bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of electromagnetic interference shielding properties between single-wall carbon nanotube and graphene sheet/polyaniline composites
Authors: Yuan Bingqing , Yu Liming , Sheng Leimei , An Kang , Zhao Xinluo 
Published: May 2012

Abstract
Single-wall carbon nanotube/polyaniline (SWCNT/PANI) and graphene sheet/polyaniline (GS/PANI) composites were prepared by a simple alcohol-assisted dispersion and pressing process. The SWCNTs and GSs were synthesized by the dc arc-discharge method. The dc electrical conductivity and the electromagnetic interference (EMI) shielding effectiveness (SE) of these two kinds of composites were measured. The experimental results reveal that the conductivity and the EMI SE of the GS/PANI composite are better than that of the SWCNT/PANI composite, and the absorption proportion of the SWCNT/PANI composite is higher than that of the GS/PANI composite. The EMI shielding results (2–18 GHz) also show that both composites present an absorption-dominant mechanism and present a wide application prospect in the field of EMI shielding and microwave absorption.
Effect of cadmium sulfide nanorod content on Freedericksz threshold voltage, splay and bend elastic constants in liquid-crystal nanocomposites
Authors: Nayek Prasenjit , Karan Santanu , Kundu Sudarshan , Lee Seung Hee , Gupta Sudeshna Das , Roy Soumen Kumar , Roy Subir Kumar 
Published: May 2012

Abstract
This report describes how doping liquid crystals (LC) with rod-like hexagonal semiconductor nanoprisms alters the dielectric and elastic properties of the composites as compared with a pristine nematic liquid crystal (NLC). Cadmium sulfide nanorods were synthesized via the solvothermal process and blended with a NLC. Nanorods were highly miscible with NLC and produced a topological defect-free texture up to a certain limit. A good dark state was achieved during the homeotropic configuration of the cell within that limit. Appreciable changes in splay and bend elastic constants of the LCs were observed after blending with nanorods. Long-range order was established in the hybrid system, and consequently the anisotropy was increased. The threshold voltage decreased dramatically by ∼31%. Dielectric study revealed a high-frequency mode, which might be due to anchoring of the LC with nanorods.
Application of survival analysis methodology to the quantitative analysis of LC-MS proteomics data
Authors: Tekwe Carmen D. , Carroll Raymond J. , Dabney Alan R. 
Published: May 2012

Abstract
Motivation: Protein abundance in quantitative proteomics is often based on observed spectral features derived from liquid chromatography mass spectrometry (LC-MS) or LC-MS/MS experiments. Peak intensities are largely non–normal in distribution. Furthermore, LC-MS-based proteomics data frequently have large proportions of missing peak intensities due to censoring mechanisms on low-abundance spectral features. Recognizing that the observed peak intensities detected with the LC-MS method are all positive, skewed and often left-censored, we propose using survival methodology to carry out differential expression analysis of proteins. Various standard statistical techniques including non-parametric tests such as the Kolmogorov–Smirnov and Wilcoxon–Mann–Whitney rank sum tests, and the parametric survival model and accelerated failure time-model with log-normal, log-logistic and Weibull distributions were used to detect any differentially expressed proteins. The statistical operating characteristics of each method are explored using both real and simulated datasets.
Results: Survival methods generally have greater statistical power than standard differential expression methods when the proportion of missing protein level data is 5% or more. In particular, the AFT models we consider consistently achieve greater statistical power than standard testing procedures, with the discrepancy widening with increasing missingness in the proportions.
Availability: The testing procedures discussed in this article can all be performed using readily available software such as R. The R codes are provided as supplemental materials.
Contact: ctekwe@stat.tamu.edu
Multi-scale computational modeling of developmental biology
Authors: Setty Yaki 
Published: May 2012

Abstract
Motivation: Normal development of multicellular organisms is regulated by a highly complex process in which a set of precursor cells proliferate, differentiate and move, forming over time a functioning tissue. To handle their complexity, developmental systems can be studied over distinct scales. The dynamics of each scale is determined by the collective activity of entities at the scale below it.
Results: I describe a multi-scale computational approach for modeling developmental systems and detail the methodology through a synthetic example of a developmental system that retains key features of real developmental systems. I discuss the simulation of the system as it emerges from cross-scale and intra-scale interactions and describe how an in silico study can be carried out by modifying these interactions in a way that mimics in vivo experiments. I highlight biological features of the results through a comparison with findings in Caenorhabditis elegans germline development and finally discuss about the applications of the approach in real developmental systems and propose future extensions.
Availability and implementation: The source code of the model of the synthetic developmental system can be found in www.wisdom.weizmann.ac.il/~yaki/MultiScaleModel.
Contact: yaki.setty@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
RAxML-Light: a tool for computing terabyte phylogenies
Authors: Stamatakis A. , Aberer A.J. , Goll C. , Smith S.A. , Berger S.A. , Izquierdo-Carrasco F. 
Published: May 2012

Abstract
Motivation: Due to advances in molecular sequencing and the increasingly rapid collection of molecular data, the field of phyloinformatics is transforming into a computational science. Therefore, new tools are required that can be deployed in supercomputing environments and that scale to hundreds or thousands of cores.
Results: We describe RAxML-Light, a tool for large-scale phylogenetic inference on supercomputers under maximum likelihood. It implements a light-weight checkpointing mechanism, deploys 128-bit (SSE3) and 256-bit (AVX) vector intrinsics, offers two orthogonal memory saving techniques and provides a fine-grain production-level message passing interface parallelization of the likelihood function. To demonstrate scalability and robustness of the code, we inferred a phylogeny on a simulated DNA alignment (1481 taxa, 20 000 000 bp) using 672 cores. This dataset requires one terabyte of RAM to compute the likelihood score on a single tree.
Code Availability: https://github.com/stamatak/RAxML-Light-1.0.5
Data Availability: http://www.exelixis-lab.org/onLineMaterial.tar.bz2
Contact: alexandros.stamatakis@h-its.org
Supplementary Information: Supplementary data are available at Bioinformatics online.
Mesalazine granules 1.5 g once‐daily maintain remission in patients with ulcerative colitis who switch from other 5‐ASA formulations: a pooled analysis from two randomised controlled trials
Authors: Lichtenstein G. R. , Zakko S. , Gordon G. L. , Murthy U. , Sedghi S. , Pruitt R. , Merchant K. , Bortey E. , Forbes W. P. 
Published: May 2012

SummaryBackgroundMesalazine (mesalamine) granules (MG) were shown to be effective for the maintenance of remission of ulcerative colitis (UC) in two double‐blind placebo‐controlled trials.AimTo evaluate the efficacy of once‐daily MG for maintenance of remission in patients with UC who switched from other 5‐aminosalicylic acid (5‐ASA) formulations.MethodsData from two independent multicenter, randomised, double‐blind, placebo‐controlled, 6‐month trials evaluating patients with UC in remission were combined for analysis of a subpopulation of patients who switched from other 5‐ASA formulations to MG 1.5 g or placebo upon randomisation. The primary endpoint was the percentage of patients who remained relapse‐free at Month 6 or end of treatment. Relapse was defined as a Sutherland Disease Activity Index (SDAI) rectal bleeding score ≥1 and mucosal appearance score ≥2, a UC flare or medication used to treat a UC flare.ResultsOf the 487 patients who received 5‐ASA maintenance therapy at enrolment, 322 were in the MG group and 165 were in the placebo group. The percentage of patients who remained relapse‐free (based on Sutherland Disease Activity Index scores) after 6 months was significantly higher with MG than placebo (78.3% vs. 58.8%, P < 0.001). Rectal bleeding, stool frequency and the physician's rating of disease activity remained unchanged after 6 months in a higher percentage of patients using MG compared with those on placebo (P < 0.004 for each endpoint).ConclusionMesalazine granules 1.5 g once‐daily is effective for maintenance of remission in UC patients who switch from other 5‐ASA formulations. ClinicalTrials.gov identifiers NCT00744016, NCT00767728.
The early gene product EUO is a transcriptional repressor that selectively regulates promoters of Chlamydia late genes
Authors: Rosario Christopher J. , Tan Ming 
Published: May 2012

SummaryThe obligate intracellular bacterium Chlamydia has an unusual developmental cycle in which there is conversion between two forms that are specialized for either intracellular replication or propagation of the infection to a new host cell. Expression of late chlamydial genes is upregulated during conversion from the replicating to the infectious form, but the mechanism for this temporal regulation is unknown. We found that EUO, which is expressed from an early gene, binds to two sites upstream of the late operon omcAB, but only the downstream site was necessary for transcriptional repression. Using gel shift and in vitro transcription assays we showed that EUO specifically bound and repressed promoters of Chlamydia trachomatis late genes, but not early or mid genes. These findings support a role for EUO as a temporal repressor that negatively regulates late chlamydial genes and prevents their premature expression. The basis of this specificity is the ability of EUO to selectively bind promoter regions of late genes, which would prevent their transcription by RNA polymerase. Thus, we propose that EUO is a master regulator that prevents the terminal differentiation of the replicating form of chlamydiae into the infectious form until sufficient rounds of replication have occurred.
Function of defensive volatiles in pedunculate oak (Quercus robur) is tricked by the moth Tortrix viridana
Authors: GHIRARDO ANDREA , HELLER WERNER , FLADUNG MATTHIAS , SCHNITZLER JÖRG‐PETER , SCHROEDER HILKE 
Published: May 2012

ABSTRACTThe indirect defences of plants are comprised of herbivore‐induced plant volatiles (HIPVs) that among other things attract the natural enemies of insects. However, the actual extent of the benefits of HIPV emissions in complex co‐evolved plant‐herbivore systems is only poorly understood. The observation that a few Quercus robur L. trees constantly tolerated (T‐oaks) infestation by a major pest of oaks (Tortrix viridana L.), compared with heavily defoliated trees (susceptible: S‐oaks), lead us to a combined biochemical and behavioural study. We used these evidently different phenotypes to analyse whether the resistance of T‐oaks to the herbivore was dependent on the amount and scent of HIPVs and/or differences in non‐volatile polyphenolic leaf constituents (as quercetin‐, kaempferol‐ and flavonol glycosides). In addition to non‐volatile metabolic differences, typically defensive HIPV emissions differed between S‐oaks and T‐oaks. Female moths were attracted by the blend of HIPVs from S‐oaks, showing significantly higher amounts of (E)‐4,8‐dimethyl‐1,3,7‐nonatriene (DMNT) and (E)‐β‐ocimene and avoid T‐oaks with relative high fraction of the sesquiterpenes α‐farnesene and germacrene D. Hence, the strategy of T‐oaks exhibiting directly herbivore‐repellent HIPV emissions instead of high emissions of predator‐attracting HIPVs of the S‐oaks appears to be the better mechanism for avoiding defoliation.
Enhancing protein stability with retained biological function in transgenic plants
Authors: Jang In‐Cheol , Niu Qi‐Wen , Deng Shulin , Zhao Pingzhi , Chua Nam‐Hai 
Published: May 2012

SummaryThe final expression level of a transgene‐derived protein in transgenic plants depends on transcriptional and post‐transcriptional processes. Here, we focus on methods to improve protein stability without comprising biological function. We found that the four isoforms of the Arabidopsis RAD23 protein family are relatively stable. The UBA2 domain derived from RAD23a can be used as a portable stabilizing signal to prolong the half‐life of two unstable transcription factors (TFs), HFR1 and PIF3. The increased stability of the TF–UBA2 fusion proteins results in an enhanced phenotype in transgenic plants compared to expression of the TF alone. Similar results were obtained for the RAD23a UBA1 domain. In addition to UBA1/2 of RAD23a, the UBA domain from the Arabidopsis DDI1 protein also increased the half‐life of the unstable protein JAZ10.1, which is involved in jasmonate signaling. Taken together, our results suggest that UBA fusions can be used to increase the stability of unstable proteins for basic plant biology research as well as crop improvement.
Asymptomatic transmission of Treponema pallidum (syphilis) through deceased donor liver transplantation
Authors: Tariciotti L. , Das I. , Dori L. , Perera M.T.P.R. , Bramhall S.R. 
Published: May 2012

AbstractA 55‐year‐old woman underwent liver transplantation (LT) with a graft from a deceased donor. Mandatory pre‐donation investigations showed positive syphilis serology that was available only after the transplant, with high Treponema pallidum particle agglutination assay titer compatible with donor syphilis infection. Despite the institution of appropriate post‐exposure prophylaxis, the recipient demonstrated latent seroconversion; however, liver graft function improved without evidence of syphilitic hepatitis or other manifestations of the disease. Through this first reported case of asymptomatic transmission of syphilis following LT, we highlight the investigations and treatment strategies for donor‐derived syphilis in liver transplant recipients. This report supplements the existing limited evidence on safe use of infected grafts from syphilitic donors through appropriate post‐exposure prophylaxis.
Deficits in inferior frontal cortex activation in euthymic bipolar disorder patients during a response inhibition task
Authors: Townsend Jennifer D , Bookheimer Susan Y , Foland‐Ross Lara C , Moody Teena D , Eisenberger Naomi I , Fischer Jeffrey S , Cohen Mark S , Sugar Catherine A , Altshuler Lori L 
Published: May 2012

Townsend JD, Bookheimer SY, Foland‐Ross LC, Moody TD, Eisenberger NI, Fischer JS, Cohen MS, Sugar CA, Altshuler LL. Deficits in inferior frontal cortex activation in euthymic bipolar disorder patients during a response inhibition task.  Bipolar Disord 2012: 14: 442–450. © 2012 The Authors. Journal compilation © 2012 John Wiley & Sons A/S.Objectives:  The inferior frontal cortical–striatal network plays an integral role in response inhibition in normal populations. While inferior frontal cortex (IFC) impairment has been reported in mania, this study explored whether this dysfunction persists in euthymia.Methods:  Functional magnetic resonance imaging (fMRI) activation was evaluated in 32 euthymic patients with bipolar I disorder and 30 healthy subjects while performing the Go/NoGo response inhibition task. Behavioral data were collected to evaluate accuracy and response time. Within‐group and between‐group comparisons of activation were conducted using whole‐brain analyses to probe significant group differences in neural function.Results:  Both groups activated bilateral IFC. However, between‐group comparisons showed a significantly reduced activation in this brain region in euthymic patients with bipolar disorder compared to healthy subjects. Other frontal and basal ganglia regions involved in response inhibition were additionally significantly reduced in bipolar disorder patients, in both the medicated and the unmedicated subgroups. No areas of greater activation were observed in bipolar disorder patients versus healthy subjects.Conclusions:  Bipolar disorder patients, even during euthymia, have a persistent reduction in activation of brain regions involved in response inhibition, suggesting that reduced activation in the orbitofrontal cortex and striatum is not solely related to the state of mania. These findings may represent underlying trait abnormalities in bipolar disorder.
Emotion processing and regulation in bipolar disorder: a review
Authors: Townsend Jennifer , Altshuler Lori L 
Published: May 2012

Townsend J, Altshuler LL. Emotion processing and regulation in bipolar disorder: a review.  Bipolar Disord 2012: 14: 326–339. © 2012 The Authors. Journal compilation © 2012 John Wiley & Sons A/S.Objectives:  Bipolar disorder (BP) is characterized by a dysfunction of mood, alternating between states of mania/hypomania and depression. Thus, the primary abnormality appears to be an inability to regulate emotion, the result of which is emotional extremes. The purpose of this paper is to review the current functional magnetic resonance imaging (fMRI) literature on adult patients with BP using emotion processing or regulation paradigms.Methods:  A search was conducted on PubMed using the keywords: bipolar disorder, fMRI, mania, bipolar depression, bipolar euthymia, emotion, and amygdala. Only those studies that were conducted in adult patients using an emotion activation task were included in the final review.Results:  Using tasks that assess neural functioning during emotion processing and emotion regulation, many fMRI studies have examined BP subjects during mania and euthymia. Fewer fMRI studies have been conducted during depression, and fewer still have included the same subjects in multiple mood states. Despite these limitations, these studies have demonstrated specific abnormalities in frontal–limbic regions. Using a variety of paradigms, investigators have specifically evaluated the amygdala (a structure within the limbic system known to be critical for emotion) and the prefrontal cortex (PFC) (a region known to have a regulatory function over the limbic system).Conclusions:  These investigations reveal that amygdala activation varies as a function of mood state, while the PFC remains persistently hypoactivated across mood states. Emotional dysregulation and lability in mania and depression may reflect disruption of a frontal–limbic functional neuroanatomical network.
Heart rate variability in the subsyndromal depressive phase of bipolar disorder
Authors: Lee Jung‐Sun , Kim Byungsu , Hong Youjin , Joo Yeon Ho 
Published: May 2012

Aims:  To compare the heart rate variability of bipolar patients in the subsyndromal depressive phase with healthy controls and to evaluate the relationship between severity of subsyndromal depressive symptoms and heart rate variability.Methods:  Thirty‐three bipolar patients in the subsyndromal depressive phase and 59 healthy controls were enrolled. A patient was considered to be in a subsyndromal depressive phase when the Montgomery–Åsberg depression rating scale score was ≤10 and the Clinical Global Impression–Severity scale (CGI‐S) was ≤3 for the previous 1 month. After approximately 10 min of supine rest, all participants underwent resting electrocardiograms for 5 min in the supine position using limb leads. Different parameters of heart rate variability were analyzed in the time and frequency domains.Results:  Bipolar patients had significantly lower standard deviation of all RR intervals (SDNN), proportion of adjacent NN intervals that differ by >50 ms (pNN50), log total power (log TP) and very low frequency power (VLF) compared to healthy controls. There were significant negative correlations between CGI‐S score and some heart rate variability parameters, including heart rate variability index, SDNN, root mean square successive difference (RMSSD), pNN50, log TP, VLF, low frequency power (LF) and high frequency power (HF).Conclusion:  Patients with bipolar disorder in the subsyndromal depressive state have reduced heart rate variability relative to healthy controls, and reduction of heart rate variability appears to be correlated with severity of symptoms in bipolar patients.
Psychological impact of the pandemic (H1N1) 2009 on general hospital workers in Kobe
Authors: Matsuishi Kunitaka , Kawazoe Ayako , Imai Hissei , Ito Atsushi , Mouri Kentaro , Kitamura Noboru , Miyake Keiko , Mino Koichi , Isobe Masanori , Takamiya Shizuo , Hitokoto Hidefumi , Mita Tatsuo 
Published: May 2012

Aims:  In order for hospitals to work efficiently in a pandemic, it is important to know how a pandemic affects the hospital staff. The aim of the present study was to investigate the psychological impact of the pandemic (H1N1) 2009 on hospital workers and how it was affected by the characteristics of the hospital, gender, age, job and work environment.Methods:  In late June 2009, soon after the pandemic had ended in Kobe city, Japan, a questionnaire was distributed consisting of questions on sociodemographic characteristics, 19 stress‐related questions and the Impact of Event Scale (IES) to all 3635 employees at three core general hospitals in Kobe. Exploratory factor analysis was applied to the 19 stress‐related questions, and this produced four factors for evaluation (anxiety about infection, exhaustion, workload, and feeling of being protected). Multiple regression models were used to evaluate the association of personal characteristics with each score of the four factors and the IES.Results:  Valid answers were received from 1625 employees. Workers at a hospital with intense liaison psychiatric services felt less psychological impact. Workers at a hospital that provided staff with information about the pandemic less frequently, felt unprotected. Workers in work environments that had a high risk of infection felt more anxious and more exhausted. The total IES score was higher in workers in high‐risk work environments.Conclusions:  It is important for hospitals to protect hospital workers during a pandemic and to rapidly share information about the pandemic. Liaison psychiatric services can help to reduce the impact of the pandemic on hospital workers.
Resting motor threshold changes and clinical response to prefrontal repetitive transcranial magnetic stimulation in depressed patients
Authors: Pretalli Jean‐Baptiste , Nicolier Magali , Chopard Gilles , Vandel Pierre , Tio Grégory , Monnin Julie , Pazart Lionel , Sechter Daniel , Haffen Emmanuel 
Published: May 2012

Aims:  Several variables are able to influence the antidepressant effects of repetitive transcranial magnetic stimulation (rTMS), particularly the intensity of stimulation, which is generally expressed according to the resting motor threshold (RMT). The aim of our study was to investigate whether or not RMT changes during the treatment of resistant depression by rTMS and whether these fluctuations could alter treatment outcome.Methods:  Seventy‐five inpatients suffering from unipolar or bipolar treatment‐resistant depression and who had been antidepressant‐free or taking a stable antidepressant drug and a daily dose of benzodiazepine for at least a month received a left prefrontal rTMS session once a day for 10 days at 10 Hz and 95% RMT.Results:  For the whole group, no significant fluctuation of RMT was observed between the first and the second week of rTMS treatment. However, RMT increased, decreased or remained constant throughout treatment depending on the patient. These RMT changes influenced the outcome of the 10 sessions concerning the severity of depressive and anxiety symptoms, measured by the Beck Depression Inventory and State Trait Anxiety, respectively.Conclusions:  Our results justify calculating RMT regularly, and suggest that its variations play a role in treatment outcome.