bluuebunny/crossref_metadata_2025_split huggingface dataset:
A 2D-proteomic analysis identifies proteins differentially regulated by two different dengue virus serotypes
Authors: Chumchanchira Chanida , Ramphan Suwipa , Paemanee Atchara , Roytrakul Sittiruk , Lithanatudom Pathrapol , Smith Duncan R. 
Published: April 2024

AbstractThe mosquito transmitted dengue virus (DENV) is a major public health problem in many tropical and sub-tropical countries around the world. Both vaccine development and drug development are complex as the species Dengue virus consist of four distinct viruses (DENV 1 to DENV 4) each of which is composed of multiple lineages and strains. To understand the interaction of DENV with the host cell machinery, several studies have undertaken in vitro proteomic analysis of different cell lines infected with DENV. Invariably, these studies have utilized DENV 2. In this study we sought to define proteins that are differentially regulated by two different DENVs, DENV 2 and DENV 4. A 2-dimensional proteomic analysis identified some 300 protein spots, of which only 11 showed differential expression by both DENVs. Of these, only six were coordinately regulated. One protein, prohibitin 1 (PHB1) was downregulated by infection with both DENVs. Overexpression of PHB1 increased DENV protein expression, level of infection and genome copy number. DENV E protein colocalized with PHB, and there was a direct interaction between DENV 2 E protein and PHB1, but not between DENV 4 E protein and PHB1. The low number of proteins showing coordinate regulation after infection by different DENVs is a cause for concern, particularly in determining new druggable targets, and suggests that studies should routinely investigate multiple DENVs.
Brownian processes in human motor control support descending neural velocity commands
Authors: Tessari Federico , Hermus James , Sugimoto-Dimitrova Rika , Hogan Neville 
Published: April 2024

AbstractThe motor neuroscience literature suggests that the central nervous system may encode some motor commands in terms of velocity. In this work, we tackle the question: what consequences would velocity commands produce at the behavioral level? Considering the ubiquitous presence of noise in the neuromusculoskeletal system, we predict that velocity commands affected by stationary noise would produce “random walks”, also known as Brownian processes, in position. Brownian motions are distinctively characterized by a linearly growing variance and a power spectral density that declines in inverse proportion to frequency. This work first shows that these Brownian processes are indeed observed in unbounded motion tasks e.g., rotating a crank. We further predict that such growing variance would still be present, but bounded, in tasks requiring a constant posture e.g., maintaining a static hand position or quietly standing. This hypothesis was also confirmed by experimental observations. A series of descriptive models are investigated to justify the observed behavior. Interestingly, one of the models capable of accounting for all the experimental results must feature forward-path velocity commands corrupted by stationary noise. The results of this work provide behavioral support for the hypothesis that humans plan the motion components of their actions in terms of velocity.
An easy to use tool for the analysis of subcellular mRNA transcript colocalisation in smFISH data
Authors: Bentley-Abbot Calum , Heslop Rhiannon , Pirillo Chiara , Chandrasegaran Praveena , McConnell Gail , Roberts Ed , Hutchinson Edward , MacLeod Annette 
Published: April 2024

AbstractSingle molecule fluorescence in situ hybridisation (smFISH) has become a valuable tool to investigate the mRNA expression of single cells. However, it requires a considerable amount of programming expertise to use currently available open-source analytical software packages to extract and analyse quantitative data about transcript expression. Here, we present FISHtoFigure, a new software tool developed specifically for the analysis of mRNA abundance and co-expression in QuPath-quantified, multi-labelled smFISH data. FISHtoFigure facilitates the automated spatial analysis of transcripts of interest, allowing users to analyse populations of cells positive for specific combinations of mRNA targets without the need for computational image analysis expertise. As a proof of concept and to demonstrate the capabilities of this new research tool, we have validated FISHtoFigure in multiple biological systems. We used FISHtoFigure to identify an upregulation in the expression of Cd4 by T-cells in the spleens of mice infected with influenza A virus, before analysing more complex data showing crosstalk between microglia and regulatory B-cells in the brains of mice infected with Trypanosoma brucei brucei. These analyses demonstrate the ease of analysing cell expression profiles using FISHtoFigure and the value of this new tool in the field of smFISH data analysis.
Photocatalytic degradation of brilliant green and 4-nitrophenol using Ni-doped Gd(OH)3 nanorods
Authors: Matussin Shaidatul Najihah , Khan Fazlurrahman , Harunsani Mohammad Hilni , Kim Young-Mog , Khan Mohammad Mansoob 
Published: April 2024

AbstractGadolinium hydroxide (Gd(OH)3) was synthesized via a microwave-assisted synthesis method. Nickel ion (Ni2+) was doped into Gd(OH)3, in which 4–12% Ni-Gd(OH)3 was synthesized, to study the effect of doping. The structural, optical, and morphological properties of the synthesized materials were analyzed. The crystallite sizes of the hexagonal structure of Gd(OH)3 and Ni-Gd(OH)3, which were 17–30 nm, were obtained from x-ray diffraction analysis. The vibrational modes of Gd(OH)3 and Ni-Gd(OH)3 were confirmed using Raman and Fourier-transform infrared spectroscopies. The band gap energy was greatly influenced by Ni-doping, in which a reduction of the band gap energy from 5.00 to 3.03 eV was observed. Transmission electron microscopy images showed nanorods of Gd(OH)3 and Ni-Gd(OH)3 and the particle size increased upon doping with Ni2+. Photocatalytic degradations of brilliant green (BG) and 4-nitrophenol (4-NP) under UV light irradiation were carried out. In both experiments, 12% Ni-Gd(OH)3 showed the highest photocatalytic response in degrading BG and 4-NP, which is about 92% and 69%, respectively. Therefore, this study shows that Ni-Gd(OH)3 has the potential to degrade organic pollutants.
Biomarker profiling to determine clinical impact of microRNAs in cognitive disorders
Authors: Zhai Weijie , Zhao Meng , Wei Chunxiao , Zhang Guimei , Qi Yiming , Zhao Anguo , Sun Li 
Published: April 2024

AbstractAlzheimer’s disease (AD) and post-stroke cognitive impairment (PSCI) are the leading causes of progressive dementia related to neurodegenerative and cerebrovascular injuries in elderly populations. Despite decades of research, patients with these conditions still lack minimally invasive, low-cost, and effective diagnostic and treatment methods. MicroRNAs (miRNAs) play a vital role in AD and PSCI pathology. As they are easily obtained from patients, miRNAs are promising candidates for the diagnosis and treatment of these two disorders. In this study, we performed complete sequencing analysis of miRNAs from 24 participants, split evenly into the PSCI, post-stroke non-cognitive impairment (PSNCI), AD, and normal control (NC) groups. To screen for differentially expressed miRNAs (DE-miRNAs) in patients, we predicted their target genes using bioinformatics analysis. Our analyses identified miRNAs that can distinguish between the investigated disorders; several of them were novel and never previously reported. Their target genes play key roles in multiple signaling pathways that have potential to be modified as a clinical treatment. In conclusion, our study demonstrates the potential of miRNAs and their key target genes in disease management. Further in-depth investigations with larger sample sizes will contribute to the development of precise treatments for AD and PSCI.
Synergistic effects of organic carbon and silica in preserving structural stability of drying soils
Authors: Barbosa Luis Alfredo Pires , Stein Mathias , Gerke Horst H. , Schaller Jörg 
Published: April 2024

AbstractPredicted climate warming and prolonged droughts pose a threat to the soil structure as organic carbon losses weaken the stability of soil aggregates. Well-structured soils are important for storage and movement of water, solutes, and air, the development of plant roots, as habitat for soil organisms, and the microbial activity. Structural stability is measured in terms of hydro-mechanical properties. This study compares effects of amorphous silica with those of organic carbon on stability parameters during drying of aggregates from relatively finer- and coarser-textured soils. Silica amendment enhanced the positive effect of organic carbon on structural stability in terms of the tensile strength. Synergistic effects between silica and organic carbon in soil colloids appear to dynamically alter aggregate density and friability (i.e., ability to crumble) during drying. Silica together with organic carbon could help soil management to reduce negative effects of predicted prolonged droughts on soil structure and stability.
Development and validation of a deep learning-based microsatellite instability predictor from prostate cancer whole-slide images
Authors: Hu Qiyuan , Rizvi Abbas A. , Schau Geoffery , Ingale Kshitij , Muller Yoni , Baits Rachel , Pretzer Sebastian , BenTaieb Aïcha , Gordhamer Abigail , Nussenzveig Roberto , Cole Adam , Leavitt Matthew O. , Jones Ryan D. , Joshi Rohan P. , Beaubier Nike , Stumpe Martin C. , Nagpal Kunal 
Published: April 2024

AbstractMicrosatellite instability-high (MSI-H) is a tumor-agnostic biomarker for immune checkpoint inhibitor therapy. However, MSI status is not routinely tested in prostate cancer, in part due to low prevalence and assay cost. As such, prediction of MSI status from hematoxylin and eosin (H&E) stained whole-slide images (WSIs) could identify prostate cancer patients most likely to benefit from confirmatory testing to evaluate their eligibility for immunotherapy and need for Lynch syndrome testing. Prostate biopsies and surgical resections from prostate cancer patients referred to our institution were analyzed. MSI status was determined by next-generation sequencing. Patients sequenced before a cutoff date formed an algorithm development set (n = 4015, MSI-H 1.8%) and a paired validation set (n = 173, MSI-H 19.7%) that consisted of two serial sections from each sample, one stained and scanned internally and the other at an external site. Patients sequenced after the cutoff date formed a temporally independent validation set (n = 1350, MSI-H 2.3%). Attention-based multiple instance learning models were trained to predict MSI-H from H&E WSIs. The predictor achieved area under the receiver operating characteristic curve values of 0.78 (95% CI [0.69–0.86]), 0.72 (95% CI [0.63–0.81]), and 0.72 (95% CI [0.62–0.82]) on the internally prepared, externally prepared, and temporal validation sets, respectively, showing effective predictability and generalization to both external staining/scanning processes and temporally independent samples. While MSI-H status is significantly correlated with Gleason score, the model remained predictive within each Gleason score subgroup.
Paired photoelectrochemical conversion of CO2/H2O and glycerol at high rate
Authors: Balog Ádám , Kecsenovity Egon , Samu Gergely F. , He Jie , Fekete Dávid , Janáky Csaba 
Published: April 2024

AbstractPhotoelectrochemistry holds the promise of directly converting sunlight to valuable chemical products. Photoelectrochemical (PEC) methods, however, lag behind their electrochemical counterparts in terms of current density. In this work, we demonstrate that, by using concentrated sunlight, we can achieve current densities similar to electrochemical methods, but with lower energy input. Specifically, we combined the direct PEC oxidation of glycerol with the dark hydrogen evolution or CO2 reduction in a membrane-separated continuous-flow PEC cell. We achieved over 110 mA cm−2 photocurrent density, which is at least an order of magnitude larger than those typically reported in the literature. We demonstrated that the product distribution of glycerol oxidation is notably different in PEC and electrochemical scenarios at the same current density, and the parasitic oxygen evolution reaction can be suppressed in the PEC case. This approach raises opportunities to drive complex electrochemical reactions in a more selective manner.
Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts
Authors: Felipe Benites L. , Stephens Timothy G. , Van Etten Julia , James Timeeka , Christian William C. , Barry Kerrie , Grigoriev Igor V. , McDermott Timothy R. , Bhattacharya Debashish 
Published: April 2024

AbstractGeothermal springs house unicellular red algae in the class Cyanidiophyceae that dominate the microbial biomass at these sites. Little is known about host-virus interactions in these environments. We analyzed the virus community associated with red algal mats in three neighboring habitats (creek, endolithic, soil) at Lemonade Creek, Yellowstone National Park (YNP), USA. We find that despite proximity, each habitat houses a unique collection of viruses, with the giant viruses, Megaviricetes, dominant in all three. The early branching phylogenetic position of genes encoded on metagenome assembled virus genomes (vMAGs) suggests that the YNP lineages are of ancient origin and not due to multiple invasions from mesophilic habitats. The existence of genomic footprints of adaptation to thermophily in the vMAGs is consistent with this idea. The Cyanidiophyceae at geothermal sites originated ca. 1.5 Bya and are therefore relevant to understanding biotic interactions on the early Earth.
PPARγ alleviates preeclampsia development by regulating lipid metabolism and ferroptosis
Authors: Lai Weisi , Yu Ling , Deng Yali 
Published: April 2024

AbstractThe study aims to explore the effect of PPARγ signaling on ferroptosis and preeclampsia (PE) development. Serum and placental tissue are collected from healthy subjects and PE patients. The PPARγ and Nrf2 decreases in the PE. Rosiglitazone intervention reverses hypoxia-induced trophoblast ferroptosis and decreases lipid synthesis by regulating Nfr2 and SREBP1. Compared to the Hypoxia group, the migratory and invasive abilities enhance after rosiglitazone and ferr1 treatment. Rosiglitazone reduces the effect of hypoxia and erastin. The si-Nrf2 treatment attenuats the effects of rosiglitazone on proliferation, migration, and invasion. The si-Nrf2 does not affect SREBP1 expression. PPARγ agonists alleviates ferroptosis in the placenta of the PE rats. The study confirms that PPARγ signaling and ferroptosis-related indicators were dysregulated in PE. PPARγ/Nrf2 signaling affects ferroptosis by regulating lipid oxidation rather than SREBP1-mediated lipid synthesis. In conclusion, our study find that PPARγ can alleviate PE development by regulating lipid oxidation and ferroptosis.
A genome-wide association study provides insights into the genetic etiology of 57 essential and non-essential trace elements in humans
Authors: Moksnes Marta R. , Hansen Ailin F. , Wolford Brooke N. , Thomas Laurent F. , Rasheed Humaira , Simić Anica , Bhatta Laxmi , Brantsæter Anne Lise , Surakka Ida , Zhou Wei , Magnus Per , Njølstad Pål R. , Andreassen Ole A. , Syversen Tore , Zheng Jie , Fritsche Lars G. , Evans David M. , Warrington Nicole M. , Nøst Therese H. , Åsvold Bjørn Olav , Flaten Trond Peder , Willer Cristen J. , Hveem Kristian , Brumpton Ben M. 
Published: April 2024

AbstractTrace elements are important for human health but may exert toxic or adverse effects. Mechanisms of uptake, distribution, metabolism, and excretion are partly under genetic control but have not yet been extensively mapped. Here we report a comprehensive multi-element genome-wide association study of 57 essential and non-essential trace elements. We perform genome-wide association meta-analyses of 14 trace elements in up to 6564 Scandinavian whole blood samples, and genome-wide association studies of 43 trace elements in up to 2819 samples measured only in the Trøndelag Health Study (HUNT). We identify 11 novel genetic loci associated with blood concentrations of arsenic, cadmium, manganese, selenium, and zinc in genome-wide association meta-analyses. In HUNT, several genome-wide significant loci are also indicated for other trace elements. Using two-sample Mendelian randomization, we find several indications of weak to moderate effects on health outcomes, the most precise being a weak harmful effect of increased zinc on prostate cancer. However, independent validation is needed. Our current understanding of trace element-associated genetic variants may help establish consequences of trace elements on human health.
Visualizing subcellular changes in the NAD(H) pool size versus redox state using fluorescence lifetime imaging microscopy of NADH
Authors: Song Angela , Zhao Nicole , Hilpert Diana C. , Perry Caroline , Baur Joseph A. , Wallace Douglas C. , Schaefer Patrick M. 
Published: April 2024

AbstractNADH autofluorescence imaging is a promising approach for visualizing energy metabolism at the single-cell level. However, it is sensitive to the redox ratio and the total NAD(H) amount, which can change independently from each other, for example with aging. Here, we evaluate the potential of fluorescence lifetime imaging microscopy (FLIM) of NADH to differentiate between these modalities.We perform targeted modifications of the NAD(H) pool size and ratio in cells and mice and assess the impact on NADH FLIM. We show that NADH FLIM is sensitive to NAD(H) pool size, mimicking the effect of redox alterations. However, individual components of the fluorescence lifetime are differently impacted by redox versus pool size changes, allowing us to distinguish both modalities using only FLIM. Our results emphasize NADH FLIM’s potential for evaluating cellular metabolism and relative NAD(H) levels with high spatial resolution, providing a crucial tool for our understanding of aging and metabolism.
Vaccine-elicited IL-1R signaling results in Th17 TRM-mediated immunity
Authors: Hoffmann Joseph P. , Srivastava Akhilesh , Yang Haoran , Iwanaga Naoki , Remcho T. Parks , Hewes Jenny L. , Sharoff Rayshma , Song Kejing , Norton Elizabeth B. , Kolls Jay K. , McCombs Janet E. 
Published: April 2024

AbstractLung tissue resident memory (TRM) cells are thought to play crucial roles in lung host defense. We have recently shown that immunization with the adjuvant LTA1 (derived from the A1 domain of E. coli heat labile toxin) admixed with OmpX from K. pneumoniae can elicit antigen specific lung Th17 TRM cells that provide serotype independent immunity to members of the Enterobacteriaceae family. However, the upstream requirements to generate these cells are unclear. Single-cell RNA-seq showed that vaccine-elicited Th17 TRM cells expressed high levels of IL-1R1, suggesting that IL-1 family members may be critical to generate these cells. Using a combination of genetic and antibody neutralization approaches, we show that Th17 TRM cells can be generated independent of caspase-1 but are compromised when IL-1α is neutralized. Moreover IL-1α could serve as a molecular adjuvant to generate lung Th17 TRM cells independent of LTA1. Taken together, these data suggest that IL-1α plays a major role in vaccine-mediated lung Th17 TRM generation.
Observation of two-dimensional acoustic bound states in the continuum
Authors: Martí-Sabaté Marc , Li Junfei , Djafari-Rouhani Bahram , Cummer Steven A. , Torrent Dani 
Published: April 2024

AbstractThe design of devices based on acoustic or optical fields requires the fabrication of cavities and structures capable of efficiently trapping these waves. A special type of cavity can be designed to support resonances with a theoretically infinite quality factor, named bound states in the continuum or BICs. The experimental measurement of such modes is still a challenging problem, as they are, by definition, not accessible from external perturbations. Here we report on the theoretical design and experimental realization of a two-dimensional, fully open acoustic resonator supporting BICs. This accidental BIC, whose symmetry is chosen during design by properly tailoring the geometrical properties of the system, is completely accessible and allows for the direct measurement of the whole pressure field and properties. We experimentally demonstrate its existence with high quality factor and field enhancement properties.
Beyond boundaries: governance considerations for climate-driven habitat shifts of highly migratory marine species across jurisdictions
Authors: Santos Bianca S. , Hazen Elliott L. , Welch Heather , Lezama-Ochoa Nerea , Block Barbara A. , Costa Daniel P. , Shaffer Scott A. , Crowder Larry B. 
Published: April 2024

AbstractThe mobile nature of migratory marine animals across jurisdictional boundaries can challenge the management of biodiversity, particularly under global environmental change. While projections of climate-driven habitat change can reveal whether marine species are predicted to gain or lose habitat in the future, geopolitical boundaries and differing governance regimes may influence animals’ abilities to thrive in new areas. Broad geographic movements and diverse governance approaches elicit the need for strong international collaboration to holistically manage and conserve these shared migratory species. In this study, we use data from the Tagging of Pacific Predators program to demonstrate the feasibility of using climate-driven habitat projections to assess species’ jurisdictional redistribution. Focusing on four species (shortfin mako shark, California sea lion, northern elephant seal, and sooty shearwater), we calculate the projected change in core habitat across jurisdictional boundaries throughout the century and highlight associated management implications. Using climate-driven habitat projections from the period of 2001 to 2010, and an RCP 8.5 climate scenario, we found that all four species are projected to face up to a 2.5-10% change in core habitat across jurisdictions in the Northeast Pacific, with the greatest gains of core habitat redistribution within the United States exclusive economic zone and in areas beyond national jurisdiction. Overall, our study demonstrates how efforts to understand the impacts of climate change on species’ habitat use should be expanded to consider how resulting shifts may provoke new management challenges in a legally bounded, yet physically borderless ocean. We discuss governance implications for transboundary habitat redistribution as highly migratory marine species potentially shift across legal jurisdictions, including new ocean areas beyond national judications, considerations which are applicable within and beyond this Pacific case study. Our study also highlights data needs and management strategies to inform high-level conservation strategies, as well as recommendations for using updated tagging data and climate models to build upon this approach in future work.