bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generating multi-atom entangled W states via light-matter interface based fusion mechanism
Authors: Zang Xue-Ping , Yang Ming , Ozaydin Fatih , Song Wei , Cao Zhuo-Liang 
Published: November 2015

AbstractW state is a key resource in quantum communication. Fusion technology has been proven to be a good candidate for preparing a large-size W state from two or more small-size W states in linear optical system. It is of great importance to study how to fuse W states via light-matter interface. Here we show that it is possible to prepare large-size W-state networks using a fusion mechanism in cavity QED system. The detuned interaction between three atoms and a vacuum cavity mode constitute the main fusion mechanism, based on which two or three small-size atomic W states can be fused into a larger-size W state. If no excitation is detected from those three atoms, the remaining atoms are still in the product of two or three new W states, which can be re-fused. The complicated Fredkin gate used in the previous fusion schemes is avoided here. W states of size 2 can be fused as well. The feasibility analysis shows that our fusion processes maybe implementable with the current technology. Our results demonstrate how the light-matter interaction based fusion mechanism can be realized and may become the starting point for the fusion of multipartite entanglement in cavity QED system.
Impact of Visual Impairment and Eye diseases on Mortality: the Singapore Malay Eye Study (SiMES)
Authors: Siantar Rosalynn Grace , Cheng Ching-Yu , Gemmy Cheung Chui Ming , Lamoureux Ecosse L. , Ong Peng Guan , Chow Khuan Yew , Mitchell Paul , Aung Tin , Wong Tien-Yin , Cheung Carol Y. 
Published: November 2015

AbstractWe investigated the relationship of visual impairment (VI) and age-related eye diseases with mortality in a prospective, population-based cohort study of 3,280 Malay adults aged 40–80 years between 2004–2006. Participants underwent a full ophthalmic examination and standardized lens and fundus photographic grading. Visual acuity was measured using logMAR chart. VI was defined as presenting (PVA) and best-corrected (BCVA) visual acuity worse than 0.30 logMAR in the better-seeing eye. Participants were linked with mortality records until 2012. During follow-up (median 7.24 years), 398 (12.2%) persons died. In Cox proportional-hazards models adjusting for relevant factors, participants with VI (PVA) had higher all-cause mortality (hazard ratio[HR], 1.57; 95% confidence interval[CI], 1.25–1.96) and cardiovascular (CVD) mortality (HR 1.75; 95% CI, 1.24–2.49) than participants without. Diabetic retinopathy (DR) was associated with increased all-cause (HR 1.70; 95% CI, 1.25–2.36) and CVD mortality (HR 1.57; 95% CI, 1.05–2.43). Retinal vein occlusion (RVO) was associated with increased CVD mortality (HR 3.14; 95% CI, 1.26–7.73). No significant associations were observed between cataract, glaucoma and age-related macular degeneration with mortality. We conclude that persons with VI were more likely to die than persons without. DR and RVO are markers of CVD mortality.
Biological and immunotoxicity evaluation of antimicrobial peptide-loaded coatings using a layer-by-layer process on titanium
Authors: Shi Jue , Liu Yu , Wang Ying , Zhang Jing , Zhao Shifang , Yang Guoli 
Published: November 2015

AbstractThe prevention and control of peri-implantitis is a challenge in dental implant surgery. Dental implants with sustained antimicrobial coating are an ideal way of preventing peri-implantitis. This study reports development of a non- immunotoxicity multilayered coating on a titanium surface that had sustained antimicrobial activity and limited early biofilm formation. In this study, the broad spectrum AMP, Tet213, was linked to collagen IV through sulfo-SMPB and has been renamed as AMPCol. The multilayer AMPCol coatings were assembled on smooth titanium surfaces using a LBL technique. Using XPS, AFM, contact angle analysis and QCM, layer-by-layer accumulation of coating thickness was measured and increased surface wetting compared to controls was confirmed. Non-cytotoxicity to HaCaT and low erythrocyte hemolysis by the AMPCol coatings was observed.In vivoimmunotoxicity assays showed IP administration of AMPCol did not effect serum immunoglobulin levels. This coating with controlled release of AMP decreased the growth of both a Gram-positive aerobe (Staphylococcus aureus) and a Gram-negative anaerobe (Porphyromonas gingivalis) up to one month. EarlyS. aureusbiofilm formation was inhibited by the coating. The excellent long-term sustained antimicrobial activity of this multilayer coating is a potential method for preventing peri-implantitis through coated on the neck of implants before surgery.
Reciprocal regulation of RORγt acetylation and function by p300 and HDAC1
Authors: Wu Qingsi , Nie Jia , Gao Yayi , Xu Peng , Sun Qijuan , Yang Jing , Han Lei , Chen Zuojia , Wang Xiuwen , Lv Ling , Tsun Andy , Shen Jijia , Li Bin 
Published: November 2015

AbstractT helper 17 (Th17) cells not only play critical roles in protecting against bacterial and fungal infections but are also involved in the pathogenesis of autoimmune diseases. The retinoic acid-related orphan receptor (RORγt) is a key transcription factor involved in Th17 cell differentiation through direct transcriptional activation of interleukin 17(A) (IL-17). How RORγt itself is regulated remains unclear. Here, we report that p300, which has histone acetyltransferase (HAT) activity, interacts with and acetylates RORγt at its K81 residue. Knockdown of p300 downregulates RORγt protein and RORγt-mediated gene expression in Th17 cells. In addition, p300 can promote RORγt-mediated transcriptional activation. Interestingly, the histone deacetylase (HDAC) HDAC1 can also interact with RORγt and reduce its acetylation level. In summary, our data reveal previously unappreciated posttranslational regulation of RORγt, uncovering the underlying mechanism by which the histone acetyltransferase p300 and the histone deacetylase HDAC1 reciprocally regulate the RORγt-mediated transcriptional activation of IL-17.
Spectroscopic characterization of charge carrier anisotropic motion in twisted few-layer graphene
Authors: Kandyba Viktor , Yablonskikh Mikhail , Barinov Alexei 
Published: November 2015

AbstractGraphene, a layer of carbon atoms in a honeycomb lattice, captures enormous interest as probably the most promising component of future electronics thanks to its mechanical robustness, flexibility and unique charge carrier quasiparticles propagating like massless high energy Dirac fermions. If several graphene layers form a stack, the interaction between them is, on the one hand, weak, allowing realization of various registries between the layers and, on the other hand, strong enough for a wide range tuning of the electronic properties. Here we grow few layer graphene with various number of layers and twist configurations and address the electronic properties of individual atomic layers in single microscopic domains using angle-resolved photoelectron spectromicroscopy. The dependence of the interlayer coupling on the twist angle is analyzed and, in the domains with tri-layers and more, if different rotations are present, the electrons in weaker coupled adjacent layers are shown to have different properties manifested by coexisting van Hove singularities, moiré superlattices with corresponding superlattice Dirac points and charge carrier group velocity renormalizations. Moreover, pronounced anisotropy in the charge carrier motion, opening a possibility to transform strongly coupled graphene bilayers into quasi one-dimensional conductors, is observed.
The genetic regulatory network centered on Pto-Wuschela and its targets involved in wood formation revealed by association studies
Authors: Yang Xiaohui , Wei Zunzheng , Du Qingzhang , Chen Jinhui , Wang Qingshi , Quan Mingyang , Song Yuepeng , Xie Jianbo , Zhang Deqiang 
Published: November 2015

AbstractTranscription factors (TFs) regulate gene expression and can strongly affect phenotypes. However, few studies have examined TF variants and TF interactions with their targets in plants. Here, we used genetic association in 435 unrelated individuals ofPopulus tomentosato explore the variants inPto-Wuschelaand its targets to decipher the genetic regulatory network ofPto-Wuschela. Our bioinformatics and co-expression analysis identified 53 genes with the motif TCACGTGA as putative targets ofPto-Wuschela. Single-marker association analysis showed thatPto-Wuschelawas associated with wood properties, which is in agreement with the observation that it has higher expression in stem vascular tissues inPopulus. Also, SNPs in the 53 targets were associated with growth or wood properties under additive or dominance effects, suggesting these genes andPto-Wuschelamay act in the same genetic pathways that affect variation in these quantitative traits. Epistasis analysis indicated that 75.5% of these genes directly or indirectly interactedPto-Wuschela, revealing the coordinated genetic regulatory network formed byPto-Wuschelaand its targets. Thus, our study provides an alternative method for dissection of the interactions between a TF and its targets, which will strength our understanding of the regulatory roles of TFs in complex traits in plants.
The Directional Observation of Highly Dynamic Membrane Tubule Formation Induced by Engulfed Liposomes
Authors: Zhang Xiaoming , Dai Luru , Wang Anhe , Wölk Christian , Dobner Bodo , Brezesinski Gerald , Tang Yunqing , Wang Xianyou , Li Junbai 
Published: November 2015

AbstractHighly dynamic tubular structures in cells are responsible for exchanges between organelles. Compared with bacterial invasion, the most affordable and least toxic lipids were found in this study to be gentle and safe exogenous stimuli for the triggering of membrane tubules. A specific lipid system was internalized by NIH3T3 cells. Following cellular uptake, the constructed liposomes traveled towards the nucleus in aggregations and were gradually distributed into moving vesicles and tubules in the cytosol. The triggered tubules proceeded, retreated or fluctuated along the cytoskeleton and were highly dynamic, moving quickly (up to several microns per second) and breaking and fusing frequently. These elongated tubules could also fuse with one another, giving rise to polygonal membrane networks. These lipid systems, with the novel property of accelerating intracellular transport, provide a new paradigm for investigating cellular dynamics.
„Psychische Gesundheit bei erwachsenen Menschen mit intellektueller Behinderung. Schutz- und Risikofaktoren in Bezug auf Depression und Angststörung“ – eine Querschnittstudie
Authors: Schmückle D. , Schmolz G. , Lindert J. 
Published: November 2015

Abstract
Hintergrund: Psychische Gesundheit bei Menschen mit intellektueller Behinderung wurde bisher nur wenig untersucht. Ziel dieser Studie ist es, Daten zu depressiven Beschwerden und pathologische Angstausprägungen bei Menschen mit intellektueller Behinderung zur Verfügung zu stellen.
Methode: In einer Querschnittstudie wurden Männer und Frauen mit intellektueller Behinderung (18–65 Jahre) mit einem standardisierten Erfassungsinstrument mit 2 Teilen befragt (Teil 1: Variablen „Wohnsituation“, „Selbstbestimmungsmöglichkeiten“, „Gewalterfahrungen“, Teil 2: Variablen „Depression“ und „Angststörungen“ mithilfe des Patient-Health-Questionaire-4 erhoben). Die Daten wurden univariat und bivariat ausgewertet.
Ergebnisse: 44 Personen (Response rate=45%) nahmen an der Studie teil (59% Männer, 41% Frauen). Insgesamt haben 20% (N=9) aller Teilnehmenden dieser Studie einen erhöhten PHQ-2 Score, der auf stärkere depressive Beschwerden hinweist. 18% (N=8) der Probanden weisen einen erhöhten GAD-2 Score auf, der als Indikator für pathologische Angstausprägungen gewertet werden kann. Risikofaktoren für depressive Störungen sind ein „erhöhter Behinderungsgrad“ (RR=11,8) „Wohnen bei den Eltern“ (RR=6,7), „eingeschränkte Selbstbestimmungsmöglichkeiten“ (RR=6,2) und „Angst vor neuen Situationen“ (RR=5,0). Gewalterfahrungen sind ein Risikofaktor (RR=13,3) in Bezug auf pathologische Angstausprägungen.
Schlussfolgerung: Die Studie ist aufgrund der besonderen methodischen Herausforderungen bei dieser Zielgruppe sehr klein. Dennoch gibt diese Studie als eine der ersten in Deutschland Hinweise auf Faktoren, die mit Depressionen und Angst bei Menschen mit intellektueller Behinderung assoziiert sind. Die Assoziation von Gewalterfahrungen und Angst bei Menschen mit intellektueller Behinderung ist eine wichtige Herausforderung für Public Health.
Entscheidungsfaktoren und Informationsquellen für die Krankenhauswahl bei Geburten in der Schweiz
Authors: Wiedenhöfer D. , Keppler S. 
Published: November 2015

ZusammenfassungSeit der Einführung von Swiss DRG im Jahr 2012 haben Frauen in der Schweiz die Möglichkeit der freien Krankenhauswahl. Das Ziel der vorliegenden Arbeit besteht darin, Entscheidungsfaktoren bei der Wahl einer Geburtsabteilung in Schweizer Krankenhäusern zu identifizieren und Informationsquellen hinsichtlich ihres Nutzungsgrades zu bewerten. Hierzu wurden Wöchnerinnen in 7 Schweizer Krankenhäusern der Deutschschweiz schriftlich befragt. Bei der Wahl des Krankenhauses werden Faktoren wie z.B. Fachkompetenz und gute Betreuung durch die Ärzte, gute geburtshilfliche Kompetenz, Fachkompetenz und gute Versorgung durch Pflegekräfte, und eine gepflegte Atmosphäre als wichtig eingestuft. Zu den wichtigsten Informationsquellen zählen Empfehlungen von Freunden, Erfahrungen im Rahmen eines früheren Aufenthaltes, die Fachärztin/der Facharzt, Familie, und die Homepage des Krankenhauses. Informationsabende für schwangere Patienten sind für ein Krankenhaus wichtig, da diese die Entscheidung positiv verstärken. Dem Internetauftritt des Krankenhauses und der Zuweiserbindung kommt zwar eine hohe Bedeutung zu, jedoch spielen Erfahrungen unmittelbarer Bezugspersonen, wie z.B. Freunde und Familie, und eigene Erfahrungen mit dem Krankenhaus eine grössere Rolle.
Automatic generation of bioinformatics tools for predicting protein–ligand binding sites
Authors: Komiyama Yusuke , Banno Masaki , Ueki Kokoro , Saad Gul , Shimizu Kentaro 
Published: November 2015

Abstract
Motivation: Predictive tools that model protein–ligand binding on demand are needed to promote ligand research in an innovative drug-design environment. However, it takes considerable time and effort to develop predictive tools that can be applied to individual ligands. An automated production pipeline that can rapidly and efficiently develop user-friendly protein–ligand binding predictive tools would be useful.
Results: We developed a system for automatically generating protein–ligand binding predictions. Implementation of this system in a pipeline of Semantic Web technique-based web tools will allow users to specify a ligand and receive the tool within 0.5–1 day. We demonstrated high prediction accuracy for three machine learning algorithms and eight ligands.
Availability and implementation: The source code and web application are freely available for download at http://utprot.net. They are implemented in Python and supported on Linux.
Contact: shimizu@bi.a.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
De novo identification of replication-timing domains in the human genome by deep learning
Authors: Liu Feng , Ren Chao , Li Hao , Zhou Pingkun , Bo Xiaochen , Shu Wenjie 
Published: November 2015

Abstract
Motivation: The de novo identification of the initiation and termination zones—regions that replicate earlier or later than their upstream and downstream neighbours, respectively—remains a key challenge in DNA replication.
Results: Building on advances in deep learning, we developed a novel hybrid architecture combining a pre-trained, deep neural network and a hidden Markov model (DNN-HMM) for the de novo identification of replication domains using replication timing profiles. Our results demonstrate that DNN-HMM can significantly outperform strong, discriminatively trained Gaussian mixture model–HMM (GMM-HMM) systems and other six reported methods that can be applied to this challenge. We applied our trained DNN-HMM to identify distinct replication domain types, namely the early replication domain (ERD), the down transition zone (DTZ), the late replication domain (LRD) and the up transition zone (UTZ), using newly replicated DNA sequencing (Repli-Seq) data across 15 human cells. A subsequent integrative analysis revealed that these replication domains harbour unique genomic and epigenetic patterns, transcriptional activity and higher-order chromosomal structure. Our findings support the ‘replication-domain’ model, which states (1) that ERDs and LRDs, connected by UTZs and DTZs, are spatially compartmentalized structural and functional units of higher-order chromosomal structure, (2) that the adjacent DTZ-UTZ pairs form chromatin loops and (3) that intra-interactions within ERDs and LRDs tend to be short-range and long-range, respectively. Our model reveals an important chromatin organizational principle of the human genome and represents a critical step towards understanding the mechanisms regulating replication timing.
Availability and implementation: Our DNN-HMM method and three additional algorithms can be freely accessed at https://github.com/wenjiegroup/DNN-HMM. The replication domain regions identified in this study are available in GEO under the accession ID GSE53984.
Contact: shuwj@bmi.ac.cn or boxc@bmi.ac.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Comparison of genetic variants in matched samples using thesaurus annotation
Authors: Konopka Tomasz , Nijman Sebastian M.B. 
Published: November 2015

Abstract
Motivation: Calling changes in DNA, e.g. as a result of somatic events in cancer, requires analysis of multiple matched sequenced samples. Events in low-mappability regions of the human genome are difficult to encode in variant call files and have been under-reported as a result. However, they can be described accurately through thesaurus annotation—a technique that links multiple genomic loci together to explicate a single variant.
Results: We here describe software and benchmarks for using thesaurus annotation to detect point changes in DNA from matched samples. In benchmarks on matched normal/tumor samples we show that the technique can recover between five and ten percent more true events than conventional approaches, while strictly limiting false discovery and being fully consistent with popular variant analysis workflows. We also demonstrate the utility of the approach for analysis of de novo mutations in parents/child families.
Availability and implementation: Software performing thesaurus annotation is implemented in java; available in source code on github at GeneticThesaurus (https://github.com/tkonopka/GeneticThesaurus) and as an executable on sourceforge at geneticthesaurus (https://sourceforge.net/projects/geneticthesaurus). Mutation calling is implemented in an R package available on github at RGeneticThesaurus (https://github.com/tkonopka/RGeneticThesaurus).
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: tomasz.konopka@ludwig.ox.ac.uk
Therapeutic antibodies that target inflammatory cytokines in autoimmune diseases
Authors: Lai Yuping , Dong Chen 
Published: November 2015

AbstractInflammatory cytokines are key regulators of immune responses. Persistent and excessive production of inflammatory cytokines underscores the development of autoimmune diseases. Therefore, neutralizing inflammatory cytokines or antagonizing their receptor function is considered as a useful therapeutic strategy to treat autoimmune diseases. To achieve the success of such a strategy, understanding of the complex actions of these cytokines and cytokine networks is required. In this review we focus on four inflammatory cytokines—tumor necrosis factor α (TNFα), interleukin-6 (IL-6), IL-23 and IL-17—and dissect how the dysregulation of these cytokines regulates autoimmune diseases. On the basis of pre-clinical and clinical data, we specifically discuss the therapeutic rationale for targeting these cytokines and describe the potential adverse effects.
The Relationship Between Insertional Torque and Pullout Strength of Surgical Screws
Authors: Rose Kyle M. , Nelson Carolyn M. , Ogden Alan L. , Morandi Massimo “Max” 
Published: November 2015

Objectives:
To investigate the role of maximal insertional torque (T
max) of surgical screws and pullout strength (POS) in human cadaveric tibiae.

Methods:
Self-tapping surgical screws (4.5 mm) were inserted into 9 segments of cadaveric tibial cortical bone, measuring T
max and POS of screws inserted at 50%, 70%, 90%, and 100% T
max. Computed tomography was also performed, allowing calculation of bone mineral density (BMD) in K2HPO4 concentration (mg/mL) and cortical thickness (mm).

Results:
POS measurements were highest and similar in screws inserted at 70% and 90% of the established T
max. Screws inserted at 90% T
max offered a significantly different POS than those inserted at 100% T
max. No significant differences were found between samples in BMD or cortical thickness. No significant correlations were found between cortical thickness or BMD and T
max.

Conclusions:
Surgeons should tighten screws to a torque less than T
max to avoid loss of purchase of the screw and reduced POS.
CYP1B1 and MYOC Mutations in Vietnamese Primary Congenital Glaucoma Patients
Authors: Do Tan , Shei William , Chau Pham Thi Minh , Trang Doan Le , Yong Victor H.K. , Ng Xiao Yu , Chen Yue Ming , Aung Tin , Vithana Eranga N. 
Published: November 2015

Purpose:
Primary congenital glaucoma (PCG, OMIM 231300), the most common glaucoma in infancy, is caused by developmental defects in the anterior chamber angle. The 3 implicated genes are cytochrome P450 family I subfamily B polypeptide 1 (CYP1B1), latent transforming growth factor β-binding protein 2 (LTBP2), and myocilin (MYOC). In this study, we sought to determine CYP1B1 and MYOC sequence variations in a Vietnamese cohort of index cases with PCG and their families.

Methods:
Thirty Vietnamese subjects with PCG and 120 normal Vietnamese subjects were recruited. PCG was defined by the presence of at least 2 of the following clinical manifestations: increased corneal diameter (>10 mm at birth), corneal edema, Haab’s striae, optic disc changes, and absence of other ocular or systemic diseases associated with childhood glaucoma. The coding exons, intron and exon boundaries, and untranslated regions of CYP1B1 and MYOC genes were PCR amplified and subjected to bidirectional sequencing in all subjects.

Results:
We identified 2 homozygous and 3 heterozygous CYP1B1 sequence alterations in our study subjects. Among the 5 mutations identified, 2 (p.H279L and p.L283F) were novel mutations, whereas 3 (p.A121_S122insDRPAFA, p.L107V, and p.V320L) had been previously reported in PCG cases. None of these mutations was observed in any of the 120 controls. Haplotypes generated with 6 non–disease-causing intragenic single nucleotide polymorphisms detected in CYP1B1 indicated that the most common haplotype in Vietnamese population is similar to that found in Chinese and Japanese. The genotype-phenotype correlation showed no significant difference between mutation and no-mutation groups for quantitative clinical features (presenting intraocular pressure, corneal diameter, number of surgeries performed, the cup-to-disc ratio) as well as for qualitative factors (bilateral cases, phenotype severity, and the prognosis) (P>0.05).

Conclusions:
Five out of 30 families with PCG (16.7%) had disease attributable to CYP1B1 alterations suggesting that CYP1B1 is not the major gene causing PCG in Vietnamese unlike in the case of Arab or Romany patients. This percentage is similar to that detected in studies of Japanese and Chinese patients with sporadic PCG. PCG has proven to be an ocular disease of genetic heterogeneity, calling for further studies to identify novel genes causing this disease.