bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated Workflows using Quantitative Colour Pattern Analysis (QCPA): A Guide to Batch Processing and Downstream Data Analysis
Authors: van den Berg Cedric P. , Condon Nicholas D. , Conradsen Cara , White Thomas E. , Cheney Karen L. 
Published: February 2023

AbstractAnimal and plant colouration presents a striking dimension of phenotypic variation, the study of which has driven general advances in ecology, evolution, and animal behaviour. Quantitative Colour Pattern Analysis (QCPA) is a dynamic framework for analysing colour patterns through the eyes of non-human observers. However, its extensive array of user-defined image processing and analysis tools means image analysis is often time-consuming. This hinders the full use of analytical power provided by QCPA and its application to large datasets. Here, we offer a robust and comprehensive batch script, allowing users to automate many QCPA workflows. We further provide a set of useful R scripts for downstream data extraction and analysis. These scripts will empower users to exploit the full analytical power of QCPA and facilitate the development of customised semi-automated workflows. Such quantitatively scaled workflows are crucial for exploring colour pattern space and developing ever-richer frameworks for analysing organismal colouration accounting for the visual perception in animals other than humans. These advances will, in turn, facilitate testing hypotheses on the function and evolution of vision and signals at quantitative and qualitative scales, which are otherwise computationally unfeasible.
Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices
Authors: Wang Gefei , Zhao Jia , Yan Yan , Wang Yang , Wu Angela Ruohao , Yang Can 
Published: February 2023

AbstractSpatial transcriptomics (ST) technologies are revolutionizing the way that researchers explore the spatial architecture of tissues. Currently, ST data analysis is often restricted to 2D space within a single tissue slice, limiting our capacity to understand biological processes that take place in 3D space. Here, we present STitch3D, a unified computational framework that integrates multiple 2D tissue slices to reconstruct 3D cellular structures from the tissue level to the whole organism level. By jointly modeling multiple 2D tissue slices and integrating them with cell-type-specific expression profiles derived from single-cell RNA-sequencing data, STitch3D simultaneously identifies 3D spatial regions with coherent gene expression levels and reveals 3D distributions of cell types. STitch3D distinguishes biological variation among slices from batch effects, and effectively borrows shared information across slices to assemble powerful 3D models of tissues. Through comprehensive experiments using diverse datasets, we demonstrate the performance of STitch3D in building comprehensive 3D tissue architectures of the mouse brain, the human heart, and theDrosophilaembryo, which allow 3D analysis in the entire tissue region or even the whole organism. To gain deeper biological insights, the outputs of STitch3D can be used for downstream tasks, such as inference of spatial trajectories, identification of spatially variable genes enriched in tissue regions or subregions, denoising or imputation of spatial gene expressions, as well as generation of virtual tissue slices.
Bifurcation Left Main Stenting with or without intracoronary imaging: Outcomes From the EBC MAIN trial
Authors: Maznyczka Annette , Arunothayaraj Sandeep , Egred Mohaned , Banning Adrian , Brunel Philippe , Ferenc Miroslaw , Hovasse Thomas , Wlodarczak Adrian , Pan Manuel , Schmitz Thomas , Silvestri Marc , Erglis Andrejs , Kretov Evgeny , Lassen Jens Flensted , Chieffo Alaide , Lefevre Thierry , Burzotta Francesco , Cockburn James , Darremont Olivier , Stankovic Goran , Morice Marie-Claude , Louvard Yves , Hildick-Smith David ,   the EBC MAIN (European Bifurcation Club Left Main Coronary Stent study) investigators
Published: February 2023

AbstractBackgroundThe impact of intracoronary imaging on outcomes, after provisional versus dual-stenting for bifurcation left main (LM) lesions, is unknown.ObjectivesWe investigated the effect of intracoronary imaging in the EBC MAIN trial (European Bifurcation Club Left Main Coronary Stent study).Methods467 patients were randomised to dual-stenting or a stepwise provisional strategy. 455 patients were included. Intravascular ultrasound (IVUS) or optical coherence tomography (OCT) was undertaken at the operator’s discretion. The primary endpoint was death, myocardial infarction or target vessel revascularisation at 1-year.ResultsIntracoronary imaging was undertaken in 179 patients (39%; IVUS n=151, OCT n=28). As a result of IVUS findings, operators re-intervened in 42 procedures. The primary outcome did not differ with intracoronary imaging versus angiographic-guidance alone (17% vs. 16%; odds ratio (OR): 1.09 [95% confidence interval (CI): 0.66-1.82] p=0.738), nor for re-intervention based on IVUS versus none (14% vs.16%; OR: 0.86 [95% CI: 0.35-2.12] p=0.745). With angiographic-guidance only, primary outcome events were more frequent with dual versus provisional stenting (21% vs. 10%; OR: 2.24 [95% CI: 1.13-4.45] p=0.022). With intracoronary imaging, there were numerically fewer primary outcome events with dual versus provisional stenting (13% vs. 21%; OR: 0.54 [95% CI: 0.24-1.22] p=0.137).ConclusionsIn EBC MAIN, the primary outcome did not differ between patients who did or did not have intracoronary imaging. However, in patients without intracoronary imaging, outcomes were worse with a dual-stent than provisional strategy, and when intracoronary imaging was used, there was a trend toward better outcomes with the dual-stent than provisional strategy.Condensed abstractWe investigated whether intracoronary imaging during LM bifurcation stenting was associated with less death, myocardial infarction and revascularisation at 1 year, for patients undergoing systematic dual versus stepwise provisional stenting. We included 455 patients from the EBC MAIN trial; 39% had intracoronary imaging. Overall, outcomes were similar between patients who did or did not have intracoronary imaging. In those with angiographic guidance only, outcomes were worse with dual versus provisional stenting (21% vs. 10%; OR: 2.24 [95% CI: 1.13-4.45] p=0.022). In those with intracoronary imaging, there was a trend toward better outcomes with dual versus provisional stenting (13% vs. 21%).
Deep learning permits imaging of multiple structures with the same fluorophores
Authors: Jin Luhong , Liu Jingfang , Zhang Heng , Zhu Yunqi , Yang Haixu , Wang Jianhang , Zhang Luhao , Xu Yingke , Kuang Cuifang , Liu Xu 
Published: February 2023

AbstractFluorescence microscopy is a powerful tool for life sciences, which employs fluorescent tags to label and observe cellular structures and their dynamics. However, due to the spectral overlap between different dyes, a limited number of structures can be separately labeled and imaged for live cell applications. Here we propose a novel double-structure network (DBSN) that consists of multiple connected models, which can extract six subcellular structures from three images with only two separate fluorescent labels. DBSN combines the intensity-balance models to compensate for uneven fluorescent labels for different structures and the structure-separation models to extract multiple different structures with the same fluorescent labels. Therefore, DBSN permits the imaging of multiple structures with only one fluorescent label. It significantly reduces photobleaching, breaks the bottleneck of the existing technologies, and would have vast applications in cell biology.
The Soil Food Web Ontology: aligning trophic groups, processes, resources, and dietary traits to support food-web research
Authors: Guillarme Nicolas Le , Hedde Mickael , Potapov Anton M. , Martínez-Muñoz Carlos A. , Berg Matty P. , Briones Maria J.I. , Calderón-Sanou Irene , Degrune Florine , Hohberg Karin , Martinez-Almoyna Camille , Pey Benjamin , Russell David J. , Thuiller Wilfried 
Published: February 2023

AbstractAlthough soil ecology has benefited from recent advances in describing the functional and trophic traits of soil organisms, data reuse for large-scale soil food-web reconstructions still faces challenges. These obstacles include: (1) most data on the trophic interactions and feeding behaviour of soil organisms being scattered across disparate repositories, without well-established standard for describing and structuring trophic datasets; (2) the existence of various competing terms, rather than consensus, to delineate feeding-related concepts such as diets, trophic groups, feeding processes, resource types, leading to ambiguities that hinder meaningful data integration from different studies; (3) considerable divergence in the trophic classification of numerous soil organisms, or even the lack of such classifications, leading to discrepancies in the resolution of reconstructed food webs and complicating the reuse and comparison of food-web models within synthetic studies. To address these issues, we introduce the Soil Food Web Ontology, a novel formal conceptual framework designed to foster agreement on the trophic ecology of soil organisms. This ontology represents a collaborative and ongoing endeavour aimed at establishing consensus and formal definitions for the array of concepts relevant to soil trophic ecology. Its primary objective is to enhance the accessibility, interpretation, combination, reuse, and automated processing of trophic data. By harmonising the terminology and fundamental principles of soil trophic ecology, we anticipate that the Soil Food Web Ontology will improve knowledge management within the field. It will help soil ecologists to better harness existing information regarding the feeding behaviours of soil organisms, facilitate more robust trophic classifications, streamline the reconstruction of soil food webs, and ultimately render food-web research more inclusive, reusable and reproducible.
The Clustered Gamma Protocadherin Pcdhγc4 Isoform Regulates Cortical Interneuron Programmed Cell Death in the Mouse Cortex
Authors: Mancia Leon Walter R , Steffen David M , Dale-Huang Fiona , Rakela Benjamin , Breevoort Arnar , Romero-Rodriguez Ricardo , Hasenstaub Andrea R , Stryker Michael P , Weiner Joshua A , Alvarez-Buylla Arturo 
Published: February 2023

AbstractCortical function critically depends on inhibitory/excitatory balance. Cortical inhibitory interneurons (cINs) are born in the ventral forebrain and migrate into cortex, where their numbers are adjusted by programmed cell death. Previously, we showed that loss of clustered gamma protocadherins (Pcdhγ), but not of genes in the alpha or beta clusters, increased dramatically cIN BAX-dependent cell death in mice. Here we show that the sole deletion of the Pcdhγc4 isoform, but not of the other 21 isoforms in the Pcdhγ gene cluster, increased cIN cell death in mice during the normal period of programmed cell death. Viral expression of thePcdhγc4isoform rescued transplanted cINs lackingPcdhγfrom cell death. We conclude thatPcdhγ, specificallyPcdhγc4, plays a critical role in regulating the survival of cINs during their normal period of cell death. This demonstrates a novel specificity in the role ofPcdhγisoforms in cortical development.
Combined multiphoton microscopy and somatostatin receptor type 2 imaging of pancreatic neuroendocrine tumors
Authors: Daigle Noelle , Knapp Thomas , Duan Suzann , Jones David W. , Azhdarinia Ali , Ghosh Sukhen C. , AghaAmiri Solmaz , Ikoma Naruhiko , Estrella Jeannelyn , Schnermann Martin J. , Merchant Juanita L. , Sawyer Travis W. 
Published: February 2023

ABSTRACTPancreatic neuroendocrine tumors (PNETs) are a rare but increasingly more prevalent cancer with heterogeneous clinical and pathological presentation. Surgery is the preferred treatment for all hormone-expressing PNETs and any PNET greater than 2 cm, but difficulties arise when tumors are multifocal, metastatic, or small in size due to lack of effective surgical localization. Existing techniques such as intraoperative ultrasound provide poor contrast and resolution, resulting in low sensitivity for such tumors.Somatostatin receptor type 2 (SSTR2) is commonly overexpressed in PNETs and presents an avenue for targeted tumor localization. SSTR2 is often used for pre-operative imaging and therapeutic treatment, with recent studies demonstrating that somatostatin receptor imaging (SRI) can be applied in radioguided surgery to aid in removal of metastatic lymph nodes and achieving negative surgical margins. However not all PNETs express SSTR2, indicating labeled SRI could benefit from using a supplemental label-free technique such as multiphoton microscopy (MPM), which has proven useful in improving the accuracy of diagnosing more common exocrine pancreatic cancers.Our work tests the suitability of combined SRI and MPM for localizing PNETs by imaging and comparing samples of PNETs and normal pancreatic tissue. Specimens were labeled with a novel SSTR2-targeted contrast agent and imaged using fluorescence microscopy, and subsequently imaged using MPM to collect four autofluo-rescent channels and second harmonic generation. Our results show that a combination of both SRI and MPM provides enhanced contrast and sensitivity for localizing diseased tissue, suggesting that this approach could be a valuable clinical tool for surgical localization and treatment of PNETs.
The tyrosine phosphatase LAR acts as a receptor of the nidogen-tetanus toxin complex
Authors: Surana Sunaina , Villarroel-Campos David , Panzi Chiara , Novoselov Sergey S. , Richter Sandy , Zanotti Giuseppe , Schiavo Giampietro 
Published: February 2023

AbstractTetanus toxin is one of the most potent neurotoxins and is the causative agent of tetanus. This neurotoxin binds to the neuromuscular junction and, after internalisation into motor neurons, undergoes long-distance axonal transport and transcytosis into spinal cord inhibitory interneurons. Inside the cytoplasm of interneurons, the catalytic chain of the toxin blocks neurotransmitter release, leading to spastic paralysis. Whilst the effects of tetanus toxin intoxication have been extensively studied, the molecular composition of its receptor complex is still poorly understood. We have previously shown that the extracellular matrix proteins nidogens are essential for binding of the toxin to the neuromuscular junction. In this study, we show that the tyrosine phosphatase LAR interacts with the nidogen-tetanus toxin complex and enables its uptake into motor neurons. Binding of LAR to the toxin complex is mediated by its fibronectin III domains, which we have harnessed to inhibit tetanus toxin entry into motor neurons. Surprisingly, this function of LAR is independent of its role in regulating the neurotrophic activity of the TrkB receptor, which has previously been shown to augment the axonal transport of signalling endosomes containing tetanus neurotoxin. These findings identify a multi-subunit complex acting as a protein receptor for tetanus neurotoxin, and demonstrate a novel endocytic trafficking route for extracellular matrix proteins in neurons. Our study paves the way for dissecting the molecular mechanisms that control the recognition and uptake of physiological ligands and pathological proteins at the neuronal plasma membrane, as well as their targeting to the axonal retrograde pathway for long-distance transport within the nervous system.
VO2maxprediction based on submaximal cardiorespiratory relationships and body composition in male runners and cyclists: a population study
Authors: Wiecha Szczepan , Kasiak Przemysław Seweryn , Szwed Piotr , Kowalski Tomasz , Cieśliński Igor , Postuła Marek , Klusiewicz Andrzej 
Published: February 2023

AbstractObjectivesOxygen uptake (VO2) is one of the most important measures of fitness and critical vital sign. CPET is a valuable method of assessing fitness in sport and clinical settings. This study aimed to: (1) derive prediction models for maximal VO2(VO2max) based on exercise variables at anaerobic threshold (AT) or respiratory compensation point (RCP) or only somatic and (2) internally validate provided equations.Methods4424 male endurance athletes (EA) underwent maximal symptom-limited CPET on a treadmill (n=3330) or cycle ergometer (n=1094). The cohort was randomly divided between: variables selection (nrunners=1998; ncyclist=656), model building (nrunners=666; ncyclist=219) and validation (nrunners=666; ncyclist=219). Random Forest was used to select the most significant variables. Models were derived and internally validated with Multiple Linear Regression.ResultsRunners were 36.24±8.45 yrs.; BMI=23.94±2.43 kg·m−2; VO2max=53.81±6.67 mL·min−1·kg−1. Cyclists were 37.33±9.13 yr.; BMI=24.34±2.63 kg·m−2; VO2max=51.74±7.99 mL·min−1·kg−1. VO2at AT and RCP were the most contributing variables to exercise equations. Body mass and body fat had the highest impact on the somatic equation. Model performance for VO2maxbased on variables at AT was R2=0.81, at RCP was R2=0.91, at AT&RCP was R2=0.91 and for somatic-only was R2=0.43.ConclusionsDerived prediction models were highly accurate and fairly replicable. Formulae allow for precise estimation of VO2maxbased on submaximal exercise performance or somatic variables. Presented models are applicable for sport and clinical settling. They are a valuable supplementary method for fitness practitioners to adjust individualised training recommendations.FundingThe author(s) received no specific funding for this work.
The BAF chromatin complex component SMARCC1 does not mediate GLI transcriptional repression of Hedgehog target genes in limb buds
Authors: Ramachandran Janani , Chen Wanlu , Lex Rachel K. , Windsor Kathryn E. , Lee Hyunji , Wang Tingchang , Zhou Weiqiang , Ji Hongkai , Vokes Steven A. 
Published: February 2023

ABSTRACTTranscriptional responses to the Hedgehog (HH) signaling pathway are primarily modulated by GLI repression in the mouse limb. Previous studies suggested a role for the BAF chromatin remodeling complex in mediating GLI repression. Consistent with this possibility, the core BAF complex protein SMARCC1 is present at most active limb enhancers including the majority of GLI enhancers. However, in contrast to GLI repression which reduces chromatin accessibility, SMARCC1 maintains chromatin accessibility at most enhancers, including those bound by GLI. Moreover, SMARCC1 binding at GLI-regulated enhancers occurs independently of GLI3. Consistent with previous studies, some individual GLI target genes are mis-regulated inSmarcc1conditional knockouts, though most GLI target genes are unaffected. Moreover, SMARCC1 is not necessary for mediating constitutive GLI repression in HH mutant limb buds. We conclude that SMARCC1 does not mediate GLI3 repression, which we propose utilizes alternative chromatin remodeling complexes.
Dopamine Dynamics Underlying Alloparental Behavioral Acquisition Facilitated by Top-down Orbitofrontal Inputs in Female Mice
Authors: Tasaka Gen-ichi , Hagihara Mitsue , Irie Satsuki , Kobayashi Haruna , Inada Kengo , Kobayashi Kenta , Kato Shigeki , Kobayashi Kazuto , Miyamichi Kazunari 
Published: February 2023

AbstractMaternal behaviors, which are crucial for the survival of mammalian infants, require the coordinated operation of multiple brain regions to process infant cues, make decisions, and execute motor plans. Although these processes likely demand higher cognitive functions, the top-down regulation of limbic parental programs remains poorly understood. Here, we show that the orbitofrontal cortex (OFC) excitatory projection neurons promote alloparental caregiving behaviors in female mice. By chronic microendoscopy, we observed robust yet adaptable representations of pup-directed anticipatory and motor-related activities within the OFC that significantly overlapped with those related to nonsocial reward signals. The inactivation of OFC output reduced the phasic activities of midbrain dopamine (DA) neurons specifically tied to pup retrieval and impaired the modulation of DA release to the ventral striatum during the acquisition of alloparental behaviors. Collectively, our study identifies top-down signals from the OFC that modulate the plasticity of the DA system, thereby promoting alloparental behaviors.TeaserOrbitofrontal cortex neurons facilitate alloparental behaviors in virgin female mice by modulating the dopamine system.
Rapid prototyping of models for COVID-19 outbreak detection in workplaces
Authors: Abell Isobel , Zachreson Cameron , Conway Eamon , Geard Nicholas , McVernon Jodie , Waring Thomas , Baker Christopher 
Published: February 2023

AbstractEarly case detection is critical to preventing onward transmission of COVID-19 by enabling prompt isolation of index infections, and identification and quarantining of contacts. Timeliness and completeness of ascertainment depend on the surveillance strategy employed. We use rapid prototype modelling to quickly investigate the effectiveness of testing strategies, to aid decision making. Models are developed with a focus on providing relevant results to policy makers, and these models are continually updated and improved as new questions are posed. The implementation of testing strategies in high risk settings in Australia was supported using models to explore the effects of test frequency and sensitivity on outbreak detection. An exponential growth model is firstly used to demonstrate how outbreak detection changes with varying growth rate, test frequency and sensitivity. From this model we see that low sensitivity tests can be compensated for by high frequency testing. This model is then updated to an Agent Based Model, which was used to test the robustness of the results from the exponential model, and to extend it to include intermittent workplace scheduling. These models help our fundamental understanding of disease detectability through routine surveillance in workplaces and evaluate the impact of testing strategies and workplace characteristics on the effectiveness of surveillance. This analysis highlights the risks of particular work patterns while also identifying key testing strategies to best improve outbreak detection in high risk workplaces.