bluuebunny/crossref_metadata_2025_split huggingface dataset:
cpPredictor: a web server for template-based prediction of RNA secondary structure
Authors: Jelínek Jan , Pánek Josef 
Published: August 2018

Abstract

Summary
We present the cpPredictor webserver that implements a novel template-based method for prediction of secondary structure of RNA. The method outperforms available prediction methods as it uses RNA structures of related molecules, either predicted or experimentally identified, as structural templates. The server aims at three major tasks: i) prediction of RNA secondary structures that are difficult to predict by available methods, ii) characterization of uncharacterized RNAs as compatible or incompatible with a chosen template structure and iii) an identification of the most relevant structure among different candidate structures of a single RNA ambiguously predicted by available methods. The web server is accompanied with a comprehensive documentation.

Availability and implementation
The web server is freely available at http://cppredictor.elixir-czech.cz/. The source code of the cpPredictor algorithm is freely available from the webserver under the Apache License, Version 2.0.
Prevalence of problem drinking and associated factors in a representative German sample of adolescents and young adults
Authors: Wartberg L , Kriston L , Thomasius R 
Published: August 2018

Abstract

Background
Alcohol use in youth is regarded as an important public health concern and in a recent survey in 35 European countries, every third student reported heavy episodic drinking. While prevalence estimates for problem drinking in adults from representative population samples are available, corresponding numbers for adolescents in Germany are currently lacking.

Methods
A representative sample of 1531 12–25 years old in Germany was investigated with a standardized questionnaire concerning problem drinking (assessed with the AUDIT-C) and psychosocial aspects (anxiety with the GAD-2, depressive symptoms with the PHQ-2 and smoking behavior). Due to missing values, we could calculate prevalence estimates, chi-square tests and logistic regression analyses for 1490 cases.

Results
The 1-year prevalence of problem drinking in 12–25 years old in Germany was 18.2%. Overall, 5.0% of the adolescents (aged 12–17 years) and 27.7% of the young adults (aged 18–25 years) reported problem drinking in the last year. Young adult males more often showed problem drinking than females, while no gender differences in adolescents were observed. Problem drinking was associated with male gender, higher age, smoking behavior and depressive symptoms.

Conclusions
According to the study findings, problem drinking is widespread in 12–25 years old in Germany.
Do Overweight Adolescent Idiopathic Scoliosis (AIS) Patients Have an Increased Perioperative Risk for Posterior Spinal Fusion (PSF) Surgery?
Authors: Chan Chris Yin Wei , Mohamad Siti Mariam , Tan Shun Herng , Loh Ling Hui , Lim Jun Ni , Chiu Chee Kidd , Hasan Mohd Shahnaz , Kwan Mun Keong 
Published: August 2018

Study Design.
A retrospective study.

Objective.
The aim of this study was to compare the perioperative outcome of posterior spinal fusion (PSF) between overweight (OW) adolescent idiopathic scoliosis (AIS) patients and the healthy-weight (HW) patients using propensity score matching analysis.

Summary of Background Data.
Obesity was found to increase postoperative surgical complications compared with the nonobese group. In scoliosis correction surgery, association of OW and perioperative risks had been explored, but most studies were retrospective in nature.

Methods.
From 374 patients, two comparable groups were matched using propensity score matching analysis with one-to-one nearest neighbor matching and a caliper of 0.2. There were 46 HW and OW patients in each group. The main outcome measures were intraoperative blood loss, use of allogeneic blood transfusion, operative time, duration of hospital stay post-surgery, total patient-controlled analgesia (PCA) morphine usage, perioperative complications, side bending flexibility (SBF), and correction rate (%).

Results.
The mean age was 13.3 ± 1.7 and 13.2 ± 1.7 years for HW and OW groups, respectively. The majority of the patients were Lenke 1 curves; 32.6% (HW) and 26.1% (OW) with an average Cobb angle of 69.0 ± 19.1° and 68.8 ± 18.4° for each group, respectively. The two groups were comparable. The operation time was 145.2 ± 42.2 and 154.4 ± 48.3 minutes for HW and OW groups, respectively (P > 0.05). The intraoperative blood loss was almost similar in both groups; 955.1 ± 497.7 mL (HW group) and 1011.8 ± 552.7 mL (OW group) (P > 0.05). Total PCA morphine used was higher in OW group (30.4 ± 22.7 mg) than in the HW group (16.2 ± 11.3 mg). No complication was observed in HW group, while in OW group, one patient (2.2%) developed intraoperative seizure.

Conclusion.
OW AIS patients (≥85th percentile) had similar mean operative time, intraoperative blood loss, allogeneic transfusion rate, length of stay, and perioperative complications compared with HW AIS patients.

Level of Evidence: 3
The use of technology in the sexual health education especially among minority adolescent girls in the United States
Authors: Brayboy Lynae M. , McCoy Katryna , Thamotharan Sneha , Zhu Emily , Gil Gabriela , Houck Christopher 
Published: August 2018

Purpose of review
The purpose of this review is to examine current sexual health education technologies for adolescents and identify gaps in knowledge. Disparities in sexual health education are prominent and mainly affect young women of color. As a result, the use of technology to reach these marginalized populations could potentially invoke change. Thus, it is crucial to determine the viability of technology as a mechanism to bridge the knowledge gap regarding sexual health for adolescents that are most at risk of sexually transmitted infections and unwanted pregnancies.

Recent findings
With a lack of standardized, evidenced-based sexual health education programs in the United States, the future of comprehensive sexual health education is moving toward smartphone apps. Many sexual health technologies exist that target adolescents, most of which have been proven to demonstrate positive effects. Use of mobile apps, especially for vulnerable populations, can be more effective because of privacy and widespread dissemination.

Summary
Ultimately, more research needs to be conducted to determine the most effective content for these sexual health apps. Additionally, more research should be conducted on effective sexual health apps for marginalized populations to determine whether technology is a viable solution.
Pneumococcal Colonization and the Nasopharyngeal Microbiota of Children in Botswana
Authors: Kelly Matthew S. , Surette Michael G. , Smieja Marek , Rossi Laura , Luinstra Kathy , Steenhoff Andrew P. , Goldfarb David M. , Pernica Jeffrey M. , Arscott-Mills Tonya , Boiditswe Sefelani , Mazhani Tiny , Rawls John F. , Cunningham Coleen K. , Shah Samir S. , Feemster Kristen A. , Seed Patrick C. 
Published: August 2018

Background:
Nasopharyngeal colonization precedes infections caused by Streptococcus pneumoniae. A more detailed understanding of interactions between S. pneumoniae and the nasopharyngeal microbiota of children could inform strategies to prevent pneumococcal infections.

Methods:
We collected nasopharyngeal swabs from children 1 to 23 months of age in Botswana between August 2012 and June 2016. We tested samples for S. pneumoniae and common respiratory viruses using polymerase chain reaction. We sequenced the V3 region of the bacterial 16S ribosomal RNA gene and used random forest models to identify clinical variables and bacterial genera that were associated with pneumococcal colonization.

Results:
Mean age of the 170 children included in this study was 8.3 months. Ninety-six (56%) children were colonized with S. pneumoniae. Pneumococcal colonization was associated with older age (P = 0.0001), a lack of electricity in the home (P = 0.02) and household use of wood as a cooking fuel (P = 0.002). Upper respiratory symptoms were more frequent in children with S. pneumoniae colonization (60% vs. 32%; P = 0.001). Adjusting for age, nasopharyngeal microbiota composition differed in colonized and noncolonized children (P = 0.001). S. pneumoniae colonization was associated with a higher relative abundance of Moraxella (P = 0.001) and lower relative abundances of Corynebacterium (P = 0.001) and Staphylococcus (P = 0.03). A decision tree model containing the relative abundances of bacterial genera had 81% sensitivity and 85% specificity for the determination of S. pneumoniae colonization status.

Conclusions:

S. pneumoniae colonization is associated with characteristic alterations of the nasopharyngeal microbiota of children. Prospective studies should determine if nasopharyngeal microbial composition alters the risk of pneumococcal colonization and thus could be modified as a novel pneumonia prevention strategy.
Randomized Trial of Tablet Computers for Education and Learning in Children and Young People with Low Vision
Authors: Gothwal Vijaya K. , Thomas Rachel , Crossland Michael , Bharani Seelam , Sharma Sujata , Unwin Hilary , Xing Wen , Khabra Komel , Dahlmann-Noor Annegret 
Published: August 2018

SIGNIFICANCE
Mobile devices such as tablet computers have become widely available as mainstream devices and are also used in some schools, but there is an absence of robust information regarding the efficacy of any optical/electronic low vision device or tablet computer in supporting education of young people with low vision.

PURPOSE
A randomized controlled trial (RCT) is needed to measure the impact of tablet computers on education, specifically on independent access to educational material, in children and young people with low vision. We conducted a pilot RCT to determine the feasibility of conducting a full-scale trial.

METHODS
This was a randomized multicenter pilot trial across two sites in the United Kingdom and one site in India. Forty children and young people aged 10 to 18 years with low vision (best-corrected visual acuity for distance between <20/60 [0.48 logMAR] and 20/400 [1.30 logMAR] in the better eye) in the United Kingdom (n = 20) and India (n = 20) were randomized to two parallel arms, with a 1:1 allocation ratio, to control (n = 20) or intervention (n = 20). Control group participants received standard low vision care. The intervention group received a tablet computer (iPad) with low vision applications and instruction in its use, including accessibility features. Four primary outcomes included (1) 6-month recruitment rate, (2) retention of participants for 3 months, (3) acceptance/usage of device, and (4) accessibility of device.

RESULTS
Nineteen participants (95%) enrolled within 6 months in the United Kingdom, and 20 participants (100%), in India. Retention at 3 months was 85% (n = 17) in the United Kingdom and 95% (n = 19) in India. More than one half of participants reported using a tablet computer at school at least once every day. The majority (90%) found it easily accessible.

CONCLUSIONS
This study demonstrated that it is feasible to recruit children and young people with low vision into an international multicenter RCT of electronic assistive technology. Regardless of geographical location, children and young people with low vision reported using tablet computers at least once a day at school and accessed them easily.
Pan-Costochondritis Caused by Aspergillus Diagnosed by 18F-FDG PET/CT
Authors: Oliván-Sasot Patricia , Martínez-Sanchis Begoña , Sánchez-Vañó Raquel , Yepes-Agudelo Ana María , Bello-Arques Pilar 
Published: August 2018

Abstract
Thoracic pain is an entity that can be difficult to diagnose etiologically. Once the cardiac origin has been ruled out, the rheumatologic, neoplastic, and infectious causes have to be taken into account. We present the case of a patient with atypical chest pain after triple-bypass surgery in whom 18F-FDG PET/CT scan showed an important uptake of the radiopharmaceutical in costal cartilages, in relation to pan-costochondritis due to Aspergillus.
Central Nervous System Myelomatosis Delineated by High-Resolution Brain Images From Fully Digital 18F-FDG PET
Authors: Bahloul Achraf , Perrin Mathieu , Amlal Samir , Marie Pierre-Yves , Verger Antoine 
Published: August 2018

AbstractCentral nervous system myelomatosis is uncommon and is associated with a particularly poor prognosis. PET images, from a 53-year-old man referred to a fully digital18F-FDG PET for relapsed multiple myeloma, revealed high18F-FDG uptakes located in the cortex and sulci of the right central area and within the meningeal envelopes of the cerebellum, the trigeminal nerves, and on the spinal canal. These particular uptakes gave evidence of a central nervous system myelomatosis subsequently confirmed by plasma cells documented in cerebrospinal fluid. Such interesting images could be obtained owing to the potential of high-resolution images provided by fully digital18F-FDG PET.
TreeBASEdmp: A Toolkit for Phyloinformatic Research
Authors: Piel William H. , Vos Rutger A. 
Published: August 2018

AbstractOver the last 20 years, TreeBASE has acquired a substantial body of phylogenetic data, including more than 20,000 published phylogenies. Given latency issues and limited options when it comes to querying the database remotely, a simplified and consolidated version of the database, here called TreeBASEdmp, is made available for download, allowing biologists to design custom analyses of the data on their local computers. The database is indexed to support searching for phylogenetic topologies using nested sets and closure tables. Here we propose a new approach to find broadly-defined phylogenetic patterns, a method we callGeneric Topological Querying, which allows the user to find hypotheses of relationship without being constrained to use particular sets of specific taxa. Additionally, we normalize as many leaf nodes as possible to an equivalent species rank identifier to assist in supertree synthesis. Our example script rapidly assembles sets of trees and generates a matrix representation of them for subsequent supertree generation.
Prediction of Choice From Competing Mechanosensory and Choice-Memory Cues During Active Tactile Decision Making
Authors: Dario Campagner , Mathew Evans H , Katarina Chlebikova , Andrea Colins-Rodriguez , Michaela Loft S E , Sarah Fox , David Pettifer , Mark Humphries D , Karel Svoboda , Rasmus Petersen S 
Published: August 2018

ABSTRACTPerceptual decision making is an active process where animals move their sense organs to extract task-relevant information. To investigate how the brain translates sensory input into decisions during active sensation, we developed a mouse active touch task where the mechanosensory input can be precisely measured and that challenges animals to use multiple mechanosensory cues. Mice were trained to localise a pole using a single whisker and to report their decision by selecting one of three choices. Using high-speed imaging and machine vision we estimated whisker-object mechanical forces at millisecond resolution. Mice solved the task by a sensory-motor strategy where both the strength and direction of whisker bending were informative cues to pole location. We found competing influences of immediate sensory input and choice memory on mouse choice. On correct trials, choice could be predicted from the direction and strength of whisker bending, but not from previous choice. In contrast, on error trials, choice could be predicted from previous choice but not from whisker bending. This study shows that animal choices during active tactile decision making can be predicted from mechanosenory and choice-memory signals; and provides a new task, well-suited for future study of the neural basis of active perceptual decisions.SIGNIFICANCE STATEMENTDue to the difficulty of measuring the sensory input to moving sense organs, active perceptual decision making remains poorly understood. The whisker system provides a way forward since it is now possible to measure the mechanical forces due to whisker-object contact during behaviour. Here we train mice in a novel behavioural task that challenges them to use rich mechanosensory cues, but can be performed using one whisker and enables task-relevant mechanical forces to be precisely estimated. This approach enables rigorous study of how sensory cues translate into action during active, perceptual decision making. Our findings provide new insight into active touch and how sensory/internal signals interact to determine behavioural choices.
Comparing the efficacy of cancer therapies between subgroups in basket trials
Authors: Palmer Adam C. , Plana Deborah , Sorger Peter K. 
Published: August 2018

SUMMARYAn increase in the number of targeted anti-cancer drugs and growing genomic stratification of patients has led to the development of basket clinical trials in which a single drug is tested simultaneously in multiple tumor subtypes under a master protocol. Basket trials typically involve few patients per type, making it difficult to rigorously compare responses across types. We describe the use of permutation testing to analyze tumor volume changes and Progression Free Survival across subtypes in basket trials for neratinib, larotrectinib, pembrolizumab, and imatinib. Permutation testing is a complement to the standard Simon’s two-stage binomial approach and can test for differences among subgroups using empirical null distributions while controlling for multiple hypothesis testing. This approach uncovers examples of therapeutic benefit missed by a binomial test; in the case of the SUMMIT trial, our analysis identifies an overlooked opportunity for use of neratinib in lung cancers carrying ERBB2 Exon 20 mutations.
The interaction between ORF18 and ORF30 is required for late gene expression in Kaposi’s sarcoma-associated herpesvirus
Authors: Castañeda Angelica F , Glaunsinger Britt A 
Published: August 2018

AbstractIn the beta- and gammaherpesviruses, a specialized complex of viral transcriptional activators (vTAs) coordinate to direct expression of virus-encoded late genes, which are critical for viral assembly and whose transcription initiates only after the onset of viral DNA replication. The vTAs in Kaposi’s sarcoma-associated herpesvirus (KSHV) are ORF18, ORF24, ORF30, ORF31, ORF34, and ORF66. While the general organization of the vTA complex has been mapped, the individual roles of these proteins, and how they coordinate to activate late gene promoters, remains largely unknown. Here, we performed a comprehensive mutational analysis of the conserved residues in ORF18, which is a highly interconnected vTA component. Surprisingly, the mutants were largely selective for disrupting the interaction with ORF30 but not the other three ORF18 binding partners. Furthermore, disrupting the ORF18-ORF30 interaction weakened the vTA complex as a whole, and an ORF18 point mutant that failed to bind ORF30 was unable to complement an ORF18 null virus. Thus, contacts between individual vTAs are critical, as even small disruptions in this complex result in profound defects in KSHV late gene expression.
Basolateral localization of MMP14 drives apicobasal polarity change during EMT independently of its catalytic activity
Authors: Andrieu Cyril , Montigny Audrey , Alfandari Dominique , Theveneau Eric 
Published: August 2018

SummaryThe transmembrane Matrix Metalloproteinase MMP14/MT1-MMP is known to promote cell migration by cleavage of the extracellular matrix. To initiate migration, epithelial cells need to gain mesenchymal attributes. They reduce cell-cell junctions and apicobasal polarity and gain migratory capabilities. This process is named epithelial-mesenchymal transition (EMT). MMP14’s implication in EMT is still ill-defined. We used chick neural crest (NC) cells as a model to explore the function of MMP14 in physiological EMT. Our results show that MMP14 is expressed by chick NC cells. However, it is its subcellular localization, rather than its expression, that correlates with EMT. MMP14 is first apical and switches to basolateral domains during EMT. Loss of function and rescue experiments show that MMP14 is involved in EMT independently of its catalytic activity. It lies downstream of pro-EMT genes and upstream of cell polarity. We found that basolateral localization of MMP14 is required and sufficient to induce polarity change in NC cells and neuroepithelial cells, respectively. These effects on polarity occur without impact on cell-cell adhesion or the extracellular matrix. Overall, our data points to a new function of MMP14 in EMT that will need to be further explored in other systems such as cancer cells.
Activation mechanism of ATP-sensitive K+channels explored with real-time nucleotide binding
Authors: Puljung Michael C. , Vedovato Natascia , Usher Samuel , Ashcroft Frances M. 
Published: August 2018

AbstractThe response of ATP-sensitive K+channels (KATP) to cellular metabolism is coordinated by three classes of nucleotide binding site (NBS). We used a novel approach involving labeling of intact channels in a native, membrane environment with a non-canonical fluorescent amino acid and measurement (using FRET with fluorescent nucleotides) of steady-state and time-resolved nucleotide binding to dissect the role of NBS2 of the accessory SUR1 subunit of KATPin channel gating. Binding to NBS2 was Mg2+-independent, but Mg was required to trigger a conformational change in SUR1. Mutation of a lysine (K1384A) in NBS2 that coordinates bound nucleotides increased the EC50for trinitrophenyl-ADP binding to NBS2, but only in the presence of Mg2+, indicating that this mutation disrupts the ligand-induced conformational change. Comparison of nucleotide-binding with ionic currents suggests a model in which each nucleotide binding event to NBS2 of SUR1 is independent and promotes KATPactivation by the same amount.