bluuebunny/crossref_metadata_2025_split huggingface dataset:
CloudMap: A Cloud-Based Pipeline for Analysis of Mutant Genome Sequences
Authors: Minevich Gregory , Park Danny S , Blankenberg Daniel , Poole Richard J , Hobert Oliver 
Published: October 2012

AbstractWhole genome sequencing (WGS) allows researchers to pinpoint genetic differences between individuals and significantly shortcuts the costly and time-consuming part of forward genetic analysis in model organism systems. Currently, the most effort-intensive part of WGS is the bioinformatic analysis of the relatively short reads generated by second generation sequencing platforms. We describe here a novel, easily accessible and cloud-based pipeline, called CloudMap, which greatly simplifies the analysis of mutant genome sequences. Available on the Galaxy web platform, CloudMap requires no software installation when run on the cloud, but it can also be run locally or via Amazon's Elastic Compute Cloud (EC2) service. CloudMap uses a series of predefined workflows to pinpoint sequence variations in animal genomes, such as those of premutagenized and mutagenized Caenorhabditis elegans strains. In combination with a variant-based mapping procedure, CloudMap allows users to sharply define genetic map intervals graphically and to retrieve very short lists of candidate variants with a few simple clicks. Automated workflows and extensive video user guides are available to detail the individual analysis steps performed (http://usegalaxy.org/cloudmap). We demonstrate the utility of CloudMap for WGS analysis of C. elegans and Arabidopsis genomes and describe how other organisms (e.g., Zebrafish and Drosophila) can easily be accommodated by this software platform. To accommodate rapid analysis of many mutants from large-scale genetic screens, CloudMap contains an in silico complementation testing tool that allows users to rapidly identify instances where multiple alleles of the same gene are present in the mutant collection. Lastly, we describe the application of a novel mapping/WGS method (“Variant Discovery Mapping”) that does not rely on a defined polymorphic mapping strain, and we integrate the application of this method into CloudMap. CloudMap tools and documentation are continually updated at http://usegalaxy.org/cloudmap.
Genomic Tests of Variation in Inbreeding Among Individuals and Among Chromosomes
Authors: Schraiber Joshua G , Shih Stephannie , Slatkin Montgomery 
Published: October 2012

Abstract
We examine the distribution of heterozygous sites in nine European and nine Yoruban individuals whose genomic sequences were made publicly available by Complete Genomics. We show that it is possible to obtain detailed information about inbreeding when a relatively small set of whole-genome sequences is available. Rather than focus on testing for deviations from Hardy–Weinberg genotype frequencies at each site, we analyze the entire distribution of heterozygotes conditioned on the number of copies of the derived (non-chimpanzee) allele. Using Levene’s exact test, we reject Hardy–Weinberg in both populations. We generalized Levene’s distribution to obtain the exact distribution of the number of heterozygous individuals given that every individual has the same inbreeding coefficient, F. We estimated F to be 0.0026 in Europeans and 0.0005 in Yorubans, but we could also reject the hypothesis that F was the same in each individual. We used a composite-likelihood method to estimate F in each individual and within each chromosome. Variation in F across chromosomes within individuals was too large to be consistent with sampling effects alone. Furthermore, estimates of F for each chromosome in different populations were not correlated. Our results show how detailed comparisons of population genomic data can be made to theoretical predictions. The application of methods to the Complete Genomics data set shows that the extent of apparent inbreeding varies across chromosomes and across individuals, and estimates of inbreeding coefficients are subject to unexpected levels of variation, which might be partly accounted for by selection.
Validation of a Short Measure of Effort‐Reward Imbalance in the Workplace: Evidence from China
Authors: Li Jian , Loerbroks Adrian , Shang Li , Wege Natalia , Wahrendorf Morten , Siegrist Johannes 
Published: October 2012

Validation of a Short Measure of Effort‐Reward Imbalance in the Workplace: Evidence from China: Jian LI, et al. Mannheim Institute of Public Health, Social and Preventive Medicine, Mannheim Medical Faculty, Heidelberg University, Germany—ObjectivesWork stress is an emergent risk in occupational health in China, and its measurement is still a critical issue. The aim of this study was to examine the reliability and validity of a short version of the effort‐reward imbalance (ERI) questionnaire in a sample of Chinese workers.MethodsA community‐based survey was conducted in 1,916 subjects aged 30−65 years with paid employment (971 men and 945 women).ResultsAcceptable internal consistencies of the three scales, effort, reward and overcommitment, were obtained. Confirmatory factor analysis showed a good model fit of the data with the theoretical structure (goodness‐of‐fit index=0.95). Evidence of criterion validity was demonstrated, as all three scales were independently associated with elevated odds ratios of both poor physical and mental health.ConclusionsBased on the findings of our study, this short version of the ERI questionnaire is considered to be a reliable and valid tool for measuring psychosocial work environment in Chinese working populations.
Smoking Rate Trends in Korean Occupational Groups: Analysis of KNHANES 1998–2009 Data
Authors: Jang Tae‐Won , Kim Hyoung‐Ryoul , Choi Sarah E. , Yim Hyeon‐Woo , Lee Hye‐Eun , Myong Jun‐Pyo , Koo Jung‐Wan 
Published: October 2012

Smoking Rate Trends in Korean Occupational Groups: Analysis of KNHANES 1998–2009 Data: Tae‐Won JANG, et al. Department of Preventive Medicine and Center for Occupational and Environmental Medicine, College of Medicine, The Catholic University of Korea, Korea—ObjectivesThis study aimed to investigate changes in the smoking rate among Korean adults from 1998–2009 by gender and occupational groups.MethodsUsing the data from the first (1998), second (2001), third (2005) and fourth (2009) waves of the Korean National Health and Nutrition Examination Survey (KNHANES), we examined men and women between 25−64 years old. Occupational groups were classified into 3 groups of non‐manual workers, 5 groups of manual workers and other workers groups. The other group included the unemployed, students and housewives. Age‐adjusted prevalence rates of cigarette smoking were calculated for 10‐year age groups in each wave of the KNHANES. Trends in the smoking rate according to occupational groups were estimated.ResultsAmong male workers, decreasing trends in smoking rates were observed in non‐manual workers, manual workers, and other workers. The odds ratios and prevalence ratios for the smoking rates of the manual workers comparing the non‐manual workers increased from 1998 to 2005, whereas decreased to 1.38 and 1.12, respectively, in 2009. Differences in smoking rates between manual and non‐manual workers increased from 1998 to 2005 but decreased from 2005 to 2009. Among female workers, the smoking rates decreased between 1998 and 2001 and increased beginning in 2001.ConclusionsThe smoking rate of the manual workers group was still higher than that of the non‐manual workers group. Anti‐smoking programs specific to each occupational group are needed.
Mechanical characterization of “blister” defects on optical oxide multilayers using nanoindentation
Authors: Mehrotra K. , Howard H.P. , Jacobs S.D. , Lambropoulos J.C. 
Published: October 2012

ABSTRACTWe characterize “blisters”, defects observed in multilayer dielectric (MLD) coatings after exposure to acid cleaning procedures. Nanoindentation is used to make site-specific indentations across blisters to measure the mechanical response, especially their compliance under different conditions of loading. Two regions of statistically different mechanical response are identified within a blister defect and compared to the undisturbed regions of the MLD coating. The indentation response of blisters can vary across samples, and we suggest reasons for this variation.
Effect of Praseodymium Species on the Structural and Functional Properties of Nanocrystalline BiFeO3 Powders and Thin Films
Authors: Albino Gina Montes , Gálvez-Saldaña Marco , Perales-Pérez Oscar 
Published: October 2012

ABSTRACTThe present study addressed the effect of the incorporation of Praseodymium species in the BiFeO3(BFO) structure on the corresponding structural and functional properties of powders and films. The level of the doping species varied from 0 at% to 4 at%. BFO powders and thin films were synthesized by a sol-gel method, where glycol was aggregated to the main solvent to increase the viscosity of the precursor solutions and promote their adhesion onto platinum substrates. The development of the host BFO structure was confirmed by XRD analyses of samples annealed at 700°C for one hour (powders) or 500°C for 2 hours (thin films), in air. The average crystallite size varied from 37 nm to 41 nm and 28nm to 40nm for powders and thin films, respectively, due to the increase of the doping level. The incorporation of specific dopant species played an important role in the ferromagnetic and ferroelectric behavior in the material.
Fabrication and Characterization of Colossal Dielectric Response of Polycrystalline Ca1-x SrxCu3Ti4O12 (0≤x≤1) Ceramics
Authors: Yun Lee Sung , Yoo Duk-Keun , Lee Jihye , Jo William , Hong Youn-Woo , Kim Young-Hwan , Yoo Sang-Im 
Published: October 2012

ABSTRACTWe report the microstructures and dielectric properties of Ca1-xSrxCu3Ti4O12 (C1-xSxCTO, 0≤x≤1) ceramics sintered at the various sintering temperatures ranging from 1000 to 1060˚C in air. The linear increase in lattice parameter in C1-xSxCTO (0≤x≤1) ceramics is observable for the full range of substitution. However, the second phases of SrTiO3 and CuO start to occur from the composition of x=0.8, implying that a stoichiometric SrCu3Ti4O12 (SCTO) compound may not exist. While the C0.6S0.4CTO and C0.4S0.6CTiO samples exhibit relatively lower dielectric constant (εr) of ∼40,000 below 1 kHz, the CaCu3Ti4O12 (CCTO) and SCTO show the extremely high εr values of ~120,000 and ∼180,000, respectively. Complex impedance (Z*) and modulus (M*) spectroscopy revealed that the capacitance (C) and resistivity (ρ) values of grain boundary in all samples are much higher than those of grains.
Improved Electrical Properties of BaTiO3 – coated CaCu3Ti4O12 Dielectrics
Authors: Kim Hui Eun , Lee Sung Yun , Yoo Sang-Im 
Published: October 2012

ABSTRACTWe report a significant improvement in the electrical properties of CaCu3Ti4O12 (CCTO) dielectrics by the BaTiO3 (BTO) additive. The addition of BTO to CCTO was performed using two different methods of a solid-state mixing and a sol-gel coating. Compared with pure CCTO ceramics (εr ∼ 52,000 and tanδ ∼ 0.38 at 100 kHz), BTO-added CCTO samples commonly showed a large improvement in the dielectric loss property although their dielectric constants were depressed around one order of magnitude; εr ∼ 5900 and tanδ ∼0.05 for 5 mol% BTO-coated CCTO sample and εr ∼ 4,075 and tanδ ∼ 0.02 for 5 mol% BTO-mixed CCTO sample. In addition, BTO-coated CCTO samples showed relatively lower leakage current than those of BTO-mixed CCTO samples, implying that the sol-gel coating is more effective for improving the electrical properties of CCTO.
Optical Properties of ATO Sol-gel Coated Carbon Fibers
Authors: Richard Brandon , Alcantar Norma , Hoff Andrew , Thomas Sylvia 
Published: October 2012

ABSTRACTRecent trends in composite research include the development of structural materials with multiple functionalities. In new studies, novel materials are being designed, developed, modified, and implemented into composite designs. Typically, an increase in functionality requires additional material phases within one system. The presence of excessive phases can result in deterioration of individual or overall properties. True multi-functional materials must maintain all properties at or above the minimum operating limit. In this project, samples of Sb-doped SnO2(ATO) sol-gel solutions are used to coat carbon fibers and are heat treated at a temperature range of 200 – 500 °C. Results from this research are used to model the implementation of sol-gel coatings into carbon fiber reinforced multifunctional composite systems. This research presents a novel thermo-responsive sol-gel/ (dopant) combination and evaluation of the actuating responses due to various heat treatment temperatures. While ATO is a well-known transparent conductive material, the implementation of ATO on carbon fibers for infrared thermal reflectivity has not been examined. These coatings serve as actuators capable of reflecting thermal infrared radiation in mid-range and near-range wavelengths (λ). By altering the ATO sol gel thickness and heat treatment temperatures, optimal optical properties are obtained. While scanning electron microscopy (SEM) is used for imaging, electron diffraction spectroscopy (EDS) is used to verify the compounds present in the coatings. Fourier transform infrared (FT-IR) spectroscopy was performed to analyze the reflectivity in the infrared spectra and analyze the crystal structures after heat treatments.
Ferroelectricity, ferromagnetism, and magnetoelectric coupling in highly textured thin films of the multiferroic Pb(Fe0.5Nb0.5)O3
Authors: Raymond-Herrera Oscar , Góngora-Lugo Paola , Ostos Carlos , Curiel-Alvarez Mario , Bueno-Baques Dario , Machorro-Mejia Roberto , Mestres-Vila Lourdes , Font-Hernández Reynaldo , Portelles-Rodriguez Jorge , Siqueiros Jesús M. 
Published: October 2012

ABSTRACTA study of the ferroelectric and magnetic properties and of the magnetoelectric coupling effects of Pb(Fe0.5Nb0.5)O3 (PFN) thin films, grown on SrRuO3/Si [(100) or (111)] substrates by the rf-magnetron sputtering technique, is presented. Structural, morphological, and compositional characterization was realized using the XRD, AFM, XPS, and TEM techniques. Highly textured single phase films with different thickness (from 45 to 270 nm) were successfully grown without Fe2+ presence. A vertically [110] oriented grainy structure was observed. Polarization vs. electric field (P-E) hysteresis loops exhibit excellent and almost constant values of the maximum (∼ 60 μC/cm2) and remanent (∼ 22 μC/cm2) polarizations in the temperature range from 4 K to room temperature; small values of the coercive field, characteristic of soft ferroelectric materials, are observed in these samples. Measurements of the zero-field cooled (ZFC) and field cooled (FC) magnetization behavior and magnetic (M-H) hysteresis loops were realized at different temperatures between 5 and 300 K. Proof of the existence of ferromagnetic order in the low temperature region (below to 50 K) is discussed and reported for the first time. Values of the maximum (∼ 3 emu/g) and remanent (∼ 1.5 emu/g) magnetizations were obtained. dc magnetic field dependence of the ferroelectric hysteresis loops are shown as evidence of the magnetoelectric coupling.
Hetero-Epitaxial Growth of YBCO and MgB2 Thin Films on Decorated Substrates with Nano-Wires and Nano-Particles
Authors: Ohshima Shigetoshi 
Published: October 2012

ABSTRACTSuperconducting NMR pickup coils have to have a low surface resistance (Rs) under a high magnetic field. One way of reducing the Rs of superconducting thin films is adding artificial pins to the films. We examined the hetero-epitaxial growth of MgB2and YBCO thin films on decorated sapphire and MgO substrates while using nano-wires and nano-particles to add pins to the films.We used ZnO nano-wire to add artificial grain boundary pins to MgB2 films. The tilted c-plane sapphire substrate with nano-step edges was used for these substrates. The terrace width with one lattice step edge can be controlled by changing the tilt angle. AFM images showed that the tilted c-plane sapphire substrate had straight nano-step edges. ZnO nono-wires were decorated on the nano-step edges by MOCVD, and then deposited on MgB2 films by sputtering. The Rs of the films was then measured with a sapphire rod resonator. The Rs of MgB2 thin films fabricated on the tilted c-plane sapphire substrate with ZnO nano-wires was lower than that of MgB2thin films on a conventional sapphire substrate under a high magnetic field.We used BaZrO3(BZO) nano-particles to add the artificial pins to YBCO thin films. The BZO particles on the MgO substrates were fabricated by laser deposition. The size and density of these particles were controlled with a pulse number of laser shot. YBCO thin films were formed on decorated MgO substrate by laser deposition. The Rs of YBCO thin films on the decorated MgO substrate was lower than that of the YBCO films formed on a conventional MgO substrate under a high magnetic field.We clarified that artificial pins in MgB2and YBCO thin films are useful for decreasing the Rs under a high magnetic field.
Proposed
DSM-5
Changes for Autism Spectrum Disorder
Authors: Lohr W. David , Le Jennifer F. 
Published: October 2012

CME Educational Objectives

1.
Identify the signs and symptoms of autism spectrum disorder (ASD).

2.

Understand the proposed criteria for ASD in the
DSM-5
.

3.

Gain awareness of the proposed advantages and concerns posed by the
DSM-5
diagnostic criteria for ASD.

The patient is a 12-year-old female diagnosed with the mainly inattentive type of attention-deficit disorder due to problems with focus and completing homework. She is treated with 54 mg per day of extended-release methylphenidate. The family presents for ongoing management of ADD but also note she has tantrums over homework and sharing with her 10-year-old sister.
An 11-Year-Old Boy with Tantrums and Head Banging
Authors: Lohr W. David , Le Jennifer F. 
Published: October 2012

CME Educational Objectives

1.
Distinguish presentations of anxiety from core autism spectrum disorder (ASD) symptoms.

2.
Become familiar with developmental differences between anxiety and anxiety in ASD.

3.
Know when either, or both, psychosocial and pharmacologic treatment of anxiety in ASD is appropriate.

The patient is an 11-year-old white male with a history of Asperger’s disorder who presents with a history of anger and tantrums that occur about twice per week in reaction to frustrations and requests made of him. The tantrums consist of balling his fists, gesturing to hit, banging his head, grunting, screaming, and crying. He struggles with transitions from preferred activities and is upset if his expectations are not met. The parents report he also has tantrums over any mistakes he makes in his schoolwork.
FcγRIIb on Liver Sinusoidal Endothelium Clears Small Immune Complexes
Authors: Ganesan Latha P. , Kim Jonghan , Wu Yun , Mohanty Sudhasri , Phillips Gary S. , Birmingham Daniel J. , Robinson John M. , Anderson Clark L. 
Published: October 2012

AbstractIt has long been known that the ITIM-bearing IgG Fc receptor (FcγRIIb, RIIb) is expressed on liver sinusoidal endothelial cells (LSEC) and that the liver is the major site of small immune complex (SIC) clearance. Thus, we proposed that RIIb of LSEC eliminates blood-borne SIC, thereby controlling immune complex-mediated autoimmune disease. Testing this hypothesis, we found most RIIb of the mouse, fully three-quarters, to be expressed in liver. Moreover, most (90%) liver RIIb was expressed in LSEC, the remainder in Kupffer cells. An absent FcRγ in LSEC implied that RIIb is the sole FcγR expressed. Testing the capacity of liver RIIb to clear blood-borne SIC, we infused mice intravenously with radio-iodinated SIC made of OVA and rabbit IgG anti-OVA. Tracking decay of SIC from the blood, we found the RIIb knockout strain to be severely deficient in eliminating SIC compared with the wild-type strain, terminal half-lives being 6 and 1.5 h, respectively. RIIb on LSEC, a major scavenger, keeps SIC blood concentrations low and minimizes pathologic deposition of inflammatory immune complex.
IL-7 Restores Lymphocyte Functions in Septic Patients
Authors: Venet Fabienne , Foray Anne-Perrine , Villars-Méchin Astrid , Malcus Christophe , Poitevin-Later Françoise , Lepape Alain , Monneret Guillaume 
Published: October 2012

Abstract
Septic syndrome is the leading cause of mortality for critically ill patients worldwide. Patients develop lymphocyte dysfunctions associated with increased risk of death and nosocomial infections. In this study, we performed preclinical experiments testing the potential of recombinant human IL-7 (rhIL-7) as a lymphostimulating therapy in sepsis. Circulating IL-7 and soluble IL-7 receptor α-chain (soluble CD127) concentrations were measured in plasma, whereas cellular CD127 expression was evaluated on circulating CD4+ and CD8+ lymphocytes from septic shock patients and healthy volunteers. Lymphocyte proliferation, IFN-γ production, STAT5 phosphorylation, and B cell lymphoma 2 induction were measured ex vivo in response to T cell stimulation in the presence or not of rhIL-7. We show that IL-7 pathway (plasmatic IL-7 concentration and cellular and soluble CD127 expressions) is not overtly altered and remains activable in septic patients. Most importantly ex vivo treatment of patients’ cells with rhIL-7 significantly improves lymphocyte functionality (CD4+ and CD8+ lymphocyte proliferations, IFN-γ production, STAT5 phosphorylation, and B cell lymphoma 2 induction after stimulation). To our knowledge, this constitutes the first report of rhIL-7 ability to restore normal lymphocyte functions in septic patients. These results support the rational for initiating a clinical trial testing rhIL-7 in septic shock.
Acute arterial infarcts in patients with severe head injuries
Authors: Garg Anil , Agrawal Deepak 
Published: October 2012

Abstract
To study the incidence, demographic profile, and outcome of patients with severe closed head injuries who develop acute arterial infarcts.
Patients with severe head injury (Glasgow coma score (GCS) ≤8) presenting within 8 h of injury in the Department of Neurosurgery over a period of 5 months were enrolled in the study. Patients with penetrating head injury, infarct due to herniation and iatrogenic arterial injuries were excluded from the study. Only arterial infarcts developing within 8 h of injury were included in the study. A computed tomography (CT) head was done on all patients within 8 h of injury and repeated if necessary. Arterial infarct was defined as well-demarcated wedge-shaped hypodensity corresponding to an arterial territory on plain CT of the head. Outcome was assessed using Glasgow outcome score (GOS) at 1 month post-injury or at death (whichever came earlier).
Forty-four patients of severe head injury were included in the study during the above period. Of these, four patients (9.1%) had arterial infarcts on the initial CT scan. The male:female ratio was 1:3. The mean age was 54 years (range 3–85 years). Two patients had infarcts in the middle cerebral artery distribution and two in the superior cerebellar artery distribution. Poor outcome (GOS 1–3) was seen in 100% of the patients with arterial infarct compared to 52.5% (n=21) in patients with severe head injury without arterial infarct.
A significant percentage of patients with severe head injury have arterial infarcts on admission, which may imply arterial injury. Our study shows that these patients have a poorer prognosis vis-à-vis patient without these findings