bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic point‐of‐care diagnosis of Mycoplasma pneumoniae infection using LAMP assay
Authors: Kakuya Fujio , Kinebuchi Takahiro , Fujiyasu Hiroaki , Tanaka Ryosuke , Kano Hiroki 
Published: March 2014

AbstractBackgroundMycoplasma pneumoniae (MP) is a major pathogen of lower respiratory tract infection (LRTI) in children. A rapid diagnostic method during the acute phase is required for the prescription of effective antibiotics.MethodsA prospective, single‐centered study was conducted on community‐acquired LRTI in children. We regarded the day of fever onset as the first day of illness. In part 1, we studied 191 patients with signs of LRTI. We compared diagnostic reliability using loop‐mediated isothermal amplification (LAMP) assay and serological testing at the first visit. In part 2, we evaluated the clinical characteristics of 117 patients with positive LAMP assay.ResultsIn part 1, 31 patients met the definite MP infection criteria. LAMP assay had a sensitivity of 96.8% and specificity of 100%, whereas enzyme immunoassay had a sensitivity of 38.7% and specificity of 76.9%, and particle agglutination test had a sensitivity of 19.4% and specificity of 93.1%. In part 2, of 106 patients with fever, 100 patients were diagnosed by the day 7 of illness. The diagnosis was made a mean of 3.5 ± 2.1 days after the onset of fever.ConclusionsLAMP assay had excellent sensitivity and specificity for the detection of acute MP infection at the first visit. This assay can diagnose MP infection during the very acute phase. LAMP assay is appropriate for genetic point‐of‐care diagnosis of MP infection in hospital laboratories.
Maternal Concern about Child Weight in a Study of Weight‐Discordant Siblings
Authors: Kral Tanja V. E. , Moore Reneé H. , Compher Charlene W. 
Published: March 2014

AbstractObjectiveThis study examined concern about child weight in mothers of weight‐discordant siblings and determined the accuracy of maternal self‐report versus measured child height, weight, and corresponding body mass index (BMI; kg/m2) z‐score.Design and SampleDiscordant sibling design. Forty‐seven mothers of 5‐ to 12‐year‐old, weight‐discordant siblings.MeasuresMothers self‐reported their concern about child weight for each child separately and for a subset of children, self‐reported their heights and weights. Siblings' height, weight, waist circumference, and adiposity were measured.ResultsThe majority (83%) of mothers expressed concern about their overweight/obese child's weight and 20% of mothers expressed concern about their normal‐weight child's weight (p < .001). Difference scores in maternal concern about child weight were positively associated with difference scores in sibling BMI z‐score (r = 0.42; p = .01) and percent body fat (r = 0.56; p < .001). For overweight/obese children only, maternal‐reported child heights and weights were significantly lower compared to the measured values (p < .03).ConclusionsOne fifth of mothers of weight‐discordant siblings were unconcerned about their overweight/obese child's weight and for overweight/obese children only, mothers tended to underreport children's height and weight. Mothers' concern for their overweight/obese child's weight was greater for sibling pairs who were more discordant in their weight.
B‐cell epitopes of antigenic proteins in Leishmania infantum: an in silico analysis
Authors: Assis L. M. , Sousa J. R. , Pinto N. F. S. , Silva A. A. , Vaz A. F. M. , Andrade P. P. , Carvalho E. M. , De Melo M. A. 
Published: March 2014

SummarySerodiagnosis of visceral leishmaniasis is often hindered by cross‐reactions to other parasitic diseases. Identifying specific B‐cell epitopes in proteins is therefore important for immunodiagnostics, as well as for disease control by vaccines. This study aimed to identify linear and conformational B‐cell epitopes and to evaluate the secondary structure of antigen proteins in Leishmania infantum using in silico analysis. Linear epitopes were predicted using the Immune Epitope Database and Analysis Resource (IEDB), BepiPred and BcePred programs. The conformational B‐cell epitopes were identified using the CBTOPE server. The combination of the predictions using IEDB, BepiPred and BcePred generated 148 linear epitopes from the calpain‐like cysteine peptidase (CP), thiol‐dependent reductase 1 (TDR1) and HSP70 proteins. In total, 164 conformational epitopes were predicted, mostly located in the linear epitope region. The predicted epitopes are located in α helix and random coil regions in the thiol‐dependent reductase 1 and HSP70 proteins. New linear and conformational B‐cell epitopes of L. infantum proteins were identified in silico, and the prediction using various programs ensures greater accuracy of the results, as suggested by confirmation of previously identified HSP70 epitopes.
Bayesian Hierarchical Structured Variable Selection Methods with Application to Molecular Inversion Probe Studies in Breast Cancer
Authors: Zhang Lin , Baladandayuthapani Veerabhadran , Mallick Bani K. , Manyam Ganiraju C. , Thompson Patricia A. , Bondy Melissa L. , Do Kim-Anh 
Published: March 2014

SummaryThe analysis of genomics alterations that may occur in nature when segments of chromosomes are copied (known as copy number alterations) has been a focus of research to identify genetic markers of cancer. One high throughput technique that has recently been adopted is the use of molecular inversion probes to measure probe copy number changes. The resulting data consist of high dimensional copy number profiles that can be used to ascertain probe-specific copy number alterations in correlative studies with patient outcomes to guide risk stratification and future treatment. We propose a novel Bayesian variable selection method, the hierarchical structured variable selection method, which accounts for the natural gene and probe-within-gene architecture to identify important genes and probes associated with clinically relevant outcomes. We propose the hierarchical structured variable selection model for grouped variable selection, where simultaneous selection of both groups and within-group variables is of interest. The hierarchical structured variable selection model utilizes a discrete mixture prior distribution for group selection and group-specific Bayesian lasso hierarchies for variable selection within groups. We provide methods for accounting for serial correlations within groups that incorporate Bayesian fused lasso methods for within-group selection. Through simulations we establish that our method results in lower model errors than other methods when a natural grouping structure exists. We apply our method to a molecular inversion probe study of breast cancer and show that it identifies genes and probes that are significantly associated with clinically relevant subtypes of breast cancer.
Inferences on Lung Cancer Mortality Rates Based on Reference Priors Under Partial Ordering
Authors: Sonksen Michael D. , Peruggia Mario 
Published: March 2014

SummaryWe present a novel analysis of a landmark table of dose–response mortality counts from lung cancer in men. The data were originally collected by Doll and Hill. Our inferences are based on Poisson models for which the rates of occurrence are partially ordered according to two covariates. The partial ordering of the mortality rates enforces the well-established knowledge that lung cancer mortality rates are higher for older men and for heavier smokers. The ordered group reference priors that we use in our analyses generalize a class of reference priors that we previously derived for models of count data in which the rates of occurrence in different categories are completely ordered with respect to the values of a single covariate. The reference models for the lung cancer data based on the proposed priors are more flexible than and can be superior, in terms of goodness of fit, to a Bayesian version of several parametric models derived from a mathematical theory of carcinogenesis that have appeared in the literature.
A Dynamic Probabilistic Principal Components Model for the Analysis of Longitudinal Metabolomics Data
Authors: Nyamundanda Gift , Gormley Isobel Claire , Brennan Lorraine 
Published: March 2014

SummaryIn a longitudinal metabolomics study, multiple metabolites are measured from several observations at many time points. Interest lies in reducing the dimensionality of such data and in highlighting influential metabolites which change over time. A dynamic probabilistic principal components analysis model is proposed to achieve dimension reduction while appropriately modelling the correlation due to repeated measurements. This is achieved by assuming an auto-regressive model for some of the model parameters. Linear mixed models are subsequently used to identify influential metabolites which change over time. The model proposed is used to analyse data from a longitudinal metabolomics animal study.
Phylogeny of Rhigonematomorpha based on the complete mitochondrial genome of Rhigonema thysanophora (Nematoda: Chromadorea)
Authors: Kim Taeho , Kim Jiyeon , Cho Soowon , Min Gi‐Sik , Park Chungoo , Carreno Ramon A. , Nadler Steven A. , Park Joong‐Ki 
Published: March 2014

We determined the complete mitochondrial genome sequence of Rhigonema thysanophora, the first representative of Rhigonematomorpha, and used this sequence along with 57 other nematode species for phylogenetic analyses. The R. thysanophora mtDNA is 15 015 bp and identical to all other chromadorean nematode mtDNAs published to date in that it contains 36 genes (lacking atp8) encoded in the same direction. Phylogenetic analyses of nucleotide and amino acid sequence data for the 12 protein‐coding genes recovered Rhigonematomorpha as the sister group to the heterakoid species, Ascaridia columbae (Ascaridomorpha). The organization of R. thysanophora mtDNA resembles the most common pattern for the Rhabditomorpha+Ascaridomorpha+Diplogasteromorpha clade in gene order, but with some substantial gene rearrangements. This similarity in gene order is in agreement with the sequence‐based analyses that indicate a close relationship between Rhigonematomorpha and Rhabditomorpha+Ascaridomorpha+Diplogasteromorpha. These results are consistent with certain analyses of nuclear SSU rDNA for R. thysanophora and some earlier classification systems that asserted phylogenetic affinity between Rhigonematomorpha and Ascaridomorpha, but inconsistent with morphology‐based phylogenetic hypotheses that suggested a close (taxonomic) relationship between rhigonematomorphs and oxyuridomorphs (pinworms). These observations must be tempered by noting that few rhigonematomorph species have been sequenced and included in phylogenetic analyses, and preliminary studies based on SSU rDNA suggest the group is not monophyletic. Additional mitochondrial genome sequences of rhigonematids are needed to characterize their phylogenetic relationships within Chromadorea, and to increase understanding of mitochondrial genome evolution.
Finiteness properties of cubulated groups
Authors: Hruska G. C. , Wise Daniel T. 
Published: March 2014

AbstractWe give a generalized and self-contained account of Haglund–Paulin’s wallspaces and Sageev’s construction of the CAT(0) cube complex dual to a wallspace. We examine criteria on a wallspace leading to finiteness properties of its dual cube complex. Our discussion is aimed at readers wishing to apply these methods to produce actions of groups on cube complexes and understand their nature. We develop the wallspace ideas in a level of generality that facilitates their application. Our main result describes the structure of dual cube complexes arising from relatively hyperbolic groups. Let $H_1,\ldots, H_s$ be relatively quasiconvex codimension-1 subgroups of a group $G$ that is hyperbolic relative to $P_1, \ldots, P_r$. We prove that $G$ acts relatively cocompactly on the associated dual CAT(0) cube complex $C$. This generalizes Sageev’s result that $C$ is cocompact when $G$ is hyperbolic. When $P_1,\ldots, P_r$ are abelian, we show that the dual CAT(0) cube complex $C$ has a $G$-cocompact CAT(0) truncation.
On the algebraic independence of generic Painlevé transcendents
Authors: Nagloo Joel , Pillay Anand 
Published: March 2014

AbstractWe prove that if$y''=f(y,y',t,\alpha ,\beta ,\ldots)$is a generic Painlevé equation from among the classes II, IV and V, and if$y_1,\ldots,y_n$are distinct solutions, then$\mathrm{tr.deg}(\mathbb{C}(t)(y_1,y'_1,\ldots,y_n,y'_n)/\mathbb{C}(t))=2n$. (This was proved by Nishioka for the single equation$P_{{\rm I}}$.) For generic Painlevé III and VI, we have a slightly weaker result:$\omega $-categoricity (in the sense of model theory) of the solution space, as described below. The results confirm old beliefs about the Painlevé transcendents.
Abstract simplicity of locally compact Kac–Moody groups
Authors: Marquis Timothée 
Published: March 2014

AbstractIn this paper, we establish that complete Kac–Moody groups over finite fields are abstractly simple. The proof makes essential use of Mathieu and Rousseau’s construction of complete Kac–Moody groups over fields. This construction has the advantage that both real and imaginary root spaces of the Lie algebra lift to root subgroups over arbitrary fields. A key point in our proof is the fact, of independent interest, that both real and imaginary root subgroups are contracted by conjugation of positive powers of suitable Weyl group elements.
IN SEARCH OF ENTREPRENEURIAL OPPORTUNITIES — AN INTEGRATED MODEL
Authors: RIQUELME HERNAN E. 
Published: March 2014

The aim of this research study is to test an integrative model of entrepreneurial opportunity recognition based on theories of cognition, social capital, environmental development and personality.240 entrepreneurs in the services industry participated in this survey. Multiple regression analysis was used to test the model and find the factors that predict entrepreneurial opportunity recognition. Overall, eight hypotheses were tested and six were supported. Schema was found to be the strongest significant variable amongst all.The study results indicate that entrepreneurs who discover opportunities organize prior knowledge and information related to their field in a manner that is easily accessible, have confidence in themselves, use social networks (both weak and strong ties) and see opportunities in changes in the economic environment.The study implies that potential entrepreneurs should be supported in terms of their social networks and instructed in the beliefs about the information and changes in the environment needed to spot opportunities. Governments play a role in providing a munificent economic environment.
Comparison of Laboratory Data of Acute Cholangitis Patients Treated with or without Immunosuppressive Drugs
Authors: Tomizawa Minoru , Shinozaki Fuminobu , Hasegawa Rumiko , Shirai Yoshinori , Ichiki Noboru , Motoyoshi Yasufumi , Sugiyama Takao , Yamamoto Shigenori , Sueishi Makoto 
Published: March 2014

Objective. Symptoms and laboratory data between acute cholangitis (AC) patients treated with and AC patients treated without immunosuppressive drugs (corticosteroids or methotrexate) were compared to identify factors that can be meaningful to the diagnosis of AC. Methods. The Wilcoxon signed-rank test was used for comparison of baseline variables between the patients with AC treated with immunosuppressive drugs and those without it. The chi-squared test was used in the analysis of the symptoms. Results. In total, 69 patients with AC were enrolled. Fifteen patients were treated with immunosuppressants due to rheumatoid arthritis or other collagen diseases. Jaundice was less frequent in the patients treated with immunosuppressive drugs (P = 0.0351). T-Bil level was marginally lower in the patients treated with immunosuppressants (P = 0.086). AST and ALT levels were lower in the patients treated with immunosuppressants (P = 0.0417 and 0.022, respectively). Conclusions. The frequency of jaundice and AST and ALT levels were lower in the patients treated with immunosuppressive drugs. It is recommended that care be taken to evaluate jaundice, AST level, and ALT level in the diagnosis of AC.
Sensitivities of the Lower-Stratospheric Transport and Mixing to Tropical SST Heating
Authors: Yang Huang , Chen Gang , Domeisen Daniela I. V. 
Published: March 2014

Abstract
The sensitivities of the Brewer–Dobson circulation (BDC) to different distributions of tropical SST heating are investigated in an idealized aquaplanet model. It is found that an increase in tropical SSTs generally leads to an acceleration of tropical upwelling and an associated reduction in the age of air (AOA) in the polar stratosphere and that the AOA near the subtropical tropopause is correlated with local isentropic mixing of tropospheric air with stratospheric air.
The zonal distribution of SST perturbations has a major impact on the vertical and meridional structure of the BDC as compared with other SST characteristics. Zonally localized SST heatings tend to generate a shallow acceleration of the stratospheric residual circulation, enhanced isentropic mixing associated with a weakened stratospheric jet, and a reduction in AOA mostly within the polar vortex. In contrast, SST heatings with a zonally symmetric structure tend to produce a deep strengthening of the stratospheric residual circulation, suppressed isentropic mixing associated with a stronger stratospheric jet, and a decrease of AOA in the entire stratosphere. The shallow versus deep strengthening of the stratospheric residual circulation change has been linked to wave propagation and dissipation in the subtropical lower stratosphere rather than wave generation in the troposphere, and the former can be strongly affected by the vertical position of the subtropical jet. These results suggest that, while the longitudinally localized SST trends under climate change may contribute to the change in the shallow branch of the BDC, the upward shift of the subtropical jet associated with the zonal SST heating can impact the deep branch of the BDC.
An Abrupt Decrease in the Late-Season Typhoon Activity over the Western North Pacific*
Authors: Hsu Pang-Chi , Chu Pao-Shin , Murakami Hiroyuki , Zhao Xin 
Published: March 2014

Abstract
In 1995 an abrupt shift in the late-season (October–December) typhoon activity over the western North Pacific (WNP) is detected by a Bayesian changepoint analysis. Interestingly, a similar change also occurs in the late-season sea surface temperature series over the western Pacific, eastern North Pacific, and portions of the Indian Ocean. All of the counts, lifespans, and accumulated cyclone energy of the late-season typhoons during the 1995–2011 epoch decreased significantly, compared with typhoons that occurred during the 1979–94 epoch. The negative vorticity anomaly is found to be the leading contributor to the genesis potential index (GPI) decrease over the southeastern sector of the WNP during 1995–2011. To elucidate the origin of the epochal change in the dynamic environmental conditions, a suite of sensitivity experiments is conducted based on the latest version of the Japan Meteorological Research Institute atmospheric general circulation model (MRI AGCM). The ensemble simulations suggest that the recent change to a La Niña–like state induces an unfavorable dynamic condition for typhoon genesis over the southeastern WNP. Warming in the Indian Ocean, however, contributes insignificantly to the circulation anomaly related to typhoon genesis over the southeastern WNP. The frequency of typhoon occurrence reveals a basinwide decrease over the WNP in the recent epoch, except for a small increase near Taiwan. An empirical statistical analysis shows that the basinwide decrease in the frequency of the typhoon occurrence is primarily attributed to a decrease in typhoon genesis, while the change in track is of less importance.
Impact of endobronchial allergen provocation on macrophage phenotype in asthmatics
Authors: Winkler Carla , Witte Lena , Moraw Natali , Faulenbach Conny , Müller Meike , Holz Olaf , Schaumann Frank , Hohlfeld Jens M 
Published: March 2014

AbstractBackgroundThe role of M2 polarized macrophages (MΦ) during the allergic airway inflammation has been discussed in various animal models. However, their presence and relevance during the chronic and acute phase of allergic airway inflammation in humans has not been fully elucidated so far. In the present study we phenotypically characterized macrophages with regard to M2 polarization in mice, a humanin vitroand a humanex vivomodel with primary lung cells after endobronchial provocation.ResultsMacrophages remained polarized beyond clearance of the acute allergic airway inflammation in mice. Alveolar macrophages of asthmatics revealed increased mRNA expression of CCL13, CCL17 and CLEC10A in response to allergen challenge as well as increased surface expression of CD86. Further, mRNA expression of CCL13, CCL17, and CLEC10A was increased in asthmatics at baseline compared to healthy subjects. The mRNA expression of CCL17 and CLEC10A correlated significantly with the degree of eosinophilia (each P < .01). Furthermore, macrophages from asthmatics released significant amounts of CCL17 proteinin vitrowhich was also found increased in BAL fluid after allergen provocation.ConclusionsThis study supports previous findings of M2 macrophage polarization in asthmatic subjects during the acute course of the allergic inflammation and provides evidence for their contribution to the Th2 inflammation.
Long-term exposure to muscarinic agonists decreases expression of contractile proteins and responsiveness of rabbit tracheal smooth muscle cells
Authors: Stamatiou Rodopi , Paraskeva Efrosini , Vasilaki Anna , Mylonis Ilias , Molyvdas Paschalis Adam , Gourgoulianis Konstantinos , Hatziefthimiou Apostolia 
Published: March 2014

Abstract

Background
Chronic airway diseases, like asthma or COPD, are characterized by excessive acetylcholine release and airway remodeling. The aim of this study was to investigate the long-term effect of muscarinic agonists on the phenotype and proliferation of rabbit tracheal airway smooth muscle cells (ASMCs).

Methods
ASMCs were serum starved before treatment with muscarinic agonists. Cell phenotype was studied by optical microscopy and indirect immunofluorescence, using smooth muscle α-actin, desmin and SM-Myosin Heavy Chain (SM-MHC) antibodies. [N-methyl-3H]scopolamine binding studies were performed in order to assess M3 muscarinic receptor expression on isolated cell membranes. Contractility studies were performed on isolated ASMCs treated with muscarinic agonists. Proliferation was estimated using methyl-[3H]thymidine incorporation, MTT or cell counting methods. Involvement of PI3K and MAPK signalling pathways was studied by cell incubation with the pathway inhibitors LY294002 and PD98059 respectively.

Results
Prolonged culture of ASMCs with acetylcholine, carbachol or FBS, reduced the expression of α-actin, desmin and SM-MHC compared to cells cultured in serum free medium. Treatment of ASMCs with muscarinic agonists for 3-15 days decreased muscarinic receptor expression and their responsiveness to muscarinic stimulation. Acetylcholine and carbachol induced DNA synthesis and increased cell number, of ASMCs that had acquired a contractile phenotype by 7 day serum starvation. This effect was mediated via a PI3K and MAPK dependent mechanism.

Conclusions
Prolonged exposure of rabbit ASMCs to muscarinic agonists decreases the expression of smooth muscle specific marker proteins, down-regulates muscarinic receptors and decreases ASMC contractile responsiveness. Muscarinic agonists are mitogenic, via the PI3K and MAPK signalling pathways.