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4,182 results for “universities”
Data from: Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods
The quantification of the biological diversity in environmental samples using high-throughput DNA sequencing is hindered by the PCR bias caused by variable primer–template mismatches of the individual species. In some dietary studies, there is the added problem that samples are enriched with predator DNA, so often a predator-specific blocking oligonucleotide is used to alleviate the problem. However, specific blocking oligonucleotides could coblock nontarget species to some degree. Here, we accurately estimate the extent of the PCR biases induced by universal and blocking primers on a mock community prepared with DNA of twelve species of terrestrial arthropods. We also compare universal and blocking primer biases with those induced by variable annealing temperature and number of PCR cycles. The results show that reads of all species were recovered after PCR enrichment at our control conditions (no blocking oligonucleotide, 45 °C annealing temperature and 40 cycles) and high-throughput sequencing. They also show that the four factors considered biased the final proportions of the species to some degree. Among these factors, the number of primer–template mismatches of each species had a disproportionate effect (up to five orders of magnitude) on the amplification efficiency. In particular, the number of primer–template mismatches explained most of the variation (~3/4) in the amplification efficiency of the species. The effect of blocking oligonucleotide concentration on nontarget species relative abundance was also significant, but less important (below one order of magnitude). Considering the results reported here, the quantitative potential of the technique is limited, and only qualitative results (the species list) are reliable, at least when targeting the barcoding COI region.
Data from: Census parcels cropping system classification from multitemporal remote imagery: a proposed universal methodology
A procedure named CROPCLASS was developed to semi-automate census parcel crop assessment in any agricultural area using multitemporal remote images. For each area, CROPCLASS consists of a) a definition of census parcels through vector files in all of the images; b) the extraction of spectral bands (SB) and key vegetation index (VI) average values for each parcel and image; c) the conformation of a matrix data (MD) of the extracted information; d) the classification of MD decision trees (DT) and Structured Query Language (SQL) crop predictive model definition also based on preliminary land-use ground-truth work in a reduced number of parcels; and e) the implementation of predictive models to classify unidentified parcels land uses. The software named CROPCLASS-2.0 was developed to semi-automatically perform the described procedure in an economically feasible manner. The CROPCLASS methodology was validated using seven GeoEye-1 satellite images that were taken over the LaVentilla area (Southern Spain) from April to October 2010 at 3- to 4-week intervals. The studied region was visited every 3 weeks, identifying 12 crops and others land uses in 311 parcels. The DT training models for each cropping system were assessed at a 95% to 100% overall accuracy (OA) for each crop within its corresponding cropping systems. The DT training models that were used to directly identify the individual crops were assessed with 80.7% OA, with a user accuracy of approximately 80% or higher for most crops. Generally, the DT model accuracy was similar using the seven images that were taken at approximately one-month intervals or a set of three images that were taken during early spring, summer and autumn, or set of two images that were taken at about 2 to 3 months interval. The classification of the unidentified parcels for the individual crops was achieved with an OA of 79.5%.
Data from: Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity
The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. Despite this popularity, the universality and specificity of PCR primers for the ITS region are not satisfactory, resulting in amplification and sequencing difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S sequences of Plantae and Fungi from GenBank, we designed new universal and plant-specific PCR primers for amplifying the whole ITS region and a part of it (ITS1 or ITS2) of plants. In silico analyses of the new and the existing ITS primers based on these highly representative data sets indicated that (i) the newly designed universal primers are suitable for over 95% of plants in most groups; and (ii) the plant-specific primers are suitable for over 85% of plants in most groups without amplification of fungi. A total of 335 samples from 219 angiosperm families, 11 gymnosperm families, 24 fern and lycophyte families, 16 moss families and 17 fungus families were used to test the performances of these primers. In vitro PCR produced similar results to those from the in silico analyses. Our new primer pairs gave PCR improvements up to 30% compared with common-used ones. The new universal ITS primers will find wide application in both plant and fungal biology, and the new plant-specific ITS primers will, by eliminating PCR amplification of nonplant templates, significantly improve the quality of ITS sequence information collections in plant molecular systematics and DNA barcoding.
Data from: Exploring the universe of protein structures beyond the Protein Data Bank
It is currently believed that the atlas of existing protein structures is faithfully represented in the Protein Data Bank. However, whether this atlas covers the full universe of all possible protein structures is still a highly debated issue. By using a sophisticated numerical approach, we performed an exhaustive exploration of the conformational space of a 60 amino acid polypeptide chain described with an accurate all-atom interaction potential. We generated a database of around 30,000 compact folds with at least 30% of secondary structure corresponding to local minima of the potential energy. This ensemble plausibly represents the universe of protein folds of similar length; indeed, all the known folds are represented in the set with good accuracy. However, we discover that the known folds form a rather small subset, which cannot be reproduced by choosing random structures in the database. Rather, natural and possible folds differ by the contact order, on average significantly smaller in the former. This suggests the presence of an evolutionary bias, possibly related to kinetic accessibility, towards structures with shorter loops between contacting residues. Beside their conceptual relevance, the new structures open a range of practical applications such as the development of accurate structure prediction strategies, the optimization of force fields, and the identification and design of novel folds.
Data from: Scientific output scales with resources. A comparison of US and European Universities
By using a comprehensive dataset of US and European universities, we demonstrate super-linear scaling between university revenues and their volume of publications and (field-normalized) citations. We show that this relationship holds both in the US and in Europe. In terms of resources, our data show that three characteristics differentiate the US system: (1) a significantly higher level of resources for the entire system, (2) a clearer distinction between education-oriented institutions and doctoral universities and (3) a higher concentration of resources among doctoral universities. Accordingly, a group of US universities receive a much larger amount of resources and have a far higher number of publications and citations when compared to their European counterparts. These results demonstrate empirically that international rankings are by and large richness measures and, therefore, can be interpreted only by introducing a measure of resources. Implications for public policies and institutional evaluation are finally discussed.
Data from: Functional diversification of Argonautes in nematodes: an expanding universe
In the last decade, many diverse RNAi (RNA interference) pathways have been discovered that mediate gene silencing at epigenetic, transcriptional and post-transcriptional levels. The diversity of RNAi pathways is inherently linked to the evolution of Ago (Argonaute) proteins, the central protein component of RISCs (RNAinduced silencing complexes). An increasing number of diverse Agos are have been identified in different species. The functions of most of these proteins are not yet known, but they are generally assumed to play roles in development, genome stability and/or protection against pathogens. Recent research in the nematode Caenorhabditis elegans has expanded the breadth of RNAi functions to include transgenerational epigenetic memory and, possibly, environmental sensing. These functions are inherently linked to the production of secondary siRNAs (small interfering RNAs) that bind to members of a clade of WAGOs (wormspecific Agos). In the present article, we review briefly what is known about the evolution and function of Ago proteins in eukaryotes, including the expansion of WAGOs in nematodes. We postulate that the rapid evolution of WAGOs enables the exceptional functional plasticity of nematodes, including their capacity for parasitism.
Data from: Difficult patient-doctor encounters in a Swiss university outpatient clinic: a cross-sectional study.
Introduction: Previous research has shown that multiple factors contribute to healthcare providers perceiving encounters as difficult, and are related to both medical and non-medical demands. Aim: To measure the prevalence and to identify predictors of encounters perceived as difficult by medical residents. Design and Setting: Cross-sectional study at the Department of Ambulatory Care and Community Medicine (DACCM), a university outpatient clinic with a long tradition of caring for vulnerable patients. Method: We identified difficult doctor-patient encounters using the validated Difficult Doctor-Patient Relationship Questionnaire (DDPRQ-10), and characterized patients using the Patient's Vulnerability Grid, a validated questionnaire measuring 5 domains of vulnerability, both completed by medical residents after each encounter. We used a multiple linear regression model with the outcome variable as the DDPRQ-10 score, controlling for resident characteristics. Participants: We analyzed 527 patient encounters performed by all 27 DACCM residents (17 women and 10 men). We asked each medical resident to evaluate 20 consecutive consultations starting on the same date. Outcome: One hundred and fifty-seven encounters (29,8%) were perceived as difficult. Results: After adjusting for differences among residents, all five domains of the Patient Vulnerability Grid were independently associated with a difficult encounter: frequent health care user; psychological comorbidity; health comorbidity; risky behaviors and a precarious social situation. Conclusion: Nearly a third of encounters were perceived as difficult by medical residents in our university outpatient clinic that cares for a high proportion of vulnerable patients. This represents twice the average ratio of difficult encounters in general practice. All five domains of patient vulnerability appear to have partial explanatory power on medical residents' perception of difficult patient encounters.
Data from: Health assessment of French university students and risk factors associated with mental health disorders
Objective: The first year of university is a particularly stressful period and can impact academic performance and students' health. The aim of this study was to evaluate the health and lifestyle of undergraduates and assess risk factors associated with psychiatric symptoms. Materials and methods: Between September 2012 and June 2013, we included all undergraduate students who underwent compulsory a medical visit at the university medical service in Nice (France) during which they were screened for potential diseases during a diagnostic interview. Data were collected prospectively in the CALCIUM database (Consultations Assistés par Logiciel pour les Centres Inter-Universitaire de Médecine) and included information about the students' lifestyle (living conditions, dietary behavior, physical activity, use of recreational drugs). The prevalence of psychiatric symptoms related to depression, anxiety and panic attacks was assessed and risk factors for these symptoms were analyzed using logistic regression. Results: A total of 4,184 undergraduates were included. Prevalence for depression, anxiety and panic attacks were 12.6%, 7.6% and 1.0%, respectively. During the 30 days preceding the evaluation, 0.6% of the students regularly drank alcohol, 6.3% were frequent-to-heavy tobacco smokers, and 10.0% smoked marijuana. Dealing with financial difficulties and having learning disabilities were associated with psychiatric symptoms. Students who were dissatisfied with their living conditions and those with poor dietary behavior were at risk of depression. Being a woman and living alone were associated with anxiety. Students who screened positively for any psychiatric disorder assessed were at a higher risk of having another psychiatric disorder concomitantly. Conclusion: The prevalence of psychiatric disorders in undergraduate students is low but the rate of students at risk of developing chronic disease is far from being negligible. Understanding predictors for these symptoms may improve students' health by implementing targeted prevention campaigns. Further research in other French universities is necessary to confirm our results.
Data from: The mouse universal genotyping array: from substrains to subspecies
Genotyping microarrays are an important resource for genetic mapping, population genetics, and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse (Mus musculus). The bulk of the content of GigaMUGA is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations, and for substrain-level identification of laboratory mice. In addition to 141,090 single nucleotide polymorphism probes, GigaMUGA contains 2006 probes for copy number concentrated in structurally polymorphic regions of the mouse genome. The performance of the array is characterized in a set of 500 high-quality reference samples spanning laboratory inbred strains, recombinant inbred lines, outbred stocks, and wild-caught mice. GigaMUGA is highly informative across a wide range of genetically diverse samples, from laboratory substrains to other Mus species. In addition to describing the content and performance of the array, we provide detailed probe-level annotation and recommendations for quality control.
Data from: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species
We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163–185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility of the primers across a diverse range of fishes, we sampled eDNA from four tanks in the Okinawa Churaumi Aquarium with known species compositions, prepared dual-indexed libraries and performed paired-end sequencing of the region using high-throughput next-generation sequencing technologies. Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3%) distributed across 59 families and 123 genera. These fishes are not only taxonomically diverse, ranging from sharks and rays to higher teleosts, but are also greatly varied in their ecology, including both pelagic and benthic species living in shallow coastal to deep waters. We also sampled natural seawaters around coral reefs near the aquarium and detected 93 fish species using this approach. Of the 93 species, 64 were not detected in the four aquarium tanks, rendering the total number of species detected to 232 (from 70 families and 152 genera). The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods. It has the potential to serve as an alternative (or complementary) tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.
Data from: A universal and reliable assay for molecular sex identification of three-spined sticklebacks (Gasterosteus aculeatus)
In heterogametic species, biological differences between the two sexes are ubiquitous, and hence, errors in sex identification can be a significant source of noise and bias in studies where sex-related sources of variation are of interest or need to be controlled for. We developed and validated a universal multi-marker assay for reliable sex identification of three-spined sticklebacks (Gasterosteus aculeatus). The assay makes use of genotype scores from three sex-linked loci, and utilizes Bayesian probabilistic inference to identify sex of the genotyped individuals. The results, validated with 286 phenotypically sexed individuals from six populations of sticklebacks representing all major genetic lineages (cf. Pacific, Atlantic and Japan Sea) indicate that in contrast to commonly used single-marker based sex identification assays, the developed multi-marker assay should be 100% accurate. Since the markers in the assay can be scored from agarose gels, it provides a quick and cost-efficient tool for universal sex identification of three-spined sticklebacks. The general principle of combining information from multiple markers to improve the reliability of sex identification is transferable and can be utilized to develop and validate similar assays for other species.
Data from: Identifying conserved genomic elements and designing universal bait sets to enrich them
Targeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic and population genetic studies. For example, two available bait sets each allow enrichment of thousands of orthologous loci from >20 000 species (Faircloth et al. Systematic Biology, 61, 717–726, 2012; Molecular Ecology Resources, 15, 489–501, 2015). Unfortunately, few open-source workflows are available to identify conserved genomic elements shared among divergent taxa and to design enrichment baits targeting these regions. Those that do exist require extensive bioinformatics expertise and significant amounts of time to use. These shortcomings limit the application of targeted enrichment methods to additional organismal groups. Here, I describe a universal workflow for identifying conserved genomic regions in available genomic data and for designing targeted enrichment baits to collect data from these conserved regions. These methods require less expertise, less time and better use commonly available information to identify conserved loci and design baits to capture them. I apply this computational approach to the understudied arthropod groups Arachnida, Coleoptera, Diptera, Hemiptera or Lepidoptera to identify thousands of conserved loci in each group and design target enrichment baits to capture these loci. I then use in silico analyses to demonstrate that targeted enrichment of the conserved loci can be used to reconstruct the accepted relationships among genome sequences from the focal arthropod orders. The software workflow I created allowed me to identify thousands of conserved loci in five diverse arthropod groups and design sequence capture baits to target them. This suite of capture bait designs should enable collection of phylogenomic data from >900 000 arthropod species. Although the examples in this manuscript focus on understudied arthropod groups, the approach I describe is applicable to all organismal groups having some form of pre-existing genomic information (e.g. other invertebrates, plants, fungi and microbes). Finally, the documentation, design steps, software code and bait sets developed here are available under an open-source license for restriction-free testing, use, and additional modification by any research group.
Use of the samples and procedures approved by the Hospital Scientific Committee and the Bioethics Committee of the University of Talca
<p>Biopsies from patients with a diagnosis of HNSCC, potentially malignant disorders of oral mucosa and normal mucosa. The use of the samples and procedures were approved by the Hospital Scientific Committee and the Bioethics Committee of the University of Talca (number 2013-051). Thesis: Universidad de Talca (master) and University of Campinas (PhD).</p>
FIGURE 3 in The Tettigoniidae (Orthoptera) described by Salvador de Toledo Piza Jr. and deposited in the collection of the University of São Paulo, Escola Superior de Agricultura " Luiz de Queiroz ", Brazil
FIGURE 3. Pizatettix sanctaecrucis (Piza, 1973) comb. nov. male habitus lateral view.
FIGURE 2 in The Tettigoniidae (Orthoptera) described by Salvador de Toledo Piza Jr. and deposited in the collection of the University of São Paulo, Escola Superior de Agricultura " Luiz de Queiroz ", Brazil
FIGURE 2. Toledopizia salesopolensis (Piza, 1980) comb. nov. male habitus lateral view.
Dataset for: Extent and types of gender-based discrimination against female medical students and physicians at five university hospitals in Germany – Results of an online survey
<p><strong><span>Objective</span></strong><span>: There is a gap in research on gender-based discrimination (GBD) in medical education and practice in Germany. This study therefore examines the extent and forms of GBD among female medical students and physicians in Germany. Causes, consequences and possible interventions of GBD are discussed.</span></p> <p><strong><span>Methods</span></strong><span>: Female medical students (n=235) and female physicians (n=157) from five university hospitals in northern Germany were asked about their personal experiences with GBD in an online survey on self-efficacy expectations and individual perceptions of the "glass ceiling effect" using an open-ended question regarding their own experiences with GBD. The answers were analyzed by content analysis using inductive category formation and relative category frequencies. </span></p> <p><strong><span>Results</span></strong><span>: From both interviewed groups, approximately 75% of each reported having experienced GBD. Their experiences fell into five main categories: sexual harassment with subcategories of verbal and physical, discrimination based on existing/possible motherhood with subcategories of structural and verbal, direct preference for men, direct neglect of women, and derogatory treatment based on gender.</span></p> <p class="MsoNoSpacing"><strong><span>Conclusion</span></strong><span>: The study contributes to filling the aforementioned research gap. At the hospitals studied, GBD is a common phenomenon among both female medical students and physicians, manifesting itself in multiple forms. Transferability of the results beyond the hospitals studied to all of Germany seems plausible. Much is known about the causes, consequences and effective countermeasures against GBD. Those responsible for training and employers in hospitals should fulfill their responsibility by implementing measures from the set of empirically evaluated interventions.</span></p>
Determinants for university students' location data sharing with public institutions during COVID-19 the Italian case
Open the record for dataset details and reuse information.
FIGURE 1 in Single syntypes of Somatochlora exuberata Bartenev, 1910 (Odonata: Corduliidae), discovered in both the Milwaukee Public Museum and the University of Michigan Museum of Zoology, U.S.A., with designation of the lectotype
FIGURE 1. Riker mount with Somatochlora specimens by A.N. Bartenev (all but the upper left).
Alasmidonta viridis Central Michigan University survey data
<p>Data collected by Central Michigan University during surveys for <i>Alasmidonta viridis </i>in Michigan in the summer of 2022. Data was analyzed for completion of Gabrielle Sanfilippo's M.S. thesis for Central Michigan University's Department of Biology, submitted December 2023. The Excel spreadsheet contains two sheets: (1) "General" with general site survey data, including person hours surveyed, number of <i>A. viridis </i>and other mussel species found, and abiotic site measurements; and (2) "A. viridis indv" which contains data collected on <i>A. viridis </i>specimens, including length, width, height, and the etch given to each <i>A. viridis </i>specimen, and other data collected within a 1x1 meter quadrat centered around the <i>A. viridis </i>individual.</p>
Figs 83-84 in New data on the Xantholinini from China. 24. New genus, new species and new records of the Shanghai Normal University collection (Coleoptera, Staphylinidae) 244° contribution to the knowledge of the Staphylinidae
Figs 83-84: forebody of Medhiama tibetana nov.sp (83) and Sinichella nov.gen chengkou nov.sp. (84) (bar scale: 0,5 mm).
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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.