bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes of an Emergency Department Program to Identify and Link Patients at Increased Risk for Acquiring HIV Infection to Outpatient HIV Prevention Services: The HIV PreventED Program
Authors: White Douglas AE , Godoy Ashley , Jewett Montana , Burns Molly , Pinto Cinthya Mujica , Packel Laura J , Garcia-Chinn Maria , Anderson Erik S , McCoy Sandra I 
Published: April 2024

Background:
Emergency departments (ED) provide care to patients at increased risk for acquiring HIV and for many of them, the ED serves as their sole point of entry into the healthcare system. We implemented the HIV PreventED Program to increase access to HIV prevention services for ED patients.

Setting:
Emergency department in Oakland, CA with an annual census of 57,000 visits.

Methods:
This cross-sectional study evaluated the first 9 months of the HIV PreventED Program. In this program, a navigator surveyed adult HIV negative ED patients to determine their risk for acquiring HIV infection, incorporating HIV prevention counseling into their assessments. Patients at higher risk for acquiring HIV were referred to outpatient prevention services, if interested. The primary outcome measure was the number and proportion of ED patients at higher risk for acquiring HIV that followed up for outpatient prevention services.

Results:
There were 1,233 HIV negative patients assessed by the navigator and who received ED-based HIV prevention counseling. Of these, 193 (15.7%) were identified at higher risk and offered an outpatient referral for prevention services, of which 104 accepted (53.9%), 23 (11.9%) attended the referral, and 13 (6.7%) were prescribed pre-exposure prophylaxis (PrEP). The median time to linkage was 28 days (interquartile range 15 to 41 days).

Conclusion:
A navigator focused on providing ED-based HIV prevention counseling and linkage to outpatient services is feasible. Strategies to more efficiently identify ED patients at higher risk for HIV acquisition, such as automated identification of risk data from the electronic health record, and policies to improve follow up and the receipt of PrEP, such as same-day PrEP initiation, should be prospectively evaluated.
Deciphering the interaction surface between the West Nile virus NS3 and NS5 proteins
Authors: Brand Carolin , Geiss Brian , Bisaillon Martin 
Published: April 2024

West Nile virus (WNV) is the most prevalent mosquito-borne disease and the leading cause of viral encephalitis in the continental United States. It belongs to the Flavivirus family which includes other important human pathogens such as dengue virus (DENV), Japanese encephalitis virus (JEV), and Zika viruses (ZIKV). Despite several decades of research, no specific antiviral drugs are available to treat Flavivirus infections. The present study characterizes the interaction between the WNV NS3 and NS5 proteins for the purpose of identifying hotspots in the protein-protein interaction which could be targeted for the development of antiviral therapeutics. We previously developed an interaction model in silico based on data available in the literature. Here, potential interacting residues on NS3 and NS5 were mutated in a WNV replicon, and seven mutations in the NS3 protein were found to drastically reduce viral replication. In addition to being well conserved among mosquito-borne Flaviviruses, these residues are located on the protein’s surface in two clusters which might be interesting new targets for future drug development.
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Authors: Southwell James W , Wilson Keith S , Thomas Gavin H , Duhme-Klair Anne-Kathrin 
Published: April 2024

Iron is an essential nutrient for microbial growth and bacteria have evolved numerous routes to solubilise and scavenge this biometal, which is often present at very low concentrations in host tissue. We recently used a MOPS-based medium to induce iron limitation in Escherichia coli K-12 during the characterisation of novel siderophore conjugated antibiotics. In this study we confirm that growth media derived from commercially-available M9 salts are unsuitable for studies of iron-limited growth, likely through the contamination of the sodium phosphate buffer components with over 100 µM iron. In contrast, MOPS-based media that are treated with metal-binding Chelex® resin, allow the free iron concentration to be reduced to growth-limiting levels. Despite these measures a small amount of E. coli growth is still observed in these iron-depleted media. By growing E. coli in conditions that theoretically increase the demand for iron-dependent enzymes, namely by replacing the glucose carbon source for acetate and by switching to a microaerobic atmosphere, we can reduce background growth even further. Finally, we demonstrate that by adding an exogeneous siderophore to the growth media which is poorly used by E. coli, we can completely prevent growth, perhaps mimicking situation in host tissue. In conclusion, this short study provides practical experimental insight into low iron media and how to augment the growth conditions of E. coli for extreme iron-limited growth.
An Evaluation of ChatGPT and Bard (Gemini) in the Context of Biological Knowledge Retrieval
Authors: Caspi Ron , Karp Peter D. 
Published: April 2024

ChatGPT and Bard (now called Gemini), two conversational AI models developed by OpenAI and Google AI, respectively, have garnered considerable attention for their ability to engage in natural language conversations and perform various language-related tasks. While the versatility of these chatbots in generating text and simulating human-like conversations is undeniable, we wanted to evaluate their effectiveness in retrieving biological knowledge for curation and research purposes. To do so we asked each chatbot a series of questions and scored their answers based on their quality. Out of a maximal score of 24, ChatGPT scored 5 and Bard scored 13. The encountered issues included missing information, incorrect answers, and instances where responses combine accurate and inaccurate details. Notably, both tools tend to fabricate references to scientific papers, undermining their usability.
In light of these findings, we recommend that biologists continue to rely on traditional sources while periodically assessing the reliability of ChatGPT and Bard. As ChatGPT aptly suggested, for specific and up-to-date scientific information, established scientific journals, databases, and subject-matter experts remain the preferred avenues for trustworthy data.
Multiomics analyses decipher intricate changes in the cellular and metabolic landscape of steatotic livers upon dietary restriction and sleeve gastrectomy
Authors: Chen Shuai , Zeng Qinghe , Cai Xiurong , Xue Jiaming , Song Peng , Tang Liming , Klein Christophe , Tacke Frank , Guillot Adrien , Liu Hanyang 
Published: April 2024

AbstractMetabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic, progressive liver disease that encompasses a spectrum of steatosis, steatohepatitis (or MASH), and fibrosis. Evidence suggests that dietary restriction (DR) and sleeve gastrectomy (SG) can lead to remission of hepatic steatosis and inflammation through weight loss, but it is unclear whether these procedures induce distinct metabolic or immunological changes in MASLD livers. This study aims to elucidate the intricate hepatic changes following DR, SG or sham surgery in rats fed a high-fat diet as a model of obesity-related MASLD, in comparison to a clinical cohort of patients undergoing SG. Single-cell and single-nuclei transcriptome analysis, spatial metabolomics, and immunohistochemistry revealed the liver landscape, while circulating biomarkers were measured in serum samples. Artificial intelligence (AI)-assisted image analysis characterized the spatial distribution of hepatocytes, myeloid cells and lymphocytes. In patients and experimental MASLD rats, SG improved BMI, circulating liver injury biomarkers and triglyceride levels. Both DR and SG attenuated liver steatosis and fibrosis in rats. Metabolism-related genes (Ppara,Cyp2e1andCyp7a1) were upregulated in hepatocytes upon DR and SG, while SG broadly upregulated lipid metabolism on cholangiocytes, monocytes, macrophages, and neutrophils. Furthermore, SG promoted myeloid cell accumulation in the liver not only ameliorating inflammation but activating liver repair processes. Regions with potent myeloid infiltration were marked with enhanced metabolic capacities upon SG. Additionally, a disruption of periportal hepatocyte functions was observed upon DR. In conclusion, this study indicates a dynamic cellular crosstalk in steatotic livers undergoing SG. Notably, PPARα- and gut-liver axis-related processes, and metabolically-active myeloid cell infiltration indicate intervention-related mechanisms supporting SG for the treatment of MASLD.
β-glucan induced trained immunity enhances antibody levels in a vaccination model in mice
Authors: Ajit Jainu , Chen Qing , Ung Trevor , Rosenberger Matthew , Kim Jeremiah , Solanki Ani , Shen Jingjing , Esser Kahn Aaron P. 
Published: April 2024

AbstractTrained immunity improves disease resistance by strengthening our first line of defense, the innate immune system. Innate immune cells, predominantly macrophages, are epigenetically and metabolically rewired by β-glucan, a fungal cell wall component, to induce trained immunity. These trained macrophages exhibit increased co-stimulatory marker expression and altered cytokine production. Signaling changes from antigen-presenting cells, including macrophages, polarize T-cell responses. Recent work has shown that trained immunity can generally enhance protection against infection, and some work has shown increased protection with specific vaccines. It has been hypothesized that the trained cells themselves potentially modulate adaptive immunity in the context of vaccines. However, the mechanistic link between trained immunity on subsequent vaccinations to enhance antibody levels has not yet been identified. We report that trained immunity induced by a single dose of β-glucan increased antigen presentation in bone-marrow-derived macrophages (BMDMs) and CD4+T cell proliferationin-vitro. Mice trained with a single dose of β-glucan a week before vaccination elicited higher antigen-specific antibody levels than untrained mice. Further experiments validate that macrophages mediate this increase. This effect persisted even after vaccinations with 100 times less antigen in trained mice. We report β-glucan training as a novel prophylactic method to enhance the effect of subsequent vaccines.
Harnessing full-text publications for deep insights intoC. elegansandDrosophilaconnectomes
Authors: Arulprakasam Karthick Raja , Toh Janelle Wing Shan , Foo Herman , Kumar Mani R , Kutevska An-Nikol , Davey Emilia Emmanuelle , Mutwil Marek , Thibault Guillaume 
Published: April 2024

SUMMARYIn the rapidly expanding domain of scientific research, tracking and synthesizing information from the rapidly increasing volume of publications pose significant challenges. To address this, we introduce a novel high-throughput pipeline that employs ChatGPT to systematically extract and analyze connectivity information from the full-texts and abstracts of 24,237 and 150,538 research publications concerningCaenorhabditis elegansandDrosophila melanogaster, respectively. This approach has effectively identified 200,219 and 1,194,587 interactions within theC. elegansandDrosophilaconnectomes, respectively. Utilizing Cytoscape Web, we have developed comprehensive, searchable online connectomes that link relevant keywords to their corresponding PubMed IDs, thus providing seamless access to an extensive knowledge network encompassingC. elegansandDrosophila. Our work highlights the transformative potential of integrating artificial intelligence with bioinformatics to deepen our understanding of complex biological systems. By revealing the intricate web of relationships among key entities inC. elegansandDrosophila, we offer invaluable insights that promise to propel advancements in genetics, developmental biology, neuroscience, longevity, and beyond. We also provide details and discuss significant nodes within both connectomes, including the insulin/IGF-1 signaling (IIS) and the notch pathways. Our innovative methodology sets a robust foundation for future research aimed at unravelling complex biological networks across diverse organisms.
Effects of abiotic and biotic drivers on tadpoles in seasonal rock pools of Western Ghats rock outcrops, India
Authors: Jithin Vijayan , Naniwadekar Rohit 
Published: April 2024

ABSTRACTWe assessed the influence of abiotic (pool size, monsoon progression) and biotic (predator abundances) factors on occurrence and abundance of three species of tadpoles by periodically monitoring rock pools in lateritic plateaus. Tadpole responses were positively associated with rock pool size and monsoon progression negatively, but not with predator abundance.
Microsaccade Selectivity as Discriminative Feature for Object Decoding
Authors: Nouri Salar , Tehrani Amirali Soltani , Faridani Niloufar , Toosi Ramin , Noroozi Jalaledin , Dehaqani Mohammad-Reza A. 
Published: April 2024

AbstractMicrosaccades, a form of fixational eye movements, maintain visual stability during stationary observations. Previous studies have provided valuable insights into the relationship between microsaccade characteristics and external stimuli. However, the dynamic nature of microsaccades provides an opportunity to explore the mechanisms of information processing, particularly object decoding. This study examines the modulation of microsaccadic rates by different stimulus categories. Our experimental approach involves an analysis of microsaccade characteristics in monkeys and human subjects engaged in a passive viewing task. The stimulus categories comprised four primary categories: human, animal, natural, and man-made. We identified distinct microsaccade patterns across different stimulus categories, successfully decoding the stimulus category based on the microsaccade rate post-stimulus distribution. Our experiments demonstrate that stimulus categories can be classified with an average accuracy and recall of up to 85%. Our study found that microsaccade rates are independent of pupil size changes. Neural data showed that category classification in the inferior temporal (IT) cortex peaks earlier than microsaccade rates, suggesting a feedback mechanism from the IT cortex that influences eye movements after stimulus discrimination. These results exhibit potential for advancing neurobiological models, developing more effective human-machine interfaces, optimizing visual stimuli in experimental designs, and expanding our understanding of the capability of microsaccades as a feature for object decoding.
Influence of advanced footwear technology spikes on middle- and long-distance running performance measures in trained runners
Authors: Rodrigo-Carranza Víctor , Muñoz de la Cruz Violeta , Hoogkamer Wouter 
Published: April 2024

ABSTRACTTwo types of track spikes are commonly used, recently: spikes with a compliant and resilient midsole foam (e.g., PEBA), and spikes that combine such modern foam with a carbon fiber plate. Here we evaluated the effect of these different spike technologies on running performance measures for middle- and long-distance track events in trained runners. Fourteen females performed a single visit with six 200m trials at self-perceived 800m race pace in three different spike conditions (Control, PEBA and PEBA+Plate) twice in a mirrored order. Sixteen males completed four visits. During the first three visits they performed six 200m trials at self-perceived 800m race pace, twice in each condition. Subsequently, they performed a 3,000m time trial in one of the three spike conditions. During visit four, participants completed six 4-minute running economy trials at 5 m/s, twice in each condition. At 800m race pace females ran faster in PEBA (2.1%) and PEBA+Plate (2.0%) compared to Control. Males ran faster in PEBA (1.4%) and PEBA+Plate (2.4%) compared to Control, and in PEBA+Plate compared to PEBA (1.1%). Similarly, males ran the 3,000m time trial faster in PEBA (1.0%) and PEBA+Plate (2.4%) than in Control. Running economy was better in PEBA (5.1%) and PEBA+Plate (4.0%) than in Control. Performance benefits from modern foam spikes with and without a plate are equivalent for female middle-distance running, and for male long-distance running, but larger from modern foam spikes with a plate for male middle-distance running.
T follicular helper cell profiles differ by malaria antigen and for children compared to adults
Authors: Forconi Catherine S. , Nixon Christina , Wu Hannah W. , Odwar Boaz , Pond-Tor Sunthorn , Ong’echa John M. , Kurtis Jonathan , Moormann Ann M. 
Published: April 2024

AbstractBackgroundCirculating T-follicular helper (cTFH) cells have the potential to provide an additional correlate of protection againstPlasmodium falciparum(Pf)as they are essential to promote B-cell production of long-lasting antibodies. Assessing the specificity of cTFHsubsets to individual malaria antigens is vital to understanding the variation observed in antibody responses and identifying promising malaria vaccine candidates.MethodsUsing spectral flow cytometry and unbiased clustering analysis, we assessed antigen-specific cTFHcell recall responsesin vitroto malaria vaccine candidatesPf-schizont egress antigen-1 (PfSEA-1A) andPf-glutamic acid-rich protein (PfGARP) within a cross-section of children and adults living in a malaria-holoendemic region of western Kenya.FindingsIn children, a broad array of cTFHsubsets (defined by cytokine and transcription factor expression) were reactive to both malaria antigens,PfSEA-1A andPfGARP, while adults had a narrow profile centering on cTFH17- and cTFH1/17-like subsets following stimulation withPfGARP only.InterpretationBecause TFH17 cells are involved in the maintenance of memory antibody responses within the context of parasitic infections, our results suggest thatPfGARP might generate longer-lived antibody responses compared toPfSEA-1A. These findings have intriguing implications for evaluating malaria vaccine candidates as they highlight the importance of including cTFHprofiles when assessing interdependent correlates of protective immunity.
Label-free structural imaging of plant roots and microbes using third-harmonic generation microscopy
Authors: Pan Daisong , Rivera Jose A. , Kim Peter , Miao Max , Tyml Tomáš , Rodríguez Cristina , Wang Bing , Yoshikuni Yasuo , Elisabeth Nathalie H. , Northen Trent , Vogel John P. , Ji Na 
Published: April 2024

ABSTRACTRoot biology is pivotal in addressing global challenges including sustainable agriculture and climate change. However, roots have been relatively understudied among plant organs, partly due to the difficulties in imaging root structures in their natural environment. Here we used microfabricated ecosystems (EcoFABs) to establish growing environments with optical access and employed nonlinear multimodal microscopy of third-harmonic generation (THG) and three-photon fluorescence (3PF) to achieve label-free,in situimaging of live roots and microbes at high spatiotemporal resolution. THG enabled us to observe key plant root structures including the vasculature, Casparian strips, dividing meristematic cells, and root cap cells, as well as subcellular features including nuclear envelopes, nucleoli, starch granules, and putative stress granules. THG from the cell walls of bacteria and fungi also provides label-free contrast for visualizing these microbes in the root rhizosphere. With simultaneously recorded 3PF fluorescence signal, we demonstrated our ability to investigate root-microbe interactions by achieving single-bacterium tracking and subcellular imaging of fungal spores and hyphae in the rhizosphere.
A transcriptome atlas of zygotic and somatic embryogenesis in Norway spruce
Authors: Stojkovič Katja , Canovi Camilla , Le Kim-Cuong , Delhomme Nicolas , Egertsdotter Ulrika , Street Nathaniel R. 
Published: April 2024

SummarySomatic embryogenesis (SE) is a powerful model system for studying embryo development and an important method for scaling up availability of elite and climate-adapted genetic material of Norway spruce (Picea abiesL. Karst). However, there are several steps during the development of the somatic embryo (Sem) that are suboptimal compared to zygotic embryo (Zem) development. These differences are poorly understood and result in substantial yield losses during plant production, which limits cost-effective large-scale production of SE plants. This study presents a comprehensive data resource profiling gene expression during zygotic and somatic embryo development to support studies aiming to advance understanding of gene regulatory programmes controlling embryo development. Transcriptome expression patterns were analysed during zygotic embryogenesis (ZE) in Norway spruce, including separated samples of the female gametophytes and Zem and at multiple stages during SE. Expression data from eight developmental stages of SE, starting with pro-embryogenic masses (PEMs) up until germination, revealed extensive modulation of the transcriptome between the early and mid-stage maturing embryos and at the transition of desiccated embryos to germination. Comparative analysis of ZE and SE identified differences in timing relative to SE development and functional enrichment of these provided insight into the associated biological processes. Orthologs of transcription factors known to regulate embryo development in angiosperms were differentially expressed during Zem and Sem development and in the different zygotic embryo tissues, providing clues to the differences in development observed between Zem and Sem. This resource represents the most comprehensive dataset available for exploring embryo development in conifers.Significance StatementSomatic embryogenesis is used as a model system to study embryo development, however detailed information to verify similarities and explain differences between somatic and zygotic embryogenesis is largely missing for conifers. This data resource provides sequential mRNA transcriptome data from nine stages of conifer zygotic embryo and female gametophyte development, and eight stages of somatic embryo development, to enable exploration of biological questions and comparisons of the two developmental processes.