bluuebunny/crossref_metadata_2025_split huggingface dataset:
The minimal behavioral time window for reward conditioning in the nucleus accumbens of mice
Authors: Yamaguchi Kenji , Maeda Yoshitomo , Sawada Takeshi , Iino Yusuke , Tajiri Mio , Nakazato Ryosuke , Kasai Haruo , Yagishita Sho 
Published: May 2019

AbstractThe temporal precision of reward-reinforcement learning is determined by the minimal time window of the reward action—theoretically known as the eligibility trace. In animal studies, however, such a minimal time window and its origin have not been well understood. Here, we used head-restrained mice to accurately control the timing of sucrose water as an unconditioned stimulus (US); we found that the reinforcement effect of the US occurred only within 1 s after a short tone of a conditioned stimulus (CS). The conditioning required the dopamine D1 receptor and CaMKII signaling in the nucleus accumbens (NAc). The time window was not reduced by replacing CS with optogenetic stimulation of the synaptic inputs to the NAc, which is in agreement with previous reports on the effective dopamine timing of NAc synapses. Thus, our data suggest that the minimal reward time window is 1 s, and is formed in the NAc.
Inverted encoding models estimate sensible channel responses for sensible models
Authors: Sprague Thomas C. , Boynton Geoffrey M. , Serences John T. 
Published: May 2019

AbstractIn a commentary published in eNeuro, Gardner & Liu (2019) discuss the role of model specification in interpreting the output of complex models of neural data. As a case study, they suggest that one variant of such analyses, the inverted encoding model (IEM) analysis framework, should not be used to assay properties of “stimulus representations” because the ability to apply linear transformations at various stages of the analysis procedure renders results ‘arbitrary’. As we discuss, the specification of all models is arbitrary to the extent that an experimenter makes choices based on current knowledge of the model system. However, the results derived from any given model, such as the reconstructed channel response profiles obtained from an IEM analysis, are uniquely defined and are arbitrary only in the sense that changes in the model can predictably change results. Moreover, with knowledge of the model used for IEM analyses, the results remain informative as comparisons between reconstructed channel response profiles across task conditions using a fixed encoding model – the most common use of the IEM technique – can generally capture changes in population-level representation magnitude across linear transformations. Thus, changes in the magnitude of the response profiles across conditions are preserved, even across unprincipled linear transforms. IEM-based channel response profiles should therefore not be considered arbitrary when the model is clearly specified and guided by our best understanding of neural population representations in the brain regions being analyzed. Intuitions derived from this case study are important to consider when interpreting results from all model-based analyses, which are similarly contingent upon the specification of the models used.
Identification of key regulators in Prostate cancer from gene expression datasets of patients
Authors: Mangangcha Irengbam Rocky , Malik Md. Zubbair , Küçük Ömer , Ali Shakir , Singh R.K. Brojen 
Published: May 2019

AbstractIdentification of key regulators and regulatory pathways is an important step in the discovery of genes involved in cancer. Here, we propose a method to identify key regulators in prostate cancer (PCa) from a network constructed from gene expression datasets of PCa patients. Overexpressed genes were identified using BioXpress, having a mutational status according to COSMIC, followed by the construction of PCa Interactome network using the curated genes. The topological parameters of the network exhibited power law nature indicating hierarchical scale-free properties and five levels of organization. Highest degreehubs(k≥65) were selected from the PCa network, traced, and 19 of them were identified as novel key regulators, as they participated at all network levels serving as backbone. Of the 19 hubs, some have been reported in literature to be associated with PCa and other cancers. Based on participation coefficient values most of these areconnectororkinless hubssuggesting significant roles in modular linkage. The observation of non-monotonicity in the rich club formation suggested the importance of intermediate hubs in network integration, and they may play crucial roles in network stabilization. The network was self-organized as evident from fractal nature in topological parameters of it and lacked a central control mechanism.
Functional brain network modeling in sub-acute stroke patients and healthy controls during rest and continuous attentive tracking
Authors: Dørum Erlend S. , Kaufmann Tobias , Alnæs Dag , Richard Geneviève , Kolskår Knut K. , Engvig Andreas , Sanders Anne-Marthe , Ulrichsen Kristine , Ihle-Hansen Hege , Nordvik Jan Egil , Westlye Lars T. 
Published: May 2019

AbstractA cerebral stroke is characterized by compromised brain function due to an interruption in cerebrovascular blood supply. Although stroke incurs focal damage determined by the vascular territory affected, clinical symptoms commonly involve multiple functions and cognitive faculties that are insufficiently explained by the focal damage alone. Functional connectivity (FC) refers to the synchronous activity between spatially remote brain regions organized in a network of interconnected brain regions. Functional magnetic resonance imaging (fMRI) has advanced this system-level understanding of brain function, elucidating the complexity of stroke outcomes, as well as providing information useful for prognostic and rehabilitation purposes.We tested for differences in brain network connectivity between a group of patients with minor ischemic strokes in sub-acute phase (n=44) and matched controls (n=100). As neural network configuration is dependent on cognitive effort, we obtained fMRI data during rest and two load levels of a multiple object tacking (MOT) task. Network nodes and time-series were estimated using independent component analysis (ICA) and dual regression, with network edges defined as the partial temporal correlations between node pairs. The full set of edgewise FC went into a cross-validated regularized linear discriminant analysis (rLDA) to classify groups and cognitive load.MOT task performance and cognitive tests revealed no significant group differences. While multivariate machine learning revealed high sensitivity to experimental condition, with classification accuracies between rest and attentive tracking approaching 100%, group classification was at chance level, with negligible differences between conditions. Repeated measures ANOVA showed significantly stronger synchronization between a temporal node and a sensorimotor node in patients across conditions. Overall, the results revealed high sensitivity of FC indices to task conditions, and suggest relatively small brain network-level disturbances after clinically mild strokes.
Functional genomics reveals extensive diversity in Staphylococcus epidermidis restriction modification systems compared to Staphylococcus aureus
Authors: Lee Jean YH , Carter Glen P , Pidot Sacha J , Guérillot Romain , Seemann Torsten , Gonçalves da Silva Anders , Foster Timothy J , Howden Benjamin P , Stinear Timothy P , Monk Ian R 
Published: May 2019

AbstractStaphylococcus epidermidis is a significant opportunistic pathogen of humans. Molecular studies in this species have been hampered by the presence of restriction-modification (RM) systems that limit introduction of foreign DNA. Here we establish the complete genomes and methylomes for seven clinically significant, genetically diverse S. epidermidis isolates and perform the first systematic genomic analyses of the type I RM systems within both S. epidermidis and Staphylococcus aureus. Our analyses revealed marked differences in the gene arrangement, chromosomal location and movement of type I RM systems between the two species. Unlike S. aureus, S. epidermidis type I RM systems demonstrate extensive diversity even within a single genetic lineage. This is contrary to current assumptions and has important implications for approaching the genetic manipulation of S. epidermidis. Using Escherichia coli plasmid artificial modification (PAM) to express S. epidermidis hsdMS, we readily overcame restriction barriers in S. epidermidis, and achieved transformation efficiencies equivalent to those of modification deficient mutants. With these functional experiments we demonstrate how genomic data can be used to predict both the functionality of type I RM systems and the potential for a strain to be transformation proficient. We outline an efficient approach for the genetic manipulation of S. epidermidis from diverse genetic backgrounds, including those that have hitherto been intractable. Additionally, we identified S. epidermidis BPH0736, a naturally restriction defective, clinically significant, multidrug-resistant ST2 isolate as an ideal candidate for molecular studies.ImportanceStaphylococcus epidermidis is a major cause of hospital-acquired infections, especially those related to implanted medical devices. Understanding how S. epidermidis causes disease and devising ways to combat these infections has been hindered by an inability to genetically manipulate “hospital-adapted” strains that cause clinical disease. Here we provide the first comprehensive analyses of the mechanisms whereby S. epidermidis resists the uptake of foreign DNA and demonstrate that these are distinct from those described for S. aureus. Until now it had been assumed that these are the same. Using these insights, we demonstrate an efficient approach for the genetic manipulation of S. epidermidis to enable the study of clinically relevant isolates for the first time.
Oncogenic and Circadian Effects of Small Molecules Directly and Indirectly Targeting the Core Circadian Clock
Authors: Lin Hui-Hsien , Robertson Kelly L. , Bisbee Heather A. , Farkas Michelle E. 
Published: May 2019

ABSTRACTCircadian rhythms are essential for controlling the cell cycle, cellular proliferation, and apoptosis, and hence, are tightly linked to cell fate. Disruption of circadian rhythms has been shown to trigger various pathological developments, including cancer. Several recent studies have used a variety of small molecules to affect circadian oscillations, however, their concomitant cellular effects were not assessed. Here, we use five molecules, grouped into direct versus indirect effectors of the circadian clock, to modulate periods in a human osteosarcoma cell line (U2OS), and determined their influences on cellular behaviors, including motility and colony formation. Luciferase reporters, whose expression were driven via Bmal1- and Per2-promoters (positive and negative protein components of the core clock), were used to facilitate the visualization and quantitative analysis of circadian oscillations. We show that all molecules significantly increase or decrease the circadian periods of Bmal1 and Per2 in a dose-dependent manner, but period length does not correlate with the extent of cell migration or proliferation. We observed that only molecules that affected circadian oscillations to a greater extent showed significant influence on cell functions (e.g. motility and colony formation). Because it is important to consider the likelihood of biological effects resulting from non-circadian targets, we also provide a thorough discussion of potential modes of action. Future studies should employ additional compounds that directly target circadian proteins and/or have different circadian effects, and evaluation in other cancer models to determine whether results obtained here remain consistent.For Table of Contents Only
Diaphragmatic Central Motor Conduction Changes In Chronic Obstructive Pulmonary Disease
Authors: El-Nemr Rehab Abdelaal , Sweed Rania Ahmad , Shafiek Hanaa 
Published: May 2019

AbstractBackground and objectivesRespiratory muscles dysfunction has been reported in COPD. Transcranial magnetic stimulation (TMS) is easy non-invasive that has been used for assessing the respiratory corticospinal pathways particularly of diaphragm. We aimed to study the cortico-diaphragmatic motor system changes in COPD using TMS and to correlate the findings with the pulmonary function.MethodsA case control study recruited 30 stable COPD from the out-patient respiratory clinic of Main Alexandria University hospital-Egypt and 17 healthy control subjects who were subjected to spirometry. Cortical conduction of the diaphragm was performed by TMS to all participants followed by cervical magnetic stimulation of the phrenic nerve roots. Diaphragmatic resting motor threshold (DRMT), cortical motor evoked potential latency (CMEPL), CMEP amplitude (CMEPA), peripheral motor evoked potential latency (PMEPL), PMEP amplitude (PMEPA) and central motor conduction time (CMCT) were measured.Results66.7% of COPD patients had severe and very severe COPD with median age of 59 (55-63) years. There was statistically significant bilateral decrease in DRMT, CMEPA and PMEPA in COPD group versus healthy subjects and significant increase in CMEPL and PMEPL (p <0.01). Left CMCT was significantly prolonged in COPD group versus healthy subjects (p <0.0001) but not right CMCT. Further, there was significant increase in CMEPL and CMCT of left versus right diaphragm in COPD group (p= 0.003 and 0.001 respectively) that inversely correlated with FEV1% and FVC% predicted.ConclusionCentral cortico-diaphragmatic motor system is affected in COPD patients with heterogeneity of both sides that is correlated with pulmonary function.SignificanceCoticospinal pathway affection could be a factor for development of diaphragmatic dysfunction in COPD patients accordingly its evaluation could help in personalization of COPD management especially pulmonary rehabilitation programs
Arabidopsis DGD1 SUPPRESSOR1 Is a Subunit of the Mitochondrial Contact Site and Cristae Organizing System and Affects Mitochondrial Biogenesis
Authors: Li Lu , Lavell Anastasiya , Meng Xiangxiang , Berkowitz Oliver , Selinski Jennifer , van de Meene Allison , Carrie Chris , Benning Christoph , Whelan James , De Clercq Inge , Wang Yan 
Published: May 2019

Abstract
Mitochondrial and plastid biogenesis requires the biosynthesis and assembly of proteins, nucleic acids, and lipids. In Arabidopsis (Arabidopsis thaliana), the mitochondrial outer membrane protein DGD1 SUPPRESSOR1 (DGS1) is part of a large multi-subunit protein complex that contains the mitochondrial contact site and cristae organizing system 60-kD subunit, the translocase of outer mitochondrial membrane 40-kD subunit (TOM40), the TOM20s, and the Rieske FeS protein. A point mutation in DGS1, dgs1-1, altered the stability and protease accessibility of this complex. This altered mitochondrial biogenesis, mitochondrial size, lipid content and composition, protein import, and respiratory capacity. Whole plant physiology was affected in the dgs1-1 mutant as evidenced by tolerance to imposed drought stress and altered transcriptional responses of markers of mitochondrial retrograde signaling. Putative orthologs of Arabidopsis DGS1 are conserved in eukaryotes, including the Nuclear Control of ATP Synthase2 (NCA2) protein in yeast (Saccharomyces cerevisiae), but lost in Metazoa. The genes encoding DGS1 and NCA2 are part of a similar coexpression network including genes encoding proteins involved in mitochondrial fission, morphology, and lipid homeostasis. Thus, DGS1 links mitochondrial protein and lipid import with cellular lipid homeostasis and whole plant stress responses.
Review article: Clinical characteristics and outcomes of patient presentations to the emergency department via police: A scoping review
Authors: Crilly Julia , Johnston Amy NB , Wallis Marianne , Polong‐Brown Josea , Heffernan Ed , Fitzgerald Gerard , Young Jesse T , Kinner Stuart 
Published: May 2019

AbstractPeople brought in by police (BIBP) to the ED are a potentially vulnerable group. This narrative scoping review aimed to identify, evaluate and summarise current literature regarding the frequency of presentation, demographic and clinical profile of patients (including reason for presentation), care delivery, and outcomes for people BIBP to the ED, and identify current gaps in knowledge. The review involved searching EMBASE, CINAHL and PubMed using a combination of terms: emergency/ED coupled with police custody/watch house or police presentation, for papers published in English language from January 2006 to November 2017. A total of 20 studies met the inclusion criteria. These included 17 observational (non‐randomised controlled trials) quantitative studies and three descriptive case reports. The proportion of presentations to ED that were BIBP varied depending on the study design and sampling frame. People BIBP often presented with mental health problems, substance use problems, aggressive behaviour and injury caused by self or others. Of studies focused specifically on patients arriving to the ED in mental health crisis (i.e. suicidal ideation or self‐harm), 18–27% were BIBP. ED presentations BIBP were mostly male and typically younger than people arriving by other means. The nature of care provided in the ED and outcomes of the acute episode of care were typically not well described. Limited research regarding people BIBP to the ED limits the ability to comprehensively understand their demographic and clinical profile and outcomes of emergency care. Further research is required to inform if and where in the patient’s journey further improvements may be targeted.
Application of Green Technology for the Acquisition of Extracts of Araçá (Psidium grandifolium Mart. ex DC.) Using Supercritical CO2 and Pressurized Ethanol: Characterization and Analysis of Activity
Authors: Bittencourt G. M. , Firmiano D. M. , Fachini R. P. , Lacaz‐Ruiz R. , Fernandes A. M. , Oliveira A. L. 
Published: May 2019

AbstractBrazil is home to a wide variety of flora, including several lesser known species, such as araçá that were processed in this study using two green technologies consecutively: supercritical fluid extraction (SFE) for nonpolar fraction and pressurized liquid extraction. For polar fraction, the experiments followed a central composite design involving ethanol as solvent, with temperature and static time in each bath as independent variables. Both extracts were analyzed for antioxidant and antimicrobial activities. Total phenolics content (TPC) was determined for all ethanol extracts. In the araçá essential oil (AEO) obtained by SFE, the extraction yield was 2.33%. The three major compounds of AEO were α‐pinene (20.75%), p‐cymene (20.50%), and o‐cymene (20.05%). In ethanol extracts, the high yield (14.49%) was obtained at 74 °C/6 min and the major TPC (136.95 mg GAE/100 g) at 60 °C/9 min. Ethanol extracts presented good antioxidant activity (EC50 = 6.37 mg/mL) at 74 °C/6 min. AEO was unable to reduce DPPH• concentration by 50%. Both extract types presented an inhibitory effect against Staphylococcus aureus, Pseudomonas aeruginosa, and Bacillus cereus, while only the ethanol extracts presented effect against Listeria monocytogenes. This work had the aim to present the innovation of the use of a whole typical Brazilian fruit that gives rise to extracts with excellent properties for employment in both the pharmaceutical and food industries.
The Discovery of Proteins Associated with Freshness of Coregonus Peled Muscle During Refrigerated Storage
Authors: Deng Xiaorong , Lei Yongdong , Yu Yawen , Lu Shiling , Zhang Jian 
Published: May 2019

AbstractThe aim of this study is to identify the protein indicator of freshness of Coregonus peled using two‐dimensional gel electrophoresis (2‐DE) and matrix‐assisted laser desorption ionization‐time‐of‐flight/time‐of‐flight mass spectrometry (MALDI‐TOF/TOF MS) methods. Samples were obtained prior to (control group) and 2, 4, 6, and 8 days after refrigerated storage for quality and proteomics analysis. Three proteins were found to have significant differential abundance in sample groups during the refrigerated storage, including l‐lactate dehydrogenase, adenylate kinase isoenzyme 1, and myosin heavy chain, which were associated with freshness changes of C. peled. The freshness of C. peled fish during the refrigerated storage can be differentiated from the comparison of the specific proteins.Practical ApplicationThe changes of food quality pose not only the relative economical loses but also the potential implications on consumer's health. Proteomics can represent a powerful tool to explore potential biomarkers that may be related to meat quality defects. The identification of key protein biomarkers linked to freshness of Coregonus peled allows to monitor the response of the food matrix during storage and try to minimizes these defects.
Camellia Oleifera Seed Extract Mildly Ameliorates Carbon Tetrachloride‐Induced Hepatotoxicity in Rats by Suppressing Inflammation
Authors: Ko Jung , Yeh Wan‐Ju , Huang Wen‐Chih , Yang Hsin‐Yi 
Published: May 2019

AbstractThe objective of this study was to evaluate the effects of a hot‐water extract of defatted Camellia oleifera seeds (CSE) in carbon tetrachloride (CCl4)‐induced liver damage in rats. Wistar rats were separated into four groups including the normal (N) and CCl4 control (C) groups, which are fed a control diet, and the CCL (low‐dose CSE) and CCH (high‐dose CSE) groups, which are fed with a control diet plus different amount of CSE for an 8‐week experimental period. Liver injury in the C, CCL, and CCH groups was induced by injecting CCl4 (i.p.) twice a week from the 5th week to the end of the study. In CCl4‐treated rats, the alanine transaminase (ALT) and aspartate transaminase (AST) activities and malondialdehyde (MDA) concentration significantly increased compared to the normal group. Lower antioxidative enzyme activities and higher proinflammatory cytokines, transforming growth factor‐β (TGF‐β) and hydroxyproline concentrations in the liver were also found in the CCl4‐treated group compared to the normal group. In contrast, the administration of CSE alleviated the biochemical and histopathological changes including inflammation, liver cell damage, and fibrosis caused by CCl4 in rats. Our results indicated that CSE exhibited hepatoprotective effects in CCl4‐induced liver hepatotoxicity through alleviating hepatic inflammation and fibrosis in rats.Practical ApplicationCamellia oleifera are widely used for edible oil production while the defatted seeds pomace is often discarded. We found that extract of C. oleifera pomace containing phenolic compounds, saponins, and polysaccharides showed protective effects chemical‐driven liver damage and, therefore, may be used in further studies and developing functional foods.