bluuebunny/crossref_metadata_2025_split huggingface dataset:
A model for trauma-informed primary care
Authors: Roberts Susan Jo , Chandler Genevieve E. , Kalmakis Karen 
Published: December 2018

ABSTRACT
Childhood trauma has been associated with negative health behaviors and conditions in adulthood. However, few primary care providers screen for trauma or alter their care to accommodate the multiple effects of trauma on patient health. The purposes of this article were to discuss the health consequences of childhood trauma and to offer a model for trauma-informed primary care (TIPC). The TIPC model provides a guide for primary care providers to screen for adverse childhood experiences and personalize the care of patients with a history of childhood trauma. The model, based on the trauma-informed care model used in mental health, has five components: (a) screening and trauma recognition, (b) understanding the health effects of trauma, (c) patient-centered communication and care, (d) emphasis on emotional safety and avoiding triggers, and (e) knowledge of helpful treatment for trauma patients. The TIPC model offers a theoretical underpinning for improving the care, health care experiences, and health outcomes for patients with a history of childhood trauma.
Analysis of nurse practitioner scope of practice in Taiwan using the Longest policy cycle model
Authors: Tsay Shiow-Luan , Tsay Shwu-Feng , Ke Chia-Yen , Chen Ching-Mei , Tung Heng-Hsin 
Published: December 2018

ABSTRACT

Background and purpose:
To date, there has been no policy analysis or review of the effectiveness of the current nurse practitioner (NP) scope of practice regulations in Taiwan. The purpose is of this article was to provide a policy analysis of NP scope of practice regulations in Taiwan.

Methods:
The Longest policy cycle model was used to analyze the NP scope of practice regulations. Policy formation, policy implementation, and policy modification are three steps in this model. Policy formation and policy implementation are described in the first two sections. Regarding policy modification, we used the data collected from a research grant to evaluate the implementation of the NP scope of practice regulations to present the effectiveness of the policy endorsement in Taiwan.

Conclusions:
The impact of health care services provided by NPs was positive from the viewpoint of the hospital. The top-ranking impact was reducing physicians' workload and increasing the effectiveness of communication and coordination among the team.

Implications for practice:
The economic value of advanced practice nurses needs to be identified, as it can result in optimal professional growth. The Taiwan Association of Nurse Practitioners can design the metrics to measure NPs' contribution and to analyze the financial benefits bestowed by the NP profession based on the study results.
Morbidity and mortality after transjugular intrahepatic portosystemic shunt placement in patients with cirrhosis
Authors: Dissegna Denis , Sponza Massimo , Falleti Edmondo , Fabris Carlo , Vit Alessandro , Angeli Paolo , Piano Salvatore , Cussigh Annarosa , Cmet Sara , Toniutto Pierluigi 
Published: December 2018

Objectives
Transjugular intrahepatic portosystemic shunt (TIPS) is adopted to treat refractory complications of portal hypertension, such as variceal bleeding and ascites. This study aimed to assess predictors of hepatic encephalopathy (HE) development and cumulative transplant-free survival after TIPS placement in patients with cirrhosis complicated by refractory ascites and major gastroesophageal bleeding.

Materials and methods
Sixty-three cirrhotic patients who underwent TIPS positioning as a secondary prophylaxis of major upper gastroesophageal bleeding (N=30) or to control refractory ascites (N=33) were enrolled.

Results
After a median follow-up of 26 months following TIPS insertion, only 1/30 (3.3%) patients developed reoccurrence of bleeding. Complete control of refractory ascites was recorded in 19/23 (82.6%) patients. Within the first month after TIPS placement, 34/63 (53.9%) patients developed clinically significant HE, which was associated with the baseline presence of type 2 hepatorenal syndrome (P=0.022). At the end of 90 months of follow-up, 35 (55.6%) patients were alive, 12 (19.0%) patients underwent liver transplantation, and 16 (25.4%) patients died. Independent predictors of transplant-free survival were a model for end-stage liver disease score up to 15 (P<0.001), the absence of a history of spontaneous bacterial peritonitis (P=0.010) pre-TIPS, and no HE within 1 month post-TIPS (P=0.040).

Conclusion
TIPS insertion can be considered a safe and effective treatment in patients with cirrhosis and severe complications of portal hypertension that are not manageable with standard treatments. Interestingly, if confirmed in future studies, the history of spontaneous bacterial peritonitis pre-TIPS could be added to the model for end-stage liver disease score as a strong baseline predictor of post-TIPS mortality.
Subtle Motor Signs in Children With Chronic Traumatic Brain Injury
Authors: Crasta Jewel E. , Sibel Jamie , Slomine Beth S. , Mahone E. Mark , Mostofsky Stewart H. , Suskauer Stacy J. 
Published: December 2018

ObjectiveThe aim of the study was to characterize subtle motor signs in children with moderate-severe traumatic brain injury in the chronic phase of injury.DesignFourteen children with moderate (n= 6) or severe (n= 8) traumatic brain injury, ages 11–18 yrs, who had sustained their injury at least 1-yr before study participation (range 1–14 yrs since injury), and 14 matched typically developing controls were examined using the Physical and Neurological Examination of Subtle Signs (PANESS). To examine the neural correlates of subtle motor signs, measures of total cerebral volume and motor/premotor volume were derived from magnetic resonance imaging.ResultsChildren with traumatic brain injury had significantly poorer PANESS performance than controls on the total timed subscore, proximal overflow, and the PANESS total score. Participants with severe traumatic brain injury had greater proximal overflow than those with moderate injury, after controlling for age at injury. Across all participants, greater proximal overflow correlated with reduced total cerebral volume, whereas within the traumatic brain injury group, reduced motor/premotor volume correlated with lower PANESS total score.ConclusionsThe study highlights the importance of examining subtle motor signs including overflow during clinical evaluation of chronic pediatric traumatic brain injury and establishes the clinical utility of the PANESS as a measure sensitive to chronic subtle motor signs in this population.To Claim CME CreditsComplete the self-assessment activity and evaluation online at http://www.physiatry.org/JournalCMECME ObjectivesUpon completion of this article, the reader should be able to: (1) Define subtle motor signs including motor overflow; (2) Identify subtle motor signs such as motor overflow during clinical evaluation of children with brain injury; and (3) Explain the relevance of examining subtle motor signs in chronic pediatric brain injury during clinical evaluations.LevelAdvanced.AccreditationThe Association of Academic Physiatrists is accredited by the Accreditation Council for Continuing Medical Education to provide continuing medical education for physicians.The Association of Academic Physiatrists designates this Journal-based CME activity for a maximum of1.0 AMA PRA Category 1 Credit(s)™. Physicians should only claim credit commensurate with the extent of their participation in the activity.
Single Suture Synostosis and Isolated Cleft Palate in Non-Apert Syndrome Patients
Authors: Pezas Theodore , Slator Rona , White Nicholas , Lloyd Mark 
Published: December 2018

Introduction:
Single suture craniosynostosis (SSC) and isolated cleft palate (ICP) in non-Apert syndrome patients rarely occur together. Management includes airway optimization, timing surgery appropriately, and assessing both cranial vault aesthetics and speech outcomes. The aim of this study was to compare treatment pathways and outcomes in patients with both conditions to standard treatment for these conditions in isolation.

Methods:
Patient hospital medical records were retrospectively reviewed for demographic data, timing of surgery, aesthetic outcome (using the Whitaker grading system for head shape), and speech outcome (from speech therapy records of general development and speech assessment).

Results:
Six patients with SSC and ICP were identified over an 18-year period. Cranial surgery was performed between 4 and 16 months and cleft surgery between 6 and 34 months of age in all cases. Documentation of cleft surgery and genetic testing was not available for 1 patient. One patient with hemi-palatal absence had an obturator inserted at 34 months. Two patients were found to have Fragile X and Emanuel syndrome, respectively.
No increased perioperative airway risk was highlighted in any case. Four cases were designated Whitaker grade 1, 1 case was designated grade 2, and 1 case was not graded as no cranial surgery was performed. Half of the patients had general and speech developmental delay, while the other half demonstrated no signs of developmental delay.

Discussion/Conclusion:
Examination of 6 patients with SSC and ICP suggests the presence of both conditions does not adversely impact management or outcome for each condition, or increase perioperative risk.
Eye Tracking as a Proxy for Perceptual Evaluation of Repaired Cleft Lip
Authors: Warne Christopher N. , Hallac Rami R. , Kane Alex A. , Derderian Christopher A. , Seaward James R. 
Published: December 2018

Abstract
Human interactions begin with near-instantaneous visual evaluation of the face, modifying emotional responses and social behavior toward the person. Eye-tracking technology can provide a potential window into how humans undertake this evaluation, and the threshold of whether a face containing a craniofacial difference is perceived as “normal.” This study's main questions were whether gaze patterns differ from normal when evaluating children with craniofacial differences, and whether these gaze patterns vary with different levels of craniofacial deformity. Two experiments tested the feasibility of using eye tracking to study facial evaluation and whether there was a difference in the gaze pattern and characteristics, correlating with the Asher McDade Aesthetic Index. Fifty-three participants’ eye movements were recorded as they gazed at photographs of children either with hemifacial microsomia or repaired cleft lip, with repaired cleft lip digitally corrected to symmetry, or with no craniofacial disorder. Recruitment and participation for this study occurred in a pediatric plastic surgery clinic and in a medical school student center. Participants gazed longer on the lip in the cleft-lip photographs compared with control photographs in the first experiment (207 ms; SD 75 versus 145 ms; SD 61, respectively; P = 0.04). This gaze bias was confirmed in the second experiment and found to correlate with severity (r = 0.042). Gaze patterns differ when individuals look at photographs with or without craniofacial differences. The degree to which these eye movement patterns differ correlates with the severity of craniofacial deformity.
Brain-behaviour modes of covariation in healthy and clinically depressed young people
Authors: Mihalik Agoston , Ferreira Fabio S. , Rosa Maria J. , Moutoussis Michael , Ziegler Gabriel , Monteiro Joao M. , Portugal Liana , Adams Rick A. , Romero-Garcia Rafael , Vértes Petra E. , Kitzbichler Manfred G. , Váša František , Vaghi Matilde M. , Bullmore Edward T. , Fonagy Peter , Goodyer Ian M. , Jones Peter B. ,   NSPN Consortium, Dolan Raymond , Mourao-Miranda Janaina 
Published: December 2018

AbstractUnderstanding how variations in dimensions of psychometrics, IQ and demographics relate to changes in brain connectivity during the critical developmental period of adolescence and early adulthood is a major challenge. This has particular relevance for mental health disorders where a failure to understand these links might hinder the development of better diagnostic approaches and therapeutics. Here, we investigated this question in 306 adolescents and young adults (14-24y, 25 clinically depressed) using a multivariate statistical framework, based on canonical correlation analysis (CCA). By linking individual functional brain connectivity profiles to self-report questionnaires, IQ and demographic data we identified two distinct modes of covariation. The first mode mapped onto an externalization/internalization axis and showed a strong association with sex. The second mode mapped onto a well-being/distress axis independent of sex. Interestingly, both modes showed an association with age. Crucially, the changes in functional brain connectivity associated with changes in these phenotypes showed marked developmental effects. The findings point to a role for the default mode, frontoparietal and limbic networks in psychopathology and depression.
MAGIC: A tool for predicting transcription factors and cofactors binding sites in gene sets using ENCODE data
Authors: Roopra A 
Published: December 2018

ABSTRACTTranscriptomic profiling is an immensly powerful hypothesis generating tool. Whether one is comparing an experimental versus control condition or collecting transcriptomes from cohorts of disease tissue, it is often necessary to determine which transcription factors (TFs) and cofactors drive programs of gene expression in the datasets. Most available tools rely on searching for TF binding motifs near promoters of genes in a gene set. This approach can work well for TFs with extended recognition elements but is less useful for shorter elements and does not work at all for cofactors. The Encyclopedia Of DNA Elements (ENCODE) archives ChIPseq tracks of 169 TFs and cofactors assayed in 91 cells lines. The algorithm presented herein, Multiple Aligned Genomic Integration of ChIP (MAGIC), uses ENCODE ChIPseq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene sets. When compared to a commonly used web resource o-Possum, MAGIC was able to more accurately predict TFs and cofactors that drive gene changes in 3 settings: 1) A cell line expressing or lacking REST, 2) Breast tumors divided along PAM50 designations and 3) Whole brain samples from WT mice or mice lacking CTCF in a particular neuronal subtype. In summary, MAGIC is a standalone application that runs on OSX machines and has a simple interface that produces meaningful predictions of which TFs and cofactors are enriched in a gene set.
Integrated genetic and methylomic analyses identify shared biology between autism and autistic traits
Authors: Massrali Aicha , Brunel Helena , Hannon Eilis , Wong Chloe ,   iPSYCH-MINERvA Epigenetics Group, Baron-Cohen Simon , Warrier Varun 
Published: December 2018

AbstractPrevious studies have identified differences in DNA methylation in autistic individuals compared to neurotypical individuals. Yet, it is unclear if this extends to autistic traits – subclinical manifestation of autism features in the general population. Here, we investigate the association between DNA methylation at birth (cord blood), and scores on the Social and Communication Disorders Checklist (SCDC), a measure of autistic traits, in 701 8-year olds, by conducting a methylome-wide association study (MWAS) using DNA methylation data from cord-blood. Whilst did not identify significant loci demonstrating differential methylation, we observe a degree of overlap between the SCDC MWAS and post-mortem brain methylation signature in autism. Validating this, we observe an enrichment for genes that are dysregulated in the post-mortem autism brain. Finally, integrating genome-wide data from more than 40,000 individuals and mQTL maps from cord-blood, we demonstrate that mQTLs of CpGs associated with SCDC scores at different P-value thresholds are significantly shifted towards lower P-values in a GWAS for autism. We validate this using a GWAS of SCDC, and demonstrate a lack of enrichment in a GWAS of Alzheimer’s disease. Our results highlight the shared cross-tissue epigenetic architecture of autism and autistic traits, and demonstrate that mQTLs associated with methylation changes in childhood autistic traits are enriched for common genetic variants associated with autism and autistic traits.
Clostridioides difficileLuxS mediates inter-bacterial interactions within biofilms
Authors: Slater Ross , Frost Lucy , Jossi Sian , Millard Andrew , Unnikrishnan Meera 
Published: December 2018

AbstractThe anaerobic gut pathogen,Clostridioides difficile, forms adherent biofilms that may play an important role in recurrentC. difficileinfections. The mechanisms underlyingC. difficilecommunity formation and inter-bacterial interactions are nevertheless poorly understood.C. difficileproduces AI-2, a quorum sensing molecule that modulates biofilm formation across many bacterial species. We found that a strain defective in LuxS, the enzyme that mediates AI-2 production, is defective in biofilm developmentin vitro. Transcriptomic analyses of biofilms formed by wild type (WT) andluxSmutant (luxS) strains revealed a downregulation of prophage loci in theluxSmutant biofilms compared to the WT. Detection of phages and eDNA within biofilms may suggest that DNA release by phage-mediated cell lysis contributes toC. difficilebiofilm formation. In order to understand if LuxS mediatesC. difficilecrosstalk with other gut species,C. difficileinteractions with a common gut bacterium,Bacteroides fragilis, were studied. We demonstrate thatC. difficilegrowth is significantly reduced when co-cultured withB. fragilisin mixed biofilms. Interestingly, the absence ofC. difficileLuxS alleviates theB. fragilismediated growth inhibition. Dual species RNA-sequencing analyses from single and mixed biofilms revealed differential modulation of distinct metabolic pathways forC. difficileWT,luxSandB. fragilisupon co-culture, indicating that AI-2 may be involved in induction of selective metabolic responses inB. fragilis. Overall, our data suggest thatC. difficileLuxS/AI-2 utilises different mechanisms to mediate formation of single and mixed species communities.
Genome sequence ofPseudomonas aeruginosaPAO1161, a PAO1 derivative with the ICEFP2 integrative and conjugative element
Authors: Kawalek Adam , Kotecka Karolina , Modrzejewska Magdalena , Jagura-Burdzy Grazyna , Bartosik Aneta Agnieszka 
Published: December 2018

ABSTRACTPseudomonas aeruginosais a common cause of nosocomial infections, especially in patients with cystic fibrosis and burn wounds. An attenuated PAO1 strain and its derivatives are widely used to study the biology of this bacterium, however recent studies indicated an ongoing evolution of the laboratory strains, highlighted by changes in the genomes of PAO1 sublines and derivatives used in different laboratories worldwide.Here we have sequenced the genome ofPseudomonas aeruginosaPAO1161 strain, aleu-, RifR, restriction-modification defective PAO1 derivative. This strain is described as the host of IncP-8 plasmid FP2, conferring the resistance to mercury and used in the past for preparation of genetic map of theP. aeruginosachromosome. Comparison of PAO1161 genome sequence with PAO1-UW reference genome revealed an inversion of the large genome segment betweenrrnAandrrnBrRNA operons and more than 100 nucleotide polymorphisms and short insertions-deletions, many of which were also found within the recently re-sequenced PAO1 sublines. The PAO1161 specific sequence variants include E108K mutation in PA3792 (leuA), which we showed is responsible for leucine auxotrophy, H531L in PA4270 (rpoB), likely conferring rifampicin resistance, as well as nonsense mutations in PA2735 encoding a DNA methyltransferase as well as a putative OLD family endonuclease PA1939. Additionally, PAO1161 genome poses a 12 kb RPG42 prophage and a 108 kbp insertion within tRNA-Lys, encompassing a putative mercury resistance and showing similarity to PAPI-1 like integrative conjugative elements (ICE). Our data indicate that the ICE can excise from the bacterial chromosome and can be transferred toPseudomonas putidacells where it integrates in the genome at three specific sites and confers the cells with mercury resistance. Overall this data provide insight into the genome variation betweenP. aeruginosalaboratory strains. Moreover, this data indicate that the FP2 element for years described as a IncP-8 plasmid is an integrative conjugative element.
Uncultured marine cyanophages encode for active NblA, phycobilisome proteolysis adaptor protein
Authors: Nadel Omer , Rozenberg Andrey , Flores-Uribe José , Larom Shirley , Schwarz Rakefet , Béjà Oded 
Published: December 2018

SummaryPhycobilisomes (PBS) are large water-soluble membrane-associated complexes in cyanobacteria and some chloroplasts that serve as a light-harvesting antennas for the photosynthetic apparatus. When short of nitrogen or sulfur, cyanobacteria readily degrade their phycobilisomes allowing the cell to replenish the vanishing nutrients. The key regulator in the degradation process is NblA, a small protein (~6 kDa) which recruits proteases to the PBS. It was discovered previously that not only do cyanobacteria possessnblAgenes but also that they are encoded by genomes of some freshwater cyanophages. A recent study, using assemblies from oceanic metagenomes, revealed genomes of a novel uncultured marine cyanophage lineage which contain genes coding for the PBS degradation protein. Here, we examine the functionality ofnblA-like genes from these marine cyanophages by testing them in a freshwater model cyanobacterialnblAknockout. One of the viral NblA variants could complement the non-bleaching phenotype and restore PBS degradation. Our findings reveal a functional NblA from a novel marine cyanophage lineage. Furthermore, we shed new light on the distribution ofnblAgenes in cyanobacteria and cyanophages.Originality-Significance StatementThis is the first study to examine the distribution and function ofnblAgenes of marine cyanophage origin. We describe as well the distribution ofnblA-like genes in marine cyanobacteria using bioinformatic methods.
Broken symmetry in the human BK channel
Authors: Tonggu Lige , Wang Liguo 
Published: December 2018

ABSTRACTVoltage-gated and ligand-modulated ion channels play critical roles in excitable cells. To understand the interplay among voltage-sensing, ligand-binding and channel opening, the structures of ion channels in various functional states need to be determined. Here, the “random spherically constrained” (RSC) single-particle cryo-EM method was employed to study the human large conductance voltage- and calcium-activated potassium (hBK or hSlo1) channels reconstituted into liposomes. The hBK structure has been determined at 3.5 Å resolution in the absence of Ca2+. Instead of the common four-fold symmetry observed in ligand-modulated ion channels, a two-fold symmetry was observed in hBK. Two opposing subunits in the Ca2+ sensing gating ring rotate around the center of each subunit, which results in the movement of the assembly and flexible interfaces and Ca2+ binding sites. Despite the significant movement, the local conformation of the assembly interfaces and Ca2+ binding sites remains the same among the four subunits.