bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell-type-specific role for nucleus accumbens neuroligin-2 in depression and stress susceptibility
Authors: Heshmati Mitra , Aleyasin Hossein , Menard Caroline , Christoffel Daniel J. , Flanigan Meghan E. , Pfau Madeline L. , Hodes Georgia E. , Lepack Ashley E. , Bicks Lucy K. , Takahashi Aki , Chandra Ramesh , Turecki Gustavo , Lobo Mary Kay , Maze Ian , Golden Sam A. , Russo Scott J. 
Published: January 2018

Significance
Although mutations in the neuroligin-3 and neuroligin-4 genes are implicated in autism syndromes, very little is known about the contribution of neuroligin-2 to neuropsychiatric disease states. We report a decrease in neuroligin-2 gene expression in the postmortem nucleus accumbens (NAc) of depressed patients. Reverse translation of this finding in chronic social defeat stress, an animal model of depression that enables investigation of both susceptibility and resiliency mechanisms, uncovers an important functional role for NAc neuroligin-2 in stress susceptibility. We detail a cell-type-specific role for NAc neuroligin-2 in modulating social avoidance behavior and dominance behaviors important for resiliency. Together, these findings describe a role for NAc neuroligin-2 in depression and chronic stress behaviors.
Standards‐based reform to senior‐secondary curriculum and metacognition in the literacy domain
Authors: Fenwick Lisl 
Published: January 2018

ABSTRACTThis study analyses the intended and enacted curricula that are produced when metacognition is included as an element within standards‐based reforms for schooling. Reformers of the senior‐secondary curriculum for South Australia (SA) and the Northern Territory (NT) hoped to improve the academic outcomes of all students, and especially those from low‐SES and Indigenous backgrounds, by creating a curriculum that required year‐10 students to reflect on their capacities. Reflection on learning in the literacy domain was a particular emphasis during the reforms. A constructionist epistemology and case‐study methodology informed the approach taken in the study. Data collection and analysis involved accessing and analysing the intended curriculum, as well as the curriculum planning documentation designed by four teachers in one NT high school. The results indicate that learning opportunities to reflect on literacy capacities will not be created when the intended curriculum provides teachers, who are not literacy specialists, with little guidance about practices associated with metacognition and literacy.
Design and validation of a microfluidic device for blood–brain barrier monitoring and transport studies
Authors: Ugolini Giovanni Stefano , Occhetta Paola , Saccani Alessandra , Re Francesca , Krol Silke , Rasponi Marco , Redaelli Alberto 
Published: January 2018

Abstract

In vitro blood–brain barrier models are highly relevant for drug screening and drug development studies, due to the challenging task of understanding the transport mechanism of drug molecules through the blood–brain barrier towards the brain tissue. In this respect, microfluidics holds potential for providing microsystems that require low amounts of cells and reagent and can be potentially multiplexed for increasing the ease and throughput of the drug screening process. We here describe the design, development and validation of a microfluidic device for endothelial blood–brain barrier cell transport studies. The device comprises of two microstructured layers (top culture chamber and bottom collection chamber) sandwiching a porous membrane for the cell culture. Microstructured layers include two pairs of physical electrodes, embedded into the device layers by geometrically defined guiding channels with computationally optimized positions. These electrodes allow the use of commercial electrical measurement systems for monitoring trans-endothelial electrical resistance (TEER). We employed the designed device for performing preliminary assessment of endothelial barrier formation with murine brain endothelial cells (Br-bEnd5). Results demonstrate that cellular junctional complexes effectively form in the cultures (expression of VE-Cadherin and ZO-1) and that the TEER monitoring systems effectively detects an increase of resistance of the cultured cell layers indicative of tight junction formation. Finally, we validate the use of the described microsystem for drug transport studies demonstrating that Br-bEnd5 cells significantly hinder the transport of molecules (40 kDa and 4 kDa dextran) from the top culture chamber to the bottom collection chamber.
A novel recession rate physics methodology for space applications at CIRA by means of CIRCE radioactive beam tracers
Authors: De Cesare M , Di Leva A , Del Vecchio A , Gialanella L 
Published: January 2018

Abstract
Thermal protection systems (TPSs) of spacecrafts, either for single use or reusable, experience wear by ablation and erosion, due to the high heat fluxes during a re-entry phase in the atmosphere. The determination of the wear rate is a crucial point, which is presently mainly possible in aerospace on-ground measurements by means of invasive diagnostics. The purpose of this paper is to present novel contactless, online, high-sensitivity and non-intrusive diagnostics for wear measurements based on radioactive tracers. We propose the technique for future on-ground experiments that might later be developed to perform in-flight TPSs monitoring, thus significantly increasing the safety of the aerospace vehicles. The basic ideas of the method, its sensitivity investigated by GEANT4 simulations, and the future experimental validation are outlined.
Inferring and analyzing module-specific lncRNA–mRNA causal regulatory networks in human cancer
Authors: Zhang Junpeng , Le Thuc Duy , Liu Lin , Li Jiuyong 
Published: January 2018

Abstract
It is known that noncoding RNAs (ncRNAs) cover ∼98% of the transcriptome, but do not encode proteins. Among ncRNAs, long noncoding RNAs (lncRNAs) are a large and diverse class of RNA molecules, and are thought to be a gold mine of potential oncogenes, anti-oncogenes and new biomarkers. Although only a minority of lncRNAs is functionally characterized, it is clear that they are important regulators to modulate gene expression and involve in many biological functions. To reveal the functions and regulatory mechanisms of lncRNAs, it is vital to understand how lncRNAs regulate their target genes for implementing specific biological functions. In this article, we review the computational methods for inferring lncRNA–mRNA interactions and the third-party databases of storing lncRNA–mRNA regulatory relationships. We have found that the existing methods are based on statistical correlations between the gene expression levels of lncRNAs and mRNAs, and may not reveal gene regulatory relationships which are causal relationships. Moreover, these methods do not consider the modularity of lncRNA–mRNA regulatory networks, and thus, the networks identified are not module-specific. To address the above two issues, we propose a novel method, MSLCRN, to infer and analyze module-specific lncRNA–mRNA causal regulatory networks. We have applied it into glioblastoma multiforme, lung squamous cell carcinoma, ovarian cancer and prostate cancer, respectively. The experimental results show that MSLCRN, as an expression-based method, could be a useful complementary method to study lncRNA regulations.
Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements
Authors: Pinello Luca , Farouni Rick , Yuan Guo-Cheng 
Published: January 2018

Abstract

Motivation
With the increasing amount of genomic and epigenomic data in the public domain, a pressing challenge is to integrate these data to investigate the role of epigenetic mechanisms in regulating gene expression and maintenance of cell-identity. To this end, we have implemented a computational pipeline to systematically study epigenetic variability and uncover regulatory DNA sequences.

Results
Haystack is a bioinformatics pipeline to identify hotspots of epigenetic variability across different cell-types, cell-type specific cis-regulatory elements, and associated transcription factors. Haystack is generally applicable to any epigenetic mark and provides an important tool to investigate the mechanisms underlying epigenetic switches during development. This software is accompanied by a set of precomputed tracks, which may be used as a valuable resource for functional annotation of the human genome.

Availability and implementation
The Haystack pipeline is implemented as an open-source, multiplatform, Python package called haystack_bio freely available at https://github.com/pinellolab/haystack_bio.

Supplementary information
Supplementary data are available at Bioinformatics online.
Predicting plant biomass accumulation from image-derived parameters
Authors: Chen Dijun , Shi Rongli , Pape Jean-Michel , Neumann Kerstin , Arend Daniel , Graner Andreas , Chen Ming , Klukas Christian 
Published: January 2018

Abstract

Background
Image-based high-throughput phenotyping technologies have been rapidly developed in plant science recently, and they provide a great potential to gain more valuable information than traditionally destructive methods. Predicting plant biomass is regarded as a key purpose for plant breeders and ecologists. However, it is a great challenge to find a predictive biomass model across experiments.

Results
In the present study, we constructed 4 predictive models to examine the quantitative relationship between image-based features and plant biomass accumulation. Our methodology has been applied to 3 consecutive barley (Hordeum vulgare) experiments with control and stress treatments. The results proved that plant biomass can be accurately predicted from image-based parameters using a random forest model. The high prediction accuracy based on this model will contribute to relieving the phenotyping bottleneck in biomass measurement in breeding applications. The prediction performance is still relatively high across experiments under similar conditions. The relative contribution of individual features for predicting biomass was further quantified, revealing new insights into the phenotypic determinants of the plant biomass outcome. Furthermore, methods could also be used to determine the most important image-based features related to plant biomass accumulation, which would be promising for subsequent genetic mapping to uncover the genetic basis of biomass.

Conclusions
We have developed quantitative models to accurately predict plant biomass accumulation from image data. We anticipate that the analysis results will be useful to advance our views of the phenotypic determinants of plant biomass outcome, and the statistical methods can be broadly used for other plant species.
Variable Rates of Simple Satellite Gains across the Drosophila Phylogeny
Authors: Wei Kevin H -C , Lower Sarah E , Caldas Ian V , Sless Trevor J S , Barbash Daniel A , Clark Andrew G 
Published: January 2018

AbstractSimple satellites are tandemly repeating short DNA motifs that can span megabases in eukaryotic genomes. Because they can cause genomic instability through nonallelic homologous exchange, they are primarily found in the repressive heterochromatin near centromeres and telomeres where recombination is minimal, and on the Y chromosome, where they accumulate as the chromosome degenerates. Interestingly, the types and abundances of simple satellites often vary dramatically between closely related species, suggesting that they turn over rapidly. However, limited sampling has prevented detailed understanding of their evolutionary dynamics. Here, we characterize simple satellites from whole-genome sequences generated from males and females of nine Drosophila species, spanning 40 Ma of evolution. We show that PCR-free library preparation and postsequencing GC-correction better capture satellite quantities than conventional methods. We find that over half of the 207 simple satellites identified are species-specific, consistent with previous descriptions of their rapid evolution. Based on a maximum parsimony framework, we determined that most interspecific differences are due to lineage-specific gains. Simple satellites gained within a species are typically a single mutation away from abundant existing satellites, suggesting that they likely emerge from existing satellites, especially in the genomes of satellite-rich species. Interestingly, unlike most of the other lineages which experience various degrees of gains, the lineage leading up to the satellite-poor D. pseudoobscura and D. persimilis appears to be recalcitrant to gains, providing a counterpoint to the notion that simple satellites are universally rapidly evolving.
Smoking Status and Survival Among a National Cohort of Lung and Colorectal Cancer Patients
Authors: Japuntich Sandra J , Kumar Pallavi , Pendergast Jane F , Juarez Caballero Grelda Yazmin , Malin Jennifer L , Wallace Robert B , Chrischilles Elizabeth A , Keating Nancy L , Park Elyse R 
Published: January 2018

Abstract

Introduction
The purpose of this study was to explore the association of smoking status and clinically relevant duration of smoking cessation with long-term survival after lung cancer (LC) or colorectal cancer (CRC) diagnosis. We compared survival of patients with LC and CRC who were never-smokers, long-term, medium-term, and short-term quitters, and current smokers around diagnosis.

Methods
We studied 5575 patients in Cancer Care Outcomes Research and Surveillance (CanCORS), a national, prospective observational cohort study, who provided smoking status information approximately 5 months after LC or CRC diagnosis. Smoking status was categorized as: never-smoker, quit >5 years prior to diagnosis, quit between 1–5 years prior to diagnosis, quit less than 1 year before diagnosis, and current smoker. We examined the relationship between smoking status around diagnosis with mortality using Cox regression models.

Results
Among participants with LC, never-smokers had lower mortality risk compared with current smokers (HR 0.71, 95% CI 0.57 to 0.89). Among participants with CRC, never-smokers had a lower mortality risk as compared to current smokers (HR 0.79, 95% CI 0.64 to 0.99).

Conclusions
Among both LC and CRC patients, current smokers at diagnosis have higher mortality than never-smokers. This effect should be further studied in the context of tumor biology. However, smoking cessation around the time of diagnosis did not affect survival in this sample.

Implications
The results from our analysis of patients in the CanCORS consortium, a large, geographically diverse cohort, show that both LC and CRC patients who were actively smoking at diagnosis have worse survival as compared to never-smokers. While current smoking is detrimental to survival, cessation upon diagnosis may not mitigate this risk.
Caregiver-Provided Physical Therapy Home Programs for Children with Motor Delay: A Scoping Review
Authors: Gorgon Edward James R 
Published: January 2018

Abstract

Background
Caregiver-provided physical therapy home programs (PTHP) play an important role in enhancing motor outcomes in pediatric patient populations.

Purpose
This scoping review systematically mapped clinical trials of caregiver–provided PTHP that were aimed at enhancing motor outcomes in children who have or who are at risk for motor delay, with the purpose of (1) describing trial characteristics; (2) assessing methodologic quality; and (3) examining the reporting of caregiver-related components.

Data Sources
Physiotherapy Evidence Database (PEDro), Cochrane CENTRAL, PubMed, Scopus, ScienceDirect, ProQuest Central, CINAHL, LILACS, and OTseeker were searched up to July 31, 2017.

Study Selection
Two reviewers independently assessed study eligibility. Randomized or quasi-randomized controlled trials on PTHP administered by parents, other family members, friends, or informal caregivers to children who had or who were at risk for motor delay were included.

Data Extraction
Two reviewers independently appraised trial quality on the PEDro scale and extracted data.

Data Synthesis
Twenty-four articles representing 17 individual trials were identified. Populations and interventions investigated were heterogeneous. Most of the trials had important research design limitations and methodological issues that could limit usefulness in ascertaining the effectiveness of caregiver-provided PTHP. Few (4 of 17) trials indicated involvement of caregivers in the PTHP planning, assessed how the caregivers learned from the training or instructions provided, or carried out both.

Limitations
Included studies were heterogeneous, and unpublished data were excluded.

Conclusions
Although caregiver-provided PTHP are important in addressing motor outcomes in this population, there is a lack of evidence at the level of clinical trials to guide practice. More research is urgently needed to determine the effectiveness of care-giver-provided PTHP. Future studies should address the many important issues identified in this scoping review to improve the usefulness of the trial results.
The Relationship Between Socioeconomic Status (SES) and NCLEX-RN: Comparing SES Indicators in Mediated Logistic Regression
Authors: Meyers Timothy W. , Karpinski Aryn C. 
Published: January 2018

Abstract
The main purpose of this study was to examine the relationship between socioeconomic status (SES), ACT test scores, and the National Council Licensure Examination–Registered Nurse (NCLEX-RN) through a mediated logistic regression model. ACT is often considered one of the strongest predictors of success on the NCLEX-RN. Data from nursing students (N = 1,176) at a large, Midwestern university were analyzed. The goal was to determine if the predictive power of ACT on the NCLEX-RN stems from the influence of SES on ACT. A significant indirect effect through the causal chain of Pell Grant eligibility (i.e., SES)→ACT→NCLEX-RN was found.
Menopausal Hormone Therapy and Long-Term All-Cause and Cause-Specific Mortality: The Women’s Health Initiative Randomized Trials
Authors: Manson JoAnn E. , Aragaki Aaron K. , Rossouw Jacques E. , Anderson Garnet L. , Prentice Ross L. , LaCroix Andrea Z. , Chlebowski Rowan T. , Howard Barbara V. , Thomson Cynthia A. , Margolis Karen L. , Lewis Cora E. , Stefanick Marcia L. , Jackson Rebecca D. , Johnson Karen C. , Martin Lisa W. , Shumaker Sally A. , Espeland Mark A. , Wactawski-Wende Jean 
Published: January 2018

(Abstracted from JAMA 2017;318(10):927–938)
This study was a further investigation of the data accumulated in the hormone trials of the Women's Health Initiative (WHI). While the general results derived from the WHI hormone trials have been reported previously, this study focused on the long-term follow-up of the all-cause mortality rates.
Update on metal-induced occupational lung disease
Authors: Wyman Anne E. , Hines Stella E. 
Published: January 2018

Purpose of review
Occupational and environmental exposures to metals can result in multiple pulmonary conditions. This article will review recent epidemiologic and mechanistic studies that have enhanced our understanding of the association between particular lung diseases and exposure to specific metals.

Recent findings
Recent studies have broadened our understanding of the mechanisms of lung diseases such as CBD in established industries and drawn attention to conditions that may arise from exposure to metals such as indium in developing technologies. New diagnostic techniques such as elemental tissue analysis may help establish a diagnosis of metal-induced occupational lung disease. Electronic cigarette devices, environmental pollutants, and the growing use of nanoparticle-sized metals pose additional risks to workers and consumers.

Summary
Recognizing the risks of pulmonary disease in workers exposed to metals and performing a thorough occupational history and diagnostic work-up in patients with unexplained respiratory findings is necessary to promote understanding and prevention of metal-induced lung disease.
Associations Between Nurse-Guided Variables and Plasma Oxytocin Trajectories in Premature Infants During Initial Hospitalization
Authors: Weber Ashley , Harrison Tondi M. , Sinnott Loraine , Shoben Abigail , Steward Deborah 
Published: January 2018

Background:
Oxytocin (OT) is a social hormone that may help researchers understand how nurse-guided interventions during initial infant hospitalization, such as supporting human milk expression, promoting comforting touch, and reducing exposure to stressors, affect preterm brain development.

Purpose:
To determine whether factors related to human milk, touch, or stressor exposure are related to plasma OT trajectories in premature infants.

Methods:
Plasma from 33 premature infants, born gestational ages 25 to

JOURNAL/ancr/04.03/00149525-201802000-00014/14FSM1/v/2023-07-21T043926Z/r/image-gif

weeks, was collected at 14 days of life and then weekly until 34 weeks' corrected gestational age (CGA). Variables related to feeding volumes of human milk and formula; touch, as indexed by skin-to-skin contact (SSC) and swaddled holding; and clinical stressors were extracted from the electronic medical record. Linear mixed-models tested associations between nurse-guided variables and plasma OT trajectories.

Results:
In the final model, same-day SSC was positively related not only to plasma OT levels at 27 weeks' CGA (β= .938, P = .002) but also to a decline in plasma OT levels over time (β=−.177, P = .001). Volume of enteral feeds (mL/kg/d), its interaction with CGA, and number of stressful procedures were not statistically significant (β= .011, P = .077; β=−.002, P = .066; and β= .007, P = .062, respectively).

Implications for Practice:
Nurse-guided interventions are associated with infant plasma OT levels, suggesting nurses may impact the neurobiology of the developing premature infant.

Implications for Research:
Replication with larger sample sizes and randomized controlled trial designs is needed to test effects of specific nursing interventions on infant OT.