bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural characterization of thePseudomonas AeruginosaMexR–mexRrepressor-operator complex: a small-angle X-ray and neutron scattering perspective
Authors: Pietras Zuzanna , Caporaletti Francesca , Jeffries Cy M. , Morad Vivian , Wallner Björn , Martel Anne , Sunnerhagen Maria 
Published: April 2024

AbstractThe rapid spread of acquired multidrug resistance (MDR) in bacteria is a world-wide health threat. The MexR protein regulates the expression of the MexAB-OprM efflux pump, which actively extrudes chemical compounds with high toxicity to the host organismPseudomonas Aeruginosa. In repression mode, two MexR dimers bind to an operator with two homologous pseudo-palindromic boxes located in proximity (named PI and PII). Here we report a first structural characterization of the complex in solution using small angle X-ray scattering (SAXS), small-angle neutron scattering (SANS) and rigid body modelling. The spacing between the PI and PII boxes is rich in AT base pairs indicate possible flexibility between the two MexR dimer binding sites. In agreement, our best modelling fits show a requirement for DNA bending between the two MexR binding sites to optimally fit SAS data as well as known biological properties of the MexR operons. Taken together, this study contributes to better understanding of the structural properties of bacterial operators and their repressor proteins.
Responses to membrane potential-modulating ionic solutions measured by magnetic resonance imaging of cultured cells andin vivorat cortex
Authors: Min Kyeongseon , Chung Sungkwon , Lee Seung-Kyun , Lee Jongho , Toi Phan Tan , Kim Daehong , Lee Jung Seung , Park Jang-Yeon 
Published: April 2024

AbstractMembrane potential plays a crucial role in various cellular functions. However, existing techniques for measuring membrane potential are often invasive or have limited recording depth. In contrast, magnetic resonance imaging (MRI) offers noninvasive imaging with desirable spatial resolution over large areas. This study investigates the feasibility of utilizing MRI to detect responses of cultured cells andin vivorat cortex to membrane potential-modulating ionic solutions by measuring magnetic resonance parameters. Our findings reveal that depolarizing (or hyperpolarizing) ionic solutions increase (or decrease) theT2relaxation time, while the ratio of bound to free water proton shows the opposite trend. These findings also suggest a potential approach to noninvasively detect changes in membrane potential using MRI.
Analysis of predation-driven inoculum loss and carbon flow in bioaugmented soils through DNA-SIP
Authors: Nieto Esteban E. , Jurburg Stephanie D. , Steinbach Nicole , Festa Sabrina , Morelli Irma S. , Coppotelli Bibiana M. , Chatzinotas Antonis 
Published: April 2024

AbstractBioaugmentation is considered as a sustainable and cost-effective methodology to recover contaminated environments, but its outcome is highly variable. Predation is a key top-down control mechanism affecting inoculum establishment, however its effects on this process have received little attention. This study focused on the impact of trophic interactions on bioaugmentation success in two soils with different pollution exposure histories We inoculated a 13C-labelled pollutant-degrading consortium in these soils and tracked the fate of the labelled biomass through stable isotope probing (SIP) of DNA. We identified active bacterial and eukaryotic inoculum-biomass consumers through amplicon sequencing of 16S rRNA and 18S rRNA genes coupled to modified enrichment factor calculation. Inoculation effectively increased PAH removal in short-term polluted soils but not in long-term polluted soils. A decrease in the relative abundance of the inoculated genera was observed already on day 15 in the long-term polluted soil, while growth of these genera was observed in the short-term polluted soil, indicating establishment of the inoculum. In both soils, eukaryotic genera dominated as early incorporators of 13C-labelled biomass, while bacteria incorporated the labelled biomass at the end of the incubation period, probably through cross-feeding. We also found different successional patterns between the two soils. In the short-term polluted soil, Cercozoa and Fungi genera predominated as early incorporators, whereas Ciliophora, Ochrophyta and Amoebozoa were the predominant genera in the long-term polluted soil. Our results showed differences in the inoculum establishment and predator community behaviours, affecting bioaugmentation efficiency. This highlights the need to further study predation effects on inoculum survival to increase the applicability of inoculation-based technologies.
A platform for mapping reactive cysteines within the immunopeptidome
Authors: Zhang Chenlu , Zhou Chen , Magassa Assa , Fang Deyu , Zhang Xiaoyu 
Published: April 2024

AbstractThe major histocompatibility complex class I (MHC-I) antigen presentation pathways play pivotal roles in orchestrating immune responses. Recent studies have begun to utilize cysteines within the immunopeptidome for therapeutic applications, such as using covalent ligands to create haptenated neoantigens for inducing an immune response. In this study, we report a platform for mapping reactive cysteines present on MHC-I-bound peptide antigens. We have developed cell-impermeable sulfonated maleimide probes capable of effectively capturing reactive cysteines on antigens. Utilizing these probes in chemoproteomic experiments, we discovered that cysteines on MHC-I-bound antigens exhibit various degrees of reactivity. Furthermore, interferon-gamma stimulation produces increased reactivity of cysteines at position 8 of 9-mer MHC-I-bound antigens. Our findings may open up new avenues for understanding the distinctive roles of cysteine within the MHC-I immunopeptidome and leveraging the differentially reactive cysteines for therapeutic intervention.
Empowering STEM Students: A University-wide Mentorship Program Fostering Retention and Belonging
Authors: Ravishankar Sumedha , Spencer-Drakes Tara C.J. , Fernandes Ivy H. , Hayes Megan I. , Coopwood Shelby , Spencer Ilya , Neal Sonya E. 
Published: April 2024

AbstractIn the face of a challenging climate that is resistant to Diversity, Equity, and Inclusion (DEI) efforts, there is a critical need for a support structure for retaining students, particularly those from historically excluded groups (HEGs), in STEM. The Biology Undergraduate and Master’s Mentorship Program (BUMMP) embodies this commitment to fostering scientific identity, efficacy, and sense of belonging for 1stgeneration and historically underserved undergraduate and master’s students at UC San Diego. The mission of BUMMP is to cultivate a sense of belonging, instill confidence, and nurture a strong scientific identity amongst all of its participants. At its core, the three pillars of BUMMP are: 1) mentorship, 2) professional development, and 3) research. Quality mentorship is provided where students receive personal guidance from faculty, graduate students, postdocs, and industry leaders in navigating their career pathways. Complementing mentorship, BUMMP provides paid research opportunities and prioritizes professional development by offering workshops designed to enhance students’ professional skills. These three pillars form the backbone of BUMMP, empowering students from all backgrounds and ensuring their retention and persistence in STEM. So far, we’ve served over 1,350 mentees, collaborated with 809 mentors, and had over 180 mentees actively engaged in BUMMP-sponsored research activities. Overall, BUMMP’s expansive efforts have made a tremendous impact at UC San Diego and will continue to foster a community of future leaders who will be prepared to make meaningful contributions to the scientific community and beyond.
Whole-brain functional connectivity predicts groupwise and sex-specific tau PET in preclincal Alzheimer’s disease
Authors: Abuwarda Hamid , Trainer Anne , Horien Corey , Shen Xilin , Ju Suyeon , Constable R. Todd , Fredericks Carolyn 
Published: April 2024

AbstractPreclinical Alzheimer’s disease, characterized by the initial accumulation of amyloid and tau pathologies without symptoms, presents a critical opportunity for early intervention. Yet, the interplay between these pathological markers and the functional connectome during this window remains understudied. We therefore set out to elucidate the relationship between the functional connectome and amyloid and tau, as assessed by PET imaging, in individuals with preclinical AD using connectome-based predictive modeling (CPM). We found that functional connectivity predicts tau PET, outperforming amyloid PET models. These models were predominantly governed by linear relationships between functional connectivity and tau. Tau models demonstrated a stronger correlation to global connectivity than underlying tau PET. Furthermore, we identify sex-based differences in the ability to predict regional tau, without any underlying differences in tau PET or global connectivity. Taken together, these results suggest tau is more closely coupled to functional connectivity than amyloid in preclinical disease, and that multimodal predictive modeling approaches stand to identify unique relationships that any one modality may be insufficient to discern.
The influence of perceived country of origin image on Chinese consumers’ purchase intention of imported wine
Authors: Zhou Yichen , Gao Lisa 
Published: April 2024

Purpose
This study aims to examine how consumers’ propensity to purchase imported wines is influenced by their attitudes and perceptions toward the countries of origin (COO) of those wines.

Design/methodology/approach
The questionnaires were distributed online and 298 valid completed questionnaires were received. This study measured the perception of the wines’ countries of origin by adopting two independent dimensions of competence and warmth in the stereotype content model.

Findings
The results show a relationship between the purchase intention and the perception of the country of origin of the wine. Furthermore, the perceived image of the country of origin impacts the brand image of the wine and the quality of wine from its country of origin.

Research limitations/implications
This study’s questionnaire was distributed online. Future research would benefit from in-depth qualitative investigation and a wider range of sample sizes across countries.

Practical implications
The results of this study guide imported wine companies in product marketing design and advertising. By promoting the countries of origin of premium wines to target consumers, trust in the quality of imported wine can be improved, thereby increasing consumers’ purchase intention.

Originality/value
This study contributes to the understanding of consumer perception of the country of origin in the context of wine marketing. It provides valuable implications for wine companies’ marketing positioning and strategy, benefiting wine marketers, distributors and importers.
How can leaders spark employee creativity? An interpersonal emotion management perspective
Authors: Yu Guangyu , Nie Qi , Peng Jian 
Published: April 2024

Purpose This paper seeks to examine how leaders shape employee creativity by using interpersonal emotion management (IEM) strategies. Drawing on the social information processing (SIP) theory, the authors argue that psychological safety translates leader problem-focused IEM into employee creativity, an impact which is moderated by organizational justice.Design/methodology/approach Data were collected in two waves from 201 employees and their leaders in China. Regression analysis was used to test the hypotheses.Findings Leader problem-focused IEM is positively related to employee creativity, and this relationship is mediated by psychological safety. Organizational justice positively moderates the relationship between leader problem-focused IEM and psychological safety as well as the indirect relationship between leader problem-focused IEM and employee creativity via psychological safety.Originality/value This paper identifies a novel and useful predictor of employee creativity from the perspective of leader problem-focused IEM and provides practical insights for organizations regarding ways of improving employee creativity.
IFRS, financial development and pollutant emissions: an empirical analysis of developed and developing countries
Authors: Akisik Orhan 
Published: April 2024

PurposeThe purpose of this study is to examine the relationship between pollutant emissions, financial development and IFRS in developed and developing countries between 1998 and 2022.Design/methodology/approachData were obtained from World Development Indicators and World Governance Indicators of the World Bank.FindingsUsing FGLS and GMM estimators, the results provide evidence that financial development has a significant positive impact on a variety of pollutant emissions. However, this positive impact is moderated by IFRS for the overall sample and country income groups.Practical implicationsGovernments and regulatory organizations should support companies’ investments in clean energy and technologies to slow down environmental degradation. Tax credits and subsidies may be helpful to achieve this goal. Also, governments may encourage companies to cooperate with universities and research institutions to develop environment-friendly production and distribution methods to reduce pollution. Although stakeholders may obtain information about environmental issues in financial statements that are prepared in accordance with IFRS, there is a need for standardization of their contents.Social implicationsGreenhouse gases are major contributors to climate change and global warming. In addition to private costs borne by producers, the production and consumption of products have social costs arising from pollution that affects air, water, and soil. Pollution adversely affects people's physiological and psychological health, which decreases labor productivity, thereby leading to a decrease in economic growth. Originality/valueAccording to the author’s knowledge, this is the first study that examines the impact of IFRS on the relationship between financial development and pollutant emissions.
Contextual bias in forensic toxicology decisions: A follow‐up empirical study from China
Authors: He Ning , Hao Hongxia 
Published: April 2024

AbstractThe impact of contextual bias has been demonstrated repeatedly across forensic domains; however, research on this topic in forensic toxicology is very limited. In our previous study, experimental data from only one context version were compared with the actual forensic biasing casework. As a follow‐up, this controlled experiment with 159 forensic toxicology practitioners was conducted, to test whether knowledge of different contextual information influenced their forensic decision‐making. Participants in different context groups were tasked to identify testing strategies for carbon monoxide and opiate drugs. The results of chi‐squared tests for their selections and two context groups exhibited statistically significant differences (p < 0.05 or p < 0.01). These findings show contextual information can bias forensic toxicology decisions about testing strategies, despite it is a relatively objective domain in forensic science.
Identifying signs and symptoms of urinary tract infection from emergency department clinical notes using large language models
Authors: Iscoe Mark , Socrates Vimig , Gilson Aidan , Chi Ling , Li Huan , Huang Thomas , Kearns Thomas , Perkins Rachelle , Khandjian Laura , Taylor R. Andrew 
Published: April 2024

AbstractBackgroundNatural language processing (NLP) tools including recently developed large language models (LLMs) have myriad potential applications in medical care and research, including the efficient labeling and classification of unstructured text such as electronic health record (EHR) notes. This opens the door to large‐scale projects that rely on variables that are not typically recorded in a structured form, such as patient signs and symptoms.ObjectivesThis study is designed to acquaint the emergency medicine research community with the foundational elements of NLP, highlighting essential terminology, annotation methodologies, and the intricacies involved in training and evaluating NLP models. Symptom characterization is critical to urinary tract infection (UTI) diagnosis, but identification of symptoms from the EHR has historically been challenging, limiting large‐scale research, public health surveillance, and EHR‐based clinical decision support. We therefore developed and compared two NLP models to identify UTI symptoms from unstructured emergency department (ED) notes.MethodsThe study population consisted of patients aged ≥ 18 who presented to an ED in a northeastern U.S. health system between June 2013 and August 2021 and had a urinalysis performed. We annotated a random subset of 1250 ED clinician notes from these visits for a list of 17 UTI symptoms. We then developed two task‐specific LLMs to perform the task of named entity recognition: a convolutional neural network‐based model (SpaCy) and a transformer‐based model designed to process longer documents (Clinical Longformer). Models were trained on 1000 notes and tested on a holdout set of 250 notes. We compared model performance (precision, recall, F1 measure) at identifying the presence or absence of UTI symptoms at the note level.ResultsA total of 8135 entities were identified in 1250 notes; 83.6% of notes included at least one entity. Overall F1 measure for note‐level symptom identification weighted by entity frequency was 0.84 for the SpaCy model and 0.88 for the Longformer model. F1 measure for identifying presence or absence of any UTI symptom in a clinical note was 0.96 (232/250 correctly classified) for the SpaCy model and 0.98 (240/250 correctly classified) for the Longformer model.ConclusionsThe study demonstrated the utility of LLMs and transformer‐based models in particular for extracting UTI symptoms from unstructured ED clinical notes; models were highly accurate for detecting the presence or absence of any UTI symptom on the note level, with variable performance for individual symptoms.
YTHDC1‐dependent m6A modification modulated FOXM1 promotes glycolysis and tumor progression through CENPA in triple‐negative breast cancer
Authors: Shen Xi , Zhong Jianxin , Yu Pan , Liu Feng , Peng Haoran , Chen Nianyong 
Published: April 2024

AbstractTriple‐negative breast cancer (TNBC) exhibits heightened aggressiveness compared with other breast cancer (BC) subtypes, with earlier relapse, a higher risk of distant metastasis, and a worse prognosis. Transcription factors play a pivotal role in various cancers. Here, we found that factor forkhead box M1 (FOXM1) expression was significantly higher in TNBC than in other BC subtypes and normal tissues. Combining the findings of Gene Ontology (GO) enrichment analysis and a series of experiments, we found that knockdown of the FOXM1 gene attenuated the ability of TNBC cells to proliferate and metastasize both in vivo and in vitro. In addition, Spearman's test showed that FOXM1 significantly correlated with glycolysis‐related genes, especially centromere protein A (CENPA) in datasets (GSE76250, GSE76124, GSE206912, and GSE103091). The effect of silencing FOXM1 on the inhibition of CENPA expression, TNBC proliferation, migration, and glycolysis could be recovered by overexpression of CENPA. According to MeRIP, the level of m6A modification on FOMX1 decreased in cells treated with cycloleucine (a m6A inhibitor) compared with that in the control group. The increase in FOXM1 expression caused by YTHDC1 overexpression could be reversed by the m6A inhibitor, which indicated that YTHDC1 enhanced FOXM1 expression depending on m6A modification. Therefore, we concluded that the YTHDC1‐m6A modification/FOXM1/CENPA axis plays an important role in TNBC progression and glycolysis.
Contemporary results from the PelvEx collaborative: improvements in surgical outcomes for locally advanced and recurrent rectal cancer
Authors:   The PelvEx Collaborative
Published: April 2024

AbstractAimThe PelvEx Collaborative collates global data on outcomes following exenterative surgery for locally advanced and locally recurrent rectal cancer (LARC and LRRC, respectively). The aim of this study is to report contemporary data from within the collaborative and benchmark it against previous PelvEx publications.MethodAnonymized data from 45 units that performed pelvic exenteration for LARC or LRRC between 2017 and 2021 were reviewed. The primary endpoints were surgical outcomes, including resection margin status, radicality of surgery, rates of reconstruction and associated morbidity and/or mortality.ResultsOf 2186 patients who underwent an exenteration for either LARC or LRRC, 1386 (63.4%) had LARC and 800 (36.6%) had LRRC. The proportion of males to females was 1232:954. Median age was 62 years (interquartile range 52–71 years) compared with a median age of 63 in both historical LARC and LRRC cohorts. Compared with the original reported PelvEx data (2004–2014), there has been an increase in negative margin (R0) rates from 79.8% to 84.8% and from 55.4% to 71.7% in the LARC and LRRC cohorts, respectively. Bone resection and flap reconstruction rates have increased accordingly in both cohorts (8.2%–19.6% and 22.6%–32% for LARC and 20.3%–41.9% and 17.4%–32.1% in LRRC, respectively). Despite this, major morbidity has not increased.ConclusionIn the modern era, patients undergoing pelvic exenteration for advanced rectal cancer are undergoing more radical surgery and are more likely to achieve a negative resection margin (R0) with no increase in major morbidity.
Engaging with peers to integrate community care: Knowledge synthesis and conceptual map
Authors: Panaite Andreea‐Cătălina , Desroches Odile‐Anne , Warren Émilie , Rouly Ghislaine , Castonguay Geneviève , Boivin Antoine 
Published: April 2024

AbstractContextEngaging with peers is gaining increasing interest from healthcare systems in numerous countries. Peers are people who offer support by drawing on lived experiences of significant challenges or ‘insider’ knowledge of communities. Growing evidence suggests that peers can serve as a bridge between underserved communities and care providers across sectors, through their ability to build trust and relationships. Peer support is thus seen as an innovative way to address core issues of formal healthcare, particularly fragmentation of care and health inequalities. The wide body of approaches, goals and models of peer support speaks volumes of such interest. Navigating the various labels used to name peers, however, can be daunting. Similar terms often hide critical differences.Objectives/BackgroundThis article seeks to disentangle the conceptual multiplicity of peer support, presenting a conceptual map based on a 3‐year knowledge synthesis project involving peers and programme stakeholders in Canada, and international scientific and grey literature.Synthesis/Main ResultsThe map introduces six key questions to navigate and situate peer support approaches according to peers' roles, pathways and settings of practice, regardless of the terms used to label them. As a tool, it offers a broad overview of the different ways peers contribute to integrating health and community care.DiscussionWe conclude by discussing the map's potential and limitations to establish a common language and bridge models, in support of knowledge exchange among practitioners, policymakers and researchers.Patient or Public ContributionOur team includes one experienced peer support worker. She contributed to the design of the conceptual map and the production of the manuscript. More than 10 peers working across Canada were also involved during research meetings to validate and refine the conceptual map.