Systematic Map of Human-Raptor Interaction and Coexistence Research.
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ABSTRACT:
SUBMITTER: Canney AC
PROVIDER: S-EPMC8749526 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundProtein-interaction maps are powerful tools for suggesting the cellular functions of genes. Although large-scale protein-interaction maps have been generated for several invertebrate species, projects of a similar scale have not yet been described for any mammal. Because many physical interactions are conserved between species, it should be possible to infer information about human protein interactions (and hence protein function) using model organism protein-interaction datasets.ResultsHere we describe a network of over 70,000 predicted physical interactions between around 6,200 human proteins generated using the data from lower eukaryotic protein-interaction maps. The physiological relevance of this network is supported by its ability to preferentially connect human proteins that share the same functional annotations, and we show how the network can be used to successfully predict the functions of human proteins. We find that combining interaction datasets from a single organism (but generated using independent assays) and combining interaction datasets from two organisms (but generated using the same assay) are both very effective ways of further improving the accuracy of protein-interaction maps.ConclusionsThe complete network predicts interactions for a third of human genes, including 448 human disease genes and 1,482 genes of unknown function, and so provides a rich framework for biomedical research.
| S-EPMC522870 | biostudies-literature
Project description:The recent pandemic caused by the novel coronavirus resulted in the greatest global health crisis since the Spanish flu pandemic of 1918. There is limited knowledge of whether SARS-CoV-2 is physically associated with human metalloproteins. Recently, high-confidence, experimentally supported protein-protein interactions between SARS-CoV-2 and human proteins were reported. In this work, 58 metalloproteins among these human targets have been identified by a structure-based approach. This study reveals that most human metalloproteins interact with the recently discovered SARS-CoV-2 orf8 protein, whose antibodies are one of the principal markers of SARS-CoV-2 infections. Furthermore, this work provides sufficient evidence to conclude that Zn2+ plays an important role in the interplay between the novel coronavirus and humans. First, the content of Zn-binding proteins in the involved human metalloproteome is significantly higher than that of the other metal ions. Second, a molecular linkage between the identified human Zn-binding proteome with underlying medical conditions, that might increase the risk of severe illness from the SARS-CoV-2 virus, has been found. Likely perturbations of host cellular metal homeostasis by SARS-CoV-2 infection are highlighted.
| S-EPMC7955571 | biostudies-literature
Project description:People believe information more if they have encountered it before, a finding known as the illusory truth effect. But what is the evidence for the generality and pervasiveness of the illusory truth effect? Our preregistered systematic map describes the existing knowledge base and objectively assesses the quality, completeness and interpretability of the evidence provided by empirical studies in the literature. A systematic search of 16 bibliographic and grey literature databases identified 93 reports with a total of 181 eligible studies. All studies were conducted at Western universities, and most used convenience samples. Most studies used verbatim repetition of trivia statements in a single testing session with a minimal delay between exposure and test. The exposure tasks, filler tasks and truth measures varied substantially across studies, with no standardisation of materials or procedures. Many reports lacked transparency, both in terms of open science practices and reporting of descriptive statistics and exclusions. Systematic mapping resulted in a searchable database of illusory truth effect studies ( https://osf.io/37xma/ ). Key limitations of the current literature include the need for greater diversity of materials as stimuli (e.g., political or health contents), more participants from non-Western countries, studies examining effects of multiple repetitions and longer intersession intervals, and closer examination of the dependency of effects on the choice of exposure task and truth measure. These gaps could be investigated using carefully designed multi-lab studies. With a lack of external replications, preregistrations, data and code, verifying replicability and robustness is only possible for a small number of studies.
| S-EPMC9166874 | biostudies-literature
Project description:Genetic interaction (GI) maps, comprising pairwise measures of how strongly the function of one gene depends on the presence of a second, have enabled the systematic exploration of gene function in microorganisms. Here, we present a two-stage strategy to construct high-density GI maps in mammalian cells. First, we use ultracomplex pooled shRNA libraries (25 shRNAs/gene) to identify high-confidence hit genes for a given phenotype and effective shRNAs. We then construct double-shRNA libraries from these to systematically measure GIs between hits. A GI map focused on ricin susceptibility broadly recapitulates known pathways and provides many unexpected insights. These include a noncanonical role for COPI, a previously uncharacterized protein complex affecting toxin clearance, a specialized role for the ribosomal protein RPS25, and functionally distinct mammalian TRAPP complexes. The ability to rapidly generate mammalian GI maps provides a potentially transformative tool for defining gene function and designing combination therapies based on synergistic pairs.
| S-EPMC3652613 | biostudies-literature
Project description:Marker positions on nine genetic linkage, radiation hybrid, and integrated maps of human chromosome 22 were compared with their corresponding positions in the completed DNA sequence. The proportion of markers whose map position is <250 kb from their respective sequence positions ranges from 100% to 35%. Several discordant markers were identified, as well as four regions that show common inconsistencies across multiple maps. These shared discordant regions surround duplicated DNA segments and may indicate mapping or assembly errors due to sequence homology. Recombination-rate distributions along the chromosome were also evaluated, with male and female meioses showing significantly different patterns of recombination, including an 8-Mb male recombination desert. The distributions of radiation-induced chromosome breakage for the GB4 and the G3 radiation hybrid panels were also evaluated. Both panels show fluctuations in breakage intensity, with different regions of significantly elevated rates of breakage. These results provide support for the common assumption that radiation-induced breaks are generally randomly distributed. The present studies detail the limitations of these important map resources and should prove useful for clarifying potential problems in the human maps and sequence assemblies, as well as for mapping and sequencing projects in and across other species.
| S-EPMC379125 | biostudies-literature
Project description:Protein kinases play a pivotal role in cell signaling, and dysregulation of many kinases has been linked to disease development. A large number of kinase inhibitors are therefore currently under investigation in clinical trials, and so far seven inhibitors have been approved as anti-cancer drugs. In addition, kinase inhibitors are widely used as specific probes to study cell signaling, but systematic studies describing selectivity of these reagents across a panel of diverse kinases are largely lacking. Here we evaluated the specificity of 156 validated kinase inhibitors, including inhibitors used in clinical trials, against 60 human Ser/Thr kinases using a thermal stability shift assay. Our analysis revealed many unexpected cross-reactivities for inhibitors thought to be specific for certain targets. We also found that certain combinations of active-site residues in the ATP-binding site correlated with the detected ligand promiscuity and that some kinases are highly sensitive to inhibition using diverse chemotypes, suggesting them as preferred intervention points. Our results uncovered also inhibitor cross-reactivities that may lead to alternate clinical applications. For example, LY333'531, a PKCbeta inhibitor currently in phase III clinical trials, efficiently inhibited PIM1 kinase in our screen, a suggested target for treatment of leukemia. We determined the binding mode of this inhibitor by x-ray crystallography and in addition showed that LY333'531 induced cell death and significantly suppressed growth of leukemic cells from acute myeloid leukemia patients.
| S-EPMC2154464 | biostudies-literature
Project description:Depression is a major public health problem among youth, currently estimated to affect as many as 9% of US children and adolescents. The recognition that both genes (nature) and environments (nurture) are important for understanding the etiology of depression has led to a rapid growth in research exploring gene-environment interactions (GxE). However, there has been no systematic review of GxE in youth depression to date.The goal of this article was to systematically review evidence on the contribution of GxE to the risk of child and adolescent depression. Through a search of PubMed and PsycINFO databases to 1 April 2010, we identified 20 candidate gene-environment interaction studies focused on depression in youth (up to age 26) and compared each study in terms of the following characteristics: research design and sample studied; measure of depression and environment used; genes explored; and GxE findings in relation to these factors.In total, 80% of studies (n = 16) found at least one significant GxE association. However, there was wide variation in methods and analyses adopted across studies, especially with respect to environmental measures used and tests conducted to estimate GxE. This heterogeneity made it difficult to compare findings and evaluate the strength of the evidence for GxE.The existing body of GxE research on depression in youth contains studies that are conceptually and methodologically quite different, which contributes to mixed findings and makes it difficult to assess the current state of the evidence. To decrease this heterogeneity, we offer 20 recommendations that are focused on: (a) reporting GxE research; (b) testing and reporting GxE effects; (c) conceptualizing, measuring and analyzing depression; (d) conceptualizing, measuring and analyzing environment; (e) increasing power to test for GxE; and (f) improving the quality of genetic data used. Although targeted to GxE research on depression, these recommendations can be adopted by GxE researchers focusing on other mental health outcomes.
| S-EPMC3202044 | biostudies-literature
Project description:BackgroundThe need to better understand implementing evidence-informed dementia care has been recognised in multiple priority-setting partnerships. The aim of this scoping review was to give an overview of the state of the evidence on implementation and dissemination of dementia care, and create a systematic evidence map.MethodsWe sought studies that addressed dissemination and implementation strategies or described barriers and facilitators to implementation across dementia stages and care settings. Twelve databases were searched from inception to October 2015 followed by forward citation and grey literature searches. Quantitative studies with a comparative research design and qualitative studies with recognised methods of data collection were included. Titles, abstracts and full texts were screened independently by two reviewers with discrepancies resolved by a third where necessary. Data extraction was performed by one reviewer and checked by a second. Strategies were mapped according to the ERIC compilation.ResultsEighty-eight studies were included (30 quantitative, 34 qualitative and 24 mixed-methods studies). Approximately 60% of studies reported implementation strategies to improve practice: training and education of professionals (94%), promotion of stakeholder interrelationships (69%) and evaluative strategies (46%) were common; financial strategies were rare (15%). Nearly 70% of studies reported barriers or facilitators of care practices primarily within residential care settings. Organisational factors, including time constraints and increased workload, were recurrent barriers, whereas leadership and managerial support were often reported to promote implementation. Less is known about implementation activities in primary care and hospital settings, or the views and experiences of people with dementia and their family caregivers.ConclusionThis scoping review and mapping of the evidence reveals a paucity of robust evidence to inform the successful dissemination and implementation of evidence-based dementia care. Further exploration of the most appropriate methods to evaluate and report initiatives to bring about change and of the effectiveness of implementation strategies is necessary if we are to make changes in practice that improve dementia care.
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Project description:In human-transformed landscapes, predators may feed on domesticated animals, and thus affect human well-being, creating negative perceptions and leading to conflict with people that can result in the persecution of the predator. We studied the factors that influence the perception of the Black-and-chestnut Eagle (Spizaetus isidori) in four rural Andean communities in Colombia and compiled historical and recent evidence on the persecution and other causes of mortality of this species in the country. We applied 267 questionnaires and conducted 16 interviews with local inhabitants, via visits to homes and schools in the surroundings of S. isidori nests. The perception of S. isidori by the inhabitants was largely negative and influenced by different socio-demographic factors such as gender, chicken (Gallus gallus) ownership, and chicken management. The records we obtained indicate that 47 eagles were shot, 16 were captured (three for illegal trafficking) and two were electrocuted on high-tension wires. The persecution of S. isidori occurs as retaliation or as a preventative measure against chicken predation, and is a significant cause of mortality of this species in Colombia. Effective conservation planning for S. isidori in Colombia needs to go further than the protected areas system, and include a socioecological perspective in conservation practices applied at landscapes scales that are dominated by people. Education programs and socioecological research, along with participatory work in local communities are key to the conservation of S. isidori in breeding territories. This approach can also prevent conflict over food resources-G. gallus and other poultry-that are shared by humans and S. isidori in rural landscapes.
| S-EPMC6953857 | biostudies-literature
Project description:To investigate methods and processes for timely, efficient and good quality peer review of research funding proposals in health.A two-stage evidence synthesis: (1) a systematic map to describe the key characteristics of the evidence base, followed by (2) a systematic review of the studies stakeholders prioritised as relevant from the map on the effectiveness and efficiency of peer review 'innovations'. Standard processes included literature searching, duplicate inclusion criteria screening, study keyword coding, data extraction, critical appraisal and study synthesis.A total of 83 studies from 15 countries were included in the systematic map. The evidence base is diverse, investigating many aspects of the systems for, and processes of, peer review. The systematic review included eight studies from Australia, Canada, and the USA, evaluating a broad range of peer review innovations. These studies showed that simplifying the process by shortening proposal forms, using smaller reviewer panels, or expediting processes can speed up the review process and reduce costs, but this might come at the expense of peer review quality, a key aspect that has not been assessed. Virtual peer review using videoconferencing or teleconferencing appears promising for reducing costs by avoiding the need for reviewers to travel, but again any consequences for quality have not been adequately assessed.There is increasing international research activity into the peer review of health research funding. The studies reviewed had methodological limitations and variable generalisability to research funders. Given these limitations it is not currently possible to recommend immediate implementation of these innovations. However, many appear promising based on existing evidence, and could be adapted as necessary by funders and evaluated. Where feasible, experimental evaluation, including randomised controlled trials, should be conducted, evaluating impact on effectiveness, efficiency and quality.
| S-EPMC5947897 | biostudies-literature