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Figure 2 in Biological and ecological aspects of Bathygobius soporator (Valenciennes, 1837) (Perciformes, Gobiidae) from Santa Catarina, Southern Brazil
Figure 2. Number of individuals (n) of the Bathygobius soporator species in the size classes. * significant for X² test with 1 degree of freedom.
Figure 1 in Biological and ecological aspects of Bathygobius soporator (Valenciennes, 1837) (Perciformes, Gobiidae) from Santa Catarina, Southern Brazil
Figure 1. Location of the sampling area (hatch area) at the Itajaí-açu river (Saco da Fazenda), the coast of Santa Catarina, Brazil.
Figure 4 in Biological and ecological aspects of Bathygobius soporator (Valenciennes, 1837) (Perciformes, Gobiidae) from Santa Catarina, Southern Brazil
Figure 4. Length – Weight relatioships for males (A, C) and females (B, D) of B. soporator in the 1997-1998 (A, B) and 2005-2006 (C, D) periods.
Dataset for article: Perakakis, P., Taylor, M., Martinez-Nieto, E., Revithi, I., Vila, J. (2009). Breathing Frequency Bias in Fractal Analysis of Heart Rate Variability. Biological Psychology, 82(1), pp. 82-88
<p>Dataset for article:</p> <p>Perakakis, P., Taylor, M., Martinez-Nieto, E., Revithi, I., Vila, J. (2009). Breathing Frequency Bias in Fractal Analysis of Heart Rate Variability. Biological Psychology, 82(1), pp. 82-88</p>
Biology and Computational Biology Papers in Pubmed, 1997-2014
<p>Downloaded from Pubmed on 12 February, 2016</p> <p>Bio:<br /> ("Biology"[Mesh]) NOT (Review[ptyp] OR Comment[ptyp] OR Editorial[ptyp] OR Letter[ptyp] OR Case Reports[ptyp] OR News[ptyp] OR "Biography" [Publication Type]) AND ("1997/01/01"[PDAT] : "2014/12/31"[PDAT]) AND english[language]</p> <p>Comp:<br /> ("Computational Biology"[Majr]) NOT (Review[ptyp] OR Comment[ptyp] OR Editorial[ptyp] OR Letter[ptyp] OR Case Reports[ptyp] OR News[ptyp] OR "Biography" [Publication Type]) AND ("1997/01/01"[PDAT] : "2014/12/31"[PDAT]) AND english[language]</p>
Figure 3a. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 3a. - Neoempheriapuncticoxa Edwards, 1940. Left wing.Figure 3a.Male.Figure 3b.Female. <br> Male.
Figure 2. from: First record of Neoempheria Osten Sacken (Diptera, Mycetophilidae) biology in the Neotropical region, with associations between its larvae and fungi - Biodiversity Data Journal 3: e5073 (08 June 2015) https://doi.org/10.3897/BDJ.3.e5073
Figure 2. - Neoempheriapuncticoxa Edwards, 1940. Female adult, lateral view.
Biological and environmental data for a study on transferability of statistical and machine learning models using North Sea Macrozoobenthos
<p>General</p> <p>Data documented here are not the product of our research but was scraped from various sources and processed - so no genuine reupload. This collection is a contribution to reproduceable reseach. All datasets are given in "RData" binary format</p> <p> </p> <p>Data description</p> <p>majornorthseabenthos </p> <p>This is macrozoobenthos data as data frame scraped from the GBIF repository (gbif.org). Species are Corbula gibba, Tellina fabula, Turritella communis, Euspira pulchella, Corystes cassive- launus, Upogebia deltaura, Lanice conchilega, Nephtys hombergii, Echinocardium cordatum, and Amphiura filiformis. data was postprocessed to have only single occurrence fon the approxinatel 1x1 km grid used for this study. Also, occurrences closer than 5 km close to shore were removed - including occurrences on land.</p> <p> </p> <p>Predictors</p> <p>A SpatialPixelsDataFrame in EPSG 4326 with five layers: Median grain size in micrometers, mud content in percent (both MUDAB database), water depth in meters above MSL (Weatherall et al, 2015), modelled average bottom shear stress from waves in N/sqrm (The Wamdi Group, 1988) and climatologival average winter bottom water temperature in deg. C (Stips et al, 2004).</p> <p> </p> <p> </p> <p>References</p> <p>Stips A, Bolding K, Pohlmann T, Burchard H (2004) Simulating the temporal and spatial dy- namics of the North Sea using the new model GETM (general estuarine transport model). Ocean Dynamics 54(2):266–283</p> <p>The Wamdi Group (1988) The WAM model-a third generation ocean wave prediction model. Journal of Physical Oceanography 18(12):1775–1810</p> <p>Weatherall P, Marks K, Jakobsson M, Schmitt T, Tani S, Arndt JE, Rovere M, Chayes D, Ferrini V, Wigley R (2015) A new digital bathymetric model of the world’s oceans. Earth and Space Science 2(8):331–345</p> <p> </p>
Dataset supporting "Violating instructed human agency: an fMRI study on oculomotor tracking of biological and nonbiological motion stimuli."
<p>Here we provide fMRI data used for the following project (for details see data description file): Gertz, H., Hilger, M., *Hegele, M., & *Fiehler, K. (2016). Violating instructed human agency: an fMRI study on oculomotor tracking of biological and nonbiological motion stimuli. Neuroimage, doi: 10.1016/j.neuroimage.2016.05.043. (*shared last authorship)</p> <p> </p> <p>Previous studies have shown that beliefs about the human origin of a stimulus are capable of modulating the coupling of perception and action. Such beliefs can be based on top-down recognition of the identity of an actor or bottom-up observation of the behavior of the stimulus. Instructed human agency has been shown to lead to superior tracking performance of a moving dot as compared to instructed computer agency, especially when the dot followed a biological velocity profile and thus matched the predicted movement, whereas a violation of instructed human agency by a nonbiological dot motion impaired oculomotor tracking (Zwickel et al., 2012). This suggests that the instructed agency biases the selection of predictive models on the movement trajectory of the dot motion. The aim of the present fMRI study was to examine the neural correlates of top-down and bottom-up modulations of perception–action couplings by manipulating the instructed agency (human action vs. computer-generated action) and the observable behavior of the stimulus (biological vs. nonbiological velocity profile). To this end, participants performed an oculomotor tracking task in an MRI environment. Oculomotor tracking activated areas of the eye movement network. A right-hemisphere occipito-temporal cluster comprising the motion-sensitive area V5 showed a preference for the biological as compared to the nonbiological velocity profile.Importantly,a mismatch between instructed human agency and a nonbiological velocity profile primarily activated medial-frontal areas comprising the frontal pole, the paracingulate gyrus, and the anterior cingulate gyrus, as well as the cerebellum and the supplementary eye field as part of the eye movement network. This mismatch effect was specific to the instructed human agency and did not occur in conditions with a mismatch between instructed computer agency and a biological velocity profile. Our results support the hypothesis that humans activate a specific predictive model for biological movements based on their own motor expertise. A violation of this predictive model causes costs as the movement needs to be corrected in accordance with incoming (nonbiological) sensory information.</p>
Database including meta data and R script for bachelor thesis biology on ground beetles as bioindicator 2017
<p>Database including meta data and R script for bachelor thesis biology on ground beetles as bioindicator 2017</p>
Effects of high dietary zinc supplementation timing on the biological responses of gestating sows and their piglets
<p class="MsoNormal">High dietary zinc (Zn) fed to gestating sows may have utility as a fetal imprinting strategy to decrease pre-weaning mortality of piglets. However, the biological action that Zn may work through is unknown. High Zn may modulate the microbiome of the sow and the microbial seeding of the offspring's gut microbiome. Additonally, high dietary Zn and piglet birth weight may alter gene expression in piglet whole blood. Sows (n = 267) were fed 1 of 3 dietary treatments: 1) Control: a corn-soybean meal-based diet containing 125 ppm total supplemental zinc, 2) Breed-to-Farrow: as Control + 141 ppm supplemental Zn as ZnSO<sub>4 </sub>fed from 5 days post-breeding to farrowing; and 3) Day 110-to-Farrow: as Control + 2,715 ppm supplemental Zn as ZnSO<sub>4 </sub>starting on day 110 of gestation until farrowing. A subset of third parity sows (n = 30) were selected to assess the microbiome of colostrum, milk, and rectal and vaginal surfaces of sows. At farrowing, 4 pigs per litter (n = 120) were selected based on birthweight (BiW), as 2 average BiW pigs and 2 pigs with BiW below the litter average were selected for assessing the piglet gut microbiome on the day of birth (day 0) and day 5 of age. 16S rRNA sequencing were implemented for milk and colostrum samples while all other sample types were sequenced using shotgun metagenomics to determine taxonomic and functional profiles. On a different subset of pigs, whole blood was collected from 9 LBW pigs per treatment and 8 ABW Control pigs for RNA-sequencing to evaluate differentially expressed genes (DEGs) and pathways. Only 2 to 3 genes were differentially expressed between Control LBW and LBW pigs born to sows fed high Zn. However, 262 DEGs were identified when comparing LBW and ABW pigs, mostly reflecting pathways associated with translation, ribosome biogenesis, and amino acid and protein synthesis. Measures of alpha diversity (richness and Shannon's H Index) and beta diversity (Bray-Curtis, PERMANOVA) were conducted along with indicator species analyses. Species with an indicator value of > 0.50 were confirmed with a generalized linear mixed model as each <em>P</em>-value was corrected for false discovery rate (FDR) to generate a Q-value. For piglet samples, the MaAsLin2 R package was used to determine multivariate associations between dietary treatment and piglet BiW. High dietary concentrations of Zn fed to gestating sows did not affect the colostrum, milk, or vaginal microbial diversity or populations of sows. Pathogenic bacteria such as <em>Shigella flexneri </em>and <em>Salmonella enterica</em> were less abundant in fecal samples from Breed-to-Farrow sows compared to Control sows. For piglets born to Breed-to-Farrow sows, their gut microbiome favored fiber fermenting, short chain fatty acid generating microbial species compared to Control pigs. Day 110-to-Farrow piglets demonstrated a lower abundance of SCFA producing bacteria compared to Control piglets. Gene families and pathways playing roles in central metabolic functions (starch, pyruvate, sucrose, amino acid metabolism) were more abundant in Breed-to-Farrow piglets compared to pigs born to Control sows. In conclusion, high Zn fed to gestating sows may influence SCFA-producing species and may reduce the abundance of potential pathogenic bacteria in the sow and piglet. Piglet birth weight may have greater effects on gene expression of neonatal pigs. </p>
Fig. 8 in Stereoscopic light-microscopy in biology - A review
Fig. 8: Spiraliform tests of a recent foraminifer (diameter: 300 µm).
Fig. 5 in Comparative Biology Of Cave-Dwelling Spitting Spiders (Araneae: Scytodidae): Parental Care, Cooperative Prey-Capture, Cannibalism, Natal Dispersal And Reproductive Behaviour
Fig. 5. Scytodes fusca female leaving her egg-sac aside to forage on the house fly.
Fig. 70 in Two new species of the genus Oryctopterus (Orthoptera: Stenopelmatidae: Oryctopinae) from India, with some notes on biology
Fig. 70. Distribution of Oryctopinae Kevan, 1986 species.
Molecular dynamics trajectories, GROMACS input files, and analysis code from "Rational optimization of a transcription factor activation domain inhibitor" by Basu et. al, Nature Structural & Molecular Biology, 2023
<p>Molecular dynamics trajectories, GROMACS input files, and analysis code from "Rational optimization of a transcription factor activation domain inhibitor" by Basu et. al, Nature Structural & Molecular Biology, 2023</p> <p> </p> <p> </p>
Data from: Fog controls biological cycling of soil phosphorus in the Coastal Cordillera of the Atacama Desert
<p>In this study, we collected topsoil samples (0‒10 cm) from each of 54 subsites, including sites in direct adjacency (< 10 cm) and in 1 m distance to plants, along an aridity gradient across the Coastal Cordillera in the Atacama Desert. The soluble salts anions (NO<sup>3</sup><sup>‒</sup>, Cl<sup>‒</sup>, and SO<sub>4</sub><sup>2</sup><sup>‒</sup>) and cations (Ca<sup>2+</sup>, Na<sup>+</sup>, Mg<sup>2+</sup> and K<sup>+</sup>) were tested. And we performed soil sequential P fractionation and the oxygen isotope values of HCl-extractable P<sub>i</sub> (δ<sup>18</sup>O<sub>HCl</sub>-<sub>Pi</sub>). </p>
Data for: A diverse parasite pool can improve effectiveness of biological control constrained by genotype-by-genotype interactions
<p>The outcomes of biological control programs can be highly variable, with natural enemies often failing to establish or spread in pest populations. This variability has posed a major obstacle in use of the bacterial parasite <em>Pasteuria</em> <em>penetrans</em> for biological control of <em>Meloidogyne</em> species, economically devastating plant-parasitic nematodes for which there are limited management options. A leading hypothesis for this variability in control is that infection is successful only for specific combinations of bacterial and nematode genotypes. Under this hypothesis, failure of biological control results from the use of <em>P</em>. <em>penetrans</em> genotypes that cannot infect local <em>Meloidogyne</em> genotypes. We tested this hypothesis using isofemale lines of <em>M</em>. <em>arenaria</em> derived from a single field population and multiple sources of <em>P</em>. <em>penetrans</em> from the same and nearby fields. In strong support of the hypothesis, susceptibility to infection depended on the specific combination of host line and parasite source, with lines of <em>M</em>. <em>arenaria</em> varying substantially in which <em>P</em>. <em>penetrans</em> source could infect them. In light of this result, we tested whether using a diverse pool of <em>P</em>. <em>penetrans</em> could increase infection and thereby control. We found that increasing the diversity of the <em>P</em>. <em>penetrans</em> inoculum from one to eight sources more than doubled the fraction of <em>M</em>. <em>arenaria</em> individuals susceptible to infection and reduced variation in susceptibility across host lines. Together, our results highlight genotype-by-genotype specificity as an important cause of variation in biological control and call for the maintenance of genetic diversity in natural enemy populations.</p>
Bryophytes enhance nitrogen content in decaying wood via biological interactions
<p>An increase in the nitrogen (N) content in coarse woody debris (CWD) facilitates its decomposition, affecting the cycling of N and other nutrients in forest ecosystems. Bryophytes may increase the N content by transferring the N in bryophyte tissues to the underlying CWD. This study examined whether and how bryophytes increase N content in the underlying CWD using N-stable isotope ratios (δ<sup>15</sup>N) as tracers for N sources. The N content and δ<sup>15</sup>N values in CWD with bryophytes were significantly higher than those in CWD without bryophytes. However, the δ<sup>15</sup>N values in CWD with bryophytes differed significantly from those in bryophytes on CWD, demonstrating that the N in bryophytes did not cause the increase in N content in CWD. The analyses using δ<sup>15</sup>N further indicated that the high N content in CWD with bryophytes may be attributed to increased N supply from wood-decomposing fungi and N-fixing bacteria. This increase in N content may result from the enhanced moisture content in CWD beneath bryophytes, which facilitates the activity of wood-decomposing fungi and N-fixing bacteria. Notably, the influence of bryophytes on the N content in CWD differed between bryophyte life forms: bryophytes that form dense mats increased the N content in CWD, whereas those with loose mats decreased the N content. This difference can be explained by the greater humidity experienced by CWD with bryophytes forming dense mats than that experienced by CWD with bryophytes forming loose mats. Given that the N content in CWD affects the decay processes, the results highlight the importance of biological interactions associated with bryophytes in forest ecosystems.</p>
The biology of prolonged lactation in wild Macaca sinica: Interbirth intervals, maternal depletion, infant mortality
<p>A sample of 442 female toque macaques distributed among 39 independent social groups were briefly captured, sedated, and released (within one day) during 13 different years in the period 1986-2002 at the natural forest site of Polonnaruwa, Sri Lanka, where long-term sociobiological research has been conducted (1968 to 2023). All macaques were individually identified and had known life-histories. Lactation was determined by testing females for the presence of absence of milk by manually massaging the mammary tissue. Female reproduction in this wild population was depicted from different perspectives. Firstly, lactation and weaning were linked to offspring age, as well as to female reproductive status (cycling, gestation, and quiescence). A second data set examines interbirth intervals in relation to lactation duration, diet, and somatic growth or parity. Differences in diet quality were also related to menarche. A third data set examined female body condition (using skinfold thickness as a measure of % body fat) to diet quality and differences in the expenditure of foraging time between lactating and non-lactating females. A fourth data set considered the relation between infant mortality during peak lactation and the depletion of female metabolic energy balance as indexed by early weaning (cessation of lactation) and a shift to female reproductive quiescence. In the publication some of these data were integrated with mother-infant behavioral relationships as cited from an independent study of the same population. A final data set indicates the names of participants who contributed to both the long-term demographic records, milk collections and estimates human effort for different phases of this research.</p>
Pathformer: a biological pathway informed Transformer for disease diagnosis and prognosis using multi-omics data
<p>Integrating multi-omics data offers a more comprehensive view of gene regulation, which would be helpful in achieving accurate diagnosis of diseases like cancer. To improve the accuracy of disease diagnosis and prognosis, we developed Pathformer, a multi-omics integration method for both tissue and liquid biopsy data. We implemented Pathformer's network architecture using the “PyTorch” package in Python v3.6.9, and our codes can be found in the GitHub repository (https://github.com/lulab/Pathformer). This repository contains preprocessed TCGA dataset data, preprocessedliquid biopsy dataset data, result of Pathformer and comparison_methods, mentioned in GitHub project and article.</p>
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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.