bluuebunny/crossref_metadata_2025_split huggingface dataset:
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps
Authors: Li Jiru , Pan Dinghao , Yang Zhihao , Sun Yuanyuan , Lin Hongfei , Wang Jian 
Published: December 2024

Abstract
Biomedical Relation Extraction (RE) is central to Biomedical Natural Language Processing and is crucial for various downstream applications. Existing RE challenges in the field of biology have primarily focused on intra-sentential analysis. However, with the rapid increase in the volume of literature and the complexity of relationships between biomedical entities, it often becomes necessary to consider multiple sentences to fully extract the relationship between a pair of entities. Current methods often fail to fully capture the complex semantic structures of information in documents, thereby affecting extraction accuracy. Therefore, unlike traditional RE methods that rely on sentence-level analysis and heuristic rules, our method focuses on extracting entity relationships from biomedical literature titles and abstracts and classifying relations that are novel findings. In our method, a multitask training approach is employed for fine-tuning a Pre-trained Language Model in the field of biology. Based on a broad spectrum of carefully designed tasks, our multitask method not only extracts relations of better quality due to more effective supervision but also achieves a more accurate classification of whether the entity pairs are novel findings. Moreover, by applying a model ensemble method, we further enhance our model’s performance. The extensive experiments demonstrate that our method achieves significant performance improvements, i.e. surpassing the existing baseline by 3.94% in RE and 3.27% in Triplet Novel Typing in F1 score on BioRED, confirming its effectiveness in handling complex biomedical literature RE tasks.
Database URL: https://codalab.lisn.upsaclay.fr/competitions/13377#learn_the_details-dataset
Exploring pectinolytic yeast diversity: toward effective polygalacturonase producers for applications in wine-making
Authors: Gazaloğlu Mehmet , Camarasa Carole , Nevoigt Elke 
Published: December 2024

Abstract
Pectinolytic enzymes secreted by yeasts have an untapped potential in industry, particularly in wine-making. This study addresses the limitations of the current screening methods in reliably predicting the capacity of pectinolytic yeast strains to secrete polygalacturonase (PGase) under industrial conditions, suggesting a novel screening approach. Using the context of wine-making as an example, a diverse collection of 512 yeast strains from 17 species was analysed for PGase secretion, a key enzyme in pectinolysis. The traditional halo assay on solid yeast–pepton–dextrose (YPD) medium revealed 118 strains from nine genera being PGase positive. Screening these strains by incubating them at 20°C on a solid synthetic grape juice medium containing polygalacturonic acid (PG) significantly reduced the number of promising strains to 35. They belong to five genera: Kluyveromyces sp., Cryptococcus, Pichia, Torulaspora, and Rhodotorula. Afterward, a newly developed pectin–iodine assay was used to precisely quantify the PGase activity of the best-performing strains in a liquid medium. Strains from Kluyveromyces and Cryptococcus sp. stood out regarding high pectinolytic activity. Our methodological advancements tailored to identify highly promising pectinolytic yeasts for industrial use open new avenues for wine-making and other industrial processes encompassing media rich in pectin and sugars.
Senolysis by GLS1 Inhibition Ameliorates Kidney Aging by Inducing Excessive mPTP Opening through MFN1
Authors: Chen Yuting , Zhao Nan , Zhang Yu , Chen Xueqi , Chen Yi , Wang Yifan , Wu Jianqing , Zhao Weihong 
Published: December 2024

Abstract
Cellular senescence is a pivotal contributor to aging and age-related diseases. The targeted elimination of senescent cells, known as senolysis, has emerged as a promising therapeutic strategy for mitigating these conditions. Glutaminase 1 (GLS1), a key enzyme in the glutaminolysis pathway, has been implicated in various cellular senescence processes. However, its specific role in senescent renal tubular epithelial cells (TECs) remains unclear. This study investigates the role and underlying mechanisms of GLS1 in senescent TECs. Using D-galactose (D-gal)-induced senescence of HK-2 cells, we found that GLS1 inhibition eliminated senescent TECs by promoting excessive mitochondrial permeability transition pore (mPTP) opening. Mechanistically, the excessive mPTP opening is associated with upregulation of mitofusin 1 (MFN1). Inhibition of GLS1 in D-gal-treated HK-2 cells induced a shift in mitochondrial dynamics from fission to fusion, accompanied by a significant increase in MFN1 expression. Knocking down MFN1 reduced the mPTP opening and the expression of mPTP-related genes (PPIF, VDAC and BAX) in cells co-treated with D-gal and the GLS1 inhibitor BPTES. Moreover, treatment of aged mice with BPTES specifically eliminated senescent TECs and ameliorated age-associated kidney disease. These findings reveal that GLS1 inhibition eliminate senescent TECs by promoting excessive mPTP opening, suggesting that targeting GLS1 may be a novel senolytic strategy for alleviating aging-related kidney diseases.
Eleven Grand Challenges for Inflammatory Bowel Disease Genetics and Genomics
Authors: Gibson Greg , Rioux John D , Cho Judy H , Haritunians Talin , Thoutam Akshaya , Abreu Maria T , Brant Steven R , Kugathasan Subra , McCauley Jacob L , Silverberg Mark , McGovern Dermot 
Published: December 2024

Abstract
The past 2 decades have witnessed extraordinary advances in our understanding of the genetic factors influencing inflammatory bowel disease (IBD), providing a foundation for the approaching era of genomic medicine. On behalf of the NIDDK IBD Genetics Consortium, we herein survey 11 grand challenges for the field as it embarks on the next 2 decades of research utilizing integrative genomic and systems biology approaches. These involve elucidation of the genetic architecture of IBD (how it compares across populations, the role of rare variants, and prospects of polygenic risk scores), in-depth cellular and molecular characterization (fine-mapping causal variants, cellular contributions to pathology, molecular pathways, interactions with environmental exposures, and advanced organoid models), and applications in personalized medicine (unmet medical needs, working toward molecular nosology, and precision therapeutics). We review recent advances in each of the 11 areas and pose challenges for the genetics and genomics communities of IBD researchers.
The need for a cancer exposome atlas: a scoping review
Authors: Young Anna S , Mullins Catherine E , Sehgal Neha , Vermeulen Roel C H , Kolijn P Martijn , Vlaanderen Jelle , Rahman Mohammad L , Birmann Brenda M , Barupal Dinesh , Lan Qing , Rothman Nathaniel , Walker Douglas I 
Published: December 2024

Abstract

Background
Despite advances in understanding genetic susceptibility to cancer, much of cancer heritability remains unidentified. At the same time, the makeup of industrial chemicals in our environment only grows more complex. This gap in knowledge on cancer risk has prompted calls to expand cancer research to the comprehensive, discovery-based study of nongenetic environmental influences, conceptualized as the “exposome.”

Methods
Our scoping review aimed to describe the exposome and its application to cancer epidemiology and to study design limitations, challenges in analytical methods, and major unmet opportunities in advanced exposome profiling methods that allow the quantification of complex chemical exposure profiles in biological matrices. To evaluate progress on incorporating measurements of the exposome into cancer research, we performed a review of such “cancer exposome” studies published through August 2023.

Results
We found that only 1 study leveraged untargeted chemical profiling of the exposome as a method to measure tens of thousands of environmental chemicals and identify prospective associations with future cancer risk. The other 13 studies used hypothesis-driven exposome approaches that targeted a set of preselected lifestyle, occupational, air quality, social determinant, or other external risk factors. Many of the included studies could only leverage sample sizes with less than 400 cancer cases (67% of nonecologic studies) and exposures experienced after diagnosis (29% of studies). Six cancer types were covered, most commonly blood (43%), lung (21%), or breast (14%) cancer.

Conclusion
The exposome is underutilized in cancer research, despite its potential to unravel complex relationships between environmental exposures and cancer and to inform primary prevention.
Shifting national interest in petroleum-producing countries during the energy transition: the Omani experience
Authors: Al Yahyai Ahad , Soliman-Hunter Tina 
Published: December 2024

Abstract
Petroleum-producing countries are at particular economic and social risk during the energy transition, primarily due to the shift from petroleum revenues that can be used to stabilize the state to the development of renewable energy sources, which do not bring revenue to the state. Exploring this conundrum within the context of the national interest, this article examines petroleum-producing countries, focusing on Oman as an example of a non-democratic rentier state. Examining the national interest as both a concept and a practice within the energy sector, the study concludes that the energy transition will place certain challenges on the Omani government, but with a focus on establishing investment opportunities and energy justice, there are many positive experiences ahead for Oman.
The Expanding Role of the U.S. Army Paramedic
Authors: Greener Robert K , Morgenweck Garrick W , Lopienski Jonathan J , Howell Chad J , Kim Jinsol , Smith Marcus F 
Published: December 2024

ABSTRACT
The combat medic (68W) will play a critical role in medical operations in the event of future large-scale combat operations (LSCOs). However, the combat medic is largely not prepared for LSCOs. The revised Medical Education and Demonstration of Individual Competence (TC 8-800) state 68Ws much be able to provide advanced airway and trauma management, medication administration, and advanced casualty movement. To meet the increased prehospital medical demands under LSCOs, the U.S. Army should require the Battalion, Brigade, and Division Medical Readiness Noncommisioned Officers (NCOs) to be Nationally Registered Paramedics (who are identified with the 3P Additional Skill Identifier [ASI]). They should have the responsibility to oversee the wartime medical skills sustainment of Combat Medic Specialists (68W) within their organization. These paramedics should drive medical simulation training events and improve current operation medical skills training. These medical readiness NCOs should attend the Medic Master Training Course and serve as advisors to commanders on the status of medic skill readiness within their organization. Commanders will be able to utilize these paramedics to augment the ongoing medical training of their medics to ensure they are operating at the fullest extent of their scope of practice.
Association between osteoarthritis-related serum biochemical markers over 10–13 years and knee symptoms in middle-aged adults
Authors: Singh Ambrish , Venn Alison , Blizzard Leigh , Fraser Brooklyn J , Jones Graeme , Burgess John , Parameswaran Venkat , March Lyn , Cicuttini Flavia , Ding Changhai , Antony Benny 
Published: December 2024

ABSTRACT

Objectives
To examine associations between osteoarthritis (OA)-related biochemical markers and knee symptoms in middle-aged adults over 10–13 year follow-up.

Methods
Blood samples were collected during the Childhood Determinants of Adult Health (CDAH)-1 study (2004–06) and follow-up at CDAH-3. Serum samples from baseline (n=156) and follow-up (n=167) were analyzed for cartilage oligomeric matrix protein (COMP), matrix metalloproteinase (MMP)-3, and hyaluronan (HA) using enzyme-linked immunosorbent assays. Knee symptoms were assessed using the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) scale at follow-up. Zero-inflated Poisson regression models adjusted for age, sex, and body mass index were used for analysis.

Results
Significant associations were observed between COMP, MMP-3, and HA with knee pain and WOMAC-total score at follow-up. Baseline MMP-3 [ratio of means (RoM): 1.013; 95% CI: 1.006, 1.020], cumulative COMP (baseline + follow-up) [RoM: 1.022; 95% CI: 1.011, 1.033], and increased HA levels over time [RoM: 1.014; 95% CI: 1.007, 1.020] were positively associated with knee pain after 10–13 years.

Conclusion
Cumulative COMP, baseline MMP-3, and changes in HA were associated with knee pain over a a 10–13 year follow-up. These markers may help predict future knee symptoms in middle-aged adults.
A case of glucocorticoid-refractory IgA vasculitis with diffuse alveolar haemorrhage: A therapeutic strategy for aberrant immunoglobulin depletion
Authors: Hirokawa Kazuhiko , Sato Shunichi , Hiraoka Eiji , Iwanami Keiichi 
Published: December 2024

ABSTRACT
Diffuse alveolar haemorrhage (DAH) is a rare and severe complication of IgA vasculitis (IgAV). Although glucocorticoids and immunosuppressive agents are used for its treatment, there is no consensus on the optimal form of treatment. We herein report the case of a 53-year-old, female patient with IgAV. She was initially resistant to glucocorticoid therapy and experienced acute respiratory failure due to DAH but responded well to rituximab (RTX) and plasma exchange (PLEX). While some previous case reports have suggested that RTX or PLEX can be effective for severe IgAV, there are no reports of a combination of RTX and PLEX being used successfully to treat IgAV-associated DAH. In the model of IgAV pathogenesis proposed herein, aberrant IgA1 and IgA-specific IgG autoantibodies play a pivotal role. PLEX may facilitate the prompt removal of these circulating, aberrant immunoglobulins while RTX inhibits their further production. Consequently, a combination of RTX and PLEX may represent an effective treatment approach for severe glucocorticoid-refractory cases of IgAV.
SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes
Authors: Nasir Jalees A , Maguire Finlay , Smith Kendrick M , Panousis Emily M , Baker Sheridan J C , Aftanas Patryk , Raphenya Amogelang R , Alcock Brian P , Maan Hassaan , Knox Natalie C , Banerjee Arinjay , Mossman Karen , Wang Bo , Simpson Jared T , Kozak Robert A , Mubareka Samira , McArthur Andrew G 
Published: December 2024

Abstract
The incorporation of sequencing technologies in frontline and public health healthcare settings was vital in developing virus surveillance programs during the Coronavirus Disease 2019 (COVID-19) pandemic caused by transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, increased data acquisition poses challenges for both rapid and accurate analyses. To overcome these hurdles, we developed the SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL) for quick bulk analyses of Illumina short-read sequencing data. SIGNAL is a Snakemake workflow that seamlessly manages parallel tasks to process large volumes of sequencing data. A series of outputs are generated, including consensus genomes, variant calls, lineage assessments and identified variants of concern (VOCs). Compared to other existing SARS-CoV-2 sequencing workflows, SIGNAL is one of the fastest-performing analysis tools while maintaining high accuracy. The source code is publicly available (github.com/jaleezyy/covid-19-signal) and is optimized to run on various systems, with software compatibility and resource management all handled within the workflow. Overall, SIGNAL illustrated its capacity for high-volume analyses through several contributions to publicly funded government public health surveillance programs and can be a valuable tool for continuing SARS-CoV-2 Illumina sequencing efforts and will inform the development of similar strategies for rapid viral sequence assessment.
HiCrayon reveals distinct layers of multi-state 3D chromatin organization
Authors: Nolan Ben , Harris Hannah L , Kalluchi Achyuth , Reznicek Timothy E , Cummings Christopher T , Rowley M Jordan 
Published: December 2024

Abstract
Chromatin contact maps are often shown as 2D heatmaps and visually compared to 1D genomic data by simple juxtaposition. While common, this strategy is imprecise, placing the onus on the reader to align features with each other. To remedy this, we developed HiCrayon, an interactive tool that facilitates the integration of 3D chromatin organization maps and 1D datasets. This visualization method integrates data from genomic assays directly into the chromatin contact map by coloring interactions according to 1D signal. HiCrayon is implemented using R shiny and python to create a graphical user interface application, available in both web and containerized format to promote accessibility. We demonstrate the utility of HiCrayon in visualizing the effectiveness of compartment calling and the relationship between ChIP-seq and various features of chromatin organization. We also demonstrate the improved visualization of other 3D genomic phenomena, such as differences between loops associated with CTCF/cohesin versus those associated with H3K27ac. We then demonstrate HiCrayon’s visualization of organizational changes that occur during differentiation and use HiCrayon to detect compartment patterns that cannot be assigned to either A or B compartments, revealing a distinct third chromatin compartment.
Initial Effectiveness of mRNA-1273 Against SARS-CoV-2 Infection and Hospitalization in Young Children
Authors: Aglipay Mary , Maguire Jonathon L , Swayze Sarah , Tuite Ashleigh , Mamdani Muhammad , Keown-Stoneman Charles , Birken Catherine S , Kwong Jeffrey C 
Published: December 2024

Abstract

Background
Data on mRNA-1273 (Moderna) vaccine effectiveness (VE) in children aged 6 months to 5 years are limited. The objectives of this study were to assess mRNA-1273 vaccine effectiveness against symptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and coronavirus disease 2019 (COVID-19)–related hospitalization among children aged 6 months to 5 years during the initial 5 months of the vaccination campaign rollout, as well as to determine whether VE varied by age group (6 months to &lt;2 years vs 2 to 5 years).

Methods
We used a test-negative study with linked health administrative data in Ontario, Canada, to evaluate vaccine effectiveness of mRNA-1273 against symptomatic SARS-CoV-2 infection and COVID-19-related hospitalization from July 28 to December 31, 2022. Participants included symptomatic children aged 6 months to 5 years who were tested by real-time polymerase chain reaction. The primary outcome was symptomatic infection, and the secondary outcome was COVID-19-related hospitalization.

Results
We included 572 test-positive cases and 3467 test-negative controls. Receipt of mRNA-1273 was associated with reduced symptomatic SARS-CoV-2 infection (VE, 90%; 95% CI, 53%–99%) and COVID-19-related hospitalization (VE, 82%; 95% CI, 4%–99%) ≥7 days after the second dose. We were unable to detect heterogeneity in VE across age groups.

Conclusions
Our findings suggest that mRNA-1273 vaccine effectiveness was initially strong against symptomatic SARS-CoV-2 infection and hospitalization in children aged 6 months to 5 years. Further research is needed to understand long-term effectiveness.
Sourcing
Authors: Dorsey David , Allen Matt 
Published: December 2024

Abstract
This chapter describes what sourcing is, why it is done, and how to do it efficiently and effectively. The authors highlight proven tactics and strategies cited by top field recruiters, organizational researchers, and recruiting analytic specialists. The authors describe how sourcing serves as the essential first step in building a talent pipeline and how core elements such as the employee value proposition and the workforce plan serve as a foundation for sourcing. Intelligent resource allocation for sourcing and related cost drivers are reviewed and tied to key components of an effective sourcing strategy such as referrals, realistic job previews, and emerging technology. The chapter concludes with a big-picture discussion of elements that will likely impact sourcing in the future. Examples are shown of effective practices and lessons of implementing them. A practical, user-friendly checklist is provided to aid in building a sourcing plan and system.
Job Postings, Ads, and the Age of the Aggregator
Authors: Streets Valerie N. 
Published: December 2024

Abstract
The first point of contact most organizations have with a potential candidate is through a job advertisement. Job ads have long created the first impression in job seekers’ eyes and thus play a crucial role in attracting or deterring individuals from the broader recruitment and selection process. While job ads have long been used, the current trend is for ads to become more interactive, customized, and engaging. Along with those changes comes a host of new issues for practitioners and researchers alike. The chapter presents an overview of the evolution of job advertisements along with some guiding principles and best practices on recruiting via job ads. In addition, the author introduces some emerging topics and issues such as integration with employee value propositions, realistic job previews, and elements of company culture.
Onboarding During Transformational Times
Authors: Ford Deborah K. , Bauer Talya N. 
Published: December 2024

Abstract
In today’s competitive climate, industry leaders must battle for top talent. Onboarding has emerged as a critical differentiator for reinforcing the employer value proposition, instilling commitment in new hires, and accelerating time to productivity. A rigorous and intimate onboarding program that reinforces interpersonal connection became critical during COVID-19 isolation, and high-touch elements add value for remote work. This chapter offers guidelines to enable speed and ease in the onboarding process by leveraging technological advances. Recommendations are made for employee-centric design decisions, and a proposed methodology is offered to create thoughtful experiences for those “moments that matter” in the employee journey.
The Geography of Taste
Authors: 9780197509081  
Published: December 2024

Abstract
Aesthetic and artistic preferences and practices vary widely between individuals and between cultures. To enjoy flamenco, for example, requires an entirely different cognitive approach and emotional attitude than that required to appreciate Bharatanatyam. In this collaborative work, four philosophers reconceive the philosophy of art and aesthetics by taking aesthetic diversity and cultural specificity, rather than universality, as the starting points of inquiry. Why are aesthetic and artistic responses so diverse? To what extent might they originate in universal human capacities? Can members of one culture enjoy and understand the artistic products of another? Or do they do each other injustice in the attempt? Is diversity a valuable feature of aesthetic and artistic engagement? To model what the turn toward diversity might look like in aesthetic inquiry, each author defends a different account of aesthetic diversity, and all engage in a collective dialogue about these issues.