bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian Modelling of Dupuytren Disease by Using Gaussian Copula Graphical Models
Authors: Mohammadi Abdolreza , Abegaz Fentaw , Heuvel Edwin , Wit Ernst C. 
Published: September 2016

SummaryDupuytren disease is a fibroproliferative disorder with unknown aetiology that often progresses and eventually can cause permanent contractures of the fingers affected. We provide a computationally efficient Bayesian framework to discover potential risk factors and investigate which fingers are jointly affected. Our Bayesian approach is based on Gaussian copula graphical models, which provide a way to discover the underlying conditional independence structure of variables in multivariate data of mixed types. In particular, we combine the semiparametric Gaussian copula with extended rank likelihood to analyse multivariate data of mixed types with arbitrary marginal distributions. For structural learning, we construct a computationally efficient search algorithm by using a transdimensional Markov chain Monte Carlo algorithm based on a birth–death process. In addition, to make our statistical method easily accessible to other researchers, we have implemented our method in C++ and provide an interface with R software as an R package BDgraph, which is freely available from http://CRAN.R-project.org/package=BDgraph.
A Semi‐parametric Transformation Frailty Model for Semi‐competing Risks Survival Data
Authors: Jiang Fei , Haneuse Sebastien 
Published: August 2016

AbstractIn the analysis of semi‐competing risks data interest lies in estimation and inference with respect to a so‐called non‐terminal event, the observation of which is subject to a terminal event. Multi‐state models are commonly used to analyse such data, with covariate effects on the transition/intensity functions typically specified via the Cox model and dependence between the non‐terminal and terminal events specified, in part, by a unit‐specific shared frailty term. To ensure identifiability, the frailties are typically assumed to arise from a parametric distribution, specifically a Gamma distribution with mean 1.0 and variance, say, σ2. When the frailty distribution is misspecified, however, the resulting estimator is not guaranteed to be consistent, with the extent of asymptotic bias depending on the discrepancy between the assumed and true frailty distributions. In this paper, we propose a novel class of transformation models for semi‐competing risks analysis that permit the non‐parametric specification of the frailty distribution. To ensure identifiability, the class restricts to parametric specifications of the transformation and the error distribution; the latter are flexible, however, and cover a broad range of possible specifications. We also derive the semi‐parametric efficient score under the complete data setting and propose a non‐parametric score imputation method to handle right censoring; consistency and asymptotic normality of the resulting estimators is derived and small‐sample operating characteristics evaluated via simulation. Although the proposed semi‐parametric transformation model and non‐parametric score imputation method are motivated by the analysis of semi‐competing risks data, they are broadly applicable to any analysis of multivariate time‐to‐event outcomes in which a unit‐specific shared frailty is used to account for correlation. Finally, the proposed model and estimation procedures are applied to a study of hospital readmission among patients diagnosed with pancreatic cancer.
Assessing the impact of defining a global priority research agenda to address HIV‐associated tuberculosis
Authors: Odone Anna , Matteelli Alberto , Chiesa Valentina , Cella Paola , Ferrari Antonio , Pezzetti Federica , Signorelli Carlo , Getahun Haileyesus 
Published: September 2016

AbstractObjectivesIn 2010, the WHO issued 77 priority research questions (PRQs) to address HIV‐associated TB. Objective of the this study was to assess the impact of defining the research agenda in stimulating and directing research around priority research questions.MethodsWe used number and type of scientific publications as a proxy to quantitatively assess the impact of research agenda setting. We conducted 77 single systematic reviews – one for every PRQ – building 77 different search strategies using PRQs’ keywords. Multivariate logistic regression models were applied to assess the quantity and quality of research produced over time and accounting for selected covariates.ResultsIn 2009–2015, PRQs were addressed by 1631 publications (median: 11 studies published per PRQ, range 1–96). The most published area was ‘Intensified TB case finding’ (median: 23 studies/PRQ, range: 2–74). The majority (62.1%, n = 1013) were published as original studies, and more than half (58%, n = 585) were conducted in the African region. Original studies’ publication increased over the study period (P trend = <0.001). They focused more on the ‘Intensified TB case finding’ (OR = 2.17, 95% CI: 1.56–2.93) and ‘Drug‐resistant TB and HIV infection’ (OR = 2.12, 95% CI: 1.47–3.06) areas than non‐original studies. Original studies were published in journals of lower impact factor and received a smaller number of citations than non‐original studies (OR = 0.54, 95% CI: 0.42‐0.69).ConclusionThe generation of evidence to address PRQs has increased over time particularly in selected fields. Setting a priority research agenda for HIV‐associated TB might have positively influenced the direction and the conduct of research and contributed to the global response to such a major threat to health.
Analysis of exome sequencing data sets reveals structural variation in the coding region of ABO in individuals of African ancestry
Authors: Fox Keolu , Johnsen Jill M. , Coe Bradley P. , Frazar Chris D. , Reiner Alexander P. ,   NHLBI Exome Sequencing Project, Minority Health‐GRID Network, Eichler Evan E. , Nickerson Deborah A. 
Published: September 2016

BACKGROUNDABO is a blood group system of high clinical significance due to the prevalence of ABO variation that can cause major, potentially life‐threatening, transfusion reactions.STUDY DESIGN AND METHODSUsing multiple large‐scale next‐generation sequence data sets, we demonstrate the application of read‐depth approaches to discover previously unsuspected structural variation (SV) in the ABO gene in individuals of African ancestry.RESULTSOur analysis of SV in the ABO gene across 6432 exomes reveals a partial deletion in the ABO gene in 32 individuals of African ancestry that predicts a novel O allele.CONCLUSIONOur study demonstrates the power that analyses of large‐scale sequencing data, particularly data sets containing underrepresented populations, can provide in identifying novel SVs.
Outcome Following Partial Unilateral Hysterectomy by Standing Flank Approach in Dairy Cattle
Authors: Marchionatti Emma , Nichols Sylvain , Babkine Marie , Lardé Hélène , Lefebvre Réjean , Desrochers André 
Published: September 2016

ABSTRACTObjectiveTo describe the clinical findings, surgical treatment, and long‐term outcome of dairy cattle undergoing partial hysterectomy with or without unilateral ovariectomy.Study DesignRetrospective case series.AnimalsDairy cattle (n = 7).MethodsMedical records (June 2007–June 2014) of dairy cattle that had partial hysterectomy with or without ipsilateral ovariectomy were reviewed. Follow‐up data were obtained by telephone interviews with owners and referring veterinarians between 6 months and 7 years following discharge.ResultsSeven dairy cattle met the inclusion criteria. Diagnoses made intra‐ or postoperatively were ovarian abscess with multiorgan adhesions (4 cows), segmental aplasia of the uterus (2 cows), and uterine lymphosarcoma (1 cow). Partial hysterectomy with or without unilateral ovariectomy was performed without surgical complications by standing flank approach. All cows were successfully discharged from the hospital (short‐term prognosis). Five cows became pregnant, and 4 delivered live calves and had a satisfactory productive life without long‐term complications.ConclusionPartial hysterectomy by standing flank approach should be considered as a viable treatment option for unilateral ovarian or uterine problems in dairy cattle. Cattle undergoing partial hysterectomy with or without ipsilateral ovariectomy are capable of satisfactory reproduction and milk production after surgery with no short‐ or long‐term complications.
Multi‐Center Retrospective Evaluation of Screw and Polymethylmethacrylate Constructs for Atlantoaxial Fixation in Dogs
Authors: Stout Steele Megan W. , Hodshon Amy W. , Hopkins Andrew L. , Tracy Gaemia M. , Cohen Noah D. , Kerwin Sharon C. , Boudreau C. Elizabeth , Thomas William B. , Mankin Joseph M. , Levine Jonathan M. 
Published: September 2016

ObjectiveTo evaluate outcome and adverse events following ventral stabilization of the atlantoaxial (AA) joint in dogs with clinical AA subluxation using screw/polymethymethacrylate (PMMA) constructs in a retrospective, multi‐center cohort study.Study DesignHistorical cohort study.Animals35 client‐owned dogs.MethodsMedical records from 3 institutions were reviewed to identify dogs with AA subluxation treated with ventral screw and PMMA constructs. Data on signalment, pre‐ and postoperative neurologic status, imaging performed, and adverse events were retrieved. Neurologic examination data were abstracted to generate a modified Frankel score at admission, discharge, and re‐examination. Telephone interview of owners >180 days postoperative was conducted.ResultsThirty‐five dogs with AA subluxation treated with ventral screw/PMMA constructs were included. Most dogs were young (median age 1 year), small breed dogs with acute onset of neurologic signs (median duration 22.5 hours). Most dogs were non‐ambulatory at the time of admission (median modified Frankel score 3). Adverse events were identified in 15/35 dogs including 9 dogs with major adverse events. Four dogs required a second surgery due to vertebral canal violation (n = 2) or implant failure (n = 2). Re‐examination at 4–6 weeks postoperative reported 15/28 dogs with improved neurologic status and 19/28 dogs were ambulatory. Telephone follow‐up was available for 23/35 dogs with 23/23 reported as ambulatory (median follow‐up 390 days).ConclusionsVentral application of screw and PMMA constructs for AA subluxation, as described here, is associated with clinical improvement in the majority of dog. Major adverse events are infrequent and the technique is considered relatively safe.
COLONIALIDAD TERRITORIAL Y EVOLUCIÓN URBANA EN LA HABANA.
Authors: Farrés Delgado Yasser 
Published: September 2016

<p>La colonialidad refiere a un conjunto de patrones de poder de larga duración que emergieron con el colonialismo en las Américas pero que se mantienen vivos más allá de los estrictos límites de las administraciones coloniales. Estos patrones se han reflejado en la evolución urbano-arquitectónica de las ciudades poscoloniales del “Sur Global”, que<br />reproducen modelos arquitectónicos, urbanos y territoriales promovidos desde los países del “Norte Global”. Esto justifica hablar de la existencia de la “colonialidad territorial”, concepto que sirve para replantear la historia urbana. En ese sentido, el artículo mostrará cómo ha ocurrido esta en el caso de La Habana (Cuba) a lo largo de su historia</p>
Aspectos de sostenibilidad de productos no maderables del bosque con uso curativo en el oeste de Pará, Brasil
Authors: May Thomas 
Published: September 2016

<p>Se analiza la sostenibilidad de los doce productos no maderables de los bosques amazónicos usados con fines curativos y más vendidos en el mercado local del oeste del estado de Pará, Brasil, en base a observaciones de campo e informaciones bibliográficas, tomando como hilo conductor los factores que inciden, de origen externo versus origen interno, y de impactos en la disponibilidad del recurso versus impactos en los aspectos económicos y sociales. Se concluye que 1) de la destrucción y degradación de los bosques cabe esperar un impacto negativo, a mediano y largo plazo, si bien a corto plazo ayuda a aumentar la oferta de ciertos productos, 2) la venta en el el mercado nacional e internacional les pone ciertas dificultades a los productores extractivistas, que no existen en el mercado local, que además parece ser relativamente estable, 3) las informaciones sobre las características biológicas de las especies indican que ellas en la mayoría de los casos permiten una utilización sostenible de los recursos no maderables por vía extractivista, y 4) en especies con características favorables de reproducción, crecimiento y desarrollo hasta la madurez reproductiva, la plantación a escala local es una estrategia promisora para la reducción de la disponibilidad del recurso, aumentando la productividad de la mano de obra local. </p>
La antropología del estado desde Akhil Gupta: a propósito de Red Tape. Burocracia, violencia estructural y pobreza en India.
Authors: Arias Vanegas Julio 
Published: September 2016

La antropología del estado desde Akhil Gupta: a propósito de Red Tape. Burocracia, violencia estructural y pobreza en India.
Synergistic Neutralization of Pertussis Toxin by a Bispecific Antibody
In Vitro
and
In Vivo
Authors: Wagner Ellen K. , Wang Xianzhe , Bui Andre , Maynard Jennifer A. 
Published: September 2016

ABSTRACT

Bispecific antibodies are a rapidly growing class of therapeutic molecules, originally developed for the treatment of cancer but recently explored for the treatment of autoimmune and infectious diseases.
Bordetella pertussis
is a reemerging pathogen, and several of the key symptoms of infection are caused by the pertussis toxin (PTx). Two humanized antibodies, hu1B7 and hu11E6, bind distinct epitopes on PTx and, when coadministered, mitigate disease severity in murine and baboon models of infection. Here we describe the generation of a bispecific human IgG1 molecule combining the hu1B7 and hu11E6 binding sites via a knobs-in-holes design. The bispecific antibody showed binding activity equivalent to that of the antibody mixture in a competition enzyme-linked immunosorbent assay (ELISA). A CHO cell neutralization assay provided preliminary evidence for synergy between the two antibodies, while a murine model of PTx-induced leukocytosis definitively showed synergistic neutralization. Notably, the bispecific antibody retained the synergy observed for the antibody mixture, supporting the conclusion that synergy is due to simultaneous blockade of both the catalytic and receptor binding activities of pertussis toxin. These data suggest that a hu1B7/hu11E6 bispecific antibody is a viable alternative to an antibody mixture for pertussis treatment.
Culture of Urine Specimens by Use of chromID CPS Elite Medium Can Expedite Escherichia coli Identification and Reduce Hands-On Time in the Clinical Laboratory
Authors: Yarbrough Melanie L. , Wallace Meghan A. , Marshall Cynthia , Mathias Erin , Burnham Carey-Ann D. 
Published: September 2016

ABSTRACT

Urine is one of the most common specimen types submitted to the clinical microbiology laboratory; the use of chromogenic agar is one method by which the laboratory might expedite culture results and reduce hands-on time and materials required for urine culture analysis. The objective of our study was to compare chromID CPS Elite (bioMérieux), a chromogenic medium, to conventional primary culture medium for evaluation of urine specimens. Remnant urine specimens (
n
= 200) were inoculated into conventional media and into chromID CPS Elite agar (chromID). The time to identification and consumables used were documented for both methods. Clinically significant pathogen(s) were recovered from 51 cultures using conventional media, with
Escherichia coli
being the most frequently recovered organism (
n
= 22). The rate of exact uropathogen agreement between conventional and chromogenic media was 82%, while overall categorical agreement was 83.5% The time interval between plating and final organism identification was decreased with chromID agar versus conventional media for
E. coli
(mean of 24.4 h versus 27.1 h,
P
< 0.001). Using chromID, clinically significant cultures required less hands-on time per culture (mean of 1 min and 2 s [1:02 min]) compared to conventional media (mean of 1:31 min). In addition, fewer consumables (2.4 versus 3.3 sticks and swabs) and rapid biochemical tests (1.0 versus 1.9) were necessary using chromID versus conventional media. Notably, antimicrobial susceptibility testing demonstrated good overall agreement (97.4%) between the chromID and conventional media for all antibiotics tested. chromID CPS Elite is accurate for uropathogen identification, reduces consumable usage, and may expedite the identification of
E. coli
in clinical specimens.
Direct Comparison of Alere i and cobas Liat Influenza A and B Tests for Rapid Detection of Influenza Virus Infection
Authors: Nolte Frederick S. , Gauld Lori , Barrett Susan B. 
Published: September 2016

ABSTRACT
We compared two rapid, point-of care nucleic acid amplification tests for detection of influenza A and B viruses (Alere i [Alere] and cobas Liat [Roche Diagnostics]) with the influenza A and B virus test components of the FilmArray respiratory panel (BioFire Diagnostics) using 129 respiratory specimens collected in universal viral transport medium (80 influenza A virus and 16 influenza B virus positive) from both adult and pediatric patients. The sensitivities of the Alere test were 71.3% for influenza A virus and 93.3% for influenza B virus, with specificities of 100% for both viruses. The sensitivities and specificities of the Liat test were 100% for both influenza A and B viruses. The poor sensitivity of the Alere test for detection of influenza A virus was likely due to a study set that included many low-positive samples that were below its limit of detection.
Intracerebral Inoculation of Mouse-Passaged Saffold Virus Type 3 Affects Cerebellar Development in Neonatal Mice
Authors: Kotani Osamu , Suzuki Tadaki , Yokoyama Masaru , Iwata-Yoshikawa Naoko , Nakajima Noriko , Sato Hironori , Hasegawa Hideki , Taguchi Fumihiro , Shimizu Hiroyuki , Nagata Noriyo 
Published: September 2016

ABSTRACTSaffold virus (SAFV), a human cardiovirus, is occasionally detected in infants with neurological disorders, including meningitis and cerebellitis. We recently reported that SAFV type 3 isolates infect cerebellar glial cells, but not large neurons, in mice. However, the impact of this infection remained unclear. Here, we determined the neuropathogenesis of SAFV type 3 in the cerebella of neonatal ddY mice by using SAFV passaged in the cerebella of neonatal BALB/c mice. The virus titer in the cerebellum increased following the inoculation of each of five passaged strains. The fifth passaged strain harbored amino acid substitutions in the VP2 (H160R and Q239R) and VP3 (K62M) capsid proteins. Molecular modeling of the capsid proteins suggested that the VP2-H160R and VP3-K62M mutations alter the structural dynamics of the receptor binding surface via the formation of a novel hydrophobic interaction between the VP2 puff B and VP3 knob regions. Compared with the original strain, the passaged strain showed altered growth characteristics in human-derived astroglial cell lines and greater replication in the brains of neonatal mice. In addition, the passaged strain was more neurovirulent than the original strain, while both strains infected astroglial and neural progenitor cells in the mouse brain. Intracerebral inoculation of either the original or the passaged strain affected brain Purkinje cell dendrites, and a high titer of the passaged strain induced cerebellar hypoplasia in neonatal mice. Thus, infection by mouse-passaged SAFV affected cerebellar development in neonatal mice. This animal model contributes to the understanding of the neuropathogenicity of SAFV infections in infants.IMPORTANCESaffold virus (SAFV) is a candidate neuropathogenic agent in infants and children, but the neuropathogenicity of the virus has not been fully elucidated. Recently, we evaluated the pathogenicity of two clinical SAFV isolates in mice. Similar to other neurotropic picornaviruses, these isolates showed mild infectivity of glial and neural progenitor cells, but not of large neurons, in the cerebellum. However, the outcome of this viral infection in the cerebellum has not been clarified. Here, we examined the tropism of SAFV in the cerebellum. We obtained anin vivo-passaged strain from the cerebella of neonatal mice and examined its genome and its neurovirulence in the neonatal mouse brain. The passaged virus showed high infectivity and neurovirulence in the brain, especially the cerebellum, and affected cerebellar development. This unique neonatal mouse model will be helpful for elucidating the neuropathogenesis of SAFV infections occurring early in life.
Virologic Differences Do Not Fully Explain the Diversification of Swine Influenza Viruses in the United States
Authors: Fabrizio Thomas P. , Sun Yilun , Yoon Sun-Woo , Jeevan Trushar , Dlugolenski Daniel , Tripp Ralph A. , Tang Li , Webby Richard J. 
Published: September 2016

ABSTRACTInfluenza A(H1N1) viruses entered the U.S. swine population following the 1918 pandemic and remained genetically stable for roughly 80 years. In 1998, there was an outbreak of influenza-like illness among swine that was caused by A(H3N2) viruses containing the triple reassortant internal gene (TRIG) cassette. Following the TRIG cassette emergence, numerous reassortant viruses were isolated in nature, suggesting that the TRIG virus had an enhanced ability to reassort compared to the classical swine virus. The present study was designed to quantify the relative reassortment capacities of classical and TRIG swine viruses. Reverse genetic viruses were generated from the classical H1N1 virus A/swine/MN/37866/1999 (MN/99), the TRIG virus A/swine/NC/18161/2002 (NC/02), and a seasonal human H3N2 virus, A/TX/6/1996 (TX/96), to measurein vitroreassortment and growth potentials. After coinfection with NC/02 or MN/99 plus TX/96, H1/H3 double-positive cells were identified. Delayed TX/96 infection was fully excluded by both swine viruses. We then analyzed reassortant H3 viruses. Seventy-seven of 81 (95.1%) TX/96-NC/02 reassortants contained at least one polymerase gene segment from NC/02, whereas only 34 of 61 (55.7%) MN/99-TX/96 reassortants contained at least one polymerase gene segment from MN/99. Additionally, 38 of 81 (46.9%) NC/02-TX/96 reassortants contained all NC/02 polymerase gene segments, while none of the MN/99-TX/96 reassortants contained all MN/99 polymerase genes. There were 21 H3 reassortants between MN/99 and TX/96, compared to only 17 H3 reassortants between NC/02 and TX/96. Overall, the results indicate that there are no distinct differences in the ability of the TRIG to reassort with a human virus compared to the classical swine virus.IMPORTANCEThere appear to be no differences in the abilities of classical swine and TRIG swine viruses to exclude a second virus, suggesting that under the right circumstances both viruses have similar opportunities to reassort. The increased percentage of TRIG polymerase gene segments in reassortant H3 viruses indicates that these viruses may be more compatible with gene segments from other viruses; however, this needs to be investigated further. Nevertheless, the classical swine virus also showed the ability to reassort, suggesting that factors other than reassortment capacity alone are responsible for the different epidemiologies of TRIG and classical swine viruses. The post-TRIG diversity was likely driven by increased intensive farming practices rather than virologic properties. Our results indicate that host ecology can be a significant factor in viral evolution.