bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oxytocinergic modulation of stress-associated amygdala-hippocampus pathways in humans is mediated by serotonergic mechanisms
Authors: Lan Chunmei , Liu Congcong , Li Keshuang , Zhao Zhiying , Yang Jiaxin , Ma Yina , Scheele Dirk , Shuxia Yao , Kendrick Keith M. , Becker Benjamin 
Published: November 2021

AbstractBackgroundThe hypothalamic neuropeptide oxytocin (OXT) may exert anxiolytic and stress-reducing actions via modulatory effects on amygdala circuits. Animal models and initial findings in humans suggest that some of these effects are mediated by interactions with other neurotransmitter systems, in particular the serotonin (5-HT) system. Against this background, the present pharmacological resting state fMRI study aimed at determining whether effects of OXT on stress-associated amygdala intrinsic networks are mediated by 5-HT.MethodsWe employed a randomized placebo-controlled double-blind parallel-group pharmacological fMRI resting state experiment during which n = 112 healthy male participants underwent a transient decrease in 5-HT signaling via acute tryptophan depletion (ATD) or the corresponding placebo-control protocols (ATDc) before the administration of intranasal OXT or placebo intranasal spray, respectively.ResultsOXT and 5-HT modulation exerted interactive effects on the coupling of the left amygdala with the ipsilateral hippocampus and adjacent midbrain. OXT increased intrinsic coupling in this pathway, while this effect of OXT was significantly attenuated during transiently decreased central serotonergic signaling induced via ATD. In the absence of OXT or 5-HT modulation this pathway showed a trend for an association with self-reported stress perception in everyday life. No interactive effects were observed for the right amygdala.ConclusionsTogether, the findings provide first evidence that effects of OXT on stress-associated amygdala-hippocampal-midbrain pathways are critically mediated by the 5-HT system in men.
specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data
Authors: Darcy John L. , Amend Anthony S. , Swift Sean O. I. , Sommers Pacifica S. , Lozupone Catherine A. 
Published: November 2021

AbstractBackgroundUnderstanding the factors that influence microbes’ environmental distributions is important for deter-mining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, “specificity” is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao’s (1982, 2010) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables.ResultsWe present our R package specificity for performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well.Conclusionsspecificity is well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers using specificity’s companion package, specificity.shiny.
Temporal variation in the behaviour of a cooperatively breeding bird, Jungle Babbler (Argya striata) at diel and seasonal scale
Authors: Yambem Soniya Devi , Jain Manjari 
Published: November 2021

AbstractTime is an important and limited resource that can drive the trade-off between various essential activities in the lives of animals. Group-living animals need to perform different behaviour to meet their individual needs and also participate in group activities. They must, therefore, partition the available time between these activities which may vary considerably with environmental and ecological conditions. We examined time-activity budget of a cooperative passerine, Jungle Babbler (Argya striata) and how their behaviour vary across diel and seasonal scales. A repertoire of 13 behaviour was recorded of which 12 behaviour that occur throughout the year were examined further in detail. This included individual behaviour such as foraging, grooming, rest, shower and group behaviour such as allogrooming, movement, play, sentinel, mobbing and inter-group fight. Our results indicate that most of the time (about 70%) was spent performing individual behaviour and the remaining time (about 30%) was allocated to social behaviour. We also found almost all behaviour varied across diel and seasonal scale with respect to proportion of time spent performing them. This highlights the impact of environmental factors on how animals partition their time to perform various activities. Our study also lays the foundation for future studies examining the role of ecological factors such as habitat type and predation pressure in driving these patterns of behaviour in Jungle Babblers.
Association between long working hours and psychological distress: The effect of sick leave criteria in the workplace during the COVID-19 pandemic
Authors: Hino Ayako , Inoue Akiomi , Mafune Kosuke , Tsuji Mayumi , Tateishi Seiichiro , Ogami Akira , Nagata Tomohisa , Muramatsu Keiji , Fujino Yoshihisa ,   for the CORoNaWork Project
Published: November 2021

AbstractObjectiveThis study investigated the effect of sick leave criteria on the association between long working hours and psychological distress.MethodsWe conducted a cross-sectional survey in December 2020, and 27,032 workers completed the questionnaire. First, after testing the interaction effect of overtime work hours and sick leave criteria on psychological distress, we conducted stratified analyses using sick leave criteria.ResultsA significant interaction effect was found. When we conducted stratified analyses, the odds ratios increased with longer working hours, both with and without sick leave criteria groups; however, the risk was greater in the without sick leave criteria group, compared with the criteria group.ConclusionWe revealed that working without sick leave criteria could strengthen the association between long working hours and psychological distress during the COVID-19 pandemic.Clinical significanceWorkers working without sick leave criteria had a significantly higher risk of psychological distress due to long working hours than those who worked with the criteria. Our findings contribute to preventing the deterioration of mental health during the COVID-19 pandemic.
Differential richness inference for 16S rRNA marker gene surveys
Authors: Kumar M. Senthil , Slud Eric V. , Hehnly Christine , Zhang Lijun , Broach James , Irizarry Rafael P. , Schiff Steven J. , Paulson Joseph N. 
Published: November 2021

AbstractIndividual and environmental health outcomes are frequently linked to changes in the diversity of associated microbial communities. This makes deriving health indicators based on microbiome diversity measures essential.While microbiome data generated using high throughput 16S rRNA marker gene surveys are appealing for this purpose, 16S surveys also generate a plethora of spurious microbial taxa. When this artificial inflation in the observed number of taxa (i.e., richness, a diversity measure) is ignored, we find that changes in the abundance of detected taxa confound current methods for inferring differences in richness.Here we argue that the evidence of our own experiments, theory guided exploratory data analyses and existing literature, support the conclusion that most sub-genus discoveries are spurious artifacts of clustering 16S sequencing reads. We proceed based on this finding to model a 16S survey’s systematic patterns of sub-genus taxa generation as a function of genus abundance to derive a robust control for false taxa accumulation.Such controls unlock classical regression approaches for highly flexible differential richness inference at various levels of the surveyed microbial assemblage: from sample groups to specific taxa collections. The proposed methodology for differential richness inference is available through an R package, Prokounter.Package availability: https://github.com/mskb01/prokounter
Distinct cell death pathways induced by granzymes collectively protect against intestinalSalmonellainfection
Authors: Chawla Amanpreet Singh , Vandereyken Maud , Arias Maykel , Santiago Llipsy , Dikovskaya Dina , Nguyen Chi , Skariah Neema , Wenner Nicolas , Golovchenko Natasha B. , Thomson Sarah J. , Ondari Edna , Garzón-Tituaña Marcela , Anderson Christopher J. , Bergkessel Megan , Hinton Jay C. D. , Edelblum Karen L. , Pardo Julian , Swamy Mahima 
Published: November 2021

ABSTRACTIntestinal intraepithelial T lymphocytes (IEL) constitutively express high amounts of the cytotoxic proteases Granzymes (Gzm) A and B and are therefore thought to protect the intestinal epithelium against infection by killing infected epithelial cells. However, the role of IEL granzymes in a protective immune response has yet to be demonstrated. We show that GzmA and GzmB are required to protect mice against oral, but not intravenous, infection withSalmonella entericaserovar Typhimurium, consistent with an intestine-specific role. IEL-intrinsic granzymes mediate the protective effects by controlling intracellular bacterial growth and aiding in cell-intrinsic pyroptotic cell death of epithelial cells. Surprisingly, we found that both granzymes play non- redundant roles.GzmB-/-mice carried significantly lower burdens ofSalmonella, as predominant GzmA-mediated cell death effectively reduced bacterial translocation across the intestinal barrier. Conversely, inGzmA-/-mice, GzmB-driven apoptosis favored luminalSalmonellagrowth by providing nutrients, while still reducing translocation across the epithelial barrier. Together, the concerted actions of both GzmA and GzmB balance cell death mechanisms at the intestinal epithelium to provide optimal control thatSalmonellacannot subvert.Abstract Figure
Sonogenetic stimulation of the brain at a spatiotemporal resolution suitable for vision restoration
Authors: Cadoni S. , Demené C. , Provansal M. , Nguyen D. , Nelidova D. , Labernede G. , Alcala I. , Lubetzki J. , Goulet R. , Burban E. , Dégardin J. , Simonutti M. , Gauvain G. , Arcizet F. , Marre O. , Dalkara D. , Roska B. , Sahel J. A. , Tanter M. , Picaud S. 
Published: November 2021

AbstractRemote, precisely controlled activation of the brain is a fundamental challenge in the development of brain-machine interfaces providing feasible rehabilitation strategies for neurological disorders. Low-frequency ultrasound stimulation can be used to modulate neuronal activity deep in the brain1–7, but this approach lacks spatial resolution and cellular selectivity and loads the brain with high levels of acoustic energy. The combination of the expression of ultrasound-sensitive proteins with ultrasound stimulation (‘sonogenetic stimulation’) can provide cellular selectivity and higher sensitivity, but such strategies have been subject to severe limitations in terms of spatiotemporal resolution in vivo8–10, precluding their use for real-life applications. We used the expression of large-conductance mechanosensitive ion channels (MscL) with high-frequency ultrasonic stimulation for a duration of milliseconds to activate neurons selectively at a relatively high spatiotemporal resolution in the rat retina ex vivo and the primary visual cortex of rodents in vivo. This spatiotemporal resolution was achieved at low energy levels associated with negligible tissue heating and far below those leading to complications in ultrasound neuromodulation6,11. We showed, in an associative learning test, that sonogenetic stimulation of the visual cortex generated light perception. Our findings demonstrate that sonogenetic stimulation is compatible with millisecond pattern presentation for visual restoration at the cortical level. They represent a step towards the precise transfer of information over large distances to the cortical and subcortical regions of the brain via an approach less invasive than that associated with current brain-machine interfaces and with a wide range of applications in neurological disorders.
Emergence and maintenance of variable-length actin filaments in a limiting pool of building blocks
Authors: Banerjee Deb Sankar , Banerjee Shiladitya 
Published: November 2021

ABSTRACTActin is one of the key structural components of the eukaryotic cytoskeleton that regulates cellular architecture and mechanical properties. Dynamic regulation of actin filament length and organization is essential for the control of many physiological processes including cell adhesion, motility and division. While previous studies have mostly focused on the mechanisms controlling the mean length of individual actin filaments, it remains poorly understood how distinct actin filament populations in cells maintain different lengths using the same set of molecular building blocks. Here we develop a theoretical model for the length regulation of multiple actin filaments by nucleation and growth rate modulation by actin binding proteins in a limiting pool of monomers. We first show that spontaneous nucleation of actin filaments naturally leads to heterogeneities in filament length distribution. We then investigate the effects of filament growth inhibition by capping proteins and growth promotion by formin proteins on filament length distribution. We find that filament length heterogeneity can be increased by growth inhibition, whereas growth promoters do not significantly affect length heterogeneity. Interestingly, a competition between filament growth inhibitors and growth promoters can give rise to bimodal filament length distribution as well as a highly heterogeneous length distribution with large statistical dispersion. We quantitatively predict how heterogeneity in actin filament length can be modulated by tuning F-actin nucleation and growth rates in order to create distinct filament subpopulations with different lengths.SIGNIFICANCEActin filaments organize into different functional network architectures within eukaryotic cells. To maintain distinct actin network architectures, it is essential to regulate the lengths of actin filaments. While the mechanisms controlling the lengths of individual actin filaments have been extensively studied, the regulation of length heterogeneity in actin filament populations is not well understood. Here we show that the modulation of actin filament growth and nucleation rates by actin binding proteins can regulate actin length distribution and create distinct sub-populations with different lengths. In particular, by tuning concentrations of formin, profilin and capping proteins, various aspects of actin filament length distribution can be controlled. Insights gained from our results may have significant implications for the regulation of actin filament length heterogeneity and architecture within a cell.
Cold protection allows local cryotherapy in a clinical-relevant model of traumatic optic neuropathy
Authors: Zhang Yikui , Li Mengyun , Yu Bo , Lu Shengjian , Zhang Lujie , Zhu Senmiao , Yu Zhonghao , Xia Tian , Huang Haoliang , Jiang WenHao , Zhang Si , Sun Lanfang , Ye Qian , Sun Jiaying , Zhu Hui , Huang Pingping , Hong Huifeng , Yu Shuaishuai , Li Wenjie , Ai Danni , Fan Jingfan , Li Wentao , Song Hong , Xu Lei , Chen Xiwen , Ou Jingxing , Li Wei , Yang Jian , Hu Yang , Wu Wencan 
Published: November 2021

AbstractTherapeutic hypothermia (TH) is potentially an important therapy for central nervous system (CNS) trauma. However, its clinical application remains controversial, hampered by two major factors: 1) Many of the CNS injury sites, such as the optic nerve (ON), are deeply buried, preventing access for local TH. The alternative is to apply TH systemically, which significantly limits the applicable temperature range. 2) Even with possible access for “local refrigeration”, cold-induced cellular damage offsets the benefit of TH. Here we present a clinically translatable model of traumatic optic neuropathy (TON) by applying clinical trans-nasal endoscopic surgery to goats and non-human primates. This model faithfully recapitulates clinical features of TON such as the injury site (pre-chiasmatic ON), the spatiotemporal pattern of neural degeneration, and the accessibility of local treatments with large operating space. We also developed a computer program to simplify the endoscopic procedure and expand this model to other large animal species. Moreover, applying a cold-protective treatment, inspired by our previous hibernation research, enables us to deliver deep hypothermia (4°C) locally to mitigate inflammation and metabolic stress (indicated by the transcriptomic changes after injury) without cold-induced cellular damage, and confers prominent neuroprotection both structurally and functionally. Intriguingly, neither treatment alone was effective, demonstrating that in situ deep hypothermia combined with hibernation-mimicking cold protection constitutes a breakthrough for TH as a therapy for TON and other CNS traumas.
Hippocampus-sensitive and striatum-sensitive learning one month after morphine or cocaine exposure in male rats
Authors: Gardner Robert S. , Korol Donna L. , Gold Paul E. 
Published: November 2021

AbstractThese experiments examined whether exposure to drugs of abuse altered the balance between hippocampal and striatal memory systems as measured long after drug treatments. Male rats received injections of morphine (5 mg/kg), cocaine (20 mg/kg), or saline for five consecutive days. One month later, rats were then trained to find food on a hippocampus-sensitive place task or a striatum-sensitive response task. Relative to saline controls, morphine-treated rats exhibited impaired place learning but enhanced response learning; prior cocaine exposure did not significantly alter learning on either task. Another set of rats was trained on a dual-solution T-maze that can be solved with either place or response strategies. While a majority (67%) of control rats used place solutions in this task, morphine treatment one month prior resulted in a shift to response solutions exclusively (100%). Prior cocaine treatment did not significantly alter strategy selection. Molecular markers related to learning and drug abuse were measured in the hippocampus and striatum one month after drug exposure in behaviorally untested rats. Protein levels of glial-fibrillary acidic protein (GFAP), an intermediate filament specific to astrocytes, increased significantly in the hippocampus after morphine, but not after cocaine exposure. Exposure to morphine or cocaine did not significantly change levels of brain-derived neurotrophic factor (BDNF) or a downstream target of BDNF signaling, glycogen synthase kinase 3β (GSK3β), in the hippocampus or striatum. Thus, exposure to morphine results in a long-lasting shift from hippocampal toward striatal dominance during learning. The effects of prior morphine injections on GFAP suggest that long-lasting alterations in hippocampal astrocytes may be associated with these behavioral strategy shifts.
Telomere length regulation by Rif1 protein from Hansenula polymorpha
Authors: Malyavko Alexander N. , Petrova Olga A. , Zvereva Maria I. , Polshakov Vladimir I. , Dontsova Olga A. 
Published: November 2021

ABSTRACTRif1 is a large multifaceted protein involved in various processes of DNA metabolism – from telomere length regulation and replication to double-strand break repair. The mechanistic details of its action, however, are often poorly understood. Here, we report functional characterization of the Rif1 homologue from methylotrophic thermotolerant budding yeast Hansenula polymorpha DL-1. We show that, similar to other yeast species, H. polymorpha Rif1 suppresses telomerase-dependent telomere elongation. We uncover two novel modes of Rif1 recruitment at H. polymorpha telomeres: via direct DNA binding and through the association with the Ku heterodimer. Both of these modes (at least partially) require the intrinsically disordered N-terminal extension – a region of the protein present exclusively in yeast species. We also demonstrate that Rif1 binds Stn1 and promotes its accumulation at telomeres in H. polymorpha.
Generation and network analysis of an RNA-seq transcriptional atlas for the rat
Authors: Summers Kim M. , Bush Stephen J. , Wu Chunlei , Hume David A. 
Published: November 2021

ABSTRACTThe laboratory rat is an important model for biomedical research. To generate a comprehensive rat transcriptomic atlas, we curated and down-loaded 7700 rat RNA-seq datasets from public repositories, down-sampled them to a common depth and quantified expression. Data from 590 rat tissues and cells, averaged from each Bioproject, can be visualised and queried athttp://biogps.org/ratatlas. Gene correlation network (GCN) analysis revealed clusters of transcripts that were tissue or cell-type restricted and contained transcription factors implicated in lineage determination. Other clusters were enriched for transcripts associated with biological processes. Many of these clusters overlap with previous data from analysis of other species whilst some (e.g. expressed specifically in immune cells, retina/pineal gland, pituitary and germ cells) are unique to these data. GCN on large subsets of the data related specifically to liver, nervous system, kidney, musculoskeletal system and cardiovascular system enabled deconvolution of cell-type specific signatures. The approach is extensible and the dataset can be used as a point of reference from which to analyse the transcriptomes of cell types and tissues that have not yet been sampled. Sets of strictly co-expressed transcripts provide a resource for critical interpretation of single cell RNA-seq data.