bluuebunny/crossref_metadata_2025_split huggingface dataset:
Principles of practice parameters for the treatment of sleep disordered breathing in the elderly and frail elderly: the consensus of the International Geriatric Sleep Medicine Task Force
Authors: Netzer Nikolaus C. , Ancoli-Israel Sonia , Bliwise Donald L. , Fulda Stephany , Roffe Christine , Almeida Fernanda , Onen Hakki , Onen Fannie , Raschke Friedhart , Martinez Garcia Miguel Angel , Frohnhofen Helmut 
Published: July 2016

Sleep disordered breathing (SDB) is a leading cause of morbidity worldwide. Its prevalence increases with age. Due to the demographic changes in industrial societies, pulmonologists and sleep physicians are confronted with a rapidly growing number of elderly SDB patients. For many physicians, it remains unclear how current guidelines for SDB management apply to elderly and frail elderly patients. The goal of this consensus statement is to provide guidance based on published evidence for SDB treatment in this specific patient group.Clinicians and researchers with expertise in geriatric sleep medicine representing several countries were invited to participate in a task force. A literature search of PubMed from the past 12 years and a systematic review of evidence of studies deemed relevant was performed.Recommendations for treatment management of elderly and frail elderly SDB patients based on published evidence were formulatedviadiscussion and consensus.In the last 12 years, there have been surprisingly few studies examining treatment of SDB in older adults and even fewer in frail older adults. Studies that have been conducted on the management of SDB in the older patient population were rarely stratified for age. Studies in SDB treatment that did include age stratification mainly focused on middle-aged and younger patient groups. Based on the evidence that is available, this consensus statement highlights the treatment forms that can be recommended for elderly SDB patients and encourages treatment of SDB in this large patient group.
The relationship between body fat and respiratory function in young adults
Authors: Sutherland Tim J.T. , McLachlan Christene R. , Sears Malcolm R. , Poulton Richie , Hancox Robert J. 
Published: July 2016

The relationship between adiposity and respiratory function is poorly understood. Most studies investigating this have used indirect measures of body fat and few have assessed how changes in adiposity influence lung function.Body fat measured by bio-electrical impedance analysis, body mass index, waist circumference, spirometry, body plethysmography and transfer factor were measured at ages 32 and 38 years in 361 non-smoking, non-asthmatic participants from a population-based birth cohort.Higher percentage body fat was associated with lower spirometric and plethysmographic lung volumes, but not with airflow obstruction, or transfer factor at 32 years. Changes in adiposity between ages 32 and 38 years were inversely associated with changes in lung volumes. These associations were generally stronger in men than women, but an association between increasing adiposity and lower airway function (forced expiratory volume in 1 s/forced vital capacity) was only found in women. Similar associations were found for body mass index and waist circumference.Higher percentage body fat is associated with lower lung volumes. Direct and indirect measures of adiposity had similar associations with lung function. Adiposity had a greater effect on lung volumes in men than women but was associated with airway function only in women. There was little evidence that adiposity influenced transfer factor.
DISMISS: detection of stranded methylation in MeDIP-Seq data
Authors: Niazi Umar , Geyer Kathrin K. , Vickers Martin J. , Hoffmann Karl F. , Swain Martin T. 
Published: July 2016

Abstract
Background
DNA methylation is an important regulator of gene expression and chromatin structure. Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is commonly used to identify regions of DNA methylation in eukaryotic genomes. Within MeDIP-Seq libraries, methylated cytosines can be found in both double-stranded (symmetric) and single-stranded (asymmetric) genomic contexts. While symmetric CG methylation has been relatively well-studied, asymmetric methylation in any dinucleotide context has received less attention. Importantly, no currently available software for processing MeDIP-Seq reads is able to resolve these strand-specific DNA methylation signals. Here we introduce DISMISS, a new software package that detects strand-associated DNA methylation from existing MeDIP-Seq analyses.

Results
Using MeDIP-Seq datasets derived from Apis mellifera (honeybee), an invertebrate species that contains more asymmetric- than symmetric- DNA methylation, we demonstrate that DISMISS can identify strand-specific DNA methylation signals with similar accuracy as bisulfite sequencing (BS-Seq; single nucleotide resolution methodology). Specifically, DISMISS is able to confidently predict where DNA methylation predominates (plus or minus DNA strands – asymmetric DNA methylation; plus and minus DNA stands – symmetric DNA methylation) in MeDIP-Seq datasets derived from A. mellifera samples. When compared to DNA methylation data derived from BS-Seq analysis of A. mellifera worker larva, DISMISS-mediated identification of strand-specific methylated cytosines is 80 % accurate. Furthermore, DISMISS can correctly (p <0.0001) detect the origin (sense vs antisense DNA strands) of DNA methylation at splice site junctions in A. mellifera MeDIP-Seq datasets with a precision close to BS-Seq analysis. Finally, DISMISS-mediated identification of DNA methylation signals associated with upstream, exonic, intronic and downstream genomic loci from A. mellifera MeDIP-Seq datasets outperforms MACS2 (Model-based Analysis of ChIP-Seq2; a commonly used MeDIP-Seq analysis software) and closely approaches the results achieved by BS-Seq.

Conclusions
While asymmetric DNA methylation is increasingly being found in growing numbers of eukaryotic species and is the predominant pattern observed in some invertebrate genomes, it has been difficult to detect in MeDIP-Seq datasets using existing software. DISMISS now enables more sensitive examinations of MeDIP-Seq datasets and will be especially useful for the study of genomes containing either low levels of DNA methylation or for genomes containing relatively high amounts of asymmetric methylation.
TopoICSim: a new semantic similarity measure based on gene ontology
Authors: Ehsani Rezvan , Drabløs Finn 
Published: July 2016

Abstract
Background
The Gene Ontology (GO) is a dynamic, controlled vocabulary that describes the cellular function of genes and proteins according to tree major categories: biological process, molecular function and cellular component. It has become widely used in many bioinformatics applications for annotating genes and measuring their semantic similarity, rather than their sequence similarity. Generally speaking, semantic similarity measures involve the GO tree topology, information content of GO terms, or a combination of both.

Results
Here we present a new semantic similarity measure called TopoICSim (Topological Information Content Similarity) which uses information on the specific paths between GO terms based on the topology of the GO tree, and the distribution of information content along these paths. The TopoICSim algorithm was evaluated on two human benchmark datasets based on KEGG pathways and Pfam domains grouped as clans, using GO terms from either the biological process or molecular function. The performance of the TopoICSim measure compared favorably to five existing methods. Furthermore, the TopoICSim similarity was also tested on gene/protein sets defined by correlated gene expression, using three human datasets, and showed improved performance compared to two previously published similarity measures. Finally we used an online benchmarking resource which evaluates any similarity measure against a set of 11 similarity measures in three tests, using gene/protein sets based on sequence similarity, Pfam domains, and enzyme classifications. The results for TopoICSim showed improved performance relative to most of the measures included in the benchmarking, and in particular a very robust performance throughout the different tests.

Conclusions
The TopoICSim similarity measure provides a competitive method with robust performance for quantification of semantic similarity between genes and proteins based on GO annotations. An R script for TopoICSim is available at http://bigr.medisin.ntnu.no/tools/TopoICSim.R.
Effectiveness of percutaneous flexor tenotomies for the management and prevention of recurrence of diabetic toe ulcers: a systematic review
Authors: Scott Jennifer E. , Hendry Gordon J. , Locke John 
Published: July 2016

AbstractBackgroundDiabetic toe ulcers are a potentially devastating complication of diabetes. In recent years, the percutaneous flexor tenotomy procedure for the correction of flexible claw and hammer‐toe contraction deformities has been proposed as a safe and effective technique for facilitating the healing of toe‐deformity related diabetic ulcers. The aim of this review is to critically appraise the evidence for the effectiveness of this surgical procedure in achieving ulcer healing, prevention of re‐ulceration, and to summarise the rate of post‐operative complications.MethodA search of medical databases, was performed to locate relevant literature. Titles were screened prior to abstract and full text review to identify articles relevant to the research question. Search terms included truncations of “tenotomy”, “toe”, “hallux”, “digit”, “diabetes” and “ulcer”. Peer reviewed primary research study designs specified as suitable for systematic reviews by the Centre for Reviews and Dissemination were included. Studies were excluded if they used a concurrent secondary procedure or included non‐diabetic patients without reporting outcomes separately. Included studies were appraised for quality using the Methodological Index for Non‐Randomised Studies tool. Levels of evidence were subsequently assigned to each outcome of interest (healing rate and prevention of re‐ulceration).ResultsFrom a total search yield of 42 articles, 5 eligible studies (all case series designs) were identified for inclusion. Included studies were of low‐to‐moderate methodological quality when assessed using the MINORS tool. A total of 250 flexor tenotomy procedures were performed in a total of 163 patients. Included studies generally reported good healing rates (92–100 % within 2 months) post‐op follow‐up), relatively few recurrences (0–18 % at 22 months median post‐op follow‐up), and low incidences of infection or new deformity. Transfer ulcers developing on adjacent areas as a result of shifted pressure were reported by several authors.The validity of these results is undermined by methodological limitations inherent to case series designs such as a lack of control groups, non‐randomised designs, as well as inconsistent reporting of post‐intervention follow‐up periods. There was level 4 evidence for the flexor tenotomy procedure in facilitating ulcer healing and preventing re‐ulceration.ConclusionMore definitive research evidence is needed in this area to determine whether or not the flexor tenotomy is a safe and effective treatment option for people with, or at risk of developing diabetic toe ulcers. Whilst the available literature reports that the procedure may be associated with high healing rates, relatively low recurrence rates and low incidences of post‐op complications, methodological limitations restrict the value of these findings.
Direct conversion of mouse embryonic fibroblasts into functional keratinocytes through transient expression of pluripotency-related genes
Authors: Iacovides Demetris , Rizki Gizem , Lapathitis Georgios , Strati Katerina 
Published: July 2016

AbstractThe insufficient ability of specialized cells such as neurons, cardiac myocytes, and epidermal cells to regenerate after tissue damage poses a great challenge to treat devastating injuries and ailments. Recent studies demonstrated that a diverse array of cell types can be directly derived from embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), or somatic cells by combinations of specific factors. The use of iPSCs and direct somatic cell fate conversion, or transdifferentiation, holds great promise for regenerative medicine as these techniques may circumvent obstacles related to immunological rejection and ethical considerations. However, producing iPSC-derived keratinocytes requires a lengthy two-step process of initially generating iPSCs and subsequently differentiating into skin cells, thereby elevating the risk of cellular damage accumulation and tumor formation. In this study, we describe the reprogramming of mouse embryonic fibroblasts into functional keratinocytes via the transient expression of pluripotency factors coupled with directed differentiation. The isolation of an iPSC intermediate is dispensable when using this method. Cells derived with this approach, termed induced keratinocytes (iKCs), morphologically resemble primary keratinocytes. Furthermore they express keratinocyte-specific markers, downregulate mesenchymal markers as well as the pluripotency factors Oct4, Sox2, and Klf4, and they show important functional characteristics of primary keratinocytes. iKCs can be further differentiated by high calcium administration in vitro and are capable of regenerating a fully stratified epidermis in vivo. Efficient conversion of somatic cells into keratinocytes could have important implications for studying genetic skin diseases and designing regenerative therapies to ameliorate devastating skin conditions.
Some fixed point results via R-functions
Authors: Nastasi Antonella , Vetro Pasquale , Radenović Stojan 
Published: July 2016

AbstractWe establish existence and uniqueness of fixed points for a new class of mappings, by using R-functions and lower semi-continuous functions in the setting of metric spaces. As consequences of this results, we obtain several known fixed point results, in metric and partial metric spaces. An example is given to support the new theory. A homotopy result for operators on a set endowed with a metric is given as application.
Partial epithelial-mesenchymal transition in keloid scars: regulation of keloid keratinocyte gene expression by transforming growth factor-β1
Authors: Hahn Jennifer M. , McFarland Kevin L. , Combs Kelly A. , Supp Dorothy M. 
Published: July 2016

Abstract

Background
Keloids are an extreme form of abnormal scarring that result from a pathological fibroproliferative wound healing process. The molecular mechanisms driving keloid pathology remain incompletely understood, hindering development of targeted, effective therapies. Recent studies in our laboratory demonstrated that keloid keratinocytes exhibit adhesion abnormalities and display a transcriptional signature reminiscent of cells undergoing epithelial-mesenchymal transition (EMT), suggesting a role for EMT in keloid pathology. In the current study, we further define the EMT-like phenotype of keloid scars and investigate regulation of EMT-related genes in keloid.

Methods
Primary keratinocytes from keloid scar and normal skin were cultured in the presence or absence of transforming growth factor beta 1 (TGF-β1) +/− inhibitors of TGF-β1 and downstream signaling pathways. Gene expression was measured using quantitative polymerase chain reaction. Migration was analyzed using an in vitro wound healing assay. Proteins in keloid scar and normal skin sections were localized by immunohistochemistry. Statistical analyses utilized SigmaPlot (SyStat Software, San Jose, CA) or SAS® (SAS Institute, Cary, NC).

Results
In keloid and normal keratinocytes, TGF-β1 regulated expression of EMT-related genes, including hyaluronan synthase 2, vimentin, cadherin-11, wingless-type MMTV integration site family, member 5A, frizzled 7, ADAM metallopeptidase domain 19, and interleukin-6. Inhibition of canonical TGF-β1 signaling in keloid keratinocytes significantly inhibited expression of these genes, and TGF-β1 stimulation of normal keratinocytes increased their expression. The inhibition of the extracellular signal-regulated kinase 1/2 (ERK1/2) signaling pathway or the p38 mitogen-activated protein kinase pathway attenuated TGF-β1-induced expression of subsets of these genes. Migration of keloid keratinocytes, previously shown to be increased compared with normal keratinocytes, was significantly reduced by inhibition of TGF-β1 or ERK1/2 signaling. Biomarkers of EMT, including reduced E-cadherin and increased active β-catenin, were observed in keloid epidermis in vivo. However, evidence of basement membrane breakdown in keloid scar was not observed.

Conclusions
The results suggest that keloid keratinocytes exist in an EMT-like metastable state, similar to activated keratinocytes in healing wounds. The EMT-like gene expression pattern of keloid keratinocytes is regulated by canonical and non-canonical TGF-β1 signaling pathways. Therefore, interventions targeting TGF-β1-regulated EMT-like gene expression in keloid keratinocytes may serve to suppress keloid scarring.
Induced polarization and pore radius — A discussion
Authors: Weller Andreas , Zhang Zeyu , Slater Lee , Kruschwitz Sabine , Halisch Matthias 
Published: July 2016

Permeability estimation from induced polarization (IP) measurements is based on a fundamental premise that the characteristic relaxation time [Formula: see text] is related to the effective hydraulic radius [Formula: see text] controlling fluid flow. The approach requires a reliable estimate of the diffusion coefficient of the ions in the electrical double layer. Others have assumed a value for the diffusion coefficient, or postulated different values for clay versus clay-free rocks. We have examined the link between a widely used single estimate of [Formula: see text] and [Formula: see text] for an extensive database of sandstone samples, in which mercury porosimetry data confirm that [Formula: see text] is reliably determined from a modification of the Hagen-Poiseuille equation assuming that the electrical tortuosity is equal to the hydraulic tortuosity. Our database does not support the existence of one or two distinct representative diffusion coefficients but instead demonstrates strong evidence for six orders of magnitude of variation in an apparent diffusion coefficient that is well-correlated with [Formula: see text] and the specific surface area per unit pore volume [Formula: see text]. Two scenarios can explain our findings: (1) the length scale defined by [Formula: see text] is not equal to [Formula: see text] and is likely much longer due to the control of pore-surface roughness or (2) the range of diffusion coefficients is large and likely determined by the relative proportions of the different minerals (e.g., silica and clays) making up the rock. In either case, the estimation of [Formula: see text] (and hence permeability) is inherently uncertain from a single characteristic IP relaxation time as considered in this study.
Modification and Validation of the Triglyceride-to–HDL Cholesterol Ratio as a Surrogate of Insulin Sensitivity in White Juveniles and Adults without Diabetes Mellitus: The Single Point Insulin Sensitivity Estimator (SPISE)
Authors: Paulmichl Katharina , Hatunic Mensud , Højlund Kurt , Jotic Aleksandra , Krebs Michael , Mitrakou Asimina , Porcellati Francesca , Tura Andrea , Bergsten Peter , Forslund Anders , Manell Hannes , Widhalm Kurt , Weghuber Daniel , Anderwald Christian-Heinz ,   the Beta-JUDO Investigators
Published: July 2016

AbstractBACKGROUNDThe triglyceride-to–HDL cholesterol (TG/HDL-C) ratio was introduced as a tool to estimate insulin resistance, because circulating lipid measurements are available in routine settings. Insulin, C-peptide, and free fatty acids are components of other insulin-sensitivity indices but their measurement is expensive. Easier and more affordable tools are of interest for both pediatric and adult patients.METHODSStudy participants from the Relationship Between Insulin Sensitivity and Cardiovascular Disease [43.9 (8.3) years, n = 1260] as well as the Beta-Cell Function in Juvenile Diabetes and Obesity study cohorts [15 (1.9) years, n = 29] underwent oral-glucose-tolerance tests and euglycemic clamp tests for estimation of whole-body insulin sensitivity and calculation of insulin sensitivity indices. To refine the TG/HDL ratio, mathematical modeling was applied including body mass index (BMI), fasting TG, and HDL cholesterol and compared to the clamp-derived M-value as an estimate of insulin sensitivity. Each modeling result was scored by identifying insulin resistance and correlation coefficient. The Single Point Insulin Sensitivity Estimator (SPISE) was compared to traditional insulin sensitivity indices using area under the ROC curve (aROC) analysis and χ2 test.RESULTSThe novel formula for SPISE was computed as follows: SPISE = 600 × HDL-C0.185/(TG0.2 × BMI1.338), with fasting HDL-C (mg/dL), fasting TG concentrations (mg/dL), and BMI (kg/m2). A cutoff value of 6.61 corresponds to an M-value smaller than 4.7 mg · kg−1 · min−1 (aROC, M:0.797). SPISE showed a significantly better aROC than the TG/HDL-C ratio. SPISE aROC was comparable to the Matsuda ISI (insulin sensitivity index) and equal to the QUICKI (quantitative insulin sensitivity check index) and HOMA-IR (homeostasis model assessment–insulin resistance) when calculated with M-values.CONCLUSIONSThe SPISE seems well suited to surrogate whole-body insulin sensitivity from inexpensive fasting single-point blood draw and BMI in white adolescents and adults.
Application of empirical mode decomposition method for characterization of random vibration signals
Authors: Parman Setyamartana , Yazid Edwar 
Published: July 2016

Characterization of finite measured signals is a great of importance in dynamical modeling and system identification. This paper addresses an approach for characterization of measured random vibration signals where the approach rests on a method called empirical mode decomposition (EMD). The applicability of proposed approach is tested in one numerical and experimental data from a structural system, namely spar platform. The results are three main signal components, comprising: noise embedded in the measured signal as the first component, first intrinsic mode function (IMF) called as the wave frequency response (WFR) as the second component and second IMF called as the low frequency response (LFR) as the third component while the residue is the trend. Band-pass filter (BPF) method is taken as benchmark for the results obtained from EMD method.
C*-simplicity of locally compact Powers groups
Authors: Raum Sven 
Published: July 2016

Abstract
In this article we initiate research on locally compact

C
*

\mathrm{C}^{*}

-simple groups. We first show that every

C
*

\mathrm{C}^{*}

-simple group must be totally disconnected. Then we study

C
*

\mathrm{C}^{*}

-algebras and von Neumann algebras associated with certain groups acting on trees. After formulating a locally compact analogue of Powers’ property, we prove that the reduced group

C
*

\mathrm{C}^{*}

-algebra of such groups is simple. This is the first simplicity result for

C
*

\mathrm{C}^{*}

-algebras of non-discrete groups and answers a question of de la Harpe. We also consider group von Neumann algebras of certain non-discrete groups acting on trees. We prove factoriality, determine their type and show non-amenability. We end the article by giving natural examples of groups satisfying the hypotheses of our work.
New copulas based on general
partitions-of-unity and their applications to
risk management
Authors: Pfeifer Dietmar , Tsatedem Hervé Awoumlac , Mändle Andreas , Girschig Côme 
Published: July 2016

Abstract
We construct new multivariate copulas on the basis of a generalized infinite partition-of-unity approach.
This approach allows, in contrast to finite partition-of-unity copulas, for tail-dependence as well as
for asymmetry. A possibility of fitting such copulas to real data from quantitative risk management is also
pointed out.