bluuebunny/crossref_metadata_2025_split huggingface dataset:
Locomotor and Reinforcing Effects of Pentedrone, Pentylone and Methylone in Rats
Authors: Javadi-Paydar Mehrak , Nguyen Jacques D. , Vandewater Sophia A. , Dickerson Tobin J. , Taffe Michael A. 
Published: July 2017

AbstractThe broad diversity of synthetic cathinone psychostimulant drugs that are available to users complicates research efforts to provide understanding of health risks. Second generation cathinones pentedrone and pentylone are distinguished from each other by the 3,4-methylenedioxy structural motif (which distinguishes methamphetamine from 3,4-methylenedioxymethamphetamine) and each incorporates the α-alkyl chain motif contained in the transporter-inhibitor cathinones (3,4-methylenedioxypyrovalerone (MDPV), α-pyrrolidinopentiophenone (α-PVP)) but not in the monoamine releasers (mephedrone, methylone). Studies were conducted in male and female Wistar rats to compare locomotor and thermoregulatory effects of pentedrone, pentylone and methylone using an implanted radiotelemetry system. Reinforcing effects were assessed in female Wistar rats trained in the intravenous self-administration (IVSA) procedure and subjected to dose-substitution (0.025-0.3 m/gkg/inf) under a fixed-ratio 1 response contingency. Pentedrone, pentylone and methylone dose-effect curves were contrasted with those for α-PVP and α-pyrrolidinohexiophenone (α-PHP). Dose dependent increases in locomotion were observed after intraperitoneal injection of pentylone (0.5-10.0 mg/kg), pentedrone (0.5-10.0 mg/kg) or mephedrone (0.5-10.0 mg/kg) in male and female rats. The maximum locomotor effect was similar across drugs but lasted longest after pentedrone. Mean body temperature did not vary systematically more than 0.5 °C after pentedrone or pentylone in either sex. A sustained hyperthermia (0.4-0.8 °C) was observed for four hours after 10 mg/kg methylone in male rats. More infusions of pentedrone or pentylone were self-administered compared with methylone, but all three were less potent than α-PVP or α-PHP. These studies support the inference that second generation cathinones pentylone and pentedrone have abuse liability greater than that of methylone.
Three-dimensional mobility and muscle attachments in the pectoral limb of the Triassic cynodontMassetognathus pascuali
Authors: Lai Phil H. , Biewener Andrew A. , Pierce Stephanie E. 
Published: July 2017

ABSTRACTThe musculoskeletal configuration of the mammalian pectoral limb has been heralded as a key anatomical feature leading to the adaptive radiation of mammals, but limb function in the cynodont outgroup remains unresolved. Conflicting reconstructions of abducted and adducted posture are based on mutually-incompatible interpretations of ambiguous osteology. We reconstruct the pectoral limb of the Triassic non-mammalian cynodontMassetognathus pascualiin three dimensions, by combining skeletal morphology from micro-computed tomography with muscle anatomy from an extended extant phylogenetic bracket. Conservative tests of maximum range of motion suggest a degree of girdle mobility, as well as substantial freedom at the shoulder and the elbow joints. The glenoid fossa supports a neutral pose in which the distal end of the humerus points 45° posterolaterally from the body wall, intermediate between classically “sprawling” and “parasagittal” limb postures.Massetognathusis reconstructed as having a near-mammalian complement of shoulder muscles, including an incipient rotator cuff (m. subscapularis, m. infraspinatus, m. supraspinatus, and m. teres minor). Based on close inspection of the morphology of the glenoid fossa, we hypothesize a posture-driven scenario for the evolution of the therian ball-and-socket shoulder joint. The musculoskeletal reconstruction presented here provides the anatomical scaffolding for more detailed examination of locomotor evolution in the precursors to mammals.
Zinc availability modulates plant growth and immune responses viaAZI1
Authors: Bouain Nadia , Satbhai Santosh B. , Saenchai Chorpet , Desbrosses Guilhem , Berthomieu Pierre , Busch Wolfgang , Rouached Hatem 
Published: July 2017

AbstractZinc is an essential micronutrient for all living organisms and is involved in a plethora of processes including growth and development, and immunity. However, it is unknown if there is a common genetic and molecular basis underlying multiple facets of zinc function. Here we used natural variation inArabidopsis thalianato study the role of zinc in regulating growth. We identify allelic variation of the systemic immunity geneAZI1as a key for determining root growth responses to low zinc conditions. We further demonstrate that this gene is important for modulating root growth depending on the zinc and defence status. Finally, we show that the interaction of the immunity signal azelaic acid and zinc level to regulate root growth is conserved in rice. This work demonstrates that there is a common genetic and molecular basis for multiple zinc dependent processes and that nutrient cues can determine the balance of plant growth and immune responses in plants.
Systematic mapping of chromatin state landscapes during mouse development
Authors: Gorkin David U. , Barozzi Iros , Zhang Yanxiao , Lee Ah Young , Li Bin , Zhao Yuan , Wildberg Andre , Ding Bo , Zhang Bo , Wang Mengchi , Strattan J. Seth , Davidson Jean M. , Qiu Yunjiang , Afzal Veena , Akiyama Jennifer A. , Plajzer-Frick Ingrid , Pickle Catherine S. , Kato Momoe , Garvin Tyler H. , Pham Quan T. , Harrington Anne N. , Mannion Brandon J. , Lee Elizabeth A. , Fukuda-Yuzawa Yoko , He Yupeng , Preissl Sebastian , Chee Sora , Williams Brian A. , Trout Diane , Amrhein Henry , Yang Hongbo , Cherry J. Michael , Shen Yin , Ecker Joseph R. , Wang Wei , Dickel Diane E. , Visel Axel , Pennacchio Len A. , Ren Bing 
Published: July 2017

SUMMARYEmbryogenesis requires epigenetic information that allows each cell to respond appropriately to developmental cues. Histone modifications are core components of a cell’s epigenome, giving rise to chromatin states that modulate genome function. Here, we systematically profile histone modifications in a diverse panel of mouse tissues at 8 developmental stages from 10.5 days post conception until birth, performing a total of 1,128 ChIP-seq assays across 72 distinct tissue-stages. We combine these histone modification profiles into a unified set of chromatin state annotations, and track their activity across developmental time and space. Through integrative analysis we identify dynamic enhancers, reveal key transcriptional regulators, and characterize the role of chromatin-based repression in developmental gene regulation. We also leverage these data to link enhancers to putative target genes, revealing connections between coding and non-coding sequence variation in disease etiology. Our study provides a compendium of resources for biomedical researchers, and achieves the most comprehensive view of embryonic chromatin states to date.
Asymmetric compression of representational space for object animacy categorization under degraded viewing conditions
Authors: Grootswagers Tijl , Ritchie J. Brendan , Wardle Susan G. , Heathcote Andrew , Carlson Thomas A. 
Published: July 2017

AbstractAnimacy is a robust organizing principle amongst object category representations in the human brain. Using multivariate pattern analysis methods (MVPA), it has been shown that distance to the decision boundary of a classifier trained to discriminate neural activation patterns for animate and inanimate objects correlates with observer reaction times for the same animacy categorization task (Carlson, Ritchie, Kriegeskorte, Durvasula, & Ma, 2014; Ritchie, Tovar, & Carlson, 2015). Using MEG decoding, we tested if the same relationship holds when a stimulus manipulation (degradation) increases task difficulty, which we predicted would systematically decrease the distance of activation patterns from the decision boundary, and increase reaction times. In addition, we tested whether distance to the classifier boundary correlates with drift rates in the Linear Ballistic Accumulator (Brown & Heathcote, 2008). We found that distance to the classifier boundary correlated with reaction time, accuracy, and drift rates in an animacy categorization task. Split by animacy, the correlations between brain and behavior were sustained for longer over the time course for animate than for inanimate stimuli. Interestingly, when examining the distance to the classifier boundary during the peak correlation between brain and behavior, we found that only degraded versions of animate, but not inanimate, objects had systematically shifted towards the classifier decision boundary as predicted. Our results support an asymmetry in the representation of animate and inanimate object categories in the human brain.
Screening and directed evolution of transporters to improve xylodextrin utilization in the yeastSaccharomyces cerevisiae
Authors: Zhang Chenlu , Acosta-Sampson Ligia , Yu Vivian Yaci , Cate Jamie H. D. 
Published: July 2017

AbstractThe economic production of cellulosic biofuel requires efficient and full utilization of all abundant carbohydrates naturally released from plant biomass by enzyme cocktails. Recently, we reconstituted theNeurospora crassaxylodextrin transport and consumption system inSaccharomyces cerevisiae, enabling growth of yeast on xylodextrins aerobically. However, the consumption rate of xylodextrin requires improvement for industrial applications, including consumption in anaerobic conditions. As a first step in this improvement, we report analysis of orthologues of theN. crassatransporters CDT-1 and CDT-2. Transporter ST16 fromTrichoderma virensenables faster aerobic growth ofS. cerevisiaeon xylodextrins compared to CDT-2. ST16 is a xylodextrin-specific transporter, and the xylobiose transport activity of ST16 is not inhibited by cellobiose. Other transporters identified in the screen also enable growth on xylodextrins including xylotriose. Taken together, these results indicate that multiple transporters might prove useful to improve xylodextrin utilization inS. cerevisiae. Efforts to use directed evolution to improve ST16 from a chromosomally-integrated copy were not successful, due to background growth of yeast on other carbon sources present in the selection medium. Future experiments will require increasing the baseline growth rate of the yeast population on xylodextrins, to ensure that the selective pressure exerted on xylodextrin transport can lead to isolation of improved xylodextrin transporters.
RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response
Authors: Krishnan Arjun , Gupta Chirag , Ambavaram Madana M.R. , Pereira Andy 
Published: July 2017

AbstractTranscriptional profiling is a prevalent and powerful approach for capturing the response of crop plants to environmental stresses, e.g. response of rice to drought. However, functionally interpreting the resulting genome-wide gene expression changes is severely hampered by the large gaps in our genomic knowledge about which genes work together in cellular pathways/processes in rice. Here, we present a new web resource – RECoN – that relies on a network-based approach to go beyond currently limited annotations in delineating functional and regulatory perturbations in new rice stress transcriptome datasets generated by a researcher. To build RECoN, we first enumerated 1,744 stress-specific gene modules covering 28,421 rice genes (>72% of the genes in the genome). Each module contains a group of genes tightly coexpressed across a large number of environmental conditions and, thus, is likely to be functionally coherent. When a user provides a new differential expression profile, RECoN identifies modules substantially perturbed in their experiment and further suggests deregulated functional and regulatory mechanisms based on the enrichment of current annotations within the predefined modules. We demonstrate the utility of this resource by analyzing new drought transcriptomes of rice in three developmental stages, which revealed large-scale insights into the cellular processes and regulatory mechanisms involved in common and stage-specific drought responses. RECoN enables biologists to functionally explore new data from all abiotic stresses on a genome-scale and to uncover gene candidates, including those that are currently functionally uncharacterized, for engineering stress tolerance.
Progesterone regulates hypothalamic-pituitary-thyroid axis
Authors: Zhong Chunyun , Xiong Kewen , Wang Xin 
Published: July 2017

AbstractProgesterone is a natural steroid hormone excreted by animals and humans, which has been frequently detected in the aquatic ecosystems. The effects of the residual progesterone on fish are unclear. In this study, we aimed to examine the effects of progesterone on the hypothalamic-pituitary-thyroid (HPT) axis by detecting the gene transcriptional expression levels. Zebrafish embryos were treated with different concentrations of progesterone from 12 hours post-fertilization (hpf) to 120 hpf. Total mRNA was extracted and the transcriptional profiles of genes involved in HPT axis were examined using qPCR. The genes related to thyroid hormone metabolism and thyroid hormone synthesis were up-regulated in zebrafish exposed to progesterone. These results indicated that progesterone affected the mRNA expression of genes involved in the HPT axis, which might interrupt the endocrine system in zebrafish. Our data also suggested that zebrafish is a useful tool for evaluating the effects of chemicals on the thyroid endocrine system.
Varying-Censoring Aware Matrix Factorization for Single Cell RNA-Sequencing
Authors: Townes F. William , Hicks Stephanie C. , Aryee Martin J. , Irizarry Rafael A. 
Published: July 2017

AbstractSingle cell RNA-Seq (scRNA-Seq) has become the most widely used high-throughput technology for gene expression profiling of individual cells. The potential of being able to measure cell-to-cell variability at a high-dimensional genomic scale opens numerous new lines of investigation in basic and clinical research. For example, by identifying groups of cells with expression profiles unlike those observed in cells with known phenotypes, new cell types may be discovered. Dimension reduction followed by unsupervised clustering are the quantitative approaches typically used to facilitate such discoveries. However, a challenge for this approach is that most scRNA-Seq datasets are sparse, with the percentages of measurements reported as zero ranging from 35% to 99% across cells, and these zeros are partially explained by experimental inefficiencies that lead to censored data. Furthermore, the observed across-cell differences in the percentages of zeros are partly due to technical artifacts rather than biological differences. Unfortunately, standard dimension reduction approaches treat these censored values as true zeros, which leads to the identification of distorted low-dimensional factors. When these factors are used for clustering, the distortion leads to incorrect identification of biological groups. Here, we propose an approach that accounts for cell-specific censoring with a varying-censoring aware matrix factorization (VAMF) model that permits the identification of factors in the presence of the above described systematic bias. We demonstrate the advantages of our approach on published scRNA-Seq data and confirm these on simulated data.
A Modular Photosynthetic Microbial Fuel Cell With Interchangeable Algae Solar Compartments
Authors: Fleury Daniel 
Published: July 2017

AbstractThis project trial provides a novel small-scale solar harnessing technology which increases environmental effectiveness while maintaining optimal energy efficiency. Although modern solar panels are purposed in producing clean energy, the materials and byproducts of solar cell manufacturing are not eco-friendly. Thus, considering an organic, renewable and energy efficient solar cell model is necessary. Investigations explored multiple highly-photosynthetic algal species which were later integrated into a controlled microbial fuel cell system (MFC). The MFC1 contained algae culture species, including Chlorella Vulgaris, Nannochloropsis, and Spirulina. Parameters, such as periodic lipid yields, algal biomass, and light absorption were assessed throughout the cultivation process while maintaining a controlled environment. After 30 days of cultivation, the culture was transferred to an anode chamber in a closed loop small-scale MFC. Following the first day of algae transfer, microwatt output was analyzed from independent test trials. Statistical comparisons were drawn between electrical energy and light absorption, finding a generally positive correlation. Thus, it is concluded that mid-high algae concentrations significantly increased electrical micro-wattage in highly absorptive algal cultures. The optimal electric levels occurred at 286 A (absorbance) and 35 mW-Nannochloropsis, 123 A-Chlorella (30.2 mW), and 142 A (31 mW)-Spirulina culture. Due to higher absorption rates in the Nannochloropsis culture, this corresponds with the record high voltage levels. The analysis of data indicates that Algae-based MFCs are proven hopeful for alternative high-yield energy production.
Competition for synaptic building blocks shapes synaptic plasticity
Authors: Triesch Jochen , Vo Anh Duong , Hafner Anne-Sophie 
Published: July 2017

AbstractChanges in the efficacies of synapses are thought to be the neurobiological basis of learning and memory. The efficacy of a synapse depends on its current number of neurotransmitter receptors. Recent experiments have shown that these receptors are highly dynamic, moving back and forth between synapses on time scales of seconds and minutes. This suggests spontaneous fluctuations in synaptic efficacies and a competition of nearby synapses for available receptors. Here we propose a mathematical model of this competition of synapses for neurotransmitter receptors from a local dendritic pool. Using minimal assumptions, the model produces a fast multiplicative scaling behavior of synapses. Furthermore, the model explains a transient form of heterosynaptic plasticity and predicts that its amount is inversely related to the size of the local receptor pool. Overall, our model reveals logistical tradeoffs during the induction of synaptic plasticity due to the rapid exchange of neurotransmitter receptors between synapses.
De NovoGenes are “Frozen Accidents” which Escaped Rapid Turnover of Pervasively Transcribed ORFs
Authors: Schmitz Jonathan , Ullrich Kristian , Bornberg-Bauer Erich 
Published: July 2017

AbstractA recent surge of studies suggested that many novel genes arisede novofrom previously non-coding DNA and not by duplication. However, since most studies concentrated on longer evolutionary time scales and rarely considered protein structural properties, it remains unclear how these properties are shaped by evolution, depend on genetic mechanisms and influence gene survival. Here we compare open reading frames (ORFs) from high coverage transcriptomes from mouse and another four mammals covering 160 million years of evolution. We find that novel ORFs pervasively emerge from intergenic and intronic regions but are rapidly lost again while relatively fewer arise from duplications but are retained over much longer times. Surprisingly, disorder and other protein properties of young ORFs do not change with gene age. Only length and nucleotide composition change, probably to avoid aggregation. Thus de novo genes resemble frozen accidents of randomly emerged ORFs which survived initial purging, likely because they are functional.
BGP: Branched Gaussian processes for identifying gene-specific branching dynamics in single cell data
Authors: Boukouvalas Alexis , Hensman James , Rattray Magnus 
Published: July 2017

AbstractHigh-throughput single-cell gene expression experiments can be used to uncover branching dynamics in cell populations undergoing differentiation through use of pseudotime methods. We develop the branching Gaussian process (BGP), a non-parametric model that is able to identify branching dynamics for individual genes and provides an estimate of branching times for each gene with an associated credible region. We demonstrate the effectiveness of our method on both synthetic data and a published single-cell gene expression hematopoiesis study. The method requires prior information about pseudotime and global cellular branching for each cell but the probabilistic nature of the method means that it is robust to errors in these global branch labels and can be used to discover early branching genes which diverge before the inferred global cell branching. The code is open-source and available at https://github.com/ManchesterBioinference/BranchedGP.
Biomass increase under zinc deficiency caused by delay of early flowering in Arabidopsis
Authors: Chen Xiaochao , Ludewig Uwe 
Published: July 2017

AbstractPlants generally produce more biomass when all nutrients are available in sufficient amounts. In addition to environmental constraints, genetic and developmental factors, such as the transition from vegetative to reproductive growth, restrict maximal yield. Here we report the peculiar observation that a subset of early flowering Arabidopsis thaliana accessions produced larger shoot rosette diameters when grown in zinc (Zn)-deficient conditions, compared with Zn-sufficient conditions. This was associated with early flowering that restricted the leaf length under Zn sufficiency. Zinc deficiency repressed FLOWERING LOCUS T (FT) expression, a major regulator of flowering. Repression or loss of FT increased the rosette diameter by a delay of the transition to flowering, a longer phase of leaf proliferation and increased leaf number. The transition to flowering reduced, but not terminated, the proliferation of established leaves. The size of individual leaf mesophyll cells was not affected by Zn deficiency or loss of FT, indicating that the larger rosette diameter was caused by maintained proliferation of vegetative tissue. As a consequence, early flowering accessions under Zn deficiency grew larger rosette diameters due to a delay of flowering, which explains the unusual increase of vegetative biomass under nutrient deficiency.HighlightAn increase in biomass of some Arabidopsis accessions under Zn-deficiency is caused by retardation of flowering, prolonging vegetative growth.AbbreviationsDASdays after sowingGWAgenome-wide associationSNPsingle nucleotide polymorphismZnzinc
Persistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists
Authors: Lentendu Guillaume , Mahé Frédéric , Bass David , Rueckert Sonja , Stoeck Thorsten , Dunthorn Micah 
Published: July 2017

AbstractAnimal and plant communities in tropical rainforests are known to have high alpha diversity within forests, but low beta diversity between forests. By contrast, it is unknown if the microbial protists inhabiting the same ecosystems exhibit similar biogeographic patterns. To evaluate the biogeographies of soil protists in three lowland Neotropical rainforests using metabarcoding data, we estimated taxa-area and distance-decay relationships for three large protist taxa and their subtaxa, at both the OTU and phylogenetic levels, with presence-absence and abundance based measures, and compared the estimates to null models. High local alpha and low regional beta diversity patterns were persistently found for both the parasitic Apicomplexa and the free-living Cercozoa and Ciliophora, even though they have different ecological functions and different dispersal modes. In comparison to the null models, both OTU and phylogenetic diversities showed spatial structures between forests, but only phylogenetic diversity showed spatial patterns within forests. These results suggest that the biogeographies of macro-and micro-organismal eukaryotes in lowland Neotropical rainforests are partially structured by the same general processes. As with arthropods, the protists’ high alpha diversity within forests presents problems for estimating their local diversity, and shows that regional diversity cannot be easily estimated because of low turnover between forests.