bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Plasmid-Mediated Reporter System for In Vivo Monitoring of Gene Expression in the Archaeon
Methanosarcina acetivorans
Authors: Apolinario Ethel E. , Jackson Karin M. , Sowers Kevin R. 
Published: August 2005

ABSTRACT

A plasmid-based gene reporter system has been developed to construct
lacZ
gene fusions for monitoring intrinsic promoter expression in
Methanosarcina acetivorans
. Constructs transform with high efficiency that can be readily screened by color selection on plates and exhibit a consistent copy number on different substrates negating the need for gene copy normalization. Expression of the CO dehydrogenase-acetyl coenzyme A synthase promoter fusion to
lacZ
revealed 18- to 54-fold down-regulation in cells grown on methylotrophic substrates compared with acetate-grown cells, which is up to an order of magnitude greater than the range of regulation previously reported by enzyme activity assays. This system complements and expands the current techniques for studying genetics of the methanosarcinal
Archaea
by providing a rapid method for monitoring and quantifying gene expression.
Genetic Analysis of Two Bile Salt Hydrolase Activities in
Lactobacillus acidophilus
NCFM
Authors: McAuliffe Olivia , Cano Raul J. , Klaenhammer Todd R. 
Published: August 2005

ABSTRACT

Two genes,
bshA
and
bshB
, encoding bile salt hydrolase enzymes (EC 3.5.1.24) were identified in the genome sequence of
Lactobacillus acidophilus
NCFM. Targeted inactivation of these genes via chromosomal insertion of an integration vector demonstrated different substrate specificities for these two enzymes.
Distribution of the
ermG
Gene among Bacterial Isolates from Porcine Intestinal Contents
Authors: Wang Yanping , Wang Gui-Rong , Shoemaker Nadja B. , Whitehead Terence R. , Salyers Abigail A. 
Published: August 2005

ABSTRACT

The
ermG
gene was first found in the soil bacterium
Bacillus sphaericus
. More recently, it was found in several human intestinal
Bacteroides
species. We report here the first finding of
ermG
genes in gram-positive bacteria isolated from porcine feces and from under-barn manure pits used to store porcine wastes. The porcine
ermG
sequences were identical to the sequence of the
B. sphaericus ermG
gene except that six of the seven
ermG
-containing strains contained an insertion sequence element insertion in the C-terminal end of the gene. The porcine
ermG
genes were found in three different gram-positive genera, an indication that it is possible that the gene is being spread by horizontal gene transfer. A segment of a
Bacteroides
conjugative transposon that carries an
ermG
gene cross-hybridized with DNA from six of the seven porcine isolates, but the restriction patterns in the porcine strains were different from that of the
Bacteroides
conjugative transposon.
Identification of Genes Involved in Cytochrome
c
Biogenesis in
Shewanella oneidensis
, Using a Modified
mariner
Transposon
Authors: Bouhenni R. , Gehrke A. , Saffarini D. 
Published: August 2005

ABSTRACT

A modified
mariner
transposon, mini
Himar RB1
, was generated to mutagenize cells of the metal-reducing bacterium
Shewanella oneidensis
. The use of this transposon led to the isolation of stable mutants and allowed rapid identification of disrupted genes. Fifty-eight mutants, including BG104 and BG148 with transposon insertions in the cytochrome
c
maturation genes
ccmC
and
ccmF1
, respectively, were analyzed. Both mutants were deficient in anaerobic respiration and cytochrome
c
production.
Farnesol Concentrations Required To Block Germ Tube Formation in
Candida albicans
in the Presence and Absence of Serum
Authors: Mosel Daniel D. , Dumitru Raluca , Hornby Jacob M. , Atkin Audrey L. , Nickerson Kenneth W. 
Published: August 2005

ABSTRACT

Concentrations of (
E
,
E
)-farnesol needed to inhibit germ tube formation were determined for
Candida albicans
strains A72 and SC5314 by using six different conditions known to trigger germination. For defined media, 1 to 2 μM farnesol was sufficient. However, with serum at 2 to 20%, up to 250 μM farnesol was required. Farnesol blocked germ tube formation but did not block elongation of existing germ tubes.
Molecular Serotyping ofEscherichia coliO26:H11
Authors: Durso Lisa M. , Bono James L. , Keen James E. 
Published: August 2005

ABSTRACTSerotyping is the foundation of pathogenicEscherichia colidiagnostics; however, few laboratories have this capacity. We developed a molecular serotyping protocol that targets, genetically, the same somatic and flagellar antigens ofE. coliO26:H11 used in traditional serotyping. It correctly serotypes strains untypeable by traditional methods, affording primary laboratories serotyping capabilities.
Prevalence and Clinical Significance of Immunoglobulin A Antibodies against Tissue Transglutaminase in Patients with Diverse Chronic Liver Diseases
Authors: Germenis Anastasios E. , Yiannaki Efthalia E. , Zachou Kalliopi , Roka Violeta , Barbanis Sotirios , Liaskos Christos , Adam Kalliopi , Kapsoritakis Andreas N. , Potamianos Spyros , Dalekos Georgios N. 
Published: August 2005

ABSTRACT

The prevalence of celiac disease (CD) and the prevalence and clinical significance of anti-tissue transglutaminase (tTG) antibodies (tTGAbs) in a large series of patients with chronic liver diseases were assessed. We studied 738 patients (462 with chronic viral hepatitis, 117 with autoimmune liver diseases, 113 with alcoholic or nonalcoholic fatty liver disease, and 46 with other liver disorders) and 1,350 healthy controls (HC). Immunoglobulin A (IgA) tTGAbs were measured by enzyme-linked immunosorbent assay and a microsphere-based flow cytometric assay. Positive sera were investigated for IgA antiendomysial antibodies (EmA). IgA tTGAb-positive subjects were invited to undergo a small-intestinal biopsy and HLA-DQ allele typing. Four of 1,350 HC (0.3%) tested tTGAb
+
EmA
+
and underwent a biopsy (CD confirmation in all). Four of 738 liver disease patients tested tTGAbs
+
EmA
+
(0.54%; not statistically significant). Two were HCV infected (1.24%; not statistically significant), and two had transaminasemia of unknown origin. Forty-three patients tested tTGAbs
+
EmA
−
(5.8%;
P
< 0.001 compared to HC). Inhibition experiments verified the existence of specific IgA anti-tTG reactivity. Twenty-six of 43 patients underwent a biopsy (all negative for CD). Binary logistic regression analysis revealed age (
P
= 0.008), cirrhosis (
P
= 0.004), alkaline phosphatase (
P
= 0.026), and antinuclear antibodies (
P
= 0.012) as independent risk factors for tTGAb reactivity among the patients. It was concluded that CD prevalence is the same in HC and patients with chronic liver diseases. The prevalence of tTGAbs is higher in hepatic patients compared to HC, but their specificity for CD diagnosis in this group of patients is low. tTGAbs in patients appear to be associated with the presence of autoimmunity, cirrhosis, and cholestasis, irrespective of the origin of the liver disease.
Optimization and Validation of a Multiplexed Luminex Assay To Quantify Antibodies to Neutralizing Epitopes on Human Papillomaviruses 6, 11, 16, and 18
Authors: Dias Dennis , Van Doren Jeff , Schlottmann Sonela , Kelly Sheri , Puchalski Derek , Ruiz Wanda , Boerckel Patricia , Kessler Joseph , Antonello Joseph M. , Green Tina , Brown Martha , Smith Judith , Chirmule Narendra , Barr Eliav , Jansen Kathrin U. , Esser Mark T. 
Published: August 2005

ABSTRACT
A human papillomavirus (HPV) multiplexed competitive Luminex immunoassay first described by Opalka et al. (D. Opalka, C. E. Lachman, S. A. MacMullen, K. U. Jansen, J. F. Smith, N. Chirmule, and M. T. Esser, Clin. Diagn. Lab. Immunol. 10:108-115, 2003) was optimized and validated for use in epidemiology studies and vaccine clinical trials. Optimization increased both the analytical sensitivity and the clinical specificity of the assay to more effectively discriminate the low-titer antibody response of HPV-infected persons from noninfected individuals. The characteristics of the assay that were optimized included monoclonal antibody (MAb) specificity, scaling up the conjugation of virus-like particles (VLPs) to microspheres, VLP concentration, MAb concentration, sample matrix, sample dilution, incubation time, heat inactivation of sample sera, and detergent effects on assay buffer. The assay was automated by use of a TECAN Genesis Workstation, thus improving assay throughput, reproducibility, and operator safety. Following optimization, the assay was validated using several distinct serum panels from individuals determined to be at low and high risk for HPV infection. The validated assay was then used to determine the clinical serostatus cutoff. This high-throughput assay has proven useful for performing epidemiology studies and evaluating the efficacy of prophylactic HPV vaccines.
Lymphocyte Proliferation Responses Induced to Broadly Reactive Th Peptides Did Not Protect against Equine Infectious Anemia Virus Challenge
Authors: Fraser Darrilyn G. , Leib Steve R. , Zhang Bao Shan , Mealey Robert H. , Brown Wendy C. , McGuire Travis C. 
Published: August 2005

ABSTRACTThe effect of immunization with five lipopeptides, three containing T-helper (Th) epitopes and two with both Th and cytotoxic T-lymphocyte (CTL) epitopes, on equine infectious anemia virus (EIAV) challenge was evaluated. Peripheral blood mononuclear cells from EIAV lipopeptide-immunized horses had significant proliferative responses to Th peptides compared with those preimmunization, and the responses were attributed to significant responses to peptides Gag from positions 221 to 245 (Gag 221-245), Gag 250-269, and Pol 326-347; however, there were no consistent CTL responses. The significant proliferative responses in the EIAV lipopeptide-immunized horses allowed testing of the hypothesis that Th responses to immunization would enhance Th and CTL responses following EIAV challenge and lessen the viral load and the severity of clinical disease. The EIAV lipopeptide-immunized group did have a significant increase in proliferative responses to Th peptides 1 week after virus challenge, whereas the control group did not. Two weeks after challenge, a significant CTL response to virus-infected cell targets occurred in the EIAV lipopeptide-immunized group compared to that in the control group. These Th and CTL responses did not significantly alter either the number of viral RNA copies/ml or disease severity. Thus, lipopeptide-induced proliferative responses and enhanced Th and CTL responses early after virus challenge were unable to control challenge virus load and clinical disease.
Clinical features and follow up of 302 patients with Mycobacterium kansasii pulmonary infection: a 50 year experience
Authors: Maliwan N , Zvetina J R 
Published: August 2005

Abstract

Aims
To analyse clinical features and treatment outcomes of patients with pulmonary Mycobacterium kansasii infection treated at Hines VA Hospital between 1952 and 1995, and followed up until 2003.

Findings
302 patients were confirmed to have M kansasii pulmonary infection; diagnosis was not made until death in 2%. The average age was 50 years old; 76% were white; all were men. Productive cough, dyspnoea, and chest pain were common; 16% were asymptomatic. Right sided, apical or subapical, thin walled cavitary infiltrate was the characteristic radiological feature. Heavy smoking, chronic obstructive pulmonary disease, alcoholism, peptic ulcer disease, coronary artery disease, prior tuberculosis, psychosis, prior pneumonia, and immunocompromising conditions were prevalent. Average follow up was 10 years and 2 months. PPD was positive in 58% of 179 tested. Two thirds of the patients required only first line drugs. Fourteen per cent required surgical intervention, none after 1977. Spontaneous resolution occurred in 1%. Aspergillosis developed in 4%. Bronchogenic carcinoma coexisted with M kansasii infection in 6% and followed it in 4%. Extrapulmonary malignancy coexisted with the infection in 4% and followed it in 6%; most involved head and neck. Eleven per cent of 224 deaths were attributed to M kansasii. Outcomes were affected by comorbidity, treatment compliance, rifampicin use, and extent of infection.

Conclusions
Prognosis of M kansasii pulmonary infection is good if diagnosed and treated early, together with control of underlying conditions. Clinicians should be aware of atypical radiological manifestations of the disease when coexisting with other pulmonary or immunocompromising conditions.
Diabetes and ethnic minorities
Authors: Oldroyd J , Banerjee M , Heald A , Cruickshank K 
Published: August 2005

Abstract
The global prevalence of diabetes for all age groups is estimated to be 2.8%. Type 2 diabetes accounts for at least 90% of diabetes worldwide. Diabetes incidence, prevalence, and disease progression varies by ethnic group. This review highlights unique aspects of the risk of developing diabetes, its overwhelming vascular complications, and their management mainly using data among South Asians and African-Caribbeans in the UK but also using non-UK data. It is concluded that although the origin of the ethnic differences in incidence need further clarification, many factors should be amenable to prevention and treatment in all ethnic groups worldwide.
Malaria in the post-genomics era: light at the end of the tunnel or just another train?
Authors: Gardiner D L , McCarthy J S , Trenholme K R 
Published: August 2005

Abstract
Malaria remains the third leading cause of death attributable to an infectious disease worldwide, with an estimated death toll of over 2 million per year, predominately in sub-Saharan Africa. The first serious attempt to eradicate this disease was unsuccessful, and 50 years later in 1998 a second programme coined “roll back malaria” was started. While this programme is at present unlikely to reach its stated aims, the completion of the genome sequencing projects on the human host, the mosquito vector, and the malaria parasite offers new hope. It is probable that the burden of disease caused by the most malignant form of the parasite Plasmodium falciparum can be, if not eliminated, then effectively suppressed within a generation through new and novel treatments aimed at all three arms of malaria control.
ENDS OF CUSP-UNIFORM GROUPS OF LOCALLY CONNECTED CONTINUA — I
Authors: GURALNIK DAN P. 
Published: August 2005

Due to works by Bestvina–Mess, Swarup and Bowditch, we now have complete knowledge of how splittings of a word-hyperbolic group G as a graph of groups with finite or two-ended edge groups relate to the cut point structure of its boundary. It is central in the theory that ∂G is a locally connected continuum (a Peano space). Motivated by the structure of tight circle packings, we propose to generalize this theory to cusp-uniform groups in the sense of Tukia. A Peano space X is cut-rigid, if X has no cut point, no points of infinite valence and no cut pairs consisting of bivalent points. We prove: Theorem. Suppose X is a cut-rigid space admitting a cusp-uniform action by an infinite group. If X contains a minimal cut triple of bivalent points, then there exists a simplicial tree T, canonically associated with X, and a canonical simplicial action of Homeo(X) on T such that any infinite cusp-uniform group G of X acts cofinitely on T, with finite edge stabilizers. In particular, if X is such that T is locally finite, then any cusp-uniform group G of X is virtually free.
Stirring by Small-Scale Vortices Caused by Patchy Mixing
Authors: Sundermeyer Miles A. , Ledwell James R. , Oakey Neil S. , Greenan Blair J. W. 
Published: August 2005

Abstract
Evidence is presented that lateral dispersion on scales of 1–10 km in the stratified waters of the continental shelf may be significantly enhanced by stirring by small-scale geostrophic motions caused by patches of mixed fluid adjusting in the aftermath of diapycnal mixing events. Dye-release experiments conducted during the recent Coastal Mixing and Optics (CMO) experiment provide estimates of diapycnal and lateral dispersion. Microstructure observations made during these experiments showed patchy turbulence on vertical scales of 1–10 m and horizontal scales of a few hundred meters to a few kilometers. Momentum scaling and a simple random walk formulation were used to estimate the effective lateral dispersion caused by motions resulting from lateral adjustment following episodic mixing events. It is predicted that lateral dispersion is largest when the scale of mixed patches is on the order of the internal Rossby radius of deformation, which seems to have been the case for CMO. For parameter values relevant to CMO, lower-bound estimates of the effective lateral diffusivity by this mechanism ranged from 0.1 to 1 m2 s−1. Revised estimates after accounting for the possibility of long-lived motions were an order of magnitude larger and ranged from 1 to 10 m2 s−1. The predicted dispersion is large enough to explain the observed lateral dispersion in all four CMO dye-release experiments examined.
A Model of the Zonally Averaged Stratification and Overturning in the Southern Ocean
Authors: Olbers Dirk , Visbeck Martin 
Published: August 2005

AbstractThe ocean area south of the Antarctic Circumpolar Current (ACC) frontal system is a region of major watermass modification. Influx of North Atlantic Deep Water (NADW), small-scale mixing, eddy transport and diffusion, as well as the fluxes of momentum and buoyancy at the sea surface combine in a complex array of processes to generate the unique stratification of the Southern Ocean with its southward uprising isopycnals and northward flux of Antarctic Intermediate Water (AAIW) and Antarctic Bottom Water. Comprehensive analytical models of this scenario are rare. The authors develop and apply a model based on zonally and temporally averaged theory to explain the conversion of NADW into AAIW with all of the aforementioned processes contained in an extremely simplified way. Eddies appear via a transformed Eulerian mean (TEM) approach with a conventional downgradient parameterization of the meridional density flux. The structure of the eddy coefficient is estimated from hydrographic and wind stress data by a simple inverse approach. Mixing is limited to a near-surface layer and is treated in a most simple entrainment form. The model determines the zonal mean density stratification in the Southern Ocean and the baroclinic transport of the ACC from the applied wind stress and the surface density flux and unravels the role and importance of the different processes responsible for shaping the stratification (Ekman and eddy-induced advection and pumping, mixing, surface buoyancy flux, and eddy-induced diffusion). All of these processes must be present to yield an agreement between the simulated stratification and the observed one, but details of their parameterization might not be too critical. The ACC transport is shown to have a contribution forced by the local wind stress as well as another contribution relating to the nonlocal forcing by wind stress and density flux over the entire Antarctic zone.
Wind Effects on Shoaling Wave Shape
Authors: Feddersen Falk , Veron Fabrice 
Published: August 2005

AbstractNear the shore, cross-shore winds strongly affect the location of the break point and the breaking-wave height. From casual observation from the beach, wind direction (onshore or offshore) and speed also appear to affect wave shape (i.e., skewness and asymmetry), although as of yet this effect has not been quantified near the shore. The effect of wind on shoaling wave shape is investigated with laboratory experiments using monochromatic waves and onshore-directed wind. Wind increases the shoaling wave energy at discrete multiples of the primary frequency and has a significant effect on the wave shape at both a deeper and shallower shoaling locations. At the shallower location, the ratio of wave energy at 2 times the primary frequency to the primary frequency is also a function of wind speed, indicating interaction between the wind and the nonlinear wave shoaling process. Nearshore wave models do not account for these wind effects. Incorrect predictions of third-order velocity moments (wave shape), believed to control wave-driven sediment transport, would result in incorrect beach morphological evolution predictions.
Potential approach to immunotherapy of chronic lymphocytic leukemia (CLL): enhanced immunogenicity of CLL cells via infection with vectors encoding for multiple costimulatory molecules
Authors: Palena Claudia , Foon Kenneth A. , Panicali Dennis , Yafal Alicia Gómez , Chinsangaram Jarasvech , Hodge James W. , Schlom Jeffrey , Tsang Kwong Y. 
Published: August 2005

AbstractChronic lymphocytic leukemia (CLL) is a disease of CD5+ B lymphocytes (designated as CLL cells) that are inefficient antigen-presenting cells. Their poor ability to present antigens to the T cells, largely due to an inadequate costimulatory capacity, is manifested as a failure to stimulate proliferation of both allogeneic and autologous T cells. We have investigated the ability of in vitro manipulated CLL cells, via hyperexpression of a triad of costimulatory molecules (B7-1, intercellular adhesion molecule 1 [ICAM-1], and leukocyte-function–associated antigen 3 [LFA-3], designated TRICOM), to stimulate effective antitumor T-cell responses. A recombinant modified vaccinia virus strain Ankara (MVA), which is a highly attenuated, replication-impaired virus variant, was successfully used to infect and deliver the simultaneous expression of the 3 human costimulatory molecules in TRICOM on the surface of the CLL cells. Proliferation of allogeneic and autologous T cells was observed when MVA-TRICOM–infected CLL cells were used as stimulators in proliferation assays. Cytotoxic T lymphocytes, generated in vitro by stimulation of autologous T cells with MVA-TRICOM–infected CLL cells, showed cytotoxicity against unmodified/uninfected CLL cells. Therefore, our findings suggest that the use of CLL cells infected ex vivo with MVA-TRICOM or direct injection of MVA-TRICOM in patients with CLL has potential for the immunotherapy of CLL.
The non-invasive documentation of coronary microcirculation impairment: role of transthoracic echocardiography
Authors: Dimitrow Pawel Petkow , Galderisi Maurizio , Rigo Fausto 
Published: August 2005

Abstract
Transthoracic Doppler echocardiographic-derived coronary flow reserve is an useful hemodynamic index to assess dysfunction of coronary microcirculation. Isolated coronary microvascular abnormalities are overt by reduced coronary flow reserve despite normal epicardial coronary arteries. These abnormalities may occur in several diseases (arterial hypertension, diabetes mellitus, hypercholesterolemia, syndrome X, aortic valve disease, hypertrophic cardiomyopathy and idiopathic dilated cardiomyopathy). The prognostic role of impaired microvascular coronary flow reserve has been shown unfavourable especially in hypertrophic or idiopathic dilated cardiomyopathies. Coronary flow reserve reduction may be reversible, for instance after regression of left ventricular hypertrophy subsequent to valve replacement in patients with aortic stenosis, after anti-hypertensive treatment or using cholesterol lowering drugs. Coronary flow reserve may increase by 30% or more after pharmacological therapy and achieve normal level >3.0. In contrast to other non invasive tools as positron emission tomography, very expensive and associated with radiation exposure, transthoracic Doppler-derived coronary flow reserve is equally non invasive but cheaper, very accessible and prone to a reliable exploration of coronary microvascular territories, otherwise not detectable by invasive coronary angiography, able to visualize only large epicardial arteries.