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8,537 results for “Openness”
Data from: The role of browsers in maintaining the openness of savanna grazing lawns
<p>1. In savannas, ruminant herbivores can have divergent impacts on tree recruitment and resulting woody cover. Heavy grazing by cattle results in woody thickening, whereas intensive grazing by wildlife instead tends to be associated with lower woody cover.</p> <p>2. To disentangle why woody cover is low in areas heavily grazed by wildlife, we tested (I) whether short-grass environments attract indigenous mammalian browsers; (II) whether preference for short grass decreases with browser body mass because of differences in predator susceptibility; and (III) whether these translate into suppression of seedlings and saplings on grazing lawns, thus maintaining their openness.</p> <p> 3. This work was conducted in Kruger National Park (KNP) and Hluhluwe iMfolozi Park (HiP), South Africa. In KNP, the effect of grass height on browser abundance (estimated using dung counts), and on the utilisation of woody plants by browsers (using a bite-score approach) was tested. An exclosure experiment tested the effect of grass height and browser removal on seedling survival and sapling growth of a dominant woody plant species in a short- and tall-grass mosaic. Finally, in HiP, the effect of grass height and browser removal were tested on the growth rates of a range of woody species, monitored over ten years, across ten sites.</p> <p>4. Steenbok and impala selected short- over tall-grass as preferred browsing sites, while elephant preferred tall grass. Browser abundance on short grass decreased with browser body mass, indicating that predator avoidance might be a key factor driving small-bodied browsers to utilize grazing lawns. Grass height did not explain variation in the utilisation of woody plants by browsers.</p> <p>5. Seedling survival was lowest in short grass and when browsers were present, with mortality occurring in two out of every three seedlings. Also, sapling growth was lowest in short grass, although browser removal had no effect. Evidence for increased browser impact on grazing lawns was clearest from our long-term exclosure experiment in HiP, which demonstrated that the effect of browsers on sapling growth rates was strongly modified by the presence of short grass.</p> <p>6. <i>Synthesis</i>. These results provide support for the hypothesis that browsers, particularly small-bodied browsers and mixed feeders, are attracted to short-grass habitats, and that, they help maintain grazing lawn openness by suppressing woody seedling survival and sapling growth where grass is kept short by grazers.</p>
Figure 2 from: Haak L, Greene S, Ratan K (2020) A New Research Economy: Socio-technical framework to open up lines of credit in the academic community. Research Ideas and Outcomes 6: e60477. https://doi.org/10.3897/rio.6.e60477
Figure 2 Collaborative Workflow of an Incremental Dataset in a Consortium Setting (click to view enlarged slide in Present mode). The workflow of an investigator's incremental dataset is shown as it is incorporated into the Facilitated Living Review (FLR), moving along a continuum from closed to open review. (1) After ideation and hypothesis formation by the team, early experimentation creates an incremental dataset. (2) The dataset is shared and discussed with the Project X research consortium, then iterated. (3) The v.3 dataset is shared with the consortium for further analysis, positioning, and citation in the context of the latest published evidence in the FLR. (4) The FLR with its cited, organically peer reviewed dataset is posted on a preprint server under the authorship of the FLR consortium. (5) Feedback from the broader community may lead to further iteration of the dataset at the discretion of the project team in the next round of the FLR revisions.
RWTHmediTEC/VSDFullBodyBoneModels: 3D surface models of the pelvis and femur created from CT datasets of the open source VSDFullBody database
<p>Was used in: Fischer <em>et al.</em> A robust method for automatic identification of femoral landmarks, axes, planes and bone coordinate systems using surface models. <em>Scientific Reports</em> <strong>10</strong>, 20859; <a href="https://doi.org/10.1038/s41598-020-77479-z">10.1038/s41598-020-77479-z</a> (2020).</p>
Phenomenon of music-induced opening of the blood-brain barrier in healthy mice
<p class="MsoBodyText">Music plays a more important role in our life than just being an entertainment. For example, it can be used as anti-anxiety therapy of human and animals. However, the unsafe listening of loud music triggers hearing loss in millions of young people and professional musicians (rock, jazz, and symphony orchestra) due to exposure to damaging sound levels using personal audio devices or at noisy entertainment venues including nightclubs, discotheques, bars, and concerts. Therefore, it is important to understand how loud music affects us.</p> <p class="MsoBodyText">In this pioneering study on healthy mice, we discover that loud rock music below the safety threshold causes opening of the blood-brain barrier (OBBB), which plays an vital role in protecting the brain from viruses, bacteria and toxins. We clearly demonstrate that listening loud music during 2 hrs in an intermittent adaptive regime is accompanied by delayed (1h after music exposure) and short-lasting (during 1-4 hrs) OBBB to low and high molecular weight compounds without cochlear and brain impairments. We present the systemic and molecular mechanisms responsible for music-induced OBBB. Finally, a revision of our traditional knowledge about the BBB nature and the novel strategies in optimizing of sound-mediated methods for brain drug delivery are discussed.</p>
Concept: Open science
<p>A 4-minute video explaining open science. Available also in https://www.helsinki.fi/fi/unitube/video/6b1aa015-452a-4a97-a501-740379e6623a</p>
Open Street Map: mapping e cartografia collaborativa in condizioni di emergenza
<p>In questo minicorso, facente parte della collezione <a href="https://www.youtube.com/playlist?list=PLXBZ0jvtlWH6qL7SOKOddJ_7MioDid_Oo">acasaconSE</a> organizzato dalla associazione <a href="http://www.successionecologica.it/">Successione Ecologica</a>, si parla di cos'è <a href="http://www.openstreetmap.org">Open Street Map</a> e come, in condizioni di emergenza (pandemie, tsunami, terremoti, siccità etc.), la cartografia colalborativa possa essere sia di supporto alle attività di soccorso che alla vita quotidiana dei singoli cittadini. In particolare, l'outline del minicorso è:<br> 1) Open Street Map: perché "insieme è meglio" e come contribuire<br> 2) Esempio di applicazione in condizioni di emergenza (il progetto HOT e il caso COVID-19)<br> 3) il civic hacking e le comunità informali</p> <p>Buona visione! </p>
Blood-brain barrier opening with focused ultrasound in Parkinson's disease dementia
<p><span><span><span><span><span><span><span><span><span><span><span>MR-guided focused ultrasound (MRgFUS), in combination with intravenous microbubble administration, <span><span>has been</span></span> applied for focal temporary BBB opening in patients with neurodegenerative disorders and brain tumors. MRgFUS could become a therapeutic tool for drug delivery of putative neurorestorative therapies. Treatment for Parkinson's disease with dementia (PDD) is an important unmet need. We <span><span>initiated a prospective, single-arm, non-randomized, proof-of-concept, safety and feasibility</span></span> phase I clinical trial <span><span>(NCT03608553), which is still in progress. The primary outcomes of the study were to demonstrate the safety, feasibility and reversibility of BBB disruption in PDD,</span></span> targeting the right parieto-occipito-temporal cortex where cortical pathology is foremost in this clinical state. <span><span>Changes in </span></span><span><span>β</span></span><span><span>-</span></span><span><span>amyloid burden, brain metabolism after treatments and neuropsychological assessments, were analyzed as exploratory measurements.</span></span> <span><span>Five patients were recruited from October 2018 until May 2019, and</span></span> received two <span><span>treatment</span></span> sessions separated by 2-3 weeks. <span><span>The results are set out in a descriptive manner.</span></span> Overall, this procedure was feasible and reversible with no serious clinical or radiological side effects. <span><span>We report BBB opening in the parieto-occipito-temporal junction in 8/10 treatments in 5 patients as demonstrated by gadolinium enhancement. In all cases the procedures were uneventful and no side effects were encountered associated with BBB opening.</span></span> From pre- to post-treatment, mild cognitive improvement was observed, and no major changes were detected in amyloid or fluorodeoxyglucose PET. MRgFUS-BBB opening in PDD is thus safe, reversible, and can be <span><span>performed</span></span> repeatedly. This study provides encouragement for the concept of BBB opening for drug delivery to treat dementia in PD and other neurodegenerative disorders.</span></span></span></span></span></span></span></span></span></span></span></p>
Reproducible results for: pmparser and PMDB: resources for large-scale, open studies of the biomedical literature
<p>The zip file contains all code and results. See the included readme.</p>
Data from: Sound attenuation in the ear of domestic chickens (Gallus gallus domesticus) as a result of beak opening
Because the quadrate and the eardrum are connected, the hypothesis was tested that birds attenuate the transmission of sound through their ears by opening the bill, which potentially serves as an additional protective mechanism for self-generated vocalizations. In domestic chickens, it was examined if a difference exists between hens and roosters, given the difference in vocalization capacity between the sexes. To test the hypothesis, vibrations of the columellar footplate were measured ex vivo with laser Doppler vibrometry (LDV) for closed and maximally opened beak conditions, with sounds introduced at the ear canal. The average attenuation was 3.5 dB in roosters and only 0.5 dB in hens. To demonstrate the importance of a putative protective mechanism, audio recordings were performed of a crowing rooster. Sound pressures levels of 133.5 dB were recorded near the ears. The frequency content of the vocalizations was in accordance with the range of highest hearing sensitivity in chickens. The results indicate a small but significant difference in sound attenuation between hens and roosters. However, the amount of attenuation as measured in the experiments on both hens and roosters is small and will provide little effective protection in addition to other mechanisms such as stapedius muscle activity.
Data from: Who shares? Who doesn't? Factors associated with openly archiving raw research data
Many initiatives encourage investigators to share their raw datasets in hopes of increasing research efficiency and quality. Despite these investments of time and money, we do not have a firm grasp of who openly shares raw research data, who doesn't, and which initiatives are correlated with high rates of data sharing. In this analysis I use bibliometric methods to identify patterns in the frequency with which investigators openly archive their raw gene expression microarray datasets after study publication. Automated methods identified 11,603 articles published between 2000 and 2009 that describe the creation of gene expression microarray data. Associated datasets in best-practice repositories were found for 25% of these articles, increasing from less than 5% in 2001 to 30%-35% in 2007-2009. Accounting for sensitivity of the automated methods, approximately 45% of recent gene expression studies made their data publicly available. First-order factor analysis on 124 diverse bibliometric attributes of the data creation articles revealed 15 factors describing authorship, funding, institution, publication, and domain environments. In multivariate regression, authors were most likely to share data if they had prior experience sharing or reusing data, if their study was published in an open access journal or a journal with a relatively strong data sharing policy, or if the study was funded by a large number of NIH grants. Authors of studies on cancer and human subjects were least likely to make their datasets available. These results suggest research data sharing levels are still low and increasing only slowly, and data is least available in areas where it could make the biggest impact. Let's learn from those with high rates of sharing to embrace the full potential of our research output.
Data from: Are extraversion and openness indicators of a slow life history strategy?
Theory and data generally concur that a slower Life History Strategy (LHS) is associated with higher Conscientiousness, Agreeableness and Emotional Stability. Whether Extraversion and Openness are indicators of a slow LH, or whether they include both fast and slow LH components, remains unresolved. I addressed these questions in two studies: one of university students observed via periodic brief audio recordings during 72 hours of their daily lives, and the second a re-analysis of data from Block and Block's (2006) longitudinal study. In both studies, I operationalized LHS as the correlation between an individual's California Q-Sort (CAQ) profile and the slow Life History (SLH) CAQ template created by Sherman et al. (2013) and Dunkel et al. (2015). I calculated Five Factor Model dimension scores using McCrae et al's (1986) method. In both samples, individuals whose CAQ profile more closely resembled the SLH template were higher in Conscientiousness, Agreeableness, and Emotional Stability than those pursuing a faster LHS. Extraversion was unrelated to LHS, while Openness in the Block and Block data set was actually associated with a faster LHS. Analysis of individual CAQ items revealed some differences between the studies. Generally, Extraversion-loading items tapping excitement-seeking and self-dramatization, and Openness-loading items tapping nonconformity, were associated with a faster LHS. Participants in the audio recording study also completed a HEXACO personality inventory and the Arizona Life History Battery. LHS as measured by the ALHB was uncorrelated with LHS as measured by the CAQ. Controlling for Extraversion yielded a significant positive relationship between the two LHS measures, suggesting that their poor convergent validity resulted from differences in their coverage of Extraversion-related content.
Data from: Arabidopsis MKK10-MPK6 mediates red-light-regulated opening of seedling cotyledons through phosphorylation of PIF3
Photomorphogenesis is an important process in which seedlings emerge from soil and begin autotrophic growth. Photomorphogenesis mechanisms include light signal perception, signal transduction, and the modulation of light-responsive genes expression, ultimately leading to cellular and developmental changes. Phytochrome-interacting factors (PIFs) play pivotal roles in negatively regulating photomorphogenesis. Light-induced activation of phytochromes triggers the rapid phosphorylation and degradation of PIFs, but the kinases responsible for the phosphorylation of PIFs are largely unknown. Here, we show that Arabidopsis MPK6 is a kinase involved in phosphorylating PIF3 and regulating red (R) light-induced cotyledon opening, a crucial process during seedling photomorphogenesis. MPK6 was activated by R light, and cotyledon opening angle in R light was reduced in mpk6 seedlings. MKK10, a MAPKK whose function is currently unclear, appears to act as a kinase upstream of MPK6 in regulating cotyledon opening. The activation of MPK6 by MKK10 led to the phosphorylation of PIF3 and accelerated its turnover in transgenic seedlings. Accordingly, the overexpression of PIF3 suppressed the MKK10-induced cotyledon opening. MKK10-MPK6 function downstream of phyB in regulating seedlings cotyledon opening in R light. Therefore, MKK10-MPK6 cascade appears to mediate the regulation of R light-controlled seedling photomorphogenesis,via a mechanism that might involve the phosphorylation of PIF3.
Data from: Catching-up but telomere loss: half-opening the black box of growth and ageing trade-off in wild king penguin chicks
One of the reasons for animals not to grow as fast as they potentially could is that fast growth has been shown to be associated with reduced lifespan. However, we are still lacking a clear description of the reality of growth-dependent modulation of ageing mechanisms in wild animals. Using the particular growth trajectory of small king penguin chicks naturally exhibiting higher-than-normal growth rate to compensate for the winter break, we tested whether oxidative stress and telomere shortening are related to growth trajectories. Plasma antioxidant defences, oxidative damages levels and telomere length were measured at the beginning and the end of the post-winter growth period in three groups of chicks (small chicks which either passed away or survived the growth period, and large chicks). Small chicks that died early during the growth period had the highest level of oxidative damage and the shortest telomere lengths prior to death. Here, we show that small chicks that grew faster did it at the detriment of body maintenance mechanisms as shown by (i) higher oxidative damage and (ii) accelerated telomere loss. Our study provides the first evidence for a mechanistic link between growth and ageing rates under natural conditions.
Data from: Has open data arrived at the British Medical Journal (BMJ)? An observational study
Objective: To quantify data sharing policy compliance at the BMJ by analysing the rate of data sharing practices, and investigate attitudes and examine barriers towards data sharing. Design: Observational study. Setting: The BMJ research archive. Participants: 160 randomly sampled BMJ research articles, excluding meta-analysis and systematic reviews. Main outcome measures: Percentages of research articles that indicated the availability of their raw datasets in their data sharing statements and those that provided their datasets upon request. Results: Fifty out of 160 (31%) research articles indicated the availability of their datasets. Twelve used publicly available data and the remaining 38 were sent email requests to access their datasets. Only 1 publicly available dataset could be accessed and only 6 out of 38 shared their data via e-mail. So only 7/160 research articles shared their datasets, 4.4% (95% confidence interval: 1.8% to 8.8%). Conclusions: Despite the BMJ's strong data sharing policy, sharing rates are low. Possible explanations for low data sharing rates could be: the wording of the BMJ data sharing policy, which leaves room for individual interpretation and possible loopholes; that our email requests ended up in researchers spam folders; and, that researchers are not rewarded in the scientific community for sharing their data. It might be time for a more effective data sharing policy and better incentives for health and medical researchers to share their data.
Data from: A novel environmental restoration method for an abandoned limestone quarry with a deep open pit and steep palisades: a case study
In general, exploitation of rock materials, such as limestone or granite exploitation, can cause serious damage to the ecological environment near a mine area. With economic development and the ever-increasing demand for ore resources, mining activities have induced very serious environmental issues in China. Therefore, environmental restoration work around mines in China is urgently required. This study explores the Chuankou open-pit limestone quarry in Tongchuan City, Shaanxi Province, Northwest China, as the engineering case. The environmental issues caused by over 40 years of limestone exploitation, including land degradation, land occupation, dust pollution and potential geological disasters, were investigated. Combining the characteristics of this quarry with a summary of previous studies on environmental restoration work, this paper proposes a novel and systematic method that was comprehensively carried out through engineering and revegetation measures. The engineering measure, that is, the construction of an artificial slope by using local abandoned construction materials, solved the environmental problems in this quarry and provided site conditions favourable for revegetation. The revegetation measure restored the local ecosystem. This method provides both a new idea for the sustainable development of a mining area and a useful reference for analogous engineering cases.
Data from: In an age of open access to research policies: physician and public health NGO staff research use and policy awareness
Introduction: Through funding agency and publisher policies, an increasing proportion of the health sciences literature is being made open access. Such an increase in access raises questions about the awareness and potential utilization of this literature by those working in health fields. Methods: A sample of physicians (N=336) and public health non-governmental organization (NGO) staff (N=92) were provided with relatively complete access to the research literature indexed in PubMed, as well as access to the point-of-care service UpToDate, for up to one year, with their usage monitored through the tracking of web-log data. The physicians also participated in a one-month trial of relatively complete or limited access. Results: The study found that participants' research interests were not satisfied by article abstracts alone nor, in the case of the physicians, by a clinical summary service such as UpToDate. On average, a third of the physicians viewed research a little more frequently than once a week, while two-thirds of the public health NGO staff viewed more than three articles a week. Those articles were published since the 2008 adoption of the NIH Public Access Policy, as well as prior to 2008 and during the maximum 12-month embargo period. A portion of the articles in each period was already open access, but complete access encouraged a viewing of more research articles. Conclusion: Those working in health fields will utilize more research in the course of their work as a result of (a) increasing open access to research, (b) improving awareness of and preparation for this access, and (c) adjusting public and open access policies to maximize the extent of potential access, through reduction in embargo periods and access to pre-policy literature.
Data from: Under the snow: a new camera trap opens the white box of subnivean ecology
Snow covers the ground over large parts of the world for a substantial portion of the year. Yet very few methods are available to quantify biotic variables below the snow, with most studies of subnivean ecological processes relying on comparisons of data before and after the snow cover season. We developed a camera trap prototype to quantify subnivean small mammal activity. The trap consists of a camera that is attached facing downward from the ceiling of a box, which is designed to function as a snow-free tunnel. We tested it by placing nine traps with passive infrared sensors in a subarctic habitat where snow cover lasted for about 6 months. The traps were functional for the whole winter, permitting continuous data collection of site-specific presence and temporal activity patterns of all three small mammal species present (the insectivorous common shrew, Sorex araneus, the herbivorous tundra vole, Microtus oeconomus, and the carnivorous stoat, Mustela erminea) as well as abiotic conditions (presence/absence of snow cover and subnivean temperature). Based on their successful functioning (only 6% of the photographs appeared empty or were of poor quality, whereas ca 80% were of small mammals and the remaining of birds and invertebrates), we discuss how the new camera trap can enable subnivean studies of small mammal communities. This greatly increases the temporal resolution and extent of data collection and thereby provides unpreceded opportunities to understand population and food web dynamics in ecosystems with snow cover.
Data from: Chromosomal loci important for cotyledon opening under UV-B in Arabidopsis thaliana
BACKGROUND: Understanding of the genetic architecture of plant UV-B responses allows extensive targeted testing of candidate genes or regions, along with combinations of those genes, for placement in metabolic or signal transduction pathways. RESULTS: Composite interval mapping and single-marker analysis methods were used to identify significant loci for cotyledon opening under UV-B in four sets of recombinant inbred lines. In addition, loci important for canalization (stability) of cotyledon opening were detected in two mapping populations. One candidate locus contained the gene HY5. Mutant analysis demonstrated that HY5 was required for UV-B-specific cotyledon opening. CONCLUSIONS: Structured mapping populations provide key information on the degree of complexity in the genetic control of UV-B-induced cotyledon opening in Arabidopsis. The loci identified using quantitative trait analysis methods are useful for follow-up testing of candidate genes.
Data from: Dynamic visual cues induce jaw opening and closing by tiger beetles during pursuit of prey
In dynamic locomotory contexts, visual cues often trigger adaptive behaviour by the viewer, yet studies investigating how animals determine impending collisions typically employ either stationary viewers or objects. Here, we describe a dynamic situation of visually guided prey pursuit in which both impending prey contact and escape elicit observable adaptive behaviours in the pursuer, a predatory beetle. We investigated which visual cues may independently control opening and closing of the beetle's jaws during chases of prey dummies. Jaw opening and closing typically occur when prey is within the 60° binocular field, but not at specific distances, angular sizes or time-to-collision. We show that a sign change in the expansion rate of the target image precedes jaw opening (16 ms) and closing (35 ms), signalling to the beetle that it is gaining on the target or that the target is getting away. We discuss the 'sloppiness' of such variation in the lag of the behavioural response, especially jaw closing, as an adaptation to uncertainty about target position due to degradation of the target image by motion blur from the fast-running beetle.
Data from: Opening the tap: increased riverine connectivity strengthens marine food web pathways.
Reduction of ecosystem connectivity has long-lasting impacts on food webs. Anadromous fish, which migrate from marine to freshwater ecosystems to complete reproduction, have seen their historically larger ecosystem role undercut by widespread riverine habitat fragmentation and other impacts mainly derived from anthropogenic sources. The result has been extensive extirpations and increased susceptibility to a suite of environmental factors that currently impede recovery. Under this present-day context of reduced productivity and connectivity, aggressive management actions and enforcement of catch limits including bycatch caps and complete moratoria on harvest have followed. What remains less understood are the implications of changes to food webs that co-occurred. What benefits restoration could provide in terms of ecosystem functioning in relation to economic costs associated with dam removal and remediation is unknown and can limit the scope and value of restoration activities. Here we employ, historical landscape-based biomass estimates of anadromous alosine for the first time in an ecosystem modeling of the Northeast US large marine ecosystem (LME), to evaluate the value of improving connectivity by measuring the increase in energy flow and population productivity. We compared a restored alosine model to a contemporary model, analyzing the impacts of the potential increase of connectivity between riverine and oceanic systems. We observed changes in ecosystem functional structure and widespread ecosystem benefits for fisheries and conservation efforts. A key advantage was the potential for a 26% biomass increase of piscivorous with high economic value, including Atlantic cod, and for a 69% increase for species of conservation concern such as pelagic sharks, seabirds and marine mammals. Our study highlights the benefits of increased connectivity between freshwater and ocean ecosystems. We demonstrate the significant role anadromous forage fish could play in improving specific fisheries and overall ecosystem functioning, mainly through the diversification of species capable of transferring primary production to upper trophic levels, adding to benefits associated with their restoration.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.