bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the Micro/Meso Scale Sheet Forming by Strain Gradient Plasticity and its Characterization of Tool Feature Size Effects
Authors: Peng Linfa , Yi Peiyun , Hu Peng , Lai Xinmin , Ni Jun 
Published: October 2014

For conventional metal forming, finite element (FE) method becomes a powerful tool in process design. However, conventional material models cannot describe material behaviors precisely in micro/meso scale due to the size/scale effects. As a result, know-how obtained in traditional macro-forming is not suitable for the micro-forming process. In micro/meso scale forming process, the reaction force, localized stress concentration and formability are not only dependent on the strain distribution and strain path but also the strain gradient and strain gradient path caused by decreased scale.
This study presented a model based on conventional mechanism based strain gradient (CMSG) plasticity. A user-defined material (UMAT) subroutine incorporating the CMSG plasticity in the ABAQUS finite element (FE) program was established. Based on the subroutine, FE simulations were performed to analyze the effects of the channel width in sheet forming process of micro-channel features. Die sets were fabricated according to the scale law and Micro/meso scale sheet forming experiments were conducted to study the effect of channel width in the die. Experimental results indicated that the CMSG plastic theory achieved better agreements compared to the conventional plastic theory. It found that the influence of the strain gradient to the forming process increased with the decrease of the geometrical parameters of the tools. Furthermore, various tool geometrical parameters were designed by Taguchi Method to explore the feature size effects caused by the decrease of tool geometrical dimensions. According the scale law, similarity difference and the similarity accuracy were calculated to evaluate the size effects. Greater equivalent strain gradient was found with the decrease of the tool geometric dimension, which lead larger maximum reaction force error due to increasing size effects. The main effect plots for equivalent strain gradient and reaction force indicated that the influence of the tools clearance was larger than punch radius, die radius and die width.
Removal of Calcified Plaque Utilizing Orbital Atherectomy
Authors: Kohler Robert , Nguyen Tri , McBroom Jeffrey 
Published: October 2014

Arterial disease occurs when plaque builds up in the arteries and limits flow of oxygen-rich blood to organs and other parts of the body reducing organ function. Atherectomy is a mechanical process in which plaque is removed from artery walls or modified to change vessel compliance. Various types of atherectomy systems exist to remove or modify plaque depending on plaque morphology. Orbital atherectomy (Diamondback 360® Orbital Atherectomy System) is a sanding process utilizing a diamond abrasive crown mounted eccentrically to a flexible drive shaft.
The effects of rotational speed, crown size, centrifugal forces and run time were evaluated. Finite element modeling and bench testing using carbon as a calcified plaque surrogate material were used.
The crown-simulated vessel wall force was calculated using a finite element model that included a rigid vessel wall and a rotating crown. Results show a small force when the crown begins to rotate at lower speeds, that increases to a peak force at maximum speed, and decreases as the orbit diameter increases with material removal.
A design of experiments plan was created and used to quantify the effects of crown size rotation speed and number of treatment passes on lumen diameter. Increasing the crown diameter increased lumen diameter nonlinearly at an increasing rate with crown rotation speed in the carbon model.
Scanning Electron Microscopy (SEM) analysis of the particulate material removed in the bench test demonstrated brittle fracture as the mode of material removal of the carbon surrogate.
Walking Reduces Postprandial Insulin Secretion in Obese Adolescents Consuming a High-Fructose or High-Glucose Diet
Authors: Heden Timothy D. , Liu Ying , Park Young-Min , Winn Nathan C. , Kanaley Jill A. 
Published: October 2014

Background:This study assessed if walking at a self-selected pace could improve postprandial glucose and insulin concentrations in obese adolescents consuming high-fructose (HF) or high-glucose (HG) diets.Methods:Seven obese male and female adolescents (18 ± 1 yr) performed 4, 15-day trials in a random order, including 1) HF-diet (50 g fructose/d added to normal diet) while being sedentary, 2) HG-diet (50 g glucose/d) while sedentary, 3) HF-diet with additional walking, and 4) HG-diet with additional walking. On the 15th day of each trial, the participants performed mixed meal testing in the laboratory in which they consumed three liquid shakes (either HF or HG) and during the HF and HG sedentary trials, the participants took < 4000 steps while in the laboratory but during the walking trials took ≥ 13,000 steps during testing.Results:Walking did not alter postprandial glucose concentrations. Although walking reduced insulin secretion by 34% and 25% during the HF- and HG-diet, respectively (P < .05), total insulin concentrations were only significantly reduced (P > .05) with walking during the HF trial, possibly because walking enhanced insulin clearance to a greater extent during the HF-diet.Conclusions:Walking reduces postprandial insulin secretion in obese adolescents consuming a high-fructose or high-glucose diet.
Genome Sequence of Coxiella burnetii Strain AuQ01 (Arandale) from an Australian Patient with Acute Q Fever
Authors: Walter Mathias C. , Vincent Gemma A. , Stenos John , Graves Stephen , Frangoulidis Dimitrios 
Published: October 2014

ABSTRACT

Coxiella burnetii
strain AuQ01 was isolated from the serum of an Australian acute Q fever patient and represents the first whole genome from this historical Q fever country. This new genome shows distinct differences from existing genomic data and will enhance the understanding of this query pathogen.
Draft Genome Sequence of Burkholderia pyrrocinia Lyc2, a Biological Control Strain That Can Suppress Multiple Plant Microbial Pathogens
Authors: Wang Xiao-Qiang , Showmaker Kurt C. , Yu Xiao-Qing , Bi Tao , Hsu Chuan-Yu , Baird Sonya M. , Peterson Daniel G. , Li Xiang-Dong , Lu Shi-En 
Published: October 2014

ABSTRACT

Burkholderia pyrrocinia
strain Lyc2 was isolated from the tobacco rhizosphere in China. This bacterium exhibits a remarkable capacity to inhibit the growth of multiple pathogens and shows strong suppression of cotton seedling damping-off. Here, we present the draft genome sequence of
Burkholderia pyrrocinia
strain Lyc2.
Draft Genome Sequence of the Organophosphorus-Degrading Bacterium
Pseudomonas
sp. Strain 1-7, Isolated from Organophosphorus-Polluted Sludge
Authors: Tian Jian , Xu Li , Zhang Shuangyu , Sun Wen , Chu Xiaoyu , Wu Ningfeng 
Published: October 2014

ABSTRACT

Pseudomonas
sp. strain 1-7, isolated from organophosphorus-polluted sludge, is able to degrade many organophosphorus compounds. Here, we report the draft genome sequence of
Pseudomonas
sp. strain 1-7.
Genome Sequence of
Maribius
sp. Strain MOLA 401, a Marine
Roseobacter
with a Quorum-Sensing Cell-Dependent Physiology
Authors: Doberva Margot , Sanchez-Ferandin Sophie , Ferandin Yoan , Intertaglia Laurent , Joux Fabien , Lebaron Philippe , Lami Raphaël 
Published: October 2014

ABSTRACT

Maribius
sp. strain MOLA401 is an alphaproteobacterium isolated from a coral reef lagoon located in New Caledonia, France. We report the genome sequence and its annotation which, interestingly, reveals the presence of genes involved in quorum sensing. This is the first report of a full genome within the genus
Maribius
.
Complete Genome Sequence of Vibrio vulnificus 93U204, a Bacterium Isolated from Diseased Tilapia in Taiwan
Authors: Lo Wen-Sui , Chen Hwajiun , Chen Chun-Yao , Kuo Chih-Horng 
Published: October 2014

ABSTRACT

Vibrio vulnificus
93U204 is a bacterium isolated from a moribund tilapia collected in Kaohsiung, Taiwan. Here, we report the complete genome sequence of this bacterium to facilitate the investigation of its pathogenicity and for comparative analyses with human-pathogenic strains within the same species.
Draft Genome Sequence of the Oyster Larval Probiotic Bacterium
Vibrio
sp. Strain OY15
Authors: Schreier Harold J. , Schott Eric J. 
Published: October 2014

ABSTRACT

We report the draft genome sequence of
Vibrio
sp. strain OY15, a Gram-negative marine bacterium isolated from an oyster (
Crassostrea virginica
) digestive tract and shown to possess probiotic activity. The availability of this genome sequence will facilitate the study of the mechanisms of probiotic activity as well as virulence capacity.
Identification of Primary Drug Resistance to Rifampin in Mycobacterium leprae Strains from Leprosy Patients in Amazonas State, Brazil
Authors: Contreras Mejía Matilde del Carmen , Porto Dos Santos Maísa , Villarouco da Silva George Allan , da Motta Passos Isabella , Naveca Felipe Gomes , Souza Cunha Maria da Graça , Moraes Milton Ozório , de Paula Lucia 
Published: October 2014

ABSTRACTThe aim of this study was to identify polymorphisms in thefolp1,gyrA, andrpoBgenes in leprosy patients treated in Amazonas State, Brazil. Among 197 slit-skin smear samples from untreated or relapsed patients, we found three cases of primary resistance to rifampin and one confirmed case of multidrug resistance.
Evaluation of the BD GeneOhm Methicillin-Resistant Staphylococcus aureus (MRSA) Assay as a Method for Detection of MRSA Isolates, Using a Large Collection of European and North African Isolates
Authors: Trouillet-Assant Sophie , Bes Michele , Meugnier Helene , Tigaud Sylvestre , Etienne Jérôme , Vandenesch François , Laurent Frédéric 
Published: October 2014

ABSTRACT

Using a large collection of European and North African methicillin-resistant
Staphylococcus aureus
(MRSA) isolates with a variety of genetic backgrounds and staphylococcal cassette chromosome
mec
(SCC
mec
) types, we evaluated the reliability of the BD GeneOhm MRSA assay. Results revealed high performance of this test for detecting MRSA strains provided from Europe and North Africa (98.3%).
Point-Counterpoint: Can Newly Developed, Rapid Immunochromatographic Antigen Detection Tests Be Reliably Used for the Laboratory Diagnosis of Influenza Virus Infections?
Authors: Dunn James J. , Ginocchio Christine C. 
Published: October 2014

ABSTRACT

Five years ago, the Point-Counterpoint series was launched. The initial article asked about the role of rapid immunochromatographic antigen testing in the diagnosis of influenza A virus 2009 H1N1 infection (D. F. Welch and C. C. Ginocchio, J Clin Microbiol 48:22–25, 2010,
http://dx.doi.org/10.1128/JCM.02268-09
). Since that article, not only have major changes been made in immunochromatographic antigen detection (IAD) testing for the influenza viruses, but there has also been rapid development of commercially available nucleic acid amplification tests (NAATs) for influenza virus detection. Further, a novel variant of influenza A, H7N9, has emerged in Asia, and H5N1 is also reemergent. In that initial article, the editor of this series, Peter Gilligan, identified two issues that required further consideration. One was how well IAD tests worked in clinical settings, especially in times of antigen drift and shift. The other was the role of future iterations of influenza NAATs and whether this testing would be available in a community hospital setting. James Dunn, who is Director of Medical Microbiology and Virology at Texas Children's Hospital, has extensive experience using IAD tests for diagnosing influenza. He will discuss the application and value of these tests in influenza diagnosis. Christine Ginocchio, who recently retired as the Senior Medical Director, Division of Infectious Disease Diagnostics, North Shore-LIJ Health System, and now is Vice President for Global Microbiology Affairs at bioMérieux, Durham, NC, wrote the initial counterpoint in this series, where she advocated the use of NAATs for influenza diagnosis. She will update us on the commercially available NAAT systems and explain what their role should be in the diagnosis of influenza infection.
HIV-1 Nef and Vpu Are Functionally Redundant Broad-Spectrum Modulators of Cell Surface Receptors, Including Tetraspanins
Authors: Haller Claudia , Müller Birthe , Fritz Joëlle V. , Lamas-Murua Miguel , Stolp Bettina , Pujol François M. , Keppler Oliver T. , Fackler Oliver T. 
Published: October 2014

ABSTRACT
HIV-1 Nef and Vpu are thought to optimize virus replication in the infected host, at least in part via their ability to interfere with vesicular host cell trafficking. Despite the use of distinct molecular mechanisms, Nef and Vpu share specificity for some molecules such as CD4 and major histocompatibility complex class I (MHC-I), while disruption of intracellular transport of the host cell restriction factor CD317/tetherin represents a specialized activity of Vpu not exerted by HIV-1 Nef. To establish a profile of host cell receptors whose intracellular transport is affected by Nef, Vpu, or both, we comprehensively analyzed the effect of these accessory viral proteins on cell surface receptor levels on A3.01 T lymphocytes. Thirty-six out of 105 detectable receptors were significantly downregulated by HIV-1 Nef, revealing a previously unappreciated scope with which HIV-1 Nef remodels the cell surface of infected cells. Remarkably, the effects of HIV-1 Vpu on host cell receptor exposure largely matched those of HIV-1 Nef in breadth and specificity (32 of 105, all also targeted by Nef), even though the magnitude was generally less pronounced. Of particular note, cell surface exposure of all members of the tetraspanin (TSPAN) protein family analyzed was reduced by both Nef and Vpu, and the viral proteins triggered the enrichment of TSPANs in a perinuclear area of the cell. While Vpu displayed significant colocalization and physical association with TSPANs, interactions of Nef with TSPANs were less robust. TSPANs thus emerge as a major target of deregulation in host cell vesicular transport by HIV-1 Nef and Vpu. The conservation of this activity in two independent accessory proteins suggests its importance for the spread of HIV-1 in the infected host.

IMPORTANCE
In this paper, we define that HIV-1 Nef and Vpu display a surprising functional overlap and affect the cell surface exposure of a previously unexpected breadth of cellular receptors. Our analyses furthermore identify the tetraspanin protein family as a previously unrecognized target of Nef and Vpu activity. These findings have implications for the interpretation of effects detected for these accessory gene products on individual host cell receptors and illustrate the coevolution of Nef and Vpu function.
Genome Analysis of the First Marseilleviridae Representative from Australia Indicates that Most of Its Genes Contribute to Virus Fitness
Authors: Doutre Gabriel , Philippe Nadège , Abergel Chantal , Claverie Jean-Michel 
Published: October 2014

ABSTRACT

The family
Marseilleviridae
consists of
Acanthamoeba
-infecting large DNA viruses with icosahedral particles ∼0.2 μm in diameter and genome sizes in the 346- to 380-kb range. Since the isolation of
Marseillevirus
from a cooling tower in Paris (France) in 2009, the family
Marseilleviridae
has expanded rapidly, with representatives from Europe and Africa. Five members have been fully sequenced that are distributed among 3 emerging
Marseilleviridae
lineages. One comprises
Marseillevirus
and
Cannes 8 virus
, another one includes
Insectomime virus
and
Tunisvirus
, and the third one corresponds to the more distant
Lausannevirus
. We now report the genomic characterization of
Melbournevirus
, the first representative of the
Marseilleviridae
isolated from a freshwater pond in Melbourne, Australia. Despite the large distance separating this sampling point from France,
Melbournevirus
is remarkably similar to
Cannes 8 virus
and
Marseillevirus
, with most orthologous genes exhibiting more than 98% identical nucleotide sequences. We took advantage of this optimal evolutionary distance to evaluate the selection pressure, expressed as the ratio of nonsynonymous to synonymous mutations for various categories of genes. This ratio was found to be less than 1 for all of them, including those shared solely by the closest
Melbournevirus
and
Cannes 8 virus
isolates and absent from
Lausannevirus
. This suggests that most of the 403 protein-coding genes composing the large
Melbournevirus
genome are under negative/purifying selection and must thus significantly contribute to virus fitness. This conclusion contrasts with the more common view that many of the genes of the usually more diverse large DNA viruses might be (almost) dispensable.

IMPORTANCE
A pervasive view is that viruses are fast-evolving parasites and carry the smallest possible amount of genomic information required to highjack the host cell machinery and perform their replication. This notion, probably inherited from the study of RNA viruses, is being gradually undermined by the discovery of DNA viruses with increasingly large gene content. These viruses also encode a variety of DNA repair functions, presumably slowing down their evolution by preserving their genomes from random alterations. On the other hand, these viruses also encode a majority of proteins without cellular homologs, including many shared only between the closest members of the same family. One may thus question the actual contribution of these anonymous and/or quasi-orphan genes to virus fitness. Genomic comparisons of
Marseilleviridae
, including a new
Marseillevirus
isolated in Australia, demonstrate that most of their genes, irrespective of their functions and conservation across families, are evolving under negative selection.
Individual differences in cognitive ability at age 20 predict pulmonary function 35 years later
Authors: Vasilopoulos Terrie , Kremen William S , Grant Michael D , Panizzon Matthew S , Xian Hong , Toomey Rosemary , Lyons Michael J , Jacobson Kristen C , Franz Carol E 
Published: October 2014

BackgroundPoor pulmonary function is associated with mortality and age-related diseases, and can affect cognitive performance. However, extant longitudinal studies indicate that early cognitive ability also affects later pulmonary function. Despite the multifaceted nature of pulmonary function, most longitudinal studies were limited to a single index of pulmonary function: forced expiratory volume in 1 s (FEV1). In this study, we examined whether early adult cognitive ability predicted five different indices of pulmonary function in mid-life.MethodsMixed modelling tested the association between young adult general cognitive ability (mean age=20), measured by the Armed Forces Qualification Test (AFQT), and mid-life pulmonary function (mean age=55), in 1019 men from the Vietnam Era Twin Study of Aging. Pulmonary function was indexed by per cent predicted values for forced vital capacity (FVC%p), FEV1%p, maximum forced expiratory flow (FEFmax%p), and maximal voluntary ventilation (MVV%p), and by the ratio of FEV1 to FVC (FEV1/FVC), an index of lung obstruction.ResultsAfter adjusting for smoking, pulmonary disease, occupation, income and education, age 20 AFQT was significantly (p<0.05) associated with mid-life FVC%p (β=0.10), FEV1%p (β=0.13), FEFmax%p (β=0.13), and MVV%p (β=0.13), but was not significantly associated with FEV1/FVC (β=0.03, p=0.34).ConclusionsEarly adult cognitive ability is a predictor of multiple indices of aging-related pulmonary function 35 years later, including lung volume, airflow and ventilator capacity. Cognitive deficits associated with impaired aging-related lung function may, thus, be partly pre-existing. However, results also highlight that early life risk factors may be differentially related to different metrics of later-life pulmonary health.
Tumor-Derived Osteopontin Suppresses Antitumor Immunity by Promoting Extramedullary Myelopoiesis
Authors: Kim Eun-Kyung , Jeon Insu , Seo Hyungseok , Park Young-Jun , Song Boyeong , Lee Kyoo-A , Jang Yongwoo , Chung Yeonseok , Kang Chang-Yuil 
Published: October 2014

Abstract
Extramedullary myelopoiesis occurs commonly in tumor-bearing animals and is known to lead to accumulation of peripheral myeloid-derived suppressor cells (MDSC), which play an important role in immune escape. However, the cellular and molecular mechanisms by which tumors induce extramedullary myelopoiesis are poorly understood. In this study, we found that osteopontin expressed by tumor cells enhances extramedullary myelopoiesis in a CD44-dependent manner through the Erk1/2–MAPK pathway. Osteopontin-mediated extramedullary myelopoiesis was directly associated with increased MDSCs in tumor-bearing hosts. More importantly, osteopontin silencing in tumor cells delayed both tumor growth and extramedullary myelopoiesis, while the same treatment did not affect tumor growth in vitro. Finally, treatment with an antibody against osteopontin inhibited tumor growth and synergized with cell-based immunotherapeutic vaccines in mediating antitumor immunity. Our findings unveil a novel immunosuppressive role for tumor-derived osteopontin and offer a rationale for its therapeutic targeting in cancer treatment. Cancer Res; 74(22); 6705–16. ©2014 AACR.
Evaluation of Human Papillomavirus Type Replacement Postvaccination Must Account for Diagnostic Artifacts: Masking of HPV52 by HPV16 in Anogenital Specimens
Authors: Tota Joseph E. , Ramanakumar Agnihotram V. , Villa Luisa L. , Richardson Harriet , Burchell Ann N. , Koushik Anita , Mayrand Marie-Hélène , Coutlée François , Franco Eduardo L. 
Published: October 2014

Abstract
It has been hypothesized that, following a reduction in human papillomavirus (HPV) vaccine–targeted genotypes, an increase in prevalence of other HPV types may occur due to reduced competition during natural infection. Any apparent postvaccination increase must be distinguished from diagnostic artifacts consequent to consensus PCR assays failing to detect HPV types present in low copy numbers in coinfected specimens (under the assumption that with a drop in vaccine-preventable types there may be increased detection of previously “masked” types). We reanalyzed anogenital specimens to evaluate unmasking of HPV52 that may be caused by elimination of HPV16. Using highly sensitive type-specific real-time HPV52 PCR, we retested 1,200 anogenital specimens (all HPV52 negative according to consensus PCR assays) from six epidemiologic studies (200 specimens/study; 100 HPV16+/study). Multivariate logistic regression, with adjustment for age and number of sexual partners, was used to evaluate the association between HPV16 positivity and detection of HPV52. In our pooled analysis (n = 1,196), the presence of HPV16 was positively associated with HPV52 detection [adjusted OR, 1.47; 95% confidence interval (CI), 0.76–2.82]. In our separate (study specific) analyses, a statistically significant association was observed in one study that included HIV-infected males (HIPVIRG study; adjusted OR, 3.82; 95% CI, 1.19–12.26). We observed a positive association between HPV16 viral load (tertiles) and detection of HPV52 (P for trend = 0.003). These results indicate that diagnostic artifacts, resulting from unmasking of HPV52, may occur in some settings in the evaluation of HPV type replacement. Additional studies exploring the extent and severity of unmasking are needed. Cancer Epidemiol Biomarkers Prev; 24(1); 286–90. ©2014 AACR.