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opencc-by-4.0Nov 2024View details →

Global Gridded Dataset of Average-state Specific Yield

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opencc-by-4.0Nov 2024View details →

Sex-specific fear acquisition following early life stress is linked to amygdala and hippocampal purine and glutamate metabolism

Motion tracking dataset used for the paper "Sex-specific fear acquisition following early life stress is linked to amygdala and hippocampal purine and glutamate metabolism", by Joeri Bordes et al. Abstract Early life stress (ELS) can negatively impact health, increasing the risk of stress-related disorders, such as post-traumatic stress disorder (PTSD). Importantly, PTSD disproportionately affects women, emphasizing the critical need to explore how sex differences influence the genetic and metabolic neurobiological pathways underlying trauma-related behaviors. This study uses the limited bedding and nesting (LBN) paradigm to model ELS and investigate its sex-specific effects on fear memory formation. Employing innovative unsupervised behavioral classification, the current study reveals distinct behavioral patterns associated with fear acquisition and retrieval in male and female mice following ELS. Females exposed to LBN display heightened active fear responses, contrasting with males. Furthermore, the study examined the crucial link between behavioral regulation and cellular metabolism in key brain regions involved in fear and stress processing. Sex-specific and stress-dependent alterations were observed in purine, pyrimidine, and glutamate metabolism within the basolateral amygdala, the dorsal hippocampus, and the ventral hippocampus. These findings provide crucial insights into the complex interplay between metabolic pathways, the neurobiological underpinnings of fear memory, and stress responses. Importantly, they emphasize the significance of considering sex-specific metabolic alterations when investigating stress-related disorders, opening potential avenues for the development of targeted interventions.

opencc-by-4.0Jun 2024View details →

cassatts in the attic - project specific files

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opencc-by-4.0Dec 2024View details →

DNA large fragment deleting by compact, sequence-motif-free and specific TaqTth-hpRNA assisted with the microhomology-mediated end joining pathway

A DNA editing tool TaqTth-hpRNA was developed in this study, composed of a compact recombinant TaqTth nuclease (832 aa) and a simple hairpin-RNA guiding probe (hpRNA). In vitro biochemical studies showed the TaqTth-hpRNA efficiently cleaves artificially synthesized ssDNA without stringent sequence motif like PAM. It can also cleave the genomic DNA of E. coli with ~80% efficiency. The TaqTth-hpRNA cleavage of genomic DNA in mammalian cells generated products with large fragment deletions mediated by the microhomology-mediated end joining (MMEJ) pathway. In addition, the cleavage was sensitive to mismatches in targeted regions, which was applied to specific damage of the APPlon mutation in Alzheimer’s disease without disrupting the APPwt locus. It is worth mentioning that the APPlon sequence has only one base difference from that of APPwt. The characteristics of small size, no PAM requirement, high specificity, and large deletion products make the TaqTth-hpRNA a potential therapeutic strategy for treating autosomal dominant disorders in the future.

opencc-by-4.0Dec 2023View details →

Lineage-Specific Class-A GPCR Dynamics Reflect Diverse Chemosensory Adaptations in Lophotrochozoa

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opencc-by-4.0Jul 2024View details →

Supplementary material - Comparison of electrified vertical trash racks – electric field and effects on species-specific fish behaviours

Videos_Rack_Interactions - Compiled videos consisting of all individual rack interactions observed for the tested configurations. Among the exploratory setups, only increasing voltages for chub with PW = 1 ms, f = 10Hz were included.      Data.xlsm- Excel document containing the following sheets: <ul> <li>Fish - Length, Height and catch date of the tested Eel, Brown Trout and Chub</li> <li>Experiments - Summary table which configuration and species was tested on which date. </li> <li>Setups - Overview of the tested setups and naming convention used in the paper (C1- C7) compared to the convention used in the dataset (R12 - R28) </li> <li>Results - Results of the experiments. Each experiment consists of three lines (three fish). For each fish, the tested configuration, lengt and height, catch date as well as reaction to the bar rack ( bypass without rack contact, bypass with rack contact, refusal and rack passage) are detailed. </li> <li>Results (Filtered) - Sheet results without formatting and without invalid experiments. </li> <li>TIme to reaction - Additional evaluation how much time fish spent in the experiment on average after the starting compartment was opened until a firsts interaction with the rack or bypass passage was observed.  </li> </ul>

opencc-by-4.0Oct 2021View details →

Subject-specific dimensions for designing clothing patterns

The data set provided as a MATLAB (R2020a) binary file consists of 4 matrices. Each matrix has the size N times 23 and corresponds to the group of the Chinese adults (matrix adults_CN), the Czech adults (matrix adults_CZ), the Czech children (matrix children_CN) and the Czech adolescents (matrix teens_CZ). N is the number of measured subjects, where on each subjects, 23 anthropometric dimensions are measured. The dimensions in millimeters are consequently the total body height, the chest circumference (widest), the waist circumference (narrowest), the waist circumference (trousers), the hip circumference (widest), the shoulder width, the back width, the front length from neck to waist, the back length from neck to waist, the length from neck to shoulder, the sleeve length from neck to wrist, the arm circumference, the forearm circumference, the wrist circumference, the neck circumference, the length from crotch to knee, the length from crotch to ankle, the thigh circumference, the knee circumference, the calf circumference (widest), the ankle circumference, the length from waist to ground and the head circumference.

opencc-zeroOct 2021View details →

Data from: The birth hour of mammals: insights from intra-specific variation in wild blue monkeys

While most mammals show birth hour peaks at times of the 24-hour cycle when they are less active, there are exceptions to this general pattern. Such exceptions have been little explored, but may clarify evolutionary reasons for the diel timing of births. We investigated intraspecific variation in birth hour in wild blue monkeys (Cercopithecus mitis stuhlmanni), a diurnal primate, to identify factors that differentiated daytime vs. nighttime births. Behavioral and life history data from 14 groups over 14 years revealed that 4% of 484 births occurred during the day. Probability of daytime birth varied with mother's age, peaking at 15.7 years. Births whose annual timing deviated most from the population's peak birth months were five times more likely to occur during daytime than those that deviated less. There was no evidence that mother's rank or infant sex influenced birth hour, and mixed evidence that daytime births were more probable in larger groups. Survivorship did not differ significantly for infants born during the day vs. night. Prime-aged mothers may be able to handle the consequences of an unusual birth hour more successfully than mothers with less experience or those weakened by age. Daytime birth may be more advantageous in the off-season because nights are colder at that time of year. These findings are consistent with hypotheses relating birth hour to the risk of losing social protection in group-living animals, but are not consistent with those emphasizing risk of conspecific harassment. Patterns of within-species variation can help in evaluating evolutionary hypotheses for non-random birth hour.

Global biogeography and diversification of a group of brown seaweeds (Phaeophyceae) driven by clade-specific evolutionary processes

Aim: Historical processes that shaped current diversity patterns of seaweeds remain poorly understood. Using Dictyotales, a globally distributed order of brown seaweeds as a model, we test if historical biogeographical and diversification patterns are comparable across clades. Dictyotales contain some 22 genera, three of which, Dictyota, Lobophora and Padina, are exceptionally diverse. Specifically we test if the evolutionary processes in these clades that shaped their latitudinal diversity patterns are in line with the tropical conservatism, the out-of-the-tropics, and diversification rate hypotheses. Location: Global coastal benthic marine environments. Taxon: Dictyotales (Phaeophyceae) Methods: Species diversity was inferred using DNA-based species delineation, addressing cryptic diversity and circumventing taxonomic problems. A six-gene time-calibrated phylogeny, distribution data of 3,755 specimens, and probabilistic modeling of geographic range evolution was used to infer historical biogeographical patterns. The phylogeny was tested against different trait dependent models in order to compare diversification rates for different geographical units as well as different thermal affinities. Results: The Dictyotales originated in the Middle Jurassic and reach a current peak of species diversity in the Central Indo-Pacific. Ancestral range estimation points to a southern hemisphere origin of Dictyotales corresponding to the tropical southern Tethys Sea. Our results demonstrate that diversification rates were generally higher in tropical regions, but increased diversification rates in different clades are driven by different processes. Three major clades underwent a major diversification burst in the early Cenozoic, with Dictyota and Padina expanding their distribution into temperate regions, while Lobophora retained a predominantly tropical niche. Main conclusions: Our results are consistent with both the tropical conservatism hypothesis, in which clades originate and remain in the tropics (Lobophora), and the out-of-the-tropics scenario, where taxa originate and expand towards the temperate regions while preserving their presence in the tropics (Dictyota, Padina).

E-scape: consumer-specific landscapes of energetic resources derived from stable isotope analysis and remote sensing

Energetic resources and habitat distribution are inherently linked. Energetic resource availability is a major driver of the distribution of consumers, but estimating how much specific habitats contribute to the energetic resource needs of a consumer can be problematic. We present a new approach that combines remote sensing information and stable isotope ecology to produce maps of energetic resources (E-scapes). E-scapes project species-specific resource use information onto the landscape to classify areas based on energetic importance. Using our E-scapes, we investigated the relationship between energetic resource distribution and white shrimp distribution and how the scale used to generate the E-scape mediated this relationship. E-scapes successfully predicted the size, abundance, biomass, and total energy of a consumer in salt marsh habitats in coastal Louisiana, USA at scales relevant to the movement of the consumer. Our E-scape maps can be used alone or in combination with existing models to improve habitat management and restoration practices and have potential to be used to test fundamental movement theory.

opencc-by-4.0Nov 2021View details →

Data repository for "Lockdown impact on age-specific contact patterns and behaviours, France, April 2020"

Aggregated contact matrices associated with the publication "Lockdown impact on age-specific contact patterns and behaviours, France, April 2020" .

Mercury accumulation in leaves of different plant types – the significance of tissue age and specific leaf area

Mercury, Hg, is one of the most problematic metals from an environmental perspective. To assess the problems caused by Hg in the environment it is crucial to understand the processes of Hg biogeochemistry, but the exchange of Hg between the atmosphere and vegetation is not sufficiently well characterised. We explored the mercury concentration, [Hg], in foliage from a diverse set of plant types, locations and sampling periods to study whether there is a continuous accumulation of Hg in leaves/needles over time. Measurements of [Hg] were made in deciduous and conifer trees in Gothenburg, Sweden (Botanical Garden and city area) as well as of evergreen trees in Rwanda. In addition, data for wheat from an ozone experiment conducted at Östad, Sweden, were included. Conifer data were quantitatively compared with literature data. In every case where older foliage was directly compared with younger, [Hg] was higher in older tissue. Covering the range of current year up to four-year old needles, there was no sign of Hg saturation in conifer needles with age. Thus, over time scales of approximately one month to several years, the Hg uptake in foliage from the atmosphere always dominated over Hg evasion. Rwandan broadleaved trees had generally older leaves due to lack of seasonal abscission and higher [Hg] than Swedish broadleaved trees. The significance of atmospheric Hg uptake in plants was shown in a wheat experiment where charcoal filtrated air lead to significantly lower leaf [Hg]. To search for general patterns, the accumulation rates of Hg in the diverse set of tree species in the Gothenburg area were related to the specific leaf area (SLA). Leaf area based [Hg] was strongly negatively and non-linearly correlated with SLA, while mass-based [Hg] had a somewhat weaker positive relationship with SLA (both relationships with p < 0.001). An elaborated understanding of the relationship behind [Hg] and SLA would support large-scale modelling of Hg uptake by vegetation and Hg circulation in general.

opencc-by-4.0Nov 2021View details →

Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

The pcYeast7.6 model and files, required to reproduce the figures, provided in the publication "Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies", accepted in Nat Commun. The Zenodo upload was created by Pranas Grigaitis, p.grigaitis [at] vu.nl. Abstract When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the relevant cellular constraints remain to be determined for such cells. Here we present a comprehensive metabolic model of the yeast cell, based on its full metabolic reaction network extended with protein synthesis and degradation reactions. The model predicts metabolic fluxes and corresponding protein expression by constraining compartment-specific protein pools and maximising growth rate. Comparing model predictions with quantitative experimental data suggests that under glucose limitation, a mitochondrial constraint limits growth at the onset of ethanol formation - known as the Crabtree effect. Under sugar excess, however, a constraint on total cytosolic volume dictates overflow metabolism. Our comprehensive model thus identifies condition-dependent and compartment-specific constraints that can explain metabolic strategies and protein expression profiles from growth rate optimization, providing a framework to understand metabolic adaptation in eukaryal cells.

Temporal and spatial variation in sex-specific abundance of the avian vampire fly (Philornis downsi)

Understanding the range and behaviour of an invasive species is critical to identify key habitat areas to focus control efforts. Patterns of range use in parasites can differ temporally, across life stages and between sexes. The invasive avian vampire fly, Philornis downsi, spends the larval stage of its life within bird nests, feeding on developing nestlings and causing high levels of mortality and deformation. However, little is known of the ecology and behaviour of the non-parasitic adult fly life stage. Here, we document sex-specific temporal and spatial patterns of abundance of adult avian vampire flies during a single Darwin's finch breeding season. We analyse fly trapping data collected across 7 weeks in the highlands (N = 405 flies) and lowlands (N = 12 flies) of Floreana Island (Galápagos). Lowland catches occurred later in the season, which supports the hypothesis that flies may migrate from the food-rich highlands to the food-poor lowlands once host breeding has commenced. Fly abundance was not correlated with host nesting density (oviposition site) but was correlated with distance to the agricultural zone (feeding site). We consistently caught more males closer to the agricultural zone and more females further away from the agricultural zone. These sex differences suggest that males may be defending or lekking at feeding sites in the agricultural zone for mating. This temporal and sex-specific habitat use of the avian vampire fly is relevant for developing targeted control methods and provides insight into the behavioural ecology of this introduced parasite on the Galápagos Archipelago.

opencc-zeroDec 2021View details →

Even more oak species in Mexico? Genetic structure and morphological differentiation support the presence of at least two specific entities within Quercus laeta

Differentiation among populations, sometimes despite ongoing gene exchange, is a key step in speciation. Therefore, comparison of intra- and interspecific differentiation patterns is of great significance to understanding speciation. The genus Quercus is an interesting system to test speciation models in the presence of gene flow, due to its weak interspecific reproductive barriers. The aim of the present study was to characterize the degree and pattern of morphological and genetic differentiation among different morphotypes in the white oak Quercus laeta, some corresponding to the previously described species Q. centralis, Q. laeta, Q. prinopsis and Q. transmontana, as well as geographically structured variation within Q. transmontana not previously described. Our goal was to evaluate if some of these can be considered distinct specific entities or are rather part of a continuum of variation. Nine microsatellite loci and two intergenic regions of chloroplast DNA were analyzed. Morphological differences were evaluated using geometric morphometrics. Chloroplast DNA showed low differentiation, suggesting introgression or sharing of ancestral haplotypes among the Q. laeta morphotypes. Nuclear microsatellites indicated differentiation into two distinct main genetic groups, which were congruent with morphological differentiation. In conclusion, nuclear markers and morphological variation suggest the existence of at least two different entities within Q. laeta.

opencc-by-4.0Dec 2021View details →

Comparative analysis of patient-specific aortic dissections through computational fluid dynamics suggests increased likelihood of degeneration in partially thrombosed aorta

Aortic dissection is a life-threatening cardiovascular disease associated with high rates of morbidity and mortality, especially in medically under-served communities. It compromises the hemodynamics of the arteries that originate from the aorta, and its outcomes include visceral ischemia and aortic rupture in the acute phase and aneurysmatic degeneration in the chronic phase. Understanding patients’ blood flow patterns is pivotal for non-invasive evidence-based treatment as they greatly influence both the disease onset and its outcome. In this paper, we combine diagnostic imaging techniques and computational fluid dynamics to analyze the flow patterns of three aorta dissections (fully perfused, partially thrombosed, and fully thrombosed), and compare them to a healthy aorta. Besides flow kinematics, we focus on time averaged wall shear stress and oscillatory shear index that are recognized risk factors for aneurysm and rupture. Our analysis shows that partially thrombosed dissection is the most prone to false lumen degeneration. In all dissections, the arteries connected to the false lumen are generally poorly supplied with blood. Further, both true and false lumens present higher turbulence levels than the healthy aorta, and critical stagnation points. Mesh sensitivity and a thorough comparison against literature data together support the methodology robustness.

opencc-by-4.0Jan 2022View details →

Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci

Trans-ethnic meta-analysis results for eGFR EWAS Description of variables: CpG             CPG name chr             Chromosome      pos_hg38         Position hg38         Beta             Effect   SE             Standard error   P             P value  totalsamplesize     number of participants  direction     direction of effect for studies        hetpval         P value for heterogeneity      hetdf            Degree of freedom    gene         Gene location Upload of this dataset was completed by The EWAS Catalog team. The data can be queried along with hundreds of other EWAS at ewascatalog.org. To upload your EWAS summary statistics and have a zenodo DOI generated for you go to ewascatalog.org/upload.

opencc-zeroJan 2022View details →

Cold winters have morph-specific effects on natal dispersal distance in a wild raptor

Dispersal is a key process with crucial implications in spatial distribution, density and genetic structure of species' populations. Dispersal strategies can vary according to both individual and environmental features, but putative phenotype-by-environment interactions have rarely been accounted for. Melanin-based color polymorphism is a phenotypic trait associated with specific behavioral and physiological profiles and is therefore a good candidate trait to study dispersal tactics in different environments. Here, using a 40 years dataset of a population of color polymorphic tawny owls (Strix aluco), we investigated natal dispersal distance of recruiting gray and pheomelanic reddish-brown (hereafter brown) color morphs in relation to post-fledging winter temperature and individual characteristics. Since morphs are differently sensitive to cold winters, we predicted that morphs' natal dispersal distances vary according to winter conditions. Winter temperature did not affect the proportion of brown (or gray) among recruits. We found that dispersal distances correlate with winter temperature in an opposite manner in the two morphs. While the gray morph undertakes larger movements in harsher conditions, likely because it copes better with winter severity, the brown morph disperses shorter distances when winters are harsher. We discuss this morph-specific natal dispersal pattern in a context of competition for territories between morphs and in terms of costs and benefits of these alternative strategies. Our results stress the importance of considering the interaction between phenotype and environment to fully disentangle dispersal movement patterns and provide further evidence that climate affects behavior and local distribution of this species.

opencc-by-4.0Jan 2022View details →

Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery

This contains data described in detail in our paper, "Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery", where we develop a novel algorithm called RPath that prioritizes drugs for a given disease by reasoning over causal paths in a knowledge graph (KG), guided by both drug-perturbed as well as disease-specific transcriptomic signatures.