bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fine-Scale Models of Bee Species Diversity and Habitat in New York State
Authors: Buckner Mark A. , White Erin L. , Howard Timothy G. , Schlesinger Matthew D. , Danforth Bryan N. 
Published: July 2024

AbstractAnthropogenic drivers of global change threaten bee diversity and the ecosystem services bees provide. Despite their importance, the conservation of bee pollinators is complicated by limited and often heavily biased occurrence data. A recent state-wide survey of insect pollinators across New York, United States generated a large spatial dataset of bee species occurrence records from community scientists, historical collections, and survey efforts. Using a combination of the state survey records with occurrence data from across the contiguous United States, we applied an ensemble modeling approach using balanced random forest and small bivariate generalized linear models to predict the distributions of most of the state’s bee species. We predicted the spatial distribution of bee species richness using a stacked species distribution model with climate, land cover, and soil covariates. To inform bee diversity conservation, we predicted spatial variation for each species and groups of species sharing similar life history traits. We also estimated statewide distribution of range-size rarity, ecological uniqueness, and climate exposure. We found that the richness of modeled species is high across the state, with the greatest richness in regions with low soil clay content and intermediate forest cover. The fine spatial scale and extent of our gridded data layers match the scale of conservation action in the state, providing an opportunity to incorporate wild bee diversity into broader statewide conservation planning. Conserving New York State’s bee pollinators is not straightforward, and decisions should be based on broader conservation priorities that incorporate bee biodiversity indicators into decision-making. Here, we encourage the inclusion of these vital pollinators in conservation decisions by leveraging the best available data and methods robust to small sample sizes to provide spatially explicit data products representing the distribution of bee diversity across the state of New York.
Classification of dinosaur footprints using machine learning
Authors: Jones Michael , Lallensack Jens N. , Jarman Ian , Falkingham Peter , Siekmann Ivo 
Published: July 2024

ABSTRACTFossilised dinosaur footprints enable us to study the behaviour of individual dinosaurs as well as interactions between dinosaurs of the same or different species. There are two principal groups of three-toed dinosaurs, ornithopods and theropods. Determining if a footprint is from an ornithopod or a theropod is a challenging problem. Based on a data set of over 300 dinosaur footprints we train several machine learning models for classifying footprints as either ornithopods or theropods. The data are provided in the form of 20 landmarks for representing each footprint which are derived from images. Variable selection using logistic forward regression demonstrates that the selected landmarks are at locations that are intuitively expected to be especially informative locations, such as the top or the bottom of a footprint. Most models show good accuracy but the recall of ornithopods, of which fewer samples were contained in the data set, was generally lower than the recall of theropods. The Multi-Layer Perceptron (MLP) stands out as the model which did best at dealing with the class imbalance. Finally, we investigate which footprints were misclassified by the majority of models. We find that some misclassified samples exhibit features that are characteristic of the other class or have a compromised shape, for example, a middle toe that points to the left or the right rather than straight ahead.
SV2A is expressed in synapse subpopulations in mouse and human brain: implications for PET radiotracer studies
Authors: Wong Theresa , Qiu Zhen , Notman Beverly , Tavares Adriana , Smith Colin , Grant Seth G.N. 
Published: July 2024

AbstractSynapse pathology is a feature of most brain diseases and there is a pressing need to monitor the onset and progression of this pathology using brain imaging in living patients. A major step toward this goal has been the development of small-molecule radiotracers that bind to synaptic vesicle glycoprotein 2A (SV2A) for use in positron emission tomography (PET). Changes in SV2A radiotracer binding in PET are widely interpreted to report differences in the density of all synapses throughout brain regions. Here, we analyse the expression of SV2A at single-synapse resolution across regions of adult mouse and human brain. We find that SV2A is expressed in fewer than 50% of excitatory and inhibitory synapses and that the density of SV2A-positive synapses differs between brain regions. Furthermore, individual synapses differ in their amounts of SV2A. These findings have important implications for the interpretation of PET imaging studies in a clinical setting and point to the need for a detailed understanding of SV2A synaptome architecture in both healthy brain and disease cases where PET imaging is being applied.
Automatic dendritic spine segmentation in widefield fluorescence images reveal synaptic nanostructures distribution with super-resolution imaging
Authors: Zhang Jiahao , Vaidya Rohit , Chung Hee Jung , Selvin Paul R. 
Published: July 2024

SUMMARYDendritic spines are the main sites for synaptic communication in neurons, and alterations in their density, size, and shapes occur in many brain disorders. Current spine segmentation methods perform poorly in conditions with low signal-to-noise and resolution, particularly in the widefield images of thick (⍰ 10 μm) brain slices. Here, we combined two open-source machine-learning models to achieve automatic 3D spine segmentation in widefield diffraction-limited fluorescence images of neurons in thick brain slices. We validated the performance by comparison with manually segmented super-resolution images of spines reconstructed from direct stochastic optical reconstruction microscopy (dSTORM). Lastly, we show an application of our approach by combining spine segmentation from diffraction-limited images with dSTORM of synaptic protein PSD-95 in the same field-of-view. This allowed us to automatically analyze and quantify the nanoscale distribution of PSD-95 inside the spine. Importantly, we found the numbers, but not the average sizes, of synaptic nanomodules and nanodomains increase with spine size.
Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes
Authors: Blaskowski Stephen , Roald Marie , Berube Paul M. , Braakman Rogier , Virginia Armbrust E. 
Published: July 2024

Microbes respond to changes in their environment by adapting their physiology through coordinated adjustments to the expression levels of functionally related genes. To detect these shifts in situ, we developed a sparse tensor decomposition method that derives gene co-expression patterns from inherently complex whole community RNA-sequencing data. Application of the method to metatranscriptomes of the abundant marine cyanobacteriaProchlorococcusandSynechococcusidentified responses to scarcity of two essential nutrients, nitrogen and iron, including increased transporter expression, restructured photosynthesis and carbon metabolism, and mitigation of oxidative stress. Further, expression profiles of the identified gene clusters suggest that both cyanobacteria populations experience simultaneous nitrogen and iron stresses in a transition zone between North Pacific oceanic gyres. The results demonstrate the power of our approach to infer organism responses to environmental pressures, hypothesize functions of uncharacterized genes, and extrapolate ramifications for biogeochemical cycles in a changing ecosystem.TeaserNew analytical approach reveals shifts in gene expression that may help cyanobacteria cope with environmental stressors.
Caregivers’ burden of care during emergency department care transitions among older adults: a mixed methods cohort study
Authors: Germain Nathalie , Jémus-Gonzalez Estephanie , Couture Vanessa , Côté Émilie , Morin Michèle , Toulouse-Fournier Annie , Bert Laetitia , Giguère Raphaëlle , Sinha Samir , Sourial Nadia , Chartier Lucas B. , Witteman Holly O. , Légaré France , Samb Rawane , Turcotte Stéphane , Chandavong Sam , Abrougui Lyna , Robitaille Joanie , Archambault Patrick M. 
Published: July 2024

AbstractObjectiveImproving care transitions for older adults can reduce emergency department (ED) revisits, and the strain placed upon caregivers. We analyzed whether caregivers felt a change in burden following a care transition, and what may be improved to reduce it.MethodsThis mixed-methods observational study nested within LEARNING WISDOM included caregivers of older patients who experienced an ED care transition. Burden was collected with the brief Zarit Burden Interview (ZBI-12), and caregivers commented on the care transition. A qualitative coding scheme of patient care transitions was created to reflect themes important to caregivers. Comments were randomly analyzed until saturation and themes were extracted from the data. We followed both the SRQR and STROBE checklists.ResultsComments from 581 caregivers (mean age (SD) 64.5 (12.3), 68% women) caring for patients (mean age (SD) 77.2 (7.54), 48% women) were analyzed. Caregivers overwhelmingly reported dissatisfaction and unmet service expectations, particularly with home care and domestic help. Communication and follow-up from the ED emerged as an area for improvement. Caregivers who reported an increased level of burden following a care recipient’s care transition had significantly higher ZBI scores than caregivers who self-reported stable burden levels, but not improved burden levels.ConclusionCaregivers with increasing, stable, and improved levels of subjective burden all reported areas for improvement in the care transition process. Themes centering on the capacity to live at home most frequently and may represent serious challenges to caregivers. Addressing these challenges could improve both caregiver burden and care transitions.Key pointsWe analyzed caregivers’ thoughts about emergency department care transitions using both qualitative and quantitative tools.Caregivers reported dissatisfaction and unmet service expectations with home care, domestic help, and coordinating follow-ups.Variance in self-reported subjective caregiver burden corresponds to Zarit Burden Interview (ZBI) scores.
Molecular profiling of primary renal diffuse large B-cell lymphoma unravels a proclivity for immune-privileged organ-tropism
Authors: Künstner Axel , von Kopylow Vera , Lohneis Philipp , Kümmel Matthias , Witte Hanno M. , Bastian Lorenz , Bernard Veronica , Stölting Stephanie , Kusch Kathrin , Krokowski Manuela , von Bubnoff Nikolas , Steinestel Konrad , Arndt Annette , Merz Hartmut , Busch Hauke , Feller Alfred C. , Gebauer Niklas 
Published: July 2024

AbstractPrimary renal manifestations of diffuse large B-cell lymphoma (PR-DLBCL) represent an exceptionally rare variant of the most common type of non-Hodgkin lymphoma (NHL). Insights into PR-DLBCL pathogenesis have been limited to small case series and methodologically limited approaches. The mechanisms driving lymphomagenesis within an organ lacking an intrinsic lymphatic niche and its proclivity for dissemination to immune-privileged sites, including testes and central nervous system, remain poorly understood. To decode the genetic and transcriptional framework of PR-DLBCL, we utilized whole exome sequencing, array-based somatic copy number alterations analysis, and RNA sequencing. Hereby we characterize the most extensive cohort of PR-DLBCL published, comprising 34 samples from 30 patients. Despite significant mutational heterogeneity with a broad distribution among molecular clusters, we observed a strong unifying enrichment in deleterious MHC class I and II aberrations and loss ofCDKN2Aat a frequency similar to primary large B-cell lymphoma of immune privileged sites (IP-LBCL) alongside significant transcriptional deregulation of interferon signaling and MYC targets in MHC class I-deficient cases.Our integrative assessment of PR-DLBCL biology expands the molecular understanding of this rare variant including similarities with IP-LBCL as an intriguing explanation for its clinical behavior and tropism. Our observations may inform future risk-adapted therapeutic approaches.
Clinical outcomes of flomoxef versus cefmetazole in hospitalized patients with urinary tract infections: Combined retrospective analyses of two real-world databases andin vitrodata
Authors: Niimura Takahiro , Goda Mitsuhiro , Nakano Satoshi , Kajihara Toshiki , Yahara Koji , Hirabayashi Aki , Miyata Koji , Ikai Marie , Shinohara Motoko , Minato Yusuke , Suzuki Masato , Ishizawa Keisuke 
Published: July 2024

AbstractBackgroundFlomoxef is active against extended-spectrum beta-lactamase (ESBL)-producing bacteria, but its clinical effectiveness has not been compared with cefmetazole. This study aimed to compare the utility of the two drugs in treating urinary tract infection (UTI) by integratingin vitrodata with a retrospective analysis of two real-world databases.MethodsThe susceptibility rates of third-generation cephalosporin-resistantEscherichia coliandKlebsiella pneumoniaeto flomoxef and cefmetazole were compared using comprehensive national antimicrobial resistance surveillance data. Combinational antimicrobial activities against an ESBL-producing multidrug-resistant bacterial strain were tested by diagonal measurement of n-way drug interactions (DiaMOND), an innovative method to assess antimicrobial interactionsin vitro. The effectiveness of the two drugs in treating UTIs was compared using hospital stay duration as the primary outcome obtained from the Japan Medical Data Center (JMDC) Claims Database.ResultsThird-generation cephalosporin-resistantE. coliandK. pneumoniae, including ESBL-producing strains, were similarly susceptible to flomoxef and cefmetazole.In vitroassessment of combinational antimicrobial activities against an ESBL-producing multidrug-resistant strain revealed that both drugs showed similar antimicrobial interaction patterns.JMDC Claims data analysis showed that the median time of hospital stay duration was 11 days (95% confidence interval [CI]: 11–11) in the cefmetazole group and 4 days (95% CI: 3– 5) in the flomoxef group, significantly shorter in the latter (log-rank test, P < 0.001). In addition, the flomoxef group had a significantly lower frequency of adverse events such asClostridioides difficileinfection.ConclusionsFlomoxef exhibits effectiveness that is comparable to cefmetazole in treating UTI without major concerns about adverse events such asC. difficileinfection or renal impairment. This evidence endorses flomoxef as a viable treatment option for UTIs in locales with high prevalence of ESBL-prodcing strains.Key PointsAn oxacephem antimicrobial agent, flomoxef, exhibited effectiveness comparable to cefmetazole in the treatment of urinary tract infections and was superior in terms of safety.
Epigenome-wide association study for dilated cardiomyopathy in left ventricular heart tissue identifies putative gene sets associated with cardiac development and early indicators of cardiac risk
Authors: Tan Konstanze , Tay Darwin , Tan Wilson , Ng Hong Kiat , Wong Eleanor , Morley Michael P , Singhera Gurpreet K , Jain Pritesh R , Tai Fei Li , Hanson Paul J , Cappola Thomas P , Margulies Kenneth B , Foo Roger , Loh Marie 
Published: July 2024

ABSTRACTBackgroundMethylation changes linked to dilated cardiomyopathy (DCM) affect cardiac gene expression. We investigate DCM mechanisms regulated by CpG methylation using multi-omics and causal analyses in the largest cohort of left ventricular tissues available.MethodsWe mapped DNA methylation at ∼850,000 CpG sites, performed array-based genotyping and RNA sequencing in left-ventricular tissue samples from failing and non-failing hearts across two independent DCM cohorts (discovery n=329, replication n=85). Summary data-based Mendelian Randomization (SMR) was applied to explore the causal contribution of sentinel CpGs to DCM. Fine-mapping of regions surrounding sentinel CpGs revealed additional signals for cardiovascular disease risk factors. Coordinated changes across multiple CpG sites were examined using weighted gene correlation network analysis (WGCNA).ResultsWe identified 194 epigenome-wide significant CpGs associated with DCM (discovery P<5.96E-08), enriched in active chromatin states in heart tissue. Amongst these, 183 sentinel CpGs significantly influenced the expression of 849 proximal genes (±1Mb). SMR suggested the causal contribution of two sentinel CpGs to DCM and 36 sentinel CpGs to the expression of 43 unique proximal genes (P<0.05). Colocalization analyses indicated that a single causal variant may underlie the methylation-gene expression relationship for three sentinel CpGs. Fine-mapping revealed additional signals linked to cardiovascular traits including hsCRP and blood pressure. Co-methylation modules were enriched in genes related to cardiac physiological and pathological processes and their corresponding transcriptional regulators.ConclusionsUsing the largest series of left ventricular tissue to date, this study investigates the causal role of cardiac methylation changes in DCM and suggests targets for experimental studies to probe DCM pathogenesis.
Prkra dimer senses double-stranded RNAs to dictate global translation efficiency
Authors: Lu Tong , Ma Pengcheng , Chen Aijun , Fang Hailing , Xu Jianlin , Wang Mingyu , Su Ling , Wang Sen , Zhang Yizhuang , Wang Jiasheng , Yang Boya , Shi De-Li , Zhou Yong , Gong Qianqian , Liu Xiangguo , Mao Bingyu , Shao Ming 
Published: July 2024

AbstractDouble-stranded RNAs (dsRNAs), known as conserved pathogen-associated molecular patterns, are recognized by interferon-induced protein kinase R (PKR) to trigger an integrated stress response, characterized by the inhibition of global translation. However, the interferon system is inactive in pluripotent cells, thus the mechanism underlying dsRNA sensing and translational control is unclear. In this study, we utilized early zebrafish embryos as a model of pluripotent cells and discovered a PKR-independent blockage of translation initiation induced by dsRNA stimulation. Prkra dimer was identified as the genuine dsRNA sensor. Upon binding to dsRNAs, the dimerized dsRNA binding domain 3 becomes activated to sequester the eIF2 complexes from the translation machinery, leading to a hindrance in global protein synthesis. This distinctive embryonic stress response restricts RNA virus SVCV replication in zebrafish embryos but is also conserved in early mouse embryos and embryonic stem cells. Therefore, the Prkra-mediated dsRNA sensing and translation blocking mechanism potentially represents a common strategy for reestablishing physiological homeostasis in response to environmental stresses.
The catheterized bladder environment induces dysregulation of macrophage polarization exacerbating bacterial UTI
Authors: Marrufo Armando M. , Molina Jonathan J. , Gager Chris , Andersen Marissa J. , LaBella Alyssa A. , Lucas Elizabeth R. , Wongso Ellsa , Urmi Tamanna , Arias-Parbul Kassandra , Webster Railyn , Stuckey Peter V. , Kohler Kurt N. , Donahue Deborah , Ploplis Victoria A. , Flick Matthew J. , Castellino Francis J. , Santiago-Tirado Felipe H. , Flores-Mireles Ana L. 
Published: July 2024

AbstractUrinary catheterization causes bladder damage, predisposing hosts to catheter-associated urinary tract infections (CAUTIs). CAUTI pathogenesis is mediated by bladder damage-induced inflammation, resulting in accumulation and deposition of the blood-clotting protein fibrinogen (Fg) and its matrix form fibrin, which are exploited by uropathogens as biofilm platforms to establish infection. Catheter-induced inflammation also results in robust immune cell recruitment, including macrophages (Mϕs). A fundamental knowledge gap is understanding the mechanisms by which the catheterized-bladder environment suppresses the Mϕ antimicrobial response, allowing uropathogen persistence. Here, we found that Fg and fibrin differentially modulate M1 and M2 Mϕ polarization, respectively. We unveiled that fibrin accumulation in catheterized mice induced an anti-inflammatory M2-like Mϕ phenotype, correlating with pathogen persistence. Even GM-CSF treatment of wildtype mice to promote M1 polarization was not sufficient to reduce bacterial burden and dissemination, indicating that the catheterized-bladder environment provides mixed signals, dysregulating Mϕ polarization, hindering its antimicrobial response against uropathogens.
Additive and partially dominant effects from genomic variation contribute to rice heterosis
Authors: Dan Zhiwu , Chen Yunping , Zhou Wei , Xu Yanghong , Huang Junran , Chen Yi , Meng Jizhou , Yao Guoxin , Huang Wenchao 
Published: July 2024

AbstractBackgroundThe molecular mechanisms of heterosis remain debated due to discrepancies in factors such as species, phenotypes, hybrid populations, developmental stages or growth environments.ResultsHere, we screened heterosis-associated genes and metabolites from molecular differences in rice inbred lines and found that the phenylpropanoid biosynthesis was involved in heterosis. The main inheritance patterns of the heterosis-associated molecules were additive and partially dominant effects, namely, at the mid-parent levels and between the parental and mid-parent levels. The additive and partially dominant effects contributed to heterosis of 17 agronomic traits in rice, including grain yield and plant height across developmental stages, and to heterosis of F1hybrids from different populations and growth environments in both rice and maize. Furthermore, the two inheritance patterns were associated with parental genomic variants, which were correlated with heterosis of agronomic traits.ConclusionsOur study systematically integrates parental genetic variation and highlights the predominant effects of additive and partially dominant in rice heterosis.