L. , O’Neill Rachel J. , Wegrzyn Jill L. , Santibáñez-López Carlos E. , Webster Cynthia N. 
Published: March 2024

AbstractOver 400 million years old, scorpions represent an ancient group of arachnids and one of the first animals to adapt to life on land. Presently, the lack of available genomes within scorpions hinders research on their evolution. This study leverages ultra-long nanopore sequencing and Pore-C to generate the first chromosome level assembly and annotation for the desert hairy scorpion,Hadrurus arizonensis. The assembled genome is 2.23 Gb in size with an N50 of 280 Mb. Pore-C scaffolding re-oriented 99.6% of bases into nine chromosomes and BUSCO identified 998 (98.6%) complete arthropod single copy orthologs. Repetitive elements represent 54.69% of the assembled bases, including 872,874 (29.39%) LINE elements. A total of 18,996 protein-coding genes and 75,256 transcripts were predicted, and extracted protein sequences yielded a BUSCO score of 97.2%. This is the first genome assembled and annotated within the family Hadruridae, representing a crucial resource for closing gaps in genomic knowledge of scorpions, resolving arachnid phylogeny, and advancing studies in comparative and functional genomics.SignificanceGenomic resources for the study of arachnids are limited. To date, only four scorpion genomes have been published; none of these are chromosome-level assemblies, and all four belong to a single family, Buthidae. In this study, we assembled the first chromosome-level, annotated genome for a non-buthid species (Hadrurus arizonensis). This high quality reference will provide a critical resource for comparative and functional genomics and contribute to the understanding of arachnid evolution.
Generative Adversarial Networks Accurately Reconstruct Pan-Cancer Histology from Pathologic, Genomic, and Radiographic Latent Features
Authors: Howard Frederick M. , Hieromnimon Hanna M. , Ramesh Siddhi , Dolezal James , Kochanny Sara , Zhang Qianchen , Feiger Brad , Peterson Joseph , Fan Cheng , Perou Charles M. , Vickery Jasmine , Sullivan Megan , Cole Kimberly , Khramtsova Galina , Pearson Alexander T. 
Published: March 2024

AbstractArtificial intelligence models have been increasingly used in the analysis of tumor histology to perform tasks ranging from routine classification to identification of novel molecular features. These approaches distill cancer histologic images into high-level features which are used in predictions, but understanding the biologic meaning of such features remains challenging. We present and validate a custom generative adversarial network – HistoXGAN – capable of reconstructing representative histology using feature vectors produced by common feature extractors. We evaluate HistoXGAN across 29 cancer subtypes and demonstrate that reconstructed images retain information regarding tumor grade, histologic subtype, and gene expression patterns. We leverage HistoXGAN to illustrate the underlying histologic features for deep learning models for actionable mutations, identify model reliance on histologic batch effect in predictions, and demonstrate accurate reconstruction of tumor histology from radiographic imaging for a ‘virtual biopsy’.
Data-driven prioritization of genetic disorders for global genomic newborn screening programs
Authors: Minten Thomas , Gold Nina B. , Bick Sarah , Adelson Sophia , Gehlenborg Nils , Amendola Laura M. , Boemer François , Coffey Alison J. , Encina Nicolas , Ferlini Alessandra , Kirschner Janbernd , Russell Bianca E. , Servais Laurent , Sund Kristen L. , Taft Ryan J. , Tsipouras Petros , Zouk Hana ,   ICoNS Gene List Contributors, Bick David , Green Robert C. ,   the International Consortium on Newborn Sequencing (ICoNS)
Published: March 2024

AbstractGenomic sequencing is poised to expand newborn screening for treatable childhood-onset disorders. Over 30 international research studies and companies are exploring its use, collectively aiming to screen more than 500,000 infants. A key challenge is determining which genes to include in screening. Among 27 newborn sequencing programs, the number of genes analyzed ranged from 134 to 4,299, with only 74 genes included by over 80% of programs. To understand this variability, we assembled a dataset with 25 characteristics of 4,389 genes included in any program and used a multivariate regression analysis to identify characteristics associated with inclusion across programs. These characteristics included presence on the US Recommended Uniform Screening panel, evidence regarding the natural history of disease, and efficacy of treatment. We then used a machine learning model to generate a ranked list of genes, offering a data-driven approach to the future prioritization of disorders for public health newborn screening efforts.
Long-Term Trajectories of Posttraumatic Stress Disorder Symptoms: A 20-Year Longitudinal Study of World Trade Center Responders
Authors: Mann Frank D. , Waszczuk Monika A. , Clouston Sean A.P. , Feltman Scott , Ruggero Camilo J. , Marx Brian P. , Schwartz Joseph E. , Bromet Evelyn J. , Luft Benjamin J. , Kotov Roman 
Published: March 2024

ABSTRACTObjectiveThe present study examined the 20-year course of posttraumatic stress disorder (PTSD) in World Trade Center (WTC) responders to address four questions: (1) How stable are symptoms of PTSD? (2) What is the average symptom trajectory? (3) How much do responders differ from the average trend? (4) How quickly do PTSD symptoms improve or worsen?MethodsData include 81,298 observations fromn= 12,822 responders, spanning from July 2002 to December 2022. Fourteen percent meet PTSD criteria. PTSD symptoms were measured using the PCL-17. Retest correlations were calculated to estimate stability, growth curve models to estimate individual trajectories, and Kaplan-Meier curves to estimate the rate of clinically significant change.ResultsRetest correlations were high overall (range =.49, .84), lower in PTSD cases (range =.21, .78), and decreased as a function of time between assessments. The best-fitting growth model represented trajectories continuously rather than multiple classes. Symptom burden peaked in 2011 and declined modestly by 2022 (Cohen’s d = -0.28 and -0.59 in all responders and PTSD cases, respectively). Median time before clinically significant improvement in responders with PTSD was 8.88 years (95% CI = 8.01, 9.79).ConclusionsIn the longest and largest study of PTSD symptoms tracked continuously since exposure, illness course was characterized to find that, while symptoms were highly stable in the short term, symptoms changed significantly over two decades. Most responders experienced clinical improvement after nine years, but 10% had poor course and should be the focus of public health efforts.
DPR-MEDIATED H2O2RESISTANCE CONTRIBUTES TO STREPTOCOCCI SURVIVAL IN A CYSTIC FIBROSIS AIRWAY MODEL SYSTEM
Authors: Rogers Rendi R. , Kesthely Christopher A. , Jean-Pierre Fabrice , Hafi Bassam El , O’Toole George A. 
Published: March 2024

ABSTRACTThe cystic fibrosis (CF) lung environment is conducive to the colonization of bacteria as polymicrobial biofilms, which are associated with poor clinical outcomes for persons with CF (pwCF).Streptococcusspp. is highly prevalent in the CF airway, but its role in the CF lung microbiome is poorly understood. Some studies have shownStreptococcusspp. to be associated with better clinical outcomes for pwCF, while others show that high abundance ofStreptococcusspp. is correlated with exacerbations. Our lab previously reported a polymicrobial culture system consisting of four CF-relevant pathogens that can be used to study microbial behavior in a more clinically relevant setting. Here, we use this model system to identify genetic pathways that are important forStreptococcus sanguinissurvival in the context of the polymicrobial community. We identified genes related to reactive oxygen species (ROS) as differentially expressed inS. sanguinismonoculture versus growth of this microbe in the mixed community. Genetic studies identified Dpr as important forS. sanguinissurvival in the community. We show that Dpr, a DNA binding ferritin-like protein, and PerR, a peroxide-responsive transcriptional regulator of Dpr, are important for protectingS. sanguinisfrom phenazine-mediated toxicity in co-culture withP. aeruginosaand when exposed to ROS, both of which mimic the CF lung environment. Characterizing such interactions in a clinically relevant model system contributes to our understanding of microbial behavior in the context of polymicrobial biofilm infections.IMPORTANCEStreptococcusspp. is recognized as a highly prevalent pathogen in CF airway infections. However, its role in clinical outcomes for pwCF is poorly understood. Here, we leverage a polymicrobial community system previously developed by our group to model CF airway infections as a tool to investigate aPseudomonas-Streptococcusinteraction involving ROS. We show that protection against ROS is required forS. sanguinissurvival in a clinically relevant polymicrobial system. Using this model system to study interspecies interactions contributes to our broader understanding of the complex role ofStreptococcusspp. in the CF lung.
Have AI-Generated Texts from LLM Infiltrated the Realm of Scientific Writing? A Large-Scale Analysis of Preprint Platforms
Authors: Cheng Huzi , Sheng Bin , Lee Aaron , Chaudary Varun , Atanasov Atanas G. , Liu Nan , Qiu Yue , Wong Tien Yin , Tham Yih-Chung , Zheng Yingfeng 
Published: March 2024

AbstractSince the release of ChatGPT in 2022, AI-generated texts have inevitably permeated various types of writing, sparking debates about the quality and quantity of content produced by such large language models (LLM). This study investigates a critical question: Have AI-generated texts from LLM infiltrated the realm of scientific writing, and if so, to what extent and in what setting? By analyzing a dataset comprised of preprint manuscripts uploaded to arXiv, bioRxiv, and medRxiv over the past two years, we confirmed and quantified the widespread influence of AI-generated texts in scientific publications using the latest LLM-text detection technique, the Binoculars LLM-detector. Further analyses with this tool reveal that: (1) the AI influence correlates with the trend of ChatGPT web searches; (2) it is widespread across many scientific domains but exhibits distinct impacts within them (highest: computer science, engineering sciences); (3) the influence varies with authors who have different language speaking backgrounds and geographic regions according to the location of their affiliations (Italy, China, etc.); (4) AI-generated texts are used in various content types in manuscripts (most significant: hypothesis formulation, conclusion summarization); (5) AI usage has a positive influence on paper’s impact, measured by its citation numbers. Based on these findings, suggestions about the advantages and regulation of AI-augmented scientific writing are discussed.
Effect of Ti and C addition on oxidation resistance of FeCoCrNiMn high entropy alloys prepared by powder metallurgy
Authors: Wang Haichao , Liu Xiaoqiang , Li Zhanjiang , Chen Li , Dai Pinqiang , Tang Qunhua 
Published: March 2024

Purpose
The purpose of this paper is to study the high temperature oxidation behavior of Ti and C-added FeCoCrNiMn high entropy alloys (HEAs).

Design/methodology/approach
Cyclic oxidation method was used to obtain the oxidation kinetic profile and oxidation rate. The microstructures of the surface and cross section of the samples after oxidation were characterized by X-ray diffraction (XRD) and scanning electron microscope (SEM).

Findings
The results show that the microstructure of the alloy mainly consisted of FCC (Face-centered Cubic Structure) main phase and carbides (M7C3, M23C6 and TiC). With the increase of Ti and C content, the microhardness, strength and oxidation resistance of the alloy were effectively improved. After oxidation at a constant temperature of 800 °C for 100 h, the preferential oxidation of chromium in the chromium carbide determined the early formation of dense chromium oxide layers compared to the HEAs substrate, resulting in the optimal oxidation resistance of the TC30 alloy.

Originality/value
More precipitated CrC can preferentially oxidize and rapidly form a dense Cr2O3 layer early in the oxidation, which will slow down the further oxidation of the alloy.
Modelling the critical challenges of quality assurance of cross-border construction logistics and supply chain during the COVID-19 pandemic
Authors: Ghansah Frank Ato , Lu Weisheng , Ababio Benjamin Kwaku 
Published: March 2024

PurposeThe COVID-19 pandemic has impacted the construction industry, yet still, it is unclear from existing studies about the critical challenges imposed on quality assurance (QA), particularly Cross-border Construction Logistics and Supply Chain (Cb-CLSC). Thus, this study aims to identify and examine the critical challenges of QA of Cb-CLSC during the COVID-19 pandemic.Design/methodology/approachThe aim is achieved via an embedded mixed-method approach pragmatically involving a desk literature review and engaging 150 experts across the globe using expert surveys, and results confirmed by semi-structured interviews. The approach is based on Interpretive Structural Modelling (ISM) as its foundation.FindingsThe study revealed ten critical challenges of QA, with the top four including “the shortage of raw construction material (C7)”, “design changes (C6)”, “collaboration and communication difficulties (C1)” and “changes in work practices (C10)”. However, examining the interrelationships among the critical challenges using ISM confirmed C7 and C10 as the most critical challenges. The study again revealed that the critical challenges are sensitive and capable of affecting themselves due to the nature of their interrelationship based on MICMAC analysis. Hence, being consistent with why all the challenges were considered critical amid the pandemic. Sentiment analysis revealed that the critical challenges have not been entirely negative but also positive by creating three areas of opportunities for improvement: technology adoption, worker management, and work process management. However, four areas of challenges in the QA include cost, raw material, time, and work process, including inspection, testing, auditing, communication, etc.Practical implicationsThe finding provides a convenient point of reference to researchers, policymakers, practitioners, and decision-makers on formulating policies to enhance the effectiveness of construction QA during the pandemic through to the post-pandemic era.Originality/valueThe study enriches the extant literature on QA, Cb-CLSC, and the COVID-19 pandemic in the construction industry by identifying the critical challenges and examining the interrelationships among them. This provides a better understanding of how the construction QA has been affected by the pandemic and the opportunities created.
How are you affected? The public’s online information behaviour patterns during the COVID-19 infodemic
Authors: Sun Jingqiong , Ming Junren , Wang Xuezhi , Zhang Yawen 
Published: March 2024

PurposeThis paper aims to examine the impact of the COVID-19 infodemic on the public’s online information behaviour, offering insights critical for shaping effective informational responses in future public health emergencies.Design/methodology/approachThis paper uses a structured online survey with 27 targeted questions using a five-point Likert scale to measure eight variables. Data analysis is conducted through structural equation modelling on 307 valid responses to rigorously test the research hypotheses.FindingsThis paper indicates that information quality significantly impacts the public’s capacity to select, share and use online information. Additionally, the comprehensibility of information plays a crucial role in shaping the public’s behaviours in terms of online information exchange and usage. The credibility of information sources emerges as a key determinant influencing the public’s online information selection, exchange and utilization behaviour. Moreover, social influence exerts a substantial effect on the public’s online information selection, acquisition, exchange and utilization behaviour. These findings highlight the presence of universality and sociality, mediation and guidance, as well as the purposefulness and selectivity performed by the public’s online information behaviour during an infodemic.Originality/valueThis paper introduces a novel research model for assessing the influence and identifies the patterns of the public’s online information behaviour during the COVID-19 infodemic. The findings have significant implications for developing strategies to tackle information dissemination challenges in future major public health emergencies.
Determinants of lean manufacturing adoption by Chinese manufacturers
Authors: Lin Chieh-Yu , Kang Cathay Kuo-Tai , Ho Yi-Hui 
Published: March 2024

Purpose
This study aims to analyze the determinants influencing Chinese manufacturing companies in implementing lean manufacturing (LM).

Design/methodology/approach
The determinants to be explored in this study consist of technological, organizational and environmental (TOE) dimensions. A questionnaire survey was conducted on Chinese manufacturing companies, and 208 samples were analyzed.

Findings
The findings show that the relative advantage of LM and organizational support have significantly positive effects on Chinese manufacturing firms’ adoption of LM. The complexity of LM, quality of human resources, organizational readiness, customer pressure, international situation, governmental support and environmental uncertainty do not have significant effects.

Originality/value
This paper contributes to the literature by using the TOE model to explore the factors influencing LM adoption in the Chinese manufacturing industry.
SIBs and the implications on the relationship between social enterprises and the public sector: a case study from the Netherlands
Authors: Patetta Valentina , Enciso-Santocildes Marta 
Published: March 2024

PurposeThe aim of this paper is to provide insights and knowledge about the motivations and implications for social enterprises' participation in SIBs, particularly in terms of collaboration and partnership with the public sector, as well as the different positions on this issue. The overall aim, therefore, is to show how social enterprises and public organisations have interacted in the context of SIBs and what has been achieved by participating.Design/methodology/approachThis multiple case study approach applies qualitative methods like observations and semi-structured and unstructured interviews.FindingsThe study shows that SIBs can be an option for financing social enterprises within a strategy of income diversification and resource dependency. Despite tensions and complexities, SIBs can renew the traditional funding relationship by adding innovation, strengthening the co-creation process and creating a stable relationship.Research limitations/implicationsResearch findings may lack generalisability due to the specific context in which the case study is rooted.Practical implicationsThe paper offers practical implications in terms of insights and suggestions for social enterprises and the public sector interested in developing the scheme.Originality/valueThis paper adds the voice and perspective of social enterprises on the relationship with the public sector within the framework of SIBs initiatives.