Towards a Shared Specification Repository
Ontology highlight
ABSTRACT:
SUBMITTER: Raschke A
PROVIDER: S-EPMC7242027 | biostudies-literature | 2020 Apr
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Successful territory defence is a prerequisite for reproduction across many taxa, and often highly sensitive to the actions of territorial neighbours. Nevertheless, to date, assessments of the significance of the behaviour of heterospecific neighbours have been infrequent and taxonomically restricted. In this field study, I examined the importance of both heterospecific and conspecific neighbours in a biparental fish, the convict cichlid, Amatitlania siquia. This was done by assessing the colonisation rates of vacant territories, the rates of aggression by the territory holders, and the overall rates of aggression towards intruders, in treatments that controlled the proximity of both neighbour types. Convict cichlid pairs colonised vacant nesting resources (territory locations) at similar rates independent of the proximity of heterospecific (moga, Hypsophrys nicaraguensis) or conspecific neighbours. However, a model of sympatric cichlid intruder was subjected to considerably higher overall levels of aggression when mogas were nearby. In contrast, the proximity of conspecifics did not have a significant effect on the overall aggression towards the intruder. These results suggest that previously demonstrated higher survival of convict cichlid broods in close proximity of mogas may be driven by aggression towards shared enemies. No conclusive evidence was found regarding whether mogas also influence convict cichlids' investment into anti-intruder aggression: the results show a marginally non-significant trend, and a moderately large effect size, to the direction of a lower investment in mogas', but not conspecifics', proximity. More generally, heterospecific neighbours may provide protective benefits in a wider range of ecological settings than commonly considered.
| S-EPMC6763407 | biostudies-other
Project description:Resistance to therapeutic treatment and metastatic progression jointly determine a fatal outcome of cancer. Cancer metastasis and therapeutic resistance are traditionally studied as separate fields using non-overlapping strategies. However, emerging evidence, including from in vivo imaging and in vitro organotypic culture, now suggests that both programmes cooperate and reinforce each other in the invasion niche and persist upon metastatic evasion. As a consequence, cancer cell subpopulations exhibiting metastatic invasion undergo multistep reprogramming that - beyond migration signalling - supports repair programmes, anti-apoptosis processes, metabolic adaptation, stemness and survival. Shared metastasis and therapy resistance signalling are mediated by multiple mechanisms, such as engagement of integrins and other context receptors, cell-cell communication, stress responses and metabolic reprogramming, which cooperate with effects elicited by autocrine and paracrine chemokine and growth factor cues present in the activated tumour microenvironment. These signals empower metastatic cells to cope with therapeutic assault and survive. Identifying nodes shared in metastasis and therapy resistance signalling networks should offer new opportunities to improve anticancer therapy beyond current strategies, to eliminate both nodular lesions and cells in metastatic transit.
| S-EPMC10399972 | biostudies-literature
Project description:Expertly collected, well-curated data sets consisting of comprehensive clinical characterization and raw structural, functional and diffusion-weighted DICOM images in schizophrenia patients and sex and age-matched controls are now accessible to the scientific community through an on-line data repository (coins.mrn.org). The Mental Illness and Neuroscience Discovery Institute, now the Mind Research Network (MRN, http://www.mrn.org/ ), comprised of investigators at the University of New Mexico, the University of Minnesota, Massachusetts General Hospital, and the University of Iowa, conducted a cross-sectional study to identify quantitative neuroimaging biomarkers of schizophrenia. Data acquisition across multiple sites permitted the integration and cross-validation of clinical, cognitive, morphometric, and functional neuroimaging results gathered from unique samples of schizophrenia patients and controls using a common protocol across sites. Particular effort was made to recruit patients early in the course of their illness, at the onset of their symptoms. There is a relatively even sampling of illness duration in chronic patients. This data repository will be useful to 1) scientists who can study schizophrenia by further analysis of this cohort and/or by pooling with other data; 2) computer scientists and software algorithm developers for testing and validating novel registration, segmentation, and other analysis software; and 3) educators in the fields of neuroimaging, medical image analysis and medical imaging informatics who need exemplar data sets for courses and workshops. Sharing provides the opportunity for independent replication of already published results from this data set and novel exploration. This manuscript describes the inclusion/exclusion criteria, imaging parameters and other information that will assist those wishing to use this data repository.
| S-EPMC3727653 | biostudies-literature
Project description:Understanding of TMZ therapy during and after treatment in a mouse model
2023-08-10 | GSE227348 | GEO
Project description:BackgroundThere is little information about the functions and behavior change techniques (BCTs) needed to implement shared decision making (SDM) in clinical practice. To guide future implementation initiatives, we sought to develop a BCT taxonomy for SDM implementation interventions.MethodsThis study is a secondary analysis of a 2018 Cochrane review on interventions for increasing the use of shared decision making by healthcare professionals. We examined all 87 studies included in the review. We extracted relevant information on each study intervention into a spreadsheet. Coders had undergone a training workshop on intervention functions and online training on BCT Taxonomy version 1 (BCTTv1). We performed functions and BCTs coding trials, and identified coding rules. We used Michie's guide for designing behavior change interventions to code the functions and BCTs used in the interventions. Coders met to compare coding and discrepancies were discussed until consensus was reached. Data was analyzed using simple descriptive statistics.ResultsOverall, 7 functions, 24 combinations of functions and 32 BCTs were used in the 87 SDM implementation interventions. The mean of functions per intervention was 2.5 and the mean of BCTs per intervention was 3.7. The functions Coercion and Restriction were not found. The most common function was Education (73 studies). Three combinations of functions were most common (e.g: Education + Persuasion, used in 10 studies). The functions associated with more effective SDM implementation interventions were Modeling and Training. The most effective combination of functions was Education + Training + Modeling + Enablement. The most commonly used BCT was Instruction on how to perform the behavior (43 studies). BCTs associated with more effective SDM implementation interventions were: Instruction on how to perform the behavior, Demonstration of the behavior, Feedback on behavior, Pharmacological support, Material reward, and Biofeedback. Twenty-five BCTs were associated with less effective SDM implementation interventions. Four new BCTs were identified: General information to support the behavior, Tailoring, Exercises to conceptually prepare for the behavior, and Experience sharing and learning.ConclusionsWe established a BCT taxonomy specific to the field of SDM to guide future SDM implementation interventions. Four new BCTs should be added to BCTTv1.
| S-EPMC7439658 | biostudies-literature
Project description:This dataset presents the results of protein sample preparation strategies for enriching a novel encyclopaedic peptide spectral library using the liquid fraction of sheep blood. The method used showed the capability of simultaneously detecting hundreds of key proteins in the liquid fraction of blood (circulating acellular proteome) using sheep as a model by: a) Prototyping of the circulating acellular proteome of healthy sheep using serum b) A comprehensive analysis of fractions of acetone precipitated sheep serum and plasma; c) A comprehensive analysis of fractions of partial organic precipitation of sheep serum and plasma proteins using acetonitrile; d) Combinatorial peptide ligand library protein enrichment of sheep serum and plasma; e) Off-gel fractionation of serum proteins; f) Extraction of protein data from ex-diagnostic sheep serum; g) Derivation of peptide data from serum and plasma of endotoxin treated sheep.
2022-11-15 | PXD005002 | Pride
Project description:The Mouse Phenome Database (MPD; https://phenome.jax.org; RRID:SCR_003212), supported by the US National Institutes of Health, is a Biomedical Data Repository listed in the Trans-NIH Biomedical Informatics Coordinating Committee registry. As an increasingly FAIR-compliant and TRUST-worthy data repository, MPD accepts phenotype and genotype data from mouse experiments and curates, organizes, integrates, archives, and distributes those data using community standards. Data are accompanied by rich metadata, including widely used ontologies and detailed protocols. Data are from all over the world and represent genetic, behavioral, morphological, and physiological disease-related characteristics in mice at baseline or those exposed to drugs or other treatments. MPD houses data from over 6000 strains and populations, representing many reproducible strain types and heterogenous populations such as the Diversity Outbred where each mouse is unique but can be genotyped throughout the genome. A suite of analysis tools is available to aggregate, visualize, and analyze these data within and across studies and populations in an increasingly traceable and reproducible manner. We have refined existing resources and developed new tools to continue to provide users with access to consistent, high-quality data that has translational relevance in a modernized infrastructure that enables interaction with a suite of bioinformatics analytic and data services.
| S-EPMC9825561 | biostudies-literature
Project description:There was an explosion in the amount of commercially available DNA in sequence repositories over the last decade. The number of such plasmids increased from 12,000 to over 300,000 among three of the largest repositories: iGEM, Addgene, and DNASU. A challenge in biodesign remains how to use these and other repository-based sequences effectively, correctly, and seamlessly. This work describes an approach to plasmid design where a plasmid is specified as simply a DNA sequence or list of features. The proposed software then finds the most cost-effective combination of synthetic and PCR-prepared repository fragments to build the plasmid via Gibson assembly®. It finds existing DNA sequences in both user-specified and public DNA databases: iGEM, Addgene, and DNASU. Such a software application is introduced and characterized against all post-2005 iGEM composite parts and all Addgene vectors submitted in 2018 and found to reduce costs by 34% versus a purely synthetic plasmid design approach. The described software will improve current plasmid assembly workflows by shortening design times, improving build quality, and reducing costs.
| S-EPMC6952187 | biostudies-literature
Project description:Teaching and learning of clinical reasoning are core principles of medical education. However, little guidance exists for faculty leaders to navigate curricular transitions between pre-clerkship and clerkship curricular phases. This study compares how educational leaders in these two phases understand clinical reasoning instruction. Previously reported cross-sectional surveys of pre-clerkship clinical skills course directors, and clerkship leaders were compared. Comparisons focused on perceived importance of a number of core clinical reasoning concepts, barriers to clinical reasoning instruction, level of familiarity across the undergraduate medical curriculum, and inclusion of clinical reasoning instruction in each area of the curriculum. Analyses were performed using the Mann Whitney U test. Both sets of leaders rated lack of curricular time as the largest barrier to teaching clinical reasoning. Clerkship leaders also noted a lack of faculty with skills to teach clinical reasoning concepts as a significant barrier (p < 0.02), while pre-clerkship leaders were more likely to perceive that these concepts were too advanced for their students (p < 0.001). Pre-clerkship leaders reported a higher level of familiarity with the clerkship curriculum than clerkship leaders reported of the pre-clerkship curriculum (p < 0.001). As faculty transition students from the pre-clerkship to the clerkship phase, a shared understanding of what is taught and when, accompanied by successful faculty development, may aid the development of longitudinal, milestone-based clinical reasoning instruction.
| S-EPMC10848998 | biostudies-literature
Project description:BackgroundThe decision about which type of general anesthetic to administer is typically made by the clinical team without patient engagement. This study examined patients' preferences, experiences, attitudes, beliefs, perceptions, and perceived social norms about anesthesia and about engaging in the decision regarding general anesthetic choice with their clinician.MethodsWe conducted a survey in the United States, sent to a panel of surgical patients through Qualtrics (Qualtrics, Provo, UT) from March 2022 through May 2022. Questions were developed based on the Theory of Planned Behavior and validated measures were used when available. A patient partner who had experienced both intravenous and inhaled anesthesia contributed to the development and refinement of the questions.ResultsA total of 806 patients who received general anesthesia for an elective procedure in the last five years completed the survey. 43% of respondents preferred a patient-led decision making role and 28% preferred to share decision making with their clinical team, yet only 7.8% reported being engaged in full shared decision making about the anesthesia they received. Intraoperative awareness, pain, nausea, vomiting and quickly returning to work and usual household activities were important to respondents. Waking up in the middle of surgery was the most commonly reported concern, despite this experience being reported only 8% of the time. Most patients (65%) who searched for information about general anesthesia noted that it took a lot of effort to find the information, and 53% agreed to feeling frustrated during the search.ConclusionsMost patients prefer a patient-led or shared decision making process when it comes to their anesthetic care and want to be engaged in the decision. However, only a small percentage of patients reported being fully engaged in the decision. Further studies should inform future shared decision-making tools, informed consent materials, educational materials and framing of anesthetic choices for patients so that they are able to make a choice regarding the anesthetic they receive.
| S-EPMC10433576 | biostudies-literature