bluuebunny/crossref_metadata_2025_split huggingface dataset:
CpG island erosion, polycomb occupancy and sequence motif enrichment at bivalent promoters in mammalian embryonic stem cells
Authors: Mantsoki Anna , Devailly Guillaume , Joshi Anagha 
Published: November 2015

AbstractIn embryonic stem (ES) cells, developmental regulators have a characteristic bivalent chromatin signature marked by simultaneous presence of both activation (H3K4me3) and repression (H3K27me3) signals and are thought to be in a ‘poised’ state for subsequent activation or silencing during differentiation. We collected eleven pairs (H3K4me3 and H3K27me3) of ChIP sequencing datasets in human ES cells and eight pairs in murine ES cells and predicted high-confidence (HC) bivalent promoters. Over 85% of H3K27me3 marked promoters were bivalent in human and mouse ES cells. We found that (i) HC bivalent promoters were enriched for developmental factors and were highly likely to be differentially expressed upon transcription factor perturbation; (ii) murine HC bivalent promoters were occupied by both polycomb repressive component classes (PRC1 and PRC2) and grouped into four distinct clusters with different biological functions; (iii) HC bivalent and active promoters were CpG rich while H3K27me3-only promoters lacked CpG islands. Binding enrichment of distinct sets of regulators distinguished bivalent from active promoters. Moreover, a ‘TCCCC’ sequence motif was specifically enriched in bivalent promoters. Finally, this analysis will serve as a resource for future studies to further understand transcriptional regulation during embryonic development.
Anti-inflammatory activity of low molecular weight polysialic acid on human macrophages
Authors: Shahraz Anahita , Kopatz Jens , Mathy Rene , Kappler Joachim , Winter Dominic , Kapoor Shoba , Schütza Vlad , Scheper Thomas , Gieselmann Volkmar , Neumann Harald 
Published: November 2015

AbstractOligosialic and polysialic acid (oligoSia and polySia) of the glycocalyx of neural and immune cells are linear chains, in which the sialic acid monomers are α2.8-glycosidically linked. Sialic acid-binding immunoglobulin-like lectin-11 (SIGLEC-11) is a primate-lineage specific receptor of human tissue macrophages and microglia that binds to α2.8-linked oligoSia. Here, we show that soluble low molecular weight polySia with an average degree of polymerization 20 (avDP20) interacts with SIGLEC-11 and acts anti-inflammatory on human THP1 macrophages involving the SIGLEC-11 receptor. Soluble polySia avDP20 inhibited the lipopolysaccharide (LPS)-induced gene transcription and protein expression of tumor necrosis factor-α (Tumor Necrosis Factor Superfamily Member 2, TNFSF2). In addition, polySia avDP20 neutralized the LPS-triggered increase in macrophage phagocytosis, but did not affect basal phagocytosis or endocytosis. Moreover, polySia avDP20 prevented the oxidative burst of human macrophages triggered by neural debris or fibrillary amyloid-β1–42. In a human macrophage-neuron co-culture system, polySia avDP20 also reduced loss of neurites triggered by fibrillary amyloid-β1–42. Thus, treatment with polySia avDP20 might be a new anti-inflammatory therapeutic strategy that also prevents the oxidative burst of macrophages.
Mutant cohesin affects RNA polymerase II regulation in Cornelia de Lange syndrome
Authors: Mannini Linda , C. Lamaze Fabien , Cucco Francesco , Amato Clelia , Quarantotti Valentina , Rizzo Ilaria M , Krantz Ian D , Bilodeau Steve , Musio Antonio 
Published: November 2015

AbstractIn addition to its role in sister chromatid cohesion, genome stability and integrity, the cohesin complex is involved in gene transcription. Mutations in core cohesin subunits SMC1A, SMC3 and RAD21, or their regulators NIPBL and HDAC8, cause Cornelia de Lange syndrome (CdLS). Recent evidence reveals that gene expression dysregulation could be the underlying mechanism for CdLS. These findings raise intriguing questions regarding the potential role of cohesin-mediated transcriptional control and pathogenesis. Here, we identified numerous dysregulated genes occupied by cohesin by combining the transcriptome of CdLS cell lines carrying mutations in SMC1A gene and ChIP-Seq data. Genome-wide analyses show that genes changing in expression are enriched for cohesin-binding. In addition, our results indicate that mutant cohesin impairs both RNA polymerase II (Pol II) transcription initiation at promoters and elongation in the gene body. These findings highlight the pivotal role of cohesin in transcriptional regulation and provide an explanation for the typical gene dysregulation observed in CdLS patients.
On the Stability and Abundance of Single Walled Carbon Nanotubes
Authors: Hedman Daniel , Reza Barzegar Hamid , Rosén Arne , Wågberg Thomas , Andreas Larsson J. 
Published: November 2015

AbstractMany nanotechnological applications, using single-walled carbon nanotubes (SWNTs), are only possible with a uniform product. Thus, direct control over the product during chemical vapor deposition (CVD) growth of SWNT is desirable and much effort has been made towards the ultimate goal of chirality-controlled growth of SWNTs. We have used density functional theory (DFT) to compute the stability of SWNT fragments of all chiralities in the series representing the targeted products for such applications, which we compare to the chiralities of the actual CVD products from all properly analyzed experiments. From this comparison we find that in 84% of the cases the experimental product represents chiralities among the most stable SWNT fragments (within 0.2 eV) from the computations. Our analysis shows that the diameter of the SWNT product is governed by the well-known relation to size of the catalytic nanoparticles and the specific chirality is normally determined by the product’s relative stability, suggesting thermodynamic control at the early stage of product formation. Based on our findings, we discuss the effect of other experimental parameters on the chirality of the product. Furthermore, we highlight the possibility to produce any tube chirality in the context of recent published work on seeded-controlled growth.
Undernourishment in utero Primes Hepatic Steatosis in Adult Mice Offspring on an Obesogenic Diet; Involvement of Endoplasmic Reticulum Stress
Authors: Muramatsu-Kato Keiko , Itoh Hiroaki , Kohmura-Kobayashi Yukiko , Ferdous Urmi J. , Tamura Naoaki , Yaguchi Chizuko , Uchida Toshiyuki , Suzuki Kazunao , Hashimoto Koshi , Suganami Takayoshi , Ogawa Yoshihiro , Kanayama Naohiro 
Published: November 2015

AbstractIn order to investigate the possible involvement of endoplasmic reticulum (ER) stress in the developmental origins of hepatic steatosis associated with undernourishment in utero, we herein employed a fetal undernourishment mouse model by maternal caloric restriction in three cohorts; cohort 1) assessment of hepatic steatosis and the ER stress response at 9 weeks of age (wks) before a high fat diet (HFD), cohort 2) assessment of hepatic steatosis and the ER stress response on a HFD at 17 wks, cohort 3) assessment of hepatic steatosis and the ER stress response at 22 wks on a HFD after the alleviation of ER stress with a chemical chaperone, tauroursodeoxycholic acid (TUDCA), from 17 wks to 22 wks. Undernourishment in utero significantly deteriorated hepatic steatosis and led to the significant integration of the ER stress response on a HFD at 17 wks. The alleviation of ER stress by the TUDCA treatment significantly improved the parameters of hepatic steatosis in pups with undernourishment in utero, but not in those with normal nourishment in utero at 22 wks. These results suggest the pivotal involvement of the integration of ER stress in the developmental origins of hepatic steatosis in association with undernourishment in utero.
Robust Photocatalytic H2O2 Production by Octahedral Cd3(C3N3S3)2 Coordination Polymer under Visible Light
Authors: Zhuang Huaqiang , Yang Lifang , Xu Jie , Li Fuying , Zhang Zizhong , Lin Huaxiang , Long Jinlin , Wang Xuxu 
Published: November 2015

AbstractHerein, we reported a octahedral Cd3(C3N3S3)2 coordination polymer as a new noble metal-free photocatalyst for robust photocatalytic H2O2 production from methanol/water solution. The coordination polymer can give an unprecedented H2O2 yield of ca. 110.0 mmol • L−1 • g−1 at pH = 2.8 under visible light illumination. The characterization results clearly revealed that the photocatalytic H2O2 production proceeds by a pathway of two-electron reduction of O2 on the catalyst surface. This work showed the potential perspective of Mx(C3N3S3)y (M = transitional metals) coordination polymers as a series of new materials for solar energy storage and conversion.
Arrays of coupled chemical oscillators
Authors: Forrester Derek Michael 
Published: November 2015

AbstractOscillating chemical reactions result from complex periodic changes in the concentration of the reactants. In spatially ordered ensembles of candle flame oscillators the fluctuations in the ratio of oxygen atoms with respect to that of carbon, hydrogen and nitrogen produces an oscillation in the visible part of the flame related to the energy released per unit mass of oxygen. Thus, the products of the reaction vary in concentration as a function of time, giving rise to an oscillation in the amount of soot and radiative emission. Synchronisation of interacting dynamical sub-systems occurs as arrays of flames that act as master and slave oscillators, with groups of candles numbering greater than two, creating a synchronised motion in three-dimensions. In a ring of candles the visible parts of each flame move together, up and down and back and forth, in a manner that appears like a “worship”. Here this effect is shown for rings of flames which collectively empower a central flame to pulse to greater heights. In contrast, situations where the central flames are suppressed are also found. The phenomena leads to in-phase synchronised states emerging between periods of anti-phase synchronisation for arrays with different columnar sizes of candle and positioning.
Ultrabroadband, More than One Order Absorption Enhancement in Graphene with Plasmonic Light Trapping
Authors: Xiong Feng , Zhang Jianfa , Zhu Zhihong , Yuan Xiaodong , Qin Shiqiao 
Published: November 2015

AbstractThis paper presents an comprehensive study of light trapping and absorption enhancement in graphene through metallic plasmonic structures and shows a strategy to realize both ultrabroadband and strong absorption enhancement. Three different plasmonic absorber designs are investigated by numerical simulations. The excitation of localized plasmons in the metallic structures significantly enhances the interactions between graphene and light at the resonances. By employing a splitted cross design for plasmonic resonant antennas and integrating two types of sub-antennas with different sizes, more than 30% of optical absorption in monolayer graphene is realized in a ultrabroad spectral range from 780 to 1760 nm. This enhancement functionality can be translated to any wavelength band from ultraviolet to terahertz ranges by modifying the geometric design of the plasmonic structure and can be applied for other two dimensional materials and their heterogeneous structures. It may significantly improve the efficiency of optical devices such as broadband photodetectors and solar cells based on graphene and other two-dimensional materials.
The conceptualization of change of state in verbs coming from gentilicios
Authors: Barrajón López Elisa 
Published: November 2015

This paper has as its aim to examine the way in which the meaning of the derivative base (regardless of its denominal or deadjectival nature, although it will be demonstrated here that it rather follows an adjectival behavior) influences the semantics of verbs coming from gentilicios (africanizar/se, gauchear, etc.) and, consequently, to identify the underlying argument structure in each case, as well as their main aspectual properties. The conceptual components involved in the process leading to the formation of these complex units can appear explicitly or amalgamate with the verb. According to the semantically conflated component, the argument scheme will be different: Hacer X a Y [To make Y become X], Hacerse X [To become X] or Comportarse X [To behave X]. Nevertheless, it is worth highlighting that the border between the last two schemes is not always clear.
Causativity and psychological verbs in Spanish
Authors: Cifuentes Honrubia José Luis 
Published: November 2015

This paper analyzes the transitive/intransitive alternation in class 2 psychological verbs of Belletti and Rizzi. The transitive variant implies an agentive subject and an aspectual change of state. The intransitive variant implies a cause and a locative state. Spanish class 2 psychological verbs are causative due to the cause component conflated in the verbal structure which gives rise to the verb: most of the psychological verbs with a transitive/intransitive alternation are denominal or deadjetival causative verbs from Romance origin. Some others come from a Latin denominal or deadjectival structure or from a causative meaning which comes as a result of an evolution in their meaning (usually agentive and local). Psychological verbs result from a conflation process by means of which the verb semantically incorporates the psychological element – as it results from a verbal lexicalization of the emotional or psychological noun or adjective, thus shaping a complex predicate. Psychological verbs are consequently complex predicates with a semantically incorporated psychological element.
Agent control over non culminating events
Authors: Demirdache Hamida , Martin Fabienne 
Published: November 2015

This paper investigates a correlation between the availability of non-culminating construals for accomplishments and the control of the agent over the described event (the Agent Control Hypothesis, ach). We consider two versions of the ach, on the basis of a new typology of non-culminating construals. On the strong version, non-culmination requires agent control whether what is being denied is the occurrence of any change of state of the type φ encoded by the verb, or merely that the change of state satisfies the property φ to degree 1. On its weak version, agent control is required in the former case only. The evidence reviewed from Romance, Germanic, Salish, and Mandarin, suggests that the weak version of the ach might indeed hold. The weak version of the ach seems, however, to be too weak for Salish languages. The final section shows how the existing analyses of non-culminating construals could capture the link between non-culmination and agentivity.
Regular Exercise and Depressive Symptoms in Community-Dwelling Elders in Northern Taiwan
Authors: Chang Shu-Hung , Chien Nai-Hui , Chen Miao-Chuan 
Published: November 2015

ABSTRACT

Background:
According to World Health Organization, depressive disorder will be a Top 2 disease in the world by 2020. In light of Taiwan’s rapidly increasing elderly population, elderly psychological health is expected to become an increasingly important issue in healthcare.

Purpose:
This study examines the association between regular exercise and depressive symptoms in community-dwelling older adults by gender in northern Taiwan.

Methods:
The participants were selected using a probability-proportional-to-size procedure from community-dwelling adults who were aged 65 years or older and living in northern Taiwan. A cross-sectional study and interviews were used to collect information about their exercise behaviors, depressive symptoms, and the factors influencing the depressive symptoms. Percentage, chi-square, t test, and logistic regression were used to analyze the data.

Result:
One thousand twenty elderly individuals completed the questionnaires. Among the participants with the average age of 73.5 years, 44.5% were men, and 55.5% were women. Two hundred seventeen of the participants (21.3%) had depressive symptoms. Five hundred eighty-five of the participants (57.4%) exercised regularly. The result of logistic regression showed that regular exercise was a significant predictor of depressive symptoms in elderly individuals (odds ratio = 3.54, 95% confidence interval [1.76, 7.12]). Other factors such as gender, chronicle diseases, and health status were not related to depressive symptoms. Moreover, both for male and female individuals, regular exercise was a significant predictor of depressive symptoms (odds ratio = 4.76, 95% confidence interval [1.65, 13.72] and odds ratio = 3.03, 95% confidence interval [1.18, 7.69], respectively). Other factors were not related to depressive symptoms.

Conclusions/Implications for Practice:
This study shows regular exercise to be a significant predictor of depressive symptoms in both men and women. Therefore, senior citizens should be encouragedto exercise regularly as a way to promote good mental health.
Validation of the Chinese Version of the Readiness for Hospital Discharge Scale on Patients Who Have Undergone Laryngectomy
Authors: Zhao Huiling , Feng Xianqiong , Yu Rong , Gu Deying , Ji Xiaoqin 
Published: November 2015

ABSTRACT

Background:
The Readiness for Hospital Discharge Scale (RHDS) was designed to assess the readiness of patients for discharge. The original English-language instrument has shown high degrees of reliability and validity, but no Chinese version of the scale has been verified.

Purpose:
The purpose of this study was to translate the RHDS into Chinese and assess the psychometric properties of this scale on laryngectomy patients in China.

Methods:
The RHDS was translated into Chinese using forward and back translation, semantic equivalence assessment, and pilot testing. The content and construct validity, internal consistency, and internal reliability of the translated scale were assessed using exploratory factor analysis and Pearson correlation analysis.

Results:
The content validity index of the developed Chinese version of the RHDS was .97, with the content validity indexes of RHDS items ranging between .75 and 1.00. The Cronbach’s α coefficient for internal consistency was .97. Exploratory factor analysis revealed a three-factor structural model. All correlations among the three factor subscales were significant. Pearson’s correlation coefficients between subscale factors and the total scale ranged from .81 to .97.

Conclusions:
The Chinese version of the RHDS is a valid and reliable instrument for assessing the discharge readiness of laryngectomy patients in China.
Centromere Detection of Human Metaphase Chromosome Images using a Candidate Based Method
Authors: Subasinghe Akila , Samarabandu Jagath , Li Yanxin , Wilkins Ruth , Flegal Farrah , Knoll Joan H. , Rogan Peter K. 
Published: November 2015

AbstractAccurate detection of the human metaphase chromosome centromere is an critical element of cytogenetic diagnostic techniques, including chromosome enumeration, karyotyping and radiation biodosimetry. Existing image processing methods can perform poorly in the presence of irregular boundaries, shape variations and premature sister chromatid separation, which can adversely affect centromere localization. We present a centromere detection algorithm that uses a novel profile thickness measurement technique on irregular chromosome structures defined by contour partitioning. Our algorithm generates a set of centromere candidates which are then evaluated based on a set of features derived from images of chromosomes. Our method also partitions the chromosome contour to isolate its telomere regions and then detects and corrects for sister chromatid separation. When tested with a chromosome database consisting of 1400 chromosomes collected from 40 metaphase cell images, the candidate based centromere detection algorithm was able to accurately localize 1220 centromere locations yielding a detection accuracy of 87%. We also introduce a Candidate Based Centromere Confidence (CBCC) metric which indicates an approximate confidence value of a given centromere detection and can be readily extended into other candidate related detection problems.
Actin activatesPseudomonas aeruginosaExoY nucleotidyl cyclase toxin and ExoY-like effector domains from MARTX toxins
Authors: Raoux-Barbot Dorothée , Saveanu Cosmin , Namane Abdelkader , Ogryzko Vasily , Worpenberg Lina , Fellous Souad , Assayag Elodie , Ladant Daniel , Renault Louis , Mechold Undine 
Published: November 2015

ABSTRACTPseudomonas aeruginosais a major cause of chronic infections in cystic fibrosis patients. The nucleotidyl cyclase toxin ExoY is a virulence factors injected by the pathogen and associated with severe damage to lung tissue. ExoY-like cyclases are also found in other Gram-negative pathogens and shown to contribute to virulence, although they remained poorly characterized. Here we demonstrate that filamentous actin (F-actin) is the hitherto unknown co-factor that activatesP. aeruginosaExoY within host target cells. Highly purified actin, when polymerized into filaments, potently stimulates (>10,000 fold) ExoY activity. ExoY co-localizesin vivowith actin filaments in transfected cells and,in vitro, it interferes with the regulation of actin assembly/disassembly-dynamics mediated by important F-actin-binding proteins. We further show that actin also activates an ExoY-like adenylate cyclase from aVibriospecies. Our results thus highlight a new sub-class within the class II adenylyl cyclase family, defined as actin-activated nucleotidyl cyclase (AA-NC) toxins.
XMRF: An R package to Fit Markov Networks to High-Throughput Genetics Data
Authors: Wan Ying-Wooi , Allen Genevera I. , Baker Yulia , Yang Eunho , Ravikumar Pradeep , Liu Zhandong 
Published: November 2015

AbstractMotivationTechnological advances in medicine have led to a rapid proliferation of high-throughput “omics” data. Tools to mine this data and discover disrupted disease networks are needed as they hold the key to understanding complicated interactions between genes, mutations and aberrations, and epi-genetic markers.ResultsWe developed an R software package,XMRF, that can be used to fit Markov Networks to various types of high-throughput genomics data. Encoding the models and estimation techniques of the recently proposed exponential family Markov Random Fields (Yang et al., 2012), our software can be used to learn genetic networks from RNA-sequencing data (counts via Poisson graphical models), mutation and copy number variation data (categorical via Ising models), and methylation data (continuous via Gaussian graphical models).AvailabilityXMRF is available from the CRAN Project and Github at:https://github.com/zhandong/XMRF