bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering intercellular signaling complexes by interaction-guided chemical proteomics
Authors: Zheng Jiangnan , Zheng Zhendong , Fu Changying , Weng Yicheng , He An , Ye Xueting , Gao Weina , Tian Ruijun 
Published: July 2023

AbstractIndirect cell–cell interactions mediated by secreted proteins and their plasma membrane receptors play essential roles for regulating intercellular signaling. However, systematic profiling of the interactions between living cell surface receptors and secretome from neighboring cells remains challenging. Here we develop a chemical proteomics approach, termed interaction-guided crosslinking (IGC), to identify ligand-receptor interactions in situ. By introducing glycan-based ligation and click chemistry, the IGC approach via glycan-to-glycan crosslinking successfully captures receptors from as few as 0.1 million living cells using only 10 ng of secreted ligand. The unparalleled sensitivity and selectivity allow systematic crosslinking and identification of ligand-receptor complexes formed between cell secretome and surfaceome in an unbiased and all-to-all manner, leading to the discovery of a ligand-receptor interaction between pancreatic cancer cell-secreted urokinase (PLAU) and neuropilin 1 (NRP1) on pancreatic cancer-associated fibroblasts. This approach is thus useful for systematic exploring new ligand-receptor pairs and discovering critical intercellular signaling events.
Overlooked riverine contributions of dissolved neodymium and hafnium to the Amazon estuary and oceans
Authors: Xu Antao , Hathorne Ed , Laukert Georgi , Frank Martin 
Published: July 2023

AbstractThe Amazon River accounts for 20% of global freshwater runoff and supplies vital trace metals to the Atlantic Ocean. Suspended particles within its plume are thought to partially dissolve, constituting a large potential source of metals, which is, however, not well constrained. Here we used combined neodymium (Nd) and hafnium (Hf) isotopes to disprove the release of Nd and Hf from particles as the cause of the observed dissolved concentration increases and isotopic variability across the plume. Instead, the changes reflect admixture of nearby Pará River freshwater with exceptionally high dissolved Nd and Hf concentrations contributing 45–100% of the riverine fraction to the southern and outer estuary. This result led us to develop an empirical relationship between riverine Nd concentration and pH to revise the global dissolved riverine Nd flux, which accordingly is at least three times higher than commonly used estimates. Future work should focus on contributions of low-pH rivers to global metal fluxes.
Oral and anal microbiome from HIV-exposed individuals: role of host-associated factors in taxa composition and metabolic pathways
Authors: Lacunza Ezequiel , Fink Valeria , Salas María E. , Canzoneri Romina , Naipauer Julián , Williams Sion , Coso Omar , Sued Omar , Cahn Pedro , Mesri Enrique A. , Abba Martín C. 
Published: July 2023

AbstractEvidence indicates that the microbiome plays a significant role in HIV immunopathogenesis and associated complications. This study aimed to characterize the oral and anal microbiome of Men who have Sex with Men (MSM) and Transgender Women (TGW), with and without HIV. One hundred and thirty oral and anal DNA-derived samples were obtained from 78 participants and subjected to shotgun metagenomics sequencing for further microbiome analysis. Significant differences in the microbiome composition were found among subjects associated with HIV infection, gender, sex behavior, CD4+ T-cell counts, antiretroviral therapy (ART), and the presence of HPV-associated precancerous anal lesions. Results confirm the occurrence of oncogenic viromes in this high HIV-risk population. The oral microbiome in HIV-associated cases exhibited an enrichment of bacteria associated with periodontal disease pathogenesis. Conversely, anal bacteria showed a significant decrease in HIV-infected subjects (Coprococcus comes, Finegoldia magna, Blautia obeum, Catenibacterium mitsuokai). TGW showed enrichment in species related to sexual transmission, which concurs that most recruited TGW are or have been sex workers. Prevotella bivia and Fusobacterium gonidiaformans were positively associated with anal precancerous lesions among HIV-infected subjects. The enrichment of Holdemanella biformis and C. comes was associated with detectable viral load and ART-untreated patients. Metabolic pathways were distinctly affected by predominant factors linked to sexual behavior or HIV pathogenesis. Gene family analysis identified bacterial gene signatures as potential prognostic and predictive biomarkers for HIV/AIDS-associated malignancies. Conclusions: Identified microbial features at accessible sites are potential biomarkers for predicting precancerous anal lesions and therapeutic targets for HIV immunopathogenesis.
Improvement of stress corrosion cracking resistance by low cycle fatigue of a CrNiMoV steel
Authors: Huang Yu-Hui , Yang Fang-Xin , Wang Nan , Zhu Ming-Liang , Xuan Fu-Zhen 
Published: July 2023

AbstractLow cycle fatigue often interacts with stress corrosion cracking behavior. In this work, the effect of low cycle fatigue on stress corrosion cracking susceptibility of a CrNiMoV steel was investigated by interrupted fatigue tests in air and slow strain rate tensile tests in 3.5 wt% NaCl solution at 180 °C. Microstructure evolution characterization verified cyclic softening and was found to improve stress corrosion cracking resistance with crack deflection along lath martensites due to a decrease of residual stress, phase transformation and increase of low-energy structures. As a semi-quantitative damage indicator, the microstructure evolution due to low cycle fatigue damage can be well described by the Kernel Average Misorientation (KAM) from the Electron Backscatter Diffraction technique. The effect of fatigue damage on stress corrosion sensitivity was found predictable based on the linear relationship between KAM and stress corrosion sensitivity factor of reduction of area.
Diverse organic-mineral associations in Jezero crater, Mars
Authors: Sharma Sunanda , Roppel Ryan D. , Murphy Ashley E. , Beegle Luther W. , Bhartia Rohit , Steele Andrew , Hollis Joseph Razzell , Siljeström Sandra , McCubbin Francis M. , Asher Sanford A. , Abbey William J. , Allwood Abigail C. , Berger Eve L. , Bleefeld Benjamin L. , Burton Aaron S. , Bykov Sergei V. , Cardarelli Emily L. , Conrad Pamela G. , Corpolongo Andrea , Czaja Andrew D. , DeFlores Lauren P. , Edgett Kenneth , Farley Kenneth A. , Fornaro Teresa , Fox Allison C. , Fries Marc D. , Harker David , Hickman-Lewis Keyron , Huggett Joshua , Imbeah Samara , Jakubek Ryan S. , Kah Linda C. , Lee Carina , Liu Yang , Magee Angela , Minitti Michelle , Moore Kelsey R. , Pascuzzo Alyssa , Rodriguez Sanchez-Vahamonde Carolina , Scheller Eva L. , Shkolyar Svetlana , Stack Kathryn M. , Steadman Kim , Tuite Michael , Uckert Kyle , Werynski Alyssa , Wiens Roger C. , Williams Amy J. , Winchell Katherine , Kennedy Megan R. , Yanchilina Anastasia 
Published: July 2023

AbstractThe presence and distribution of preserved organic matter on the surface of Mars can provide key information about the Martian carbon cycle and the potential of the planet to host life throughout its history. Several types of organic molecules have been previously detected in Martian meteorites1 and at Gale crater, Mars2–4. Evaluating the diversity and detectability of organic matter elsewhere on Mars is important for understanding the extent and diversity of Martian surface processes and the potential availability of carbon sources1,5,6. Here we report the detection of Raman and fluorescence spectra consistent with several species of aromatic organic molecules in the Máaz and Séítah formations within the Crater Floor sequences of Jezero crater, Mars. We report specific fluorescence-mineral associations consistent with many classes of organic molecules occurring in different spatial patterns within these compositionally distinct formations, potentially indicating different fates of carbon across environments. Our findings suggest there may be a diversity of aromatic molecules prevalent on the Martian surface, and these materials persist despite exposure to surface conditions. These potential organic molecules are largely found within minerals linked to aqueous processes, indicating that these processes may have had a key role in organic synthesis, transport or preservation.
Mast cells link immune sensing to antigen-avoidance behaviour
Authors: Plum Thomas , Binzberger Rebecca , Thiele Robin , Shang Fuwei , Postrach Daniel , Fung Candice , Fortea Marina , Stakenborg Nathalie , Wang Zheng , Tappe-Theodor Anke , Poth Tanja , MacLaren Duncan A. A. , Boeckxstaens Guy , Kuner Rohini , Pitzer Claudia , Monyer Hannah , Xin Cuiyan , Bonventre Joseph V. , Tanaka Satoshi , Voehringer David , Vanden Berghe Pieter , Strid Jessica , Feyerabend Thorsten B. , Rodewald Hans-Reimer 
Published: July 2023

AbstractThe physiological functions of mast cells remain largely an enigma. In the context of barrier damage, mast cells are integrated in type 2 immunity and, together with immunoglobulin E (IgE), promote allergic diseases. Allergic symptoms may, however, facilitate expulsion of allergens, toxins and parasites and trigger future antigen avoidance1–3. Here, we show that antigen-specific avoidance behaviour in inbred mice4,5 is critically dependent on mast cells; hence, we identify the immunological sensor cell linking antigen recognition to avoidance behaviour. Avoidance prevented antigen-driven adaptive, innate and mucosal immune activation and inflammation in the stomach and small intestine. Avoidance was IgE dependent, promoted by Th2 cytokines in the immunization phase and by IgE in the execution phase. Mucosal mast cells lining the stomach and small intestine rapidly sensed antigen ingestion. We interrogated potential signalling routes between mast cells and the brain using mutant mice, pharmacological inhibition, neural activity recordings and vagotomy. Inhibition of leukotriene synthesis impaired avoidance, but overall no single pathway interruption completely abrogated avoidance, indicating complex regulation. Collectively, the stage for antigen avoidance is set when adaptive immunity equips mast cells with IgE as a telltale of past immune responses. On subsequent antigen ingestion, mast cells signal termination of antigen intake. Prevention of immunopathology-causing, continuous and futile responses against per se innocuous antigens or of repeated ingestion of toxins through mast-cell-mediated antigen-avoidance behaviour may be an important arm of immunity.
Large language models encode clinical knowledge
Authors: Singhal Karan , Azizi Shekoofeh , Tu Tao , Mahdavi S. Sara , Wei Jason , Chung Hyung Won , Scales Nathan , Tanwani Ajay , Cole-Lewis Heather , Pfohl Stephen , Payne Perry , Seneviratne Martin , Gamble Paul , Kelly Chris , Babiker Abubakr , Schärli Nathanael , Chowdhery Aakanksha , Mansfield Philip , Demner-Fushman Dina , Agüera y Arcas Blaise , Webster Dale , Corrado Greg S. , Matias Yossi , Chou Katherine , Gottweis Juraj , Tomasev Nenad , Liu Yun , Rajkomar Alvin , Barral Joelle , Semturs Christopher , Karthikesalingam Alan , Natarajan Vivek 
Published: July 2023

AbstractLarge language models (LLMs) have demonstrated impressive capabilities, but the bar for clinical applications is high. Attempts to assess the clinical knowledge of models typically rely on automated evaluations based on limited benchmarks. Here, to address these limitations, we present MultiMedQA, a benchmark combining six existing medical question answering datasets spanning professional medicine, research and consumer queries and a new dataset of medical questions searched online, HealthSearchQA. We propose a human evaluation framework for model answers along multiple axes including factuality, comprehension, reasoning, possible harm and bias. In addition, we evaluate Pathways Language Model1(PaLM, a 540-billion parameter LLM) and its instruction-tuned variant, Flan-PaLM2on MultiMedQA. Using a combination of prompting strategies, Flan-PaLM achieves state-of-the-art accuracy on every MultiMedQA multiple-choice dataset (MedQA3, MedMCQA4, PubMedQA5and Measuring Massive Multitask Language Understanding (MMLU) clinical topics6), including 67.6% accuracy on MedQA (US Medical Licensing Exam-style questions), surpassing the prior state of the art by more than 17%. However, human evaluation reveals key gaps. To resolve this, we introduce instruction prompt tuning, a parameter-efficient approach for aligning LLMs to new domains using a few exemplars. The resulting model, Med-PaLM, performs encouragingly, but remains inferior to clinicians. We show that comprehension, knowledge recall and reasoning improve with model scale and instruction prompt tuning, suggesting the potential utility of LLMs in medicine. Our human evaluations reveal limitations of today’s models, reinforcing the importance of both evaluation frameworks and method development in creating safe, helpful LLMs for clinical applications.
Spatially resolved multiomics of human cardiac niches
Authors: Kanemaru Kazumasa , Cranley James , Muraro Daniele , Miranda Antonio M. A. , Ho Siew Yen , Wilbrey-Clark Anna , Patrick Pett Jan , Polanski Krzysztof , Richardson Laura , Litvinukova Monika , Kumasaka Natsuhiko , Qin Yue , Jablonska Zuzanna , Semprich Claudia I. , Mach Lukas , Dabrowska Monika , Richoz Nathan , Bolt Liam , Mamanova Lira , Kapuge Rakeshlal , Barnett Sam N. , Perera Shani , Talavera-López Carlos , Mulas Ilaria , Mahbubani Krishnaa T. , Tuck Liz , Wang Lu , Huang Margaret M. , Prete Martin , Pritchard Sophie , Dark John , Saeb-Parsy Kourosh , Patel Minal , Clatworthy Menna R. , Hübner Norbert , Chowdhury Rasheda A. , Noseda Michela , Teichmann Sarah A. 
Published: July 2023

AbstractThe function of a cell is defined by its intrinsic characteristics and its niche: the tissue microenvironment in which it dwells. Here we combine single-cell and spatial transcriptomics data to discover cellular niches within eight regions of the human heart. We map cells to microanatomical locations and integrate knowledge-based and unsupervised structural annotations. We also profile the cells of the human cardiac conduction system1. The results revealed their distinctive repertoire of ion channels, G-protein-coupled receptors (GPCRs) and regulatory networks, and implicated FOXP2 in the pacemaker phenotype. We show that the sinoatrial node is compartmentalized, with a core of pacemaker cells, fibroblasts and glial cells supporting glutamatergic signalling. Using a custom CellPhoneDB.org module, we identify trans-synaptic pacemaker cell interactions with glia. We introduce a druggable target prediction tool, drug2cell, which leverages single-cell profiles and drug–target interactions to provide mechanistic insights into the chronotropic effects of drugs, including GLP-1 analogues. In the epicardium, we show enrichment of both IgG+ and IgA+ plasma cells forming immune niches that may contribute to infection defence. Overall, we provide new clarity to cardiac electro-anatomy and immunology, and our suite of computational approaches can be applied to other tissues and organs.
Fatigue database of complex metallic alloys
Authors: Zhang Zian , Tang Haoxuan , Xu Zhiping 
Published: July 2023

AbstractThe past few decades have witnessed rapid progresses in the research and development of complex metallic alloys such as metallic glasses and multi-principal element alloys, which offer new solutions to tackle engineering problems of materials such as the strength-toughness conflict and deployment in harsh environments and/or for long-term service. A fatigue database (FatigueData-CMA2022) is compiled from the literature by the end of 2022. Data for both metallic glasses and multi-principal element alloys are included and analyzed for their statistics and patterns. Automatic extraction and manual examination are combined in the workflow to improve the efficiency of processing, the quality of published data, and the reusability. The database contains 272 fatigue datasets of S-N (the stress-life relation), ε-N (the strain-life relation), and da/dN-ΔK (the relation between the fatigue crack growth rate and the stress intensity factor range) data, together with the information of materials, processing and testing conditions, and mechanical properties. The database and scripts are released in open repositories, which are designed in formats that can be continuously expanded and updated.
A dataset on energy efficiency grade of white goods in mainland China at regional and household levels
Authors: Li Zonghan , Wang Chunyan , Liu Yi 
Published: July 2023

AbstractTo improve energy-saving management, the energy efficiency grade (EEG) was introduced by the Chinese government in the 2000s and mainly implemented for white goods (WGs) in early stages. However, due to the lack of actual statistics, how effective the promotion of high EEG WGs has been in China is still not clear. The China Energy Efficiency Grade (CEEG) of WGs dataset described here comprises (i) EEG-related data on 5 kinds of WGs at the regional (national, provincial) and household levels in China and (ii) predictions of future average EEG trends. By web crawling, retrieving and processing in SQL, the average EEG data weighted by sales in 30 provinces in mainland China from 2012 to 2019 are provided. Household WG survey data, including household information and average EEG, were collected by distributing questionnaires to 1327 households in Beijing, China. The CEEG dataset will facilitate the advancement of research on household energy consumption, household appliance consumer choice, and the assessment of energy efficiency-related policies.
Development and validation of asthma risk prediction models using co-expression gene modules and machine learning methods
Authors: Dessie Eskezeia Y. , Gautam Yadu , Ding Lili , Altaye Mekibib , Beyene Joseph , Mersha Tesfaye B. 
Published: July 2023

AbstractAsthma is a heterogeneous respiratory disease characterized by airway inflammation and obstruction. Despite recent advances, the genetic regulation of asthma pathogenesis is still largely unknown. Gene expression profiling techniques are well suited to study complex diseases including asthma. In this study, differentially expressed genes (DEGs) followed by weighted gene co-expression network analysis (WGCNA) and machine learning techniques using dataset generated from airway epithelial cells (AECs) and nasal epithelial cells (NECs) were used to identify candidate genes and pathways and to develop asthma classification and predictive models. The models were validated using bronchial epithelial cells (BECs), airway smooth muscle (ASM) and whole blood (WB) datasets. DEG and WGCNA followed by least absolute shrinkage and selection operator (LASSO) method identified 30 and 34 gene signatures and these gene signatures with support vector machine (SVM) discriminated asthmatic subjects from controls in AECs (Area under the curve: AUC = 1) and NECs (AUC = 1), respectively. We further validated AECs derived gene-signature in BECs (AUC = 0.72), ASM (AUC = 0.74) and WB (AUC = 0.66). Similarly, NECs derived gene-signature were validated in BECs (AUC = 0.75), ASM (AUC = 0.82) and WB (AUC = 0.69). Both AECs and NECs based gene-signatures showed a strong diagnostic performance with high sensitivity and specificity. Functional annotation of gene-signatures from AECs and NECs were enriched in pathways associated with IL-13, PI3K/AKT and apoptosis signaling. Several asthma related genes were prioritized including SERPINB2 and CTSC genes, which showed functional relevance in multiple tissue/cell types and related to asthma pathogenesis. Taken together, epithelium gene signature-based model could serve as robust surrogate model for hard-to-get tissues including BECs to improve the molecular etiology of asthma.
Allogenic adipose derived mesenchymal stem cells are effective than antibiotics in treating endometritis
Authors: Bhaskar Vinay , Saini Sikander , Ansari Shama , Ghai Shubham , Thakur Abhishek , Chopra Suman , Verma Vivekananda , Malakar Dhruba 
Published: July 2023

AbstractEndometritis is a uterine inflammatory disease that causes reduced livestock fertility, milk production and lifespan leading to significant economic losses to the dairy industry. Mesenchymal stem cells (MSC) may act as an alternative for inefficacy of antibiotics and rising antibiotic resistance in endometritis. The present study aimed to cure the chronic endometritic buffaloes using allogenic adipose-derived MSCs (AD-MSC). AD-MSCs were isolated from buffalo adipose tissue and characterized by multilineage differentiation as well as MSC-specific markers. The in vivo safety and efficacy were assessed after infusion of AD-MSCs. In safety trial, cells were administered in healthy buffaloes via different routes (IV and IC) followed by examination of clinical and hematological parameters. In efficacy study, AD-MSCs treatments (IV and IC) and antibiotic therapy (ABT) in endometritic buffaloes were comparatively evaluated. AD-MSCs did not induced any immunological reaction in treated buffaloes. PMN count, CRP levels and VDS were significantly (p ≤ 0.05) reduced after AD-MSCs infusions in IV and IC groups and no significant difference was observed in antibiotic group. The IV group was marked with 50% absolute risk reduction in endometritis and 50% live calf births after artificial insemination in comparison with ABT group. Anti-inflammatory cytokines (IL4 and IL10) and anti-microbial peptides (PI3, CATHL4, LCN2 and CST3) expressions were significantly (p ≤ 0.05) upregulated in IV group. The calf delivery rate after the treatments in IV group was higher (50%, 3 calves) than the other groups (IC: 33.3%, 2 calves; ABT: 16.6%, 1 calf). In conclusion, the administration of AD-MSCs through IV route was found to be safe and efficacious for alleviating chronic endometritis in dairy buffaloes.
Quantifying the effect of isolation and negative certification on COVID-19 transmission
Authors: Takeshita Jun-ichi , Murakami Michio , Kamo Masashi , Naito Wataru , Yasutaka Tetsuo , Imoto Seiya 
Published: July 2023

AbstractIsolation of close contact people and negative test certification are used to manage the spread of new coronavirus infections worldwide. These effectively prevent the spread of infection in advance, but they can lead to a decline in socio-economic activity. Thus, the present study quantified the extent to which isolation and negative test certification respectively reduce the risk of infection. To this end, a discrete-time SEIR model was used as the infectious disease model, and equations for calculating the conditional probability of non-infection status given negative test results on two different days were derived. Then the respective non-infection probabilities with two negative PCR test results, and with one negative PCR test result and one antigen test result, were quantified. By substituting initial parameters of the SEIR model into these probabilities, the present study revealed the following: (1) isolating close contact individuals can reduce by$$80\%$$80%the risk of infection during the first 5 days, but five more days are needed to reduce the risk$$10\%$$10%more, and seven more days to reduce the risk$$20\%$$20%more; and (2) if an individual with a negative PCR test result has a negative antigen test result the next day, then his or her infection probability is between 0.6 and$$0.7\%$$0.7%. Our results show that 5-day isolation has a proportionally greater effect on risk reduction, compared to longer isolation; and thus, if an isolation period of longer than 5 days is contemplated, both the risk reduction and the negative effects from such increased isolation should be considered. Regarding negative test certification, our results provide those in managerial positions, who must decide whether to accept the risk and hold mass-gathering events, with quantitative information that may be useful in their decision-making.