bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relating Working Memory to Compression Parameters in Clinically Fit Hearing Aids
Authors: Souza Pamela E. , Sirow Lynn 
Published: August 2014

Purpose
Several laboratory studies have demonstrated that working memory may influence response to compression speed in controlled (i.e., laboratory) comparisons of compression. In this study, the authors explored whether the same relationship would occur under less controlled conditions, as might occur in a typical audiology clinic.

Method
Participants included 27 older adults who sought hearing care in a private practice audiology clinic. Working memory was measured for each participant using a reading span test. The authors examined the relationship between working memory and aided speech recognition in noise, using clinically fit hearing aids with a range of compression speeds.

Results
Working memory, amount of hearing loss, and age each contributed to speech recognition, but the contribution depended on the speed of the compression processor. For fast-acting compression, the best performance was obtained by patients with high working memory. For slow-acting compression, speech recognition was affected by age and amount of hearing loss but was not affected by working memory.

Conclusions
Despite the expectation of greater variability from differences in compression implementation, number of compression channels, or attendant signal processing, the relationship between working memory and compression speed showed a similar pattern as results from more controlled, laboratory-based studies.
Molecular architecture of mammalian nitric oxide synthases
Authors: Campbell Melody G. , Smith Brian C. , Potter Clinton S. , Carragher Bridget , Marletta Michael A. 
Published: August 2014

Significance
In mammals, NO produced by NOS acts as a signaling molecule in the nervous and cardiovascular systems and as a cytotoxin in the immune system’s response to infection. Although structures of smaller portions of NOS have been solved, the structures of the entire NOS homodimer have remained elusive. In this study, we use single-particle EM to directly visualize the 3D structures, domain organization, and conformations accessed by all three mammalian NOSs. The observed conformational changes provide insight into the mechanisms through which calmodulin binding results in efficient NO formation.
Tropical forest transitions: structural changes in forest area, composition and landscape.
Authors: Wiersum K. F. 
Published: August 2014

Abstract
Most studies on tropical forest dynamics focus on the processes of deforestation and forest degradation and its associated ecological impacts; comparatively little attention is given to the emergence of forest transitions. This review gives an overview of forest transitions in the tropics as involving a structural reversal from a decreasing to expanding forest area as well as related changes in forest quality and forest landscape. After introducing the concept of forest transition it first summarizes the changing forest area in tropical countries. It then discusses how the identification of a forest transition greatly depends on how forests are defined. Three types of forests with contrasting forest composition are distinguished, i.e. natural forests, modified forests and transformed forests, and forest transitions are characterized as involving either forest conversion or forest restoration. Next, forest transitions are related to changes in forested landscapes and described as involving either forest extension at a retracting agricultural frontier or incorporation of forests in forested mosaic landscapes. These processes are driven by either macro-scale socio-ecological feedbacks or socio-economic changes or by location-specific development of rural forests as part of farming intensification. This paper concludes that forest transitions do not just involve a return of natural forests and/or extension of forest plantations on forest lands, but also a multidimensional co-evolution in social and ecological conditions involving an increasing incorporation of socialized forests in forested landscapes.
Mechanical compression insults induce nanoscale changes of membrane-skeleton arrangement which could cause apoptosis and necrosis in dorsal root ganglion neurons
Authors: Quan Xin , Guo Kai , Wang Yuqing , Huang Liangliang , Chen Beiyu , Ye Zhengxu , Luo Zhuojing 
Published: August 2014

Abstract
In a primary spinal cord injury, the amount of mechanical compression insult that the neurons experience is one of the most critical factors in determining the extent of the injury. The ultrastructural changes that neurons undergo when subjected to mechanical compression are largely unknown. In the present study, using a compression-driven instrument that can simulate mechanical compression insult, we applied mechanical compression stimulation at 0.3, 0.5, and 0.7 MPa to dorsal root ganglion (DRG) neurons for 10 min. Combined with atomic force microscopy, we investigated nanoscale changes in the membrane-skeleton, cytoskeleton alterations, and apoptosis induced by mechanical compression injury. The results indicated that mechanical compression injury leads to rearrangement of the membrane-skeleton compared with the control group. In addition, mechanical compression stimulation induced apoptosis and necrosis and also changed the distribution of the cytoskeleton in DRG neurons. Thus, the membrane-skeleton may play an important role in the response to mechanical insults in DRG neurons. Moreover, sudden insults caused by high mechanical compression, which is most likely conducted by the membrane-skeleton, may induce necrosis, apoptosis, and cytoskeletal alterations.
Identification of catalytic residues of a very large NAD-glutamate dehydrogenase from Janthinobacterium lividum by site-directed mutagenesis
Authors: Kawakami Ryushi , Sakuraba Haruhiko , Ohshima Toshihisa 
Published: August 2014

Abstract
We previously found a very large NAD-dependent glutamate dehydrogenase with approximately 170 kDa subunit from Janthinobacterium lividum (Jl-GDH) and predicted that GDH reaction occurred in the central domain of the subunit. To gain further insights into the role of the central domain, several single point mutations were introduced. The enzyme activity was completely lost in all single mutants of R784A, K810A, K820A, D885A, and S1142A. Because, in sequence alignment analysis, these residues corresponded to the residues responsible for glutamate binding in well-known small GDH with approximately 50 kDa subunit, very large GDH and well-known small GDH may share the same catalytic mechanism. In addition, we demonstrated that C1141, one of the three cysteine residues in the central domain, was responsible for the inhibition of enzyme activity by HgCl2, and HgCl2 functioned as an activating compound for a C1141T mutant. At low concentrations, moreover, HgCl2 was found to function as an activating compound for a wild-type Jl-GDH. This suggests that the mechanism for the activation is entirely different from that for the inhibition.
Environmentally benign process for the preparation of antimicrobial α-methylene-β-hydroxy-γ-butyrolactone (tulipalin B) from tulip biomass
Authors: Nomura Taiji , Hayashi Emiko , Kawakami Shohei , Ogita Shinjiro , Kato Yasuo 
Published: August 2014

Abstract
Tulipalin B (α-methylene-β-hydroxy-γ-butyrolactone, PaB) is an antimicrobial natural product occurring in tulip (Tulipa gesneriana). PaB is directly formed from the precursor glucose ester 6-tuliposide B (PosB) by endogenous Pos-converting enzyme (TCE). Despite the potential usefulness of antibacterial PaB in various industrial applications, lack of facile synthetic schemes hampers its practical use. Herein, we describe an environmentally benign and facile process for the preparation of PaB using tulip biomass materials based on one-step enzyme reaction catalyzed by TCE without the use of petroleum-derived solvents. By screening 115 tulip cultivars, we found three elite cultivars, which accumulated PosB almost exclusively in flower tissues. The flower extracts with aqueous ethanol were partially purified with activated charcoal and subjected to the enzyme reaction with reusable immobilized TCE prepared from bulb crude extracts. The reaction was completed in a few hours at room temperature, and PaB was purified with activated charcoal and ethanol in a batch-wise manner.
READemption—a tool for the computational analysis of deep-sequencing–based transcriptome data
Authors: Förstner Konrad U. , Vogel Jörg , Sharma Cynthia M. 
Published: August 2014

Abstract
Summary: RNA-Seq has become a potent and widely used method to qualitatively and quantitatively study transcriptomes. To draw biological conclusions based on RNA-Seq data, several steps, some of which are computationally intensive, have to be taken. Our READemption pipeline takes care of these individual tasks and integrates them into an easy-to-use tool with a command line interface. To leverage the full power of modern computers, most subcommands of READemption offer parallel data processing. While READemption was mainly developed for the analysis of bacterial primary transcriptomes, we have successfully applied it to analyze RNA-Seq reads from other sample types, including whole transcriptomes and RNA immunoprecipitated with proteins, not only from bacteria but also from eukaryotes and archaea.
Availability and implementation: READemption is implemented in Python and is published under the ISC open source license. The tool and documentation is hosted at http://pythonhosted.org/READemption (DOI:10.6084/m9.figshare.977849).
Contact: cynthia.sharma@uni-wuerzburg.de and konrad.foerstner@uni-wuerzburg.de
gCUP: rapid GPU-based HIV-1 co-receptor usage prediction for next-generation sequencing
Authors: Olejnik Michael , Steuwer Michel , Gorlatch Sergei , Heider Dominik 
Published: August 2014

Abstract
Summary: Next-generation sequencing (NGS) has a large potential in HIV diagnostics, and genotypic prediction models have been developed and successfully tested in the recent years. However, albeit being highly accurate, these computational models lack computational efficiency to reach their full potential.
In this study, we demonstrate the use of graphics processing units (GPUs) in combination with a computational prediction model for HIV tropism. Our new model named gCUP, parallelized and optimized for GPU, is highly accurate and can classify &gt;175 000 sequences per second on an NVIDIA GeForce GTX 460. The computational efficiency of our new model is the next step to enable NGS technologies to reach clinical significance in HIV diagnostics. Moreover, our approach is not limited to HIV tropism prediction, but can also be easily adapted to other settings, e.g. drug resistance prediction.
Availability and implementation: The source code can be downloaded at http://www.heiderlab.de
Contact: d.heider@wz-straubing.de
HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations
Authors: Usuyama Naoto , Shiraishi Yuichi , Sato Yusuke , Kume Haruki , Homma Yukio , Ogawa Seishi , Miyano Satoru , Imoto Seiya 
Published: August 2014

Abstract
Motivation: Identifying somatic changes from tumor and matched normal sequences has become a standard approach in cancer research. More specifically, this requires accurate detection of somatic point mutations with low allele frequencies in impure and heterogeneous cancer samples. Although haplotype phasing information derived by using heterozygous germ line variants near candidate mutations would improve accuracy, no somatic mutation caller that uses such information is currently available.
Results: We propose a Bayesian hierarchical method, termed HapMuC, in which power is increased by using available information on heterozygous germ line variants located near candidate mutations. We first constructed two generative models (the mutation model and the error model). In the generative models, we prepared candidate haplotypes, considering a heterozygous germ line variant if available, and the observed reads were realigned to the haplotypes. We then inferred the haplotype frequencies and computed the marginal likelihoods using a variational Bayesian algorithm. Finally, we derived a Bayes factor for evaluating the possibility of the existence of somatic mutations. We also demonstrated that our algorithm has superior specificity and sensitivity compared with existing methods, as determined based on a simulation, the TCGA Mutation Calling Benchmark 4 datasets and data from the COLO-829 cell line.
Availability and implementation: The HapMuC source code is available from http://github.com/usuyama/hapmuc.
Contact: imoto@ims.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
MindTheGap: integrated detection and assembly of short and long insertions
Authors: Rizk Guillaume , Gouin Anaïs , Chikhi Rayan , Lemaitre Claire 
Published: August 2014

Abstract
Motivation: Insertions play an important role in genome evolution. However, such variants are difficult to detect from short-read sequencing data, especially when they exceed the paired-end insert size. Many approaches have been proposed to call short insertion variants based on paired-end mapping. However, there remains a lack of practical methods to detect and assemble long variants.
Results: We propose here an original method, called M ind T he G ap , for the integrated detection and assembly of insertion variants from re-sequencing data. Importantly, it is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. M ind T he G ap uses an efficient k -mer-based method to detect insertion sites in a reference genome, and subsequently assemble them from the donor reads. M ind T he G ap showed high recall and precision on simulated datasets of various genome complexities. When applied to real Caenorhabditis elegans and human NA12878 datasets, M ind T he G ap detected and correctly assembled insertions &gt;1 kb, using at most 14 GB of memory.
Availability and implementation: http://mindthegap.genouest.org
Contact: guillaume.rizk@inria.fr or claire.lemaitre@inria.fr
Public Employment and Access to Justice in Employment Law
Authors: Rodgers Lisa 
Published: August 2014

Abstract
This paper discusses and analyses the current evolution of the exceptional employment law rules governing (certain) public sector employment and the implication of that evolution for access to justice for public employees. It starts with an analysis of the origins and justifications for the separation of the regulation of ‘private’ as opposed to ‘public’ employees and how that separation has evolved over time. The article then proceeds to outline some of the possible critiques of that separation and the potential for the challenge to that separation in theoretical terms. In the third section, there is an assessment of the practical ways in which way public employees have recently sought to challenge this separation, and particularly their exclusion from private employment law rights. It discusses the reasons for the varying degrees of success of that challenge. The final section proceeds to discuss how far public law may step in to counteract the exclusion of public employees from the employment law regime. In particular, there is a discussion of the realisation within the public law arena of a need to relax the strict separation of the public/private regime and the need to cater for particular individual circumstances.
Drug-Induced Liver Injury
Authors: Leise Michael D. 
Published: August 2014

Abstract
Despite increased awareness through the efforts of public and regulatory agencies, the syndrome known as drug-induced liver injury (DILI) is still a major public health problem in the United States and the world. Moreover, it is the single most common reason for US Food and Drug Administration (FDA) regulatory actions, including the removal of drugs from the marketplace because of DILI. Although the frequency of this clinical syndrome is low within populations, a significant clinical and economic burden is generated by DILI. This chapter highlights new developments in the field of idiosyncratic DILI and provides information about DILI from acetaminophen.
What sodium absorption lines tell us about Type Ia supernovae
Authors: Soker Noam 
Published: August 2014

Abstract
We propose that the sodium responsible for the variable Na iD absorption lines in some Type Ia supernovae (SN Ia) originate mainly from dust residing at ∼1 pc from the supernovae. In this Na-from-dust absorption (NaDA) model, the process by which the SN Ia peak luminosity releases sodium from dust at ∼1 pc from the SN is similar to the processes by which solar radiation releases sodium from cometary dust when comets approach a distance of ≲ 1 au from the Sun. The dust grains are not sublimated but rather stay intact, and release sodium by photon-stimulated desorption (or photosputtering). Some of the Na might start in the gas phase before the explosion. Weakening in absorption strength is caused by Na-ionizing radiation of the SN. We apply the NaDA model to SN 2006X and SN 2007le, and find it to comply better with the observed time variability of the Na iD absorption lines than the Na recombination model. The mass in the dusty shell of the NaDA model is much too high to be accounted for in the single-degenerate scenario for SN Ia. Therefore, the presence of variable Na iD lines in some SN Ia further weakens the already very problematic single-degenerate scenario for SN Ia.
7SL RNA represses p53 translation by competing with HuR
Authors: Abdelmohsen Kotb , Panda Amaresh C , Kang Min-Ju , Guo Rong , Kim Jiyoung , Grammatikakis Ioannis , Yoon Je-Hyun , Dudekula Dawood B , Noh Ji Heon , Yang Xiaoling , Martindale Jennifer L , Gorospe Myriam 
Published: August 2014

Abstract
Noncoding RNAs (ncRNAs) and RNA-binding proteins are potent post-transcriptional regulators of gene expression. The ncRNA 7SL is upregulated in cancer cells, but its impact upon the phenotype of cancer cells is unknown. Here, we present evidence that 7SL forms a partial hybrid with the 3′-untranslated region (UTR) of TP53 mRNA, which encodes the tumor suppressor p53. The interaction of 7SL with TP53 mRNA reduced p53 translation, as determined by analyzing p53 expression levels, nascent p53 translation and TP53 mRNA association with polysomes. Silencing 7SL led to increased binding of HuR to TP53 mRNA, an interaction that led to the promotion of p53 translation and increased p53 abundance. We propose that the competition between 7SL and HuR for binding to TP53 3′UTR contributes to determining the magnitude of p53 translation, in turn affecting p53 levels and the growth-suppressive function of p53. Our findings suggest that targeting 7SL may be effective in the treatment of cancers with reduced p53 levels.
The importance of study design for detecting differentially abundant features in high-throughput experiments
Authors: Huaien Luo , Juntao Li , Hui Burton Chia Kuan , Robson Paul , Nagarajan Niranjan 
Published: August 2014

ABSTRACTThe use of high-throughput experiments, such as RNA-seq, to simultaneously identify differentially abundant entities across conditions has become widespread, but the systematic planning of such studies is currently hampered by the lack of general-purpose tools to do so. Here we demonstrate that there is substantial variability in performance across statistical tests, normalization techniques and study conditions, potentially leading to significant wastage of resources and/or missing information in the absence of careful study design. We present a broadly applicable experimental design tool called EDDA, and the first for single-cell RNA-seq, Nanostring and Metagenomic studies, that can be used to i) rationally choose from a panel of statistical tests, ii) measure expected performance for a study and iii) plan experiments to minimize mis-utilization of valuable resources. Using case studies from recent single-cell RNA-seq, Nanostring and Metagenomics studies, we highlight its general utility and, in particular, show a) the ability to correctly model single-cell RNA-seq data and do comparisons with 1/5ththe amount of sequencing currently used and b) that the selection of suitable statistical tests strongly impacts the ability to detect biomarkers in Metagenomic studies. Furthermore, we demonstrate that a novel mode-based normalization employed in EDDA uniformly improves in robustness over existing approaches (10-20%) and increases precision to detect differential abundance by up to 140%.
Estimating Premium Sensitivity for Children's Public Health Insurance Coverage: Selection but No Death Spiral
Authors: Marton James , Ketsche Patricia G. , Snyder Angela , Adams E. Kathleen , Zhou Mei 
Published: August 2014

ObjectiveTo estimate the effect of premium increases on the probability that near‐poor and moderate‐income children disenroll from public coverage.Data SourcesEnrollment, eligibility, and claims data for Georgia's PeachCare for Kids™ (CHIP) program for multiple years.Study DesignWe exploited policy‐induced variation in premiums generated by cross‐sectional differences and changes over time in enrollee age, family size, and income to estimate the duration of enrollment as a function of the effective (per child) premium. We classify children as being of low, medium, or high illness severity.Principal FindingsA dollar increase in the per‐child premium is associated with a slight increase in a typical child's monthly probability of exiting coverage from 7.70 to 7.83 percent. Children with low illness severity have a significantly higher monthly baseline probability of exiting than children with medium or high illness severity, but the enrollment response to premium increases is similar across all three groups.ConclusionsSuccess in achieving coverage gains through public programs is tempered by persistent problems in maintaining enrollment, which is modestly affected by premium increases. Retention is subject to adverse selection problems, but premium increases do not appear to significantly magnify the selection problem in this case.
Serum soluble toll‐like receptor 2: a novel biomarker for systemic lupus erythematosus disease activity and lupus‐related cardiovascular dysfunction
Authors: Houssen Maha E. , El‐Mahdy Rasha H. , Shahin Dina A. 
Published: August 2014

AbstractAimTo assess the serum levels of soluble toll‐like receptor (sTLR2) as an endogenous negative regulator of TLR2 signaling in systemic lupus erythematosus (SLE) patients, to investigate the correlation between sTLR2 and SLE disease activity index (SELDAI), SLE‐related cardiovascular risk factors and ventricular dysfunction and to evaluate the effect of different therapeutic regimens on serum sTLR2 levels.MethodsNinety‐six SLE patients, along with 30 healthy controls, were enrolled in the study. Echocardiography measurements were performed. Serum levels of (sTLR2) were measured using enzyme‐linked immunosorbent assay (ELISA). Serum lipid profiles, uric acid and creatinine were also detected.ResultsMean serum levels of sTLR2 in SLE patients was 3.98 ± 4.4 ng/mL, which was significantly decreased as compared with that of the control group (11.3 ± 4.9 ng/mL; P < 0.0001). sTLR2 was negatively correlated with SELDAI, low‐density lipoprotein (LDL) and left ventricular diastolic dysfunction. sTLR2 levels were increased in patients receiving hydroxychloroquine, statins and corticosteroids.ConclusionSerum sTLR2 can attenuate disease activity and negatively impact left ventricular diastolic dysfunction and hypercholersterelemia in SLE patients. Statins, corticosteroids and chloroquine increase sTLR2 levels.