bluuebunny/crossref_metadata_2025_split huggingface dataset:
Turning old foes into new allies – harnessing drainage canals for biodiversity conservation in desiccated novel ecosystems
Authors: Tölgyesi Csaba , Torma Attila , Bátori Zoltán , Šeat Jelena , Popović Miloš , Gallé Róbert , Gallé-Szpisjak Nikolett , Erdős László , Vinkó Tamás , Kelemen András , Török Péter 
Published: April 2020

AbstractDrainage canals are ubiquitous components of agricultural landscapes worldwide. Although canals have greatly contributed to biodiversity loss by desiccating wetlands, they have recently attracted conservation attention due to their potential to function as refugia for native wetland-dependent species in intensively managed landscapes. However, their conservation role in complex landscapes comprising a mosaic of agricultural and desiccated semi-natural habitats, on which canals still pose a heavy burden, is unknown. Improved understanding of drainage canals and related biodiversity in these landscapes could help unlock their potential and support synergistic land management for nature conservation and water management.We applied a multitaxon approach, including plants, butterflies, true bugs, spiders and birds, to (1) assess the conservation value of drainage canals in a heavily drained European lowland region, (2) to test landscape-level and local canal parameters for aiding prioritization among canal types, and (3) to propose a reconciliation-based management framework that suits the interest of all stakeholders.We found that drainage canals concentrate more species across most taxa than adjacent semi-natural habitats, owing to the micro-environmental heterogeneity and the comparatively low management intensity in the canals. The species-concentrating capacity is particularly high in canals that traverse semi-natural habitats, although agricultural canals also support remarkable species diversity. However, agricultural canals are important dispersal corridors for invasive plants, which may negatively affect native species. Canal size has little effect on biodiversity but habitat stress is an important determinant. The higher the stress (due to sandiness and salinity), the higher is the added value of canals to landscape-wide biodiversity.Synthesis and applicationsWe provide evidence that drainage canals can harbour surprisingly high levels of biodiversity and should therefore be recognized as important novel ecosystems with high conservation value, even within semi-natural habitats. Canals have previously been considered detrimental to nature conservation due to their association with loss of wetlands. However, by reducing water loss with reversible obstructions, controlling invasive species and applying specific conservation measures, they may be turned into conservation allies without compromising long-term interests of water management and agricultural land use.
Disentangling the Independent Contributions of Visual and Conceptual Features to the Spatiotemporal Dynamics of Scene Categorization
Authors: Greene Michelle R. , Hansen Bruce C. 
Published: April 2020

AbstractHuman scene categorization is characterized by its remarkable speed. While many visual and conceptual features have been linked to this ability, significant correlations exist between feature spaces, impeding our ability to determine their relative contributions to scene categorization. Here, we employed a whitening transformation to decorrelate a variety of visual and conceptual features and assess the time course of their unique contributions to scene categorization. Participants (both sexes) viewed 2,250 full-color scene images drawn from 30 different scene categories while having their brain activity measured through 256-channel EEG. We examined the variance explained at each electrode and time point of visual event-related potential (vERP) data from nine different whitened encoding models. These ranged from low-level features obtained from filter outputs to high-level conceptual features requiring human annotation. The amount of category information in the vERPs was assessed through multivariate decoding methods. Behavioral similarity measures were obtained in separate crowdsourced experiments. We found that all nine models together contributed 78% of the variance of human scene similarity assessments and was within the noise ceiling of the vERP data. Low-level models explained earlier vERP variability (88 ms post-image onset), while high-level models explained later variance (169 ms). Critically, only high-level models shared vERP variability with behavior. Taken together, these results suggest that scene categorization is primarily a high-level process, but reliant on previously extracted low-level features.Significance StatementIn a single fixation, we glean enough information to describe a general scene category. Many types of features are associated with scene categories, ranging from low-level properties such as colors and contours, to high-level properties such as objects and attributes. Because these properties are correlated, it is difficult to understand each property’s unique contributions to scene categorization. This work uses a whitening transformation to remove the correlations between features and examines the extent to which each feature contributes to visual event-related potentials (vERPs) over time. We found that low-level visual features contributed first, but were not correlated with categorization behavior. High-level features followed 80 ms later, providing key insights into how the brain makes sense of a complex visual world.
Parallel visual pathways with topographic versus non-topographic organization connect theDrosophilaeyes to the central brain
Authors: Timaeus Lorin , Geid Laura , Sancer Gizem , Wernet Mathias F. , Hummel Thomas 
Published: April 2020

SummaryOne hallmark of the visual system is the strict retinotopic organization from the periphery towards the central brain, spanning multiple layers of synaptic integration. RecentDrosophilastudies on the computation of distinct visual features have shown that retinotopic representation is often lost beyond the optic lobes, due to convergence of columnar neuron types onto optic glomeruli. Nevertheless, functional imaging revealed a spatially accurate representation of visual cues in the central complex (CX), raising the question how this is implemented on a circuit level. By characterizing the afferents to a specific visual glomerulus, the anterior optic tubercle (AOTU), we discovered a spatial segregation of topographic versus non-topographic projections from molecularly distinct classes of medulla projection neurons (medullo-tubercular, or MeTu neurons). Distinct classes of topographic versus non-topographic MeTus form parallel channels, terminating in separate AOTU domains. Both types then synapse onto separate matching topographic fields of tubercular-bulbar (TuBu) neurons which relay visual information towards the dendritic fields of central complex ring neurons in the bulb neuropil, where distinct bulb sectors correspond to a distinct ring domain in the ellipsoid body. Hence, peripheral topography is maintained due to stereotypic circuitry within each TuBu class, providing the structural basis for spatial representation of visual information in the central complex. Together with previous data showing rough topography of lobula projections to a different AOTU subunit, our results further highlight the AOTUs role as a prominent relay station for spatial information from the retina to the central brain.
Role of Differential Expression of miRNAs miR-125a, miR-200a and miR-199a in Metastatic Property of Ovarian Cancer Cell lines and Relationship between miR-199a and its Predicted Target Protein GSK3β
Authors: Rana Divya RSJB , Xu Lin , Zhang Jie 
Published: April 2020

AbstractOvarian cancer is a gynecological cancer of high mortality rate. Most of the ovarian cancer origin from the surface epithelium of the ovaries. Ovarian cancers gain metastatic and invasive properties from various biochemical events taking place during tumorogenesis. MicroRNAs (miRNA) are non-coding RNAs and they have an important function of inhibiting translation of specific mRNAs in the cytoplasm. Present study uses two ovarian cancer cell lines as model to study the differential expression of miR-125a, miR-200a, and miR-199a, and provides indirect proof for possible relationship between miR-199a and its predicted target gene Glycogen Synthase Kinase 3 β (GSK3β). As expected the expression of these three microRNAs are decreased in metastatic ovarian cancer cell line A2780 compared to epithelial ovarian cancer OVCAR3. Reciprocal expression pattern of miR-199a and its predicted target GSK3β was found in two different cell lines providing information on possible inhibitory role of miR-199a against GSK3β.
Potentials of Aqueous Extract ofBambusa vulgaristo Reactivate β-Cells of Pancreas in Alloxan-Induced Diabetic Wistar Rats
Authors: Akiibinu MO. , Folawuyo OS. , Oyekan IO. , Ibikunle I. , Kolawole OT. , Adesiyan A. , Anetor J. , Akiibinu SO. , Tayo F. 
Published: April 2020

AbstractAbility of the damaged pancreas to generate new β-cells when activated with external stimuli has been documented. This study assessed the potentials of aqueous extract ofbambusa vulgarisleaf to reactivate damaged β-cells in insulin dependent diabetes mellitus (IDDM). Eighteen healthy male Wistar rats (12 weeks old; weight= between 150 and 200g) were used for this study. The rats were randomly divided into three groups (six per group); group A (un-induced); group B (untreated alloxan-induced diabetics); group C (alloxan-induced diabetics treated with 200mg/kg body weight of freshly prepared extract ofbambusa vulgarisleaf). Fasting blood sugar (FBS) and plasma insulin levels were determined in all animals using glucometer and enzyme linked immunosorbent assay methods respectively. Sections of pancreas tissues were prepared for histology. IDDM was confirmed in groups B and C (FBS increased significantly=p<0.05) after 2 days of alloxan administration). The FBS remained significantly (p>0.05) higher in group B, compared to group A, but reduced significantly (p<0.05) in group C after 7 days of treatment withbambusa vulgarisleaf extract. On the 7th day, plasma insulin level decreased significantly (p<0.05) in group B, but no significant difference observed in group C compared with group A. Histology reports showed damaged pancreas in group B, while Group C showed normal islet cells after 7 days of oral administration ofbambusa vulgarisextract. In conclusion, aqueous extract ofBambusa vulgariscould restore the activities of alloxan-damaged pancreas. The extract could be a reliable alternative to synthetic pharmaceuticals in the treatment IDDM.
An analytical framework for interpretable and generalizable ‘quasilinear’ single-cell data analysis
Authors: Zhou Jian , Troyanskaya Olga G. 
Published: April 2020

AbstractScaling single-cell data exploratory analysis with the rapidly growing diversity and quantity of single-cell omics datasets demands more interpretable and robust data representation that is generalizable across datasets. To address this challenge, here we developed a novel ‘quasilinear’ framework that combines the interpretability and transferability of linear methods with the representational power of nonlinear methods. Within this framework, we introduce a data representation and visualization method, GraphDR, and a structure discovery method, StructDR, that unifies cluster, trajectory, and surface estimation and allows their confidence set inference. We applied both methods to diverse single-cell RNA-seq datasets from whole embryos and tissues. Unlike PCA and t-SNE, GraphDR and StructDR generated representations that both distinguished highly specific cell types and were comparable across datasets. In addition, GraphDR is at least an order of magnitude faster than commonly used nonlinear methods. Our visualizations of scRNA-seq data from developing zebrafish and Xenopus embryos revealed extruding branches of lineages from a continuum of cell states, suggesting that the current branch view of cell specification may be oversimplified. Moreover, StructDR identified a novel neuronal population using scRNA-seq data from mouse hippocampus. An open-source python library and a user-friendly graphical interface for 3D data visualization and analysis with these methods are available athttps://github.com/jzthree/quasildr.
Differential localization patterns of pyruvate kinase isoforms in murine naïve, formative and primed pluripotent states
Authors: Dierolf Joshua G. , Watson Andrew J. , Betts Dean H. 
Published: April 2020

AbstractMouse embryonic stem cells (mESCs) and mouse epiblast stem cells (mEpiSCs) represent opposite ends of a pluripotency continuum, referred to as naïve and primed pluripotent states, respectively. These divergent pluripotent states differ in several ways including growth factor requirements, transcription factor expression, DNA methylation patterns, and metabolic profiles. Naïve cells employ both glycolysis and oxidative phosphorylation (OXPHOS), whereas primed cells preferentially utilize aerobic glycolysis, a trait shared with cancer cells referred to as the Warburg effect. Until recently, metabolism has been regarded as a by-product of cell fate; however, evidence now supports metabolism as being a driver of stem cell state and fate decisions. Pyruvate kinase muscle isoforms (PKM1 and PKM2) are important for generating and maintaining pluripotent stem cells (PSCs) and mediating the Warburg effect. Both isoforms catalyze the last step of glycolysis generating adenosine triphosphate and pyruvate, however, the precise role(s) of PKM1/2 in naïve and primed pluripotency is not well understood. The primary objective was to characterize the cellular expression and localization patterns of PKM1 and PKM2 in mESCs, chemically transitioned epiblast-like cells (mEpiLCs) representing formative pluripotency, and mEpiSCs using immunoblotting, flow cytometry and confocal microscopy. The results indicate that PKM1 and PKM2 are not only localized to the cytoplasm but also accumulate in differential subnuclear regions of mESC, mEpiLCs and mEpiSCs as determined by a quantitative, confocal microscopy colocalization employing orthogonal projections and airyscan processing. Importantly, we discovered that the subnuclear localization of PKM1/2 shifts during the transition from mESCs, mEpiLCs and mEpiSCs. We have also authenticated a new method of selecting formative pluripotency cells from naïve and primed populations using the cell surface markers SSEA1 and CD24. Finally, we have comprehensively validated the appropriateness and power of the Pearson’s correlation coefficient and Manders’ overlap coefficient for assessing nuclear and cytoplasmic protein colocalization in PSCs by immunofluorescence confocal microscopy. We propose that nuclear PKM1/2 assists with distinct pluripotency state maintenance and lineage priming by non-canonical mechanisms. These results advance our understanding of the overall mechanisms controlling naïve, formative and primed pluripotency.
Microvascular Injury in Mild Traumatic Brain Injury Accelerates Alzheimer-like Pathogenesis in Mice
Authors: Wu Yingxi , Zeng Jianxiong , Pluimer Brock , Dong Shirley , Xie Xiaochun , Guo Xinying , Liang Xinyan , Feng Sudi , Wu Haijian , Yan Youzhen , Chen Jian-Fu , Maria Naomi Sta , Ma Qingyi , Gomez-Pinilla Fernando , Zhao Zhen 
Published: April 2020

AbstractIntroductionTraumatic brain injury (TBI) is considered as the most robust environmental risk factor for Alzheimer’s disease (AD). Besides direct neuronal injury and neuroinflammation, vascular impairment is also a hallmark event of the pathological cascade after TBI. However, the vascular connection between TBI and subsequent AD pathogenesis remains underexplored.MethodsWe established a closed-head mild TBI (mTBI) model in mice with controlled cortical impact, and examined the time courses of microvascular injury, blood-brain barrier (BBB) dysfunction, gliosis and motor function impairment in wild type C57BL/6 mice. We also determined the brain clearance of β-amyloid, as well as amyloid pathology and cognitive functions after mTBI in the 5xFAD mouse model of AD.ResultsmTBI induced microvascular injury with BBB breakdown, pericyte loss and cerebral blood flow reduction in mice, which preceded gliosis. mTBI also impaired brain amyloid clearance via the vascular pathways. More importantly, mTBI accelerated amyloid pathology and cognitive impairment in the 5xFAD mice.DiscussionOur data demonstrated that microvascular injury plays a key role in the pathogenesis of AD after mTBI. Therefore, restoring vascular functions might be beneficial for patients with mTBI, and potentially reduce the risk of developing AD.
Identification of 38 novel loci for systemic lupus erythematosus and genetic heterogeneity that may underly population disparities in this disease
Authors: Wang Yong-Fei , Zhang Yan , Lin Zhiming , Zhang Huoru , Wang Ting-You , Cao Yujie , Morris David L. , Sheng Yujun , Yin Xianyong , Zhong Shi-Long , Gu Xiaoqiong , Lei Yao , He Jing , Wu Qi , Shen Jiangshan Jane , Yang Jing , Lam Tai-Hing , Lin Jia-Huang , Mai Zhi-Ming , Guo Mengbiao , Tang Yuanjia , Chen Yanhui , Song Qin , Ban Bo , Chiu Mok Chi , Cui Yong , Lu Liangjing , Shen Nan , Sham Pak C. , Lau Chak Sing , Smith David K. , Vyse Timothy J. , Zhang Xuejun , Lau Yu Lung , Yang Wanling 
Published: April 2020

AbstractSystemic lupus erythematosus (SLE), a worldwide autoimmune disease with high heritability, shows differences in prevalence, severity and age of onset among different ancestral groups. Previous genetic studies have focused more on European populations, which appear to be the least affected. Consequently, the genetic variations that underly the commonalities, differences and treatment options in SLE among ancestral groups have not been well elucidated. To address this, we undertook a genome-wide association study, increasing the sample size of Chinese populations to the level of existing European studies. Thirty-eight novel SLE-associated loci and incomplete sharing of genetic architecture were identified. Nine disease loci showed clear ancestral group heterogeneity and implicated antibody production as a potential mechanism for differences in disease manifestation. Polygenic risk scores performed significantly better when trained on matched ancestral data sets. These analyses help to reveal the genetic bases for disparities in SLE among ancestral groups.
DNA Sequence Preference forDe NovoCentromere Formation on aCaenorhabditis elegansArtificial Chromosome
Authors: Lin Zhongyang , Yuen Karen Wing Yee 
Published: April 2020

ABSTRACTCentromeric DNA sequences vary in different species, but share common characteristics, like high AT-content, repetitiveness, and low, but not no, transcriptional activity. Yet, neocentromeres can be found on non-centromeric, ectopic sequences, suggesting that centromeres can be established and maintained epigenetically. In contrast, canonical centromeric DNA sequences are more competent inde novocentromere formation on artificial chromosomes (ACs). To determine if specific DNA sequence features are preferred for new centromere formation, we injected different DNA sequences into the gonad of a holocentric model organism,Caenorhabditis elegans, to form ACs in embryos, and monitored mitotic AC segregation. We demonstrated that AT-rich sequences, but not repetitive sequences, acceleratedde novocentromere formation on ACs. We also injected fragmentedSaccharomyces cerevisiaegenomic DNA to construct a less repetitive, more complex AC that can propagate through generations. By whole-genome sequencing andde novoassembly of AC sequences, we deduced that this AC was formed through non-homologous end joining. By CENP-AHCP-3chromatin immunoprecipitation followed by sequencing (ChIP-seq), we found that CENP-AHCP-3domain width on both the AC and endogenous chromosomes is positively correlated with AT-content. Besides, CENP-AHCP-3binds to unexpressed gene loci or non-genic regions on the AC, consistent with the organization of endogenous holocentromeres.
Single-cell copy number lineage tracing enabling gene discovery
Authors: Wang Fang , Wang Qihan , Mohanty Vakul , Liang Shaoheng , Dou Jinzhuang , Han Jincheng , Minussi Darlan Conterno , Gao Ruli , Ding Li , Navin Nicholas , Chen Ken 
Published: April 2020

AbstractAneuploidy plays critical roles in genome evolution.Alleles, whose dosages affect the fitness of an ancestor, will have altered frequencies in the descendant populations upon perturbation.Single-cell sequencing enables comprehensive genome-wide copy number profiling of thousands of cells at various evolutionary stage and lineage. That makes it possible to discover dosage effects invisible at tissue level, provided that the cell lineages can be accurately reconstructed.Here, we present a Minimal Event Distance Aneuploidy Lineage Tree (MEDALT) algorithm that infers the evolution history of a cell population based on single-cell copy number (SCCN) profiles. We also present a statistical routine named lineage speciation analysis (LSA), which facilitates discovery of fitness-associated alterations and genes from SCCN lineage trees.We assessed our approaches using a variety of single-cell datasets. Overall, MEDALT appeared more accurate than phylogenetics approaches in reconstructing copy number lineage. From the single-cell DNA-sequencing data of 20 triple-negative breast cancer patients, our approaches effectively prioritized genes that are essential for breast cancer cell fitness and are predictive of patient survival, including those implicating convergent evolution. Similar benefits were observed when applying our approaches on single-cell RNA sequencing data obtained from cancer patients.The source code of our study is available athttps://github.com/KChen-lab/MEDALT.
Resistance, resilience, and functional redundancy of freshwater bacterioplankton communities facing a gradient of agricultural stressors in a mesocosm experiment
Authors: Barbosa da Costa Naíla , Fugère Vincent , Hébert Marie-Pier , Xu Charles C.Y. , Barrett Rowan D.H. , Beisner Beatrix E. , Bell Graham , Yargeau Viviane , Fussmann Gregor F. , Gonzalez Andrew , Shapiro B. Jesse 
Published: April 2020

AbstractAgricultural pollution with fertilizers and pesticides is a common disturbance to freshwater biodiversity. Bacterioplankton communities are at the base of aquatic food webs, but their responses to these potentially interacting stressors are rarely explored. To test the extent of resistance and resilience in bacterioplankton communities faced with agricultural stressors, we exposed freshwater mesocosms to single and combined gradients of two commonly used pesticides: the herbicide glyphosate (0-15 mg/L) and the neonicotinoid insecticide imidacloprid (0-60 μg/L), in high or low nutrient backgrounds. Over the 43-day experiment, we tracked variation in bacterial density with flow cytometry, carbon substrate use with Biolog EcoPlates, and taxonomic diversity and composition with environmental 16S rRNA gene amplicon sequencing. We show that only glyphosate (at the highest dose, 15 mg/L), but not imidacloprid, nutrients, or their interactions measurably changed community structure, favoring members of the Proteobacteria including the genus Agrobacterium. However, no change in carbon substrate use was detected throughout, suggesting functional redundancy despite taxonomic changes. We further show that communities are resilient at broad, but not fine taxonomic levels: 24 days after glyphosate application the precise amplicon sequence variants do not return, and tend to be replaced by phylogenetically close taxa. We conclude that high doses of glyphosate – but still within commonly acceptable regulatory guidelines – alter freshwater bacterioplankton by favoring a subset of higher taxonomic units (i.e. genus to phylum) that transiently thrive in the presence of glyphosate. Longer-term impacts of glyphosate at finer taxonomic resolution merit further investigation.