bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of conserved long-range RNA-RNA interactions in full viral genomes
Authors: Fricke Markus , Marz Manja 
Published: June 2016

Abstract
Motivation: Long-range RNA-RNA interactions (LRIs) play an important role in viral replication, however, only a few of these interactions are known and only for a small number of viral species. Up to now, it has been impossible to screen a full viral genome for LRIs experimentally or in silico. Most known LRIs are cross-reacting structures (pseudoknots) undetectable by most bioinformatical tools.
Results: We present LRIscan, a tool for the LRI prediction in full viral genomes based on a multiple genome alignment. We confirmed 14 out of 16 experimentally known and evolutionary conserved LRIs in genome alignments of HCV, Tombusviruses, Flaviviruses and HIV-1. We provide several promising new interactions, which include compensatory mutations and are highly conserved in all considered viral sequences. Furthermore, we provide reactivity plots highlighting the hot spots of predicted LRIs.
Availability and Implementation: Source code and binaries of LRIscan freely available for download at http://www.rna.uni-jena.de/en/supplements/lriscan/, implemented in Ruby/C ++ and supported on Linux and Windows.
Contact: manja@uni-jena.de
Supplementary information: Supplementary data are available at Bioinformatics online.
GenVisR: Genomic Visualizations in R
Authors: Skidmore Zachary L. , Wagner Alex H. , Lesurf Robert , Campbell Katie M. , Kunisaki Jason , Griffith Obi L. , Griffith Malachi 
Published: June 2016

Abstract
Summary: Visualizing and summarizing data from genomic studies continues to be a challenge. Here, we introduce the GenVisR package to addresses this challenge by providing highly customizable, publication-quality graphics focused on cohort level genome analyses. GenVisR provides a rapid and easy-to-use suite of genomic visualization tools, while maintaining a high degree of flexibility by leveraging the abilities of ggplot2 and Bioconductor.
Availability and Implementation: GenVisR is an R package available via Bioconductor (https://bioconductor.org/packages/GenVisR) under GPLv3. Support is available via GitHub (https://github.com/griffithlab/GenVisR/issues) and the Bioconductor support website.
Contacts: obigriffith@wustl.edu or mgriffit@wustl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Inferring the perturbation time from biological time course data
Authors: Yang Jing , Penfold Christopher A. , Grant Murray R. , Rattray Magnus 
Published: June 2016

Abstract
Motivation: Time course data are often used to study the changes to a biological process after perturbation. Statistical methods have been developed to determine whether such a perturbation induces changes over time, e.g. comparing a perturbed and unperturbed time course dataset to uncover differences. However, existing methods do not provide a principled statistical approach to identify the specific time when the two time course datasets first begin to diverge after a perturbation; we call this the perturbation time. Estimation of the perturbation time for different variables in a biological process allows us to identify the sequence of events following a perturbation and therefore provides valuable insights into likely causal relationships.
Results: We propose a Bayesian method to infer the perturbation time given time course data from a wild-type and perturbed system. We use a non-parametric approach based on Gaussian Process regression. We derive a probabilistic model of noise-corrupted and replicated time course data coming from the same profile before the perturbation time and diverging after the perturbation time. The likelihood function can be worked out exactly for this model and the posterior distribution of the perturbation time is obtained by a simple histogram approach, without recourse to complex approximate inference algorithms. We validate the method on simulated data and apply it to study the transcriptional change occurring in Arabidopsis following inoculation with Pseudomonas syringae pv. tomato DC3000 versus the disarmed strain DC3000hrpA.
Availability and Implementation: An R package, DEtime, implementing the method is available at https://github.com/ManchesterBioinference/DEtime along with the data and code required to reproduce all the results.
Contact: Jing.Yang@manchester.ac.uk or Magnus.Rattray@manchester.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
RTFBSDB: an integrated framework for transcription factor binding site analysis
Authors: Wang Zhong , Martins André L. , Danko Charles G. 
Published: June 2016

Abstract
Summary: Transcription factors (TFs) regulate complex programs of gene transcription by binding to short DNA sequence motifs. Here, we introduce rtfbsdb, a unified framework that integrates a database of more than 65 000 TF binding motifs with tools to easily and efficiently scan target genome sequences. Rtfbsdb clusters motifs with similar DNA sequence specificities and integrates RNA-seq or PRO-seq data to restrict analyses to motifs recognized by TFs expressed in the cell type of interest. Our package allows common analyses to be performed rapidly in an integrated environment.
Availability and Implementation: rtfbsdb available at (https://github.com/Danko-Lab/rtfbs_db).
Contact: dankoc@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data
Authors: Stokowy Tomasz , Garbulowski Mateusz , Fiskerstrand Torunn , Holdhus Rita , Labun Kornel , Sztromwasser Pawel , Gilissen Christian , Hoischen Alexander , Houge Gunnar , Petersen Kjell , Jonassen Inge , Steen Vidar M. 
Published: June 2016

Abstract
Motivation: The search for causative genetic variants in rare diseases of presumed monogenic inheritance has been boosted by the implementation of whole exome (WES) and whole genome (WGS) sequencing. In many cases, WGS seems to be superior to WES, but the analysis and visualization of the vast amounts of data is demanding.
Results: To aid this challenge, we have developed a new tool—RareVariantVis—for analysis of genome sequence data (including non-coding regions) for both germ line and somatic variants. It visualizes variants along their respective chromosomes, providing information about exact chromosomal position, zygosity and frequency, with point-and-click information regarding dbSNP IDs, gene association and variant inheritance. Rare variants as well as de novo variants can be flagged in different colors. We show the performance of the RareVariantVis tool in the Genome in a Bottle WGS data set.
Availability and implementation: https://www.bioconductor.org/packages/3.3/bioc/html/RareVariantVis.html
Contact: tomasz.stokowy@k2.uib.no
Supplementary information: Supplementary data are available at Bioinformatics online.
Quark deconfinement in the proto-magnetar model of long gamma-ray bursts
Authors: Pili A. G. , Bucciantini N. , Drago A. , Pagliara G. , Del Zanna L. 
Published: June 2016

Abstract
We investigate the possible implications of quark deconfinement on the phenomenology of long gamma-ray bursts focusing, in particular, on the possibility to describe multiple prompt emission phases in the context of the proto-magnetar model. Starting from numerical models of rotating Hadron Stars and Quark Stars in full general relativity we track the electromagnetic spin-down evolution in both the hadronic and quark phase, linking the two families through conservation of baryon number and angular momentum. We give estimates of the time-scales and the energetics involved in the spin-down process deriving, in the relevant spin range, the relation between the initial and the final masses and rotational energies, whenever hadron-quark conversion is possible. We show how the results can be used in relevant astrophysical cases such as the double burst GRB 110709B.
Immunopathogenesis and risk factors for allopurinol severe cutaneous adverse reactions
Authors: Wang Chuang-Wei , Dao Ro-Lan , Chung Wen-Hung 
Published: June 2016

Purpose of review
The article reviews the immunopathogenesis and risk factors related to allopurinol-induced severe cutaneous adverse reactions (SCARs).

Recent findings
For years, allopurinol remains one of the leading cause for SCARs worldwide. The pathogenesis of allopurinol-induced SCARs have been discovered in recent years. HLA-B∗58 : 01 has been found to be strongly associated with allopurinol-SCARs with functional interactions between allopurinol/its metabolite-oxypurinol and the T-cell receptor (TCR). However, the genetic strength of HLA-B∗58 : 01 may vary among different ethnic populations. In addition to HLA-B∗58 : 01, specific T cells with preferential TCR clonotypes, which have no cross-reactivity with new xanthine oxidase inhibitors structurally different from allopurinol, are found to play a crucial role for allopurinol-induced SCARs. Furthermore, other nongenetic factors such as renal impairment are also found to be an important factor resulting in allopurinol-induced SCARs of greater severity and poorer prognosis.

Summary
There are multiple risk factors for allopurinol-induced SCARs, including genetic and nongenetic factors. Activation of specific T cells with preferential TCR and its functional interaction of HLA-B∗58 : 01 molecule and allopurinol/oxypurinol are involved in the immune mechanism of allopurinol-induced SCAR. Patients with allopurinol-induced SCARs with renal impairment have significantly higher risk of mortality. A structurally different new generation xanthine oxidase inhibitor can provide a safer alternative for patients intolerant to allopurinol.
Ebola
Authors: Kiser Erin 
Published: June 2016

ABSTRACT:
Two U.S. nurses relay their experience of deciding to serve and work in Sierra Leone during the 2015 Ebola crisis. The nurses' heartbreaking experiences convey the devastation of Ebola in West Africa and the privilege of answering God's call to serve. Learn about the current status and known outcomes of Ebola Virus Disease (EVD) as of March 2016 for infected patients and the people of West Africa.
Reciprocal Service-Learning Benefits Students, Educators, and the University
Authors: Forehand Jeffery W. , Vardaman Shellye A. , Outlaw Kerri L. 
Published: June 2016

ABSTRACT:
Service-learning offers an opportunity to educate nursing students and foster important personal and professional characteristics. A different kind of service-learning project was developed and implemented in a nursing school. Community/public health nursing students and nurse educators taught cardiopulmonary resuscitation (CPR) and epilepsy training to faculty and staff members of another university department in a Good Samaritan Training project. The multiple benefits of the project to nursing students, educators, and the project recipients are discussed.
Salvaging the Infected Breast Tissue Expander: A Standardized Multidisciplinary Approach
Authors: Viola George M. , Selber Jesse C. , Crosby Melissa , Raad Issam I. , Butler Charles E. , Villa Mark T. , Kronowitz Steven J. , Clemens Mark W. , Garvey Patrick , Yang Wei , Baumann Donald P. 
Published: June 2016

Background:
Infections of breast tissue expander (TE) are complex, often requiring TE removal and hospitalization, which can delay further adjuvant therapy and add to the overall costs of breast reconstruction. Therefore, to reduce the rate of TE removal, hospitalization, and costs, we created a standardized same-day multidisciplinary outpatient quality improvement protocol for diagnosing and treating patients with early signs of TE infection.

Methods:
We prospectively evaluated 26 consecutive patients who developed a surgical site infection between February 2013 and April 2014. On the same day, patients were seen in the Plastic Surgery and Infectious Diseases clinics, underwent breast ultrasonography with or without periprosthetic fluid aspiration, and were prescribed a standardized empiric oral or intravenous antimicrobial regimen active against biofilm-embedded microorganisms. All patients were managed as per our established treatment algorithm and were followed up for a minimum of 1 year.

Results:
TEs were salvaged in 19 of 26 patients (73%). Compared with TE-salvaged patients, TE-explanted patients had a shorter median time to infection (20 vs 40 days; P = 0.09), a significantly higher median temperature at initial presentation [99.8°F; interquartile range (IQR) = 2.1 vs 98.3°F; IQR = 0.4°F; P = 0.01], and a significantly longer median antimicrobial treatment duration (28 days; IQR = 27 vs 21 days; IQR = 14 days; P = 0.05). The TE salvage rates of patients whose specimen cultures yielded no microbial growth, Staphylococcus species, and Pseudomonas were 92%, 75%, and 0%, respectively. Patients who had developed a deep-seated pocket infection were significantly more likely than those with superficial cellulitis to undergo TE explantation (P = 0.021).

Conclusions:
Our same-day multidisciplinary diagnostic and treatment algorithm not only yielded a TE salvage rate higher than those previously reported but also decreased the rate of hospitalization, decreased overall costs, and identified several clinical scenarios in which TE explantation was likely.
Cardiovascular diseases in mega-countries: the challenges of the nutrition, physical activity and epidemiologic transitions, and the double burden of disease
Authors: Barquera Simon , Pedroza-Tobias Andrea , Medina Catalina 
Published: June 2016

Purpose of review
There are today 11 mega-countries with more than 100 million inhabitants. Together these countries represent more than 60% of the world's population. All are facing noncommunicable chronic disease (NCD) epidemic where high cholesterol, obesity, diabetes, and cardiovascular diseases are becoming the main public health concerns. Most of these countries are facing the double burden of malnutrition where undernutrition and obesity coexist, increasing the complexity for policy design and implementation. The purpose of this study is to describe diverse sociodemographic characteristics of these countries and the challenges for prevention and control in the context of the nutrition transition.

Recent findings
Mega-countries are mostly low or middle-income and are facing important epidemiologic, nutrition, and physical activity transitions because of changes in food systems and unhealthy lifestyles. NCDs are responsible of two-thirds of the 57 million global deaths annually. Approximately, 80% of these are in low and middle-income countries. Only developed countries have been able to reduce mortality rates attributable to recognized risk factors for NCDs, in particular high cholesterol and blood pressure.

Summary
Mega-countries share common characteristics such as complex bureaucracies, internal ethnic, cultural and socioeconomic heterogeneity, and complexities to implement effective health promotion and education policies across population. Priorities for action must be identified and successful lessons and experiences should be carefully analyzed and replicated.
Diagnostic scoring for familial hypercholesterolaemia in practice
Authors: Haralambos Kate , Ashfield-Watt Pauline , McDowell Ian F.W. 
Published: June 2016

Purpose of review
Diagnostic scoring for familial hypercholesterolaemia (FH) can be used either to screen for possible FH or guide the selection of patients for genetic (DNA) testing. We review the published diagnostic criteria and discuss the options for future development.

Recent findings
Scoring systems have been developed internationally based on lipid values and various combinations of clinical signs and cardiovascular history. The predictive value varies according to the test population, be it lipid clinic referrals, general population, or relatives of patients with FH. Also, there is increasing recognition of genetic heterogeneity in FH so that criteria are of differing predictive value depending on the genetic variant of FH.

Summary
These clinical scoring systems are increasingly used to guide selection of patients for FH genetic testing but no single approach has yet emerged as the system of choice. Further refinement of these scoring tools using more sophisticated calculators are superseding the more manual approaches. These are well suited to web-based tools or smartphone applications.
Long-term neurodevelopmental benefits of breastfeeding
Authors: Bar Sari , Milanaik Ruth , Adesman Andrew 
Published: June 2016

Purpose of review
The American Academy of Pediatrics recommends exclusive breastfeeding for the first 6 months of an infant#$#apos;s life, with continuation of breastfeeding for at least a year or as mutually desired by mother and child. A robust body of research literature documenting the short-term medical, developmental, and emotional benefits of breastfeeding for infants and toddlers supports this position. This article reviews the neurodevelopmental benefits of breastfeeding as it relates to preschool and school-age children, with particular emphasis on cognitive development, attention-deficit/hyperactivity disorder, and autism spectrum disorder.

Recent findings
The majority of research studies examining breastfeeding and long-term neurodevelopmental outcomes suggest that children who breastfeed for longer than 6 months have better cognitive outcomes, lower risk of developing attention-deficit/hyperactivity disorder, and lower risk of being diagnosed with autism spectrum disorder.

Summary
Pediatricians play a critical role in educating and counseling families about infant nutrition and feeding. Along with the many positive short-term medical effects that breastfeeding confers, physicians should be aware of the growing body of research suggesting that there are also significant long-term neurodevelopmental benefits of breastfeeding.
Hypoxic-Ischemic Encephalopathy With Clinical and Imaging Abnormalities Limited to Occipital Lobe
Authors: Parmar Hemant A. , Trobe Jonathan D. 
Published: June 2016

Background:
The vulnerable brain areas in hypoxic-ischemic encephalopathy (HIE) following systemic hypotension are typically the neocortex, deep cerebral gray nuclei, hippocampus, cerebellum, and the parieto-occipital arterial border zone region. The visual cortex is not commonly recognized as a target in this setting.

Methods:
Single-institution review from 2007 to 2015 of patients who suffered cortical visual loss as an isolated clinical manifestation following systemic hypotension and whose brain imaging showed abnormalities limited to the occipital lobe.

Results:
Nine patients met inclusion criteria. Visual loss at outset ranged from hand movements to 20/20, but all patients had homonymous field loss at best. In 1 patient, imaging was initially normal but 4 months later showed encephalomalacia. In 2 patients, imaging was initially subtle enough to be recognized as abnormal only when radiologists were advised that cortical visual loss was present.

Conclusions:
The occipital lobe may be an isolated target in HIE with cortical visual loss as the only clinical manifestation. Imaging performed in the acute period may appear normal or disclose abnormalities subtle enough to be overlooked. Radiologists informed of the clinical manifestations may be more attune to these abnormalities, which will become more apparent months later when occipital volume loss develops.
To what extent are the terminal stages of sepsis, septic shock, SIRS, and multiple organ dysfunction syndrome actually driven by a prion/amyloid form of fibrin?
Authors: Kell Douglas B. , Pretorius Etheresia 
Published: June 2016

AbstractA well-established development of increasing disease severity leads from sepsis through septic shock, SIRS, multiple organ dysfunction syndrome and cellular and organismal death. We argue that a chief culprit is the LPS-induced anomalous coagulation of fibrinogen to produce a form of fibrin that is at once inflammatory, resistant to fibrinolysis, and underpins the disseminated intravascular coagulation commonly observed in sepsis. In particular, we argue that the form of fibrin produced is anomalous because much of its normal α-helical content is transformed to β-sheets, as occurs in established amyloidogenic and prion diseases. We hypothesise that these processes play a major role in the passage along the above pathways to organismal death, and that inhibiting them would be of great therapeutic value, a claim for which there is emerging evidence.
Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel
Authors: Mohandesan Elmira , Speller Camilla F. , Peters Joris , Uerpmann Hans‐Peter , Uerpmann Margarethe , De Cupere Bea , Hofreiter Michael , Burger Pamela A. 
Published: June 2016

AbstractThe performance of hybridization capture combined with next‐generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient‐domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187‐fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient‐domestic dromedaries with 17–95% length coverage and 1.27–47.1‐fold read depths for the covered regions. Using whole‐genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1–1.06‐fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.