bluuebunny/crossref_metadata_2025_split huggingface dataset:
A global ecological signal of extinction risk in marine ray-finned fishes (class Actinopterygii)
Authors: Bak Trevor M. , Camp Richard J. , Heim Noel A. , McCauley Douglas J. , Payne Jonathan L. , Knope Matthew L. 
Published: November 2023

Abstract
Many marine fish species are experiencing population declines, but their extinction risk profiles are largely understudied in comparison to their terrestrial vertebrate counterparts. Selective extinction of marine fish species may result in rapid alteration of the structure and function of ocean ecosystems. In this study, we compiled an ecological trait dataset for 8,185 species of marine ray-finned fishes (class Actinopterygii) from FishBase and used phylogenetic generalized linear models to examine which ecological traits are associated with increased extinction risk, based on the International Union for the Conservation of Nature Red List. We also assessed which threat types may be driving these species toward greater extinction risk and whether threatened species face a greater average number of threat types than non-threatened species. We found that larger body size and/or fishes with life histories involving movement between marine, brackish, and freshwater environments are associated with elevated extinction risk. Commercial harvesting threatens the greatest number of species, followed by pollution, development, and then climate change. We also found that threatened species, on average, face a significantly greater number of threat types than non-threatened species. These results can be used by resource managers to help address the heightened extinction risk patterns we found.
Involuntary memory signals in the medial temporal lobe
Authors: Yang Haopei , Martin Chris B. , Köhler Stefan 
Published: November 2023

Abstract
We highlight recent progress in neuroimaging and neuropsychological research on memory mechanisms in the medial temporal lobe that speaks to the involuntary nature of memory retrieval processes. We suggest that evidence form these studies supports Barzykowski and Moulin's proposal that memory signals involved in experiences of familiarity and déjà vu can be generated in the absence of retrieval intentionality.
Sediment Compaction in Experimental Deltas: Toward a Meso‐Scale Understanding of Coastal Subsidence Patterns
Authors: Zapp Samuel M. , Sanks Kelly M. , Silvestre Jose , Shaw John B. , Dutt Ripul , Straub Kyle M. 
Published: November 2023

AbstractWe present the first investigation of subsidence due to sediment compaction and consolidation in two laboratory‐scale river delta experiments. Spatial and temporal trends in subsidence rates in the experimental setting may elucidate behavior which cannot be directly observed at sufficiently long timescales, except for in reduced scale models such as the ones studied. We compare subsidence between a control experiment using steady boundary conditions, and an otherwise identical experiment which has been treated with a proxy for highly compressible marsh deposits. Both experiments have non‐negligible compactional subsidence rates across the delta‐top, comparable in magnitude to our boundary condition relative sea level rise rate of 250 μm/hr. Subsidence in the control experiment (on average 54 μm/hr) is concentrated in the lowest elevation (<10 mm above sea level) areas near the coast and is likely related to creep induced by a rising water table near the shoreface. The treatment experiment exhibits larger (on average 126 μm/hr) and more spatially variable subsidence rates controlled mostly by compaction of recent marsh deposits within one channel depth (∼10 mm) of the sediment surface. These rates compare favorably with field and modeling based subsidence measurements both in relative magnitude and location. We find that subsidence “hot spots” may be relatively ephemeral on longer timescales, but average subsidence across the entire delta can be variable even at our shortest measurement window. This suggests that subsidence rates over a short time frame may exceed thresholds for marsh platform drowning, even if the long term trend does not.
The long noncoding RNA nHOTAIRM1 is necessary for differentiation and activity of iPSC-derived spinal motor neurons
Authors: Tollis Paolo , Vitiello Erika , Migliaccio Francesco , D’Ambra Eleonora , Rocchegiani Anna , Garone Maria Giovanna , Bozzoni Irene , Rosa Alessandro , Carissimo Annamaria , Laneve Pietro , Caffarelli Elisa 
Published: November 2023

AbstractThe mammalian nervous system is made up of an extraordinary array of diverse cells that form intricate functional connections. The programs underlying cell lineage specification, identity and function of the neuronal subtypes are managed by regulatory proteins and RNAs, which coordinate the succession of steps in a stereotyped temporal order. In the central nervous system (CNS), motor neurons (MNs) are responsible for controlling essential functions such as movement, breathing, and swallowing by integrating signal transmission from the cortex, brainstem, and spinal cord (SC) towards peripheral muscles. A prime role in guiding the progression of progenitor cells towards the MN fate has been largely attributed to protein factors. More recently, the relevance of a class of regulatory RNAs abundantly expressed in the CNS - the long noncoding RNAs (lncRNAs) - has emerged overwhelmingly. LncRNA-driven gene expression control is key to regulating any step of MN differentiation and function, and its derangement profoundly impacts neuronal pathophysiology. Here, we uncover a novel function for the neuronal isoform of HOTAIRM1 (nHOTAIRM1), a lncRNA specifically expressed in the SC. Using a model system that recapitulates spinal MN (spMN) differentiation, we show that nHOTAIRM1 intervenes in the binary cell fate decision between MNs and interneurons, acting as a pro-MN factor. Furthermore, human iPSC-derived spMNs without nHOTAIRM1 display altered neurite outgrowth, with a significant reduction of both branch and junction numbers. Finally, the expression of genes essential for synaptic connectivity and neurotransmission is also profoundly impaired when nHOTAIRM1 is absent in spMNs. Mechanistically, nHOTAIRM1 establishes both direct and indirect interactions with a number of target genes in the cytoplasm, being a novel post-transcriptional regulator of MN biology. Overall, our results indicate that the lncRNA nHOTAIRM1 is essential for the specification of MN identity and the acquisition of proper morphology and synaptic activity of post-mitotic MNs.
Mechanistic insights into glycoside 3-oxidases involved in C-glycoside metabolism in soil microorganisms
Authors: Taborda André , Frazão Tomás , Rodrigues Miguel V. , Fernández-Luengo Xavier , Sancho Ferran , Lucas Maria Fátima , Frazão Carlos , Melo Eduardo P. , Ventura M. Rita , Masgrau Laura , Borges Patrícia T. , Martins Lígia O. 
Published: November 2023

AbstractC-glycosides are natural products with important biological activities but are recalcitrant to degradation. Glycoside 3-oxidases (G3Oxs) are recently identified bacterial flavo-oxidases from the glucose-methanol-coline (GMC) superfamily that catalyze the oxidation of C-glycosides with the concomitant reduction of O2 to H2O2. This oxidation is followed by C-C acid/base-assisted bond cleavage in two-step C-deglycosylation pathways. Soil and gut microorganisms have different oxidative enzymes, but the details of their catalytic mechanisms are largely unknown. Here, we report that PsG3Ox oxidizes at 50,000-fold higher specificity (kcat/Km) the glucose moiety of mangiferin to 3-keto-mangiferin than free D-glucose to 2-keto-glucose. Analysis of PsG3Ox X-ray crystal structures and PsG3Ox in complex with glucose and mangiferin, combined with mutagenesis and molecular dynamics simulations, reveal distinctive features in the topology surrounding the active site that favor catalytically competent conformational states suitable for recognition, stabilization, and oxidation of the glucose moiety of mangiferin. Furthermore, their distinction to pyranose 2-oxidases (P2Oxs) involved in wood decay and recycling is discussed from an evolutionary, structural, and functional viewpoint.
The GET insertase exhibits conformational plasticity and induces membrane thinning
Authors: McDowell Melanie A. , Heimes Michael , Enkavi Giray , Farkas Ákos , Saar Daniel , Wild Klemens , Schwappach Blanche , Vattulainen Ilpo , Sinning Irmgard 
Published: November 2023

AbstractThe eukaryotic guided entry of tail-anchored proteins (GET) pathway mediates the biogenesis of tail-anchored (TA) membrane proteins at the endoplasmic reticulum. In the cytosol, the Get3 chaperone captures the TA protein substrate and delivers it to the Get1/Get2 membrane protein complex (GET insertase), which then inserts the substrate via a membrane-embedded hydrophilic groove. Here, we present structures, atomistic simulations and functional data of human and Chaetomium thermophilum Get1/Get2/Get3. The core fold of the GET insertase is conserved throughout eukaryotes, whilst thinning of the lipid bilayer occurs in the vicinity of the hydrophilic groove to presumably lower the energetic barrier of membrane insertion. We show that the gating interaction between Get2 helix α3’ and Get3 drives conformational changes in both Get3 and the Get1/Get2 membrane heterotetramer. Thus, we provide a framework to understand the conformational plasticity of the GET insertase and how it remodels its membrane environment to promote substrate insertion.
TLR7 promotes smoke-induced experimental lung damage through the activity of mast cell tryptase
Authors: Liu Gang , Haw Tatt Jhong , Starkey Malcolm R. , Philp Ashleigh M. , Pavlidis Stelios , Nalkurthi Christina , Nair Prema M. , Gomez Henry M. , Hanish Irwan , Hsu Alan CY. , Hortle Elinor , Pickles Sophie , Rojas-Quintero Joselyn , Estepar Raul San Jose , Marshall Jacqueline E. , Kim Richard Y. , Collison Adam M. , Mattes Joerg , Idrees Sobia , Faiz Alen , Hansbro Nicole G. , Fukui Ryutaro , Murakami Yusuke , Cheng Hong Sheng , Tan Nguan Soon , Chotirmall Sanjay H. , Horvat Jay C. , Foster Paul S. , Oliver Brian GG. , Polverino Francesca , Ieni Antonio , Monaco Francesco , Caramori Gaetano , Sohal Sukhwinder S. , Bracke Ken R. , Wark Peter A. , Adcock Ian M. , Miyake Kensuke , Sin Don D. , Hansbro Philip M. 
Published: November 2023

AbstractToll-like receptor 7 (TLR7) is known for eliciting immunity against single-stranded RNA viruses, and is increased in both human and cigarette smoke (CS)-induced, experimental chronic obstructive pulmonary disease (COPD). Here we show that the severity of CS-induced emphysema and COPD is reduced in TLR7-deficient mice, while inhalation of imiquimod, a TLR7-agonist, induces emphysema without CS exposure. This imiquimod-induced emphysema is reduced in mice deficient in mast cell protease-6, or when wild-type mice are treated with the mast cell stabilizer, cromolyn. Furthermore, therapeutic treatment with anti-TLR7 monoclonal antibody suppresses CS-induced emphysema, experimental COPD and accumulation of pulmonary mast cells in mice. Lastly,TLR7mRNA is increased in pre-existing datasets from patients with COPD, while TLR7+mast cells are increased in COPD lungs and associated with severity of COPD. Our results thus support roles for TLR7 in mediating emphysema and COPD through mast cell activity, and may implicate TLR7 as a potential therapeutic target.
Microscopic theory of colour in lutetium hydride
Authors: Kim Sun-Woo , Conway Lewis J. , Pickard Chris J. , Pascut G. Lucian , Monserrat Bartomeu 
Published: November 2023

AbstractNitrogen-doped lutetium hydride has recently been proposed as a near-ambient-conditions superconductor. Interestingly, the sample transforms from blue to pink to red as a function of pressure, but only the pink phase is claimed to be superconducting. Subsequent experimental studies have failed to reproduce the superconductivity, but have observed pressure-driven colour changes including blue, pink, red, violet, and orange. However, discrepancies exist among these experiments regarding the sequence and pressure at which these colour changes occur. Given the claimed relationship between colour and superconductivity, understanding colour changes in nitrogen-doped lutetium hydride may hold the key to clarifying the possible superconductivity in this compound. Here, we present a full microscopic theory of colour in lutetium hydride, revealing that hydrogen-deficient LuH2is the only phase which exhibits colour changes under pressure consistent with experimental reports, with a sequence blue-violet-pink-red-orange. The concentration of hydrogen vacancies controls the precise sequence and pressure of colour changes, rationalising seemingly contradictory experiments. Nitrogen doping also modifies the colour of LuH2but it plays a secondary role compared to hydrogen vacancies. Therefore, we propose hydrogen-deficient LuH2as the key phase for exploring the superconductivity claim in the lutetium-hydrogen system. Finally, we find no phonon-mediated superconductivity near room temperature in the pink phase.
Imaging cellular forces with photonic crystals
Authors: Li Qiwei , Chen Zaozao , Zhang Ying , Ding Shuang , Ding Haibo , Wang Luping , Xie Zhuoying , Fu Yifu , Wei Mengxiao , Liu Shengnan , Chen Jialun , Wang Xuan , Gu Zhongze 
Published: November 2023

AbstractCurrent techniques for visualizing and quantifying cellular forces have limitations in live cell imaging, throughput, and multi-scale analysis, which impede progress in cell force research and its practical applications. We developed a photonic crystal cellular force microscopy (PCCFM) to image vertical cell forces over a wide field of view (1.3 mm ⨯ 1.0 mm, a 10 ⨯ objective image) at high speed (about 20 frames per second) without references. The photonic crystal hydrogel substrate (PCS) converts micro-nano deformations into perceivable color changes, enabling in situ visualization and quantification of tiny vertical cell forces with high throughput. It enabled long-term, cross-scale monitoring from subcellular focal adhesions to tissue-level cell sheets and aggregates.
Dietary L-Tryptophan consumption determines the number of colonic regulatory T cells and susceptibility to colitis via GPR15
Authors: Van Nguyen T. , Zhang Karen , Wigmore Rachel M. , Kennedy Anne I. , DaSilva Carolina R. , Huang Jialing , Ambelil Manju , Villagomez Jose H. , O’Connor Gerald J. , Longman Randy S. , Cao Miao , Snook Adam E. , Platten Michael , Kasenty Gerard , Sigal Luis J. , Prendergast George C. , Kim Sangwon V. 
Published: November 2023

AbstractEnvironmental factors are the major contributor to the onset of immunological disorders such as ulcerative colitis. However, their identities remain unclear. Here, we discover that the amount of consumed L-Tryptophan (L-Trp), a ubiquitous dietary component, determines the transcription level of the colonic T cell homing receptor, GPR15, hence affecting the number of colonic FOXP3+ regulatory T (Treg) cells and local immune homeostasis. Ingested L-Trp is converted by host IDO1/2 enzymes, but not by gut microbiota, to compounds that induce GPR15 transcription preferentially in Treg cells via the aryl hydrocarbon receptor. Consequently, two weeks of dietary L-Trp supplementation nearly double the colonic GPR15+ Treg cells via GPR15-mediated homing and substantially reduce the future risk of colitis. In addition, humans consume 3–4 times less L-Trp per kilogram of body weight and have fewer colonic GPR15+ Treg cells than mice. Thus, we uncover a microbiota-independent mechanism linking dietary L-Trp and colonic Treg cells, that may have therapeutic potential.
Epidermal growth factor receptor activation is essential for kidney fibrosis development
Authors: Cao Shirong , Pan Yu , Terker Andrew S. , Arroyo Ornelas Juan Pablo , Wang Yinqiu , Tang Jiaqi , Niu Aolei , Kar Sarah Abu , Jiang Mengdi , Luo Wentian , Dong Xinyu , Fan Xiaofeng , Wang Suwan , Wilson Matthew H. , Fogo Agnes , Zhang Ming-Zhi , Harris Raymond C. 
Published: November 2023

AbstractFibrosis is the progressive accumulation of excess extracellular matrix and can cause organ failure. Fibrosis can affect nearly every organ including kidney and there is no specific treatment currently. Although Epidermal Growth Factor Receptor (EGFR) signaling pathway has been implicated in development of kidney fibrosis, underlying mechanisms by which EGFR itself mediates kidney fibrosis have not been elucidated. We find that EGFR expression increases in interstitial myofibroblasts in human and mouse fibrotic kidneys. Selective EGFR deletion in the fibroblast/pericyte population inhibits interstitial fibrosis in response to unilateral ureteral obstruction, ischemia or nephrotoxins. In vivo and in vitro studies and single-nucleus RNA sequencing analysis demonstrate that EGFR activation does not induce myofibroblast transformation but is necessary for the initial pericyte/fibroblast migration and proliferation prior to subsequent myofibroblast transformation by TGF-ß or other profibrotic factors. These findings may also provide insight into development of fibrosis in other organs and in other conditions.
The evolution of the COVID-19 pandemic through the lens of google searches
Authors: Marty Robert , Ramos-Maqueda Manuel , Khan Nausheen , Reichert Arndt 
Published: November 2023

AbstractReal-time data is essential for policymakers to adapt to a rapidly evolving situation like the COVID-19 pandemic. Using data from 221 countries and territories, we demonstrate the capacity of Google search data to anticipate reported COVID-19 cases and understand how containment policies are associated with changes in socioeconomic indicators. First, search interest in COVID-specific symptoms such as “loss of smell” strongly correlated with cases initially, but the association diminished as COVID-19 evolved; general terms such as “COVID symptoms” remained strongly associated with cases. Moreover, trends in search interest preceded trends in reported cases, particularly in the first year of the pandemic. Second, countries with more restrictive containment policies experienced greater search interest in unemployment and mental health terms after policies were implemented, indicating socio-economic externalities. Higher-income countries experienced a larger increase in searches related to unemployment and a larger reduction in relationship and family planning keywords relative to lower-income countries. The results demonstrate that real-time search interest can be a valuable tool to inform policies across multiple stages of the pandemic.
Asbestos-related cancer in naval personnel: findings from participants in the British nuclear tests 1952–1967
Authors: Gun Richard T. , Kendall Gerry M. 
Published: November 2023

AbstractAsbestos-containing materials (ACM) were present in British and Australian naval vessels throughout the twentieth century. The aim of this study was to identify and quantify the incidence of cancer in naval personnel from onboard asbestos exposure. Subjects were four cohorts of subjects who had served in the armed forces of the United Kingdom and Australia in the 1950s and 1960s. All cohorts had previously been studied, three of them in relation to radiation exposures from British nuclear testing. Comparisons of SIRs between services were made to identify cancers attributable to asbestos exposure. Excess mesotheliomas were found in naval personnel in all cohorts. In all but one cohort the lung cancer incidence was highest in navy personnel. Comparison of other smoking-related conditions indicated that the excess in navy personnel was not smoking-related. The relatively high SIRs for mesothelioma and the occurrence of deaths from asbestosis were indicative of high levels of asbestos exposure, with an expectation of cases of asbestos-related lung cancer. The findings are consistent with the occurrence of significant excesses of mesotheliomas. In addition, notwithstanding some inconsistencies in the results between the cohorts, we estimated that approximately 27% of lung cancers in Australian seamen and 12% in British seamen were related to onboard asbestos exposure.
Efficient estimation of population variance of a sensitive variable using a new scrambling response model
Authors: Saleem Iram , Sanaullah Aamir , Al-Essa Laila A. , Bashir Shakila , Al Mutairi Aned 
Published: November 2023

AbstractThis study introduces a pioneering scrambling response model tailored for handling sensitive variables. Subsequently, a generalized estimator for variance estimation, relying on two auxiliary information sources, is developed following this novel model. Analytical expressions for bias, mean square error, and minimum mean square error are meticulously derived up to the first order of approximation, shedding light on the estimator’s statistical performance. Comprehensive simulation experiments and empirical analysis unveil compelling results. The proposed generalized estimator, operating under both scrambling response models, consistently exhibits minimal mean square error, surpassing existing estimation techniques. Furthermore, this study evaluates the level of privacy protection afforded to respondents using this model, employing a robust framework of simulations and empirical studies.
Genome-wide transcriptional profiling and physiological investigation elucidating the molecular mechanism of multiple abiotic stress response in Stevia rebaudiana Bertoni
Authors: Pal Poonam , Masand Mamta , Sharma Shikha , Seth Romit , Singh Gopal , Singh Sanatsujat , Kumar Ashok , Sharma Ram Kumar 
Published: November 2023

AbstractConsidering the major source of plant-derived low/non-calorie steviol glycosides (SGs), comprehensive physiological, biochemical, and deep transcriptional investigations were conducted to explicit deeper insight into multiple abiotic stress responses in Stevia rebaudiana. The physiological indicators including photosynthesis, chlorophyll, relative water content, shoot growth, electrolyte leakage, and SG biosynthesis were negatively impacted under drought (DS), followed by salinity (SS) and waterlogging (WS). Global transcriptional analysis revealed significant upregulated expression of the genes encoding for ROS detoxification (GST, SOD, APX, glutathione peroxidase), osmotic adjustment (alpha-trehalose-phosphate and S-adenosylmethionine decarboxylase), ion transporters (CAX, NHX, CNGS, VPPase, VATPase), water channel (PIP1, TIP) and abiotic stress-responsive candidate genes (LEA, HSPs, and Dehydrins) regulating abiotic stress response in S. rebaudiana. These inferences were complemented with predicted interactome network that revealed regulation of energy metabolism by key stress-responsive genes (GST, HKT1, MAPKs, P5CSs, PIP), transcription factors (HSFA2, DREB1A, DREB2A), and abiotic stress responsive pathways (ABA, ethylene, ion stress). This is the first detailed study to comprehend the molecular regulation of stress response and their interplay under DS, SS, and WS. The key genes and regulators can be functionally validated, and will facilitate targeted gene editing for genetic improvement of crop sustainability under changing environmental conditions in S. rebaudiana.