bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulatory T‐cells promote hepatitis B virus infection and hepatocellular carcinoma progression
Authors: Li Wei , Han Jun , Wu Hong 
Published: November 2016

AbstractRegulatory T‐cells (Tregs), known for their immune suppressive function, have been reported in higher numbers, with activated phenotypes and greater potency, in hepatitis B virus (HBV)‐related liver diseases than in normal conditions. The numbers, phenotypes, and function of intrahepatic and/or tumor‐infiltrating Tregs in HBV‐related liver diseases also differ from those of Tregs in the peripheral blood. By inhibiting the function of effector T‐cells (Teffs), Tregs play a substantial role in the formation and maintenance of the liver's suppressive microenvironment, which might account for the progression of HBV‐related hepatitis and hepatocellular carcinoma (HCC). In acute hepatitis B virus infection, Tregs can safeguard the liver from damage at the cost of prolonged antiviral processes, which results in chronic HBV infection in the liver. Furthermore, Tregs play a role in the development of cirrhosis, the transformation of cirrhosis to HCC, and the progression and metastasis of HCC. Higher levels of Tregs in the peripheral blood and/or tumor sites signify a poorer prognosis in HBV‐related liver conditions, and observational data from mouse models and human patients support the theory that depleting Tregs may be therapeutic in HBV‐related liver diseases by inducing antiviral and antitumor immunity.
The complexity of millennial-scale variability in southwestern Europe during MIS 11
Authors: Oliveira Dulce , Desprat Stephanie , Rodrigues Teresa , Naughton Filipa , Hodell David , Trigo Ricardo , Rufino Marta , Lopes Cristina , Abrantes Fatima , Goni Maria Fernanda Sánchez 
Published: November 2016

AbstractClimatic variability of Marine Isotope Stage (MIS) 11 is examined using a new high-resolution direct land—sea comparison from the SW Iberian margin Site U1385. This study, based on pollen and biomarker analyses, documents regional vegetation, terrestrial climate and sea surface temperature (SST) variability. Suborbital climate variability is revealed by a series of forest decline events suggesting repeated cooling and drying episodes in SW Iberia throughout MIS 11. Only the most severe events on land are coeval with SST decreases, under larger ice volume conditions. Our study shows that the diverse expression (magnitude, character and duration) of the millennial-scale cooling events in SW Europe relies on atmospheric and oceanic processes whose predominant role likely depends on baseline climate states. Repeated atmospheric shifts recalling the positive North Atlantic Oscillation mode, inducing dryness in SW Iberia without systematical SST changes, would prevail during low ice volume conditions. In contrast, disruption of the Atlantic meridional overturning circulation (AMOC), related to iceberg discharges, colder SST and increased hydrological regime, would be responsible for the coldest and driest episodes of prolonged duration in SW Europe.
On the generation of large-scale eddy-driven patterns: the average eddy model
Authors: Radko Timour 
Published: November 2016

A theoretical model is developed which illustrates the dynamics of the spontaneous generation of large-scale structures in baroclinically unstable eddying flows. Techniques of asymptotic multiscale analysis are used to identify instabilities resulting from the positive feedback of the background eddies on large-scale perturbations. The novelty of the proposed approach lies in the choice of a dynamically consistent time-dependent background eddy field, which is taken from simulations of baroclinic instability in the Phillips two-layer system. The resulting solutions differ considerably from those of traditional multiscale models, in which the background eddy field is represented by steady analytical patterns. The present formulation makes it possible to (i) test the multiscale theory against the corresponding numerical simulations, (ii) unambiguously interpret the key physical processes at play and (iii) rationalize the emergence of large-scale patterns for certain background parameters. While the proposed approach to multiscale modelling is illustrated on a particular example of the Phillips baroclinic instability model, it is our belief that the presented technique is readily adaptable to a wide range of applications.
Flow and Heat Transfer of Gold-Blood Nanofluid in a Porous Channel with Moving/Stationary Walls
Authors: Srinivas S. , Vijayalakshmi A. , Subramanyam Reddy A. 
Published: November 2016

AbstractThe present study investigates the flow and heat transfer characteristics of blood carrying gold nanoparticles in a porous channel with moving/stationary walls in the presence of thermal radiation. Blood is considered as Newtonian fluid which is the base fluid and gold (Au) as nanoparticles. The governing equations are transformed into system of ordinary differential equations by using similarity transformations. The analytical solutions are obtained for the flow variables by employing homotopy analysis method (HAM). The analytical solutions are compared with the numerical solutions which are obtained by shooting technique along with Runge-Kutta scheme. It was noticed that there is a good agreement between analytical and numerical results. The influence of various parameters on velocity, temperature and heat transfer rate of gold-blood nanofluid has been discussed in detail. The temperature of the nanofluid increases with increasing the nanoparticle volume fraction. The heat transfer rate at the top wall increases with increasing nanoparticle volume fraction while it decreases for a given increase in radiation parameter.
Nonlinear Rupture of Thin Micropolar Liquid Film Under a Magnetic Field
Authors: Cheng P.-J. , Chen C.-K. , Wang Y.-C. , Lin M.-C. , Yang C.-K. 
Published: November 2016

AbstractThis paper investigates the rupture problem of a thin micropolar liquid film under a magnetic field on a horizontal plate, using long-wave perturbation to resolve nonlinear evolution equations with a free film interface. The governing equation is resolved using a finite difference method as part of an initial value problem for spatial periodic boundary conditions. The effect of a micropolar liquid under a magnetic field on the nonlinear rupture mechanism is studied in terms of the micropolar parameter, R, the Hartmann constant, m and the initial disturbance amplitude, H0. Modeling results indicate that the R, m and H0 parameters strongly affect the film flow. Enhancing the micropolar and magnetic effects is found to delay the rupture time. In addition, the results show that the film rupture time increases as the values of initial disturbance magnitude decrease. The micropolar and magnetic parameters indeed play a significant role in the film flow on a horizontal plate. Moreover, the optimum conditions can be found to alter stability of the film flow by controlling the applied magnetic field.
Good practice guide to setting inputs for operational risk models
Authors: Kelliher P. O. J. , Acharyya M. , Couper A. , Grant K. , Maguire E. , Nicholas P. , Smerald C. , Stevenson D. , Thirlwell J. , Cantle N. 
Published: November 2016

AbstractThis paper seeks to establish good practice in setting inputs for operational risk models for banks, insurers and other financial service firms. It reviews Basel, Solvency II and other regulatory requirements as well as publicly available literature on operational risk modelling. It recommends a combination of historic loss data and scenario analysis for modelling of individual risks, setting out issues with these data, and outlining good practice for loss data collection and scenario analysis. It recommends the use of expert judgement for setting correlations, and addresses information requirements for risk mitigation allowances and capital allocation, before briefly covering Bayesian network methods for modelling operational risks.
Increasing the density of passive photonic-integrated circuits via nanophotonic cloaking
Authors: Shen Bing , Polson Randy , Menon Rajesh 
Published: November 2016

AbstractPhotonic-integrated devices need to be adequately spaced apart to prevent signal cross-talk. This fundamentally limits their packing density. Here we report the use of nanophotonic cloaking to render neighbouring devices invisible to one another, which allows them to be placed closer together than is otherwise feasible. Specifically, we experimentally demonstrated waveguides that are spaced by a distance of ∼λ0/2 and designed waveguides with centre-to-centre spacing as small as 600 nm (<λ0/2.5). Our experiments show a transmission efficiency >−2 dB and an extinction ratio >15 dB over a bandwidth larger than 60 nm. This performance can be improved with better design algorithms and industry-standard lithography. The nanophotonic cloak relies on multiple guided-mode resonances, which render such devices very robust to fabrication errors. Our devices are broadly complimentary-metal-oxide-semiconductor compatible, have a minimum pitch of 200 nm and can be fabricated with a single lithography step. The nanophotonic cloaks can be generally applied to all passive integrated photonics.
Contracting CAG/CTG repeats using the CRISPR-Cas9 nickase
Authors: Cinesi Cinzia , Aeschbach Lorène , Yang Bin , Dion Vincent 
Published: November 2016

AbstractCAG/CTG repeat expansions cause over 13 neurological diseases that remain without a cure. Because longer tracts cause more severe phenotypes, contracting them may provide a therapeutic avenue. No currently known agent can specifically generate contractions. Using a GFP-based chromosomal reporter that monitors expansions and contractions in the same cell population, here we find that inducing double-strand breaks within the repeat tract causes instability in both directions. In contrast, the CRISPR-Cas9 D10A nickase induces mainly contractions independently of single-strand break repair. Nickase-induced contractions depend on the DNA damage response kinase ATM, whereas ATR inhibition increases both expansions and contractions in a MSH2- and XPA-dependent manner. We propose that DNA gaps lead to contractions and that the type of DNA damage present within the repeat tract dictates the levels and the direction of CAG repeat instability. Our study paves the way towards deliberate induction of CAG/CTG repeat contractions in vivo.
Chaperone addiction of toxin–antitoxin systems
Authors: Bordes Patricia , Sala Ambre Julie , Ayala Sara , Texier Pauline , Slama Nawel , Cirinesi Anne-Marie , Guillet Valérie , Mourey Lionel , Genevaux Pierre 
Published: November 2016

AbstractBacterial toxin–antitoxin (TA) systems, in which a labile antitoxin binds and inhibits the toxin, can promote adaptation and persistence by modulating bacterial growth in response to stress. Some atypical TA systems, known as tripartite toxin–antitoxin–chaperone (TAC) modules, include a molecular chaperone that facilitates folding and protects the antitoxin from degradation. Here we use a TAC module from Mycobacterium tuberculosis as a model to investigate the molecular mechanisms by which classical TAs can become ‘chaperone-addicted’. The chaperone specifically binds the antitoxin at a short carboxy-terminal sequence (chaperone addiction sequence, ChAD) that is not present in chaperone-independent antitoxins. In the absence of chaperone, the ChAD sequence destabilizes the antitoxin, thus preventing toxin inhibition. Chaperone–ChAD pairs can be transferred to classical TA systems or to unrelated proteins and render them chaperone-dependent. This mechanism might be used to optimize the expression and folding of heterologous proteins in bacterial hosts for biotechnological or medical purposes.
BMI1 regulates PRC1 architecture and activity through homo- and hetero-oligomerization
Authors: Gray Felicia , Cho Hyo Je , Shukla Shirish , He Shihan , Harris Ashley , Boytsov Bohdan , Jaremko Łukasz , Jaremko Mariusz , Demeler Borries , Lawlor Elizabeth R. , Grembecka Jolanta , Cierpicki Tomasz 
Published: November 2016

AbstractBMI1 is a core component of the polycomb repressive complex 1 (PRC1) and emerging data support a role of BMI1 in cancer. The central domain of BMI1 is involved in protein–protein interactions and is essential for its oncogenic activity. Here, we present the structure of BMI1 bound to the polyhomeotic protein PHC2 illustrating that the central domain of BMI1 adopts an ubiquitin-like (UBL) fold and binds PHC2 in a β-hairpin conformation. Unexpectedly, we find that the UBL domain is involved in homo-oligomerization of BMI1. We demonstrate that both the interaction of BMI1 with polyhomeotic proteins and homo-oligomerization via UBL domain are necessary for H2A ubiquitination activity of PRC1 and for clonogenic potential of U2OS cells. Here, we also emphasize need for joint application of NMR spectroscopy and X-ray crystallography to determine the overall structure of the BMI1–PHC2 complex.
Recurrence Rates and Risk Factors for Primary Giant Cell Tumors around the Knee: A Multicentre Retrospective Study in China
Authors: Hu Pan , Zhao Liming , Zhang Huilin , Yu Xiuchun , Wang Zhen , Ye Zhaoming , Wu Sujia , Guo Shibing , Zhang Guochuan , Wang Jinghua , Ning Xianjia , Hu Yongcheng , Zhang Yingze 
Published: November 2016

AbstractGiant cell tumors of the bone (GCTBs) are commonly diagnosed in Asian populations, usually around the knee. Herein, we aimed to determine the clinical characteristics, local recurrence rates, and relevant risk factors of primary GCTB around the knee. Univariate and multivariate survival analyses were used to identify the risk factors for local recurrence. Four hundred ten patients with primary GCTB around the knee, treated between March 2000 and June 2014, were recruited from 7 institutions in China. The overall local recurrence rate was 23.4%, but was higher in patients aged 20–39 years (28.5%; P = 0.039). The local recurrence rate was the highest in patients treated with intralesional curettage (53.4%), and the lowest in those treated with resection (4.9%). We found a higher risk of tumor recurrence in the proximal fibula compared to the distal femur (hazard ratio: 28.52, 95% confidence interval: 5.88–138.39; P < 0.0001), and in patients treated with curettage compared to those treated with resection (hazard ratio: 12.07, 95% confidence interval: 4.99–29.18; P < 0.0001). Thus, the tumor location must be considered when selecting the optimal surgical treatment approach to reduce the risk of local recurrence and preserve joint function, especially in young patients.
Heterogeneity of executive functions among comorbid neurodevelopmental disorders
Authors: Dajani Dina R. , Llabre Maria M. , Nebel Mary Beth , Mostofsky Stewart H. , Uddin Lucina Q. 
Published: November 2016

AbstractExecutive functions (EFs) are used to set goals, plan for the future, inhibit maladaptive responses, and change behavior flexibly. Although some studies point to specific EF profiles in autism spectrum disorder (ASD) and attention-deficit/hyperactivity disorder (ADHD) — prevalent and often highly comorbid neurodevelopmental disorders — others have not differentiated them. The objective of the current study was to identify distinct profiles of EF across typically developing (TD) children and children with ASD and ADHD. We employed a latent profile analysis using indicators of EF (e.g., working memory, inhibition, and flexibility) in a mixed group of 8–13 year-olds including TD children (n = 128), children with ASD without ADHD (n = 30), children with ADHD (n = 93), and children with comorbid ASD and ADHD (n = 66). Three EF classes emerged: “above average,” “average,” and “impaired.” EF classes did not reproduce diagnostic categories, suggesting that differences in EF abilities are present within the ASD and ADHD groups. Further, greater EF dysfunction predicted more severe socioemotional problems, such as anxiety/depression. These results highlight the heterogeneity of current diagnostic groups and identify an “impaired” EF group, consisting of children with both ASD and ADHD, which could specifically be targeted for EF intervention.
Micrometre-scale deformation observations reveal fundamental controls on geological rifting
Authors: Thun Johannes , Lokmer Ivan , Bean Christopher J. , Eibl Eva P. S. , Bergsson Bergur H. , Braiden Aoife 
Published: November 2016

AbstractMany of the world’s largest volcanic eruptions are associated with geological rifting where major fractures open at the Earth’s surface, yet fundamental controls on the near-surface response to the rifting process are lacking. New high resolution observations gleaned from seismometer data during the 2014 Bárðarbunga basaltic dyke intrusion in Iceland allow us unprecedented access to the associated graben formation process on both sub-second and micrometre scales. We find that what appears as quasi steady-state near-surface rifting on lower resolution GPS observation comprises discrete staccato-like deformation steps as the upper crust unzips through repetitive low magnitude (MW < 0) failures on fracture patches estimated between 300 m2and 1200 m2in size. Stress drops for these events are one to two orders of magnitude smaller than expected for tectonic earthquakes, demonstrating that the uppermost crust in the rift zone is exceptionally weak.
TM1-IR680 peptide for assessment of surgical margin and lymph node metastasis in murine orthotopic model of oral cancer
Authors: Suganya S. Annie A. , Kochurani K. J. , Nair Madhumathy G. , Louis Jiss Maria , Sankaran Santhosh , Rajagopal R. , Kumar K. Santhosh , Abraham Parvin , P. G. Balagopal , Sebastian Paul , Somananthan Thara , Maliekal Tessy Thomas 
Published: November 2016

AbstractTreatment outcome after surgical removal in oral carcinoma is poor due to inadequate methodologies available for marking surgical margins. Even though some methodologies for intraoperative margin assessment are under clinical and preclinical trials for other solid tumours, a promising modality for oral cancer surgery is not developed. Fluorescent-based optical imaging using Near Infrared (NIR) dyes tagged to tumour specific target will be an optimal tool for this purpose. One such target, Gastrin Releasing Peptide Receptor (GRPR) was selected for the study, and its binding peptide, TM1-IR680, was tested for its efficacy for surgical margin prediction in murine orthotopic model of oral cancer, derived from primary samples. Here, for the first time in a preclinical analysis, we show that the size and margin of oral cancer can be predicted, as revealed by 3D-imaging. Interestingly, the peptide was sensitive enough to detect lymph nodes that harboured dispersed tumour cells before colonization, which was impossible to identify by conventional histopathology. We recommend the use of TM1-NIR dyes alone or in combination with other technologies to improve the clinical outcome of oral cancer surgery.
Decrease in fMRI brain activation during working memory performed after sleeping under 10 lux light
Authors: Kang Seung-Gul , Yoon Ho-Kyoung , Cho Chul-Hyun , Kwon Soonwook , Kang June , Park Young-Min , Lee Eunil , Kim Leen , Lee Heon-Jeong 
Published: November 2016

AbstractThe aim of this study was to investigate the effect of exposure to dim light at night (dLAN) when sleeping on functional brain activation during a working-memory tasks. We conducted the brain functional magnetic resonance imaging (fMRI) analysis on 20 healthy male subjects. All participants slept in a polysomnography laboratory without light exposure on the first and second nights and under a dim-light condition of either 5 or 10 lux on the third night. The fMRI scanning was conducted during n-back tasks after second and third nights. Statistical parametric maps revealed less activation in the right inferior frontal gyrus (IFG) after exposure to 10-lux light. The brain activity in the right and left IFG areas decreased more during the 2-back task than during the 1- or 0-back task in the 10-lux group. The exposure to 5-lux light had no significant effect on brain activities. The exposure to dLAN might influence the brain function which is related to the cognition.
FUEL-mLoc: feature-unified prediction and explanation of multi-localization of cellular proteins in multiple organisms
Authors: Wan Shibiao , Mak Man-Wai , Kung Sun-Yuan 
Published: November 2016

Abstract
Although many web-servers for predicting protein subcellular localization have been developed, they often have the following drawbacks: (i) lack of interpretability or interpreting results with heterogenous information which may confuse users; (ii) ignoring multi-location proteins and (iii) only focusing on specific organism. To tackle these problems, we present an interpretable and efficient web-server, namely FUEL-mLoc, using Feature-Unified prediction and Explanation of multi-Localization of cellular proteins in multiple organisms. Compared to conventional localization predictors, FUEL-mLoc has the following advantages: (i) using unified features (i.e. essential GO terms) to interpret why a prediction is made; (ii) being capable of predicting both single- and multi-location proteins and (iii) being able to handle proteins of multiple organisms, including Eukaryota, Homo sapiens, Viridiplantae, Gram-positive Bacteria, Gram-negative Bacteria and Virus. Experimental results demonstrate that FUEL-mLoc outperforms state-of-the-art subcellular-localization predictors.

Availability and Implementation
http://bioinfo.eie.polyu.edu.hk/FUEL-mLoc/

Supplementary information
Supplementary data are available at Bioinformatics online.
SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets
Authors: Mao Hongliang , Wang Hao 
Published: November 2016

Abstract

Motivation
Short Interspersed Nuclear Elements (SINEs) are transposable elements (TEs) that amplify through a copy-and-paste mode via RNA intermediates. The computational identification of new SINEs are challenging because of their weak structural signals and rapid diversification in sequences.

Results
Here we report SINE_Scan, a highly efficient program to predict SINE elements in genomic DNA sequences. SINE_Scan integrates hallmark of SINE transposition, copy number and structural signals to identify a SINE element. SINE_Scan outperforms the previously published de novo SINE discovery program. It shows high sensitivity and specificity in 19 plant and animal genome assemblies, of which sizes vary from 120 Mb to 3.5 Gb. It identifies numerous new families and substantially increases the estimation of the abundance of SINEs in these genomes.

Availability and Implementation
The code of SINE_Scan is freely available at http://github.com/maohlzj/SINE_Scan, implemented in PERL and supported on Linux.

Supplementary information
Supplementary data are available at Bioinformatics online.