bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laboratory Investigation of the First Case of Botulism Caused by Clostridium butyricum Type E Toxin in the United States
Authors: Dykes Janet K. , Lúquez Carolina , Raphael Brian H. , McCroskey Loretta , Maslanka Susan E. 
Published: August 2015

ABSTRACT

We report here the laboratory investigation of the first known case of botulism in the United States caused by
Clostridium butyricum
type E. This investigation demonstrates the importance of extensive microbiological examination of specimens, which resulted in the isolation of this organism.
Application of Isothermal Amplification Techniques for Identification of Madurella mycetomatis, the Prevalent Agent of Human Mycetoma
Authors: Ahmed Sarah A. , van de Sande Wendy W. J. , Desnos-Ollivier Marie , Fahal Ahmed H. , Mhmoud Najwa A. , de Hoog G. S. 
Published: August 2015

ABSTRACT

Appropriate diagnosis and treatment of eumycetoma may vary significantly depending on the causative agent. To date, the most common fungus causing mycetoma worldwide is
Madurella mycetomatis
. This species fails to express any recognizable morphological characteristics, and reliable identification can therefore only be achieved with the application of molecular techniques. Recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP) are proposed as alternatives to phenotypic methods. Species-specific primers were developed to target the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region of
M. mycetomatis
. Both isothermal amplification techniques showed high specificity and sufficient sensitivity to amplify fungal DNA and proved to be appropriate for detection of
M. mycetomatis
. Diagnostic performance of the techniques was assessed in comparison to conventional PCR using biopsy specimens from eumycetoma patients. RPA is reliable and easy to operate and has the potential to be implemented in areas where mycetoma is endemic. The techniques may be expanded to detect fungal DNA from environmental samples.
Lab-on-Chip-Based Platform for Fast Molecular Diagnosis of Multidrug-Resistant Tuberculosis
Authors: Cabibbe Andrea M. , Miotto Paolo , Moure Raquel , Alcaide Fernando , Feuerriegel Silke , Pozzi Gianni , Nikolayevskyy Vladislav , Drobniewski Francis , Niemann Stefan , Reither Klaus , Cirillo Daniela M. 
Published: August 2015

ABSTRACT

We evaluated the performance of the molecular lab-on-chip-based VerePLEX Biosystem for detection of multidrug-resistant tuberculosis (MDR-TB), obtaining a diagnostic accuracy of more than 97.8% compared to sequencing and MTBDR
plus
assay for
Mycobacterium tuberculosis
complex and rifampin and isoniazid resistance detection on clinical isolates and smear-positive specimens. The speed, user-friendly interface, and versatility make it suitable for routine laboratory use.
Hemagglutinin-Neuraminidase Balance Influences the Virulence Phenotype of a Recombinant H5N3 Influenza A Virus Possessing a Polybasic HA
0
Cleavage Site
Authors: Diederich Sandra , Berhane Yohannes , Embury-Hyatt Carissa , Hisanaga Tamiko , Handel Katherine , Cottam-Birt Colleen , Ranadheera Charlene , Kobasa Darwyn , Pasick John 
Published: August 2015

ABSTRACT

Although a polybasic HA
0
cleavage site is considered the dominant virulence determinant for highly pathogenic avian influenza (HPAI) H5 and H7 viruses, naturally occurring virus isolates possessing a polybasic HA
0
cleavage site have been identified that are low pathogenic in chickens. In this study, we generated a reassortant H5N3 virus that possessed the hemagglutinin (HA) gene from H5N1 HPAI A/swan/Germany/R65/2006 and the remaining gene segments from low pathogenic A/chicken/British Columbia/CN0006/2004 (H7N3). Despite possessing the HA
0
cleavage site GERRRKKR/GLF, this rH5N3 virus exhibited a low pathogenic phenotype in chickens. Although rH5N3-inoculated birds replicated and shed virus and seroconverted, transmission to naive contacts did not occur. To determine whether this virus could evolve into a HPAI form, it underwent six serial passages in chickens. A progressive increase in virulence was observed with the virus from passage number six being highly transmissible. Whole-genome sequencing demonstrated the fixation of 12 nonsynonymous mutations involving all eight gene segments during passaging. One of these involved the catalytic site of the neuraminidase (NA; R293K) and is associated with decreased neuraminidase activity and resistance to oseltamivir. Although introducing the R293K mutation into the original low-pathogenicity rH5N3 increased its virulence, transmission to naive contact birds was inefficient, suggesting that one or more of the remaining changes that had accumulated in the passage number six virus also play an important role in transmissibility. Our findings show that the functional linkage and balance between HA and NA proteins contributes to expression of the HPAI phenotype.

IMPORTANCE
To date, the contribution that hemagglutinin-neuraminidase balance can have on the expression of a highly pathogenic avian influenza virus phenotype has not been thoroughly examined. Reassortment, which can result in new hemagglutinin-neuraminidase combinations, may have unpredictable effects on virulence and transmission characteristics of a virus. Our data show the importance of the neuraminidase in complementing a polybasic HA
0
cleavage site. Furthermore, it demonstrates that adaptive changes selected for during the course of virus evolution can result in unexpected traits such as antiviral drug resistance.
Neuraminidase of Influenza A Virus Binds Lysosome-Associated Membrane Proteins Directly and Induces Lysosome Rupture
Authors: Ju Xiangwu , Yan Yiwu , Liu Qiang , Li Ning , Sheng Miaomiao , Zhang Lifang , Li Xiao , Liang Zhu , Huang Fengming , Liu Kangtai , Zhao Yan , Zhang Yanxu , Zou Zhen , Du Jianchao , Zhong Ying , Zhou Huandi , Yang Peng , Lu Huijun , Tian Mingyao , Li Dangsheng , Zhang Jianming , Jin Ningyi , Jiang Chengyu 
Published: August 2015

ABSTRACT
As a recycling center, lysosomes are filled with numerous acid hydrolase enzymes that break down waste materials and invading pathogens. Recently, lysosomal cell death has been defined as “lysosomal membrane permeabilization and the consequent leakage of lysosome contents into cytosol.” Here, we show that the neuraminidase (NA) of H5N1 influenza A virus markedly deglycosylates and degrades lysosome-associated membrane proteins (LAMPs; the most abundant membrane proteins of lysosome), which induces lysosomal rupture, and finally leads to cell death of alveolar epithelial carcinoma A549 cells and human tracheal epithelial cells. The NA inhibitors peramivir and zanamivir could effectively block the deglycosylation of LAMPs, inhibit the virus cell entry, and prevent cell death induced by the H5N1 influenza virus. The NA of seasonal H1N1 virus, however, does not share these characteristics. Our findings not only reveal a novel role of NA in the early stage of the H5N1 influenza virus life cycle but also elucidate the molecular mechanism of lysosomal rupture crucial for influenza virus induced cell death.

IMPORTANCE
The integrity of lysosomes is vital for maintaining cell homeostasis, cellular defense and clearance of invading pathogens. This study shows that the H5N1 influenza virus could induce lysosomal rupture through deglycosylating lysosome-associated membrane proteins (LAMPs) mediated by the neuraminidase activity of NA protein. NA inhibitors such as peramivir and zanamivir could inhibit the deglycosylation of LAMPs and protect lysosomes, which also further interferes with the H5N1 influenza virus infection at early stage of life cycle. This work is significant because it presents new concepts for NA's function, as well as for influenza inhibitors' mechanism of action, and could partially explain the high mortality and high viral load after H5N1 virus infection in human beings and why NA inhibitors have more potent therapeutic effects for lethal avian influenza virus infections at early stage.
Importation and Recombination Are Responsible for the Latest Emergence of Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus in China
Authors: Zhao Kuan , Ye Chao , Chang Xiao-Bo , Jiang Cheng-Gang , Wang Shu-Jie , Cai Xue-Hui , Tong Guang-Zhi , Tian Zhi-Jun , Shi Mang , An Tong-Qing 
Published: August 2015

ABSTRACT
In China, a majority of the highly pathogenic porcine reproductive and respiratory syndrome (HP-PRRSV) strains were seeded by the 2006 outbreak. However, the most recently emerged (2013-2014) HP-PRRSV strain has a very different genetic background. It is a NADC30-like PRRSV strain recently introduced from North America that has undergone genetic exchange with the classic HP-PRRSV strains in China. Subsequent isolation and characterization of this variant suggest high pathogenicity, so it merits special attention in control and vaccine strategies.
Constitutive Activation of Interleukin-13/STAT6 Contributes to Kaposi's Sarcoma-Associated Herpesvirus-Related Primary Effusion Lymphoma Cell Proliferation and Survival
Authors: Wang Chong , Zhu Caixia , Wei Fang , Zhang Liming , Mo Xiaohui , Feng Yanling , Xu Jianqing , Yuan Zhenghong , Robertson Erle , Cai Qiliang 
Published: August 2015

ABSTRACT

Activation of the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling pathway has been associated with numerous human malignancies, including primary effusion lymphomas (PELs). PEL, a cancerous proliferation of B cells, is caused by Kaposi's sarcoma-associated herpesvirus (KSHV). Previously we identified constitutive phosphorylation of STAT6 on tyrosine 641 (p-STAT6
C
) in PEL cell lines BC3 and BCBL1; however, the molecular mechanism leading to this activation remains unclear. Here we demonstrate that STAT6 activation tightly correlates with interleukin-13 (IL-13) secretion, JAK1/2 tyrosine phosphorylation, and reduced expression of SHP1 due to KSHV infection. Moreover, p-STAT6
C
and reduction of SHP1 were also observed in KS patient tissue. Notably, blockade of IL-13 by antibody neutralization dramatically inhibits PEL cell proliferation and survival. Taken together, these results suggest that IL-13/STAT6 signaling is modulated by KSHV to promote host cell proliferation and viral pathogenesis.

IMPORTANCE
STAT6 is a member of signal transducer and activator of transcription (STAT) family, whose activation is linked to KSHV-associated cancers. The mechanism through which STAT6 is modulated by KSHV remains unclear. In this study, we demonstrated that constitutive activation of STAT6 in KSHV-associated PEL cells results from interleukin-13 (IL-13) secretion and reduced expression of SHP1. Importantly, we also found that depletion of IL-13 reduces PEL cell growth and survival. This discovery provides new insight that IL-13/STAT6 plays an essential role in KSHV pathogenesis.
Topography of the Human Papillomavirus Minor Capsid Protein L2 during Vesicular Trafficking of Infectious Entry
Authors: DiGiuseppe Stephen , Keiffer Timothy R. , Bienkowska-Haba Malgorzata , Luszczek Wioleta , Guion Lucile G. M. , Müller Martin , Sapp Martin 
Published: August 2015

ABSTRACT

The human papillomavirus (HPV) capsid is composed of the major capsid protein L1 and the minor capsid protein L2. During entry, the HPV capsid undergoes numerous conformational changes that result in endosomal uptake and subsequent trafficking of the L2 protein in complex with the viral DNA to the
trans
-Golgi network. To facilitate this transport, the L2 protein harbors a number of putative motifs that, if capable of direct interaction, would interact with cytosolic host cell factors. These data imply that a portion of L2 becomes cytosolic during infection. Using a low concentration of digitonin to selectively permeabilize the plasma membrane of infected cells, we mapped the topography of the L2 protein during infection. We observed that epitopes within amino acid residues 64 to 81 and 163 to 170 and a C-terminal tag of HPV16 L2 are exposed on the cytosolic side of intracellular membranes, whereas an epitope within residues 20 to 38, which are upstream of a putative transmembrane region, is luminal. Corroborating these findings, we also found that L2 protein is sensitive to trypsin digestion during infection. These data demonstrate that the majority of the L2 protein becomes accessible on the cytosolic side of intracellular membranes in order to interact with cytosolic factors to facilitate vesicular trafficking.

IMPORTANCE
In order to complete infectious entry, nonenveloped viruses have to pass cellular membranes. This is often achieved through the viral capsid protein associating with or integrating into intracellular membrane. Here, we determine the topography of HPV L2 protein in the endocytic vesicular compartment, suggesting that L2 becomes a transmembrane protein with a short luminal portion and with the majority facing the cytosolic side for interaction with host cell transport factors.
A Druggable Pocket at the Nucleocapsid/Phosphoprotein Interaction Site of Human Respiratory Syncytial Virus
Authors: Ouizougun-Oubari Mohamed , Pereira Nelson , Tarus Bogdan , Galloux Marie , Lassoued Safa , Fix Jenna , Tortorici M. Alejandra , Hoos Sylviane , Baron Bruno , England Patrick , Desmaële Didier , Couvreur Patrick , Bontems François , Rey Félix A. , Eléouët Jean-François , Sizun Christina , Slama-Schwok Anny , Duquerroy Stéphane 
Published: August 2015

ABSTRACT

Presently, respiratory syncytial virus (RSV), the main cause of severe respiratory infections in infants, cannot be treated efficiently with antivirals. However, its RNA-dependent polymerase complex offers potential targets for RSV-specific drugs. This includes the recognition of its template, the ribonucleoprotein complex (RNP), consisting of genomic RNA encapsidated by the RSV nucleoprotein, N. This recognition proceeds via interaction between the phosphoprotein P, which is the main polymerase cofactor, and N. The determinant role of the C terminus of P, and more particularly of the last residue, F241, in RNP binding and viral RNA synthesis has been assessed previously. Here, we provide detailed structural insight into this crucial interaction for RSV polymerase activity. We solved the crystallographic structures of complexes between the N-terminal domain of N (N-NTD) and C-terminal peptides of P and characterized binding by biophysical approaches. Our results provide a rationale for the pivotal role of F241, which inserts into a well-defined N-NTD pocket. This primary binding site is completed by transient contacts with upstream P residues outside the pocket. Based on the structural information of the N-NTD:P complex, we identified inhibitors of this interaction, selected by
in silico
screening of small compounds, that efficiently bind to N and compete with P
in vitro
. One of the compounds displayed inhibitory activity on RSV replication, thereby strengthening the relevance of N-NTD for structure-based design of RSV-specific antivirals.

IMPORTANCE
Respiratory syncytial virus (RSV) is a widespread pathogen that is a leading cause of acute lower respiratory infections in infants worldwide. RSV cannot be treated efficiently with antivirals, and no vaccine is presently available, with the development of pediatric vaccines being particularly challenging. Therefore, there is a need for new therapeutic strategies that specifically target RSV. The interaction between the RSV phosphoprotein P and the ribonucleoprotein complex is critical for viral replication. In this study, we identified the main structural determinants of this interaction, and we used them to screen potential inhibitors
in silico
. We found a family of molecules that were efficient competitors of P
in vitro
and showed inhibitory activity on RSV replication in cellular assays. These compounds provide a basis for a pharmacophore model that must be improved but that holds promises for the design of new RSV-specific antivirals.
An external validation study of a clinical prediction rule for medical patients with suspected bacteraemia
Authors: Hodgson Luke Eliot , Dragolea Nicholas , Venn Richard , Dimitrov Borislav D , Forni Lui G 
Published: August 2015

ObjectiveThe objective of this study was to externally validate a clinical prediction rule (CPR)—the ‘Shapiro criteria’—to predict bacteraemia in an acute medical unit (AMU).MethodsProspectively collected data, retrospectively evaluated over 11 months in an AMU in the UK. From 4810 admissions, 635 patients (13%) had blood cultures (BCs) performed. The 100 cases of true bacteraemia were compared with a randomly selected sample of 100 control cases where BCs were sterile.ResultsTo predict bacteraemia (at a cut-off score of two points), the Shapiro criteria had a sensitivity of 97% (95% CIs 91% to 99%), specificity 37% (28% to 47%), positive likelihood ratio 1.54 (1.3 to 1.8) and a negative likelihood ratio of 0.08 (0.03 to 0.25). The area under the receiver operating curve was 0.80 (0.74 to 0.86), and the Hosmer–Lemeshow p value was 0.45.ConclusionsA cut-off score of two points on the Shapiro criteria had high sensitivity to predict bacteraemia in a study of acute general medical admissions. Application of the rule in patients being considered for a BC could identify those at low risk of bacteraemia. Though the model demonstrated good discrimination, the lengthy number of variables (13) and difficulty automating the CPR may limit its use.
Deaths of teenagers in car crashes: a child death review
Authors: Jones Sarah J , Heatman Beverley 
Published: August 2015

MVCs are a leading cause of death and disability for teenagers. In Wales, a child death review process has been established to carry out thematic reviews of deaths; this approach is believed to highlight opportunities for prevention that individual case review could not. Cases were 13-year-old to 17-year-old Welsh residents who died as car drivers or passengers between 1 January 2006 and 31 December 2010. An expert panel was convened to review these cases. 28 MVCs occurred and 34 13–17 year olds died; 24 males, 10 females. 51 vehicles were involved; 23 driven by 17-year-old to 19-year-old males. 19 of the 28 MVCs occurred between 21:00 and 05:00. The risk factors identified were consistent with global research on MVC deaths and injuries to teenagers. However, there is a lack of effective interventions to tackle these in the UK. It is recommended that the implementation of Graduated Driver Licensing is considered.
Shifting abortion care from a hospital to a community sexual and reproductive health care setting
Authors: Cameron Sharon T , Glasier Anna , Johnstone Anne 
Published: August 2015

BackgroundCommunity sexual and reproductive health (SRH) services are well placed to deliver abortion assessment services and early medical abortion (EMA), but comparative data on safety and acceptability from both settings are important for future service planning.MethodsRetrospective review of computerised records of 1342 women undergoing outpatient EMA (≤9 weeks) in a community SRH or hospital department of gynaecology in the same city, and a self-completed, anonymous survey of 303 women requesting abortion at both sites. Primary outcome was safety in terms of re-attendance rates for a complication related to EMA. Secondary outcomes were telephone contact with each site for an EMA-related concern and satisfaction with information about abortion (defined as score out of 10) received at each site.ResultsThere was no difference in re-attendance rates to either service for a complication following outpatient EMA (2.7%). A higher proportion of women undergoing EMA at the SRH site made telephone contact compared to women at the hospital site (18.8% vs 10.8%;p=0.033). Women rated both settings highly in terms of information received before abortion (9.2 and 9.6 out of 10) at the hospital and SRH sites, respectively.ConclusionsThis study suggests that provision of outpatient EMA in a community SRH setting is as safe as that delivered from a hospital setting, and that women are similarly satisfied with the information they receive about abortion from each setting. More abortion assessment and outpatient EMA services in Great Britain could shift from hospital to community SRH settings.
Lower–Middle Jurassic facies patterns in the NW Afghan–Tajik Basin of southern Uzbekistan and their geodynamic context
Authors: Fürsich Franz T. , Brunet Marie-Françoise , Auxiètre Jean-Luc , Munsch Hermann 
Published: August 2015

Abstract
Based on 11 sections, the palaeoenvironments and depositional history of the NW Afghan–Tajik Basin in southern Uzbekistan have been reconstructed for the time interval of the Early Jurassic–Early Callovian. The earliest sediments, resting on Palaeozoic basement rocks, date from the Early Jurassic Period. Up to the end of the Early Bajocian time, more than 500 m of non-marine sediments accumulated as a result of extensional tectonics inducing active subsidence. In the Late Bajocian time interval, transgression led to the establishment of siliciclastic ramps that were influenced by storm processes. After a condensed unit in the Middle Bathonian, sedimentation resumed in an outer carbonate ramp–basinal setting as the subsidence rate outpaced the diminished siliciclastic sediment supply. The change from siliciclastic to carbonate sedimentation in the Middle Jurassic Period is thought to be multifactorial, reflecting levelling of relief in the hinterland, the subsidence moving to a thermally more quiet stage and a change from humid to arid climatic conditions. These features are also observed in the area of present-day Iran. Similarly, the timing of the transgression coincides with that in eastern and northern Iran, stressing the regional significance of this event.
A Molecular Portrait of High-Grade Ductal Carcinoma In Situ
Authors: Abba Martin C. , Gong Ting , Lu Yue , Lee Jaeho , Zhong Yi , Lacunza Ezequiel , Butti Matias , Takata Yoko , Gaddis Sally , Shen Jianjun , Estecio Marcos R. , Sahin Aysegul A. , Aldaz C. Marcelo 
Published: August 2015

Abstract
Ductal carcinoma in situ (DCIS) is a noninvasive precursor lesion to invasive breast carcinoma. We still have no understanding on why only some DCIS lesions evolve to invasive cancer whereas others appear not to do so during the life span of the patient. Here, we performed full exome (tumor vs. matching normal), transcriptome, and methylome analysis of 30 pure high-grade DCIS (HG-DCIS) and 10 normal breast epithelial samples. Sixty-two percent of HG-DCIS cases displayed mutations affecting cancer driver genes or potential drivers. Mutations were observed affecting PIK3CA (21% of cases), TP53 (17%), GATA3 (7%), MLL3 (7%) and single cases of mutations affecting CDH1, MAP2K4, TBX3, NF1, ATM, and ARID1A. Significantly, 83% of lesions displayed numerous large chromosomal copy number alterations, suggesting they might precede selection of cancer driver mutations. Integrated pathway-based modeling analysis of RNA-seq data allowed us to identify two DCIS subgroups (DCIS-C1 and DCIS-C2) based on their tumor-intrinsic subtypes, proliferative, immune scores, and in the activity of specific signaling pathways. The more aggressive DCIS-C1 (highly proliferative, basal-like, or ERBB2+) displayed signatures characteristic of activated Treg cells (CD4+/CD25+/FOXP3+) and CTLA4+/CD86+ complexes indicative of a tumor-associated immunosuppressive phenotype. Strikingly, all lesions showed evidence of TP53 pathway inactivation. Similarly, ncRNA and methylation profiles reproduce changes observed postinvasion. Among the most significant findings, we observed upregulation of lncRNA HOTAIR in DCIS-C1 lesions and hypermethylation of HOXA5 and SOX genes. We conclude that most HG-DCIS lesions, in spite of representing a preinvasive stage of tumor progression, displayed molecular profiles indistinguishable from invasive breast cancer. Cancer Res; 75(18); 3980–90. ©2015 AACR.