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38 results for “discernment”
◂Fig. 5 Gametogenesis in male and female Veneriserva pygoclava. A–D Semi-thin histological sections of female Veneriserva pygoclava, stained with toluidine blue. A Cross-section of a female Veneriserva. B Close-up of large mature oocytes without discernible nurse cells. C Developing oocytes attached to mesenteries (mes), and oogonia proliferating from the ventral side of the dorsal blood vessel (bv). D Details of vitellogenic oocytes and nurse cells. Arrowheads indicate brownstained yolk platelets and yolk bodies. E Live sperm cells captured in a light micrograph. F–G Cross-sections of male Veneriserva. Note the absence of a gut in the cross-sections. Abbreviations—ac acicula, acr acrosome, bv blood vessel, coe coelomic cavity, mes mesentery, nc nurse cell, nn nurse cell nucleus, nu sperm cell nucleus, Oo oocyte, on oocyte nucleus, sp spermatogonia, vnc ventral nerve cord in Hardly Venus's servant-morphological adaptations of Veneriserva to an endoparasitic lifestyle and its phylogenetic position within Dorvilleidae (Annelida)
◂Fig. 5 Gametogenesis in male and female Veneriserva pygoclava. A–D Semi-thin histological sections of female Veneriserva pygoclava, stained with toluidine blue. A Cross-section of a female Veneriserva. B Close-up of large mature oocytes without discernible nurse cells. C Developing oocytes attached to mesenteries (mes), and oogonia proliferating from the ventral side of the dorsal blood vessel (bv). D Details of vitellogenic oocytes and nurse cells. Arrowheads indicate brownstained yolk platelets and yolk bodies. E Live sperm cells captured in a light micrograph. F–G Cross-sections of male Veneriserva. Note the absence of a gut in the cross-sections. Abbreviations—ac acicula, acr acrosome, bv blood vessel, coe coelomic cavity, mes mesentery, nc nurse cell, nn nurse cell nucleus, nu sperm cell nucleus, Oo oocyte, on oocyte nucleus, sp spermatogonia, vnc ventral nerve cord
Text-fig. 1. Rhinoppioides quadrituberculatus MIKO gen. et sp. nov. A – dorsal view of holotype (prodorsal setae largely missing except right lamellar seta, notogastral setae missing and their insertions not discernable); B – ventral view of holotype (genital and anal valves missing, only insertions of ventral setae visible, gnathosoma missing); C – lateral view of paratype (notogaster missing). Bar indicates 100 µm. For explanation of acronyms see page 31. in Oribatid Mite Fossils From Quaternary And Pre-Quaternary Sediments In Slovenian Caves I.Two New Genera And Two New Species Of The Family Oppiidae From The Early Pleistocene
Text-fig. 1. Rhinoppioides quadrituberculatus MIKO gen. et sp. nov. A – dorsal view of holotype (prodorsal setae largely missing except right lamellar seta, notogastral setae missing and their insertions not discernable); B – ventral view of holotype (genital and anal valves missing, only insertions of ventral setae visible, gnathosoma missing); C – lateral view of paratype (notogaster missing). Bar indicates 100 µm. For explanation of acronyms see page 31.
Bioinformatic pipeline from: Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River
<p>Community composition data are essential for conservation management, facilitating identification of rare native and invasive species, along with abundant ones. However, traditional capture-based morphological surveys require considerable taxonomic expertise, are time consuming and expensive, can kill rare taxa and damage habitats, and often are prone to false negatives. Alternatively, metabarcode assays can be used to assess the genetic identity and compositions of entire communities from environmental samples, comprising a more sensitive, less damaging, and relatively time- and cost-efficient approach. However, there is a trade-off between the stringency of bioinformatic filtering needed to remove false positives and the potential for false negatives. The present investigation thus evaluated use of four mitochondrial (mt) DNA metabarcode assays and a customized bioinformatic pipeline to increase confidence in species identifications by removing false positives, while achieving high detection probability. Positive controls were used to calculate sequencing error, and results that fell below those cutoff values were removed, unless found with multiple assays. The performance of this approach was tested to discern and identify North American freshwater fishes using lab experiments (mock communities and aquarium experiments) and processing of a bulk ichthyoplankton sample. The method then was applied to field environmental (e)DNA water samples taken concomitant with electrofishing surveys and morphological identifications. This protocol detected 100% of species present in concomitant electrofishing surveys in the Wabash River and an additional 21 that were absent from traditional sampling. Using single 1 L water samples collected from just four locations, the metabarcoding assays discerned 73% of the total fish species that were discerned in comparison to four months of an extensive electrofishing river survey in the Maumee River, along with an additional nine species. In both rivers, total fish species diversity was best resolved when all four metabarcode assays were used together, which identified 35 additional species missed by electrofishing. Ecological distinction and diversity levels among the fish communities also were better resolved with the metabarcode assays than with morphological sampling and identifications, especially with the combined assays. At the population-level, metabarcode analyses targeting the invasive round goby <i>Neogobius melanostomus</i> and the silver carp <i>Hypophthalmichthys molitrix</i> identified all population haplotype variants found using Sanger sequencing of morphologically sampled fish, along with additional intra-specific diversity, meriting further investigation. Overall findings demonstrated that the use of multiple metabarcode assays and custom bioinformatics that filter potential error from true positive detections improves confidence in evaluating biodiversity.</p>
Data from: A trait-based framework for discerning drivers of species co-occurrence across heterogeneous landscapes
Null model analysis of species co-occurrence patterns has long been used to gain insight into community assembly but is often limited to identifying non-random patterns without providing clarity about underlying ecological mechanisms. This challenge is especially apparent when sampling units are spread across a heterogeneous landscape or along an environmental gradient because multiple mechanisms can produce similar co-occurrence patterns. We developed a trait-based approach for discriminating between environmental filtering and biotic interactions as the probable driver of co-occurrence patterns across environmentally heterogeneous sites. We demonstrate our framework by analyzing the co-occurrence of small mammals over elevation in three independent mountain ranges in the Great Basin of the western United States. Our sampling design accounts for landscape scale environmental variability and within-site habitat heterogeneity. We identified 52 non-random species pairs, of which 36 were aggregated and 16 were segregated. For each pair, we determined which mechanism was the likely ecological explanation using a hypothesis-testing framework based on functional trait similarity. Expectations of biotic interactions were based on similarity of diet and body size whereas habitat affinity and geographic range were used for environmental filtering. Only four pairs were consistent with expectations under biotic interactions, including pairs for which competitive exclusion has previously been documented. In addition to analyzing individual pairs, we used binomial tests of observed versus expected totals of intra- and inter-guild pairs to determine assemblage-wide deviations from random community structure. Signatures of environmental filtering were consistent across mountain ranges and scales. Despite differences in species composition and significant pairs among data sets, our approach revealed consistent mechanistic conclusions, emphasizing the value of trait-based methods to co-occurrence and community assembly.
Data from: Evaluating the use of lidar to discern snag characteristics important for wildlife
<p>Standing dead trees (known as snags) are historically difficult to map and model using airborne laser scanning (ALS), or lidar. Specific snag characteristics are important for wildlife; for instance, a larger snag with a broken top can serve as a nesting platform for raptors. The objective of this study was to evaluate whether characteristics such as top intactness could be inferred from discrete-return ALS data. We collected structural information for 198 snags in closed-canopy conifer forest plots in Idaho. We selected 13 lidar metrics within 5 m diameter point clouds to serve as predictor variables in random forest (RF) models to classify snags into four groups by size (small [<40 cm diameter] or large [≥40 cm diameter]) and intactness (intact or broken top) across multiple iterations. We conducted these models first with all snags combined, and then ran the same models with only small or large snags. Overall accuracies were highest in RF models with large snags only (77%), but kappa statistics for all models were low (0.29–0.49). ALS data alone were not sufficient to identify top intactness for large snags; future studies combining ALS data with other remotely sensed data to improve classification of snag characteristics important for wildlife is encouraged.</p>
DISCERN 2: Duke Innovation & SCientific Enterprises Research Network
<p>The DISCERN dataset was developed to support academic research on corporate innovation by linking data on U.S. publicly listed firms from Standard & Poor’s Compustat database to their patents and scientific publications. A key feature of DISCERN is its comprehensive coverage of firms’ subsidiaries and their ownership changes over time, which is crucial for accurately mapping corporate innovation. Patents and publications may be assigned to various legal entities within a firm’s organizational structure. Subsidiaries may change ownership in M&A events. By accounting for these ownership linkages over time, DISCERN enables researchers to construct more precise measures of firms’ knowledge production and examine the factors influencing their R&D investment decisions.</p> <p>Version 2.0 incorporates several key improvements over the previous version of DISCERN. First, we shift to using the PatentsView database as the main source of patent data and OpenAlex as the main source of scientific publication data. PatentsView is publicly available and continuously maintained directly by the United States Patents & Trademarks Office (USPTO). OpenAlex is currently the only open data source of scientific publication metadata. Using freely available data sources allows us to share both the patent and the publication datasets openly. This enhances data access, which was previously limited due to the use of propriety data. Second, the updated dataset now covers the period from 1980 to 2021, providing an additional six years of data. Third, we transition to using Securities and Exchange Commission (SEC) filings as the primary source of subsidiary data, allowing us to trace ownership linkages further back to the mid-1990s and ensuring a higher degree of reliability compared to the Orbis data used in the original version, which was less reliable and had comprehensive coverage only from 2008. Finally, by transitioning to PatentsView and additional data sourced from the USPTO, we expand the scope of the dataset to include pre-grant patent applications and patent re-assignment information. This addition allows users to study patent applications regardless of grant status and to observe ownership transitions beyond those related to mergers and acquisitions.</p> <p>A special thanks and appreciation go to Sanskriti Purohit and Ron Rabi for their diligent work and dedication to this effort.</p> <p>The dataset is freely available under the<a href="https://cdla.dev/open-use-of-data-agreement-v1-0/"> O-UDA-1.0 License</a>, permitting unrestricted use for research and commercial purposes. We request that users provide proper citations when utilizing the dataset. The license also allows for the creation of derivative datasets based on DISCERN, with the condition that creators ask their downstream users to cite the original authors appropriately.</p> <p><strong>If you use the data, please add these citations:</strong></p> <p>1. Arora, A., Belenzon, S., Cioaca, L., Sheer, L, Shin, H.M. & Shvadron, D. (2024). DISCERN 2.0: Duke Innovation & SCientific Enterprises Research Network [Dataset]. In Zenodo (CERN European Organization for Nuclear Research). <a href="../doi/10.5281/zenodo.3594642">https://doi.org/10.5281/zenodo.3594642</a></p> <p>2. Arora, A., Belenzon, S., Cioaca, L., Sheer, L, & Shvadron, D. (2024). Back to the Future: Are Big Firms Regaining their Scientific and Technological Dominance? Evidence from DISCERN 2.0 (available soon)</p> <p> </p>
Bioinformatic pipeline from: Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River
Open the record for dataset details and reuse information.
Data from: A trait-based framework for discerning drivers of species co-occurrence across heterogeneous landscapes
Open the record for dataset details and reuse information.
Data from: Evaluating the use of lidar to discern snag characteristics important for wildlife
Open the record for dataset details and reuse information.
Data from: Repurposing population genetics data to discern genomic architecture: a case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)
Genetic surveys of the population structure of species can be used as resources for exploring their genomic architecture. By adjusting filtering assumptions, genome-wide single nucleotide polymorphism (SNP) datasets can be reused to give new insights into the genetic basis of divergence and speciation without targeted re-sampling of specimens. Filtering only for missing data and minor allele frequency, we used a combination of principle components analysis and linkage disequilibrium network analysis to distinguish three cohorts of variable SNPs in the mountain pine beetle in western Canada, including one that was sex-linked and one that was geographically associated. These marker cohorts indicate genomically localized differentiation, and their detection demonstrates an accessible and intuitive method for discovering potential islands of genomic divergence without a priori knowledge of a species' genomic architecture. Thus, this method has utility for directly addressing the genomic architecture of species and generating new hypotheses for functional research.
Data from: Rapid light-induced shifts in opsin expression: finding new opsins, discerning mechanisms of change, and implications for visual sensitivity
Light induced shifts in cone frequency and opsin expression occur in many aquatic species. Yet little is known about how quickly animals can alter opsin expression and, thereby, track their visual environments. Similarly, little is known about whether adult animals can alter opsin expression or whether shifts in opsin expression are limited to critical developmental windows. We took adult wild caught bluefin killifish (Lucania goodei) from three different lighting environments (spring, swamp, variable), placed them under two different lighting treatments (clear vs. tea-stained water), and monitored opsin expression over four weeks. We measured opsin expression for five previously described opsins (SWS1, SWS2B, SWS2A, RH2-1, LWS) as well as RH2-2 which we discovered via 454 sequencing. We used two different metrics of opsin expression. We measured expression of each opsin relative to a housekeeping gene and the proportional expression of each opsin relative to the total pool of opsins. Population and lighting environment had large effects on opsin expression which were present at the earliest time points indicating rapid shifts in expression. The two measures of expression produced radically different patterns. Proportional measures indicated large effects of light on the SWS1 expression whereas relative measures indicated no such effect. Instead, light had large effects on the relative expression of SWS2B, RH2-2, RH2-1, and LWS. We suggest that proportional measures of opsin expression are best for making inferences about color vision, but that measures relative to a house keeping gene are better for making conclusions about which opsins are differentially regulated.
Supporting information for "Discerning TGF and leader current pulse in ASIM observation"
<p>Data files for the paper "Discerning TGF and leader current pulse in ASIM observation".</p>
FIG. 2 in Discerning the Environmental Drivers of Annual Migrations in an Endangered Amphibian
FIG. 2. Comparison of arrival dates for male and female flatwoods salamanders. Plots are standardized from 1 October and separated by year, i.e., 10–11 is the fall 2010–spring 2011 breeding season. Within year comparisons are made with Wilcoxon rank-sum tests.
FIG. 1 in Discerning the Environmental Drivers of Annual Migrations in an Endangered Amphibian
FIG. 1. Daily counts of individuals as a proportion of the total number of individuals available for capture for each year. Major tick marks are set at January 1, and minor tick marks are months.
Discerning Symptomatic and Asymptomatic Episodes Pre and Post Radiofrequency Ablation of Atrial Fibrillation
ClinicalTrials.gov study NCT00745706. IPD Sharing: Not stated. Countries: 1. Publications: 1.
DiSCERN: Advanced PD Therapy Candidacy and Evaluation System
ClinicalTrials.gov study NCT05351580. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Repurposing population genetics data to discern genomic architecture: a case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)
Open the record for dataset details and reuse information.
Data from: Rapid light-induced shifts in opsin expression: finding new opsins, discerning mechanisms of change, and implications for visual sensitivity
Open the record for dataset details and reuse information.
Supplementary material 1 from: Snyder MR, Stepien CA (2020) Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River. Metabarcoding and Metagenomics 4: e53455. https://doi.org/10.3897/mbmg.4.53455
Supplementary material: Additional methods, results, figures, and tables
Simulation files for 'Discerning Rise Time Constants: Connecting the Time and Frequency Domain Response of Perovskite Solar Cells'
<p>.parx files for SETFOS simulations and .py file for equivalent circuit simulations</p>
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