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Figure 7 in Wanted, tracked down and identified: Mesozoic non-biting midges of the subfamily Chironominae (Chironomidae, Diptera)
Figure 7. Palaeocentron krzeminskii, adult male, MP/4020 (ISEZ PAN); mid-Cretaceous, probably Albian–Cenomanian; Hukawng Valley, Kachin State, Myanmar. A, B, hypopygium in dorsolateral (A) and ventrolateral aspect (B). C, D, anal point photographed (C) and drawn (D). E, superior volsellae. F, G, inferior volsellae drawn (F) and photographed (G).
Figure 1 in Wanted, tracked down and identified: Mesozoic non-biting midges of the subfamily Chironominae (Chironomidae, Diptera)
Figure 1. Mesoacentron kaluginae, adult male, PIN 3130/224; Late Cretaceous, Santonian; Yantardakh, Taimyr Peninsula, Russia. A, inclusion in amber embedded in epoxy resin. B, habitus. C, head. D, antenna (arrowheads indicate borders between flagellomeres fm 1–14: black – distinctly separated, grey – weakly separated or partially fused). E, head and thorax in lateral aspect.
Fluctuating starvation conditions modify host-symbiont relationship between a leaf beetle and its newly identified gregarine species
<p class="MsoNormal"><span>Gregarines are ubiquitous endosymbionts in invertebrates, including terrestrial insects. However, the biodiversity of gregarines is probably vastly underestimated and the knowledge about their role in shaping fitness-related traits of their host in dependence of fluctuating environmental conditions is limited. Using morphological and molecular analyses, we identified a new gregarine species, <em>Gregarina cochlearium</em> sp. n., in the mustard leaf beetle, <em>Phaedon cochleariae</em>. Applying a full-factorial design, we investigated the effects of a gregarine infection in combination with fluctuating starvation conditions during the larval stage on the development time and fitness-related traits of adult beetles. Under benign environmental conditions, the relationship between gregarines and the host seemed neutral, as host development, body mass, reproduction and survival were not altered by a gregarine infection. However, when additionally exposed to starvation, the combination of gregarine infection and this stress resulted in the lowest reproduction and survival of the host, which points to a parasitic relationship. Furthermore, when the host experienced starvation, the development time was prolonged and the adult females were lighter compared to non-starved individuals, independent of the presence of gregarines. Counting of gregarines in the guts of larvae revealed a lower gregarine load with increasing host body mass under stable food conditions, which indicates a regulation of the gregarine burden in dependence of the host condition. Contrary, in starved individuals the number of gregarines was the highest, hence the already weakened host suffered additionally from a higher gregarine burden. This interactive effect between gregarine infection and fluctuating starvation conditions led to an overall reduced fitness of <em>P. cochleariae</em>. Our study emphasises the need to study endosymbionts as important components of the natural environment and to investigate the role of host-symbiont relationships under fluctuating environmental conditions in an evolutionary and ecological context.</span></p>
Supplementary materials of the paper Identifying benchmark units for research management and evaluation
<p>Supplementary materials of the paper Identifying benchmark units for research management and evaluation</p> <p>Supplementary1 Rsearch topics of Hero-m and SciLifeLab</p> <p>Supplementary2 Topics of benchmarks</p> <p>Supplementary3 Measures of connectivity</p>
Application of GIS and Spatial Statistics in identifying the rental value of shop lot in a shopping mall based on location factor
<p>GIS Property Data</p>
Supplemental material for: Validation of intraluminal filling defect length to identify carotid free-floating thrombus in patients with stroke/TIA
<p><strong>Objective: </strong>To validate a previously proposed filling defect length threshold of >3.8 mm on CT-angiography (CTA) to discriminate between free-floating thrombus (FFT) and plaque of atheroma.</p> <p><b>Materials and Methods: </b>Prospective multicenter observational study of 100 participants presenting with TIA/stroke symptoms and a carotid intraluminal filling defect on initial CTA. Follow-up CTA was obtained within one week, and at weeks 2 and 4 if the intraluminal filling defect was unchanged in length. Resolution or decreased length was diagnostic of FFT, whereas its static appearance after 4 weeks was indicative of plaque. Diagnostic accuracy of FFT length was assessed by receiver operating characteristic analysis.</p> <p><b>Results: </b>Ninety-five participants (mean age [standard deviation], 68 [13] years; 61 men; 83 participants with FFT; 12 participants with a plaque) were evaluated. The >3.8 mm threshold had a sensitivity of 88% (73/83) (95% confidence interval {CI}: 78%, 94%) and specificity of 83% (10/12) (95% CI, 51%, 97%) (area under the curve [AUC], 0.91, p<.001) for the diagnosis of FFT. The optimal length threshold was >3.64 mm with a sensitivity of 89%( 74/83) (95% CI, 80%, 95%) and specificity of 83% (10/12) (95% CI, 51%, 97%). Adjusted logistic regression showed that every 1 mm increase in intraluminal filling defect length is associated with an increase in odds of FFT of 4.6 ([95% CI] 1.9-11.1; <i>p</i>=.01).</p> <p><b>Conclusion: </b>CTA enables accurate differentiation of FFT versus plaque using craniocaudal length thresholds.</p> <p><strong>Clinical Trial Identifier:</strong> <a href="http://www.clinicaltrials.gov">www.clinicaltrials.gov</a> NCT02405845.</p> <p><b>Classification of Evidence: </b>This study provides Class I evidence that in patients with TIA/stroke symptoms, the presence of a carotid intraluminal filling defect with length > 3.8 mm on CTA accurately discriminates free-floating thrombus from atheromatous plaque.</p>
Subspecies and Distribution. M.s.swillaTemminck,1840—MalayPeninsula(includingLangkawiI),Borneo,Suma-tra,Java,andthePhilippines(Luzon,Cebu,Mindanao,andPalawanIs). M. s. canescens Thomas, 1923 — Nias I, off W Sumatra. Apparently also in C Sulawesi, Peleng I, and New Guinea because these specimens are similar to this speciesin size, although they were originally identified as the Flores Tube-nosed Bat (M. florium). These records are not mapped here. in Vespertilionidae
Subspecies and Distribution. M.s.swillaTemminck,1840—MalayPeninsula(includingLangkawiI),Borneo,Suma-tra,Java,andthePhilippines(Luzon,Cebu,Mindanao,andPalawanIs). M. s. canescens Thomas, 1923 — Nias I, off W Sumatra. Apparently also in C Sulawesi, Peleng I, and New Guinea because these specimens are similar to this speciesin size, although they were originally identified as the Flores Tube-nosed Bat (M. florium). These records are not mapped here.
Distribution. Manus, New Britain, Duke of York, and Umboi Is; a specimen from Wetar I was identified as this species, but specific status of this specimen needs to be confirmed. in Vespertilionidae
Distribution. Manus, New Britain, Duke of York, and Umboi Is; a specimen from Wetar I was identified as this species, but specific status of this specimen needs to be confirmed.
RegEl corpus: Identifying DNA regulatory elements in the scientific literature
<pre>@article{garda2022regel, title={RegEl corpus: identifying DNA regulatory elements in the scientific literature}, author={Garda, Samuele and Lenihan-Geels, Freyda and Proft, Sebastian and Hochmuth, Stefanie and Sch{\"u}lke, Markus and Seelow, Dominik and Leser, Ulf}, journal={Database}, volume={2022}, year={2022}, publisher={Oxford Academic} } </pre>
Binding networks identify targetable protein pockets for mechanism-based drug design
<p>This repository contains supporting files for the manuscript entitled: Binding networks identify targetable protein pockets for mechanism-based drug design.</p>
Data from: Identifying conservation priorities for gorgonian forests in Italian coastal waters with multiple methods including citizen science and social media content analysis
<div> <div> <div> <div> <p>Gorgonian forests are among the most complex of subtidal habitats in the Mediterranean Sea, supporting high biodiversity and providing diverse ecosystem services. Despite their iconic status, the geographical distribution and condition of gorgonian species is poorly known. Using multiple online data sources, our primary aims were to compile, map and analyse observations of gorgonian forests in Italian coastal waters to assess the biological complexity of gorgonian forests; evaluate impacts and vulnerable species, and identify areas of special interest inside and outside of existing MPAs to help prioritise conservation strategies and actions.</p> </div> </div> </div> </div>
FASTA file of sequences of identified proteins in Anastrepha ludens reproductive tissues
<p>Seminal fluid proteins (Sfps) modify female phenotypes and have wide-ranging evolutionary implications on fitness in many insects. However, in the Mexican fruit fly, <em>Anastrepha ludens</em>, a highly destructive agricultural pest, the functions of Sfps are still largely unknown. To gain insights into female phenotypes regulated by Sfps, we used nano liquid chromatography mass spectrometry to conduct a proteomic analysis of the soluble proteins from reproductive organs of <em>A. ludens</em>. The proteins predicted to be transferred from males to females during copulation were 100 proteins from the accessory glands, 69 from the testes, and 20 from the ejaculatory bulb, resulting in 141 unique proteins after accounting for redundancies from multiple tissues. These 141 included orthologs to <em>Drosophila melanogaster</em> proteins involved mainly in oogenesis, spermatogenesis, immune response, lifespan, and fecundity. In particular, we found one protein associated with female olfactory response to repellent stimuli (Scribble), and two related to memory formation (aPKC, Shibire). Together, these results raise the possibility that <em>A. ludens</em> Sfps could play a role in regulating female olfactory responses and memory formation and could be indicative of novel evolutionary functions in this important agricultural pest.</p>
Aesthetic Trends and Semantic Web Adoption of Media Outlets Identified through Automated Archival Data Extraction
<p>This dataset includes a variety of structured data gathered via various Web data extraction techniques which were employed in order to collect current and archival data from almost a thousand news websites that are popular in Greece, for the purpose of monitoring and recording their progress through time. The collected information, that took the form of a website’s source code and an impression of their homepage in different time instances of the last decade, has been used to identify trends concerning Semantic Web integration, DOM structure complexity, number of graphics, color usage and more. In total more than ten thousands impressions (including screenshots and source code) were analyzed which resulted to conclusions regarding the evolution of aesthetics and the adoption of new technologies.</p>
Subspecies and Distribution. S.s.sciureusLinnaeus,1758—GuianasandNBrazil,NoftheAmazonRiverfromtheriosNegroandDemini(AmazonasState),Etotherivermouth,andSoftheAmazonRiverbetweentheRioXingu-Iriri(ParaState)EtotheRioPindaré(MaranhaoState),extendingStoc.6°SalongtheupperreachesoftheRioXingu. S. s. collins: Osgood, 1916 — N Brazil, Marajo I in the estuary of the Amazon River (Para State), but further studies are needed to identify the extent of its occurrence, which may well be much larger; the identity of the squirrel monkeys on other islands in the Amazon estuary (Gurupa, Caviana, and Mexiana) has yet to be ascertained. in Cebidae
Subspecies and Distribution. S.s.sciureusLinnaeus,1758—GuianasandNBrazil,NoftheAmazonRiverfromtheriosNegroandDemini(AmazonasState),Etotherivermouth,andSoftheAmazonRiverbetweentheRioXingu-Iriri(ParaState)EtotheRioPindaré(MaranhaoState),extendingStoc.6°SalongtheupperreachesoftheRioXingu. S. s. collins: Osgood, 1916 — N Brazil, Marajo I in the estuary of the Amazon River (Para State), but further studies are needed to identify the extent of its occurrence, which may well be much larger; the identity of the squirrel monkeys on other islands in the Amazon estuary (Gurupa, Caviana, and Mexiana) has yet to be ascertained.
Linking camera-trap data to taxonomy: Identifying photographs of morphologically similar chipmunks
<p>Remote cameras are a common method for surveying wildlife and recently have been promoted for implementing large-scale regional biodiversity monitoring programs. The use of camera-trap data depends on the correct identification of animals captured in the photographs, yet misidentification rates can be high, especially when morphologically similar species co-occur, and this can lead to faulty inferences and hinder conservation efforts. Correct identification is dependent on diagnosable taxonomic characters, photograph quality, and the experience and training of the observer. However, keys rooted in taxonomy are rarely used for the identification of camera-trap images and error rates are rarely assessed, even when morphologically similar species are present in the study area. We tested a method for ensuring high identification accuracy using two sympatric and morphologically similar chipmunk (<i>Neotamias</i>) species as a case study. We hypothesized that the identification accuracy would improve with use of the identification key, and with observer training, resulting in higher levels of observer confidence and higher levels of agreement among observers. We developed an identification key and tested identification accuracy based on photographs of verified museum specimens. Our results supported predictions for each of these hypotheses. In addition, we validated the method in the field by comparing remote camera data with live-trapping data. We recommend use of these methods to evaluate error rates and to exclude ambiguous records in camera-trap datasets. We urge that ensuring correct and scientifically defensible species identifications is incumbent on researchers and should be incorporated into the camera-trap workflow.</p>
Replication package for identifying four types of SATD from four different sources
<p>This dataset includes pre-trained word embeddings and the weighted file for identifying four types (i.e., code/design, requirement, documentation, and test debt) of SATD (self-admitted technical debt) from four different sources (i.e., code comments, issue tracking systems, commit messages, and pull requests).</p>
Astrometrically identified nearby binary stars
<p>22,699 astrometric binary candidates identified via Gaia astrometry from the <a href="https://ui.adsabs.harvard.edu/abs/2021A%26A...649A...6G/abstract">Gaia Catalog of Nearby Stars</a>.</p> <p>Details of the specific data products and how the sample was selected can be found in <a href="https://ui.adsabs.harvard.edu/abs/2022MNRAS.513.5270P/abstract">Penoyre, Belokurov & Evans 2022</a>, with a description of the specific data included here provided in Table 2.</p>
Distribution. Known with certainty from Costa Rica, Panama, NW Ecuador, and Suriname, as determined by genetic analyses. Morphologically identified specimens from Colombia and Peru require propervalidation. in Phyllostomidae
Distribution. Known with certainty from Costa Rica, Panama, NW Ecuador, and Suriname, as determined by genetic analyses. Morphologically identified specimens from Colombia and Peru require propervalidation.
Elevation-Dependent Warming Identified During the Abrupt Shift at the Last Ice Age Termination
<p>The current Earth’s surface warming rate may increase with elevation, known as Elevation-Dependent Warming, which has profound environmental impacts on the fragile environments in high-elevation mountainous regions. However, Elevation-Dependent Warming has not been well constrained due to the short duration and sparse distribution of available instrumental data. Here we report quantitative paleotemperature reconstructions for three lakes within the elevational range of 1800–3800 m above sea level in the Hengduan Mountains, southeastern Tibetan Plateau, to show that abrupt warming occurred during ~14500–14000 years ago, and the warming rate was higher at higher elevations. We also find a prolonged cold interval from ~24000 to ~14000 years ago at high elevations, which coincides with the timing of the regional mountain glacier advances. We conclude that the observed Elevation-Dependent Warming was probably driven by the surface snow-albedo feedback caused by the rapidly shrinking mountain glaciers, which had a stronger influence at higher elevations.</p>
"A link model approach to identify congestion hotspots"
<p>Congestion emerges when high demand peaks put transportation systems under stress. Understanding the interplay between the spatial organization of demand, the route choices of citizens, and the underlying infrastructures is thus crucial to locate congestion hotspots and mitigate the delay. Here we develop a model where links are responsible for the processing of vehicles, that can be solved analytically before and after the onset of congestion, and providing insights into the global and local congestion. We apply our method to synthetic and real transportation networks, observing a strong agreement between the analytical solutions and the Monte Carlo simulations, and a reasonable agreement with the travel times observed in 12~cities under congested phase. Our framework can incorporate any type of routing extracted from real trajectory data to provide a more detailed description of congestion phenomena, and could be used to dynamically adapt the capacity of road segments according to the flow of vehicles, or reduce congestion through hotspot pricing.</p>
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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.