bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring Alternative Biomaterials for Diagnosis of Pulmonary Tuberculosis in HIV-Negative Patients by Use of the GeneXpert MTB/RIF Assay
Authors: Shenai Shubhada , Amisano Danielle , Ronacher Katharina , Kriel Magdalena , Banada Padmapriya P. , Song Taeksun , Lee Myungsun , Joh Joon Sung , Winter Jill , Thayer Rich , Via Laura E. , Kim Soyeon , Barry Clifton E. , Walzl Gerhard , Alland David 
Published: October 2013

ABSTRACT

The utility of the GeneXpert MTB/RIF (Xpert) assay for detection of
Mycobacterium tuberculosis
in sputum samples has been extensively studied. However, the performance of the Xpert assay as applied to other readily accessible body fluids such as exhaled breath condensate (EBC), saliva, urine, and blood has not been established. We used the Xpert assay to test EBC, saliva, urine, and blood samples from HIV-negative, smear- and culture-positive pulmonary tuberculosis (TB) patients for the presence of
M. tuberculosis
. To compare the ability of the assay to perform bacterial load measurements on sputum samples with versus without sample processing, the assay was also performed on paired direct and processed sputum samples from each patient. The Xpert assay detected
M. tuberculosis
in none of the 26 EBC samples (sensitivity, 0.0%; 95% confidence interval [95% CI], 0.0%, 12.9%), 10 of the 26 saliva samples (sensitivity, 38.5%; 95% CI, 22.4%, 57.5%), 1 of 26 urine samples (sensitivity, 3.8%; 95% CI, 0.7%, 18.9%), and 2 of 24 blood samples (sensitivity, 8.3%; 95% CI, 2.3%, 25.8%). For bacterial load measurements in the different types of sputum samples, the cycle thresholds of the two
M. tuberculosis
-positive sputum types were well correlated (Spearman correlation of 0.834). This study demonstrates that the Xpert assay should not be routinely used to detect
M. tuberculosis
in EBC, saliva, urine, or blood samples from HIV-negative patients suspected of having pulmonary tuberculosis. As a test of bacterial load, the assay produced similar results when used to test direct versus processed sputum samples. Sputum remains the optimal sample type for diagnosing pulmonary tuberculosis in HIV-negative patients with the Xpert assay.
Epidemiology, Species Distribution, Antifungal Susceptibility, and Outcome of Candidemia across Five Sites in Italy and Spain
Authors: Bassetti Matteo , Merelli Maria , Righi Elda , Diaz-Martin Ana , Rosello Eva Maria , Luzzati Roberto , Parra Anna , Trecarichi Enrico Maria , Sanguinetti Maurizio , Posteraro Brunella , Garnacho-Montero Jose , Sartor Assunta , Rello Jordi , Tumbarello Mario 
Published: October 2013

ABSTRACT

Candidemia has become an important bloodstream infection that is frequently associated with high rates of mortality and morbidity, and its growing incidence is related to complex medical and surgical procedures. We conducted a multicenter study in five tertiary care teaching hospitals in Italy and Spain and evaluated the epidemiology, species distribution, antifungal susceptibilities, and outcomes of candidemia episodes. In the period of 2008 to 2010, 995 episodes of candidemia were identified in these hospitals. The overall incidence of candidemia was 1.55 cases per 1,000 admissions and remained stable during the 3-year analysis.
Candida albicans
was the leading agent of infection (58.4%), followed by
Candida parapsilosis
complex (19.5%),
Candida tropicalis
(9.3%), and
Candida glabrata
(8.3%). The majority of the candidemia episodes were found in the internal medicine department (49.6%), followed by the surgical ward, the intensive care unit (ICU), and the hemato-oncology ward. Out of 955 patients who were eligible for evaluation, 381 (39.9%) died within 30 days from the onset of candidemia. Important differences in the 30-day mortality rates were noted between institutions: the lowest mortality rate was in the Barcelona hospital, and the highest rate was in the Udine hospital (33.6% versus 51%, respectively;
P
= 0.0005). Overall, 5.1% of the 955 isolates tested were resistant or susceptible dose dependent (SDD) to fluconazole, with minor differences between the hospitals in Italy and Spain (5.7% versus 3.5%, respectively;
P
= 0.2). Higher MICs for caspofungin were found, especially with
C. parapsilosis
complex (MIC
90
, 1 μg/ml). Amphotericin B had the lowest MICs. This report shows that candidemia is a significant source of morbidity in Europe, causing a substantial burden of disease and mortality.
Aspergillus PCR-Based Investigation of Fresh Tissue and Effusion Samples in Patients with Suspected Invasive Aspergillosis Enhances Diagnostic Capabilities
Authors: Reinwald M. , Spiess B. , Heinz W. J. , Heussel C. P. , Bertz H. , Cornely O. A. , Hahn J. , Lehrnbecher T. , Kiehl M. , Laws H. J. , Wolf H. H. , Schwerdtfeger R. , Schultheis B. , Burchardt A. , Klein M. , Dürken M. , Claus B. , Schlegel F. , Hummel M. , Hofmann W.-K. , Buchheidt D. 
Published: October 2013

ABSTRACTAlthough it is a severe complication in immunocompromised patients, diagnosing invasive fungal disease (IFD), especially invasive aspergillosis (IA), remains difficult. In certain clinical scenarios, examining tissue samples for identification of the infectious organism becomes important. As culture-based methods rarely yield results, the performance of anAspergillus-specific nested PCR in fresh tissue or pleural effusion samples was evaluated. Fresh tissue (n= 59) and effusion (n= 47) specimens from 79 immunocompromised patients were subjected to anAspergillus-specific PCR assay. Twenty-six patients had proven (n= 20) or probable (n= 6) IFD, according to the European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) criteria, while the remaining patients were classified as having either possible IFD (n= 30) or no IFD (n= 23). IA was identified as the underlying IFD in 21/26 proven/probable cases. PCR positivity was observed for 18/21 proven/probable and 6 possible IA cases; cases classified as no IA did not show positive signals. Patients with proven IFD (n= 5) with cultures positive for non-Aspergillusmolds also had negativeAspergillusPCR results.AspergillusPCR performance analysis yielded sensitivity and specificity values of 86% (95% confidence interval [CI], 65% to 95%) and 100% (95% CI, 86% to 100%), respectively, thus leading to a diagnostic odds ratio of >200. In this analysis, good diagnostic performance of the PCR assay for detection of IA was observed for tissue samples, while effusion samples showed lower sensitivity rates. PCR testing represents a complementary tool; a positive PCR result strengthens the likelihood of IA, whereas IA seems unlikely in cases with negative results but findings could indicate non-AspergillusIFD. Thus, PCR testing of these specimens enhances the diagnostic capabilities.
Sensitivity, Specificity, and Reproducibility of the Capilia TB-Neo Assay
Authors: Muyoyeta Monde , Mwanza Winnie C. , Kasese Nkatya , Cheeba-Lengwe Maina , Moyo Maureen , Kaluba-Milimo Deborah , Ayles Helen 
Published: October 2013

ABSTRACT
The performance of the Capilia TB-Neo assay, a new-generation assay, was assessed by determining its sensitivity, specificity, reproducibility, and cross-reaction with contaminating organisms. The sensitivity and specificity were 99.2 and 96.4% and 89.3 and 100% in pure and mixed-culture isolates, respectively. The kappa statistic was 95.0 and 77.9% in pure and mixed culture isolates, respectively. There was no cross-reaction with contaminating organisms.
Effect of Multimerization on Membrane Association of Rous Sarcoma Virus and HIV-1 Matrix Domain Proteins
Authors: Dick Robert A. , Kamynina Elena , Vogt Volker M. 
Published: October 2013

ABSTRACT

In most retroviruses, plasma membrane (PM) association of the Gag structural protein is a critical step in viral assembly, relying in part on interaction between the highly basic Gag MA domain and the negatively charged inner leaflet of the PM. Assembly is thought to begin with Gag dimerization followed by multimerization, resulting in a hexameric lattice. To directly address the role of multimerization in membrane binding, we fused the MA domains of Rous sarcoma virus (RSV) and HIV-1 to the chemically inducible dimerization domain FK506-binding protein (FKBP) or to the hexameric protein CcmK4 from cyanobacteria. The cellular localization of the resulting green fluorescent protein (GFP)-tagged chimeric proteins was examined by fluorescence imaging, and the association of the proteins with liposomes was quantified by flotation in sucrose gradients, following synthesis in a reticulocyte extract or as purified proteins. Four lipid compositions were tested, representative of liposomes commonly reported in flotation experiments. By themselves, GFP-tagged RSV and HIV-1 MA proteins were largely cytoplasmic, but both hexamerized proteins were highly concentrated at the PM. Dimerization led to partial PM localization for HIV-1 MA. These
in vivo
effects of multimerization were reproduced
in vitro
. In flotation analyses, the intact RSV and HIV-1 Gag proteins were more similar to multimerized MA than to monomeric MA. RNA is reported to compete with acidic liposomes for HIV-1 Gag binding, and thus we also examined the effects of RNase treatment or tRNA addition on flotation. tRNA competed with liposomes in the case of some but not all lipid compositions and ionic strengths. Taken together, our results further underpin the model that multimerization is critical for PM association of retroviral Gag proteins. In addition, they suggest that the modulation of membrane binding by RNA, as previously reported for HIV-1, may not hold for RSV.
HSP90 Protects the Human T-Cell Leukemia Virus Type 1 (HTLV-1) Tax Oncoprotein from Proteasomal Degradation To Support NF-κB Activation and HTLV-1 Replication
Authors: Gao Linlin , Harhaj Edward William 
Published: October 2013

ABSTRACT
Human T-cell leukemia virus type 1 (HTLV-1) is the causative agent of adult T-cell leukemia (ATL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). The HTLV-1 genome encodes the Tax protein that plays essential regulatory roles in HTLV-1 replication and oncogenic transformation of T lymphocytes. Despite intensive study of Tax, how Tax interfaces with host signaling pathways to regulate virus replication and drive T-cell proliferation and immortalization remains poorly understood. To gain new insight into the mechanisms of Tax function and regulation, we used tandem affinity purification and mass spectrometry to identify novel cellular Tax-interacting proteins. This screen identified heat shock protein 90 (HSP90) as a new binding partner of Tax. The interaction between HSP90 and Tax was validated by coimmunoprecipitation assays, and colocalization between the two proteins was observed by confocal microscopy. Treatment of HTLV-1-transformed cells with the HSP90 inhibitor 17-DMAG elicited proteasomal degradation of Tax in the nuclear matrix with concomitant inhibition of NF-κB and HTLV-1 long terminal repeat (LTR) activation. Knockdown of HSP90 by lentiviral shRNAs similarly provoked a loss of Tax protein in HTLV-1-transformed cells. Finally, treatment of HTLV-1-transformed cell lines with 17-DMAG suppressed HTLV-1 replication and promoted apoptotic cell death. Taken together, our results reveal that Tax is a novel HSP90 client protein and HSP90 inhibitors may exert therapeutic benefits for ATL and HAM/TSP patients.
Merkel Cell Polyomavirus Small T Antigen Targets the NEMO Adaptor Protein To Disrupt Inflammatory Signaling
Authors: Griffiths David A. , Abdul-Sada Hussein , Knight Laura M. , Jackson Brian R. , Richards Kathryn , Prescott Emma L. , Peach A. Howard S. , Blair G. Eric , Macdonald Andrew , Whitehouse Adrian 
Published: October 2013

ABSTRACT
Merkel cell carcinoma (MCC) is a highly aggressive nonmelanoma skin cancer arising from epidermal mechanoreceptor Merkel cells. In 2008, a novel human polyomavirus, Merkel cell polyomavirus (MCPyV), was identified and is strongly implicated in MCC pathogenesis. Currently, little is known regarding the virus-host cell interactions which support virus replication and virus-induced mechanisms in cellular transformation and metastasis. Here we identify a new function of MCPyV small T antigen (ST) as an inhibitor of NF-κB-mediated transcription. This effect is due to an interaction between MCPyV ST and the NF-κB essential modulator (NEMO) adaptor protein. MCPyV ST expression inhibits IκB kinase α (IKKα)/IKKβ-mediated IκB phosphorylation, which limits translocation of the NF-κB heterodimer to the nucleus. Regulation of this process involves a previously undescribed interaction between MCPyV ST and the cellular phosphatase subunits, protein phosphatase 4C (PP4C) and/or protein phosphatase 2A (PP2A) Aβ, but not PP2A Aα. Together, these results highlight a novel function of MCPyV ST to subvert the innate immune response, allowing establishment of early or persistent infection within the host cell.
The Cytoprotective Enzyme Heme Oxygenase-1 Suppresses Ebola Virus Replication
Authors: Hill-Batorski Lindsay , Halfmann Peter , Neumann Gabriele , Kawaoka Yoshihiro 
Published: October 2013

ABSTRACT
Ebola virus (EBOV) is the causative agent of a severe hemorrhagic fever in humans with reported case fatality rates as high as 90%. There are currently no licensed vaccines or antiviral therapeutics to combat EBOV infections. Heme oxygenase-1 (HO-1), an enzyme that catalyzes the rate-limiting step in heme degradation, has antioxidative properties and protects cells from various stresses. Activated HO-1 was recently shown to have antiviral activity, potently inhibiting the replication of viruses such as hepatitis C virus and human immunodeficiency virus. However, the effect of HO-1 activation on EBOV replication remains unknown. To determine whether the upregulation of HO-1 attenuates EBOV replication, we treated cells with cobalt protoporphyrin (CoPP), a selective HO-1 inducer, and assessed its effects on EBOV replication. We found that CoPP treatment, pre- and postinfection, significantly suppressed EBOV replication in a manner dependent upon HO-1 upregulation and activity. In addition, stable overexpression of HO-1 significantly attenuated EBOV growth. Although the exact mechanism behind the antiviral properties of HO-1 remains to be elucidated, our data show that HO-1 upregulation does not attenuate EBOV entry or budding but specifically targets EBOV transcription/replication. Therefore, modulation of the cellular enzyme HO-1 may represent a novel therapeutic strategy against EBOV infection.
Fatal Measles Virus Infection Prevented by Brain-Penetrant Fusion Inhibitors
Authors: Welsch Jeremy C. , Talekar Aparna , Mathieu Cyrille , Pessi Antonello , Moscona Anne , Horvat Branka , Porotto Matteo 
Published: October 2013

ABSTRACTMeasles virus (MV) infection causes an acute childhood disease that can include infection of the central nervous system and can rarely progress to severe neurological disease for which there is no specific treatment. We generated potent antiviral peptide inhibitors of MV entry and spreading and MV-induced cell fusion. Dimers of MV-specific peptides derived from the C-terminal heptad repeat region of the MV fusion protein, conjugated to cholesterol, efficiently protect SLAM transgenic mice from fatal MV infection. Fusion inhibitors hold promise for the prophylaxis of MV infection in unvaccinated and immunocompromised people, as well as potential for the treatment of grave neurological complications of measles.
NFX1-123 and Human Papillomavirus 16E6 Increase Notch Expression in Keratinocytes
Authors: Vliet-Gregg Portia A. , Hamilton Jennifer R. , Katzenellenbogen Rachel A. 
Published: October 2013

ABSTRACT
The high-risk human papillomavirus (HR HPV) E6 oncoprotein binds host cell proteins to dysregulate multiple regulatory pathways, including apoptosis and senescence. HR HPV16 E6 (16E6) interacts with the cellular protein NFX1-123, and together they posttranscriptionally increase hTERT expression, the catalytic subunit of telomerase. NFX1-123 interacts with hTERT mRNA and stabilizes it, leading to greater telomerase activity and the avoidance of cellular senescence. Little is known regarding what other transcripts are dependent on or augmented by the association of NFX1-123 with 16E6. Microarray analysis revealed enhanced expression of Notch1 mRNA in 16E6-expressing keratinocytes when NFX1-123 was overexpressed. A moderate increase in Notch1 mRNA was seen with overexpression of NFX1-123 alone, but with 16E6 coexpression the increase in Notch1 was enhanced. The PAM2 motif and R3H protein domains in NFX1-123, which were important for increased hTERT expression, were also important in the augmentation of Notch1 expression by 16E6. These findings identify a second gene coregulated by 16E6 and NFX1-123 and the protein motifs in NFX1-123 that are important for this effect.
Human Coronavirus OC43 Nucleocapsid Protein Binds MicroRNA 9 and Potentiates NF-κB Activation
Authors: Lai Frances W. , Stephenson Kyle B. , Mahony James , Lichty Brian D. 
Published: October 2013

ABSTRACT
The human coronavirus OC43 is a major contributor to the common cold worldwide, though due to its low mortality rate, little research has focused on this human pathogen. The nucleocapsid is an essential structural protein with conserved functions across the coronavirus family. While a multitude of studies have examined nucleocapsid function, none have described the effects of OC43 nucleocapsid on the transcription factor NF-κB. We report that the nucleocapsid protein of OC43 causes potentiation of NF-κB activation. This prolonged activation is the direct result of the ability of the nucleocapsid to bind RNA, specifically microRNA 9 (miR-9), which is a negative regulator of NF-κB. This previously undescribed interaction between virus and host is a potential mechanism of immune evasion in RNA viruses.
Reversible Inactivation and Desiccation Tolerance of Silicified Viruses
Authors: Laidler James R. , Shugart Jessica A. , Cady Sherry L. , Bahjat Keith S. , Stedman Kenneth M. 
Published: October 2013

ABSTRACT

Long-distance host-independent virus dispersal is poorly understood, especially for viruses found in isolated ecosystems. To demonstrate a possible dispersal mechanism, we show that bacteriophage T4, archaeal virus
Sulfolobus
spindle-shaped virus Kamchatka, and vaccinia virus are reversibly inactivated by mineralization in silica under conditions similar to volcanic hot springs. In contrast, bacteriophage PRD1 is not silicified. Moreover, silicification provides viruses with remarkable desiccation resistance, which could allow extensive aerial dispersal.
Risk of fatal unintentional injuries in children by migration status: a nationwide cohort study with 46 years’ follow-up
Authors: Karimi Najmeh , Beiki Omid , Mohammadi Reza 
Published: October 2013

BackgroundInjuries are responsible for much child and adolescent mortality in the world.ObjectiveTo study the effect of parental birth country on the risk of fatal unintentional injuries.MethodsWe established a cohort by linkages between Swedish national registers through personal identification number. The main variable was country of birth of parents. Children with both parents born in Sweden were the reference group. The cohort was followed up from the starting date of the study (1 January 1961) or date of birth, whichever occurred last, until the exit date, which was death due to unintentional injury, first emigration or end of the follow-up (31 December 2007), whichever came first. We calculated HRs with 95% CIs adjusted for age at exit, parental education and calendar period of birth by Cox proportional hazards models.ResultsWe found a significantly higher risk of fatal unintentional injuries among children with a foreign background than among native children. We found a higher risk of fatal transportation-related injuries and drowning among boys with a foreign background and a higher risk of fatal burns/fire and falls among girls with a foreign background than among same sex native children. We also found a higher risk of fatal unintentional injuries among children with a foreign background at older ages than among native children at the same ages.ConclusionsInjury prevention work against unintentional injuries among children of foreign origin is more complex than that among native children. We recommend designing specific studies to find out the factors responsible and planning preventive interventions aiming at this particular group of children with a foreign background.
Four cases of solitary fibrous tumour of the eye and orbit: one with sarcomatous transformation after radiotherapy and one in a 5-year-old child’s eyelid
Authors: Blandamura Stella , Alaggio Rita , Bettini Giordana , Guzzardo Vincenza , Valentini Elisa , Bedogni Alberto 
Published: October 2013

BackgroundSolitary fibrous tumour (SFT) is quite a rare neoplasm involving the eye and the orbit. It is described as showing benign behaviour in adults, but malignant cases are exceptionally reported in this location. This report describes four new cases of SFT/giant cell angiofibroma (GCA) of the eyelid and orbit, one in a 5-year-old child, and one with sarcomatous dedifferentiated transformation occurring 9 years after radiotherapy.MethodsFour cases of ocular SFT/GCA were retrieved from the database of the Pathological Anatomy Unit, University of Padova; immunohistochemistry and RT-PCR were used to identify COL1A1—PDBGF fusion gene transcripts in all cases.ResultsIn case 1, late relapse 9 years later was characterised by abrupt transition into a high-grade component, associated with a non-distinctive high-grade sarcomatous area. The latter component was CD34, CD99 and Bcl2 negative and smooth muscle actin positive. Molecular characterisation showed the absence of COL1A1-PDGFB fusion transcripts in cases 1, 3 and 4, excluded diagnosis of giant cell fibroblastoma in all cases. Analysis could not be performed in case 2.ConclusionsAn eyelid SFT/GCA in a 5-year-old child is the youngest case reported in the literature, indicating that the tumour is not exclusive to adults. The case with sarcomatous transformation, with dedifferentiated features occurring 9 years after radiotherapy, raises some questions about the choice of treatment for ocular SFT, in which excision is sometimes difficult without devastating surgery.