bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effectiveness of Emollient Therapy in Pediatric Patients With Atopic Dermatitis
Authors: Barfield Amanda , Brown Hope , Pernell Paige , Woodard Jessica 
Published: April 2017

ABSTRACT

Background and Purpose
Atopic dermatitis is a chronic inflammatory skin disease that can develop in early childhood and affects 15%–30% of children. The purposes of this research were to review the literature and critique the evidence to better understand the use of emollient therapy in atopic dermatitis.

Methods
A literature review was performed using the databases CINAHL, Cochrane, and MEDLINE and the clinical decision-making resource UptoDate.

Findings
Recent specialty research has begun to focus on the multifactorial triggers that predispose a child to develop atopic dermatitis and subsequent burden of sequelae later in life. Evidence is beginning to show that long-term control of atopic conditions is better achieved using primary prevention measures.

Conclusions
Emollient therapy is a low-risk primary prevention intervention that has been shown to have a steroid-sparing effect. Effective emollient therapy may also prevent the development of atopic dermatitis in at-risk populations. An algorithm or clinical tool is needed to assist primary care providers in the selection of an emollient, how to apply an emollient when used concurrently with a topical rescue medication, and how to adequately educate parents of the importance of primary prevention in the long-term management of atopic dermatitis.
Quality of Antiepileptic Treatment Among Older Medicare Beneficiaries With Epilepsy
Authors: Pisu Maria , Richman Joshua , Piper Kendra , Martin Roy , Funkhouser Ellen , Dai Chen , Juarez Lucia , Szaflarski Jerzy P. , Faught Edward 
Published: April 2017

Background:
Enzyme-inducing antiepileptic drugs (EI-AEDs) are not recommended for older adults with epilepsy. Quality Indicator for Epilepsy Treatment 9 (QUIET-9) states that new patients should not receive EI-AEDs as first line of treatment. In light of reported racial/ethnic disparities in epilepsy care, we investigated EI-AED use and QUIET-9 concordance across major racial/ethnic groups of Medicare beneficiaries.

Research Design:
Retrospective analyses of 2008–2010 Medicare claims for a 5% random sample of beneficiaries 67 years old and above in 2009 augmented for minority representation. Logistic regressions examined QUIET-9 concordance differences by race/ethnicity adjusting for individual, socioeconomic, and geography factors.

Subjects:
Epilepsy prevalent (≥1 International Classification of Disease-version 9 code 345.x or ≥2 International Classification of Disease-version 9 code 780.3x, ≥1 AED), and new (same as prevalent+no seizure/epilepsy events nor AEDs in 365 d before index event) cases.

Measures:
Use of EI-AEDs and QUIET-9 concordance (no EI-AEDs for the first 2 AEDs).

Results:
Cases were 21% white, 58% African American, 12% Hispanic, 6% Asian, 2% American Indian/Alaskan Native. About 65% of prevalent, 43.6% of new cases, used EI-AEDs. QUIET-9 concordance was found for 71% Asian, 65% white, 61% Hispanic, 57% African American, 55% American Indian/Alaskan new cases: racial/ethnic differences were not significant in adjusted model. Beneficiaries without neurology care, in deductible drug benefit phase, or in high poverty areas were less likely to have QUIET-9 concordant care.

Conclusions:
EI-AED use is high, and concordance with recommendations low, among all racial/ethnic groups of older adults with epilepsy. Potential socioeconomic disparities and drug coverage plans may affect treatment quality and opportunities to live well with epilepsy.
Long non-coding RNAs in leukemia: biology and clinical impact
Authors: Lammens Tim , Durinck Kaat , Wallaert Annelynn , Speleman Frank , Van Vlierberghe Pieter 
Published: April 2017

Purpose of review
Over the last years, long non-coding RNAs (lncRNAs) have emerged as putative regulators of malignant hematopoietic development. Here, we review recent literature on the involvement of lncRNAs in leukemia, including their role in driving or sustaining disease and their potential impact on diagnosis, classification, and prognosis.

Recent findings
Leukemogenesis is a complex process resulting from the accumulation of multiple genetic alterations. Over the last years, advances in high-throughput sequencing and transcriptome profiling have enabled the identification of lncRNAs involved in leukemia development. lncRNAs are able to distinguish different subtypes of human leukemia and several reports have identified specific patterns of lncRNA expression associated with clinical patient characteristics. Although functional studies on the actual role of these lncRNAs during transformation remain scarce, emerging evidence suggests that complex interactions between coding and non-coding transcript are truly involved in leukemia development.

Summary
Introduction of lncRNAs as an additional layer of complexity in human leukemia might provide new molecular genetic insights in the biology of this disease and could create unique opportunities for the identification of novel drug targets and diagnostic or prognostic biomarkers.
Epigenetic regulatory mutations and epigenetic therapy for multiple myeloma
Authors: Dupéré-Richer Daphné , Licht Jonathan D. 
Published: April 2017

Purpose of review
Next generation sequencing and large-scale analysis of patient specimens has created a more complete picture of multiple myeloma (MM) revealing that epigenetic deregulation is a prominent factor in MM pathogenesis.

Recent findings
Over half of MM patients have mutations in genes encoding epigenetic modifier enzymes. The DNA methylation profile of MM is related to the stage of the disease and certain classes of mutations in epigenetic modifiers are more prevalent upon disease relapse, suggesting a role in disease progression. Many small molecules targeting regulators of epigenetic machinery have been developed and clinical trials are underway for some of these in MM.

Summary
Recent findings suggest that epigenetic targeting drugs could be an important strategy to cure MM. Combining these agents along with other strategies to affect the MM cell such as immunomodulatory drugs and proteasome inhibitors may enhance efficacy of combination regimens in MM.
Do triglyceride-lowering drugs decrease risk of cardiovascular disease?
Authors: Maki Kevin C. , Dicklin Mary R. 
Published: April 2017

Purpose of review
This review summarizes the evidence supporting a relationship between lowering triglycerides (TGs) and TG-rich lipoprotein cholesterol (TGRL-C) levels and reduced atherosclerotic cardiovascular disease (ASCVD) event risk.

Recent findings
Data from observational investigations, including studies of genetic variants, provide evidence consistent with a causal relationship between elevations in TG and TGRL-C and greater risk for ASCVD. Randomized controlled trial evidence of ASCVD risk reduction with therapies that substantially lower TG and TGRL-C is limited by the fact that no large-scale trial results have been published from a study that enrolled subjects selected specifically on the basis of TG or TGRL-C elevation, although three such trials are underway or in the planning stages. Subgroup analyses from randomized controlled trials are suggestive of a reduction in coronary heart disease and ASCVD event rates with statins, fibrates, omega-3 fatty acid concentrates, and niacin in subjects with elevated TGs, particularly if accompanied by low high-density lipoprotein-cholesterol. Mechanistic studies also support the biologic plausibility of this relationship.

Summary
In conclusion, the available data are suggestive of a benefit of ASCVD reduction with therapies that lower TG and TGRL-C; results from ongoing outcomes trials are expected to provide definitive evidence of this relationship.
Clarifying complex inheritance: apolipoprotein C3 and atherosclerosis
Authors: Galton David J. 
Published: April 2017

Purpose of review
To describe some steps in the progress in the molecular biology of a peptide, apolipoprotein C3; its gene mutations that render individuals susceptible or resistant to developing hyperlipidaemia and atherosclerosis.

Recent findings
Data that lead to the development of a new therapeutic agent volanesorsen.

Summary
The agent blocks the function of the mRNA of apolipoprotein C3 and successfully treats severe hypertriglyceridaemia in phase 3 trials (Ionis Pharmaceuticals).
Dilator Use After Vaginal Brachytherapy for Endometrial Cancer
Authors: Hanlon Alexandra , Small William , Strauss Jonathan , Lin Lilie L. , Hanisch Laura , Huang Liming , Bai Jinbing , Wells Jessica , Bruner Deborah Watkins 
Published: April 2017

Background:
Vaginal brachytherapy, a common treatment of endometrial cancer, is associated with high rates of vaginal stenosis. Recommendations for vaginal dilator use to minimize stenosis generally include 3 times per week for approximately 10 minutes per use. However, adherence rates range widely and are generally well less than 50%.

Objectives:
The aims of this study were to assess feasibility of recruitment to a study of dilator use and test a theoretically driven enhanced educational program (EEP) to increase adherence.

Methods:
Eligibility included women treated with postoperative vaginal brachytherapy for stage I to IIIc endometrial cancer. Patients were randomized to either nurse-delivered standard institutional instruction or EEP.

Results:
Of eligible patients, 76% consented, 42 were randomized, and 69% completed the 6-month assessment. Mean age was 58.2 years; 48% were sexually active. There was no difference in adherence between arms. Overall, 20% and 8.3% were adherent to the prescribed use of 3 times per week, and 64% and 16% were adherent to use at least once per week at 6 weeks and 6 months, respectively. Adherence was greater among those motivated by vaginal health and having lower body mass index. Nonadherence was significantly higher among those who are college educated, in the EEP group, and with higher weight.

Conclusions:
Feasibility of recruitment into a study of vaginal dilator use was high. Adherence was low, and there was no difference between groups. Adherence to vaginal dilator use requires novel interventions to test.

Implications for Practice:
Nursing education that includes how dilators may maintain vaginal health may improve use because it was a motivator for adherence in this study.
Reconstructing the Gigabase Plant Genome ofSolanum pennelliiusing Nanopore Sequencing
Authors: Schmidt Maximilian H.-W. , Vogel Alxander , Denton Alisandra K. , Istace Benjamin , Wormit Alexandra , van de Geest Henri , Bolger Marie E. , Alseekh Saleh , Maβ Janina , Pfaff Christian , Schurr Ulrich , Chetelat Roger , Maumus Florian , Aury Jean-Marc , Fernie Alisdair R. , Zamir Dani , Bolger Anthony M. , Usadel Bjöern 
Published: April 2017

Recent updates in sequencing technology have made it possible to obtain Gigabases of sequence data from one single flowcell. Prior to this update, the nanopore sequencing technology was mainly used to analyze and assemble microbial samples1-3. Here, we describe the generation of a comprehensive nanopore sequencing dataset with a median fragment size of 11,979 bp for the wild tomato speciesSolanum pennelliifeaturing an estimated genome size of ca 1.0 to 1.1 Gbases. We describe its genome assembly to a contig N50 of 2.5 MB using a pipeline comprising a Canu4pre-processing and a subsequent assembly using SMARTdenovo. We show that the obtained nanopore basedde novogenome reconstruction is structurally highly similar to that of the referenceS. pennelliiLA7165genome but has a high error rate caused mostly by deletions in homopolymers. After polishing the assembly with Illumina short read data we obtained an error rate of <0.02 % when assessed versus the same Illumina data. More importantly however we obtained a gene completeness of 96.53% which even slightly surpasses that of the referenceS. pennelliigenome5. Taken together our data indicate such long read sequencing data can be used to affordably sequence and assemble Gbase sized diploid plant genomes.Raw data is available athttp://www.plabipd.de/portal/solanum-pennelliiand has been deposited as PRJEB19787.
Amygdala input differentially influences prefrontal local field potential and single neuron encoding of reward-based decisions
Authors: Stoll Frederic M. , Mosher Clayton P. , Tamang Sarita , Murray Elisabeth A. , Rudebeck Peter H. 
Published: April 2017

ABSTRACTReward-guided behaviors require functional interaction between amygdala, orbital (OFC), and medial (MFC) divisions of prefrontal cortex, but the neural mechanisms underlying these interactions are unclear. Here, we used a decoding approach to analyze local field potentials (LFPs) recorded from OFC and MFC of monkeys engaged in a stimulus-choice task, before and after excitotoxic amygdala lesions. Whereas OFC LFP responses were strongly modulated by the amount of reward associated with each stimulus, MFC responses best represented which stimulus subjects decided to choose. This was counter to what we observed in the level of single neurons where their activity was closely associated with the value of the stimuli presented on each trial. After lesions of the amygdala, stimulus-reward value and choice encoding were reduced in OFC and MFC, respectively. However, while the lesion-induced decrease in OFC LFP encoding of stimulus-reward value mirrored changes in single neuron activity, reduced choice encoding in MFC LFPs was distinct from changes in single neuron activity. Thus, LFPs and single neurons represent different information required for decision-making in OFC and MFC. At the circuit-level, amygdala input to these two areas play a distinct role in stimulus-reward encoding in OFC and choice encoding in MFC.
How does mixed reality affect quiet stance?
Authors: Kong Gaiqing , Wei Kunlin , Kording Konrad P. 
Published: April 2017

AbstractMixed reality (MR) has promise for learning, design, and entertainment, and for use during everyday life. However, when interacting with objects in mixed reality, will moving objects make us fall or perturb our postural stability? To address this question, we recruited participants, instructed them to stand quietly, and measured how much virtual objects presented in mixed reality (Microsoft HoloLens) affected their stance. We analyzed the effects of solid object and text, in both a static and a dynamic setting. Mixed reality events induced some movements, but the effect, while significant, was exceptionally small (< 1mm & < 0.5° perturbations in terms of mean distance and angle rotations). We conclude that induced movement in “real reality” should not be too much of a concern when designing mixed reality applications.
BROCKMAN: Deciphering variance in epigenomic regulators byk-mer factorization
Authors: de Boer Carl G. , Regev Aviv 
Published: April 2017

AbstractBackgroundVariation in chromatin organization across single cells can help shed important light on the mechanisms controlling gene expression, but scale, noise, and sparsity pose significant challenges for interpretation of single cell chromatin data. Here, we develop BROCKMAN (Brockman Representation Of Chromatin byK-mers in Mark-Associated Nucleotides), an approach to infer variation in transcription factor (TF) activity across samples through unsupervised analysis of the variation in DNA sequences associated with an epigenomic mark.ResultsBROCKMAN represents each sample as a vector of epigenomic-mark-associated DNA word frequencies, and decomposes the resulting matrix to find hidden structure in the data, followed by unsupervised grouping of samples and identification of the TFs that distinguish groups. Applied to single cell ATAC-seq, BROCKMAN readily distinguished cell types, treatments, batch effects, experimental artifacts, and cycling cells. We show that each variable component in thek-mer landscape reflects a set of co-varying TFs, which are often known to physically interact. For example, in K562 cells, AP-1 TFs were central determinant of variability in chromatin accessibility through their variable expression levels and diverse interactions with other TFs. We provide a theoretical basis for why cooperative TF binding – and any associated epigenomic mark – is inherently more variable than non-cooperative binding.ConclusionsBROCKMAN and related approaches will help gain a mechanistic understanding of thetransdeterminants of chromatin variability between cells, treatments, and individuals.
Allometric derivation and estimation ofGuadua weberbaueriandG. sarcocarpabiomass in the bamboo-dominated forests of SW Amazonia
Authors: Yavit Noah 
Published: April 2017

AbstractBamboo-dominated forests in Southwestern Amazonia encompass an estimated 180,000 km2of nearly contiguous primary, tropical lowland forest. This area, largely composed of two bamboo species,Guadua weberbaueriPilger andG. sarcocarpaLondoño & Peterson, comprises a significant portion of the Amazon Basin and has a potentially important effect on regional carbon storage. Numerous local REDD(+) projects would benefit from the development of allometric models for these species, although there has been just one effort to do so. The aim of this research was to create a set of improved allometric equations relating the above and belowground biomass to the full range of natural size and growth patterns observed. Four variables (DBH, stem length, small branch number and branch number ≥ 2cm diameter) were highly significant predictors of stem biomass (N≤ 278, p< 0.0001 for all predictors,complete modelR2=0.93). A secondaryfield model(containing DBH and branch number > 2cm diameter), proved highly significant as well (N= 278, p< 0.0001 for both predictors, R2=0.84). The belowground biomass was estimated to be 19.2±6.2% of the total dry biomass of the bamboo species examined. To demonstrate the utility of these models in the field and derive stand-level estimates of bamboo biomass, ten 0.36-ha plots were analyzed (N= 3,966 culms), yielding above + belowground biomass values ranging from 4.3–14.5 Mg·ha-1. The results of this research provide novel allometric models and estimates of the contribution ofG. weberbaueriandG. sarcocarpato the total carbon budget of this vast and largely unexplored Amazonian habitat.
Base-specific mutational intolerance near splice-sites clarifies role of non-essential splice nucleotides
Authors: Zhang Sidi , Samocha Kaitlin E. , Rivas Manuel A. , Karczewski Konrad J. , Daly Emma , Schmandt Ben , Neale Benjamin M. , MacArthur Daniel G. , Daly Mark J. 
Published: April 2017

AbstractVariation in RNA splicing (i.e., alternative splicing) plays an important role in many diseases. Variants near 5′ and 3′ splice sites often affect splicing, but the effects of these variants on splicing and disease have not been fully characterized beyond the 2 “essential” splice nucleotides flanking each exon. Here we provide quantitative measurements of tolerance to mutational disruptions by position and reference allele-alternative allele combination. We show that certain reference alleles are particularly sensitive to mutations, regardless of the alternative alleles into which they are mutated. Using public RNA-seq data, we demonstrate that individuals carrying such variants have significantly lower levels of the correctly spliced transcript compared to individuals without them, and confirm that these specific substitutions are highly enriched for known Mendelian mutations. Our results propose a more refined definition of the “splice region” and offer a new way to prioritize and provide functional interpretation of variants identified in diagnostic sequencing and association studies.
With our powers combined: integrating behavioral and genetic data to estimate mating success and sexual selection
Authors: Gauthey Zoé , Tentelier Cédric , Lepais Olivier , Elosegi Arturo , Royer Laura , Glise Stéphane , Labonne Jacques 
Published: April 2017

AbstractThe analysis of sexual selection classically relies on the regression of individual phenotypes against the marginal sums of a males × females matrix of pairwise reproductive success, assessed by genetic parentage analysis. When the matrix is binarized, the marginal sums give the individual mating success. Because such analysis treats male and female mating/reproductive success independently, it ignores that the success of a male × female sexual interaction can be attributable to the phenotype of both individuals. Also, because it is based on genetic data only, it is oblivious to costly yet unproductive matings, which may be documented by behavioral observations. To solve these problems, we propose a statistical model which combines matrices of offspring numbers and behavioral observations. It models reproduction on each mating occasion of a mating season as three stochastic and interdependent pairwise processes, each potentially affected by the phenotype of both individuals and by random individual effect: encounter (Bernoulli), concomitant gamete emission (Bernoulli), and offspring production (Poisson). Applied to data from a mating experiment on brown trout, the model yielded different results from the classical regression analysis, with only a limited effect of male body size on the probability of gamete release and a negative effect of female body size on the probability of encounter and gamete release. Because the general structure of the model can be adapted to other partitioning of the reproductive process, it can be used for a variety of biological systems where behavioral and genetic data are available.
Bayesian phylogenetic analysis for diploid and allotetraploid species networks
Authors: Jones Graham 
Published: April 2017

AbstractAllopolyploid species are formed by genome doubling after hybridization between otherwise intersterile parental species. Allopolyploidy is a common speciation mechanism in land plants. Here we describe and evaluate a Bayesian approach to the phylogenetic analysis of species relationships when both ordinary speciation and allopolyploidy are present. The approach takes incomplete lineage sorting into account using the multi-species coalescent model, and extends this to deal with the extra complications due to allopolyploidy. The number of hybridizations is not assumed, which means that the number of parameters varies and a reversible-jump MCMC algorithm is needed to sample from the posterior. The main restriction is that only diploids and allotetraploids are considered. The model is implemented in the BEAST framework and is an extension of Jones et al. (2013). Simulations show that the topology of the network can be reliably inferred along with estimates of other parameters.