bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recurrence of primary biliary cirrhosis and development of autoimmune hepatitis after liver transplant: A blind histologic study
Authors: Hytiroglou Prodromos , Gutierrez Julio A. , Freni Maria , Odin Joseph A. , Stanca Carmen M. , Merati Sukma , Schiano Thomas D. , Branch Andrea D. , Thung Swan N. 
Published: January 2009

Aim:  This long‐term study aimed to evaluate recurrence and evolution of primary biliary cirrhosis (PBC) after orthotopic liver transplantation (OLT).Methods:  We reviewed “blindly” allograft biopsy specimens of women who underwent transplantation for PBC (n = 84), and women who received a transplant for chronic hepatitis C virus infection (CHCV ) (n = 108). All needle liver biopsy specimens obtained more than 6 months post‐OLT were examined, including 83 specimens from 44 PBC patients and 152 specimens from 58 CHCV patients.Results:  Granulomatous destructive cholangitis was found in five biopsies from four PBC patients (P = 0.0048). Non‐necrotizing epithelioid cell granulomas were present in four biopsies from four PBC patients, and in two biopsies from one CHCV patient. Piecemeal necrosis (P = 0.0002), lobular necroinflammatory activity (P < 0.0001), steatosis (P < 0.0001) and fibrosis (P < 0.0001) were more prevalent in CHCV patients than PBC patients. Four PBC patients developed histologic evidence of autoimmune hepatitis (AIH), at a mean time of 3.66 years post‐OLT. One of these patients had histologic features of AIH/PBC overlap syndrome. All four patients developed bridging fibrosis (n = 2) or cirrhosis (n = 2). No other PBC patient had evidence of cirrhosis after OLT.Conclusions:  Histologic findings indicative of recurrent PBC were present in 15.9% of the PBC patients undergoing biopsy in this series. However, this group of patients did not suffer significant bile duct loss or fibrosis, as compared to the control group, suggesting that recurrent PBC is a mild or slowly progressive disease. Histologic evidence of AIH was observed in allograft biopsies of some PBC patients.
Activity of Anidulafungin in a Murine Model of
Candida krusei
Infection: Evaluation of Mortality and Disease Burden by Quantitative Tissue Cultures and Measurement of Serum (1,3)-β-
d
-Glucan Levels
Authors: Ostrosky-Zeichner Luis , Paetznick Victor L. , Rodriguez Jose , Chen Enuo , Sheehan Daniel J. 
Published: January 2009

ABSTRACT

Experience with anidulafungin against
Candida krusei
is limited. Immunosuppressed mice were injected with 1.3 × 10
7
to 1.5 × 10
7
CFU of
C. krusei
. Animals were treated with saline, 40 mg/kg fluconazole, 1 mg/kg amphotericin B, or 10 and 20 mg/kg anidulafungin for 5 days. Anidulafungin improved survival and significantly reduced the number of CFU/g in kidneys and serum β-glucan levels.
Tigecycline Therapy Significantly Reduces the Concentrations of Inflammatory Pulmonary Cytokines and Chemokines in a Murine Model of
Mycoplasma pneumoniae
Pneumonia
Authors: Salvatore C. M. , Techasaensiri C. , Tagliabue C. , Katz K. , Leos N. , Gomez A. M. , McCracken G. H. , Hardy R. D. 
Published: January 2009

ABSTRACT

Mycoplasma pneumoniae
is one of the causative agents of atypical community-acquired pneumonia. Tigecycline belongs to a new class of glycylcycline antimicrobials that have activity against a wide range of microorganisms, including in vitro activity against
M. pneumoniae
. We investigated the effect of tigecycline on microbiologic, histologic, and immunologic indices in a murine model of
M. pneumoniae
pneumonia. BALB/c mice were inoculated intranasally with
M. pneumoniae
and treated subcutaneously with tigecycline or placebo for 6 days. Outcome variables included quantitative bronchoalveolar lavage (BAL)
M. pneumoniae
culture, lung histopathologic score (HPS), BAL cytokine and chemokine concentrations (tumor necrosis factor alpha [TNF-α], gamma interferon [IFN-γ], interleukin 1β [IL-1β], IL-2, IL-4, IL-5, IL-6, IL-10, IL-12 [p40/p70], granulocyte-macrophage colony-stimulating factor, MIP-1α, MIG, KC, MCP-1, and IP-10). BAL
M. pneumoniae
concentrations in mice treated with tigecycline (MpTige) tended to be reduced compared with mice treated with placebo (MpPl); however this did not reach statistical significance. The lung HPS was significantly lower, as well as the parenchymal-pneumonia subscore, in the MpTige mice than in the MpPl mice. MpTige mice had significantly lower BAL cytokine concentrations of IL-1β, IL-12 (p40/p70), IFN-γ, and TNF-α; of the chemokines, MIG, MIP-1α, and IP-10 were statistically lower in MpTige mice. While tigecycline treatment demonstrated a modest microbiologic effect, it significantly improved lung histologic inflammation and reduced pulmonary cytokines and chemokines.
Voriconazole Use for Endemic Fungal Infections
Authors: Freifeld Alison , Proia Laurie , Andes David , Baddour Larry M. , Blair Janis , Spellberg Brad , Arnold Sandra , Lentnek Arnold , Wheat L. Joseph 
Published: January 2009

ABSTRACT
In a retrospective review of 24 patients with histoplasmosis, blastomycosis, or coccidioidomycosis treated with voriconazole (most for salvage therapy), the outcome was favorable (improved or stable) for 22 (95.8%) within 2 months of starting voriconazole and for 20 (83.3%) at the last follow-up. Prospective studies are required to determine its role in the treatment of endemic mycoses.
Polyanionic Microbicides Modify Toll-Like Receptor-Mediated Cervicovaginal Immune Responses
Authors: Trifonova R. T. , Doncel G. F. , Fichorova R. N. 
Published: January 2009

ABSTRACT

Topical microbicides are being developed as a preventative approach to reduce the sexual transmission of human immunodeficiency virus type 1 (HIV-1) and other infections. For them to be efficacious, it is believed that they should avoid inducing inflammation while allowing the vaginal epithelium to initiate protective Toll-like receptor (TLR)-mediated innate responses against pathogens. In this study, human cervical and vaginal epithelial cells were exposed to polyanionic HIV entry inhibitors and the following synthetic TLR ligands: (i) the bacterial lipoprotein Pam
3
CSK
4
, binding cell surface TLR1/TLR2; (ii) macrophage activating lipopeptide 2 (MALP-2), binding cell surface TLR2/TLR6; and (iii) the viral double-stranded RNA analog poly(I:C), recognized by intracellular TLR3. Cell activation was assessed by nuclear factor κB (NF-κB) reporter gene transactivation and cytokine production. In spite of enhancing TLR-triggered NF-κB activation, the polyanionic microbicide compounds dextran sulfate and polystyrene sulfonate significantly inhibited TLR-mediated cytokine production. They decreased cytokine mRNA and protein levels of proinflammatory (interleukin-8 [IL-8] and IL-1β) and antiviral (beta interferon) cytokines following epithelial cell stimulation with Pam
3
CSK
4
, MALP-2, or poly(I:C). These activities were associated with the sulfate/sulfonate moieties of the polyanionic compounds, since the unsulfated dextran control did not show any effects. Our data demonstrate that these microbicide compounds are capable of selectively interfering with TLR-mediated epithelial responses at different points in their signaling pathways and underscore the importance of expanding the assessment of microbicide compatibility with vaginal innate immune function. Further studies are warranted to determine the impact of this interference on HIV-1 transmission risk.
A
bla
VEB-1
Variant,
bla
VEB-6
, Associated with Repeated Elements in a Complex Genetic Structure
Authors: Zong Zhiyong , Partridge Sally R. , Iredell Jonathan R. 
Published: January 2009

ABSTRACT

bla
VEB-6
was found on the
Proteus mirabilis
chromosome in a context similar to those of
bla
VEB-1a
and
bla
VEB-1b
, in a truncated gene cassette flanked by 135-bp elements and duplications of the 3′-conserved segment of class 1 integrons. A linked
aacA4-aadB-dfrA1-orfC
cassette array includes components of Tn
1331
, illustrating the complex mosaicism of multiresistance regions.
In Vitro Activity of Iclaprim against Respiratory and Bacteremic Isolates of
Streptococcus pneumoniae
Authors: Zhanel George G. , Karlowsky James A. 
Published: January 2009

ABSTRACT

Iclaprim, a novel dihydrofolate reductase inhibitor, inhibited 90% of the clinical isolates (MIC
90
) of
Streptococcus pneumoniae
(
n
= 785) collected by a national surveillance program at a concentration of 1 μg/ml. The MIC
90
for iclaprim was 7 doubling dilutions lower for trimethoprim-sulfamethoxazole-susceptible isolates (
n
= 670; MIC
90
, 0.06 μg/ml) than for trimethoprim-sulfamethoxazole-resistant isolates (
n
= 115; MIC
90
, ≥8 μg/ml). The potential clinical utility of iclaprim to treat patients with pneumococcal infections may depend upon the current prevalence of resistance to trimethoprim-sulfamethoxazole in this pathogen.
Associations between Antimicrobial Resistance Phenotypes, Antimicrobial Resistance Genes, and Virulence Genes of Fecal
Escherichia coli
Isolates from Healthy Grow-Finish Pigs
Authors: Rosengren Leigh B. , Waldner Cheryl L. , Reid-Smith Richard J. 
Published: January 2009

ABSTRACT

Escherichia coli
often carries linked antimicrobial resistance genes on transmissible genetic elements. Through coselection, antimicrobial use may select for unrelated but linked resistance or virulence genes. This study used unconditional statistical associations to investigate the relationships between antimicrobial resistance phenotypes and antimicrobial resistance genes in 151
E. coli
isolates from healthy pigs. Phenotypic resistance to each drug was significantly associated with phenotypic resistance to at least one other drug, and every association found that the probability of observing the outcome resistance was increased by the presence of the predictor resistance. With one exception, each statistical association that was identified between a pair of resistance genes had a corresponding significant association identified between the phenotypes mediated by those genes. This suggests that associations between resistance phenotypes might predict coselection. If this hypothesis is confirmed, evaluation of the associations between resistance phenotypes could improve our knowledge of coselection dynamics and provide a cost-effective way to evaluate existing data until large-scale genotypic data collection becomes feasible. This could enable policy makers and users of antimicrobials to consider coselection in antimicrobial use decisions. This study also considered the unconditional relationships between resistance and virulence genes in
E. coli
from healthy pigs (
aidA-1
,
eae
,
elt
,
estA
,
estB
,
fedA1
,
stx1
, and
stx2
). Positive statistical associations would suggest that antimicrobial use may select for virulence in bacteria that may contaminate food or cause diarrhea in pigs. Fortunately, the odds of detecting a virulence gene were rarely increased by the presence of an antimicrobial resistance gene. This suggests that on-farm antimicrobial use did not select for the examined virulence factors in
E. coli
carried by this population of healthy pigs.
Biogeographic Patterns in Genomic Diversity among a Large Collection ofVibrio choleraeIsolates
Authors: Keymer Daniel P. , Lam Lilian H. , Boehm Alexandria B. 
Published: January 2009

ABSTRACTVibrio choleraestrains are capable of inhabiting multiple niches in the aquatic environment and in some cases cause disease in humans. However, the ecology and biodiversity of these bacteria in environmental settings remains poorly understood. We used the genomic fingerprinting technique enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) to profile 835 environmental isolates from waters and sediments obtained at nine sites along the central California coast. We identified 115 ERIC-PCR genotypes from 998 fingerprints, with a reproducibility of 98.5% and a discriminatory power of 0.971. When the temporal dynamics at a subset of sampling sites were explored, several genotypes provided evidence for cosmopolitan or geographically restricted distributions, and other genotypes displayed nonrandom patterns of cooccurrence. Partial Mantel tests confirmed that genotypic similarity of isolates across all sampling events was correlated with environmental similarity (0.04 ≤r≤ 0.05), temporal proximity (r= 0.09), and geographic distance (r= 0.09). A neutral community model for all sampling events explained 61% of the variation in genotype abundance. Cooccurrence indices (C-score, C-board, and Combo) were significantly different than expected by chance, suggesting that theV. choleraepopulation may have a competitive structure, especially at the regional scale. Even though stochastic processes are undoubtedly important in generating biogeographic patterns in diversity, deterministic factors appear to play a significant, albeit small, role in shaping theV. choleraepopulation structure in this system.
Sulfolobus tokodaiiST0053 Produces a Novel Thermostable, NAD-Dependent Medium-Chain Alcohol Dehydrogenase
Authors: Yanai Hisaaki , Doi Katsumi , Ohshima Toshihisa 
Published: January 2009

ABSTRACTAn alcohol dehydrogenase (ADH) gene, ST0053, fromSulfolobus tokodaiiwas expressed inEscherichia coli. The purified recombinant enzyme was an NAD-dependent medium-chain ADH with high thermostability and tolerance of a wide range of pHs. This is the first step in creating an experimental functionality library of 10 genes annotated as ADHs in theS. tokodaiigenome.
Evaluation of Genotypic and Phenotypic Methods To Distinguish Clinical from Environmental
Vibrio vulnificus
Strains
Authors: Sanjuán Eva , Fouz Belén , Oliver James D. , Amaro Carmen 
Published: January 2009

ABSTRACT

Vibrio vulnificus
is a heterogeneous bacterial species that comprises virulent and avirulent strains from environmental and clinical sources that have been grouped into three biotypes. To validate the typing methods proposed to distinguish clinical from environmental isolates, we performed phenotypic (API 20E, API 20NE, and BIOLOG tests) and genetic (ribotyping and DNA polymorphism at several loci) studies with a large strain collection representing different biotypes, origins, and host ranges. No phenotypic method was useful for biotyping or grouping strains with regard to the origin of an isolate, and only the BIOLOG system was reliable for identifying the strains at the species level. DNA polymorphisms divided the population into three major profiles. Profile 1 strains were
vcg
type C, 16S rRNA type B, and
vvh
type 1 and included most of the biotype 1 human septicemic isolates; profile 2 strains were
vcg
type E, 16S rRNA type A, and
vvh
type 2 and included all biotype 2 isolates together with biotype 1 isolates from fish and water and some human isolates; and profile 3 strains were
vcg
type E, 16S rRNA type AB, and
vvh
type 2 and included biotype 3 strains. Ribotyping divided the species into two groups: one group that included profile 1 biotype 1 isolates and one group that included isolates of all three biotypes with the three profiles described above. In conclusion, no genotyping system was able to distinguish either clinical strains from environmental strains or biogroups within the species
V. vulnificus
, which suggests that new typing methodologies useful for public health have to be developed for this species.
Longitudinal Study ofSalmonellaDispersion and the Role of Environmental Contamination in Commercial Swine Production Systems
Authors: Dorr Paul M. , Tadesse Daniel A. , Zewde Bayleyegn Molla , Fry Pamela , Thakur Siddhartha , Gebreyes Wondwossen A. 
Published: January 2009

ABSTRACTThis study investigated the roles of various environmental sources, such as truck-washing systems, waste-processing lagoons, and other sources, as potential contributors to the exposure and dissemination ofSalmonellain commercial swine production systems. Four cohorts of nursery age swine herds which originated from distinct farm flows were selected. In addition, cross-sectional sampling of four truck wash stations selected based on the types of disinfectants and sources of water used for sanitizing trucks were tested.Salmonellaisolates were recovered from pigs (feces, cecal contents, and mesenteric lymph nodes) and environmental sources (barn floor, lagoon, barn flush, trucks, and holding pens). Antimicrobial susceptibility testing and genotyping were conducted using Kirby-Bauer disk diffusion and amplified fragment length polymorphism, respectively.Salmonellaprevalence significantly increased with age from late nursery to slaughter for all of the cohorts (P= 0.007). In two of three instances, all three pig holding pens (lairage) sampled at processing wereSalmonellapositive. The predominant antibiotypes for all sources included ACSSuT (51.8%), SSuT (16.8%), T (6%), and pansusceptible (7.4%). For the isolates obtained at the farms, the ACSSuT phenotype was 5.6 times more likely to be found in the animals than in the environment (95% confidence interval, 4.4 to 7.2 times). Serogroup B was the most common serogroup (79%), followed by serogroup E (10.4%). Despite the fact that the four production flows were independent, 1 of the 11 genotypic clusters (cluster A1) was commonly detected in any type of sample regardless of its origin. Five of the genotypic clusters (clusters A3, A4, A5, A6, and A7) contained isolates that originated from trucks and lairage swabs and also from cecal contents and/or mesenteric lymph nodes. More interestingly, genotypic clusters A3, A4, and A6 (but not clusters A5 and A7) were not detected on the farms. They originated from the trucks and lairage swabs and then were identified from the cecal contents and/or mesenteric lymph nodes. These findings underscore the significance of various environmental factors, including inadequate truck-washing systems, and emphasize the role of lairage contamination bySalmonellathat has food safety significance.
Development of a Test System To Apply Virus-Containing Particles to Filtering Facepiece Respirators for the Evaluation of Decontamination Procedures
Authors: Fisher Edward , Rengasamy Samy , Viscusi Dennis , Vo Evanly , Shaffer Ronald 
Published: January 2009

ABSTRACT

A chamber to apply aerosolized virus-containing particles to air-permeable substrates (coupons) was constructed and validated as part of a method to assess the virucidal efficacy of decontamination procedures for filtering facepiece respirators. Coliphage MS2 was used as a surrogate for pathogenic viruses for confirmation of the efficacy of the bioaerosol respirator test system. The distribution of virus applied onto and within the coupons was characterized, and the repeatability of applying a targeted virus load was examined. The average viable virus loaded onto 90 coupons over the course of 5 days was found to be 5.09 ± 0.19 log
10
PFU/coupon (relative standard deviation, 4%). To determine the ability to differentiate the effectiveness of disinfecting procedures with different levels of performance, sodium hypochlorite and steam treatments were tested in experiments by varying the dose and time, respectively. The role of protective factors was assessed by aerosolizing the virus with various concentrations of the aerosol-generating medium. A sodium hypochlorite (bleach) concentration of 0.6% and steam treatments of 45 s and longer resulted in log reductions (>4 logs) which reached the detection limits for both levels of protective factors. Organic matter (ATCC medium 271) as a protective factor afforded some protection to the virus in the sodium hypochlorite experiments but was not a factor in the steam experiments. The evaluation of the bioaerosol respirator test system demonstrated a repeatable method for applying a targeted viral load onto respirator coupons and provided insight into the properties of aerosols that are of importance to the development of disinfection assays for air-permeable materials.
Transcriptional Regulation and Signal-Peptide-Dependent Secretion of Exolevanase (LsdB) in the Endophyte
Gluconacetobacter diazotrophicus
Authors: Menéndez Carmen , Banguela Alexander , Caballero-Mellado Jesús , Hernández Lázaro 
Published: January 2009

ABSTRACT

Gluconacetobacter diazotrophicus
utilizes plant sucrose with a constitutively expressed levansucrase (LsdA), producing extracellular levan, which may be degraded under energetically unfavored conditions. Reverse transcriptase-PCR analysis revealed that
lsdA
and the downstream exolevanase gene (
lsdB
) form an operon.
lsdB
transcription was induced during growth with low fructose concentrations (0.44 to 33 mM) and repressed by glucose. Transport of LsdB to the periplasm involved N-terminal signal peptide cleavage. Type II secretion mutants failed to transfer LsdB across the outer membrane, impeding levan hydrolysis.
Molecular Subtyping and Distribution of the Serine Protease from Shiga Toxin-Producing
Escherichia coli
among Atypical Enteropathogenic
E. coli
Strains
Authors: Cookson Adrian L. , Bennett Jenny , Nicol Carolyn , Thomson-Carter Fiona , Attwood Graeme T. 
Published: January 2009

ABSTRACT

Atypical enteropathogenic
Escherichia coli
(aEPEC) and Shiga toxin-producing
E. coli
(STEC) were examined to determine the prevalence and sequence of
espP
, which encodes a serine protease. These analyses indicated shared
espP
sequence types between the two
E. coli
pathotypes and thus provide further insights into the evolution of aEPEC and STEC.
Image Analysis Software Based on Color Segmentation for Characterization of Viability and Physiological Activity of Biofilms
Authors: Chávez de Paz Luis E. 
Published: January 2009

ABSTRACT

The novel image analysis software package
bio
Image_L was tested to calculate biofilm structural parameters in oral biofilms stained with dual-channel fluorescent markers. By identifying color tonalities in situ, the software independently processed the color subpopulations and characterized the viability and metabolic activity of biofilms.
Reengineering of a
Corynebacterium glutamicum
l
-Arginine and
l
-Citrulline Producer
Authors: Ikeda Masato , Mitsuhashi Satoshi , Tanaka Kenji , Hayashi Mikiro 
Published: January 2009

ABSTRACT

Toward the creation of a robust and efficient producer of
l
-arginine and
l
-citrulline (arginine/citrulline), we have performed reengineering of a
Corynebacterium glutamicum
strain by using genetic information of three classical producers. Sequence analysis of their
arg
operons identified three point mutations (
argR123, argG92
up
, and
argG45
) in one producer and one point mutation (
argB26
or
argB31
) in each of the other two producers. Reconstitution of the former three mutations or of each
argB
mutation on a wild-type genome led to no production. Combined introduction of
argB26
or
argB31
with
argR123
into a wild type gave rise to arginine/citrulline production. When
argR123
was replaced by an
argR
-deleted mutation (Δ
argR
), the production was further increased. The best mutation set, Δ
argR
and
argB26
, was used to screen for the highest productivity in the backgrounds of different wild-type strains of
C. glutamicum
. This yielded a robust producer, RB, but the production was still one-third of that of the best classical producer. Transcriptome analysis revealed that the
arg
operon of the classical producer was much more highly upregulated than that of strain RB. Introduction of
leuC456
, a mutation derived from a classical
l
-lysine producer and provoking global induction of the amino acid biosynthesis genes, including the
arg
operon, into strain RB led to increased production but incurred retarded fermentation. On the other hand, replacement of the chromosomal
argB
by heterologous
Escherichia coli argB
, natively insensitive to arginine, caused a threefold-increased production without retardation, revealing that the limitation in strain RB was the activity of the
argB
product. To overcome this, in addition to
argB26
, the
argB31
mutation was introduced into strain RB, which caused higher deregulation of the enzyme and resulted in dramatically increased production, like the strain with
E. coli argB
. This reconstructed strain displayed an enhanced performance, thus allowing significantly higher productivity of arginine/citrulline even at the suboptimal 38°C.