bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of long- and short-range fiber depletion on the cognitive deficits of fronto-temporal dementia
Authors: Savard Melissa , Pascoal Tharick A. , Dhollander Thijs , Iturria-Medina Yasser , Vitali Paolo , Therriault Joseph , Mathotaarachchi Sulantha , Benedet Andrea L. , Gauthier Serge , Rosa-Neto Pedro ,   for the Frontotemporal Lobar Degeneration Neuroimaging Initiative
Published: May 2020

AbstractFronto-temporal dementia (FTD) is a neurodegenerative disease characterized by focal atrophy of the gray matter (GM), especially in the frontal and temporal regions. Recent studies suggest a framework where white matter (WM) atrophy plays an important role in FTD pathophysiology. However, these studies often overlook the fact that WM tracts bridging different brain regions may have different vulnerabilities to the disease and the relative contribution of GM atrophy to this WM model, resulting in a less comprehensive understanding of the relationship between clinical symptoms and pathology. Here, by leveraging the sensitivity of advanced diffusion MRI modelling and metrics to precise white matter microstructural properties, we aim to clarify the relative contributions of WM fibers and GM atrophy to the cognitive symptoms typically found in FTD. A total of 155 participant from the Frontotemporal Lobar Degeneration Neuroimaging Initiative (FTLDNI) were analysed, including 68 normal elderly controls (CN), 28 behavioral variants (BV), 26 sematic variants (SV) and 30 progressive non fluent aphasia variants (PNFA) of FTD. Diffusion MRI analysis was performed using two complementary techniques: whole brain fixel-based analysis (FBA) and structural connectivity based on probabilistic tractography. Whole brain GM atrophy was assessed using voxel-based morphometry (VBM). Using a common factor analysis to extract a semantic and an executive factor, we aim to test the relative contribution of WM and GM of specific tracts in predicting cognition. We found that semantic symptoms were mainly dependent on short-range WM fiber disruption, while damage to long-range WM fibers was preferentially associated to executive dysfunction with the GM contribution to cognition being predominant for local processing. Our results support the importance of the disruption of specific WM tracts to the core cognitive symptoms associated with FTD. As large-scale WM tracts, which are particularly vulnerable to vascular disease, were highly associated with executive dysfunction, our findings highlight the importance of controlling for risk factors associated with deep white matter disease, such as vascular risk factors, in patients with FTD in order not to potentiate underlying executive dysfunction.
Equine synovial fluid small non-coding RNA signatures in early osteoarthritis
Authors: Castanheira Catarina , Balaskas Panagiotis , Falls Charlotte , Ashraf-Kharaz Yalda , Clegg Peter , Burke Kim , Fang Yongxiang , Dyer Philip , Welting Tim JM , Peffers Mandy J 
Published: May 2020

ABSTRACTBackgroundOsteoarthritis remains one of the greatest causes of morbidity and mortality in the equine population. The inability to detect pre-clinical changes in osteoarthritis has been a significant impediment to the development of effective therapies against this disease. Synovial fluid represents a potential source of disease-specific small non-coding RNAs (sncRNAs) that could aid in the understanding of the pathogenesis of osteoarthritis. We hypothesised that early stages of osteoarthritis would alter the expression of sncRNAs, facilitating the understanding of the underlying pathogenesis and potentially provide early biomarkers.MethodsSmall RNA sequencing was performed using synovial fluid from the metacarpophalangeal joints of both control and early osteoarthritic non-Thoroughbred horses. A group of differentially expressed sncRNAs was selected for further validation through qRT-PCR using an independent cohort of synovial fluid samples from control and early osteoarthritic horses. Bioinformatic analysis was performed in order to identify putative targets of the differentially expressed microRNAs and to explore potential associations with specific biological processes.ResultsResults revealed 22 differentially expressed sncRNAs including 13 microRNAs; miR-10a, miR-223, let7a, miR-99a, miR-23b, miR-378, miR-143 (and six novel microRNAs), four small nuclear RNAs; U2, U5, U11, U12, three small nucleolar RNAs; U13, snoR38, snord96, and one small cajal body-specific RNA; scarna3. Five sncRNAs were validated; miR-223 was significantly reduced in early OA and miR-23b, let-7a-2, snord96A and snord13 were significantly upregulated. Significant cellular functions deduced by the differentially expressed microRNAs included apoptosis (P < 0.0003), necrosis (P < 0.0009), autophagy (P < 0.0007) and inflammation (P < 0.00001). A conservatively filtered list of 57 messenger RNA targets was obtained; the top biological processes associated were regulation of cell population proliferation (P < 0.000001), cellular response to chemical stimulus (P < 0.000001) and cell surface receptor signalling pathway (P < 0.000001).ConclusionsSynovial fluid sncRNAs can be used as molecular biomarkers for early disease in equine osteoarthritic joints. The biological processes they regulate may play an important role in understanding early osteoarthritis pathogenesis. Characterising these dynamic molecular changes could provide novel insights on the process and mechanism of early osteoarthritis development and is critical for the development of new therapeutic approaches.
Artificially selecting microbial communities using propagule strategies
Authors: Chang Chang-Yu , Osborne Melisa L. , Bajic Djordje , Sanchez Alvaro 
Published: May 2020

AbstractArtificial selection is a promising approach to manipulate the function of microbial communities. Here, we report the outcome of two artificial selection experiments at the microbial community level. Both experiments used “propagule” strategies, in which a set of the best-performing communities are used as the inocula to form a new generation of communities. In both cases, the selected communities are compared to a control treatment where communities are randomly selected. The first experiment used a defined set of strains as the starting inoculum, and the function under selection was the amylolytic activity of the consortia. The second experiment used a diverse set of natural communities as the inoculum, and the function under selection was the cross-feeding potential of the resulting communities towards a reference bacterial strain. In both experiments, the selected communities reached a higher mean and a higher maximum function than the control. In the first experiment this is caused by a decline in function of the control, rather than an improvement of the selected line. In the second experiment, the strong response of the mean is caused by the large initial variance in function across communities, and is the immediate consequence of the spread of the top-performing community in the starting group, whose function does not increase. Our results are in agreement with basic expectations of artificial selection theory, pointing out some of the limitations of community-level selection experiments which can inform the design of future studies.
Submodular sketches of single-cell RNA-seq measurements
Authors: Yang Wei , Schreiber Jacob , Bilmes Jeffrey , Noble William Stafford 
Published: May 2020

AbstractAnalyzing and sharing massive single-cell RNA-seq data sets can be facilitated by creating a “sketch” of the data—a selected subset of cells that accurately represent the full data set. Using an existing benchmark, we demonstrate the utility of submodular optimization in efficiently creating high quality sketches of scRNA-seq data.
Oxygen radicals and cytoplasm zoning in growing lily pollen tubes
Authors: Podolyan Alexandra , Luneva Oksana , Breygina Maria 
Published: May 2020

AbstractRecently redox-regulation of tip growth has been extensively studied, but differential sensitivity of growing cells to particular ROS and their subcellular localization is still unclear. Here we used specific dyes to provide mapping of H2O2and O•2−in short and long pollen tubes. We found apical accumulation of H2O2and H2O2–producing organelles in the shank that were not colocalized with O•2−-producing mitochondria. Differential modulation of ROS content of the germination medium affected both growth speed and pollen tube morphology. Oxygen radicals affected ionic zoning: membrane potential and pH gradients. OH• caused depolarization all along the tube while O•2−provoked hyperpolarization and cytoplasm alkalinization. O•2−accelerated growth and reduced tube diameter, indicating that this ROS can be considered as pollen tube growth stimulator along with H2O2. Serious structural disturbances were observed upon exposure to OH• and H2O2and O•2−quencher MnTMPP: pollen tube growth slowed down and ballooned tips formed in both cases, but in the presence of OH• membrane transport and organelle distribution was affected as well. OH•, thus, can be considered as a negative influence on pollen tubes which, presumably, have mechanisms for leveling it. The assumption was confirmed by EPR spectroscopy: pollen tubes actively reduce OH• content in the incubation medium.
Transcriptomic expression patterns of two contrasting lowland rice varieties reveal high iron stress tolerance
Authors: Kar Saradia , Mai Hans-Jörg , Khalouf Hadeel , Ben Abdallah Heithem , Flachbart Samantha , Fink-Straube Claudia , Bräutigam Andrea , Xiong Guosheng , Shang Lianguang , Panda Sanjib Kumar , Bauer Petra 
Published: May 2020

AbstractIron (Fe) toxicity is a major challenge for plant cultivation in acidic water-logged soil environments, where lowland rice is a major staple food crop. Only few studies addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance in the studied varieties.Here, we screened 16 lowland rice varieties for excess Fe stress growth responses to identify contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. Hacha and Lachit differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation, Fe and metal contents. These responses were mirrored by differential gene expression patterns, obtained through RNA-sequencing, and corresponding GO term enrichment in tolerant versus susceptible lines. From the comparative transcriptomic profiles between Lachit and Hacha in response to excess Fe stress, individual genes of the category metal homeostasis, mainly root-expressed, may contribute to the tolerance of Lachit. 22 out of these 35 metal homeostasis genes are present in selection sweep genomic regions, in breeding signatures and/or differentiated during rice domestication. These findings will serve to design targeted Fe tolerance breeding of rice crops.Summary statementLowland rice varieties Hacha and Lachit were selected for contrasting abilities to cope with iron excess stress. Morphological and physiological phenotypes were mirrored by molecular transcriptome changes, indicating altered metal homeostasis in the root as an adaptive tolerance mechanism in Lachit.
Social play is critical for the development of prefrontal inhibitory synapses and cognitive flexibility in rats
Authors: Bijlsma Ate , Omrani Azar , Spoelder Marcia , Verharen Jeroen P.H. , Bauer Lisa , Cornelis Cosette , de Zwart Beleke , van Dorland René , Vanderschuren Louk J.M.J. , Wierenga Corette J. 
Published: May 2020

AbstractSensory driven activity during early life is critical for setting up the proper connectivity of the sensory cortices. Here we ask if social play behavior, a particular form of social interaction that is highly abundant during post-weaning development, is equally important for setting up connections in the developing prefrontal cortex (PFC). Young rats were deprived from social play with peers for 3 weeks during the period in life when social play behavior normally peaks (P21-42; SPD rats), followed by resocialization until adulthood. We recorded synaptic currents in L5 cells in slices from medial PFC of adult SPD and control rats and observed that inhibitory synaptic currents were reduced in SPD slices, while excitatory synaptic currents were unaffected. This was associated with a decrease in perisomatic inhibitory synapses from parvalbumin-positive GABAergic cells. In parallel experiments, adult SPD rats achieved more reversals in a probabilistic reversal learning task (PRL), which depends on the integrity of the PFC. They appeared to use a different cognitive strategy than controls. One hour of intense play during SPD did not prevent the decrease in inhibitory synaptic inputs and had only a limited effect on behavioral outcomes in the PRL. Our data demonstrate the importance of unrestricted social play for the development of inhibitory synapses in the PFC and cognitive skills in adulthood.
Kaleidoscope: A New Bioinformatics Pipeline Web Application for In Silico Hypothesis Exploration of Omics Signatures
Authors: Alganem Khaled , Shukla Rammohan , Eby Hunter , Abel Mackenzie , Zhang Xiaolu , McIntyre William Brett , Lee Jiwon , Au-Yeung Christy , Asgariroozbehani Roshanak , Panda Roshni , O’Donovan Sinead M , Funk Adam , Hahn Margaret , Meller Jarek , McCullumsmith Robert 
Published: May 2020

AbstractBackgroundIn silicodata exploration is a key first step of exploring a research question. There are many publicly available databases and tools that offer appealing features to help with such a task. However, many applications lack exposure or are constrained with unfriendly or outdated user interfaces. Thus, it follows that there are many resources that are relevant to investigation of medical disorders that are underutilized.ResultsWe developed an R Shiny web application, called Kaleidoscope, to address this challenge. The application offers access to several omics databases and tools to let users explore research questionsin silico. The application is designed to be user- friendly with a unified user interface, while also scalable by offering the option of uploading user-defined datasets. We demonstrate the application features with a starting query of a single gene (Disrupted in schizophrenia 1, DISC1) to assess its protein-protein interactions network. We then explore expression levels of the gene network across tissues and cell types in the brain, as well as across 34 schizophrenia versus control differential gene expression datasets.ConclusionKaleidoscope provides easy access to several databases and tools under a unified user interface to explore research questionsin silico. The web application is open-source and freely available athttps://kalganem.shinyapps.io/Kaleidoscope/. This application streamlines the process ofin silicodata exploration for users and expands the efficient use of these tools to stakeholders without specific bioinformatics expertise.
A Proposed Drought Response Equation Added to the Münch-Horwitz Theory of Phloem Transport
Authors: Goeschl John D. , Han Lifeng 
Published: May 2020

AbstractTheoretical and experimental evidence for an effect of sieve tube turgor pressure on the mechanisms of phloem unloading near the root tips during moderate levels of drought stress is reviewed. An additional, simplified equation is proposed relating decreased turgor pressure to decreased rate kinetics of membrane bound transporters. The effect of such a mechanism would be to decrease phloem transport Speed, but increase Concentration and Pressure, and thus prevent or delay negative Pressure in the phloem. Experimental evidence shows this mechanism precedes and exceeds a reduction in stomatal conductance.
CoV-Seq: SARS-CoV-2 Genome Analysis and Visualization
Authors: Liu Boxiang , Liu Kaibo , Zhang He , Zhang Liang , Bian Yuchen , Huang Liang 
Published: May 2020

AbstractSummaryCOVID-19 has become a global pandemic not long after its inception in late 2019. SARS-CoV-2 genomes are being sequenced and shared on public repositories at a fast pace. To keep up with these updates, scientists need to frequently refresh and reclean datasets, which is ad hoc and labor-intensive. Further, scientists with limited bioinformatics or programming knowledge may find it difficult to analyze SARS-CoV-2 genomes. In order to address these challenges, we developed CoV-Seq, a webserver to enable simple and rapid analysis of SARS-CoV-2 genomes. Given a new sequence, CoV-Seq automatically predicts gene boundaries and identifies genetic variants, which are presented in an interactive genome visualizer and are downloadable for further analysis. A command-line interface is also available for high-throughput processing.Availability and ImplementationCoV-Seq is implemented in Python and Javascript. The webserver is available athttp://covseq.baidu.com/and the source code is available fromhttps://github.com/boxiangliu/covseq.Contactjollier.liu@gmail.comSupplementary informationSupplementary information are available atbioRxivonline.
Sex-dependent effects of chronic intermittent voluntary alcohol consumption on attentional, not motivational, measures during probabilistic learning and reversal
Authors: Aguirre Claudia G. , Stolyarova Alexandra , Das Kanak , Kolli Sriya , Marty Vincent , Ray Lara , Spigelman Igor , Izquierdo Alicia 
Published: May 2020

AbstractBackgroundForced alcohol (ethanol, EtOH) exposure has been shown to cause significant impairments on reversal learning, a widely-used assay of cognitive flexibility, specifically on fully-predictive, deterministic versions of this task. However, previous studies have not adequately considered voluntary EtOH consumption and sex effects on probabilistic reversal learning. The present study aimed to fill this gap in the literature.MethodsMale and female Long-Evans rats underwent either 10 weeks of voluntary intermittent 20% EtOH access or water only (H2O) access. Rats were then pretrained to initiate trials and learn stimulus-reward associations via touchscreen response, and subsequently required to select between two visual stimuli, rewarded with probability 0.70 or 0.30. In the final phase, reinforcement contingencies were reversed.ResultsWe found significant sex differences on several EtOH-drinking variables, with females reaching a higher maximum EtOH consumption, exhibiting more high-drinking days, and escalating their EtOH at a quicker rate compared to males. During early abstinence, EtOH drinkers made more initiation omissions and were slower to initiate trials than H2O drinking controls, particularly during pretraining. EtOH drinking females were most affected. A similar pattern in trial initiations was also observed in discrimination, but not in reversal learning. EtOH drinking rats were unaffected in their reward collection and stimulus response times, indicating intact motivation and motor responding. Although there were sex differences in discrimination and reversal phases, performance improved over time. We also observed sex-independent drinking group differences in win-stay and lose-shift strategies specific to the reversal phase.ConclusionsFemales exhibit increased vulnerability to EtOH effects in early learning: there were sex-dependent EtOH effects on attentional measures during pretraining and discrimination phases. We also found sexindependent EtOH effects on exploration strategies during reversal. Future studies should aim to uncover the neural mechanisms for changes in attention and exploration in both acute and prolonged EtOH withdrawal.
No evidence for transient transformation via pollen magnetofection in several monocot species
Authors: Vejlupkova Zuzana , Warman Cedar , Sharma Rita , Scheller Henrik Vibe , Mortimer Jenny C. , Fowler John E. 
Published: May 2020

ABSTRACTThe development of rapid and efficient transformation methods for many plant species remains an obstacle in both the basic and applied plant sciences. A novel method described by Zhao et al. (2017) used magnetic nanoparticles to deliver DNA into pollen grains of several dicot species, and one monocot (lily), to achieve transformation (“pollen magnetofection”). Using the published protocol, extensive trials by two independent research groups showed no indication of transient transformation success with pollen from two monocots, maize and sorghum. To further address the feasibility of magnetofection, lily pollen was used for side-by-side trials of magnetofection with a proven methodology for transient transformation, biolistics. Using a Green Fluorescent Protein reporter plasmid, transformation efficiency with the biolistic approach averaged 0.7% over three trials. However, the same plasmid produced no recognizable transformants via magnetofection, despite screening >3500 individual pollen grains. We conclude that pollen magnetofection is not effective for transient transformation of pollen for at least three species of monocots, and suggest that efforts to replicate the magnetofection protocol in dicot species would be useful to fully assess its potential.ARISING FROM Zhao et al.Nature Plantshttps://doi.org/10.1038/s41477-017-0063-z(2017)
The microbiota promotes social behavior by modulating microglial remodeling of forebrain neurons
Authors: Bruckner Joseph J. , Stednitz Sarah J. , Grice Max Z. , Zaidan Dana , Massaquoi Michelle S. , Larsch Johannes , Tallafuss Alexandra , Guillemin Karen , Washbourne Philip , Eisen Judith S. 
Published: May 2020

AbstractHost-associated microbiotas guide the trajectory of developmental programs, and microbial dysbiosis is linked to neurodevelopmental conditions such as autism spectrum disorder. Recent work suggests that microbiotas modulate behavioral phenotypes associated with these disorders. We discovered that the zebrafish microbiota is required for normal social behavior, and reveal a molecular pathway linking the microbiota, microglial remodeling of neural circuits, and social behavior in this experimentally tractable model vertebrate. Examining neuronal correlates of behavior, we found that the microbiota restrains neurite complexity and targeting of forebrain neurons required for normal social behavior and is necessary for localization of forebrain microglia, brain resident phagocytes that remodel neuronal arbors. The microbiota also influences microglial molecular functions, including promoting expression of the remodeling factorc1q, which we find is required for normal forebrain neurite complexity. Several distinct bacterial taxa are individually sufficient for normal microglial and neuronal phenotypes, suggesting that host neuroimmune development is sensitive to a feature common among many bacteria. Our results demonstrate that the microbiota influences zebrafish social behavior by stimulating microglial remodeling of forebrain circuits during early neurodevelopment, and suggest pathways for new interventions in multiple neurodevelopmental disorders.