bluuebunny/crossref_metadata_2025_split huggingface dataset:
A qualitative evaluation of a multi-modal cancer prehabilitation programme for colorectal, head and neck and lung cancers patients
Authors: Bingham Sharon Linsey , Small Sarah , Semple Cherith 
Published: November 2022

Background Growing evidence indicates patients’ survivorship outcomes can be enhanced through active engagement in a multi-modal cancer prehabilitation programme (MCPP), although this intervention is not uniformly embedded as a standard of care. MCPP aims to optimise patients physiologically and psychologically for cancer treatments, shorten recovery time, reduce complications, promote healthier lifestyles and improve quality of life. South Eastern Health and Social Care Trust (SET) developed and evaluated a system-wide collaborative approach to MMCP across three tumour groups (colorectal, lung, head and neck cancer). Addressing the lack of qualitative evaluation of MCPPs, this paper explores mechanisms promoting feasibility and acceptability of MCPP from patients’ and interdisciplinary professionals’ perspectives. Methods Semi-structured virtual one-to-one interviews were conducted with 24 interdisciplinary professionals and nine patients. Transcripts were recorded, transcribed verbatim and themes developed using Framework Analysis. Results Analysis of findings identified four themes providing an in-depth understanding of key elements required to develop and deliver a MCPP: 1) Planning: Building the team, 2) Shared vision to develop and tailor the MCPP to meet patient needs, 3) Delivering the MCPP and 4) Moving forward - improving the MCPP. Conclusion The system-wide collaborative approach to developing a MCPP at SET was deemed both feasible and acceptable. Success was attributed to visionary leadership, alongside a diverse group of interdisciplinary professionals being engaged, motivated and committed to improving patient outcomes. Iterative, responsive troubleshooting during delivery facilitated successful implementation. Greater adherence to provision of prescriptive high intensity exercise within the programme may further promote enhanced patient outcomes.
Fine-scale variability in coral bleaching and mortality during a marine heatwave
Authors: Yadav Shreya , Roach Ty NF , McWilliam Michael J , Caruso Carlo , de Souza Mariana Rocha , Foley Catherine , Allen Corinne , Dilworth Jenna , Huckeba Joel , Santoro Erika P , Wold Renee , Simpson Jacqueline , Miller Spencer , Hancock Joshua R , Drury Crawford , Madin Joshua S 
Published: November 2022

AbstractCoral bleaching and mortality can show significant spatial and taxonomic heterogeneity at local scales, highlighting the need to understand the fine-scale drivers and impacts of thermal stress. In this study, we used structure-from-motion photogrammetry to track coral bleaching, mortality, and changes in community composition during the 2019 marine heatwave in Kāne‘ohe Bay, Hawai‘i. We surveyed 30 shallow reef patches every 3 weeks for the duration of the bleaching event (August-December) and one year after, resulting in a total of 210 large-area, high-resolution photomosaics that enabled us to follow the fate of thousands of coral colonies through time. We also measured environmental variables such as temperature, sedimentation, depth, and wave velocity at each of these sites, and extracted estimates of habitat complexity (rugosity R and fractal dimension D) from digital elevation models to better understand their effects on patterns of bleaching and mortality. We found that up to 80% of corals experienced moderate to severe bleaching in this period, with peak bleaching occurring in October when heat stress (DHW) reached its maximum. Mortality continued to accumulate as bleaching levels dropped, driving large declines in more heat-susceptible species (77% loss ofPocilloporacover) and moderate declines in heat-tolerant species (19% and 23% forPorites compressaandMontipora capitata, respectively). Declines in live coral were accompanied by a rapid increase in algal cover across the survey sites. Spatial differences in bleaching were significantly linked to habitat complexity and coral species composition, with reefs that were dominated byPocilloporaexperiencing the most severe bleaching. Mortality was also influenced by species composition, fractal dimension, and site-level differences in thermal stress. Our results show that spatial heterogeneity in the impacts of bleaching are driven by a mix of environmental variation, habitat complexity, and differences in assemblage composition.
TreeTerminus - Creating transcript trees using inferential replicate counts
Authors: Singh Noor Pratap , Love Michael I. , Patro Rob 
Published: November 2022

AbstractThe accuracy and robustness of many types of analyses performed using RNA-seq data are directly impacted by the quality of the transcript and gene abundance estimates inferred from this data. However, a certain degree of uncertainty is always associated with the transcript abundance estimates. This uncertainty may make many downstream analyses, such as differential testing, difficult for certain transcripts. Conversely, gene-level analysis, though less ambiguous, is often too coarse-grained. To circumvent this problem, methods have proposed grouping transcripts together into distinct inferential units that should be used as a base unit for analysis. However, these methods don’t take downstream analysis into account.We introduceTreeTerminus, a data-driven approach for grouping transcripts into a tree structure where leaves represent individual transcripts and internal nodes represent an aggregation of a transcript set.TreeTerminusconstructs trees such that, on average, the inferential uncertainty decreases as we ascend the tree topology. The tree provides the flexibility to analyze data at nodes that are at different levels of resolution in the tree and can be tuned depending on the analysis of interest. To obtain fixed groups for the downstream analysis, we provide a dynamic programming (DP) approach that can be used to find a cut through the tree that optimizes one of several different objectives.We evaluatedTreeTerminuson two simulated and two experimental datasets, and observed an improved performance compared to transcripts (leaves) and other methods under several different metrics.
Memory for a day: Olfactory place episodic-like memory for dung droppings by the domestic horse (Equus ferus caballus)
Authors: Guyonnet Audrey EM , Whishaw Ian Q 
Published: November 2022

AbstractThe domestic horse (Equus ferus caballus) makes dung deposits to form “stud-piles” and investigates dung droppings more generally, suggesting that dung contains species-relevant communicative information. This natural behavior provides a behavior with which to examine a species-typical form of memory used by horses in relation to their social behavior. Horses were video recorded in indoor and outdoor riding arenas as they were lightly taken on a lead line to experimenter-determined objects or dung-piles. Frame-by-frame video analysis was used to measure sniffing duration and spatial memory of dung dropping visitations. Horses readily approached and sniffed dung for longer durations than they sniffed other objects. They always approached dung at new locations, made head movements across the extent of dung-piles as they sniffed, showed no preference in the nostril directed to the target, and might blink during sniffing and always blinked when disengaging from sniffing. Horses did remember dung visited withing a day by reducing visits and sniff duration but displayed little retention between days. The results are discussed in relation to the idea that this form of episodic-like memory is time limited because it competes with safety-related behavior related to horse movement within foraging areas.
When should coevolution among competitors promote coexistence versus exclusion?
Authors: Nell Lucas A. , Phillips Joseph S. , Ives Anthony R. 
Published: November 2022

AbstractCoevolution of competitors can lead to niche partitioning promoting coexistence or to heightened conflicts promoting competitive exclusion. If both are possible, when should coevolution favor coexistence versus exclusion? We investigated this question with a general eco-evolutionary model in which species can reduce the interspecific competition they experience through evolutionary investments in two types of competitive traits: partitioning traits that promote coexistence and conflict traits that promote exclusion. We found that communities were generally mixed, consisting of species investing in both trait types or mixtures of species specializing in one type. For each species, its competitors’ abundances and investments determined its experienced competition, and stronger competition begot greater competitive trait investment. Species investing in conflict traits strengthened competition for other species both directly and indirectly, whereas partitioning traits only weakened competition via direct effects. Conflict traits were therefore the stronger driver of community-wide investments in all traits. However, species investing most in conflict traits experienced less competition, so they ultimately evolved least investment, making them most likely to be excluded by the next invader. Thus, coevolution may provide an open door for species that play nice and a revolving door of exclusion for those that do not.
Is exposure to chemical pollutants associated with sleep outcomes? A systematic review
Authors: Wallace Danielle A. , Gallagher Jayden Pace , Peterson Shenita R. , Ndiaye-Gueye Seyni , Fox Kathleen , Redline Susan , Johnson Dayna A. 
Published: November 2022

ABSTRACTBackgroundSleep disruption is a public health concern and environmental exposures that influence the biological processes underpinning sleep may contribute to impaired sleep health. However, the contributions of environmental chemical pollutants to sleep health have not been systematically investigated.ObjectivesThis systematic literature review sought to identify, evaluate, summarize, and synthesize the existing evidence between environmental chemical pollutant exposure and dimensions of sleep health in humans. We sought to evaluate potential mechanisms underlying exposure-outcome relationships and recommend areas for future research.MethodsDatabases were searched for peer-reviewed published research on chemical environmental pollutants and sleep health and disorders with no date restriction up to the last search date of April 2021 (registered protocol PROSPERO # CRD42021256918), resulting in 9,918 records. Two reviewers independently screened identified records against inclusion and exclusion criteria, extracted study information, and performed risk of bias assessments.ResultsWe identified 204 studies of exposure to air pollution, exposures related to the Gulf War and other conflicts, endocrine disruptors, metals, pesticides, and solvents with dimensions of sleep health (architecture, duration, quality, timing) and sleep disorders (sleeping pill use, insomnia, sleep-disordered breathing) for inclusion in this review. Metals were the most frequently evaluated pollutants, while sleep maintenance/insomnia and quality were the most reported sleep outcomes. Synthesis of the evidence suggests mechanisms related to cholinergic signaling, neurotransmission, and inflammation as the most shared pathways.DiscussionEvidence indicates that exposure to particulate matter, secondhand smoke, dioxins and dioxin- like compounds, lead, mercury, pesticides, solvents, and exposures related to the Gulf War are associated with worse sleep health and disorders. Chemical pollutants are likely key environmental determinants of sleep health and disorders; thus, there is a need to improve measurement of pollutants and sleep, study rigor, and determine the populations most vulnerable to the effects of exposure.
Identification of an early hippocampal recognition system using intracerebral evoked potentials in humans
Authors: López-Madrona Víctor J. , Trébuchon Agnès , Mindruta Ioana , Barbeau Emmanuel J. , Barborica Andrei , Pistol Costi , Oane Irina , Alario F. Xavier , Bénar Christian G. 
Published: November 2022

ABSTRACTThe role of the hippocampal formation in memory recognition has been well studied in animals, with different pathways and structures linked to specific memory processes. In contrast, the hippocampus is commonly analyzed as a unique responsive area in most electrophysiological studies in humans, and the specific activity of its subfields remains unexplored. We combined intracerebral electroencephalogram recordings from epileptic patients with independent component analysis (ICA) during a memory recognition task involving the recognition of old and new images to disentangle the activities of multiple neuronal sources within the hippocampus. We identified two sources with different responses emerging from the hippocampus: a fast one (maximum at ∼250 ms) that could not be directly identified from raw recordings, and a later one, peaking at ∼400 ms. The earliest component was found in 12 out of 15 electrodes, with different amplitudes for old and new items in half of the electrodes. The latter component, identified in 13 out of 15 electrodes, had different delays for each condition, with a faster activation (∼290 ms after stimulus onset) for recognized items. We hypothesize that both sources represent two steps of hippocampal memory recognition, the faster reflecting the input from other structures and the latter the hippocampal internal processing. Recognized images evoking early activations would facilitate neural computation in the hippocampus, accelerating memory retrieval of complementary information. Overall, our results suggest that hippocampal activity is composed by several sources, including an early system for memory recognition, that can be disentangled with ICA methods.SIGNIFICANCE STATEMENTIn the human memory circuit, the hippocampus is considered as a relatively late structure, associated to the retrieval of elaborated memories. In most electrophysiological studies, it is analyzed as a unique responsive area, and the specific activity of its subfields remains unexplored. In this work, we combined intracerebral recordings with independent component analysis to separate the electrophysiological activity from two different substructures of the hippocampus. We analyzed the responses of both sources in a memory task involving the recognition of old and new images. Our results revealed new hippocampal dynamics associated to different subfields, with memory recognition occurring much faster than previously reported. Importantly, we confirmed the potential of independent component analysis, which can be extended to other brain areas.
Imaging the Neural Substrate of Trigeminal Neuralgia Pain Using Deep Learning
Authors: Liang Yun , Zhao Qing , Hu Zhenhong , Bo Ke , Meyyappan Sreenivasan , Neubert John K. , Ding Mingzhou 
Published: November 2022

AbstractTrigeminal neuralgia (TN) is a severe and disabling facial pain condition and is characterized by intermittent, severe, electric shock-like pain in one (or more) trigeminal subdivisions. This pain can be triggered by an innocuous stimulus or can be spontaneous. Presently available therapies for TN include both surgical and pharmacological management; however, the lack of a known etiology for TN contributes to the unpredictable response to treatment and the variability in long-term clinical outcomes. Given this, a range of peripheral and central mechanisms underlying TN pain remain to be understood. We acquired functional magnetic resonance imaging (fMRI) data from TN patients who (1) rested comfortably in the scanner during a resting state session and (2) rated their pain levels in real time using a calibrated tracking ball-controlled scale in a pain tracking session. Following data acquisition, the data was analyzed using the conventional correlation analysis and two artificial intelligence (AI)-inspired deep learning methods: convolutional neural network (CNN) and graph convolutional neural network (GCNN). Each of the three methods yielded a set of brain regions related to the generation and perception of pain in TN. There were six regions that were identified by all three methods, including the superior temporal cortex, the insula, the fusiform, the precentral gyrus, the superior frontal gyrus, and the supramarginal gyrus. Additionally, 17 regions, including dorsal anterior cingulate cortex(dACC) and the thalamus, were identified by at least two of the three methods. Collectively, these 23 regions represent signature centers of TN pain and provide target areas for future studies relating to central mechanisms of TN.
Single-cell multi-omics decodes regulatory programs during development of mouse secondary palate
Authors: Yan Fangfang , Suzuki Akiko , Iwaya Chihiro , Pei Guangsheng , Chen Xian , Yoshioka Hiroki , Yu Meifang , Simon Lukas M. , Iwata Junichi , Zhao Zhongming 
Published: November 2022

SUMMARYThe abnormal perturbation in gene regulation during palatogenesis may lead to cleft palate, a major congenital birth defect in humans and mice. However, a comprehensive multi-omic map of the developing secondary palate at single-cell resolution is lacking. In this study, we performed single-cell multiome sequencing and profiled chromatin accessibility and gene expression simultaneously within the same cells (n = 36,154) isolated from mouse secondary palate across embryonic days (E) 12.5, E13.5, E14.0, and E14.5. Application of optimal transport reconstructed five trajectories, representing continuous differentiation of multipotent cells into different subpopulations in later stages. By linking open chromatin signals to gene expression changes, we discovered a list of lineage-determining transcription factors, such as Shox2 for the anterior and Dlx1/2 for the posterior palatal mesenchymal trajectories. In conclusion, this study charted epigenetic and transcriptional dynamics during palatogenesis, which provides a valuable resource for the community and facilitate future research in cleft palate.HighlightsThe first report on building a single-cell multi-omics atlas with joint chromatin accessibility and gene expression measurements from the same cells during the development of mouse secondary palate.Application of optimal transport calculated fate probabilities to different terminal states and recovered continuous landscapes during mouse secondary palate development.By linkingcis-regulatory DNA elements to target genes, we characterized a series of transcription factors governing the differentiation of cranial neural crest-derived multipotent cells to the anterior and posterior palatal mesenchymal trajectories, respectively.Transcription factors Shox2 and Dlx1/2 exhibited top regulatory roles for the anterior and posterior palatal mesenchymal trajectories, respectively, showing significant enrichment in both motif accessibility and gene expression.
Multisensory integration (MSI) by polymodal sensory neurons dictates larval settlement in a brainless cnidarian larva
Authors: Birch Sydney , Plachetzki David 
Published: November 2022

SummaryMultisensory integration (MSI) combines information from more than one sensory modality to elicit behaviors distinct from unisensory behaviors. MSI is best understood in animals with complex brains and specialized centers for parsing sensory information, but the dispersive larvae of sessile marine invertebrates utilize multimodal environmental sensory stimuli to base irreversible settlement decisions on, and most lack complex brains. Here, we examined the sensory determinants of settlement in actinula larvae of the hydrozoanEctopleura crocea(Cnidaria), which possess a diffuse nerve net. A factorial settlement study revealed that photo-, chemo-, and mechano-sensory cues each influence the settlement response, which was complex and dependent on specific combinations of cues, therefore indicating MSI. Mechanosensory cues either inhibited or enhanced settlement rates depending on the presence or absence of chemical and light cues in the environment. Sensory gene expression over development peaked with developmental competence to settle, which in actinulae, requires cnidocyte discharge. Transcriptome analyses also highlighted several deep homological links between cnidarian and bilaterian mechano- chemo- and photo-sensory pathways. Fluorescentin situhybridization studies of candidate transcripts suggested cellular partitioning of sensory function among the few cell types that comprise the actinula nervous system, where ubiquitous polymodal sensory neurons with putative chemo- and photo-sensitivity interface with mechanoreceptive cnidocytes. We propose that a simple multisensory processing circuit, involving polymodal chemo/photosensory neurons and mechanoreceptive cnidocytes, is sufficient to explain MSI in actinulae settlement. Our study demonstrates that MSI is not exclusive to complex brains, but likely predated and contextualized their evolution.
Sashimi.py: a flexible toolkit for combinatorial analysis of genomic data
Authors: Zhang Yiming , Zhou Ran , Wang Yuan 
Published: November 2022

AbstractSimultaneously visualizing how isoform expression, protein–DNA/RNA interactions, accessibility, and architecture of chromatin differs across condition and cell types could inform our understanding on regulatory mechanisms and functional consequences of alternative splicing. However, the existing versions of tools generating sashimi plots remain inflexible, complicated, and user-unfriendly for integrating data sources from multiple bioinformatic formats or various genomics assays. Thus, a more scalable visualization tool is necessary to broaden the scope of sashimi plots. Here, we introduce sashimi.py, a Python package for generating publication-quality visualization by a programmable and interactive web-based approach. Sashimi.py is a platform to visually interpret genomic data from a large variety of data sources including single-cell RNA-seq, protein–DNA/RNA interactions, long-reads sequencing data, and Hi-C data without any preprocessing, and also offers a broad degree of flexibility for formats of output files that satisfy the requirements of major journals. The Sashimi.py package is an open-source software which is freely available on Bioconda (https://anaconda.org/bioconda/sashimi-py), Docker, PyPI (https://pypi.org/project/sashimi.py/) and GitHub (https://github.com/ygidtu/sashimi.py), and a built-in web server for local deployment is also provided.