bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Pragmatic Approach to HIV-1 Drug Resistance Determination in Resource-Limited Settings by Use of a Novel Genotyping Assay Targeting the Reverse Transcriptase-Encoding Region Only
Authors: Aitken Susan C. , Bronze Michelle , Wallis Carole L. , Stuyver Lieven , Steegen Kim , Balinda Sheila , Kityo Cissy , Stevens Wendy , Rinke de Wit Tobias F. , Schuurman Rob 
Published: March 2013

ABSTRACT

In resource-limited settings (RLS), reverse transcriptase (RT) inhibitors form the backbone of first-line treatment regimens. We have developed a simplified HIV-1 drug resistance genotyping assay targeting the region of RT harboring all major RT inhibitor resistance mutation positions, thus providing all relevant susceptibility data for first-line failures, coupled with minimal cost and labor. The assay comprises a one-step RT-PCR amplification reaction, followed by sequencing using one forward and one reverse primer, generating double-stranded coverage of RT amino acids (aa) 41 to 238. The assay was optimized for all major HIV-1 group M subtypes in plasma and dried blood spot (DBS) samples using a panel of reference viruses for HIV-1 subtypes A to D, F to H, and circulating recombinant form 01_AE (CRF01_AE) and applied to 212 clinical plasma samples and 25 DBS samples from HIV-1-infected individuals from Africa and Europe. The assay was subsequently transferred to Uganda and applied locally on clinical plasma samples. All major HIV-1 subtypes could be detected with an analytical sensitivity of 5.00E+3 RNA copies/ml for plasma and DBS. Application of the assay on 212 clinical samples from African subjects comprising subtypes A to D, F to H (rare), CRF01_AE, and CRF02_AG at a viral load (VL) range of 6.71E+2 to 1.00E+7 (median, 1.48E+5) RNA copies/ml was 94.8% (
n
= 201) successful. Application on clinical samples in Uganda demonstrated a comparable success rate. Genotyping of clinical DBS samples, all subtype C with a VL range of 1.02E+3 to 4.49E+5 (median, 1.42E+4) RNA copies/ml, was 84.0% successful. The described assay greatly reduces hands-on time and the costs required for genotyping and is ideal for use in RLS, as demonstrated in a reference laboratory in Uganda and its successful application on DBS samples.
First Case of Pseudoclavibacter bifida Bacteremia in an Immunocompromised Host with Chronic Obstructive Pulmonary Disease (COPD)
Authors: Oyaert Matthijs , De Baere Thierry , Breyne Joke , De Laere Emmanuel , Mariën Stan , Waets Peter , Laffut Wim 
Published: March 2013

ABSTRACT

Pseudoclavibacter
spp. are Gram-positive, aerobic, catalase-positive, coryneform bacteria belonging to the family of
Microbacteriaceae
. Identification of these species with conventional biochemical assays is difficult. This case report of a
Pseudoclavibacter bifida
bacteremia occurring in an immunocompromised host diagnosed with an acute exacerbation of chronic obstructive pulmonary disease, with a lethal outcome, confirms that this organism may be a human pathogen.
Molecular Characterization of Achromobacter Isolates from Cystic Fibrosis and Non-Cystic Fibrosis Patients in Madrid, Spain
Authors: Barrado Laura , Brañas Patricia , Orellana M. Ángeles , Martínez M. Teresa , García Gloria , Otero Joaquín R. , Chaves Fernando 
Published: March 2013

ABSTRACT

Multilocus sequence typing and
nrdA
sequence analysis identified 6 different species or genogroups and 13 sequence types (STs) among 15
Achromobacter
isolates from cystic fibrosis (CF) patients and 7 species or genogroups and 11 STs among 11 isolates from non-CF patients.
Achromobacter xylosoxidans
was the most frequently isolated species among CF patients.
Quantitative PCR for Detection of Shigella Improves Ascertainment of Shigella Burden in Children with Moderate-to-Severe Diarrhea in Low-Income Countries
Authors: Lindsay Brianna , Ochieng John B. , Ikumapayi Usman N. , Toure Aliou , Ahmed Dilruba , Li Shan , Panchalingam Sandra , Levine Myron M. , Kotloff Karen , Rasko David A. , Morris Carolyn R. , Juma Jane , Fields Barry S. , Dione Michel , Malle Dramane , Becker Stephen M. , Houpt Eric R. , Nataro James P. , Sommerfelt Halvor , Pop Mihai , Oundo Joe , Antonio Martin , Hossain Anowar , Tamboura Boubou , Stine O. Colin 
Published: March 2013

ABSTRACTEstimates of the prevalence ofShigellaspp. are limited by the suboptimal sensitivity of current diagnostic and surveillance methods. We used a quantitative PCR (qPCR) assay to detectShigellain the stool samples of 3,533 children aged <59 months from the Gambia, Mali, Kenya, and Bangladesh, with or without moderate-to-severe diarrhea (MSD). We compared the results from conventional culture to those from qPCR for theShigella ipaHgene. Using MSD as the reference standard, we determined the optimal cutpoint to be 2.9 × 104ipaHcopies per 100 ng of stool DNA for set 1 (n= 877). One hundred fifty-eight (18%) specimens yielded >2.9 × 104ipaHcopies. Ninety (10%) specimens were positive by traditional culture forShigella. Individuals with ≥2.9 × 104ipaHcopies have 5.6-times-higher odds of having diarrhea than those with <2.9 × 104ipaHcopies (95% confidence interval, 3.7 to 8.5;P< 0.0001). Nearly identical results were found using an independent set of samples. qPCR detected 155 additional MSD cases with high copy numbers ofipaH, a 90% increase from the 172 cases detected by culture in both samples. Among a subset (n= 2,874) comprising MSD cases and their age-, gender-, and location-matched controls, the fraction of MSD cases that were attributable toShigellainfection increased from 9.6% (n= 129) for culture to 17.6% (n= 262) for qPCR when employing our cutpoint. We suggest that qPCR with a cutpoint of approximately 1.4 × 104ipaHcopies be the new reference standard for the detection and diagnosis of shigellosis in children in low-income countries. The acceptance of this new standard would substantially increase the fraction of MSD cases that are attributable toShigella.
Substitutions T200A and E227A in the Hemagglutinin of Pandemic 2009 Influenza A Virus Increase Lethality but Decrease Transmission
Authors: Martínez-Romero Carles , de Vries Erik , Belicha-Villanueva Alan , Mena Ignacio , Tscherne Donna M. , Gillespie Virginia L. , Albrecht Randy A. , de Haan Cornelis A. M. , García-Sastre Adolfo 
Published: March 2013

ABSTRACT
We report that swine influenza virus-like substitutions T200A and E227A in the hemagglutinin (HA) of the 2009 pandemic influenza virus alter its pathogenesis and transmission. Viral replication is increased in mammalian cells. Infected mice show increased disease as measured by weight loss and lethality. Transmission in ferrets is decreased in the presence of both substitutions, suggesting that amino acids 200T and 227E are adaptive changes in the HA of swine origin influenza viruses associated with increased transmission and decreased pathogenesis.
Rotavirus Prevents the Expression of Host Responses by Blocking the Nucleocytoplasmic Transport of Polyadenylated mRNAs
Authors: Rubio Rosa M. , Mora Silvia I. , Romero Pedro , Arias Carlos F. , López Susana 
Published: March 2013

ABSTRACT
Rotaviruses are the most important agent of severe gastroenteritis in young children. Early in infection, these viruses take over the host translation machinery, causing a severe shutoff of cell protein synthesis while viral proteins are efficiently synthesized. In infected cells, there is an accumulation of the cytoplasmic poly(A)-binding protein in the nucleus, induced by the viral protein NSP3. Here we found that poly(A)-containing mRNAs also accumulate and become hyperadenylated in the nuclei of infected cells. Using reporter genes bearing the untranslated regions (UTRs) of cellular or viral genes, we found that the viral UTRs do not determine the efficiency of translation of mRNAs in rotavirus-infected cells. Furthermore, we showed that while a polyadenylated reporter mRNA directly delivered into the cytoplasm of infected cells was efficiently translated, the same reporter introduced as a plasmid that needs to be transcribed and exported to the cytoplasm was poorly translated. Altogether, these results suggest that nuclear retention of poly(A)-containing mRNAs is one of the main strategies of rotavirus to control cell translation and therefore the host antiviral and stress responses.
Differentiation of Human Fetal Multipotential Neural Progenitor Cells to Astrocytes Reveals Susceptibility Factors for JC Virus
Authors: Ferenczy Michael W. , Johnson Kory R. , Marshall Leslie J. , Monaco Maria Chiara , Major Eugene O. 
Published: March 2013

ABSTRACT
Viral infections of the central nervous system (CNS) are of increasing concern, especially among immunocompromised populations. Rodent models are often inappropriate for studies of CNS infection, as many viruses, including JC virus (JCV) and HIV, cannot replicate in rodent cells. Consequently, human fetal brain-derived multipotential CNS progenitor cells (NPCs) that can be differentiated into neurons, oligodendrocytes, or astrocytes have served as a model in CNS studies. NPCs can be nonproductively infected by JCV, while infection of progenitor-derived astrocytes (PDAs) is robust. We profiled cellular gene expression at multiple times during differentiation of NPCs to PDAs. Several activated transcription factors show commonality between cells of the brain, in which JCV replicates, and lymphocytes, in which JCV is likely latent. Bioinformatic analysis determined transcription factors that may influence the favorable transcriptional environment for JCV in PDAs. This study attempts to provide a framework for understanding the functional transcriptional profile necessary for productive JCV infection.
Generation of Genetically Stable Recombinant Rotaviruses Containing Novel Genome Rearrangements and Heterologous Sequences by Reverse Genetics
Authors: Navarro Aitor , Trask Shane D. , Patton John T. 
Published: March 2013

ABSTRACT

The rotavirus (RV) genome consists of 11 segments of double-stranded RNA (dsRNA). Typically, each segment contains 5′ and 3′ untranslated regions (UTRs) that flank an open reading frame (ORF) encoding a single protein. RV variants with segments of atypical size owing to sequence rearrangements have been described. In many cases, the rearrangement originates from a partial head-to-tail sequence duplication that initiates after the stop codon of the ORF, leaving the protein product of the segment unaffected. To probe the limits of the RV genome to accommodate additional genetic sequence, we used reverse genetics to insert duplications (analogous to synthetic rearrangements) and heterologous sequences into the 3′ UTR of the segment encoding NSP2 (gene 8). The approach allowed the recovery of recombinant RVs that contained sequence duplications (up to 200 bp) and heterologous sequences, including those for FLAG, the hepatitis C virus E2 epitope, and the internal ribosome entry site of cricket paralysis virus. The recombinant RVs grew to high titer (>10
7
PFU/ml) and remained genetically stable during serial passage. Despite their longer 3′ UTRs, rearranged RNAs of recombinant RVs expressed wild-type levels of protein
in vivo
. Competitive growth experiments indicated that, unlike RV segments with naturally occurring sequence duplications, genetically engineered segments were less efficiently packaged into progeny viruses. Thus, features of naturally occurring rearranged segments, other than their increased length, contribute to their enhanced packaging phenotype. Our results define strategies for developing recombinant RVs as expression vectors, potentially leading to next-generation RV vaccines that induce protection against other infectious agents.
Qualitative and Quantitative Analysis of Adenovirus Type 5 Vector-Induced Memory CD8 T Cells: Not as Bad as Their Reputation
Authors: Steffensen Maria Abildgaard , Holst Peter Johannes , Steengaard Sanne Skovvang , Jensen Benjamin Anderschou Holbech , Bartholdy Christina , Stryhn Anette , Christensen Jan Pravsgaard , Thomsen Allan Randrup 
Published: March 2013

ABSTRACTIt has been reported that adenovirus (Ad)-primed CD8 T cells may display a distinct and partially exhausted phenotype. Given the practical implications of this claim, we decided to analyze in detail the quality of Ad-primed CD8 T cells by directly comparing these cells to CD8 T cells induced through infection with lymphocytic choriomeningitis virus (LCMV). We found that localized immunization with intermediate doses of Ad vector induces a moderate number of functional CD8 T cells which qualitatively match those found in LCMV-infected mice. The numbers of these cells may be efficiently increased by additional adenoviral boosting, and, importantly, the generated secondary memory cells cannot be qualitatively differentiated from those induced by primary infection with replicating virus. Quantitatively, DNA priming prior to Ad vaccination led to even higher numbers of memory cells. In this case, the vaccination led to the generation of a population of memory cells characterized by relatively low CD27 expression and high CD127 and killer cell lectin-like receptor subfamily G member 1 (KLRG1) expression. These memory CD8 T cells were capable of proliferating in response to viral challenge and protecting against infection with live virus. Furthermore, viral challenge was followed by sustained expansion of the memory CD8 T-cell population, and the generated memory cells did not appear to have been driven toward exhaustive differentiation. Based on these findings, we suggest that adenovirus-based prime-boost regimens (including Ad serotype 5 [Ad5] and Ad5-like vectors) represent an effective means to induce a substantially expanded, long-lived population of high-quality transgene-specific memory CD8 T cells.
Phylogenetic Considerations in Designing a Broadly Protective Multimeric L2 Vaccine
Authors: Jagu Subhashini , Kwak Kihyuck , Schiller John T. , Lowy Douglas R. , Kleanthous Harold , Kalnin Kirill , Wang Chenguang , Wang Hsu-Kun , Chow Louise T. , Huh Warner K. , Jaganathan Kilvani S. , Chivukula Sudha V. , Roden Richard B. S. 
Published: March 2013

ABSTRACT
While the oncogenic human papillomavirus (HPV) types with the greatest medical impact are clustered within the α9 and α7 species, a significant fraction of cervical cancers are caused by α5, α6, and α11 viruses. Benign genital warts are caused principally by the α10 viruses HPV6 and HPV11. In an effort to achieve broad protection against both cervical cancer- and genital wart-associated types, we produced at high levels in bacteria a multimeric protein (α11-88x8) fusing eight polypeptides corresponding to a protective domain comprising L2 residues ∼11 to 88 derived from HPV6 (α10), HPV16 (α9), HPV18 (α7), HPV31 (α9), HPV39 (α7), HPV51 (α5), HPV56 (α6), and HPV73 (α11) and a truncated derivative with the last three units deleted (α11-88x5). Mice were immunized three times with α11-88x8 or α11-88x5 adjuvanted with alum or the licensed HPV vaccines and challenged intravaginally with HPV6, HPV16, HPV26, HPV31, HPV33, HPV35, HPV45, HPV51, HPV56, HPV58, or HPV59 pseudovirions. The α11-88x5 and α11-88x8 vaccines induced similarly robust protection against each HPV type tested and indistinguishable HPV16-neutralizing antibody titers. Passive transfer of α11-88x8 antisera was protective. Further, rabbit antisera to α11-88x8 and α11-88x5 similarly neutralized native HPV18 virions. These findings suggest that immunologic competition between units is not a significant issue and that it is not necessary to include a unit of L2 derived from each species to achieve broader protection against diverse medically significant HPV types than is achieved with the licensed HPV vaccines.
The Cellular Decapping Activators LSm1, Pat1, and Dhh1 Control the Ratio of Subgenomic to Genomic Flock House Virus RNAs
Authors: Giménez-Barcons Mireia , Alves-Rodrigues Isabel , Jungfleisch Jennifer , Van Wynsberghe Priscilla M. , Ahlquist Paul , Díez Juana 
Published: March 2013

ABSTRACT

Positive-strand RNA viruses depend on recruited host factors to control critical replication steps. Previously, it was shown that replication of evolutionarily diverse positive-strand RNA viruses, such as hepatitis C virus and brome mosaic virus, depends on host decapping activators LSm1-7, Pat1, and Dhh1 (J. Diez et al., Proc. Natl. Acad. Sci. U. S. A. 97:3913–3918, 2000; A. Mas et al., J. Virol. 80:246 –251, 2006; N. Scheller et al., Proc. Natl. Acad. Sci. U. S. A. 106:13517–13522, 2009). By using a system that allows the replication of the insect Flock House virus (FHV) in yeast, here we show that LSm1-7, Pat1, and Dhh1 control the ratio of subgenomic RNA3 to genomic RNA1 production, a key feature in the FHV life cycle mediated by a long-distance base pairing within RNA1. Depletion of
LSM1
,
PAT1
, or
DHH1
dramatically increased RNA3 accumulation during replication. This was not caused by differences between RNA1 and RNA3 steady-state levels in the absence of replication. Importantly, coimmunoprecipitation assays indicated that LSm1-7, Pat1, and Dhh1 interact with the FHV RNA genome and the viral polymerase. By using a strategy that allows dissecting different stages of the replication process, we found that LSm1-7, Pat1, and Dhh1 did not affect the early replication steps of RNA1 recruitment to the replication complex or RNA1 synthesis. Furthermore, their function on RNA3/RNA1 ratios was independent of the membrane compartment, where replication occurs and requires ATPase activity of the Dhh1 helicase. Together, these results support that LSm1-7, Pat1, and Dhh1 control RNA3 synthesis. Their described function in mediating cellular mRNP rearrangements suggests a parallel role in mediating key viral RNP transitions, such as the one required to maintain the balance between the alternative FHV RNA1 conformations that control RNA3 synthesis.
The TobamovirusTurnip Vein Clearing Virus30-Kilodalton Movement Protein Localizes to Novel Nuclear Filaments To Enhance Virus Infection
Authors: Levy Amit , Zheng Judy Y. , Lazarowitz Sondra G. 
Published: March 2013

ABSTRACTPlant viruses overcome the barrier of the plant cell wall by encoding cell-to-cell movement proteins (MPs), which direct newly replicated viral genomes to, and across, the wall. The paradigm for how a single MP regulates and coordinates these activities is theTobacco mosaic virus(TMV) 30-kDa protein (MPTMV). Detailed studies demonstrate that TMV multiplies exclusively in the cytoplasm and have documented associations of MPTMVwith endoplasmic reticulum (ER) membrane, microtubules, and plasmodesmata throughout the course of infection. As TMV poorly infectsArabidopsis thaliana,Turnip vein clearing virus(TVCV) is the tobamovirus of choice for studies in this model plant. A key problem, which has contributed to confusion in the field, is the unproven assumption that the TVCV and TMV life cycles are identical. We engineered an infectious TVCV replicon that expressed a functional fluorescence-tagged MPTVCVand report here the unexpected discovery that MPTVCV, beyond localizing to ER membrane and plasmodesmata, targeted to the nucleus in a nuclear localization signal (NLS)-dependent manner, where it localized to novel F-actin-containing filaments that associated with chromatin. The MPTVCVNLS appeared to be conserved in the subgroup 3 tobamoviruses, and our mutational analyses showed that nuclear localization of MPTVCVwas necessary for efficient TVCV cell-to-cell movement and systemic infection inNicotiana benthamianaandArabidopsis thaliana. Our studies identify a novel nuclear stage in TVCV infection and suggest that nuclear MP encoded by TVCV and other subgroup 3 tobamoviruses interacts with F-actin and chromatin to modulate host defenses or cellular physiology to favor virus movement and infection.
Screening athletes for cardiovascular disease in Africa: a challenging experience
Authors: Schmied Christian , Di Paolo Fernando M , Zerguini A Yacine , Dvorak Jiri , Pelliccia Antonio 
Published: March 2013

AimsPreparticipation cardiovascular (CV) screening has been advocated as an efficient strategy to reduce sudden cardiac death in Caucasian athletes. At present, uncertainty remains if such strategy is feasible and efficient in native African athletes. To this scope, we performed a CV screening in an African setting.Methods210 male Gabonian football players were examined with history, physical examination, ECG and echocardiography.ResultsOn history, 19 players (9%) referred atypical chest discomfort/oppression. Familial sudden death was referred by 36 (17%). No anomalies were detected at physical examination. ECG showed large proportions of ‘training-related’ abnormalities, that is, ST-segment elevation in precordial leads in 150 (71.4%), and isolated increase in R/S-wave voltage in 116 (55.2%). A substantial subset (12.4%) showed ‘training-unrelated’ abnormalities, that is, inverted T-waves in 10 (4.8%), left atrial enlargement in 8 (4%), deep Q-waves in 3 (1.4%). On echocardiography, one athlete meet criteria for hypertrophic cardiomyopathy (HCM); none showed evidence for arrhythmogenic right ventricular cardiomyopathy (ARVC) or dilated cardiomyopathy (DCM). Other abnormalities included mitral valve prolapse in three, atrial septal defect in two and pulmonary hypertension in one.ConclusionsAbout 12% of native African athletes showed ECG abnormalities unrelated to training and requiring additional testing and periodical follow-up. Structural abnormalities were found, however, in a minority (5%), including HCM in one, but no ARVC or DCM. In conclusion, this study demonstrates that preparticipation CV screening is efficient to identify (or raise suspicion) for CV abnormalities in native African athletes, but challenging for conclusive identification of cardiac diseases in the difficult scenario of a developing African country.
Impact of isoniazid preventive therapy on mortality among children less than 5 years old following exposure to tuberculosis at home in Guinea-Bissau: a prospective cohort study
Authors: Gomes Victor Francisco , Andersen Andreas , Lemvik Grethe , Wejse Christian , Oliveira Ines , Vieira Fina J , Carlos Luis José , Vieira Cesaltina da Silva , Aaby Peter , Gustafson Per 
Published: March 2013

ObjectiveIn a cohort of children less than 5 years old exposed to adult intrathoracic tuberculosis (TB) in 1996–1998, we found 66% increased mortality compared with community controls. In 2005, we implemented isoniazid preventive therapy (IPT) for children exposed to TB at home, and the present study evaluates the effect of this intervention on mortality.SettingThis prospective cohort study was conducted in six suburban areas included in the demographic surveillance system of the Bandim Health Project in Bissau, the capital city of Guinea-Bissau.ParticipantsAll children less than 5 years of age and living in the same house as an adult with intrathoracic TB registered for treatment in the study area between 2005 and 2007 were evaluated for inclusion in the IPT programme.Main outcome measures (end points)The all-cause mortality rate ratio (MRR) between exposed children on IPT, exposed without IPT and unexposed community control children.ResultsA total of 1396 children were identified as living in the same houses as 416 adult TB cases; of those, 691 were enrolled in the IPT programme. Compared with community controls, the IPT children had an MRR of 0.30 (95%CI 0.1 to 1.2). The MRR comparing exposed children with and without IPT was 0.21 (0.0 to 1.1). The relative mortality in IPT children compared with community controls in 2005–2008 differed significantly from the relative mortality of exposed untreated children compared with the community controls in 1996–1998 (test of interaction, p=0.01).ConclusionsIn 2005–2008, exposed children on IPT had 70% lower mortality than the community control children, though not significantly. Relative to the community control children, the mortality among TB-exposed children on IPT in 2005–2008 was significantly lower than the mortality among TB-exposed children not on IPT in 1996–1998.