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opencc-zeroNov 2023View details →

Female chacma baboons modulate their sexual receptivity in response to male intrasexual competition

Research in social mammals has revealed the complexity of strategies females use in response to female-female reproductive competition and sexual conflict. One point at which competition and conflict manifest acutely is during sexual receptivity, indicated by swellings in some primates. Whether females can adjust their sexual receptivity from cycle to cycle to decrease reproductive competition and sexual conflict in response to social pressures has not been tested. As a first step, this study explores whether sexual receptivity duration is predicted social pressures in wild female chacma baboons (Papio ursinus). Given that female baboons face intense reproductive competition and sexual coercion, we predicted that: females could shorten the duration of their sexual receptive period to reduce female-female aggression and male coercion or increase it to access multiple or their preferred male(s). We quantified 157 ovulatory cycles from 46 wild females living in central Namibia recorded over 15 years. We found no support for our hypothesis; however, our analyses revealed a negative correlation between maximal-swelling duration and group size, a proxy of within-group competition. This study provides further evidence that swelling is costly as well as a testable framework for future investigations of 'cycle length manipulation'.

opencc-zeroNov 2023View details →

Data from: Mechanical morphotype switching as an adaptive response in Mycobacteria

Invading microbes face a myriad of cidal mechanisms of phagocytes that inflict physical damage to microbial structures. How intracellular bacterial pathogens adapt to these stresses is not fully understood. Here, we report a new virulence mechanism by which changes to the mechanical stiffness of the mycobacterial cell surface confers refraction to killing during infection. Long-Term Time-Lapse Atomic Force Microscopy was used to reveal a process of "mechanical morphotype switching" in mycobacteria exposed to host intracellular stress. A "soft" mechanical morphotype switch enhances tolerance to intracellular macrophage stress, including cathelicidin. Both pharmacologic treatment, with bedaquiline, and a genetic mutant lacking uvrA modified the basal mechanical state of mycobacteria into a "soft" mechanical morphotype, enhancing survival in macrophages. Our study proposes microbial cell mechanical adaptation as a critical axis for surviving host-mediated stressors.

Data for "Predicting the charge density response in metal electrodes"

Dataset associated with the manuscript "Predicting the charge density response in metal electrodes", as published in https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.7.125403.

Dataset for: Hug et al. Unexpected behavioural adaptation of yellow fever mosquitoes in response to high temperatures

Dataset for the manuscript: Hug et al. Unexpected behavioural adaptation of yellow fever mosquitoes in response to high temperatures

Genetic variants regulating the immune response improve the prediction of COVID-19 severity provided by clinical variables

Data set generated to evaluate the association between SNPs from genes related to SARS-CoV-2 pathogenesis and their clinical outcome.

Single-Cell RNA-Sequencing Reveals Placental Response under Environmental Stress

This repository provides scRNA-seq data corresponding to the manuscript "Single-Cell RNA-Sequencing Reveals Placental Response under Environmental Stress" by Van Buren, Azzara, Rangel-Moreno, de la Luz Garcia-Hernandez, Murphy, Cohen, Lin, and Park. The repository includes both count by gene matrices output from CellRanger version 6.0.1 (file names *_filtered_feature_matrix.h5 for each of the eight samples Control_1_M, Control_1_F, Control_2_M, Control_2_F, As_1_M, As_1_F, As_2_M, As_2_F), and a finalized Seurat object including cell type assignments as used for analyses in the manuscript (file name final_Seurat_obj.RData). Accompanying code used in analysis can be found at https://github.com/edvanburen/placenta_code.

The role of bottom friction in mediating the response of the Weddell Gyre circulation to changes in surface stress and buoyancy fluxes

This repository contains code to reproduce the figures in the paper titled "The role of bottom friction in mediating the response of the Weddell Gyre circulation to changes in surface stress and buoyancy fluxes" published in the Journal of Physical Oceanography (DOI: <a href="https://doi.org/10.1175/JPO-D-23-0165.1">https://doi.org/10.1175/JPO-D-23-0165.1</a>), as well as the barotropic vorticity budget terms for each of simulation in the paper.

Dataset from "Impact of intercepted and sub-canopy snow microstructure on snowpack response to rain-on-snow events under a boreal canopy"

The dataset presented below is described in the paper "Impact of rain-on-snow events on snowpack structure and runoff under a boreal canopy" by Bouchard et al. (submitted in December 2023) in the journal The Cryosphere.The original dataset includes sub-canopy snow monitoring data collected at the Montmorency Forest site (MF; 47.29°N, 71.17°W, elev. » 850 m above mean sea level (AMSL)) from 2018 to 2023 and at the Bernard River Valley site (BRV; 50.91°N; 63.37°W, elev. » 250 m. AMSL) from 2019 to 2023. MF is a balsam fir-white birch stand on a 12° northeast-facing slope. BRV is a valley surrounded by plateaus 200 m higher. The dataset covers the period from October 15 to June 15 of each year. In the monitoring dataset you can find the hourly time step:<ul><li>Snow height (cm) – all years at both sites</li><li>Soil-snow interface temperature (°C) – 2020 to 2023 at both sites</li><li>Snow temperature every 15 cm from the ground surface (°C) – 2020 to 2023 at both sites</li><li>Snow surface temperature (°C) – 2018-19 and from 2020 to 2023 at MF site</li><li>Air temperature (°C) – 2020 to 2023 at both sites</li></ul>The dataset also includes a total of 48 sub-canopy snow pit observations taken at the MF (42 snow pits) and BRV (6 snow pits) sites during the study period. Each snow pit contains the vertical profile of snow stratigraphy (grain type) and snow density. The snow pit height corresponds to the upper limit of the top snow layer in the stratigraphic profile. For density measurements, the height value corresponds to the center of the 3 cm thick box cutter. Grain type codes for the snowpack stratigraphy correspond to the International Classification for Seasonal Snow (Fierz et al., 2009):<ul><li>PP: precipitation particles</li><li>DF: decomposed and fragmented precipitation particles</li><li>RG: rounded grains</li><li>FC: faceted crystals</li><li>FCxr: rounding faceted particles</li><li>DH: depth hoar</li><li>MFpc: melt forms – rounded polycrystals</li><li>MF: melt forms – clustered rounded grains</li><li>MFcr: melt forms – melt-freeze crusts</li><li>IF: ice formations</li></ul>Finally, the dataset includes all observed rain-on-snow (ROS) events at both sites from November to March, covering the period 2018-2023 at the MF site and the period 2019-2023 at the BRV site. In the ROS dataset, we present the start and end dates, as well as the duration, rainfall amount, and mean air temperature of each event.

Data for: Effects of reproductive status on behavioral and neural responses to isolated pup stimuli in female California mice

The transition to motherhood in mammals is marked by changes in females' perception of and responsiveness to sensory stimuli from infants. Our understanding of maternally induced sensory plasticity relies most heavily on studies in uniparental, promiscuous house mice and rats, which may not be representative of rodent species with different life histories. We exposed biparental, monogamous California mouse (Peromyscus californicus) mothers and ovariectomized virgin females to one of four acoustic and olfactory stimulus combinations (Control: clean cotton and white noise; Call: clean cotton and pup vocalizations; Odor: pup-scented cotton and white noise; Call + Odor: pup-scented cotton and pup vocalizations) and quantified females' behavior and Fos expression in select brain regions. Behavior did not differ between mothers and ovariectomized virgins. Among mothers, however, those exposed to the Control condition took the longest to sniff the odor stimulus, and mothers exposed to the Odor condition were quicker to sniff the odor ball compared to those in the Call condition. Behavior did not differ among ovariectomized virgins exposed to the different conditions. Fos expression differed across conditions only in the anterior hypothalamic nucleus (AHN), which response to aversive stimuli: among mothers, the Control condition elicited the highest AHN Fos and Call + Odor elicited the lowest. Among ovariectomized virgin females, Call elicited the lowest Fos in the AHN. Thus, reproductive status in California mice alters females' behavioral responses to stimuli from pups, especially odors, and results in the inhibition of defense circuitry in response to pup stimuli.

Strong plastic responses in aerenchyma formation in F1 hybrids of Imperata cylindrica under different soil moisture conditions

There is insufficient evidence demonstrating how phenotypic plasticity in specific traits mediates hybrid performance. Two ecotypes of Imperata cylindrica produce F1 hybrids. The early flowering type (E-type) in wet habitats has larger internal gas spaces (aerenchyma) than the common type (C-type) in dry habitats. This study evaluated the relationships between the habitat utilisation, aerenchyma plasticity, and growth of I. cylindrica accessions. We hypothesize that plasticity in expressing parental traits explains hybrid establishment in habitats with various soil moisture conditions. Aerenchyma formation was examined in the leaf midribs, rhizomes, and roots of two parental ecotypes and their F1 hybrids in their natural habitats. In common garden experiments, we examined plastic aerenchyma formation in the leaf midribs, rhizomes and roots of natural and artificial F1 hybrids and parental ecotypes. Their vegetative growth performance was also quantified. In the natural habitats where soil moisture content varied widely, the F1 hybrids showed larger variation of aerenchyma formation in the rhizomes than their parental ecotypes. In the common garden experiments, the F1 hybrids showed high plasticity of aerenchyma formation in the rhizomes, and their growth was similar to that of C-type and E-type under drained and flooded conditions, respectively. The results demonstrate that the F1 hybrids of I. cylindrica exhibit plasticity in aerenchyma development in response to varying local soil moisture content. This characteristic allows the hybrids to thrive in diverse soil moisture conditions.

opengpl-3.0-or-laterNov 2023View details →

Multiomics analyses reveal a Type III-associated immune response in immunotherapy-induced toxicity in melanoma and identifies potential new therapeutic targets

Immune checkpoint inhibitors (ICIs) are standard-of-care for the treatment of advanced melanoma, but their use is limited by immune-related adverse events (irAEs). Proteomic analyses and multiplex cytokine/chemokine assays from serum at baseline and at irAEs onset in melanoma patients indicated aberrant T-cell activity with differential expression of Type I and III immune signatures. This was in line with an increase in the proportions of monocytes and decrease of IL-17A-producing CD4+ T-cells in the peripheral blood using single cell RNA sequencing. Multiplex immunohistochemistry and spatial transcriptomics on ICI-induced skin rash and colitis showed an increase in the proportion of CD4+ T-cells with IL-17A expression.   Anti-IL-17A mAbs were administered in two patients with myocarditis, colitis and skin rash with resolution of the irAE. This study highlights the potential role of Type III CD4+ T-cells in irAEs development and provides proof-of-principle evidence for a corresponding clinical trial using anti-IL17A for treating irAEs. Code to generate the figures are located at https://github.com/pcheng84/AE_analysis/

Contrasting responses of fine root biomass and traits to large-scale nitrogen and phosphorus addition in tropical forests in the Guiana shield

Fine roots mediate plant nutrient acquisition and growth. Depending on soil nutrient availability, plants can regulate fine root biomass and morphological traits to optimise nutrient acquisition. Little is known, however, about the importance of these parameters influencing forest functioning. In this study, we measured root responses to nutrient additions to gain a mechanistic understanding of plant adaptations to nutrient limitation in two tropical forests in French Guiana, differing two-fold in their soil nutrient statuses. We analysed the responses of root biomass, mean root diameter (RD), specific root length (SRL), specific root area (SRA), root tissue density (RTD) and carbon (C), nitrogen (N) and phosphorus (P) concentrations in roots down to 15 cm soil depth after three years of N and P additions. At the lower-fertility site Paracou, no changes in root biomass or morphological traits were detected with either N or P addition, although P concentrations in roots increased with P addition. In the higher fertility site, Nouragues, root biomass and P concentrations in roots increased with P addition, with no changes in morphological traits. In contrast, N addition shifted root traits from acquisitive to more conservative by increasing RTD. A significant interaction between N and P in Nouragues pointed to stronger responses to P addition in the absence of N. Our results suggest that the magnitude and direction of root biomass and trait expression were regulated by soil fertility, corroborated by the response to N or P additions. At low fertility sites, we found lower plasticity in root trait expression compared to more fertile conditions, where N and P additions caused stronger and antagonistic responses. Identifying the exact role of mechanisms affecting root nutrient uptake in Amazon forests growing in different soils will be crucial to foresee if and how rapid global changes can affect their carbon allocation.

Responses of avian predators to polymorphic harlequin ladybird (Harmonia axyridis)

Harlequin ladybird (Harmonia axyridis) shows high level of colour polymorphism. Particular forms differ in their colour combination, pattern and abundance. We tested the willingness of native, wild-caught passerines to attack and eat particular forms. We predicted that those forms that are more abundant in the wild are better protected, as they are more familiar to the predators. We compared the forms novemdecimsignata and spectabilis, which represent 97 % of individuals in the wild population, but importantly differ in their visual appearance (mostly orange vs. mostly black). Further, we examined three intermediate forms: axyridis, which is very scarce in the wild, and two forms not occurring in the wild – originating from laboratory breedings: suturalis and aninkae. As predators, we used great tit (Parus major), which is very aversive towards ladybirds, and tree sparrow (Passer montanus), which is quite willing to attack and even eat ladybirds. We compared their responses to particular ladybird forms, with artificially brown-painted ladybird to test for the effect of visual signal. We showed that both bird species attacked all forms of ladybird equally and usually very scarcely. The brown-painted novemdecimsignata form was attacked more often, showing that the visual appearance prevents birds from attacking any conspicuous colour combination. Sparrows tended to eat the attacked ladybirds of forms novemdecimsignata, spectabilis and brown painted. Scarce axyridis form and laboratory forms were very well protected from the attack, very likely due to neophobia.

opencc-by-4.0Jul 2023View details →

The response of silicon carbide composites to He ion implantation and ramifications for use as a fusion reactor structural material

Raw datasets for the publication "The response of silicon carbide composites to He ion implantation and ramifications for use as a fusion reactor structural material".

Data from: Temporal dynamics in psychological assessments: a novel dataset with scales and response times

This dataset is collected from February 27 to March 17, 2021, it includes responses from 24,292 students to four recognized psychological scales: PHQ-9, GAD-7, ISI, and PSS. A unique aspect of this dataset is the inclusion of response time data, which reflects the duration students took to answer each question. This temporal information offers a new dimension in understanding respondent behavior and enhances the reliability of these scales.

opencc-by-4.0Jan 2024View details →

Multi-omics analysis of innate and adaptive responses to BCG vaccination reveals epigenetic cell states that predict trained immunity

This repository contains personal immune profiles of 323 healthy individuals (300BCG) subjected to Bacillus Calmette-Guérin (BCG) with blood samples collected immediately before (day 0), and 14 and 90 days after the vaccination. The personal immune profiles comprise: <ul> <li>immune cell concentrations measured with flow cytometry and a hematology analyzer</li> <li>plasma concentrations of 73 circulating inflammatory markers</li> <li>30 measurements of cytokine and lactate production capacity of peripheral blood mononuclear cells (PBMCs) in response to four microbial stimuli (Candida albicans, Escherichia coli lipopolysaccharide [LPS], Staphylococcus aureus, Mycobacterium tuberculosis).</li> </ul> Visit <a href="http://300BCG.bocklab.org/">http://300BCG.bocklab.org/</a> to learn more.

Vocalization Patterns in Laying Hens - An Analysis of Stress-Induced Audio Responses

This repository houses a comprehensive collection of data and resources from the study "Vocalization Patterns in Laying Hens - An Analysis of Stress-Induced Audio Responses." Led by Dr. Suresh Neethirajan at Mooanalytica, Department of Agriculture & Aquaculture, Faculty of Agriculture & Computer Science, Dalhousie University, this research represents a significant foray into the field of poultry ethology and welfare monitoring using advanced machine learning techniques. Key Components of the Repository <ol> <li> Experimental Audio Data <ul> <li>Control and Treatment Vocalizations: Audio recordings of laying hens under two different stress conditions – sudden umbrella opening (Treatment 1) and simulated dog barking sounds (Treatment 2), along with control groups. The processed dataset is approximately 460 MB for the control group experimental data and about 2 GB for the 2 treatment group experimental data, capturing the nuanced responses of hens to these stressors.</li> <li>Original Raw Data: The original, unprocessed audio data is around 9 GB in size. Though not included in the repository, it can be made available upon reasonable request.</li> </ul> </li> <li> Algorithm and Code Files <ul> <li>CNN Feature Extraction and Classification Algorithms Python scripts used for the extraction of features from the audio data using Convolutional Neural Networks (CNN) and subsequent classification.</li> <li>Supplementary Algorithms Additional code files that support the processing and analysis of the audio data.</li> </ul> </li> <li> MFCC Feature Dataset <ul> <li>An Excel file containing the 40 Mel Frequency Cepstral Coefficients (MFCC) features extracted from the vocalization data. This dataset provides a detailed spectral analysis of the hen's vocalizations, crucial for understanding their response to stress.</li> </ul> </li> </ol> Study Overview This study aimed to classify and analyze the vocalization patterns of laying hens subjected to different stressors. Using a CNN model, the research identified distinct vocal patterns between control and treated groups, indicating unique vocal responses to different types of stressors. This study is pivotal in understanding the impact of environmental stressors on poultry welfare and behavior. The age of the chickens and the timing of stressor application were also critical factors influencing vocalization patterns. Implications and Applications: The findings from this study have significant implications for poultry welfare monitoring and management. By providing a non-invasive method to assess the well-being of chickens, this research contributes valuable insights into enhancing poultry management practices and welfare standards. The resources in this repository are intended for researchers, academicians, and professionals in animal behavior, veterinary science, and poultry management. We encourage the use of these data and tools for further research and practical applications in the field of precision (Digital) livestock farming and animal welfare. For any queries or requests related to the raw dataset, please contact Dr. Suresh Neethirajan.

Data from: A cucumber protein, Phloem Phosphate Stress Repressed 1, rapidly degrades in response to a phosphate stress condition

Under depleted external phosphate (Pi), many plant species adapt to this stress by initiating downstream signalling cascades. In plants, the vascular system delivers nutrients and signalling agents to control physiological and developmental processes. Currently, limited information is available regarding the direct role of phloem-borne long-distance signals in plant growth and development under Pi-stress conditions. Here, we report on the identification and characterization of a cucumber protein, Cucumis sativus Phloem Phosphate-Stress-Repressed 1 (CsPPSR1), whose level in the phloem translocation stream rapidly responds to imposed Pi-limiting conditions. CsPPSR1 degradation is mediated by the 26S proteasome; under Pi-sufficient conditions, CsPPSR1 is stabilized by its phosphorylation, within the sieve tube system, through the action of CsPPSR1 Kinase. Further, we discovered that CsPPSR1 Kinase was susceptible to Pi-starvation-induced degradation, in the sieve tube system. Our findings offer insight into a molecular mechanism underlying the response of phloem-borne proteins to Pi-limited stress conditions.

opencc-zeroJan 2024View details →

Supplementary material from: Alpine extremophytes in evolutionary turmoil: Complex diversification patterns and demographic responses of a Halophilic grass in a Central Asian biodiversity hotspot

Diversification and demographic responses are key processes shaping species evolutionary history. Yet we still lack a full understanding of ecological mechanisms that shape genetic diversity at different spatial scales upon rapid environmental changes. In this study, we examined genetic differentiation in an extremophilic grass Puccinellia pamirica and factors affecting its population dynamics among the occupied hypersaline alpine wetlands on the arid Pamir Plateau in Central Asia. Using genomic data, we found evidence of fine-scale population structure and gene flow among the localities established across the high-elevation plateau as well as fingerprints of historical demographic expansion. We showed that an increase in the effective population size could coincide with the Last Glacial Period, which was followed by the species demographic decline during the Holocene. Geographic distance plays a vital role in shaping the spatial genetic structure of P. pamirica alongside with isolation-by-environment and habitat fragmentation. Our results highlight a complex history of divergence and gene flow in this species-poor alpine region during the Late Quaternary. We demonstrate that regional climate specificity and a shortage of nonclimate data largely impede predictions of future range changes of the alpine extremophile using ecological niche modeling. This study emphasizes the importance of fine-scale environmental heterogeneity for population dynamics and species distribution shifts.