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Specific conductance and temperature data from Peat Inlet near Toolik Field Station, Alaska, summer 2010
As a part of the CSASN project, background (or ambient) specific conductance and stream water temperature was continuously monitored in three streams within the Toolik Inlet watershed from 2010 - 2012 summer/fall seasons. HOBO U24 data loggers were used for data acquisition. The data included in this file is from Peat Inlet stream, 2010 season.
Specific conductance and temperature data from Peat Inlet near Toolik Field Station, Alaska, summer 2011
As a part of the CSASN project, background (or ambient) specific conductance and stream water temperature was continuously monitored in three streams within the Toolik Inlet watershed from 2010 - 2012 summer/fall seasons. HOBO U24 data loggers were used for data acquisition. The data included in this file is from Peat Inlet stream, 2011 season.
Specific Leaf Area: BioCON : Biodiversity, Elevated CO2, and N Enrichment
BioCON (Biodiversity, CO2, and Nitrogen) is an ecological experiment started in 1997 at the University of Minnesota's Cedar Creek Ecosystem Science Reserve. BioCON's goal is to explore the ways in which plant communities will respond to three environmental changes that are known to be occurring on a global scale: increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity. Why Biodiversity, CO2, and Nitrogen? While there are many uncertainties in global change biology, there are also some well documented facts. Some of these are: 1. The amount of carbon dioxide (CO2) in the atmosphere is rising. Since the industrial revolution, the CO2 concentration in the atmosphere has increased from approximately 275 parts per million (ppm) to about 378 ppm today. This has been largely the result of fossil fuel burning. It is expected that CO2 levels will continue to rise, and that by the year 2050 these levels will be approximately 550 ppm. CO2 is the raw material for photosynthesis and is known to affect plant growth and development. 2. The amount of nitrogen moving through terrestrial ecosystems has increased in the recent past. While natural "background" levels of nitrogen fixation have remained constant, human additions to the system through fertilizer production and fossil fuel use have increased dramatically. Nitrogen is a key nutrient for plant growth and plays a critical role in plant community structure and composition in many environments. 3. Biodiversity levels are falling. While the research and data are not as complete as they are for CO2 and nitrogen, data indicate that the number of species globally, is being reduced. Perhaps more important for ecosystem function, diversity levels on local to regional scales have fallen due to land use change, biotic invasion and many other drivers. While much is known about how each of these factors affects ecosystem functioning, many questions remain. There is also little data on how these issues affe
Specific Leaf Area for a chronosquence of Morella cerifera shrub thickets on Hog Island, VA, 2012
Leaf area and mass for Morella cerifera leaves were measured inside and outside shrub thickets of different age (ranging from ~12 to ~50 years old) on Hog Island Virginia and Specific Leaf Area (SLA) was calculated.
Dataset Chronic water restriction triggers sex-specific oxidative stress and telomere shortening in lizards
<p>This dataset is related to "Chronic water restriction triggers sex-specific oxidative stress and telomere shortening in lizards" (Dupoué A., Angelier F., Ribout C., Meylan S., Rozen-Rechels D., Decencière B., Agostini S., Le Galliard J.-F.) </p> <p>The file reports the information on the responses of 100 yearling lizards identified with their code (lizard_ID), depending on their sex and hydric treatment. Abrevations: </p> <p>SVL: Snout-vent length</p> <p>ROM: Reactive Oxygen Metabolites (an index of oxidative damages)</p> <p>OXY: Non-enzymatic antioxydant activities (an index of defences)</p> <p>TL: Telomere length</p>
Time series measurements of group-specific picophytoplankton primary production
<p>14C-based primary production by flow cytometrically determined pico plankton (Prochlorococcus, Synechococcus, and photosynthetic picoeukaryotes) were measured at six discrete depths (5, 25, 45, 75, 100, and 125 m) at Station ALOHA. Seawater samples from each depth were subsampled into triplicate 30-mL polycarbonate centrifuge tubes from a pre-dawn cast, inoculated under subdued light with 70 µL of NaH14CO3-, then incubated over the full photoperiod (~12-14 hours). At the end of the incubation period (after sundown), 5 mL of each radiolabeled sample was preserved in cryotubes containing 30 µL of 16% (final concentration 0.24% w/v) microscopy-grade paraformaldehyde, flash-frozen in liquid nitrogen, and stored at -80°C for subsequent flow cytometric sorting. Group-specific rates of 14C-assimilation by Prochlorococcus, Synechococcus, and PPE were determined by measuring the amount of 14C assimilated into populations sorted using a BD Influx sorting flow cytometer. </p>
Trait-specific trade-offs prevent niche expansion in two parasites
<p>Data and analyses for a condensed version of the manuscript "Trait-specific trade-offs prevent niche expansion in two parasites" by Lievens et al., on bioRxiv at https://doi.org/10.1101/621581. The only difference with the previous version of this package (doi 10.5281/zenodo.3476544) is that some lines were analyzed separately to improve the readability of the manuscript (i.e. a slightly different analysis file).</p>
Fig. 3 in Gender-Specific Reproductive Tissue in Ratites and Tyrannosaurus rex
Fig. 3. Dinosaur and ratite MB. (A) MOR 1125, (B) emu, and (C) ostrich demineralized (14) MB. The coloration in (B) and (C) results from infiltration of tissues with blood sinuses. (D) MOR 1125, partially demineralized, showing enlarged, randomly arranged vascular openings surrounded by circumferential matrix fibers. Partially demineralized (E) emu and (F) ostrich medullary tissues show extensive vascular penetration, with randomly spaced and varyingly sized vessel openings. (G) Plane view of undemineralized dinosaur tissues shows fibrous matrix and an unusual pattern of vascular doublets or triplets within osteonlike structures (arrows). The inset shows variation in depth and diameter of vascular sinuses. (H) Undemineralized emu MB shows similar doublet pattern (arrows) and fibrous matrix. The greater depth of field makes focusing difficult. (I) Ostrich MB is denser closer to the cortex (inset), where the doublet/triplet pattern of vessels (arrows) is evident, but this becomes obscured by the increasing development of bony tubes and spicules as bone extends further into the medullary cavity. (J) Plane view of MOR 1125 shows the partially eroded, fibrous MB distributed across the cortex in a mazelike fashion. (K) Emu MB shows white (chloroform-altered) and cream-colored MB in the same mazelike pattern. (L) Thicker, randomly oriented tubular spicules of ostrich MB, showing deep penetration and intimate association of blood-containing sinuses.
(G) Higher magnification of dinosaur femur fragment in oblique view shows dense CB lined with newly described bone tissue, also seen in oblique view of emu (H) and ostrich (I) tibia. Ostrich MB is apparently unique in forming longitudinal tubules. in Gender-Specific Reproductive Tissue in Ratites and Tyrannosaurus rex
(G) Higher magnification of dinosaur femur fragment in oblique view shows dense CB lined with newly described bone tissue, also seen in oblique view of emu (H) and ostrich (I) tibia. Ostrich MB is apparently unique in forming longitudinal tubules.
Fast and sensitive flow-injection mass spectrometry metabolomics by analyzing sample specific ion distributions
<p>Data generated and analyzed in "Fast and sensitive flow-injection mass spectrometry metabolomics by analyzing sample specific ion distributions"</p> <p>Boris Sarvin<sup>‡1</sup>, Shoval Lagziel<sup>‡2</sup>, Nikita Sarvin<sup>1</sup>, Dzmitry Mukha<sup>1</sup>, Praveen Kumar<sup>1</sup>, Elina Aizenshtein<sup>3</sup>, Tomer Shlomi *<sup>123</sup></p> <p><sup>1</sup> Faculty of Biology, Technion – Israel Institute of Technology, 32000 Haifa, Israel.</p> <p><sup>2</sup> Faculty of Computer Science, Technion – Israel Institute of Technology, 32000 Haifa, Israel.</p> <p><sup>3</sup> Lokey Center for Life Science and Engineering, Technion – Israel Institute of Technology, 32000 Haifa, Israel.</p> <p><sup>‡</sup> BS and SL contributed equally to this work.</p>
Early Requirements Traceability with Domain-Specific Taxonomies - A Pilot Experiment
<p>Experiment instrumentation (code), raw data, and R analysis scripts.</p> <p>Github repository: https://github.com/munterkalmsteiner/inception/tree/CoClassRecommender</p>
Figure 5 in Chemistry supports the identification of gender-specific reproductive tissue in Tyrannosaurus rex
Figure 5. Immunochemical staining of bone using monoclonal antibodies raised against the sulfated glycosaminoglycan keratan sulfate. (A,C,E,G,I,K,M,O) are overlay images showing tissue and localized binding; (B,D,F,H,},L,N,P) are fluorescent images using FITC label. Chicken CB (A,B) shows no binding; chicken MB (C,D) shows positive staining, with green fluorescent signal representing antibody-antigen complexes, arranged in globular clusters. Similarly, ostrich femoral CB (E,F) does not bind antibodies, but ostrich MB (G,H) is positive for binding using the same data collection parameters. T. rex CB (I,}), does not show evidence of localized antibody binding, but sections of isolated MB (K,L) show localized specific binding to antibodies in a globular pattern, as seen in the chicken. (M,N) cortical region of tarsometatarsus and (O,P) internal (medullary) region of chicken genetically diagnosed with avian osteopetrosis (Materials and Methods) exposed to anti-keratan sulfate antibodies. No binding is seen, using same data collection parameters.
Figure 3 in Chemistry supports the identification of gender-specific reproductive tissue in Tyrannosaurus rex
Figure 3. Alcian blue histochemical stain capitalizes on the differential presence of sulfated glycosaminoglycans found in MB vs CB. Low (A) and high (B) magnification of demineralized, sectioned bone from a laying hen femur show MB (black arrows), forming along the borders of CB. Alcian blue stains MB intensely, but only lightly stains CB and TB, reflecting the differences in matrix composition. MB is shown to form around ovate vacancies that may represent vessels (red arrowheads). MB is sometimes found as islands within spicules of TB or CB (yellow arrows), possibly representing centripetal infilling of pre-existing vessel channels or erosion rooms with forming MB. Ostrich (C), shown at a lower magnification to encompass internal-most cortical bone and developing spicules of MB. The developmental pattern differs from that of chicken, reflecting macroscopic differences seen in hand sample, where MB and CB are not distinct, but more gradational in nature. Forming MB (black arrows) can be seen lining secondary osteons (leftmost black arrow), and as pockets of bone within pre-existing cortical bone (yellow arrows). Ovate open spaces within completely formed MB spicules are also seen (red arrowheads). Low (D) and high (E) magnifications of demineralized and sectioned T. rex CB show fibrous matrix that is lightly stained. Dinosaur MB in low (F), and high (G) magnifications show much more intense staining (black arrows). Matrix is fibrous, but is penetrated by ovate forms within deeply staining bone (F, red arrows). White spaces in F are sectioning artifact, where tissue and embedding material have pulled away from bone. Scale bars as indicated.
Figure 2 in Chemistry supports the identification of gender-specific reproductive tissue in Tyrannosaurus rex
Figure 2. Computed tomographic imaging of MOR 1125 femur bone fragment showing morphological differentiation between MB and CB. (A–D) volumetric renderings and (E–G) cross sections. (A,B) High density cortical bone rendered transparent to visually isolate lower density medullary bone. (E) Density shown as spectrum from high (black) to low (white). Fragment is (C,D,G) color and (F) heat mapped. Color mapping key: (C,D,G) medullary bone (orange/red) and cortical bone (beige/yellow); heat mapping key (F): highest density (red) lowest density (blue). Sample shown in (A,C,E–G) cross sectional and (B,D) medial views.
FIG. 6. The specific synanthropic setting where the holotype and a in A new species of Scotophilus (Chiroptera: Vespertilionidae) from western Madagascar
FIG. 6. The specific synanthropic setting where the holotype and a portion of the type series of S. marovaza were collected. The arrow indicates the site and the direction bats would have entered into the day roost site within the palm leaves. (Photograph taken by Mamy Ravokatra)
Antibody Watch: Text Mining Antibody Specificity from the Literature
<p><strong>Abstract </strong></p> <p><strong>Motivation</strong>: Antibodies are widely used reagents to test for expression of proteins. However, they might not always reliably produce results when they do not specifically bind to the target proteins that their providers designed them for, leading to unreliable research results.</p> <p><strong>Results</strong>: We developed a deep neural network system and tested its performance with a corpus of more than two thousand articles that reported uses of antibodies. We divided the problem into two tasks. Given an input article, the first task is to identify snippets about antibody specificity and classify if the snippets report any antibody that is nonspecific, and thus problematic. The second task is to link each of these snippets to one or more antibodies that the snippet referred to. We leveraged the Research Resource Identifiers (RRID) to precisely identify antibodies linked to the extracted specificity snippets. The result shows that it is feasible to construct a reliable knowledge base about problematic antibodies by text mining.</p>
Data from: Stage- and thermal-specific genetic architecture for preadult viability in natural populations of Drosophila melanogaster
Studying the processes affecting variation for preadult viability is essential to understand the evolutionary trajectories followed by natural populations. This task requires focusing on the complex nature of the phenotype-genotype relationship by taking into account usually neglected aspects of the phenotype and recognizing the modularity between different ontogenetic stages. Here we describe phenotypic variability for viability during the larval and pupal stages in lines derived from three natural populations of Drosophila melanogaster, as well as the variability for phenotypic plasticity and canalization at two different rearing temperatures. The observed phenotypic differences between populations can be attributed both to adaptation to environmental conditions and lack of gene flow between them. According to our results, different aspects of the phenotype (means, plasticity, canalization, plasticity of canalization) are affected by different genetic bases underlying changes in viability in a stage- and environment-specific manner. These findings explain the generalized maintenance of genetic variability for this fitness trait.
Data from: Population-specific effect of Wolbachia on the cost of fungal infection in spider mites
<p>Many studies have revealed the ability of the endosymbiotic bacterium <i>Wolbachia </i>to protect its arthropod hosts against diverse pathogens. However, as <i>Wolbachia </i>may also increase the susceptibility of its host to infection, predicting the outcome of a particular <i>Wolbachia</i>-host-pathogen interaction remains elusive. Yet, understanding such interactions and their eco-evolutionary consequences is crucial for disease and pest control strategies. Moreover, how natural <i>Wolbachia </i>infections affectartificially introduced pathogens for biocontrol has never been studied. <i>Tetranychus urticae </i>spider mites are herbivorous crop pests, causing severe damage on numerous economically important crops. Due to the rapid evolution of pesticide resistance, biological control strategies using entomopathogenic fungi are being developed. However, although spider mites are infected with various <i>Wolbachia </i>strains worldwide, whether this endosymbiont protects them from fungi is as yet unknown. Here, we compared the survival of two populations, treated with antibiotics or naturally harbouring different <i>Wolbachia </i>strains, after exposure to the fungal biocontrol agents <i>Metarhizium brunneum </i>and <i>Beauveria bassiana</i>. To control for potential effects of the bacterial community of spider mites, we also compared the susceptibility of two populations naturally uninfected by <i>Wolbachia</i>, treated with antibiotics or not. In one population, <i>Wolbachia</i>-infected mites had a better survival than uninfected ones in absence of fungi but not in their presence, whereas in the other population <i>Wolbachia </i>increased the mortality induced by <i>B. bassiana</i>. In one naturally <i>Wolbachia</i>-uninfected populations, the antibiotic treatment increased the susceptibility of spider mites to <i>M. brunneum</i>, but it had no effect in the other treatments. These results suggest that natural <i>Wolbachia </i>infections may not hamper and may even improve the success of biological control using entomopathogenic fungi. However, they also draw caution on the generalization of such effects, given the complexity of within-host pathogens interaction and the potential eco-evolutionary consequences of the use of biocontrol agents for <i>Wolbachia</i>-host associations.</p>
Application specific network traffic with specified activities
<p>This dataset contains network traffic of 12 different containerized, isolated applications. It includes headers of network traffic data in the initial two minutes of execution of the application.<br> We have specified each network traffic with an activity that the application was involved in during traffic capturing.<br> </p> <p>------------------------------------<br> Application name, No. of samples, Engaged activity while capturing<br> ------------------------------------<br> Curl, 60, downloading<br> Firefox, 47, browsing<br> mpg123, 99, audio streaming<br> mplayer, 82, audio streaming<br> mpv, 48, video streaming<br> Slack, 58, no chatting (just opening the app and menus)<br> streamlink, 57, video streaming<br> Trello, 46, just opening the app (just opening the app and menus)<br> Vlc, 102, audio streaming<br> w3m, 60, downloading<br> wget, 20, file downloading<br> wgetaudio, 20, file downloading(audio)<br> wgetvideo, 20, file downloading(video)<br> ydm (mplayer + youtube-dl),61, video streaming</p>
Data from: Social effects on age-related and sex-specific immune cell profiles in a wild mammal
<p>Evidence for age-related changes in innate and adaptive immune responses is increasing in wild populations. Such changes have been linked to fitness, and knowledge of the factors driving immune response variation is important for understanding the evolution of immunity. Age-related changes in immune profiles may be due to factors such as immune system development, sex-specific behaviour and responses to environmental conditions. Social environments may also contribute to variation in immunological responses, for example, through transmission of pathogens and stress arising from resource and mate competition. Yet, the impact of the social environment on age-related changes in immune cell profiles is currently understudied in the wild. Here, we tested the relationship between leukocyte cell composition (proportion of neutrophils and lymphocytes [innate and adaptive immunity, respectively] that were lymphocytes) and age, sex, and group size in a wild population of European badgers (<i>Meles meles</i>). We found that the proportion of lymphocytes in early-life was greater in males in smaller groups compared to larger groups, but with a faster age-related decline in smaller groups. In contrast, the proportion of lymphocytes in females was not significantly related to age or group size. Our results provide evidence of sex-specific age-related changes in immune cell profiles in a wild mammal, which are influenced by the social environment.</p>
ScienceDex guides
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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.