bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classifying patients by their characteristics and clinical presentations; the use of latent class analysis
Authors: Wraith Darren , Wolfe Rory 
Published: October 2014

AbstractIn this article, we introduce the general statistical analysis approach known as latent class analysis and discuss some of the issues associated with this type of analysis in practice. Two recent examples from the respiratory health literature are used to highlight the types of research questions that have been addressed using this approach.
Combining Data from Multiple Spatially Referenced Prevalence Surveys Using Generalized Linear Geostatistical Models
Authors: Giorgi Emanuele , Sesay Sanie S. S. , Terlouw Dianne J. , Diggle Peter J. 
Published: October 2014

SummaryData from multiple prevalence surveys can provide information on common parameters of interest, which can therefore be estimated more precisely in a joint analysis than by separate analyses of the data from each survey. However, fitting a single model to the combined data from multiple surveys is inadvisable without testing the implicit assumption that all of the surveys are directed at the same inferential target. We propose a multivariate generalized linear geostatistical model that accommodates two sources of heterogeneity across surveys to correct for spatially structured bias in non-randomized surveys and to allow for temporal variation in the underlying prevalence surface between consecutive survey periods. We describe a Monte Carlo maximum likelihood procedure for parameter estimation and show through simulation experiments how accounting for the different sources of heterogeneity among surveys in a joint model leads to more precise inferences. We describe an application to multiple surveys of the prevalence of malaria conducted in Chikhwawa District, Southern Malawi, and discuss how this approach could inform hybrid sampling strategies that combine data from randomized and non-randomized surveys to make the most efficient use of all available data.
Evaluation of soil and water conservation measures in a semi‐arid river basin in Tunisia using SWAT
Authors: Abouabdillah A. , White M. , Arnold J. G. , De Girolamo A. M. , Oueslati O. , Maataoui A. , Lo Porto A. 
Published: October 2014

AbstractThe Merguellil catchment (central Tunisia) is a typical Mediterranean semi‐arid basin, which suffers from regular water shortage aggravated by current droughts. Over recent decades, the continuous construction of small and large dams and soil and water conservation works (i.e. contour ridges) have taken place within this watershed. However, little is known about the effect of these water‐harvesting systems on the water balance components of arid or semi‐arid basins. In this paper, we present the results of a study, which evaluates the impact of the contour ridges on water balance components and erosion at basin scale by using the soil and water assessment tool model (SWAT). Large dams were modelled as reservoirs, small dams as ponds and contour ridges as potholes that fill with water and increase the percolation into the aquifer. The model predicts that contour ridges produce annually a reduction of 32 and 21% in surface run‐off and river discharge, respectively, and an increase in aquifer recharge of 50%. At the same time, retention of a large proportion of entrained sediment (26%) was modelled.
Influence of basin‐based conservation agriculture on selected soil quality parameters under smallholder farming inZimbabwe
Authors: Nyamangara J. , Marondedze A. , Masvaya E. N. , Mawodza T. , Nyawasha R. , Nyengerai K. , Tirivavi R. , Nyamugafata P. , Wuta M. 
Published: October 2014

AbstractThe research was carried out to determine the effect of basin‐based conservation agriculture (CA) on selected soil quality parameters. Paired plots (0.01 ha) ofCAand conventional tillage based on the animal‐drawn mouldboard plough (CONV) were established between 2004 and 2007 on farm fields on soils with either low (12–18% – sandy loams and sandy clay loams) or high clay levels (>18–46% – sandy clays and clays) as part of an ongoing project promotingCAin six districts in the smallholder farming areas of Zimbabwe. We hypothesized thatCAwould improve soil organic carbon (SOC), bulk density, aggregate stability, soil moisture retention and infiltration rate. Soil samples forSOCand aggregate stability were taken from 0 to 15 cm depth and for bulk density and soil moisture retention from 0 to 5, 5 to 10 and 10 to 15 cm depths in 2011 from maize plots. LargerSOCcontents,SOCstocks and improved aggregate stability, decreased bulk density, increased pore volume and moisture retention were observed inCAtreatments. Results were consistent with the hypothesis, and we conclude thatCAimproves soil quality under smallholder farming. Benefits were, however, greater in high clay soils, which is relevant to the targeting of practices on smallholder farming areas of sub‐Saharan Africa.
Changing microbial epidemiology in hematopoietic stem cell transplant recipients: increasing resistance over a 9‐year period
Authors: Macesic N. , Morrissey C.O. , Cheng A.C. , Spencer A. , Peleg A.Y. 
Published: October 2014

AbstractInfections remain important contributors to mortality in hematopoietic stem cell transplantation (HSCT).MethodWe studied the evolving epidemiology and trends in susceptibility of bacterial and Candida isolates at an Australian HSCT center. A total of 528 HSCTs in 508 patients were performed from April 2001 to May 2010. A total of 605 isolates were eligible for study inclusion; 318 (53%) were gram‐positive, 268 (44%) were gram‐negative, and 19 (3%) were Candida species.ResultsThe most common site for isolates was blood (380 isolates, 63%). Staphylococcus aureus was the most common gram‐positive organism (n = 107, 34%), but trends to increasing coagulase‐negative staphylococci (P = 0.002) and vancomycin‐resistant Enterococcus (P < 0.001) were observed. Escherichia coli was the most common gram‐negative isolate (n = 74, 28%). Fluoroquinolone resistance increased with widespread use of protocol fluoroquinolone prophylaxis (P = 0.001). Carbapenem resistance was found in 44% of Pseudomonas or Acinetobacter isolates. Bloodstream infection with a multidrug‐resistant organism (odds ratio 3.61, 95% confidence interval: 1.40–9.32, P = 0.008) was an independent predictor of mortality at 7 days after a positive blood culture.ConclusionsAntimicrobial resistance is an increasing problem in this vulnerable patient population, and not only has an impact on choice of empiric therapy for febrile neutropenia but also on mortality.
Genome Sequence of a Bornavirus Recovered from an African Garter Snake (
Elapsoidea loveridgei
)
Authors: Stenglein Mark D. , Leavitt Eli B. , Abramovitch Michael A. , McGuire Jimmy A. , DeRisi Joseph L. 
Published: October 2014

ABSTRACT

Bornaviruses are known to infect mammals and birds, and they have been associated with disease in both groups of animals. Here, we report the genome sequence of a bornavirus identified in a wild-caught Loveridge's garter snake (
Elapsoidea loveridgei
).
Draft Genome Sequence of Necropsobacter rosorum Strain P709
T
Authors: Padmanabhan Roshan , Robert Catherine , Fenollar Florence , Raoult Didier , Fournier Pierre-Edouard 
Published: October 2014

ABSTRACT

Necropsobacter
is a recently described genus that contains a single species,
N. rosorum
, and belongs to the family
Pasteurellaceae
. Here, we present the draft genome of
N. rosorum
strain P709
T
, which is the first genome sequence from this species.
Genome Sequences of Simian Hemorrhagic Fever Virus Variant NIH LVR42-0/M6941 Isolates (
Arteriviridae
:
Arterivirus
)
Authors: Lauck Michael , Palacios Gustavo , Wiley Michael R. , Lǐ Yànhuá , Fāng Yīng , Lackemeyer Matthew G. , Caì Yíngyún , Bailey Adam L. , Postnikova Elena , Radoshitzky Sheli R. , Johnson Reed F. , Alkhovsky Sergey V. , Deriabin Petr G. , Friedrich Thomas C. , Goldberg Tony L. , Jahrling Peter B. , O'Connor David H. , Kuhn Jens H. 
Published: October 2014

ABSTRACT
Simian hemorrhagic fever virus (SHFV) variant NIH LVR42-0/M6941 is the only remaining SHFV in culture, and only a single genome sequence record exists in GenBank/RefSeq. We compared the genomic sequence of NIH LVR42-0/M6941 acquired from the ATCC in 2011 to NIH LVR42-0/M6941 genomes sequenced directly from nonhuman primates experimentally infected in 1989.
Complete Genome Sequence of the RmInt1 Group II Intronless Sinorhizobium meliloti Strain RMO17
Authors: Toro Nicolás , Martínez-Abarca Francisco , Nisa-Martínez Rafael 
Published: October 2014

ABSTRACT

We report the complete genome sequence of the RmInt1 group II intronless
Sinorhizobium meliloti
strain RMO17 isolated from
Medicago orbicularis
nodules from Spanish soil. The genome consists of 6.73 Mb distributed between a single chromosome and two megaplasmids (the chromid pSymB and pSymA).
Commentaries: Name Changes in Medically Important Fungi and Their Implications for Clinical Practice
Authors: de Hoog G. Sybren , Chaturvedi Vishnu , Denning David W. , Dyer Paul S. , Frisvad Jens Christian , Geiser David , Gräser Yvonne , Guarro Josep , Haase Gerhard , Kwon-Chung Kyung-Joo , Meis Jacques F. , Meyer Wieland , Pitt John I. , Samson Robert A. , Taylor John W. , Tintelnot Kathrin , Vitale Roxana G. , Walsh Thomas J. , Lackner Michaela 
Published: October 2014

ABSTRACT
Recent changes in the Fungal Code of Nomenclature and developments in molecular phylogeny are about to lead to dramatic changes in the naming of medically important molds and yeasts. In this article, we present a widely supported and simple proposal to prevent unnecessary nomenclatural instability.
Tumor Necrosis Factor Alpha and Interleukin-6 Facilitate Corneal Lymphangiogenesis in Response to Herpes Simplex Virus 1 Infection
Authors: Bryant-Hudson Katie M. , Gurung Hem R. , Zheng Min , Carr Daniel J. J. 
Published: October 2014

ABSTRACTHerpes simplex virus 1 (HSV-1) is a common human pathogen of clinical significance due to its association with vision impairment and encephalitis. In a mouse model of ocular neovascularization, we have previously shown that HSV-1 elicits the genesis of lymphatic vessels into the cornea proper through epithelial cell expression of vascular endothelial growth factor A (VEGFA) dependent upon expression of VEGFR2 during acute infection. We hypothesized that other factors may be involved in lymphangiogenesis, with proinflammatory cytokines as the leading candidates. In the absence of infection or inflammation, intrastromal administration of tumor necrosis factor alpha (TNF-α) coupled with VEGFA elicited lymphatic vessel genesis significantly above either factor alone as well as a vehicle control. Consistent with this observation, anti-TNF-α antibody (Ab) blocked HSV-1-mediated corneal lymphangiogenesis within the first 5 days postinfection. However, TNF-α-deficient (TNF-α−/−) mice displayed a level of corneal vessel growth similar to that shown by wild-type (WT) controls. To investigate the likely redundant nature of cytokines, PCR array analysis of HSV-1-infected TNF-α−/−mice was conducted, and it revealed several factors elevated above those found in HSV-1-infected WT mice, including interleukin-1β (IL-1β), platelet-derived growth factor, angiopoietin 2, insulin-like growth factor 2, and IL-6. Subconjunctival administration of neutralizing Ab to IL-6 blocked lymphangiogenesis in TNF-α−/−mice. Whereas the cornea levels of IL-6 were significantly reduced, there was no appreciable change in the level of IL-1β or other proangiogenic factors analyzed. Collectively, the results suggest in addition to VEGFA, TNF-α and IL-6 promote and likely synergize with VEGFA in corneal lymphangiogenesis during acute HSV-1 infection.IMPORTANCEWe have identified at least two proinflammatory cytokines expressed locally that are involved in the genesis of lymphatic vessels in the normally avascular cornea in response to HSV-1 infection. This finding provides the basis to target IL-6 and TNF-α as additional proangiogenic factors in the cornea during the development of herpetic stromal keratitis as a means to alleviate further neovascularization and tissue pathology associated with the host immune response to the pathogen.
Putative Domain-Domain Interactions in the Vesicular Stomatitis Virus L Polymerase Protein Appendage Region
Authors: Ruedas John B. , Perrault Jacques 
Published: October 2014

ABSTRACT
The multidomain polymerase protein (L) of nonsegmented negative-strand (NNS) RNA viruses catalyzes transcription and replication of the virus genome. The N-terminal half of the protein forms a ring-like polymerase structure, while the C-terminal half encoding viral mRNA transcript modifications consists of a flexible appendage with three distinct globular domains. To gain insight into putative transient interactions between L domains during viral RNA synthesis, we exchanged each of the four distinct regions encompassing the appendage region of vesicular stomatitis virus (VSV) Indiana serotype L protein with their counterparts from VSV New Jersey and analyzed effects on virus polymerase activity in a minigenome system. The methyltransferase domain exchange yielded a fully active polymerase protein, which functioned as well as wild-type L in the context of a recombinant virus. Exchange of the downstream C-terminal nonconserved region abolished activity, but coexchanging it with the methyltransferase domain generated a polymerase favoring replicase over transcriptase activity, providing strong evidence of interaction between these two regions. Exchange of the capping enzyme domain or the adjacent nonconserved region thought to function as an “unstructured” linker also abrogated polymerase activity even when either domain was coexchanged with other appendage domains. Further probing of the putative linker segment using in-frame enhanced green fluorescent protein (EGFP) insertions similarly abrogated activity. We discuss the implications of these findings with regard to L protein appendage domain structure and putative domain-domain interactions required for polymerase function.

IMPORTANCE
NNS viruses include many well-known human pathogens (e.g., rabies, measles, and Ebola viruses), as well as emerging viral threats (e.g., Nipah and Hendra viruses). These viruses all encode a large L polymerase protein similarly organized into multiple domains that work in concert to enable virus genome transcription and replication. But how the unique L protein carries out the multiplicity of individual steps in these two distinct processes is poorly understood. Using two different approaches, i.e., exchanging individual domains in the C-terminal appendage region of the protein between two closely related VSV serotypes and inserting unrelated protein domains, we shed light on requirements for domain-domain interactions and domain contiguity in polymerase function. These findings further our understanding of the conformational dynamics of NNS L polymerase proteins, which play an essential role in the pathogenic properties of these viruses and represent attractive targets for the development of antiviral measures.
Assessing the suitability of 8-OHdG and micronuclei as genotoxic biomarkers in chromate-exposed workers: a cross-sectional study
Authors: Li Ping , Gu Yongen , Yu Shanfa , Li Yang , Yang Jinglin , Jia Guang 
Published: October 2014

ObjectivesWe aimed to investigate suitable conditions of 8-hydroxy-2′-deoxyguanosine (8-OHdG) and micronucleus (MN) as genotoxic biomarkers at different levels of occupational chromate exposure.DesignA cross-sectional study was used.Participants84 workers who were exposed to chromate for at least 1 year were chosen as the chromate exposed group, while 30 non-exposed individuals were used as controls.Main outcome measuresEnvironmental and biological exposure to chromate was respectively assessed by measuring the concentration of chromate in the air (CrA) and blood (CrB) by inductively coupled plasma mass spectrometer (ICP-MS) in all participants. MN indicators, including micronucleus cell count (MNCC), micro-nucleus count (MNC), nuclear bridge (NPB) and nuclear bud (NBUD) were calculated by the cytokinesis-block micronucleus test (CBMN), while the urinary 8-OHdG was measured by the ELISA method and normalised by the concentration of Cre.ResultsCompared with the control group, the levels of CrA, CrB, MNCC, MNC and 8-OHdG in the chromate-exposed group were all significantly higher (p<0.05). There were positive correlations between log(8-OHdG) and LnMNCC or LnMNC (r=0.377 and 0.362). The levels of LnMNCC, LnMNC and log (8-OHdG) all have parabola correlations with the concentration of CrB. However, there was a significantly positive correlation between log (8-OHdG) and CrB when the CrB level was below 10.50 µg/L (r=0.355), while a positive correlation was also found between LnMNCC or LnMNC and CrB when the CrB level was lower than 9.10 µg/L (r=0.365 and 0.269, respectively).ConclusionsMN and 8-OHdG can be used as genotoxic biomarkers in the chromate-exposed group, but it is only when CrB levels are lower than 9.10 and 10.50 µg/L, respectively, that they can accurately reflect the degree of genetic damage.
Euthanasia in a no‐kill shelter
Authors: Ashall Vanessa 
Published: October 2014

THIS series gives readers the opportunity to consider and contribute to discussion of some of the ethical dilemmas that can arise in veterinary practice. Each month, a case scenario is presented, followed by discussion of some of the issues involved.In addition, a possible way forward is suggested; however, there is rarely a cut‐and‐dried answer in such cases, and readers may wish to suggest an alternative approach. This month's dilemma, ‘Euthanasia in a no‐kill shelter’, was submitted and is discussed by Vanessa Ashall. Readers with comments to contribute are invited to send them as soon as possible, so that they can be considered for publication in the next issue. Discussion of the dilemma ‘Little nippers’, which was published in the September issue of In Practice, appears on page 479.The series is being coordinated by Siobhan Mullan, of the University of Bristol. It is hoped it will provide a framework that will help practices find solutions when facing similar dilemmas.
The Age Distribution of Type-Specific High-Risk Human Papillomavirus Incidence in Two Population-Based Screening Trials
Authors: Veldhuijzen Nienke J. , Berkhof Johannes , Gillio-Tos Anna , De Marco Laura , Carozzi Francesca , Del Mistro Annarosa , Snijders Peter J.F. , Meijer Chris J.L.M , Ronco Guglielmo 
Published: October 2014

Abstract
Background: Age- and type-specific high-risk human papillomavirus (hrHPV) incidence estimates in screen-eligible women are relevant from a public health perspective because they provide an indication of the effect of vaccination on the occurrence of screen-positives in HPV-based screening. However, limited data from women over 25 years of age are available.
Methods: In 24,105 hrHPV-negative women participating in Dutch (Population-Based Screening Study Amsterdam: POBASCAM) and Italian (New Technologies for Cervical Cancer: NTCC) population-based randomized controlled screening trials the age- and type-specific distribution of incident hrHPV infections detected at the next screening round was assessed. HPV types were grouped into vaccine (bivalent: HPV16/18; polyvalent HPV16/18/31/33/45/52/58) and nonvaccine types.
Results: The incidence of screen-detected hrHPV among women ages 29 to 56 years was 2.54% (95% confidence interval, 2.30–2.78) in POBASCAM and 2.77% (2.36–3.19) in NTCC. In both studies, the incidence of bivalent, polyvalent, and nonpolyvalent infections decreased with age (P &lt; 0.0001). Among women with incident infection(s), vaccine-type positivity changed quadratically with age, in particular for the polyvalent vaccine (P values: POBASCAM: bivalent 0.264, polyvalent 0.038; NTCC bivalent 0.039, polyvalent 0.005). However, more than 20% and 50% of women with incident hrHPV were positive for bivalent and polyvalent vaccine types, respectively, in all ages in both studies.
Conclusions: We observed decreasing age trends of hrHPV vaccine and nonvaccine type incidences and age-related differences in the vaccine-type positivity among women with incident infections. Most importantly, hrHPV infections continued to be detected in all ages and the contribution of vaccine types remained substantial.
Impact: Our results indicate a considerable reduction of new hrHPV infections in vaccinated cohorts, ensuing revision of screening guidelines. Cancer Epidemiol Biomarkers Prev; 24(1); 111–8. ©2014 AACR.
Reproducible, Quantitative, and Flexible Molecular Subtyping of Clinical DLBCL Samples Using the NanoString nCounter System
Authors: Veldman-Jones Margaret H. , Lai Zhongwu , Wappett Mark , Harbron Chris G. , Barrett J. Carl , Harrington Elizabeth A. , Thress Kenneth S. 
Published: October 2014

Abstract
Purpose: Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease with distinct molecular subtypes. The most established subtyping approach, the “Cell of Origin” (COO) algorithm, categorizes DLBCL into activated B-cell (ABC) and germinal center B-cell (GCB)-like subgroups through gene expression profiling. Recently developed immunohistochemical (IHC) techniques and other established methodologies can deliver discordant results and have various technical limitations. We evaluated the NanoString nCounter gene expression system to address issues with current platforms.
Experimental Design: We devised a scoring system using 145 genes from published datasets to categorize DLBCL samples. After cell line validation, clinical tissue segmentation was tested using commercially available diagnostic DLBCL samples. Finally, we profiled biopsies from patients with relapsed/refractory DLBCL enrolled in the fostamatinib phase IIb clinical trial using three independent RNA expression platforms: NanoString, Affymetrix, and qNPA.
Results: Diagnostic samples showed a typical spread of subtypes with consistent gene expression profiles across matched fresh, frozen, and formalin-fixed paraffin-embedded tissues. Results from biopsy samples across platforms were remarkably consistent, in contrast to published IHC data. Interestingly, COO segmentation of longitudinal fostamatinib biopsies taken at initial diagnosis and then again at primary relapse showed 88% concordance (15/17), suggesting that COO designation remains stable over the course of disease progression.
Conclusions: DLBCL segmentation of patient tumor samples is possible using a number of expression platforms. However, we found that NanoString offers the most flexibility and fewest limitations in regards to robust clinical tissue subtype characterization. These subtype distinctions should help guide disease prognosis and treatment options within DLBCL clinical practice. Clin Cancer Res; 21(10); 2367–78. ©2014 AACR.
See related commentary by Rimsza, p. 2204