bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of cognitive-motor function in women who have experienced intimate partner violence-related brain injury
Authors: Maldonado-Rodriguez Naomi , Val Crocker Clara , Taylor Edward , Jones K. Elisabeth , Rothlander Krystal , Smirl Jon , Wallace Colin , van Donkelaar Paul 
Published: February 2021

ABSTRACTIntimate partner violence (IPV) affects at least 1 in 3 women worldwide and up to 92% report symptoms consistent with brain injury (BI). Although a handful of studies have examined different aspects of brain structure and function in this population, none has characterized potential deficits in cognitive-motor function. This knowledge gap was addressed in the current study by having participants who had experienced IPV complete the bimanual Object Hit & Avoid (OHA) task on a Kinarm End-Point Lab. BI load, as assessed by the Brain Injury Severity Assessment (BISA) tool as well as measures of comorbidities (PTSD, anxiety, depression, substance use, history of abuse) were also collected. Results demonstrated BI load accounted for a significant amount of variability in the number of targets hit and average hand speed. PTSD, anxiety, and depression also contributed significantly to the variability in these measures as well as to the number and proportion of distractor hits, and the object processing rate. Taken together, these findings suggest IPV-related BI, as well as comorbid PTSD, anxiety, and depression, disrupt the processing required to quickly and accurately hit targets while avoiding distractors. This pattern of results reflects the complex interaction between the physical injuries induced by the episodes of IPV and the resulting impacts these experiences have on mental health.
Small size of recorded neuronal structures confines the accuracy in direct axonal voltage measurements
Authors: Oláh Viktor János , Tarcsay Gergely , Brunner János 
Published: February 2021

AbstractPatch-clamp instruments including amplifier circuits and pipettes affect the recorded voltage signals. We hypothesized that realistic and completein silicorepresentation of recording instruments together with detailed morphology and biophysics of small recorded structures will precisely reveal signal distortions and provides a tool that predicts native signals from distorted voltage recordings. Therefore, we built a model that was verified by small axonal recordings. The model accurately recreated actual action potential measurements with typical recording artefacts and predicted the native electrical behavior. The simulations verified that recording instruments substantially filter voltage recordings. Moreover, we revealed that instrumentation directly interferes with local signal generation depending on the size of the recorded structures, which complicates the interpretation of recordings from smaller structures, such as axons. However, our model offers a straightforward approach that predicts the native waveforms of fast voltage signals and the underlying conductances even from the smallest neuronal structures.
MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics
Authors: Amamuddy Olivier Sheik , Glenister Michael , Bishop Özlem Tastan 
Published: February 2021

AbstractMDM-TASK-web is the web server for the MD-TASK and MODE-TASK software suites. It simplifies the set-up required to perform and visualize results from dynamic residue network analysis, perturbation-response scanning, dynamic cross-correlation, essential dynamics and normal mode analysis. In a nutshell, the server gives access to updated versions of the tool suites, and offers new functionalities and integrated 2D/3D visualization. An embedded work-flow, integrated documentation and visualization tools shortens the number of steps to follow, starting from calculations to result visualization. The web server (available athttps://mdmtaskweb.rubi.ru.ac.za/) is powered by Django and a MySQL database, and is compatible with all major web browsers. All scripts implemented in the web platform are freely available athttps://github.com/RUBi-ZA/MD-TASK/tree/mdm-task-webandhttps://github.com/RUBi-ZA/MODE-TASK/tree/mdm-task-web.HighlightsMDM-TASK-web is the web server for highly utilized MD-TASK and MODE-TASK with updatesEight residue network centrality metrics are available to analyze static and dynamic proteinsNovel comparative essential dynamics is established to compare independent MD simulationsCommunication propensity tool to evaluate residue communication efficiency is implemented.Normal mode analysis from static and protein MD simulations is provided
Management of altered metabolic activity inDrosophilamodel of Huntington’s disease by curcumin
Authors: Aditi Kumari , Singh Akanksha , Shakarad Mallikarjun N , Agrawal Namita 
Published: February 2021

ABSTRACTHuntington’s disease (HD) is a devastating polyglutamine (polyQ) disorder characterized by extensive neurodegeneration and metabolic abnormalities at systemic, cellular and intracellular levels. Metabolic alterations in HD manifest as abnormal body weight, dysregulated biomolecule levels, impaired adipocyte functions and defective energy state which exacerbate disease progression and pose acute threat to the health of challenged individuals in form of insulin resistance, cardiovascular disease and energy crisis. To colossally mitigate disease symptoms, we tested the efficacy of curcumin inDrosophilamodel of HD. Curcumin is bioactive component of turmeric (Curcuma longaLinn), well-known for its ability to modulate metabolic activities. We found that curcumin effectively managed abnormal body weight, dysregulated lipid content and carbohydrate level in HD flies. In addition, curcumin administration lowered elevated reactive-oxygen-species (ROS) levels in adult adipose tissue of diseased flies, and improved survival and locomotor function in HD flies at advanced disease stage. Altogether, these findings clearly suggest that curcumin efficiently attenuates metabolic derangements in HD flies and can prove beneficial in alleviating the complexities associated with HD. Phytochemicals like curcumin that can regulate multiple targets in complex diseases like HD, with least side-effects and maximum benefits, provide a better hope for the treatment of terminally-ill HD patients.
Effect of urbanization and its environmental stressors on the intraspecific variation of flight functional traits in two bumblebee species
Authors: Tommasi Nicola , Pioltelli Emiliano , Biella Paolo , Labra Massimo , Casiraghi Maurizio , Galimberti Andrea 
Published: February 2021

ABSTRACTThe way urbanization shapes the intraspecific variation of pollinator functional traits is little understood. However, this topic is relevant for investigating ecosystem services and pollinator health. Here, we studied how urbanization affects the functional traits of workers in two bumblebee species (Bombus terrestrisandB. pascuorum) sampled in 37 sites along a gradient of urbanization in North Italy (an area of 1800 km2including the metropolitan context of Milan and other surrounding capital districts). Namely, we investigated the role played by land-use composition, configuration, temperature, flower resource abundance, and air pollutants on the variation of traits related to flight performance (i.e., body size, wing shape and size fluctuating asymmetry). These traits are relevant because they are commonly used as indicators of stress during insect development. The functional traits of the two bumblebees responded idiosyncratically to urbanization. Urban temperatures were associated with smaller wing sizes inB. pascuorumand with more accentuated fluctuating asymmetry of wing size inB. terrestris. Moreover, flower abundance correlated with bigger wings inB. terrestrisand with less asymmetric wing sizes inB. pascuorum. Other traits did not vary significantly and other urban variables played minor effects. These patterns highlight that environmental stressors linked to urbanization negatively impact traits related to flight performance and development stability of these species with possible consequences on the pollination service they provide.Overall, this study found species-specific variation patterns in syntopic taxa, expanding our understanding about the effects of anthropic disturbance in shaping relevant functional traits of pollinator model species.
Just-in-time: gaze guidance in natural behavior
Authors: Keshava Ashima , Nezami Farbod Nosrat , Neumann Henri , Izdebski Krzysztof , Schüler Thomas , König Peter 
Published: February 2021

ABSTRACTNatural eye movements have primarily been studied for over-learned activities such as tea-making, sandwich-making, and hand-washing, which have a fixed sequence of associated actions. These studies indicate a sequential activation of low-level cognitive schemas facilitating task completion. However, it is unclear if these action schemas are activated in the same pattern when a task is novel and a sequence of actions must be planned in the moment. Here, we recorded gaze and body movements in a naturalistic task to study action-oriented gaze behavior. In a virtual environment, subjects moved objects on a life-size shelf to achieve a given order. In order to compel cognitive planning, we added complexity to the sorting tasks. Fixations aligned with the action onset showed gaze as tightly coupled with the action sequence, and task complexity moderately affected the proportion of fixations on the task-relevant regions. Our analysis further revealed that the gaze was allocated to action-relevant targets just in time. Planning behavior predominantly corresponded to a greater visual search for task-relevant objects before the action onset. The results support the idea that natural behavior relies very little on working memory, and humans refrain from encoding objects in the environment to plan long-term actions. Instead, they prefer just-in-time planning by searching for action-relevant items in the moment, directing their body and hand to it, monitoring the action until it is terminated, and moving on to the next action.Author SummaryEye movements in the natural environment have primarily been studied for over-learned and habitual everyday activities (tea-making, sandwich-making, hand-washing) with a fixed sequence of associated actions. These studies show eye movements correspond to a specific order of actions learned over time. In this study, we were interested in how humans plan and execute actions for tasks that do not have an inherent action sequence. To that end, we asked subjects to sort objects based on object features on a life-size shelf in a virtual environment as we recorded their eye and body movements. We investigated the general characteristics of gaze behavior while acting under natural conditions. Our paper provides a comprehensive approach to preprocess naturalistic gaze data in virtual reality. Furthermore, we provide a data-driven method of analyzing the different action-oriented functions of gaze. The results show that bereft of a predefined action sequence, humans prefer to plan only their immediate actions where eye movements are used to search for the target object to immediately act on, then to guide the hand towards it, and to monitor the action until it is terminated. Such a simplistic approach ensures that humans choose sub-optimal behavior over planning under sustained cognitive load.
Experimental sexual selection reveals rapid evolutionary divergence in sex-specific transcriptomes and their interactions following mating
Authors: Veltsos Paris , Porcelli Damiano , Fang Yongxiang , Cossins Andrew R. , Ritchie Michael G. , Snook Rhonda R. 
Published: February 2021

AbstractPostcopulatory interactions between the sexes in internally fertilizing species elicits both sexual conflict and sexual selection. Macroevolutionary and comparative studies have linked these processes to rapid transcriptomic evolution in sex-specific tissues and substantial transcriptomic postmating responses in females, patterns of which are altered when mating between reproductively isolated species. Here we test multiple predictions arising from sexual selection and conflict theory about the evolution of sex-specific and tissue-specific gene expression and the postmating response at the microevolutionary level. Following over 150 generations of experimental evolution under either reduced (enforced monogamy) or elevated (polyandry) sexual selection inDrosophila pseudoobscura, we found a substantial effect of sexual selection treatment on transcriptomic divergence in virgin male and female reproductive tissues (testes, male accessory glands, the female reproductive tract and ovaries). Sexual selection treatment also had a dominant effect on the postmating response, particularly in the female reproductive tract – the main arena for sexual conflict - compared to ovaries. This affect was asymmetric with monandry females typically showing more postmating responses than polyandry females, with enriched gene functions varying across treatments. The evolutionary history of the male partner had a larger effect on the postmating response of monandry females, but females from both sexual selection treatments showed unique patterns of gene expression and gene function when mating with males from the alternate treatment. Our microevolutionary results mostly confirm comparative macroevolutionary predictions on the role of sexual selection on transcriptomic divergence and altered gene regulation arising from divergent coevolutionary trajectories between sexual selection treatments.
Functional inactivation of pulmonary MAIT cells following 5-OP-RU treatment of non-human primates
Authors: Sakai Shunsuke , Lora Nickiana E. , Kauffman Keith D. , Dorosky Danielle E. , Oh Sangmi , Namasivayam Sivaranjani , Gomez Felipe , Fleegle Joel D. ,   Tuberculosis Imaging Program, Lindestam Arlehamn Cecilia S. , Sette Alessandro , Sher Alan , Freeman Gordon J. , Via Laura E. , Barry Clifton E. , Barber Daniel L. 
Published: February 2021

ABSTRACTTargeting MAIT cells holds promise for the treatment of different diseases and infections. We previously showed that treatment ofMycobacterium tuberculosisinfected mice with 5-OP-RU, a major antigen for MAIT cells, expands MAIT cells and enhances bacterial control. Here we treatedM. tuberculosisinfected rhesus macaques with 5-OP-RU intratracheally but found no clinical or microbiological benefit inM. tuberculosisinfected macaques. In fact, after 5-OP-RU treatment MAIT cells did not expand, but rather upregulated PD-1 and lost the ability to produce multiple cytokines, a phenotype resembling T cell exhaustion. Furthermore, we show that vaccination of uninfected macaques with 5-OP-RU+CpG instillation into the lungs also drives MAIT cell dysfunction, and PD-1 blockade during vaccination partly prevents the loss of MAIT cell function without facilitating their expansion. Thus, in rhesus macaques MAIT cells are prone to the loss of effector functions rather than expansion after TCR stimulationin vivo, representing a significant barrier to therapeutically targeting these cells.
Modeling Vertical Migrations of Zooplankton Based on Maximizing Fitness
Authors: Kuzenkov O. , Ryabova E. , Garcia A. , Degtyarev A. 
Published: February 2021

AbstractThe purpose of the work is to calculate the evolutionarily stable strategy of zooplankton diel vertical migrations from known data of the environment using principles of evolutionary optimality and selection.At the first stage of the research, the fitness function is identified using artificial neural network technologies. The training sample is formed based on empirical observations. It includes pairwise comparison results of the selective advantages of a certain set of species. Key parameters of each strategy are calculated: energy gain from ingested food, metabolic losses, energy costs on movement, population losses from predation and unfavorable living conditions. The problem of finding coefficients of the fitness function is reduced to a classification problem. The single-layer neural network is built to solve this problem. The use of this technology allows one to construct the fitness function in the form of a linear convolution of key parameters with identified coefficients.At the second stage, an evolutionarily stable strategy of the zooplankton behavior is found by maximizing the identified fitness function. The maximization problem is solved using optimal control methods. A feature of this work is the use of piecewise linear approximations of environmental factors: the distribution of food and predator depending on the depth. As a result of the study, mathematical and software tools have been created for modeling and analyzing the hereditary behavior of living organisms in an aquatic ecosystem. Mathematical modeling of diel vertical migrations of zooplankton in Saanich Bay has been carried out.
Proton egress pathway during the S1–S2transition of the Oxygen Evolving Complex of Photosystem II
Authors: Kaur Divya , Zhang Yingying , Reiss Krystle M. , Mandal Manoj , Brudvig Gary W. , Batista Victor S. , Gunner M. R. 
Published: February 2021

AbstractPhotosystem II uses water as the ultimate electron source of the photosynthetic electron transfer chain. Water is oxidized to dioxygen at the Oxygen Evolving Complex (OEC), a Mn4CaO5inorganic core embedded in the lumenal side of PSII. Water-filled channels are thought to bring in substrate water molecules to the OEC, remove the substrate protons to the lumen, and may transport the product oxygen. Three water-filled channels, denoted large, narrow, and broad, that extend from the OEC towards the aqueous surface more than 15 Å away are seen. However, the actual mechanisms of water supply to the OEC, the removal of protons to the lumen and diffusion of oxygen away from the OEC have yet to be established. Here, we combine Molecular Dynamics (MD), Multi Conformation Continuum Electrostatics (MCCE) and Network Analysis to compare and contrast the three potential proton transfer paths during the S1to S2transition of the OEC. Hydrogen bond network analysis shows that the three channels are highly interconnected with similar energetics for hydronium as calculated for all paths near the OEC. The channels diverge as they approach the lumen, with the water chain in the broad channel better interconnected that in the narrow and large channels, where disruptions in the network are observed at about 10 Å from the OEC. In addition, the barrier for hydronium translocation is lower in the broad channel, suggesting that a proton from the OEC could access the paths near the OEC, and likely exit to the lumen via the broad channel, passing through PsbO.
DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species
Authors: Hu Yanhui , Tattikota Sudhir Gopal , Liu Yifang , Comjean Aram , Gao Yue , Forman Corey , Kim Grace , Rodiger Jonathan , Papatheodorou Irene , dos Santos Gilberto , Mohr Stephanie E. , Perrimon Norbert 
Published: February 2021

AbstractWith the advent of single-cell RNA sequencing (scRNA-seq) technologies, there has been a spike in studies involving scRNA-seq of several tissues across diverse species includingDrosophila.Although a few databases exist for users to query genes of interest within the scRNA-seq studies, search tools that enable users to find orthologous genes and their cell type-specific expression patterns across species are limited. Here, we built a new search database, called DRscDB (https://www.flyrnai.org/tools/single_cell/web/) to address this need. DRscDB serves as a comprehensive repository for published scRNA-seq datasets forDrosophilaand the relevant datasets from human and other model organisms. DRscDB is based on manual curation ofDrosophilascRNA-seq studies of various tissue types and their corresponding analogous tissues in vertebrates including zebrafish, mouse, and human. Of note, our search database provides most of the literature-derived marker genes, thus preserving the original analysis of the published scRNA-seq datasets. DRscDB serves as a web-based user interface that allows users to mine, utilize and compare gene expression data pertaining to scRNA-seq datasets from the published literature.
Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions
Authors: Findley Anthony S , Monziani Alan , Richards Allison L , Rhodes Katie , Ward Michelle C , Kalita Cynthia A , Alazizi Adnan , Pazokitoroudi Ali , Sankararaman Sriram , Wen Xiaoquan , Lanfear David E , Pique-Regi Roger , Gilad Yoav , Luca Francesca 
Published: February 2021

AbstractGenetic effects on gene expression and splicing can be modulated by cellular and environmental factors; yet interactions between genotypes, cell type and treatment have not been comprehensively studied together. We used an induced pluripotent stem cell system to study multiple cell types derived from the same individuals and exposed them to a large panel of treatments. Cellular responses involved different genes and pathways for gene expression and splicing processes, and were also highly variable across cell types and treatments. For thousands of genes, we identified variable allelic expression across contexts, and characterized different types of gene-environment interactions. Many of these G×E genes are associated with complex traits. We characterized promoter functional and evolutionary features that distinguish genes with elevated allelic imbalance mean and variance. More than 47% of the genes with dynamic regulatory interactions were missed by GTEx, but we identified them using a suitable allelic imbalance study design. This indicates the importance of exploring multiple treatments to reveal previously unrecognized regulatory loci that may be important for disease.
Morphological Metrics of Magnetic Resonance Imaging of Glioblastoma as Biomarkers of Prognosis
Authors: Curtin Lee , Whitmire Paula , White Haylye , Mrugala Maciej M. , Hu Leland S. , Swanson Kristin R. 
Published: February 2021

AbstractMorphological characteristics have been linked to outcomes across a variety of cancers. Lacunarity is a quantitative morphological measure of how shapes fill space while fractal dimension is a morphological measure of the complexity of pixel arrangement. Glioblastoma is the most aggressive primary brain tumor with a short expected survival given the current standard-of-care treatment. Due to the sensitive location of the tumor, there is a heavy reliance on imaging to assess the state of the disease in the clinic. In this project, we computed lacunarity and fractal dimension values for glioblastoma-induced abnormalities on gadolinium-enhanced T1-weighted magnetic resonance imaging (T1Gd MRI) as well as T2-weighted (T2) and fluid-attenuated inversion recovery (FLAIR) MRIs. In our patient cohort (n=402), we aim to connect these morphological metrics calculated on pretreatment MRI with the survival of patients with GBM. We calculated lacunarity and fractal dimension across all MRI slices on necrotic regions (n=390) and abnormalities on T1Gd MRI (n=402), as well as on enhancing abnormalities present on T2/FLAIR MRI (n=257). We also explored the relationship between these metrics and age at diagnosis, as well as abnormality volume. We found statistically significant relationships to outcome across all three imaging subtypes, with the shape of T2/FLAIR abnormalities showing the strongest relationship with overall survival. The link between morphological and survival metrics could be driven by underlying biological phenomena, tumor location or microenvironmental factors that should be further explored.