bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Porcine Model of Peripheral Nerve Injury Enabling Ultra-Long Regenerative Distances: Surgical Approach, Recovery Kinetics, and Clinical Relevance
Authors: Burrell Justin C. , Browne Kevin D. , Dutton John L. , Das Suradip , Brown Daniel P. , Laimo Franco A. , Roberts Sanford , Petrov Dmitriy , Ali Zarina , Ledebur Harry C. , Rosen Joseph M. , Kaplan Hilton M. , Wolf John A. , Smith Douglas H. , Chen H. Isaac , Cullen D. Kacy 
Published: April 2019

AbstractApproximately 20 million Americans currently experience residual deficits from traumatic peripheral nerve injury. Despite recent advancements in surgical technique, peripheral nerve repair typically results in poor functional outcomes due to prolonged periods of denervation resulting from long regenerative distances coupled with relatively slow rates of axonal regeneration. Development of novel surgical solutions requires valid preclinical models that adequately replicate the key challenges of clinical peripheral nerve injury. Our team has developed a porcine model using Yucatan minipigs that provides an opportunity to investigate peripheral nerve regeneration using different nerves tailored for a specific mechanism of interest, such as (1) nerve modality: motor, sensory, and mixed-modality; (2) injury length: short versus long gap; and (3) total regenerative distance: proximal versus distal injury. Here, we describe a comprehensive porcine model of two challenging clinically relevant procedures for repair of long segmental lesions (≥ 5 cm) – the deep peroneal nerve repaired using a sural nerve autograft and the common peroneal nerve repaired using a saphenous nerve autograft – each featuring ultra-long total regenerative distances (up to 20 cm and 27 cm, respectively) to reach distal targets. This paper includes a detailed characterization of the relevant anatomy, surgical approach/technique, functional/electrophysiological outcomes, and nerve morphometry for baseline and autograft repaired nerves. These porcine models of major peripheral nerve injury are suitable as preclinical, translatable models for evaluating the efficacy, safety, and tolerability of next-generation artificial nerve grafts prior to clinical deployment.
Routing of non-mnemonic hippocampal ripples to subcortical structures
Authors: Tingley David , Buzsáki György 
Published: April 2019

SummaryThe mnemonic functions of hippocampal sharp wave ripples (SPW-Rs) have been studied extensively. Because hippocampal outputs affect not only downsteam cortical structures but also subcortical targets, we examined the impact of SPW-Rs on the firing patterns of lateral septal (LS) neurons in behaving rats. A large fraction of SPW-Rs were temporally locked to high frequency oscillations (HFOs; 120-180 Hz) in LS. SPW-R to LS HFOs coupling was strongest during NREM sleep, followed by waking immobility. However, coherence and spike-LFP coupling between the two events were low, suggesting that HFOs are generated locally within the LS GABAergic population. This hypothesis was supported by optogenetic induction of HFOs in LS. Spiking of LS neurons was independent from the sequential order of spiking in SPW-Rs but, instead, correlated strongly with the magnitude of excitatory synchrony of the hippocampal output. Thus, LS is strongly activated by SPW-Rs and may convey hippocampal population events to its motivation and action-inducing targets in the hypothalamus and brainstem.
Three-Dimensional Reconstructions of Mouse Circumvallate Taste Buds Using Serial Blockface Scanning Electron Microscopy: I. Cell Types and the Apical Region of the Taste Bud
Authors: Yang Ruibiao , Dzowo Yannick K. , Wilson Courtney E. , Russell Rae L. , Kidd Grahame J. , Salcedo Ernesto , Lasher Robert S. , Kinnamon John C. , Finger Thomas E. 
Published: April 2019

ABSTRACTTaste buds comprise four types of taste cells: 3 mature, elongate types: Type I, Type II, Type III; and basally-situated, immature post-mitotic Type IV cells. We employed serial blockface scanning electron microscopy to delineate the characteristics and interrelationships of the taste cells in the circumvallate papillae of adult mice. Type I cells have an indented, elongate nucleus with invaginations, folded plasma membrane, and multiple apical microvilli in the taste pore. Type I microvilli may be either restricted to the bottom of the pore or extend outward reaching midway up into the taste pore. Type II cells (aka receptor cells) are characterized by a large round or oval nucleus, a single apical microvillus extending through the taste pore, and specialized “atypical” mitochondria at functional points of contact with nerve fibers. Type III cells (aka “synaptic cells”) are elongate with an indented nucleus, possess a single, apical microvillus extending through the taste pore and are characterized by a small accumulation of synaptic vesicles at points of contact with nerve fibers. About one-quarter of Type III cells also exhibit an atypical mitochondrion amidst the presynaptic vesicle clusters at the synapse. Type IV cells (non-proliferative “basal cells”) have a nucleus in the lower quarter of the taste bud but have a foot process extending to the basement membrane often contacting nerve processes along the way. Type I cells represent just over 50% of the population, whereas Type II, Type III, and Type IV (basal cells) represent 19%, 15%, and 14% respectively.
Collective aggressiveness limits colony persistence in high but not low elevation sites in Amazonian social spiders
Authors: Lichtenstein James L. L. , Fisher David N. , McEwen Brendan L. , Nondorf Daniel T. , Calvache Esteban , Schmitz Clara , Elässer Jana , Pruitt Jonathan N. 
Published: April 2019

AbstractIdentifying the traits that foster group survival in contrasting environments is important for understanding local adaptation in social systems. Here we evaluate the relationship between the aggressiveness of social spider colonies and their persistence along an elevation gradient using the Amazonian spider,Anelosimus eximius. We found that colonies ofA. eximiusexhibit repeatable differences in their collective aggressiveness, and that colony aggressiveness is linked with persistence in a site-specific manner. Less aggressive colonies are better able to persist at high-elevation sites, which lack colony-sustaining large-bodied prey, whereas colony aggression was not related to chance of persistence at low-elevation sites. This suggests resistance to resource limitation through docility promotes colony survival at high elevations. These data reveal that the collective phenotypes that relate to colony persistence vary by site, and thus, the path of social evolution in these environments is likely to be affected.
Arabidopsis glutathione reductase 2 is indispensable in plastids, while mitochondrial glutathione is safeguarded by additional reduction and transport systems
Authors: Marty Laurent , Bausewein Daniela , Müller Christopher , Bangash Sajid Ali Khan , Moseler Anna , Schwarzländer Markus , Müller-Schüssele Stefanie J. , Zechmann Bernd , Riondet Christophe , Balk Janneke , Wirtz Markus , Hell Rüdiger , Reichheld Jean-Philippe , Meyer Andreas J. 
Published: April 2019

SummaryA highly negative glutathione redox potential (EGSH) is maintained in the cytosol, plastids and mitochondria of plant cells to support fundamental processes, including antioxidant defence, redox regulation and iron-sulfur cluster biogenesis. Out of two glutathione reductase (GR) proteins in Arabidopsis, GR2 is predicted to be dual-targeted to plastids and mitochondria, but its differential roles in these organelles remain unclear.We dissected the role of GR2 in organelle glutathione redox homeostasis and plant development using a combination of genetic complementation and stacked mutants, biochemical activity studies, immunogold labelling and in vivo biosensing.Our data demonstrate that GR2 is dual-targeted to plastids and mitochondria, but embryo lethality of gr2 null mutants is caused specifically in plastids. Whereas lack of mitochondrial GR2 leads to a partially oxidised glutathione pool in the matrix, the ABC transporter ATM3 and the mitochondrial thioredoxin system provide functional backup and maintain plant viability.We identify GR2 as essential in the plastid stroma, where it counters GSSG accumulation and developmental arrest. By contrast a functional triad of GR2, ATM3 and the thioredoxin system in the mitochondria provides resilience to excessive glutathione oxidation.
Altered structural hub connectivity and its clinical relevance in glioma
Authors: Douw Linda , Miller Julie J. , Steenwijk Martijn D. , Stufflebeam Steven M. , Gerstner Elizabeth R. 
Published: April 2019

AbstractBackground and PurposeStructural network analysis of diffusion imaging is increasingly used to study neurological disease, its pathophysiology and symptoms. We therefore evaluate structural hub connectivity in glioma patients and its association with molecular subtype and clinical status.Materials and MethodsUsing retrospective diffusion imaging, structural connectivity was investigated in 65 newly diagnosed glioma patients (36 males; mean age 52 ± 14 years) and 60 healthy controls (23 males; mean age 50 ± 7 years). Probabilistic tractography was performed between 39 cortical nodes per hemisphere. In patients, tumors were drawn in to exclude each tumor-containing voxel from analysis. As previous connectomic research in glioma and other neurological diseases has shown particular importance of ‘hub’ nodes and connections, the numbers of connections between hubs, hubs and non-hubs, and non-hubs were calculated for each hemisphere separately. Clinical and molecular characteristics were assessed as part of routine clinical care. Group differences in connectivity and its associations with performance and molecular subtypes were tested non-parametrically through Mann-Whitney U-tests, corrected for multiple comparisons.ResultsGlioma patients had more hub-related connections in the hemisphere contralateral to the tumor (hub-hub P = 0.002, hub-non-hub P = 0.005), despite being comparable to controls in terms of total and ipsilateral connections. Within patients, hub-related connectivity related to performance status (P = 0.009) and molecular subtype (P = 0.045).ConclusionWe present experimental evidence for the relevance of structural connectomics as a tool to pick up on the clinical impact of glioma on the rest of the brain.
Plasma membrane associated Receptor Like Kinases relocalise to plasmodesmata in response to osmotic stress
Authors: Grison Magali S. , Kirk Philip , Brault Marie , Wu Xu Na , Schulze Waltraud X , Benitez-Alfonso Yoselin , Immel Françoise , Bayer Emmanuelle M. 
Published: April 2019

AbstractPlasmodesmata act as key elements in intercellular communication, coordinating processes related to plant growth, development and responses to environmental stresses. While many of the developmental, biotic and abiotic signals are primarily perceived at the plasma membrane (PM) by receptor proteins, plasmodesmata also cluster receptor-like activities and whether or not these two pathways interact is currently unknown.Here we show that specific PM-located Leucine-Rich-Repeat Receptor-Like-Kinases (LRR-RLKs), KIN7 and IMK2, which under optimal growth conditions are absented from plasmodesmata, rapidly relocate and cluster to the pores in response to osmotic stress. This process is remarkably fast, it is not a general feature of PM-associated proteins and is independent of sterol- and sphingolipid-membrane composition. Focusing on KIN7, previously reported to be involved in stress responses, we show that relocalisation upon mannitol depends on KIN7 phosphorylation. Loss-of-function mutation in KIN7 induces delay in lateral root (LR) development and the mutant is affected in the root response to mannitol stress. Callose-mediated plasmodesmata regulation is known to regulate LR development. We found that callose levels are reduced inkin7mutant background with a root phenotype resembling ectopic expression of PdBG1, an enzyme that degrades callose at the pores. Both the LR and callose phenotypes can be complemented by expression of KIN7 -wild-type and –phosphomimic variants but not by KIN7 phosphodead mutant which fails to relocalise at plasmodesmata. Together the data indicate that re-organisation of RLKs to plasmodesmata is important for the regulation of callose and LR development as part of the plant response to osmotic stress.
A combination of Interferon Stimulated Genes is more effective than IFNα and IFNβ in reducing HIV-1 replication in human cervicovaginal tissues
Authors: Rollenhagen Christiane , Gui Jiang , Doncel Gustavo F. , Asin Susana N. 
Published: April 2019

AbstractEnhancing antiviral responses while controlling immune cell activation is an attractive strategy to reduce HIV-1 replication in the cervicovaginal mucosae, a primary site of heterosexual transmission. Interferon alpha and beta (IFNα/β) signaling up-regulates expression of inflammatory factors and Interferon-Stimulated Genes (ISGs). The simultaneous induction of both IFNs by pathogen-bound molecular pattern recognition receptors and the paucity of data on the anti-HIV-1 efficacy of a combination of these antiviral factors or their downstream targets in human experimental models taking into account mucosal and submucosal cell populations, motivated us to determine whether combined IFNα/β or ISGs could decrease HIV-1 replication in cervicovaginal tissues.IFNα/β reduced HIV-1 p24 release. This reduction was associated with upregulation of expression of a subset of ISGs, the type I IFN receptor and interferon regulatory factor seven. IFNα/β also enhanced immune cell activation. In contrast, when added directly to CV tissues, a combination of ISGs was more effective than IFNα/β in reducing HIV-1 p24 release. The ISG combination demonstrated early kinetics and a more robust reduction in HIV-1 p24 release. Opposite to IFNα/β, the combination of ISGs did not induce immune cell activation.IFNα/β-induced ISGs provide novel mucosal therapeutic targets with a greater capacity to reduce HIV-1 compared to IFNα/β, without inducing immune cell activation.
Human co-transcriptional splicing kinetics and coordination revealed by direct nascent RNA sequencing
Authors: Drexler Heather L. , Choquet Karine , Churchman L. Stirling 
Published: April 2019

AbstractHuman genes have numerous exons that are differentially spliced within pre-mRNA. Understanding how multiple splicing events are coordinated across nascent transcripts requires quantitative analyses of transient RNA processing events in living cells. We developed nanopore analysis of CO-transcriptional Processing (nano-COP), in which nascent RNAs are directly sequenced through nanopores, exposing the dynamics and patterns of RNA splicing without biases introduced by amplification. nano-COP showed that in both human andDrosophilacells, co-transcriptional splicing occurs after RNA polymerase II transcribes several kilobases of pre-mRNA, suggesting that metazoan splicing transpires distally from the transcription machinery. Inhibition of the branch-site recognition complex SF3B globally abolished co-transcriptional splicing in both species. Our findings revealed that splicing order does not strictly follow the order of transcription and is influenced by cis-regulatory elements. In human cells, introns with delayed splicing frequently neighbor alternative exons and are associated with RNA-binding factors. Moreover, neighboring introns in human cells tend to be spliced concurrently, implying that splicing occurs cooperatively. Thus, nano-COP unveils the organizational complexity of metazoan RNA processing.
Characterization of aroma-active compounds in delicious apples juices by gas chromatography-mass spectrometry (GC-MS), gas chromatography–olfactometry (GC-O) and odor activity value (OAV)
Authors: deshou Mao , liu Hong , zhengfeng Li , yunwei Niu , zuobing Xiao , fengmei Zhang , jiancai Zhu 
Published: April 2019

AbstractVolatile aroma compounds of delicious apple juice in three cultivars were obtained by gas chromatography-mass spectrometry (GC-MS), gas chromatography-olfactometry (GC-O), and GC-flame photometric detection (FPD). Quantitatively, the major volatiles of the delicious apple juice were detected by GC-MS, such as esters, alcohols, aldehydes. In addition, GC-O and OAV were used to determine the aroma-active compounds in fruit. Amongst these compounds, ethyl 2-methylbutanoate (47-229), butyl 2-methylbutanoate (8-208), (E)-2-hexenal (25-120), butyl propanoate (14-54), methyl 2-methylbutanoate (28-41), ethyl hexanoate (4-32), ethyl butanoate (5-17) showed high OAVs in three delicious apple juices, which contributed greatly to the aroma of delicious apple juice. Beside those compounds, methanethiol (OAV: 1.1-1.6), dimethyl sulfide (OAV: 2.5-3.6), methional (OAV: 4.2-11.7) and 2-(methylthio)ethanol (OAV: 1.2-1.9) also presented relatively high OAVs. Finally, four compounds (ethyl 2-methylbutanoate, ethyl octanoate, ethyl butanoate and ethyl hexanoate) were selected to investigate the possible interactions occurring in the delicious apple juice. The resultants demonstrated that those aroma volatile compounds can decrease threshold of the solution to dissimilar degrees before and after their addition.
Benchmarking of alignment-free sequence comparison methods
Authors: Zielezinski Andrzej , Girgis Hani Z. , Bernard Guillaume , Leimeister Chris-Andre , Tang Kujin , Dencker Thomas , Lau Anna K. , Röhling Sophie , Choi JaeJin , Waterman Michael S. , Comin Matteo , Kim Sung-Hou , Vinga Susana , Almeida Jonas S. , Chan Cheong Xin , James Benjamin T. , Sun Fengzhu , Morgenstern Burkhard , Karlowski Wojciech M. 
Published: April 2019

ABSTRACTAlignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference and reconstruction of species trees under horizontal gene transfer and recombination events. The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions.
Cloning, Biochemical Characterization and Inhibition of Alanine racemase fromStreptococcus iniae
Authors: Muhammad Murtala , Li Yangyang , Gong Siyu , Shi Yanmin , Ju Jiansong , Zhao Baohua , Liu Dong 
Published: April 2019

ABSTRACTStreptococcus iniaeis a pathogenic and zoonotic bacteria that impacted high mortality to many fish species, as well as capable of causing serious disease to humans. Alanine racemase (Alr, EC 5.1.1.1) is a pyridoxal-5′-phosphate (PLP)-containing homodimeric enzyme that catalyzes the racemization of L-alanine and D-alanine. In this study, we purified alanine racemase from the pathogenic strain ofS. iniae, determined its biochemical characteristics and inhibitors. Thealrgene has an open reading frame (ORF) of 1107 bp, encoding a protein of 369 amino acids, which has a molecular mass of 40 kDa. The optimal enzyme activity occurred at 35°C and a pH of 9.5. The enzyme belongs to the PLP dependent enzymes family and is highly specific to L-alanine.S.iniaeAlr can be inhibited by some metal ions, hydroxylamine and dithiothreitol (DTT). The kinetic parametersKmandVmaxof the enzyme were 33.11 mM, 2426 units/mg for L-alanine and 14.36 mM, 963.6 units/mg for D-alanine. Finally, the 50% inhibitory concentrations (IC50) values and antibiotic activity of two alanine racemase inhibitors, were determined and found to be effective against both gram positive and gram negative bacteria employed in this study. The important role of alanine racemase as a target of developing new antibiotics againstS. iniaehighlighted the usefulness of the enzyme for new antibiotics discovery.
Empowering small industry of wood carving handicraft in Bangli district
Authors: Marhaeni A.A.I.N. , Yuliarmi Ni Nyoman , Setiawina Nyoman Djinar 
Published: April 2019

PurposeThe purpose of this study is to analyze the influence of social capital on human capital; the effect of social capital on transaction costs; the influence of social capital, human capital and transaction costs on empowerment; the indirect effect of social capital on empowerment through human capital; and the indirect effect of social capital on empowerment through transaction costs in Bangli Regency.Design/methodology/approachThe population in this research is all wood carving business in Bangli Regency, in all districts some 366 business units. The number of respondents surveyed were 191 business units in all sub-districts. The sampling technique used is stratified random sampling, with strata of business area. Inferential analysis is preceded by using factor analysis techniques to obtain factor scores on each latent variable, followed by path analysis to answer the research objectives.FindingBased on the analysis, the following conclusions are drawn: social capital has a positive and significant impact on human resources; positive social capital and significant positive to transaction costs; social capital and human resources have a positive and significant effect while transaction costs and no significant positive effect on empowerment; human resources partially mediate the influence of social capital on empowerment; and transaction costs do not act as a variable, mediating the influence of social capital on empowering small woodcraft industry in Bangli Regency.Originality/valueThis study is one of the few to investigate the role of social capital, human capital and transaction cost on empowerment of small industries, especially wood carving in Bangli District. This small woodcraft industry is famous for its uniqueness that characterizes Balinese carving ornaments. But lately, the productivity of handicrafts wood carving, especially in Bangli District, fluctuates tend to decline. Social capital, in addition to human capital and technology, also plays an important role in the production process. Social capital equals other physical capital and can increase productivity and economic efficiency. Higher social capital owned by individuals or groups can reduce transaction costs; thus economic activity can run efficiently. Social capital is the information, trust and norms of reciprocity inherent in social networks.