bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrically switchable polymer stabilised broadband infrared reflectors and their potential as smart windows for energy saving in buildings
Authors: Khandelwal Hitesh , Loonen Roel C. G. M. , Hensen Jan L. M. , Debije Michael G. , Schenning Albertus P. H. J. 
Published: July 2015

AbstractElectrically switchable broadband infrared reflectors that are relatively transparent in the visible region have been fabricated using polymer stabilised cholesteric liquid crystals. The IR reflectors can change their reflection/transmission properties by applying a voltage in response to changes in environmental conditions. Simulations predict that a significant amount of energy can be saved on heating, cooling and lighting of buildings in places such as Madrid by using this switchable IR reflector. We have also fabricated a switchable IR reflector which can also generate electricity. These polymer based switchable IR reflectors are of high potential as windows of automobiles and buildings to control interior temperatures and save energy.
Chromosome Scaffold is a Double-Stranded Assembly of Scaffold Proteins
Authors: Poonperm Rawin , Takata Hideaki , Hamano Tohru , Matsuda Atsushi , Uchiyama Susumu , Hiraoka Yasushi , Fukui Kiichi 
Published: July 2015

AbstractChromosome higher order structure has been an enigma for over a century. The most important structural finding has been the presence of a chromosome scaffold composed of non-histone proteins; so-called scaffold proteins. However, the organization and function of the scaffold are still controversial. Here, we use three dimensional-structured illumination microscopy (3D-SIM) and focused ion beam/scanning electron microscopy (FIB/SEM) to reveal the axial distributions of scaffold proteins in metaphase chromosomes comprising two strands. We also find that scaffold protein can adaptably recover its original localization after chromosome reversion in the presence of cations. This reversion to the original morphology underscores the role of the scaffold for intrinsic structural integrity of chromosomes. We therefore propose a new structural model of the chromosome scaffold that includes twisted double strands, consistent with the physical properties of chromosomal bending flexibility and rigidity. Our model provides new insights into chromosome higher order structure.
Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase
Authors: Goulas Theodoros , Mizgalska Danuta , Garcia-Ferrer Irene , Kantyka Tomasz , Guevara Tibisay , Szmigielski Borys , Sroka Aneta , Millán Claudia , Usón Isabel , Veillard Florian , Potempa Barbara , Mydel Piotr , Solà Maria , Potempa Jan , Gomis-Rüth F. Xavier 
Published: July 2015

AbstractCitrullination is a post-translational modification of higher organisms that deiminates arginines in proteins and peptides. It occurs in physiological processes but also pathologies such as multiple sclerosis, fibrosis, Alzheimer’s disease and rheumatoid arthritis (RA). The reaction is catalyzed by peptidylarginine deiminases (PADs), which are found in vertebrates but not in lower organisms. RA has been epidemiologically associated with periodontal disease, whose main infective agent is Porphyromonas gingivalis. Uniquely among microbes, P. gingivalis secretes a PAD, termed PPAD (Porphyromonas peptidylarginine deiminase), which is genetically unrelated to eukaryotic PADs. Here, we studied function of PPAD and its substrate-free, substrate-complex and substrate-mimic-complex structures. It comprises a flat cylindrical catalytic domain with five-fold α/β-propeller architecture and a C-terminal immunoglobulin-like domain. The PPAD active site is a funnel located on one of the cylinder bases. It accommodates arginines from peptide substrates after major rearrangement of a “Michaelis loop” that closes the cleft. The guanidinium and carboxylate groups of substrates are tightly bound, which explains activity of PPAD against arginines at C-termini but not within peptides. Catalysis is based on a cysteine-histidine-asparagine triad, which is shared with human PAD1-PAD4 and other guanidino-group modifying enzymes. We provide a working mechanism hypothesis based on 18 structure-derived point mutants.
Reorganization of corticospinal tract fibers after spinal cord injury in adult macaques
Authors: Nakagawa Hiroshi , Ninomiya Taihei , Yamashita Toshihide , Takada Masahiko 
Published: July 2015

AbstractPrevious studies have shown that sprouting of corticospinal tract (CST) fibers after spinal cord injury (SCI) contributes to recovery of motor functions. However, the neuroanatomical mechanism underlying the functional recovery through sprouting CST fibers remains unclear. Here we investigated the pattern of reorganization of CST fibers below the lesion site after SCI in adult macaques. Unilateral lesions were made at the level between the C7 and the C8 segment. The extent of spontaneous recovery of manual dexterity was assessed with a reaching/grasping task. The impaired dexterous manual movements were gradually recovered after SCI. When anterograde tract tracing with biotinylated dextran amine was performed to identify the intraspinal reinnervation of sprouting CST fibers, it was found that the laminar distribution of CST fibers was changed. The sprouting CST fibers extended preferentially into lamia IX where the spinal motor neuron pool was located, to innervate the motor neurons directly. Instead, few, if any, CST fibers were distributed in the dorsal laminae. The present results indicate that CST fibers below the lesion site after SCI in macaques are reorganized in conjunction with the recovery of dexterous manual movements.
Distinct roles for GABA across multiple timescales in mammalian circadian timekeeping
Authors: DeWoskin Daniel , Myung Jihwan , Belle Mino D. C. , Piggins Hugh D. , Takumi Toru , Forger Daniel B. 
Published: July 2015

Significance
Each day, over 50 billion synaptic signals, mediated by the neurotransmitter GABA, are sent between neurons in the central circadian pacemaker in the mammalian brain to time and coordinate daily events. Although GABA is the only signaling molecule sent and received by most, if not all of these neurons, its role is not well understood. Past studies have shown paradoxically that GABA can synchronize and desynchronize, as well as excite and inhibit, clock neurons. Through experiments and modeling characterizing the role of GABA in timekeeping, we propose the existence of two types of differentially regulated GABA signaling—fast signaling that regulates neuronal output, and slow signaling that modulates synchrony between neurons—a hypothesis that can explain many previous experimental results.
Delicate conformational balance of the redox enzyme cytochrome P450cam
Authors: Skinner Simon P. , Liu Wei-Min , Hiruma Yoshitaka , Timmer Monika , Blok Anneloes , Hass Mathias A. S. , Ubbink Marcellus 
Published: July 2015

Significance
The ubiquitous enzymes called cytochromes P450 catalyze a broad range of chemical reactions using molecular oxygen. For example, in humans, these enzymes are involved in breakdown of foreign compounds, including drugs. The bacterial cytochrome P450cam is thought to open up to allow substrate to enter the active site, and then to close during catalysis to keep reactive intermediates inside. Surprisingly, recent crystal structures suggested that the enzyme is open during the reaction. We have studied the enzyme in solution using paramagnetic NMR spectroscopy, demonstrating that, in fact, the enzyme is closed. This finding indicates that the subtle balance between open and closed is affected by crystallization, which can lead to the wrong conclusions about the protein dynamics.
Structural characterization of the interaction of Ubp6 with the 26S proteasome
Authors: Aufderheide Antje , Beck Florian , Stengel Florian , Hartwig Michaela , Schweitzer Andreas , Pfeifer Günter , Goldberg Alfred L. , Sakata Eri , Baumeister Wolfgang , Förster Friedrich 
Published: July 2015

Significance
In eukaryotic cells the 26S proteasome is responsible for the regulated degradation of intracellular proteins. The function of this large macromolecular machine is regulated by many cofactors, most notably the deubiquitylating enzyme ubiquitin C-terminal hydrolase 6 (Ubp6). Here, we investigate the structure of Ubp6 bound to the 26S proteasome and explore its influence on the conformational landscape of the 26S proteasome. Our structure reveals that Ubp6’s active site may contribute to a large composite active site, also formed by the mouth of the proteasomal ATPase ring and the active site of deubiquitylating enzyme regulatory particle non-ATPase 11. Moreover, Ubp6 modulates the conformational landscape of the proteasome, favoring an intermediate state, which may explain the effects of Ubp6 on proteasomal degradation.
THE HCN/HNC ABUNDANCE RATIO TOWARD DIFFERENT EVOLUTIONARY PHASES OF MASSIVE STAR FORMATION
Authors: Jin Miwha , Lee Jeong-Eun , Kim Kee-Tae 
Published: July 2015

ABSTRACT
Using the H13CN and HN13C J = 1–0 line observations, the abundance ratio of HCN/HNC has been estimated for different evolutionary stages of massive star formation: infrared dark clouds (IRDCs), high-mass protostellar objects (HMPOs), and ultracompact H ii regions (UCH iis). IRDCs were divided into “quiescent IRDC cores (qIRDCc)” and “active IRDC cores (aIRDCc),” depending on star formation activity. The HCN/HNC ratio is known to be higher at active and high temperature regions related to ongoing star formation, compared to cold and quiescent regions. Our observations toward 8 qIRDCc, 16 aIRDCc, 23 HMPOs, and 31 UCH iis show consistent results; the ratio is 0.97 (±0.10), 2.65 (±0.88), 4.17 (±1.03), and 8.96 (±3.32) in these respective evolutionary stages, increasing from qIRDCc to UCH iis. The change of the HCN/HNC abundance ratio, therefore, seems directly associated with the evolutionary stages of star formation, which have different temperatures. One suggested explanation for this trend is the conversion of HNC to HCN, which occurs effectively at higher temperatures. To test the explanation, we performed a simple chemical model calculation. In order to fit the observed results, the energy barrier of the conversion must be much lower than the value provided by theoretical calculations.
Integrating full spectrum of sequence features into predicting functional microRNA–mRNA interactions
Authors: Wang Zixing , Xu Wenlong , Liu Yin 
Published: July 2015

AbstractMotivation: MicroRNAs (miRNAs) play important roles in general biological processes and diseases pathogenesis. Identifying miRNA target genes is an essential step to fully understand the regulatory effects of miRNAs. Many computational methods based on the sequence complementary rules and the miRNA and mRNA expression profiles have been developed for this purpose. It is noted that there have been many sequence features of miRNA targets available, including the context features of the target sites, the thermodynamic stability and the accessibility energy for miRNA-mRNA interaction. However, most of current computational methods that combine sequence and expression information do not effectively integrate full spectrum of these features; instead, they perceive putative miRNA–mRNA interactions from sequence-based prediction as equally meaningful. Therefore, these sequence features have not been fully utilized for improving miRNA target prediction.Results: We propose a novel regularized regression approach that is based on the adaptive Lasso procedure for detecting functional miRNA–mRNA interactions. Our method fully takes into account the gene sequence features and the miRNA and mRNA expression profiles. Given a set of sequence features for each putative miRNA–mRNA interaction and their expression values, our model quantifies the down-regulation effect of each miRNA on its targets while simultaneously estimating the contribution of each sequence feature to predicting functional miRNA–mRNA interactions. By applying our model to the expression datasets from two cancer studies, we have demonstrated our prediction results have achieved better sensitivity and specificity and are more biologically meaningful compared with those based on other methods.Availability and implementation: The source code is available at: http://nba.uth.tmc.edu/homepage/liu/miRNALasso.Supplementary information: Supplementary data are available at Bioinformatics online.Contact: Yin.Liu@uth.tmc.edu
Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics
Authors: Ren Jie , Song Kai , Deng Minghua , Reinert Gesine , Cannon Charles H. , Sun Fengzhu 
Published: July 2015

Abstract
Motivation: Next-generation sequencing (NGS) technologies generate large amounts of short read data for many different organisms. The fact that NGS reads are generally short makes it challenging to assemble the reads and reconstruct the original genome sequence. For clustering genomes using such NGS data, word-count based alignment-free sequence comparison is a promising approach, but for this approach, the underlying expected word counts are essential.
A plausible model for this underlying distribution of word counts is given through modeling the DNA sequence as a Markov chain (MC). For single long sequences, efficient statistics are available to estimate the order of MCs and the transition probability matrix for the sequences. As NGS data do not provide a single long sequence, inference methods on Markovian properties of sequences based on single long sequences cannot be directly used for NGS short read data.
Results: Here we derive a normal approximation for such word counts. We also show that the traditional Chi-square statistic has an approximate gamma distribution, using the Lander-Waterman model for physical mapping. We propose several methods to estimate the order of the MC based on NGS reads and evaluate those using simulations. We illustrate the applications of our results by clustering genomic sequences of several vertebrate and tree species based on NGS reads using alignment-free sequence dissimilarity measures. We find that the estimated order of the MC has a considerable effect on the clustering results, and that the clustering results that use an MC of the estimated order give a plausible clustering of the species.
Availability and implementation: Our implementation of the statistics developed here is available as R package ‘NGS.MC’ at http://www-rcf.usc.edu/∼fsun/Programs/NGS-MC/NGS-MC.html.
Contact: fsun@usc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Differences Between New Immigrants From the Former Soviet Union and Veteran Residents in Knowledge, Perception, and Risk Factors of Stroke
Authors: Melnikov Semyon , Itzhaki Michal , Koton Silvia 
Published: July 2015

Background:
Stroke is the fourth most common cause of death in developed countries and a leading cause of acquired disability in adults. Awareness of risk factors and warning signs for stroke has a considerable impact on early arrival at the hospital and early thrombolytic treatment. Delays in seeking medical treatment following the onset of stroke symptoms have been shown to be more common among ethnic minorities.

Objective:
The aim of the current study was to examine stroke awareness and knowledge among new immigrants from the Former Soviet Union (IFSUs) compared with veteran residents (VRs).

Methods:
The study was conducted by students of the nursing master of arts program. Data were collected during March 2010 and June 2014. Trained registered nurses conducted interviews, using a structured, pretested, open-ended questionnaire. Participants were recruited by a snowball method from among the interviewers’ friends and family members, 40 years or older with no history of stroke.

Results:
A total of 643 Israelis, 420 VRs (65.3%) and 223 IFSUs (34.7%), were interviewed; 40.7% were men, with a mean age of 52.6 (SD, 9.3) years. Compared with VRs, IFSUs were more likely to report previous myocardial infarction (P = .022), hypertension (P < .001), and diabetes (P = .012). The mean number of stroke warning signs reported by IFSUs was higher than that reported by VRs (P = .031). When asked about risk factors for stroke, IFSUs more often stated hypertension (P = .03), whereas VRs more often reported family history (P = .03). Immigrants from the Former Soviet Union were more aware of strategies for the prevention of stroke than VRs (P = .02). The preferred sources of information about stroke for IFSUs, as distinguished from VRs, were personal doctors (P = .001) and radio programs (P = .03).

Conclusions:
Veteran residents showed lower levels of knowledge about stroke. Educational campaigns aimed at increasing knowledge of stroke among Israel’s general population in Israel, as well as culturally targeting specific subgroups, are recommended.
Pantoea intestinalis sp. nov., isolated from the human gut
Authors: Prakash Om , Nimonkar Yogesh , Vaishampayan Ankita , Mishra Mrinal , Kumbhare Shreyas , Josef Neetha , Shouche Yogesh S. 
Published: July 2015

A novel bacterial strain, 29Y89BT, was isolated from a faecal sample of a healthy human subject. Cells were Gram-stain-negative, motile, non-spore-forming and rod-shaped. Strain 29Y89BT formed cream-coloured colonies 2 mm in diameter on trypticase soy agar and showed optimum growth at 35 °C. Strain 29Y89BT showed highest 16S rRNA gene sequence similarity to Pantoea gaviniae A18/07T (98.4 %) followed by Pantoea calida 1400/07T (97.2 %). Multi-locus sequence analysis using atpD (ATP synthase β subunit), gyrB (DNA gyrase), infB (initiation translation factor 2) and rpoB (RNA polymerase β subunit) genes also supported the result of 16S rRNA gene sequence based phylogeny. Strain 29Y89BT showed 62 and 40.7 % DNA–DNA relatedness with P. calida DSM 22759T and P. gaviniae DSM 22758T. Strain 29Y89BT contained C17
: 0 cyclo, C19
: 0 cyclo ω8c, C16 : 0, C14 : 0 and C12 : 0 as predominant fatty acids. In addition, strain 29Y89BT showed physiological and phenotypic differences from its closest relatives P. gaviniae DSM 22758T and P. calida DSM 22759T. The polar lipid profile mainly comprised phospholipids. The DNA G+C content was 59.1 mol%. Thus, based on the findings of the current study, strain 29Y89BT showed clear delineations from its closest relatives P. gaviniae DSM 22758T and P. calida DSM 22759T, and is thus considered to represent a novel species of the genus Pantoea, for which the name Pantoea intestinalis sp. nov. is proposed. The type strain is 29Y89BT ( = DSM 28113T = MCC 2554T).
SARTools: a DESeq2- and edgeR-based R pipeline for comprehensive differential analysis of RNA-Seq data
Authors: Varet Hugo , Coppée Jean-Yves , Dillies Marie-Agnès 
Published: July 2015

AbstractBackgroundSeveral R packages exist for the detection of differentially expressed genes from RNA-Seq data. The analysis process includes three main steps, namely normalization, dispersion estimation and test for differential expression. Quality control steps along this process are recommended but not mandatory, and failing to check the characteristics of the dataset may lead to spurious results. In addition, normalization methods and statistical models are not exchangeable across the packages without adequate transformations the users are often not aware of. Thus, dedicated analysis pipelines are needed to include systematic quality control steps and prevent errors from misusing the proposed methods.ResultsSARTools is an R pipeline for differential analysis of RNA-Seq count data. It can handle designs involving two or more conditions of a single biological factor with or without a blocking factor (such as a batch effect or a sample pairing). It is based on DESeq2 and edgeR and is composed of an R package and two R script templates (for DESeq2 and edgeR respectively). Tuning a small number of parameters and executing one of the R scripts, users have access to the full results of the analysis, including lists of differentially expressed genes and a HTML report that (i) displays diagnostic plots for quality control and model hypotheses checking and (ii) keeps track of the whole analysis process, parameter values and versions of the R packages used.ConclusionsSARTools provides systematic quality controls of the dataset as well as diagnostic plots that help to tune the model parameters. It gives access to the main parameters of DESeq2 and edgeR and prevents untrained users from misusing some functionalities of both packages. By keeping track of all the parameters of the analysis process it fits the requirements of reproducible research.
Confirmation and evaluation of performance measurement model for the Thai frozen shrimp chain
Authors: Pungchompoo Sirirat , Sopadang Apichat 
Published: July 2015

Purpose
– The purpose of this paper is to investigate and evaluate the new performance measurement model for the Thai frozen shrimp chain.

Design/methodology/approach
– The performance measurement model was developed by the combination method between a structural equation modeling and an analytical hierarchy process, which the method confirmed and proved the construction of the framework and identified the important key performance indicators of the chain from different supply chain members’ point of views.

Findings
– The results showed that the model is reliable and valid as well as being theoretically acceptable on the basis of performance measurement foundations. Furthermore, the financial and the customer perspectives are demonstrated as the first to be prioritized in order to evaluate the performance.

Research limitations/implications
– Two limitations should be considered. First, small sample size of this study is a limitation. Hence, further study should consider on enough sample size. A next limitation, different points of view from participants has effect on factor loading which represented minus value on the research model. Therefore, the future research should apply several techniques, such as the fuzzy set and data envelopment analysis.

Originality/value
– The contribution of this study is the new performance measurement model which based on the integrated conceptual ideas and the synthesizing methods for evaluating the Thai frozen shrimp chain.