bluuebunny/crossref_metadata_2025_split huggingface dataset:
Movement and Performance Explain Widespread Cortical Activity in a Visual Detection Task
Authors: Salkoff David B , Zagha Edward , McCarthy Erin , McCormick David A 
Published: August 2019

Abstract
Recent studies in mice reveal widespread cortical signals during task performance; however, the various task-related and task-independent processes underlying this activity are incompletely understood. Here, we recorded wide-field neural activity, as revealed by GCaMP6s, from dorsal cortex while simultaneously monitoring orofacial movements, walking, and arousal (pupil diameter) of head-fixed mice performing a Go/NoGo visual detection task and examined the ability of task performance and spontaneous or task-related movements to predict cortical activity. A linear model was able to explain a significant fraction (33–55% of variance) of widefield dorsal cortical activity, with the largest factors being movements (facial, walk, eye), response choice (hit, miss, false alarm), and arousal and indicate that a significant fraction of trial-to-trial variability arises from both spontaneous and task-related changes in state (e.g., movements, arousal). Importantly, secondary motor cortex was highly correlated with lick rate, critical for optimal task performance (high d′), and was the first region to significantly predict the lick response on target trials. These findings suggest that secondary motor cortex is critically involved in the decision and performance of learned movements and indicate that a significant fraction of trial-to-trial variation in cortical activity results from spontaneous and task-related movements and variations in behavioral/arousal state.
Effects of Developmental Nicotine Exposure on Frontal Cortical GABA-to-Non-GABA Neuron Ratio and Novelty-Seeking Behavior
Authors: Martin Melissa M , McCarthy Deirdre M , Schatschneider Chris , Trupiano Mia X , Jones Sara K , Kalluri Aishani , Bhide Pradeep G 
Published: August 2019

AbstractCigarette smoking during pregnancy is a major public health concern, resulting in detrimental health effects in the mother and her offspring. The adverse behavioral consequences for children include increased risk for attention deficit hyperactivity disorder, working memory deficits, epilepsy, novelty-seeking, and risk-taking behaviors. Some of these behavioral conditions are consistent with an imbalance in frontal cortical excitatory (glutamate) and inhibitory (GABA) neurotransmitter signaling. We used a GAD67-GFP knock-in mouse model to examine if developmental nicotine exposure alters frontal cortical GABA neuron numbers, GABA-to-non-GABA neuron ratio and behavioral phenotypes. Female mice were exposed to nicotine (100 or 200 μg/mL) in drinking water beginning 3 weeks prior to breeding and until 3 weeks postpartum. Male and female offspring were examined beginning at 60 days of age. The nicotine exposure produced dose-dependent decreases in GABA-to-non-GABA neuron ratios in the prefrontal and medial prefrontal cortices without perturbing the intrinsic differences in cortical thickness and laminar distribution of GABA or non-GABA neurons between these regions. A significant increase in exploratory behavior and a shift toward “approach” in the approach–avoidance paradigm were also observed. Thus, developmental nicotine exposure shifts the cortical excitation–inhibition balance toward excitation and produces behavioral changes consistent with novelty-seeking behavior.
Recurrence and Occurrence of Kaposi’s Sarcoma in Patients Living With Human Immunodeficiency Virus (HIV) and on Antiretroviral Therapy, Despite Suppressed HIV Viremia
Authors: Palich Romain , Veyri Marianne , Valantin Marc-Antoine , Marcelin Anne-Geneviève , Guihot Amélie , Pourcher Valérie , Jary Aude , Solas Caroline , Makinson Alain , Poizot-Martin Isabelle , Costagliola Dominique , Spano Jean-Philippe , Katlama Christine ,   for the CancerVIH Study Group, Autran B , Boué F , Choquet S , Cadranel J , Costagliola D , Garraffo R , Guihot A , Jary A , Katlama C , Lambotte O , Lavolé A , Makinson A , Marcelin A-G , Palich R , Poizot-Martin I , Solas C , Spano J-P , Valantin M-A , Veyri M , Ait-Mohand H , Baillat V , Belhouari K , Canestri A , Chiarello P , El Hajj Lise , Gras G , Hitoto H , Makhloufi D , Pourcher V , Pacanowski J , Patrat-Delon S , Pavel S , Psomas C , Vareil M-O 
Published: August 2019

Abstract
In 21 cutaneous and/or visceral Kaposi’s sarcoma cases, occurring in patients living with human immunodeficiency virus (HIV) who were on antiretroviral therapy with suppressed HIV viremia and high CD4 T cell counts, the efficacy of conventional chemotherapies was limited due to cumulative toxicities, comedications, and a lack of immune improvement.
Natural History and Evolution of Anti-Interferon-γ Autoantibody-Associated Immunodeficiency Syndrome in Thailand and the United States
Authors: Hong Gloria H , Ortega-Villa Ana M , Hunsberger Sally , Chetchotisakd Ploenchan , Anunnatsiri Siriluck , Mootsikapun Piroon , Rosen Lindsey B , Zerbe Christa S , Holland Steven M 
Published: August 2019

Abstract

Background
The natural history of anti-interferon-γ (IFN-γ) autoantibody-associated immunodeficiency syndrome is not well understood.

Methods
Data of 74 patients with anti-IFN-γ autoantibodies at Srinagarind Hospital, Thailand, were collected annually (median follow-up duration, 7.5 years). Annual data for 19 patients and initial data for 4 patients with anti-IFN-γ autoantibodies at the US National Institutes of Health were collected (median follow-up duration, 4.5 years). Anti-IFN-γ autoantibody levels were measured in plasma samples.

Results
Ninety-one percent of US patients were of Southeast Asian descent; there was a stronger female predominance (91%) in US than Thai (64%) patients. Mycobacterium abscessus (34%) and Mycobacterium avium complex (83%) were the most common nontuberculous mycobacteria in Thailand and the United States, respectively. Skin infections were more common in Thailand (P = .001), whereas bone (P &lt; .0001), lung (P = .002), and central nervous system (P = .03) infections were more common in the United States. Twenty-four percent of Thai patients died, most from infections. None of the 19 US patients with follow-up data died. Anti-IFN-γ autoantibody levels decreased over time in Thailand (P &lt; .001) and the United States (P = .017), with either cyclophosphamide (P = .01) or rituximab therapy (P = .001).

Conclusions
Patients with anti-IFN-γ autoantibodies in Thailand and the United States had distinct demographic and clinical features. While titers generally decreased with time, anti-IFN-γ autoantibody disease had a chronic clinical course with persistent infections and death. Close long-term surveillance for new infections is recommended.
Clinical Manifestations of Nipah Virus–Infected Patients Who Presented to the Emergency Department During an Outbreak in Kerala State in India, May 2018
Authors: Chandni Radhakrishnan , Renjith T P , Fazal Arshad , Yoosef Noufel , Ashhar C , Thulaseedharan N K , Suraj K P , Sreejith M K , Sajeeth Kumar K G , Rajendran V R , Remla Beevi A , Sarita R L , Sugunan Attayur P , Arunkumar Govindakarnavar , Mourya D T , Murhekar Manoj 
Published: August 2019

Abstract

Background
An outbreak of Nipah virus (NiV) disease occurred in the Kozhikode district of Kerala State in India in May 2018. Several cases were treated at the emergency medicine department (ED) of the Government Medical College, Kozhikode (GMCK). The clinical manifestations and outcome of these cases are described.

Methods
The study included 12 cases treated in the ED of GMCK. Detailed clinical examination, laboratory investigations, and molecular testing for etiological diagnosis were performed.

Results
The median age of the patients was 30 years and the male to female ratio was 1.4:1.0. All the cases except the index case contracted the infection from hospitals. The median incubation period was 10 days, and the case fatality ratio was 83.3%. Ten (83.3%) patients had encephalitis and 9 out of 11 patients whose chest X-rays were obtained had bilateral infiltrates. Three patients had bradycardia and intractable hypotension requiring inotropes. Encephalitis, acute respiratory distress syndrome, and myocarditis were the clinical prototypes, but there were large overlaps between these. Ribavirin therapy was given to a subset of the patients. Although there was a 20% reduction in NiV encephalitis cases treated with the drug, the difference was not statistically significant. The outbreak ended soon after the introduction of total isolation of patients and barrier nursing.

Conclusion
The outbreak of NiV disease in Kozhikode in May 2018 presented as encephalitis, acute respiratory distress and myocarditis or combinations of these. The CFR was high. Ribavirin therapy was tried but no evidence for its benefit could be obtained.
Frequent Methicillin-Resistant Staphylococcus aureus Introductions Into an Inner-city Jail: Indications of Community Transmission Networks
Authors: Popovich Kyle J , Snitkin Evan S , Zawitz Chad , Aroutcheva Alla , Payne Darjai , Thiede Stephanie N , Schoeny Michael , Green Stefan J , Hayden Mary K , Hota Bala , Weinstein Robert A 
Published: August 2019

Abstract

Background
Jails may facilitate spread of methicillin-resistant Staphylococcus aureus (MRSA) in urban areas. We examined MRSA colonization upon entrance to a large urban jail to determine if there are MRSA transmission networks preceding incarceration.

Methods
Males incarcerated in Cook County Jail (Chicago) were enrolled, with enrichment for people living with human immunodeficiency virus (PLHIV), within 72 hours of intake. Surveillance cultures assessed prevalence of MRSA colonization. Whole-genome sequencing (WGS) identified preincarceration transmission networks.
We examined methicillin-resistant Staphylococcus aureus (MRSA) isolates to determine if there are transmission networks that precede incarceration. A large proportion of individuals enter jail colonized with MRSA. Molecular epidemiology and colonization risk factors provide clues to community reservoirs for MRSA.

Results
There were 718 individuals (800 incarcerations) enrolled; 58% were PLHIV. The prevalence of MRSA colonization at intake was 19%. In multivariate analysis, methamphetamine use, unstable housing, current/recent skin infection, and recent injection drug use were predictors of MRSA. Among PLHIV, recent injection drug use, current skin infection, and HIV care at outpatient clinic A that emphasizes comprehensive care to the lesbian, gay, bisexual, transgender community were predictors of MRSA. Fourteen (45%) of 31 detainees with care at clinic A had colonization. WGS revealed that this prevalence was not due to clonal spread in clinic but rather to an intermingling of distinct community transmission networks. In contrast, genomic analysis supported spread of USA500 strains within a network. Members of this USA500 network were more likely to be PLHIV (P &lt; .01), men who have sex with men (P &lt; .001), and methamphetamine users (P &lt; .001).

Conclusions
A large proportion of individuals enter jail colonized with MRSA. Molecular epidemiology and colonization risk factors provide clues to identify colonized detainees entering jail and potential community reservoirs of MRSA.
Sri Lanka’s Quest for a Reformed Constitution: Lessons from a Lost Opportunity
Authors: Pullé Austin I , Ratnapala Suri 
Published: August 2019

Abstract
The history of Sri Lanka is highly instructive of the dynamics of constitutional evolution in a post-colonial, multi-ethnic, and economically challenged Asian nation. Sri Lanka is one of the few ex-colonies where constitutional change has happened without military involvement. Citizens have changed their government 10 times by generally fair and free elections. In the first three decades after independence, the country’s judiciary enjoyed an enviable reputation for independence, integrity, and competence. The public service, though poorly rewarded and resourced, maintained a praiseworthy standard of administrative impartiality and competence. Sri Lanka had, and still has, one of the highest rates of literacy in the developing world and scores creditably on human development indicators. Despite these impressive achievements, the country has a chequered record of constitutional government since independence. It has been ruled for long periods under emergency rule, and the nation’s two republican constitutions have a poor record of maintaining constitutional democracy and basic rights and freedoms. The nation’s most recent efforts at constitutional reform, despite some notable successes, have stalled as a consequence of hyper-partisanship and opportunistic political strategizing. This article examines the post-independence constitutional history of the nation, prognosticates its prospects of constitutional revival, and draws important lessons from the failure of the current constitutional project.
Hydrographical Flow Modelling of the River Severn Using Particle Swarm Optimization
Authors: Kenny Ian 
Published: August 2019

Abstract
A model is presented to model hydrographical flow, which we apply to flood forecasting in the River Severn catchment area. The approach uses Particle Swarm Optimization (PSO), a swarm computation heuristic, to produce a predictive model of hydrographical flow. Hydrological flow data from 1980 to 1990 are considered, comprising the daily average flow through the River Severn and its tributaries. PSO models are developed from each year of data and are applied to predict flow in the other 10 years; model performance is shown to be largely independent of the training year, suggesting the catchment system is stable and the approach is robust. Importantly, and in contrast to most of the existing alternatives, flow is derived from data measurements taken 2 days previously, as demanded for early-warning flood prediction. The cross-validated model for prediction of extreme (Q95) events R2 = 0.96, significantly improving upon multiple linear regression R2 = 0.93, the best performing of current existing methods.
Discovery and validation of candidate smoltification gene expression biomarkers across multiple species and ecotypes of Pacific salmonids
Authors: Houde Aimee Lee S , Günther Oliver P , Strohm Jeffrey , Ming Tobi J , Li Shaorong , Kaukinen Karia H , Patterson David A , Farrell Anthony P , Hinch Scott G , Miller Kristina M 
Published: August 2019

AbstractEarly marine survival of juvenile salmon is intimately associated with their physiological condition during smoltification and ocean entry. Smoltification (parr–smolt transformation) is a developmental process that allows salmon to acquire seawater tolerance in preparation for marine living. Traditionally, this developmental process has been monitored using gill Na+/K+-ATPase (NKA) activity or plasma hormones, but gill gene expression offers the possibility of another method. Here, we describe the discovery of candidate genes from gill tissue for staging smoltification using comparisons of microarray studies with particular focus on the commonalities between anadromous Rainbow trout and Sockeye salmon datasets, as well as a literature comparison encompassing more species. A subset of 37 candidate genes mainly from the microarray analyses was used for TaqMan quantitative PCR assay design and their expression patterns were validated using gill samples from four groups, representing three species and two ecotypes: Coho salmon, Sockeye salmon, stream-type Chinook salmon and ocean-type Chinook salmon. The best smoltification biomarkers, as measured by consistent changes across these four groups, were genes involved in ion regulation, oxygen transport and immunity. Smoltification gene expression patterns (using the top 10 biomarkers) were confirmed by significant correlations with NKA activity and were associated with changes in body brightness, caudal fin darkness and caudal peduncle length. We incorporate gene expression patterns of pre-smolt, smolt and de-smolt trials from acute seawater transfers from a companion study to develop a preliminary seawater tolerance classification model for ocean-type Chinook salmon. This work demonstrates the potential of gene expression biomarkers to stage smoltification and classify juveniles as pre-smolt, smolt or de-smolt.
Prolonged exposure to low oxygen improves hypoxia tolerance in a freshwater fish
Authors: Gilmore Kayla L , Doubleday Zoe A , Gillanders Bronwyn M 
Published: August 2019

Lay summary
It is poorly understood whether fish can acclimate to prolonged low-oxygen conditions (or hypoxia). Our study shows that prior long-term exposure to low-oxygen conditions improves tolerance to low-oxygen in a freshwater fish. The results of our study aid our understanding of long-term responses of freshwater fish to low-oxygen to hypoxic events.
Effects of traffic noise exposure on corticosterone, glutathione and tonic immobility in chicks of a precocial bird
Authors: Flores Romina , Penna Mario , Wingfield John C , Cuevas Elfego , Vásquez Rodrigo A , Quirici Verónica 
Published: August 2019

AbstractRepeated exposure to traffic noise may be perceived as a succession of stressors, and therefore, noisy urban environments could lead to a state of chronic stress. In developing animals, glucocorticoids can have organizational effects on the hypothalamic–pituitary–adrenal axis in addition to the classic activation effects, so evaluating the effect of traffic noise during development is urgently needed. To our knowledge, to date six studies have investigated the effects of traffic noise on baseline corticosterone (CORT) and/or the stress response in birds during development; however, these studies were performed in nestling (altricial species), where confounding factors (e.g. communication between nestlings and parents) could mask the real impact of traffic noise on stress. In this study, we evaluated the effect of traffic noise (traffic noise group vs. rural noise group) on baseline levels of CORT and stress responses in chicks of a precocial bird species, the Japanese quail (Coturnix japonica). Because CORT can also decrease glutathione (GSH) levels (antioxidant and neurotransmitter/modulator), secondly by means of path analysis we investigated whether the strength of the association between CORT levels, GSH levels and tonic immobility (TI) varied in relation to treatment. We observed (i) similar baseline levels of CORT in both groups, (ii) a trend toward higher stress response in the traffic noise group (P = 0.08), (iii) similar TI duration in both groups, (iv) higher GSH levels in the traffic noise group and (v) differences in the strength and sign of the associations in relation to the treatment (traffic vs. rural). We conclude that the acoustic environment perceived during development has implications for physiology and behaviour; as more research is done on this topic, the need for sustainable urban planning will become clearer.
A Flattened Protagonist: Sleep and Environmental Mitigation in Lydia Millet’s How the Dead Dream
Authors: Bateman Benjamin 
Published: August 2019

AbstractThinking with contemporary American novelist Lydia Millet’s How the Dead Dream (2007), this essay explores sleep as a form of ecological relief and argues that the form of the novel can critically expose the limitations of a “set-aside” approach to environmental conservation. As the protagonist T. loses the ability to sequester personal losses, he pursues co-sleeping opportunities with critically endangered animals both in zoos and in the wild. Through his somnolent form, the novel imagines sustainable and rehabilitative alternatives to traditional character development.
RumimiR: a detailed microRNA database focused on ruminant species
Authors: Bourdon Céline , Bardou Philippe , Aujean Etienne , Le Guillou Sandrine , Tosser-Klopp Gwenola , Le Provost Fabienne 
Published: August 2019

Abstract
The ever-increasing use of next-generation sequencing technologies to explore the genome has generated large quantities of data in recent years. Numerous publications have described several thousand sequences of microRNAs, all species included. A new database (RumimiR) has been created from the literature to provide a detailed description of microRNAs for three ruminant species: cattle, goats and sheep. To date, 2887, 2733 and 5095 unique microRNAs from bovine, caprine and ovine species, respectively, are included. In addition to the most recent reference genomic position and sequence of each microRNA, this database contains details about the animals, tissue origins and experimental conditions mentioned in the publications. Identity to human or mouse microRNA is also indicated. The RumimiR database allows data filtering by selecting microRNAs on the basis of defined criteria such as animal status or tissue origin. For ruminant studies, RumimiR supplements the widely used miRBase database, by using complementary criteria to allow browsing and filtering, and integrates all newly described published sequences. The principal goal of this database is to provide easy access to all the ruminant microRNAs described in the literature.
KOFFI and Anabel 2.0—a new binding kinetics database and its integration in an open-source binding analysis software
Authors: Norval Leo William , Krämer Stefan Daniel , Gao Mingjie , Herz Tobias , Li Jianyu , Rath Christin , Wöhrle Johannes , Günther Stefan , Roth Günter 
Published: August 2019

Abstract
The kinetics of featured interactions (KOFFI) database is a novel tool and resource for binding kinetics data from biomolecular interactions. While binding kinetics data are abundant in literature, finding valuable information is a laborious task. We used text extraction methods to store binding rates (association, dissociation) as well as corresponding meta-information (e.g. methods, devices) in a novel database. To date, over 270 articles were manually curated and binding data on over 1705 interactions was collected and stored in the (KOFFI) database. Moreover, the KOFFI database application programming interface was implemented in Anabel (open-source software for the analysis of binding interactions), enabling users to directly compare their own binding data analyses with related experiments described in the database.
PopTargs: a database for studying population evolutionary genetics of human microRNA target sites
Authors: Hatlen Andrea , Helmy Mohab , Marco Antonio 
Published: August 2019

AbstractThere is an increasing interest in the study of polymorphic variants at gene regulatory motifs, including microRNA target sites. Understanding the effects of selective forces at specific microRNA target sites, together with other factors like expression levels or evolutionary conservation, requires the joint study of multiple datasets. We have compiled information from multiple sources and compared it with predicted microRNA target sites to build a comprehensive database for the study of microRNA targets in human populations. PopTargs is a web-based tool that allows the easy extraction of multiple datasets and the joint analyses of them, including allele frequencies, ancestral status, population differentiation statistics and site conservation. The user can also compare the allele frequency spectrum between two groups of target sites and conveniently produce plots. The database can be easily expanded as new data becomes available and the raw database as well as code for creating new custom-made databases is available for downloading. We also describe a few illustrative examples.