bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeting the Treponemal Microbiome of Digital Dermatitis Infections by High-Resolution Phylogenetic Analyses and Comparison with Fluorescent
In Situ
Hybridization
Authors: Klitgaard Kirstine , Foix Bretó Antoni , Boye Mette , Jensen Tim K. 
Published: May 2013

ABSTRACT

Modern pyrosequencing technology allows for a more comprehensive approach than traditional Sanger sequencing for elucidating the etiology of bovine digital dermatitis. We sought to describe the composition and diversity of treponemes in digital dermatitis lesions by using deep sequencing of the V3 and V4 hypervariable regions of the 16S rRNA gene coupled with species-level taxonomic identification.
Treponema
-specific 16S rRNA gene PCRs and pyrosequencing were performed on biopsy specimens originating from 10 different Catalan dairy herds (
n
= 36) with digital dermatitis, and this analysis yielded 75,297 sequences. We identified 20 different taxa, including a potentially novel phylotype that displayed 95% sequence identity to members of the
Treponema denticola
/
Treponema pedis
-like cluster. Species frequencies and abundances that were determined by pyrosequencing analysis were highly correlated with the results of fluorescent
in situ
hybridization using phylotype-specific oligonucleotide probes. In a limited number of animals from a single geographic region, we detected most of the
Treponema
phylotypes that were described in previous investigations of digital dermatitis. Additionally, we identified a number of phylotypes that mapped to oral treponemes of humans and dogs that had not been reported for digital dermatitis lesions. The results presented here support previous observations of a polytreponemal etiology of infections, with
Treponema phagedenis
-like,
Treponema medium
/
Treponema vincentii
-like, and
T. denticola
/
T. pedis
-like phylotypes being highly associated with disease. Using this new approach, it has become feasible to study large herds and their surrounding environments, which might provide a basis for a better understanding of the pathogenesis of this disease.
Highly Sensitive Detection of Hepatitis B Virus Surface Antigen by Use of a Semiautomated Immune Complex Transfer Chemiluminescence Enzyme Immunoassay
Authors: Takeda Kazuhiko , Maruki Mari , Yamagaito Takahiro , Muramatsu Machiko , Sakai Yasuhiro , Tobimatsu Hiroaki , Kobayashi Hironori , Mizuno Yoshiteru , Hamaguchi Yukio 
Published: May 2013

ABSTRACT
The performance of hepatitis B surface antigen (HBsAg) screening assays is continuously improved to reduce the risk of transfusion-associated hepatitis B. In this study, a semiautomated immune complex transfer chemiluminescence enzyme immunoassay (ICT-CLEIA) for the detection of HBsAg, which is as sensitive as hepatitis B virus (HBV) DNA PCR, was developed; the ICT-CLEIA assay performance was compared with the performance of the Architect HBsAg QT assay and HBV DNA PCR. The specificities in the initial assay and after retesting were 99.50% (1,988/1,998 samples) and 99.95% (1,997/1,998 samples), respectively. The analytical detection limit was determined to be 0.2 mIU/ml using the 2nd International WHO HBsAg standard, and the cutoff value (0.5 mIU/ml) of the ICT-CLEIA assay was 8.0 standard deviations (SD) above the mean of the HBsAg-negative specimens. The ICT-CLEIA assay could detect HBsAg even in the presence of anti-HBs antibodies and demonstrated a 23.6-day-shorter window period using commercially available HBsAg seroconversion panels than the Architect HBsAg QT assay. Furthermore, the monitoring of the viral kinetics by the ICT-CLEIA assay and the HBV DNA PCR produced very similarly shaped curves during both the HBsAg seroconversion and reverse seroconversion periods. Therefore, the ICT-CLEIA assay may be useful not only for an earlier detection of HBV reactivation but also for the monitoring of hepatitis B patients.
Rapid Molecular Microbiologic Diagnosis of Prosthetic Joint Infection
Authors: Cazanave Charles , Greenwood-Quaintance Kerryl E. , Hanssen Arlen D. , Karau Melissa J. , Schmidt Suzannah M. , Gomez Urena Eric O. , Mandrekar Jayawant N. , Osmon Douglas R. , Lough Lindsay E. , Pritt Bobbi S. , Steckelberg James M. , Patel Robin 
Published: May 2013

ABSTRACT

We previously showed that culture of samples obtained by prosthesis vortexing and sonication was more sensitive than tissue culture for prosthetic joint infection (PJI) diagnosis. Despite improved sensitivity, culture-negative cases remained; furthermore, culture has a long turnaround time. We designed a genus-/group-specific rapid PCR assay panel targeting PJI bacteria and applied it to samples obtained by vortexing and sonicating explanted hip and knee prostheses, and we compared the results to those with sonicate fluid and periprosthetic tissue culture obtained at revision or resection arthroplasty. We studied 434 subjects with knee (
n
= 272) or hip (
n
= 162) prostheses; using a standardized definition, 144 had PJI. Sensitivities of tissue culture, of sonicate fluid culture, and of PCR were 70.1, 72.9, and 77.1%, respectively. Specificities were 97.9, 98.3, and 97.9%, respectively. Sonicate fluid PCR was more sensitive than tissue culture (
P
= 0.04). PCR of prosthesis sonication samples is more sensitive than tissue culture for the microbiologic diagnosis of prosthetic hip and knee infection and provides same-day PJI diagnosis with definition of microbiology. The high assay specificity suggests that typical PJI bacteria may not cause aseptic implant failure.
Predictive Value of Molecular Drug Resistance Testing of Mycobacterium tuberculosis Isolates in Valle del Cauca, Colombia
Authors: Ferro Beatriz E. , García Pamela K. , Nieto Luisa Maria , van Soolingen Dick 
Published: May 2013

ABSTRACT

Previous evaluations of the molecular GenoType tests have promoted their use to detect resistance to first- and second-line antituberculosis drugs in different geographical regions. However, there are known geographic variations in the mutations associated with drug resistance in
Mycobacterium tuberculosis
, and especially in South America, there is a paucity of information regarding the frequencies and types of mutations associated with resistance to first- and second-line antituberculosis drugs. We therefore evaluated the performance of the GenoType kits in this region by testing 228
M. tuberculosis
isolates in Colombia, including 134 resistant and 94 pansusceptible strains. Overall, the sensitivity and specificity of the GenoType MTBDR
plus
test ranged from 92 to 96% and 97 to 100%, respectively; the agreement index was optimal (Cohen's kappa, >0.8). The sensitivity of the GenoType MTBDR
sl
test ranged from 84 to 100% and the specificity from 88 to 100%. The most common mutations were
katG
S315T1,
rpoB
S531L,
embB
M306V,
gyrA
D94G, and
rrs
A1401G. Our results reflect the utility of the GenoType tests in Colombia; however, as some discordance still exists between the conventional and molecular approaches in resistance testing, we adhere to the recommendation that the GenoType tests serve as early guides for therapy, followed by phenotypic drug susceptibility testing for all cases.
Clustering of Tuberculosis Cases Based on Variable-Number Tandem-Repeat Typing in Relation to the Population Structure of Mycobacterium tuberculosis in the Netherlands
Authors: Sloot Rosa , Borgdorff Martien W. , de Beer Jessica L. , van Ingen Jakko , Supply Philip , van Soolingen Dick 
Published: May 2013

ABSTRACT

The population structure of 3,776
Mycobacterium tuberculosis
isolates was determined using variable-number tandem-repeat (VNTR) typing. The degree of clonality was so high that a more relaxed definition of clustering cannot be applied. Among recent immigrants with non-Euro-American isolates, transmission is overestimated if based on identical VNTR patterns.
Ward-Specific Rates of Nasal Cocolonization with Methicillin-Susceptible and -Resistant Staphylococcus spp. and Potential Impact on Molecular Methicillin-Resistant Staphylococcus aureus Screening Tests
Authors: Trouillet-Assant Sophie , Rasigade Jean-Philippe , Lustig Sebastien , Lhoste Yannick , Valour Florent , Guerin Claude , Aubrun Frederic , Tigaud Sylvestre , Laurent Frederic 
Published: May 2013

ABSTRACT

We report that the rates of nasal cocolonization with methicillin-susceptible
Staphylococcus aureus
and methicillin-resistant coagulase-negative staphylococci can vary widely between patients admitted to different wards within a single hospital. Such cocolonization can greatly influence the performance of molecular methicillin-resistant
S. aureus
(MRSA) screening tests depending on the methods used and targets selected.
Rapid Molecular Detection of Macrolide Resistance in the Mycobacterium avium Complex: Are We There Yet?
Authors: Christianson Sara , Grierson William , Wolfe Joyce , Sharma Meenu K. 
Published: May 2013

ABSTRACT

Macrolides are an important tool in the treatment of
Mycobacterium avium
complex infections. Here, we evaluate the use of 23S rRNA gene sequencing for the rapid detection of macrolide resistance. Routine sequencing of the 23S rRNA gene is highly specific for macrolide resistance but lacks in sensitivity.
Multicenter Study Evaluating the Vitek MS System for Identification of Medically Important Yeasts
Authors: Westblade Lars F. , Jennemann Rebecca , Branda John A. , Bythrow Maureen , Ferraro Mary Jane , Garner Omai B. , Ginocchio Christine C. , Lewinski Michael A. , Manji Ryhana , Mochon A. Brian , Procop Gary W. , Richter Sandra S. , Rychert Jenna A. , Sercia Linda , Burnham Carey-Ann D. 
Published: May 2013

ABSTRACT

The optimal management of fungal infections is correlated with timely organism identification. Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) is revolutionizing the identification of yeasts isolated from clinical specimens. We present a multicenter study assessing the performance of the Vitek MS system (bioMérieux) in identifying medically important yeasts. A collection of 852 isolates was tested, including 20
Candida
species (626 isolates, including 58
C. albicans
, 62
C. glabrata
, and 53
C. krusei
isolates), 35
Cryptococcus neoformans
isolates, and 191 other clinically relevant yeast isolates; in total, 31 different species were evaluated. Isolates were directly applied to a target plate, followed by a formic acid overlay. Mass spectra were acquired using the Vitek MS system and were analyzed using the Vitek MS v2.0 database. The gold standard for identification was sequence analysis of the D2 region of the 26S rRNA gene. In total, 823 isolates (96.6%) were identified to the genus level and 819 isolates (96.1%) were identified to the species level. Twenty-four isolates (2.8%) were not identified, and five isolates (0.6%) were misidentified. Misidentified isolates included one isolate of
C. albicans
(
n
= 58) identified as
Candida dubliniensis
, one isolate of
Candida parapsilosis
(
n
= 73) identified as
Candida pelliculosa
, and three isolates of
Geotrichum klebahnii
(
n
= 6) identified as
Geotrichum candidum
. The identification of clinically relevant yeasts using MS is superior to the phenotypic identification systems currently employed in clinical microbiology laboratories.
Identification of
bla
OXA-51-like
,
bla
OXA-58
,
bla
DIM-1
, and
bla
VIM
Carbapenemase Genes in Hospital Enterobacteriaceae Isolates from Sierra Leone
Authors: Leski Tomasz A. , Bangura Umaru , Jimmy David H. , Ansumana Rashid , Lizewski Stephen E. , Li Robert W. , Stenger David A. , Taitt Chris R. , Vora Gary J. 
Published: May 2013

ABSTRACT

We describe the results of a molecular epidemiological survey of 15 carbapenemase-encoding genes from a recent collection of clinical isolates from Mercy Hospital in Bo, Sierra Leone. The most salient findings revealed that (i) 60% of the isolates harbored multiple carbapenemase genes; (ii) the
bla
DIM-1
gene, which has previously only been reported in The Netherlands, is also circulating in this environment; and (iii)
bla
OXA-51-like
and
bla
OXA-58
genes, which were thought to reside exclusively in
Acinetobacter
species, can also be found in members of the
Enterobacteriaceae
.
Asymptomatic Carriage of Sequence Type 398,
spa
Type t571 Methicillin-Susceptible Staphylococcus aureus in an Urban Jail: a Newly Emerging, Transmissible Pathogenic Strain
Authors: David Michael Z. , Siegel Jane , Lowy Franklin D. , Zychowski Diana , Taylor Alexis , Lee Caroline J. , Boyle-Vavra Susan , Daum Robert S. 
Published: May 2013

ABSTRACT

Sequence type 398 (ST398)
Staphylococcus aureus
, frequently carried by livestock, has caused severe human infections and often carries transmissible antibiotic resistance genes. Among methicillin-susceptible
S. aureus
isolates colonizing Dallas County Jail detainees, 13.2% were ST398,
spa
type t571, and were genetically similar to human colonization isolates from New York, Chicago, and the Dominican Republic.
The CD225 Domain of IFITM3 Is Required for both IFITM Protein Association and Inhibition of Influenza A Virus and Dengue Virus Replication
Authors: John Sinu P. , Chin Christopher R. , Perreira Jill M. , Feeley Eric M. , Aker Aaron M. , Savidis George , Smith Sarah E. , Elia Andrew E. H. , Everitt Aaron R. , Vora Mehul , Pertel Thomas , Elledge Stephen J. , Kellam Paul , Brass Abraham L. 
Published: May 2013

ABSTRACT

The interferon-induced transmembrane protein 3 (IFITM3) gene is an interferon-stimulated gene that inhibits the replication of multiple pathogenic viruses
in vitro
and
in vivo
. IFITM3 is a member of a large protein superfamily, whose members share a functionally undefined area of high amino acid conservation, the CD225 domain. We performed mutational analyses of IFITM3 and identified multiple residues within the CD225 domain, consisting of the first intramembrane domain (intramembrane domain 1 [IM1]) and a conserved intracellular loop (CIL), that are required for restriction of both influenza A virus (IAV) and dengue virus (DENV) infection
in vitro
. Two phenylalanines within IM1 (F75 and F78) also mediate a physical association between IFITM proteins, and the loss of this interaction decreases IFITM3-mediated restriction. By extension, similar IM1-mediated associations may contribute to the functions of additional members of the CD225 domain family. IFITM3's distal N-terminal domain is also needed for full antiviral activity, including a tyrosine (Y20), whose alteration results in mislocalization of a portion of IFITM3 to the cell periphery and surface. Comparative analyses demonstrate that similar molecular determinants are needed for IFITM3's restriction of both IAV and DENV. However, a portion of the CIL including Y99 and R87 is preferentially needed for inhibition of the orthomyxovirus. Several IFITM3 proteins engineered with rare single-nucleotide polymorphisms demonstrated reduced expression or mislocalization, and these events were associated with enhanced viral replication
in vitro
, suggesting that possessing such alleles may impact an individual's risk for viral infection. On the basis of this and other data, we propose a model for IFITM3-mediated restriction.
Contribution of Follicular Dendritic Cells to Persistent HIV Viremia
Authors: Zhang Jingshan , Perelson Alan S. 
Published: May 2013

ABSTRACTHIV-1 infections cannot be completely eradicated by drug therapy, as the virus persists in reservoirs. Low-level plasma viremia has been detected in patients treated for over 7 years, but the cellular compartments that support this low-level viremia have not been identified. The decay of HIV-1 during treatment appears to occur in four phases, with the 3rd and 4th phases occurring when the virus is below the limit of detection of conventional assays. Here, we focus on the 3rd phase of decay, which has been estimated to have a half-life of 39 months. We show that follicular dendritic cells (FDC), which have been identified as an HIV reservoir, can be the main source of the low-level viremia detected during the 3rd phase of decay and contribute to viremia at even longer times. Our calculations show that the kinetics of leakage of virus from FDC is consistent with three types of available clinical data.
NS3 of Bluetongue Virus Interferes with the Induction of Type I Interferon
Authors: Chauveau Emilie , Doceul Virginie , Lara Estelle , Breard Emmanuel , Sailleau Corinne , Vidalain Pierre-Olivier , Meurs Eliane F. , Dabo Stéphanie , Schwartz-Cornil Isabelle , Zientara Stéphan , Vitour Damien 
Published: May 2013

ABSTRACTUpon infection with Bluetongue virus (BTV), an arthropod-borne virus, type I interferon (IFN-I) is producedin vivoandin vitro. IFN-I is essential for the establishment of an antiviral cellular response, and most if not all viruses have elaborated strategies to counteract its action. In this study, we assessed the ability of BTV to interfere with IFN-I synthesis and identified the nonstructural viral protein NS3 as an antagonist of the IFN-I system.
Comparison of the Levels of Infectious Virus in Respirable Aerosols Exhaled by Ferrets Infected with Influenza Viruses Exhibiting Diverse Transmissibility Phenotypes
Authors: Gustin Kortney M. , Katz Jacqueline M. , Tumpey Terrence M. , Maines Taronna R. 
Published: May 2013

ABSTRACT
Influenza viruses pose a major public health burden to communities around the world by causing respiratory infections that can be highly contagious and spread rapidly through the population. Despite extensive research on influenza viruses, the modes of transmission occurring most often among humans are not entirely clear. Contributing to this knowledge gap is the lack of an understanding of the levels of infectious virus present in respirable aerosols exhaled from infected hosts. Here, we used the ferret model to evaluate aerosol shedding patterns and measure the amount of infectious virus present in exhaled respirable aerosols. By comparing these parameters among a panel of human and avian influenza viruses exhibiting diverse respiratory droplet transmission efficiencies, we are able to report that ferrets infected by highly transmissible influenza viruses exhale a greater number of aerosol particles and more infectious virus within respirable aerosols than ferrets infected by influenza viruses that do not readily transmit. Our findings improve our understanding of the ferret transmission model and provide support for the potential for influenza virus aerosol transmission.
Abstract A10: CaMKK2 regulates cellular proliferation and androgen receptor activity during prostate cancer progression
Authors: Karacosta Loukia G. , Foster Barbara A. , Gissou Azabdaftari , Feliciano David M. , Edelman Arthur M. 
Published: May 2013

Abstract
Mounting evidence suggests that the androgen receptor (AR) plays a critical role in prostate cancer (PCa) progression. However, the molecular mechanisms by which the AR regulates cell proliferation in androgen-dependent and castration-resistant PCa are incompletely understood. We report here that calcium/calmodulin-dependent kinase kinase 2 (CaMKK2) expression increases during progression of human PCa and becomes nuclear or perinuclear in advanced disease. In a mouse model of PCa (transgenic adenocarcinoma of mouse prostate, TRAMP), CaMKK2 expression increases with progression and is predominantly nuclear. CaMKK2 expression is markedly higher in the AR-expressing, tumorigenic cell line LNCaP compared to cell lines which are AR-nonexpressing and/or nontumorigenic. Silencing of CaMKK2 expression by RNA interference (RNAi) reduces cell proliferation in LNCaP cells but not in AR-non-expressing PC3 cells. In LNCaP cells, dihydrotestosterone (DHT) induces CaMKK2 mRNA and protein expression while androgen withdrawal suppresses CaMKK2 expression. RNAi of CaMKK2 reduces expression of the AR target, prostate specific antigen (PSA) and the cell cycle regulators cyclin D1 and phospho-pRB. Our results suggest that in PCa progression, CaMKK2 is transcriptionally induced by the AR to maintain AR activity, AR-dependent cell cycle control and continued cell proliferation.
Citation Format: Loukia G. Karacosta, Barbara A. Foster, Azabdaftari Gissou, David M. Feliciano, Arthur M. Edelman. CaMKK2 regulates cellular proliferation and androgen receptor activity during prostate cancer progression [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr A10.
Abstract A15: A phase 2 study of neoadjuvant metformin in prostatic carcinoma
Authors: Joshua Anthony Michael , Fleshner Neil , Pollak Michael , Zannella Vanessa , Bowes Barbara , Koritzinsky Marianne , Sweet Joan , Evans Andrew , Trachtenberg John , Jewett Michael , Finelli Antonio 
Published: May 2013

Abstract
Background: Metformin is an inhibitor of the complex 1 in the respiratory chain, and is widely used in diabetes due to its effect on reducing insulin resistance. It has also been recently described to have effects via AMPK on inhibiting the mTOR kinase. Significant preclinical and epidemiological studies suggest its role in chemoprevention. These actions provide significant rationale to evaluate its utility in prostate cancer. We conducted a phase II single centre study of neoadjuvant metformin in localized prostate cancer.
Methods: Men were required to have histologically confirmed prostate cancer involving at least 20% of at least 1 unfragmented biopsy core. Exclusion criteria included patients who on initial assessment are found to be on treatment with any drug used for the treatment of any form of diabetes, or patients that begin treatment for any form of diabetes during the course of the study. Pts were treated with up to 500mg tid of metformin. The primary objectives were to demonstrate safety and tolerability of neoadjuvant metformin administration in men with prostate cancer and to document changes in phospho-AKT signaling indices.
Results: 24 patients were enrolled with 22 evaluable; median age was 64 yrs (range, 45-70 yrs). Baseline characteristics included median PSA 6 ng/mL (range, 3.22–36.11 ng/mL). Median duration of drug treatment was 41 days (range 18–81). No grade 3 adverse events were reported, all patients underwent subsequent radical prostatectomy with adverse effects related to metformin. Significant pre-and post changes were noted in serum IGF1 (p=0.02), fasting glucose (p=0.03), BMI (p &lt; 0.01) and waist/hip ratio (p &lt; 0.01). There was a trend for a PSA reduction (p=0.08). There were no correlations between any metabolic, morphometric or cancer-related serum indices.
Conclusions: Neoadjuvant metformin is well tolerated prior to radical prostatectomy. Data to date indicates promising effects on metabolic parameters, tissue results will be presented including proliferation indices and signaling pathway assessments.
Citation Format: Anthony Michael Joshua, Neil Fleshner, Michael Pollak, Vanessa Zannella, Barbara Bowes, Marianne Koritzinsky, Joan Sweet, Andrew Evans, John Trachtenberg, Michael Jewett, Antonio Finelli. A phase 2 study of neoadjuvant metformin in prostatic carcinoma [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr A15.