bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic Signature of Multidrug-Resistant Salmonella enterica Serovar Typhi Isolates Related to a Massive Outbreak in Zambia between 2010 and 2012
Authors: Hendriksen Rene S. , Leekitcharoenphon Pimlapas , Lukjancenko Oksana , Lukwesa-Musyani Chileshe , Tambatamba Bushimbwa , Mwaba John , Kalonda Annie , Nakazwe Ruth , Kwenda Geoffrey , Jensen Jacob Dyring , Svendsen Christina A. , Dittmann Karen K. , Kaas Rolf S. , Cavaco Lina M. , Aarestrup Frank M. , Hasman Henrik , Mwansa James C. L. 
Published: November 2014

ABSTRACT

Retrospectively, we investigated the epidemiology of a massive
Salmonella enterica
serovar Typhi outbreak in Zambia during 2010 to 2012. Ninety-four isolates were susceptibility tested by MIC determinations. Whole-genome sequence typing (WGST) of 33 isolates and bioinformatic analysis identified the multilocus sequence type (MLST), haplotype, plasmid replicon, antimicrobial resistance genes, and genetic relatedness by single nucleotide polymorphism (SNP) analysis and genomic deletions. The outbreak affected 2,040 patients, with a fatality rate of 0.5%. Most (83.0%) isolates were multidrug resistant (MDR). The isolates belonged to MLST ST1 and a new variant of the haplotype, H58B. Most isolates contained a chromosomally translocated region containing seven antimicrobial resistance genes,
catA1
,
bla
TEM-1
,
dfrA7
,
sul1
,
sul2
,
strA
, and
strB
, and fragments of the incompatibility group Q1 (IncQ1) plasmid replicon, the class 1 integron, and the
mer
operon. The genomic analysis revealed 415 SNP differences overall and 35 deletions among 33 of the isolates subjected to whole-genome sequencing. In comparison with other genomes of H58, the Zambian isolates separated from genomes from Central Africa and India by 34 and 52 SNPs, respectively. The phylogenetic analysis indicates that 32 of the 33 isolates sequenced belonged to a tight clonal group distinct from other H58 genomes included in the study. The small numbers of SNPs identified within this group are consistent with the short-term transmission that can be expected over a period of 2 years. The phylogenetic analysis and deletions suggest that a single MDR clone was responsible for the outbreak, during which occasional other
S
. Typhi lineages, including sensitive ones, continued to cocirculate. The common view is that the emerging global
S
. Typhi haplotype, H58B, containing the MDR IncHI1 plasmid is responsible for the majority of typhoid infections in Asia and sub-Saharan Africa; we found that a new variant of the haplotype harboring a chromosomally translocated region containing the MDR islands of IncHI1 plasmid has emerged in Zambia. This could change the perception of the term “classical MDR typhoid” currently being solely associated with the IncHI1 plasmid. It might be more common than presently thought that
S
. Typhi haplotype H58B harbors the IncHI1 plasmid or a chromosomally translocated MDR region or both.
Whole-Genome Sequencing Confirms that Burkholderia pseudomallei Multilocus Sequence Types Common to Both Cambodia and Australia Are Due to Homoplasy
Authors: De Smet Birgit , Sarovich Derek S. , Price Erin P. , Mayo Mark , Theobald Vanessa , Kham Chun , Heng Seiha , Thong Phe , Holden Matthew T. G. , Parkhill Julian , Peacock Sharon J. , Spratt Brian G. , Jacobs Jan A. , Vandamme Peter , Currie Bart J. 
Published: November 2014

ABSTRACT

Burkholderia pseudomallei
isolates with shared multilocus sequence types (STs) have not been isolated from different continents. We identified two STs shared between Australia and Cambodia. Whole-genome analysis revealed substantial diversity within STs, correctly identified the Asian or Australian origin, and confirmed that these shared STs were due to homoplasy.
A Taxonomically Unique Acinetobacter Strain with Proteolytic and Hemolytic Activities Recovered from a Patient with a Soft Tissue Injury
Authors: Almuzara Marisa , Traglia German Matías , Krizova Lenka , Barberis Claudia , Montaña Sabrina , Bakai Romina , Tuduri Alicia , Vay Carlos , Nemec Alexandr , Ramírez María Soledad 
Published: November 2014

ABSTRACT

A taxonomically unique bacterial strain,
Acinetobacter
sp. A47, has been recovered from several soft tissue samples from a patient undergoing reconstructive surgery owing to a traumatic amputation. The results of 16S rRNA,
rpoB
, and
gyrB
gene comparative sequence analyses showed that A47 does not belong to any of the hitherto-known taxa and may represent an as-yet-unknown
Acinetobacter
species. The recognition of this novel organism contributes to our knowledge of the taxonomic complexity underlying infections caused by
Acinetobacter
.
Ebola Virus: a Clear and Present Danger
Authors: Burd Eileen M. 
Published: November 2014

ABSTRACT
An epidemic of Ebola virus disease is occurring in Western Africa on a scale not seen before, particularly in the countries of Guinea, Liberia, and Sierra Leone. The continued spread is facilitated by insufficient medical facilities, poor sanitation, travel, and unsafe burial practices. Several patients diagnosed with Ebola virus disease in Africa have been evacuated to the United States for treatment, and several other patients have been diagnosed in the United States. It is important for laboratories to be aware of available tests, especially those granted emergency use authorization, as hospitals prepare protocols for the diagnosis and management of high-risk patients.
Distinct Characteristics of Endometrial and Decidual Macrophages and Regulation of Their Permissivity to HIV-1 Infection by SAMHD1
Authors: Quillay Héloïse , El Costa Hicham , Marlin Romain , Duriez Marion , Cannou Claude , Chrétien Fabrice , Fernandez Hervé , Lebreton Anne , Ighil Julien , Schwartz Olivier , Barré-Sinoussi Françoise , Nugeyre Marie-Thérèse , Menu Elisabeth 
Published: November 2014

ABSTRACT

In order to develop strategies to prevent HIV-1 (human immunodeficiency virus type 1) transmission, it is crucial to better characterize HIV-1 target cells in the female reproductive tract (FRT) mucosae and to identify effective innate responses. Control of HIV-1 infection in the decidua (the uterine mucosa during pregnancy) can serve as a model to study natural mucosal protection. Macrophages are the main HIV-1 target cells in the decidua. Here we report that
in vitro
, macrophages and T cells are the main HIV-1 targets in the endometrium in nonpregnant women. As reported for decidual macrophages (dM), endometrial macrophages (eM) were found to have an M2-like phenotype (CD68
+
CD163
+
CD206
+
IL-10
high
). However, eM and dM may belong to different subpopulations, as they differently express certain markers and secrete different amounts of proinflammatory and anti-inflammatory cytokines. We observed strong expression of the SAMHD1 restriction factor and weak expression of its inactive form (pSAMHD1, phosphorylated at residue Thr592) in both eM and dM. Infection of macrophages from both tissues was enhanced in the presence of the viral protein Vpx, suggesting a role for SAMHD1 in the restriction of HIV-1 infection. This study and further comparisons of the decidua with FRT mucosae in nonpregnant women should help to identify mechanisms of mucosal protection against HIV-1 infection.

IMPORTANCE
The female reproductive tract mucosae are major portals of HIV-1 entry into the body. The decidua (uterine mucosa during pregnancy) can serve as a model for studying natural mucosal protection against HIV-1 transmission. A comparison of target cells and innate responses in the decidua versus the endometrium in nonpregnant women could help to identify protective mechanisms. Here, we report for the first time that macrophages are one of the main HIV-1 target cells in the endometrium and that infection of macrophages from both the endometrium and the decidua is restricted by SAMHD1. These findings might have implications for the development of vaccines to prevent HIV-1 mucosal transmission.
Less Is More: Ebola Virus Surface Glycoprotein Expression Levels Regulate Virus Production and Infectivity
Authors: Mohan Gopi S. , Ye Ling , Li Wenfang , Monteiro Ana , Lin Xiaoqian , Sapkota Bishu , Pollack Brian P. , Compans Richard W. , Yang Chinglai 
Published: November 2014

ABSTRACT

The Ebola virus (EBOV) surface glycoprotein (GP
1,2
) mediates host cell attachment and fusion and is the primary target for host neutralizing antibodies. Expression of GP
1,2
at high levels disrupts normal cell physiology, and EBOV uses an RNA-editing mechanism to regulate expression of the GP gene. In this study, we demonstrate that high levels of GP
1,2
expression impair production and release of EBOV virus-like particles (VLPs) as well as infectivity of GP
1,2
-pseudotyped viruses. We further show that this effect is mediated through two mechanisms. First, high levels of GP
1,2
expression reduce synthesis of other proteins needed for virus assembly. Second, viruses containing high levels of GP
1,2
are intrinsically less infectious, possibly due to impaired receptor binding or endosomal processing. Importantly, proteolysis can rescue the infectivity of high-GP
1,2
-containing viruses. Taken together, our findings indicate that GP
1,2
expression levels have a profound effect on factors that contribute to virus fitness and that RNA editing may be an important mechanism employed by EBOV to regulate GP
1,2
expression in order to optimize virus production and infectivity.

IMPORTANCE
The Ebola virus (EBOV), as well as other members of the
Filoviridae
family, causes severe hemorrhagic fever that is highly lethal, with up to 90% mortality. The EBOV surface glycoprotein (GP
1,2
) plays important roles in virus infection and pathogenesis, and its expression is tightly regulated by an RNA-editing mechanism during virus replication. Our study demonstrates that the level of GP
1,2
expression profoundly affects virus particle production and release and uncovers a new mechanism by which Ebola virus infectivity is regulated by the level of GP
1,2
expression. These findings extend our understanding of EBOV infection and replication in adaptation of host environments, which will aid the development of countermeasures against EBOV infection.
Specificity of Coxsackievirus B3 Interaction with Human, but Not Murine, Decay-Accelerating Factor: Replacement of a Single Residue within Short Consensus Repeat 2 Prevents Virus Attachment
Authors: Pan Jieyan , Zhang Lili , Organtini Lindsey J. , Hafenstein Susan , Bergelson Jeffrey M. 
Published: November 2014

ABSTRACTMany coxsackievirus B (CVB) isolates bind to human decay-accelerating factor (DAF) as well as to the coxsackievirus and adenovirus receptor (CAR). However, the virus does not interact with murine DAF. To understand why CVB3 binds specifically to human DAF, we constructed a series of chimeric molecules in which specific regions of the human DAF molecule were replaced by the corresponding murine sequences. We found that replacement of human short consensus repeat 2 (SCR2) with murine SCR2 ablated virus binding to human DAF, as did deletion of human SCR2. Although replacement of human SCR4 had a partial inhibitory effect, deletion of SCR4 had no effect. Within human SCR2, replacement of serine 104 (S104) with the proline residue found in murine DAF eliminated virus binding. On the basis of the structure of the CVB3-DAF complex determined by cryo-electron microscopy, DAF S104 is in close contact with a viral capsid residue, a threonine at VP1 position 271. Replacement of this capsid residue with larger amino acids specifically eliminated virus attachment to human DAF but had no effect on attachment to CAR or replication in HeLa cells. Taken together, these results support the current model of virus-DAF interaction and point to a specific role for VP1 T271 and DAF S104 at the virus-DAF interface.IMPORTANCEThe results of the present study point to a specific role for VP1 T271 and DAF S104 at the interface between CVB3 and DAF, and they demonstrate how subtle structural changes can dramatically influence virus-receptor interactions. In addition, the results support a recent pseudoatomic model of the CVB3-DAF interaction obtained by cryo-electron microscopy.
Biological and Protective Properties of Immune Sera Directed to the Influenza Virus Neuraminidase
Authors: Halbherr Stefan J. , Ludersdorfer Thomas H. , Ricklin Meret , Locher Samira , Berger Rentsch Marianne , Summerfield Artur , Zimmer Gert 
Published: November 2014

ABSTRACTThe envelope of influenza A viruses contains two large antigens, hemagglutinin (HA) and neuraminidase (NA). Conventional influenza virus vaccines induce neutralizing antibodies that are predominantly directed to the HA globular head, a domain that is subject to extensive antigenic drift. Antibodies directed to NA are induced at much lower levels, probably as a consequence of the immunodominance of the HA antigen. Although antibodies to NA may affect virus release by inhibiting the sialidase function of the glycoprotein, the antigen has been largely neglected in past vaccine design. In this study, we characterized the protective properties of monospecific immune sera that were generated by vaccination with recombinant RNA replicon particles encoding NA. These immune sera inhibited hemagglutination in an NA subtype-specific and HA subtype-independent manner and interfered with infection of MDCK cells. In addition, they inhibited the sialidase activities of various influenza viruses of the same and even different NA subtypes. With this, the anti-NA immune sera inhibited the spread of H5N1 highly pathogenic avian influenza virus and HA/NA-pseudotyped viruses in MDCK cells in a concentration-dependent manner. When chickens were immunized with NA recombinant replicon particles and subsequently infected with low-pathogenic avian influenza virus, inflammatory serum markers were significantly reduced and virus shedding was limited or eliminated. These findings suggest that NA antibodies can inhibit virus dissemination by interfering with both virus attachment and egress. Our results underline the potential of high-quality NA antibodies for controlling influenza virus replication and place emphasis on NA as a vaccine antigen.IMPORTANCEThe neuraminidase of influenza A viruses is a sialidase that acts as a receptor-destroying enzyme facilitating the release of progeny virus from infected cells. Here, we demonstrate that monospecific anti-NA immune sera inhibited not only sialidase activity, but also influenza virus hemagglutination and infection of MDCK cells, suggesting that NA antibodies can interfere with virus attachment. Inhibition of both processes, virus release and virus binding, may explain why NA antibodies efficiently blocked virus disseminationin vitroandin vivo. Anti-NA immune sera showed broader reactivity than anti-HA sera in hemagglutination inhibition tests and demonstrated cross-subtype activity in sialidase inhibition tests. These remarkable features of NA antibodies highlight the importance of the NA antigen for the development of next-generation influenza virus vaccines.
Causes of mortality and unintentional poisoning in predatory and scavenging birds in California
Authors: Kelly Terra R. , Poppenga Robert H. , Woods Leslie A. , Hernandez Yvette Z. , Boyce Walter M. , Samaniego Francisco J. , Torres Steve G. , Johnson Christine K. 
Published: November 2014

ObjectivesWe documented causes of mortality in an opportunistic sample of golden eagles, turkey vultures and common ravens, and assessed exposure to several contaminants that have been found in carrion and common prey for these species.MethodsDead birds were submitted for testing through wildlife rehabilitation centres and a network of wildlife biologists in California from 2007 to 2009.ResultsThe leading causes of mortality in this study were collision‐related trauma (63 per cent), lead intoxication (17 per cent) and anticoagulant rodenticide poisoning (8 per cent). Elevated liver lead concentration (≥2 µg/g) and bone lead concentration (>6 µg/g) were detected in 25 and 49 per cent of birds tested, respectively. Approximately 84 per cent of birds tested had detectable rodenticide residues. The majority of rodenticide exposure occurred in peri‐urban areas, suggesting that retail sale and use of commensal rodent baits, particularly in residential and semi‐residential areas in California, may provide a pathway of exposure.ConclusionsMonitoring anthropogenic causes of mortality in predatory and scavenging bird species provides important data needed to inform on mitigation and regulatory efforts aimed at reducing threats to these populations.
Thrombin generation and low-molecular-weight heparin prophylaxis in pregnant women with thrombophilia
Authors: Selmeczi Anna , Roach Rachel E. J. , Móré Csaba , Batta Zoltán , Hársfalvi Jolán , Bom van der Johanna G. , Boda Zoltán , Oláh Zsolt 
Published: November 2014

SummaryPregnancy is associated with increased risk of venous thromboembolism, especially in the presence of thrombophilia. However, there is no consensus on the optimal approach for thromboprophylaxis in this population. Recent evidence suggests that thrombin generation correlates with the overall procoagulant state of the plasma. Our aim was to evaluate thrombin generation in a prospective cohort of thrombophilic pregnant women, and investigate the effectiveness of low-molecular- weight heparin (LMWH) prophylaxis in pregnancy. Women with severe (n=8), mild (n=47) and no (n=15) thrombophilia were followed throughout their pregnancies. Thrombin generation was evaluated in each trimester as well as five days and eight weeks postpartum (as a reference category). In women undergoing LMWH prophylaxis, thrombin generation and anti-Factor-Xa activity were measured just before and 4 hours after administration (peak effect). Thrombin generation was determined using Technothrombin TGA assay system. For the analysis, median peak thrombin and endogenous thrombin potential were used. Peak thrombin and endogenous thrombin potential were increased during pregnancy compared to the non-pregnant state with the highest results in the severe thrombophilia group. In women receiving LMWH prophylaxis a decrease was observed in thrombin generation at peak effect but over the progression of pregnancy the extent of this decrease reduced in a stepwise fashion. Our results show that thrombin generation demonstrates the hypercoagulable state in thrombophilic pregnancies. In addition, we found the effect of LMWH prophylaxis to progressively decrease with advancing stages of pregnancy.
Serum NOX2 and urinary isoprostanes predict vascular events in patients with atrial fibrillation
Authors: Carnevale Roberto , Farcomeni Alessio , Cangemi Roberto , Nocella Cristina , Bartimoccia Simona , Vicario Tommasa , Saliola Mirella , Lip Gregory , Pignatelli Pasquale , Pastori Daniele , Violi Francesco 
Published: November 2014

SummaryThere are limited prospective data evaluating the role of urinary F2-IsoP and NOX2 as predictive markers in atrial fibrillation (AF). The aim of this study was to analyse the role of urinary prostaglandin PGF2alpha (8-iso-PGF2α) and NOX2, markers of systemic oxidative stress, in predicting cardiovascular (CV) events and mortality in anticoagulated non-valvular AF patients. This was a prospective study including 1,002 anticoagulated AF patients, followed for a median time of 25.7 months (interquartile range: 14.8–50.9). All major CV events, CV deaths and all-cause deaths were considered as primary outcomes of the study. CV events included fatal/nonfatal ischaemic stroke, fatal/ nonfatal myocardial infarction (MI), cardiac revascularisation and transient ischaemic attack (TIA). Oxidative stress biomarkers, such as urinary 8-iso-PGF2α and serum sNOX2-dp, a marker of NOX2 activation, were measured. A CV event occurred in 125 patients (12.5 %); 78 CV deaths and 31 non-CV deaths were registered. 8-iso-PGF2α and sNOX2-dp were correlated (Rs=0.765 p> 0.001). A significant increased cumulative incidence of CV events and CV deaths was observed across tertiles for 8-iso-PGF2α and sNOX2-dp. An increased rate of all-cause death was observed across tertiles of urinary 8-iso-PGF2α.In Cox or Fine and Gray models, 8-iso-PGF2α predicted CV events and CV and non-CV deaths. The addition of tertiles of 8-iso-PGF2α to CHA2DS2-VASc score improved ROC curves for each outcome and NRI for CV events (0.24 [0.06–0.53] p=0.0067). The study shows that in AF patients 8-iso-PGF2α and NOX2 levels are predictive of CV events and total mortality. F2-IsoP may complement conventional risk factors in prediction of CV events.Note: The review process for this manuscript was fully handled by Christian Weber, Editor in Chief. Clinical Trial Registration: ClinicalTrials.gov NCT01882114.
A dissolved oxygen dressing: A pilot study in an ischemic skin flap model
Authors: Zellner Susan , Manabat Rowena , Roe David F 
Published: November 2014

Objectives To determine if skin flap failure rates could be improved with the use of a dissolved oxygen wound dressing in a porcine model. Methods Full-thickness skin flaps (4 × 16 cm) were raised on pigs. Flaps were randomly assigned after surgery to experimental treatment with a dissolved oxygen dressing (treatment group) or a hydrogel dressing (control group). Flaps were evaluated daily for 14 days. Skin flaps that failed any one of four key clinical outcomes were considered failures. Histological parameters (including skin and subcutaneous necrosis, inflammation, ischemia, fibrosis, and bacterial load) were compared by a blinded histopathologist. Results Sixteen full-thickness skin flaps were raised on four pigs. All animals survived surgery and all incisions were evaluable. Clinical flap failure was observed in six (75%) control-treated wounds and in two (25%) dissolved oxygen-treated wounds. Histological evaluation demonstrated no significant differences in the proximal 75% of the flaps. There were significant differences in a number of histological parameters in the distal 25% in favor of the dissolved oxygen dressing. Conclusions Flaps treated with a dissolved oxygen dressing had fewer clinical failures and improved histological profiles compared with control-treated flaps, suggesting that increasing local oxygen supply may improve the local wound healing environment.
Evaluating the progress of the UK’s Material Recycling Facilities: A mini review
Authors: Ali Muhammad , Courtenay Peter 
Published: November 2014

Over the last 15 years, the UK has made great strides in reducing the amount of waste being sent to landfill while also increasing the amount of waste being recycled. The key drivers for this change are the European Union Landfill Directive (1999/31/EC) and the UK Landfill Tax. However, also playing their part are the growing numbers of Material Recycling Facilities (MRFs), which process recyclables. This mini review evaluates the current state of MRFs in the UK, through extensive secondary research, and detailed primary data analysis focussing on MRFs located in South-East England, UK. This study also explores technologies that aim to generate energy from waste, including Waste-to-Energy (WtE) and Refuse-derived Fuel (RDF) facilities. These facilities can have a huge appetite for waste, which can be detrimental to recycling efforts as some of the waste being sent there should be recycled. It was found that the waste sent to a typical UK MRF would recycle around 92% of materials while 6% was sent to energy recovery and the remaining 2% ended up in landfill. Therefore, the total estimated rejected or non-compliance materials from MRFs are around 8%. A key recommendation from this study is to adopt a strategy to combine MRFs with a form of energy generation, such as WtE or RDF. This integrated approach would ensure any residual waste arising from the recycling process can be used as a sustainable fuel, while also increasing the recycling rates.