bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples
Authors: Domanskyi Sergii , Srivastava Anuj , Kaster Jessica , Li Haiyin , Herlyn Meenhard , Rubinstein Jill C. , Chuang Jeffrey H. 
Published: July 2023

HighlightsWe have developed an automated data processing pipeline to quantify mouse and human data from patient-derived xenograft samples assayed by Visium spatial transcriptomics with matched hematoxylin and eosin (H&E) stained image. We enable deconvolution of reads with Xenome, quantification of spatial gene expression from host and graft species with Space Ranger, extraction of B-allele frequencies, and splicing quantification with Velocyto. In the H&E image processing sub-workflow, we generate morphometric and deep learning-derived feature quantifications complementary to the Visium spots, enabling multi-modal H&E/expression comparisons. We have wrapped the pipeline into Nextflow DSL2 in a scalable, portable, and easy-to-use framework.SummaryWe designed a Nextflow DSL2-based pipeline, Spatial Transcriptomics Quantification (STQ), for simultaneous processing of 10x Genomics Visium spatial transcriptomics data and a matched hematoxylin and eosin (H&E)-stained whole slide image (WSI), optimized for Patient-Derived Xenograft (PDX) cancer specimens. Our pipeline enables the classification of sequenced transcripts for deconvolving the mouse and human species and mapping the transcripts to reference transcriptomes. We align the H&E WSI with the spatial layout of the Visium slide and generate imaging and quantitative morphology features for each Visium spot. The pipeline design enables multiple analysis workflows, including single or dual reference genomes input and stand-alone image analysis. We showed the utility of our pipeline on a dataset from Visium profiling of four melanoma PDX samples. The clustering of Visium spots and clustering of imaging features of H&E data reveal similar patterns arising from the two data modalities.
Sustained Effects of Developmental Exposure to Inorganic Arsenic on Hepatic Gene Expression and Mating Success in Zebrafish
Authors: Koomson Abigail Ama , Delaney Patrice , Sadler Kirsten C. 
Published: July 2023

ABSTRACTThe impacts of exposure to the pervasive environmental toxicant, inorganic arsenic (iAs), on human and fish health are well characterized and several lines of evidence suggest that some impacts can manifest years after exposure cessation. Using a developmental exposure protocol whereby zebrafish embryos were exposed to 0.5 and 1.5 mM iAs from 4-120 hours post fertilization (hpf) and then was removed, we investigated the sustained effects of iAs on gene expression in the liver, survival, reproductive success, and susceptibility to iAs toxicity in the subsequent generation. Developmental exposure to iAs has massive effects on the hepatic transcriptome, with 23% of genes differentially expressed at the end of exposure at 120 hpf, and some of these genes remain deregulated in the liver 9 months after iAs was removed. Developmental exposure to 1.5 mM iAs, but not 0.5 mM, increased mortality through 3 months by over 50%. Adults that were developmentally exposed to 0.5 mM iAs had reduced mating success, but their offspring had no differences in observable aspects of development or their susceptibility to iAs toxicity. This demonstrates that developmental exposure of zebrafish to iAs reduces long-term survival, reproductive success and causes sustained changes to gene expression in the liver.SUMMARY STATEMENTThis work investigates the long-term effects of developmental exposure to inorganic arsenic (iAs) using zebrafish. Months after iAs-exposure was terminated, we found increased mortality, changes in gene expression in the liver and decreased mating success.
A multiplex, prime editing framework for identifying drug resistance variants at scale
Authors: Chardon Florence M. , Suiter Chase C. , Daza Riza M. , Smith Nahum T. , Parrish Phoebe , McDiarmid Troy , Lalanne Jean-Benoît , Martin Beth , Calderon Diego , Ellison Amira , Berger Alice H. , Shendure Jay , Starita Lea M. 
Published: July 2023

AbstractCRISPR-based genome editing has revolutionized functional genomics, enabling screens in which thousands of perturbations of either gene expression or primary genome sequence can be competitively assayed in single experiments. However, for libraries of specific mutations, a challenge of CRISPR-based screening methods such as saturation genome editing is that only one region (e.g.one exon) can be studied per experiment. Here we describe prime-SGE (“prime saturation genome editing”), a new framework based on prime editing, in which libraries of specific mutations can be installed into genes throughout the genome and functionally assessed in a single, multiplex experiment. Prime-SGE is based on quantifying the abundance of prime editing guide RNAs (pegRNAs) in the context of a functional selection, rather than quantifying the mutations themselves. We apply prime-SGE to assay thousands of single nucleotide changes in eight oncogenes for their ability to confer drug resistance to three EGFR tyrosine kinase inhibitors. Although currently restricted to positive selection screens by the limited efficiency of prime editing, our strategy opens the door to the possibility of functionally assaying vast numbers of precise mutations at locations throughout the genome.
The molecular mechanism of positive allosteric modulation at the dopamine D1 receptor
Authors: Goldberg Alexander , Xie Bing , Shi Lei 
Published: July 2023

AbstractThe dopamine D1 receptor (D1R) is a promising target for treating various psychiatric disorders. While upregulation of D1R activity has shown potential in alleviating motor and cognitive symptoms, orthosteric agonists have limitations, restricting their clinical applications. However, the discovery of several allosteric compounds specifically targeting the D1R, such as LY3154207, has opened new therapeutic avenues. Based on the cryo-EM structures of the D1R, we conducted molecular dynamics simulations to investigate the binding and allosteric mechanisms of LY3154207. Our simulations revealed that LY3154207 preferred the horizontal orientation above intracellular loop 2 (IL2) and stabilized the helical conformation of IL2. Moreover, LY3154207 binding induced subtle yet significant changes in key structural motifs and their neighboring residues. Notably, a cluster of residues centered around the Na+binding site became more compact, while interactions involving the PIF motif and its neighboring residues were loosened upon LY3154207 binding, consistent with their role in opening the intracellular crevice for receptor activation. Additionally, we identified an allosteric pathway likely responsible for the positive allosteric effect of LY3154207 in enhancing Gs protein coupling. This mechanistic understanding of LY3154207’s allosteric action at the D1R pave the way for the rational design of more potent and effective allosteric modulators.
A prospective observational cohort study to investigate the effect of frailty on mortality of adults following lower limb amputation
Authors: Welsh S , Gale J , Carter B , Hussey K , Orr D , Quinn T , Braude P 
Published: July 2023

AbstractIntroductionFrailty is common in patients with atherosclerotic disease and is associated with substantially increased morbidity, mortality and significant economic and resource implications. Major limb amputation (MLA) secondary to critical limb threatening ischaemia (CLTI) is also associated with high mortality rates. This study aims to examine the association between frailty, as defined by the Rockwood Clinical Frailty Scale (CFS), on mortality rates in patients undergoing MLA for CLTI.MethodsThis multi-centre, prospective observational cohort study will collect data on MLA performed for CLTI between November 2017 to December 2021 (North Bristol Trust) and January 2016 to October 2021 (NHS Greater Glasgow & Clyde). All patients undergoing MLA for CLTI will be included. Exclusion criteria are MLA for other aetiology, insufficient data to generate CFS score and minor lower limb amputations. Data collected includes age, sex, deprivation index and Charlson Comorbidity Index variables. A consultant/registrar with specialist-interest in frailty will allocate CFS scores based on pre-operative functional status. Three categories will be used: robust (CFS 1-3), mildly frail (CFS 4-5) and frail (CFS 6-8). CFS 9, ‘terminally ill’, will be presented separately. Primary outcome is all-cause mortality following MLA. Secondary outcome is length of stay. Sample size calculation assumed a mortality of 30% in robust and 40% in frail patients (HR=0.7) in a 1:2 ratio (robust:frail), calculating 1000 patients required, using a 0.05 significance level and 90% power. Outcome data will be analysed by multivariable Cox proportional baseline hazards regression controlling for demographic and operative variables (e.g., sex, age, deprivation index, comorbidity index, urgency of operation).DiscussionIt is expected the study results will inform clinical decision-making and contribute toward an evidence pool which will inform service planning.KEY STUDY CONTACTSSTUDY SUMMARYFUNDING AND SUPPORT IN KINDPROTOCOL CONTRIBUTORSStudy contributorsNBT vascular department – proving data on all patients that have undergone LLA in the last 5 years.NHSGGC vascular department – proving data on all patients that have undergone LLA in the last 5 years.
Community Support for Injured Patients: A Scoping Review and Narrative Synthesis
Authors: Jhunjhunwala Rashi , Jayaram Anusha , Mita Carol , Davies Justine , Chu Kathryn 
Published: July 2023

AbstractBACKGROUNDCommunity-based support groups have been effective in facilitating access to and retention in the healthcare system for patients with HIV/AIDS, cancer, diabetes, and other communicable and non-communicable diseases. Given the high incidence of morbidity that results from traumatic injuries, and the barriers to reaching and accessing care for injured patients, community-based support groups may prove to be similarly effective in this population.OBJECTIVESThe objective of this review is to identify the extent and impact of community and peer support groups for injured patients.ELIGIBILITYWe included primary research on studies that evaluated community support groups that were solely based in the community. Hospital-based or healthcare-professional led groups were excluded.EVIDENCESources were identified from a systematic search of Medline / PubMed, CINAHL, and Web of Science Core Collection.CHARTING METHODSWe utilized a narrative synthesis approach to data analysis.RESULTS4,989 references were retrieved from database search; 25 were included in final data extraction. There was a variety of methodologies represented, and the groups represented patients with spinal cord injury (N=2), traumatic brain or head injury (N=7), burns (N=4), intimate partner violence (IPV) (N=5), mixed injuries (N=5), torture (N=1), and brachial plexus injury (N=1). Multiple benefits were reported by support group participants; categorized as social, emotional, logistical, or educational benefits.CONCLUSIONScommunity-based peer support groups can provide education, community, and may have implications for retention in care for injured patients.
Ploidy-specific transcriptomes shed light on the heterogeneous identity and metabolism of developing pericarp cells
Authors: Tourdot Edouard , Maza Elie , Djari Anis , Martin Pascal GP , Gévaudant Frédéric , Chevalier Christian , Pirrello Julien , Gonzalez Nathalie 
Published: July 2023

SummaryEndoreduplication, during which cells increase their DNA content through successive rounds of full genome replication without cell division, is the major source of endopolyploidy in higher plants. Endoreduplication plays pivotal roles in plant growth and development and is associated with the activation of specific transcriptional programs that are characteristic to each cell type, thereby defining their identity. In plants, endoreduplication is found in numerous organs and cell types and especially in agronomically valuable ones, such as the fleshy fruit (pericarp) of tomato presenting high ploidy levels. We used the tomato pericarp tissue as a model system to explore the transcriptomes associated with endoreduplication progression during fruit growth. We confirmed that expression globally scales with ploidy level and identified sets of genes differentially expressed when comparing ploidy levels at a specific developmental stage. We found that non-endoreduplicated cells are defined by cell division state and cuticle synthesis while endoreduplicated cells are mainly defined by their metabolic activity changing rapidly over time. By combining this dataset with publicly available spatiotemporal pericarp expression data, we proposed a map describing the distribution of ploidy levels within the pericarp. These transcriptome-based predictions were validated by quantifying ploidy levels within the pericarp tissue. Thisin situploidy quantification revealed the dynamic progression of endoreduplication and its cell layer specificity during early fruit development. In summary, the study sheds light on the complex relationship between endoreduplication, cell differentiation, and gene expression patterns in the tomato pericarp.Significance statementThe progression of endoreduplication is very dynamic during early fruit development and displays cell layer specific patterns. The integration of ploidy distribution maps with ploidy-specific transcriptome data revealed that gene expression in the pericarp is controlled in a ploidy-specific manner during the early stages of tomato fruit development, resulting in the spatialization of transcriptional programs.
Developmental noise and phenotypic plasticity are correlated inDrosophila simulans
Authors: Saito Keita , Tsuboi Masahito , Takahashi Yuma 
Published: July 2023

AbstractNon-genetic variation is the phenotypic variation induced by the differential expression of a genotype in response to varying environmental cues and is broadly categorized into two types: phenotypic plasticity and developmental noise. These variation aspects have been suggested to play an important role in adaptive evolution; however, the mechanisms by which these two types of non-genetic variations influence the evolutionary process are currently poorly understood. Using a machine-learning based phenotyping tool, we independently quantified the phenotypic plasticity and developmental noise in the wing morphological traits of a fruit flyDrosophila simulans.Utilizing a rearing experiment, we demonstrated plastic responses in both wing size and shape as well as non-zero heritability of both phenotypic plasticity and developmental noise, which suggests that adaptive phenotypic plasticity can evolve via genetic accommodation in the wing morphology ofD. simulans. We found a positive correlation between phenotypic plasticity and developmental noise, while the correlation between the plastic response to three kinds of environmental factors that were examined (nutrient condition, temperature, and light–dark cycle) were poor. These results suggest that phenotypic plasticity and developmental noise contribute to evolvability in a similar manner, however, the mechanisms that underlie the correspondence between these two variation types remains to be elucidated.Lay SummaryNon-genetic variations consist of phenotypic plasticity and developmental noise, and these variations have been suggested to influence the direction and the rate of evolution. However, the role of phenotypic plasticity and developmental noise in evolutionary process is still poorly understood. Using a rearing experiment, we examined the heritability of plasticity and developmental noise, the correlation of the strength of plastic response to three kinds of environmental factors, and the relationship between plasticity and developmental noise in wing size and wing shape inDrosophila simulans. We found that the degree of phenotypic plasticity and developmental noise were heritable, and positively correlated with each other. Our results suggest that there two non-genetic variations dependently affect the direction and the rate of evolution together.
napari-threedee: a toolkit for human-in-the-loop 3D image analysis in napari
Authors: Yamauchi Kevin A. , Burt Alister 
Published: July 2023

AbstractWith recent advances in three-dimensional bioimaging acquisition and analysis methods, imaging data are an important tool for unveiling the complex architecture of biological organisms. However, extracting insights from these complex datasets requires interactive exploration as well as annotation for training supervised analytical methods. Here we present napari-threedee, a library of composable components and napari plugins for interactively exploring and annotating image data in 3D. We demonstrate how napari-threedee can be used for human-in-the-loop 3D image analysis in diverse image data including fluorescence microscopy and cryoelectron tomography.
Analysis of human BBS protein homologues in insects support alternative non-ciliary functions
Authors: Ewerling Alexander , Graebling Isa , Wierczeiko Anna , Kotzurek Elisa , Foitzik Susanne , Gerber Susanne , Colgan Thomas J. , May-Simera Helen 
Published: July 2023

ABSTRACTCilia and flagella were one of the characteristic traits of the last eukaryotic common ancestor and as such, are highly conserved among eukaryotes. Their proteomic makeup is consequently remarkably similar throughout all eukaryotic lineages. Recently, one subgroup of ciliary transport proteins in mammalian cells, the Bardet-Biedl Syndrome (BBS) proteins, was shown to have the ability to traverse the nuclear envelope, and to engage in protein-protein-interactions that modulate gene expression, signalling cascades, and cell homeostasis. Insects have been critically understudied in cilia biology because of their highly specialised cilia being localised on only a small subset of cell types. In this study, we present evidence that the BBSome, a hetero-octameric ciliary transport complex of BBS proteins, is largely conserved in multiple insect lineages. Using the honeybeeApis melliferaas a study system to explore BBS-associated gene expression, our analyses suggest that not all BBSome-associated genes are expressed equally, indicating possible non-ciliary functions. We also demonstrate that the expression of individual BBS proteins varies significantly between the tissues of queens and males inA. mellifera, especially in neuronal tissue. This result raises the question of what role BBS proteins play in these tissues and whether they are involved in gene regulation in insects. The potential gene regulatory function of BBS proteins should be explored in other eukaryotes due to their high degree of conservation.
Multi-omic study of genome-edited human colonoid models of colorectal cancer reveal genotype-specific patterns of microRNA regulation
Authors: Villanueva Jonathan W. , Pan Fong Cheng , Rice Edward J. , Hung Yu-Han , Winnicki Mary , Chen Shuibing , Danko Charles G. , Sethupathy Praveen 
Published: July 2023

AbstractCombinations of oncogenic mutations drive inter-tumor heterogeneity in colorectal cancer (CRC), which promotes distinct phenotypes and affects therapeutic efficacy. We recently demonstrated that combinations of mutations in mouse small intestinal organoids lead to unique changes in microRNA (miRNA) expression profiles. However, it remains unknown how different mutational backgrounds shape miRNA profiles in the human colon. We leveraged human colonic organoid models, termed colonoids, with gene edits targeting genes commonly mutated in CRC to profile genotype-specific changes in miRNA expression. By small RNA-sequencing we characterized genotype-specific miRNA profiles. We identified one group of miRNAs, including mir-34a-5p and mir-10a-5p, that is strongly downregulated inAPC/KRAS/TP53mutant (AKP-mutant) colonoids. Using chromatin run-on sequencing, we showed that most miRNA alterations in AKP-mutant colonoids are concordant with transcriptional changes. Transcription factor (TF) motif enrichment analysis using transcriptional regulatory elements with increased activity in AKP-mutant colonoids revealed an enrichment of binding sites for multiple oncogenic TFs. Several of these harbor predicted binding sites for mir-10a-5p and/or mir-34a-5p, suggesting these miRNAs may play a role in regulating transcriptional programs in AKP-mutant contexts. Ultimately, our study offers a glimpse into regulatory mechanisms that drive inter-tumor heterogeneity, and we highlight candidate therapeutic targets for the advancement of precision medicine.
A seven-year record of fluctuating core body temperatures of nesting leatherback and hawksbill sea turtles
Authors: Kennedy Malcolm W. 
Published: July 2023

AbstractSea turtles experience changes in water temperatures during migrations and seasonal movements that will influence their body temperatures. Nothing is known of how sea turtles’ core body temperatures vary from season to season at nesting sites. Over seven consecutive seasons we measured the surface temperatures of freshly laid eggs as proxies of core temperatures of sea turtles using non-contact infrared thermometers. We measured egg temperatures of two species that have contrasting lifestyles - leatherbacks, the largest, which are adapted to migrate between tropical breeding sites to cold temperate waters, and the smaller hawksbills that are confined to the tropics and sub-tropics. We found considerable year-to-year variations in temperatures in both species (year means 30.4 °C to 31.5 °C in leatherbacks), hawksbills the more so (28.1 °C to 30.3 °C). These differences will likely be modified by both natural seasonal variations and anthropogenic changes in global ocean temperatures and resulting changes in currents and water temperatures local to nesting beaches. These previously unrecognised diversities in body temperatures of nesting turtles are pertinent to predicting environmental tolerances, reproductive success, and nest site selection by sea turtles, and could contribute to predicting which rookeries may remain viable or not during future ocean warming.