bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hemodynamic, Echocardiographic, and Exercise‐Related Effects of the HeartWare Left Ventricular Assist Device in Advanced Heart Failure
Authors: McDiarmid Adam , Gordon Brian , Wrightson Neil , Robinson‐Smith Nicola , Pillay Thasee , Parry Gareth , Schueler Stephan , MacGowan Guy A. 
Published: July 2012

©2012 Wiley Periodicals, Inc.The aim of this study was to determine the effects of the HeartWare left ventricular assist device (HVAD) (HeartWare International, Inc, Framingham, MA) on hemodynamics, ventricular function, and exercise capacity. Between July 2009 and March 2011, 46 patients with advanced heart failure had implantation of the HVAD. Of these patients, 30 had subsequent assessments for transplantation and these patients formed the study cohort. Thirty patients had assessments at a mean of 201±86 days and 13 went on to have a second assessment at 351±86 days. There were marked improvements in hemodynamics and exercise capacity at both assessments, with significant decreases in right and left heart filling pressures; increases in cardiac index, New York Heart Association class, and peak exercise oxygen consumption; and reduction in pulmonary vascular resistance (all P<.05). Left ventricular end‐diastolic and end‐systolic dimensions were unchanged at the first assessment, although there was a significant reduction in end‐diastolic diameter at the second assessment (P<.01). There were no significant changes in a visual grade of right ventricular function. After up to 1 year of support, the HVAD system results in significant benefits in overall heart failure status, with improved hemodynamics and exercise capacity. This occurs in the absence of marked changes in left ventricular size or right ventricular function.
EvolMarkers: a database for mining exon and intron markers for evolution, ecology and conservation studies
Authors: LI CHENHONG , RIETHOVEN JEAN‐JACK M. , NAYLOR GAVIN J. P. 
Published: July 2012

AbstractRecent innovations in next‐generation sequencing have lowered the cost of genome projects. Nevertheless, sequencing entire genomes for all representatives in a study remains expensive and unnecessary for most studies in ecology, evolution and conservation. It is still more cost‐effective and efficient to target and sequence single‐copy nuclear gene markers for such studies. Many tools have been developed for identifying nuclear markers, but most of these have focused on particular taxonomic groups. We have built a searchable database, EvolMarkers, for developing single‐copy coding sequence (CDS) and exon‐primed‐intron‐crossing (EPIC) markers that is designed to work across a broad range of phylogenetic divergences. The database is made up of single‐copy CDS derived from BLAST searches of a variety of metazoan genomes. Users can search the database for different types of markers (CDS or EPIC) that are common to different sets of input species with different divergence characteristics. EvolMarkers can be applied to any taxonomic group for which genome data are available for two or more species. We included 82 genomes in the first version of EvolMarkers and have found the methods to be effective across Placozoa, Cnidaria, Arthropod, Nematoda, Annelida, Mollusca, Echinodermata, Hemichordata, Chordata and plants. We demonstrate the effectiveness of searching for CDS markers within annelids and show how to find potentially useful intronic markers within the lizard Anolis.
Laminar Regulation of STAT1 and STAT3 in Black Walnut Extract and Carbohydrate Overload Induced Models of Laminitis
Authors: Leise B.S. , Watts M. , Tanhoff E. , Johnson P.J. , Black S.J. , Belknap J.K. 
Published: July 2012

Background
STAT1 and STAT3 are important signaling molecules in disorders of systemic inflammation and are likely to be involved in laminitis, as laminar and systemic inflammation have been well documented in experimental models of laminitis.HypothesisThe STAT1 and STAT3 activation (via phosphorylation of tyrosine and serine moieties) is occurring in the laminar tissue during the developmental and onset of lameness time points in both the black walnut extract (BWE) and carbohydrate overload (CHO) models of laminitis.AnimalsArchived laminar tissue from horses.MethodsExperimental studies of induced laminitis (BWE and CHO administration) in horses were conducted and laminar tissue samples archived. Western hybridization was performed to determine concentrations of Tyr‐ and Ser‐phosphorylated STAT1 and STAT3 from these archived samples. The RT‐qPCR was also performed to assess mRNA concentrations of target genes of STAT1 and STAT3.ResultsIncreases (P < .05) in phosphorylation of tyrosine705 and serine727 of STAT3, demonstrated by band intensity ratios, are present in laminar tissue from both the BWE and CHO models at the DEV and OG1 time points. No change in phosphorylation of tyrosine701 or serine727 of STAT1 was present in the laminar tissue from either the BWE or the CHO models. The SOCS3 mRNA concentrations were increased at the onset of lameness in both the CHO and BWE models.Conclusions and Clinical RelevanceThe STAT3 activation likely plays a role in equine laminitis, similar to its reported involvement in organ injury/failure in human sepsis. Regulation of JAK‐STAT, through STAT3 inhibitors, might serve as potential therapeutic target for controlling the inflammatory response in the septic horse.
Left Atrial Function in Cats with Left‐Sided Cardiac Disease and Pleural Effusion or Pulmonary Edema
Authors: Johns S.M. , Nelson O.L. , Gay J.M. 
Published: July 2012

BackgroundCongestive heart failure (CHF) in cats with left‐sided heart disease is sometimes manifest as pleural effusion, in other cases as pulmonary edema.HypothesisThose cats with pleural effusion have more severe left atrial (LA) dysfunction than cats with pulmonary edema.Animals30 healthy cats, 22 cats with pleural effusion, and 12 cats with pulmonary edema. All cats were client owned.MethodsRetrospective study. Measurements ofLAsize and function were made using commercial software on archived echocardiograms. Cases were identified through searches of medical records and of archived echocardiograms for cats with these conditions.ResultsThere was no difference (P = .3) inLAsize between cats with pleural effusion and cats with pulmonary edema. Cats with pleural effusion had poorer (P = .04)LAactive emptying and increased (P = .006) right ventricular (RV) diameter when compared with cats with pulmonary edema and healthy cats. Cats that exhibitedLAactive emptying of <7.9%, total emptying of <13.6% (diameter) or <19.4% (area), orRVdiameter of >3.6 mm were significantly (P < .001) more likely to manifest pleural effusion.Conclusions and Clinical ImportancePoorerLAfunction and increasedRVdimensions are associated with pleural effusion in cats with left‐sided heart disease.
Overexpression of
ShCYP51B
and
ShatrD
in Sclerotinia homoeocarpa Isolates Exhibiting Practical Field Resistance to a Demethylation Inhibitor Fungicide
Authors: Hulvey Jon , Popko James T. , Sang Hyunkyu , Berg Andrew , Jung Geunhwa 
Published: July 2012

ABSTRACT

We investigated genetic factors that govern the reduced propiconazole sensitivity of
Sclerotinia homoeocarpa
field isolates collected during a 2-year field efficacy study on dollar spot disease of turf in five New England sites. These isolates displayed a >50-fold range of
in vitro
sensitivity to a sterol demethylation inhibitor (DMI) fungicide, propiconazole, making them ideal for investigations of genetic mechanisms of reduced DMI sensitivity. The
CYP51
gene homolog in
S. homoeocarpa
(
ShCYP51B
), encoding the enzyme target of DMIs, is likely a minor genetic factor for reduced propiconazole sensitivity, since there were no differences in constitutive relative expression (RE) values and only 2-fold-higher induced RE values for insensitive than for sensitive isolate groups. Next, we mined RNA-Seq transcriptome data for additional genetic factors and found evidence for the overexpression of a homolog of
Botrytis cinerea atrD
(
BcatrD
),
ShatrD
, a known efflux transporter of DMI fungicides. The
ShatrD
gene showed much higher constitutive and induced RE values for insensitive isolates. Several polymorphisms were found upstream of
ShatrD
but were not definitively linked to overexpression. The screening of constitutive RE values of
ShCYP51B
and
ShatrD
in isolates from two golf courses that exhibited practical field resistance to propiconazole uncovered evidence for significant population-specific overexpression of both genes. However, linear regression demonstrated that the RE of
ShatrD
displays a more significant relationship with propiconazole sensitivity than that of
ShCYP51B
. In summary, our results suggest that efflux is a major determinant of the reduced DMI sensitivity of
S. homoeocarpa
genotypes in New England, which may have implications for the emergence of practical field resistance in this important turfgrass pathogen.
Characterization of a Leuconostoc Bacteriophage Infecting Flavor Producers of Cheese Starter Cultures
Authors: Kleppen Hans Petter , Nes Ingolf F. , Holo Helge 
Published: July 2012

ABSTRACT

Dairy siphovirus φLmd1, which infects starter culture isolate
Leuconostoc mesenteroides
subsp.
dextranicum
A1, showed resistance to pasteurization and was able to grow on 3 of the 4 commercial starter cultures tested. Its 26,201-bp genome was similar to that of
Leuconostoc
phage of vegetable origin but not to those of dairy phages infecting
Lactococcus
.
Identification of Soil Bacteria Susceptible to TiO
2
and ZnO Nanoparticles
Authors: Ge Yuan , Schimel Joshua P. , Holden Patricia A. 
Published: July 2012

ABSTRACT

Because soil is expected to be a major sink for engineered nanoparticles (ENPs) released to the environment, the effects of ENPs on soil processes and the organisms that carry them out should be understood. DNA-based fingerprinting analyses have shown that ENPs alter soil bacterial communities, but specific taxon changes remain unknown. We used bar-coded pyrosequencing to explore the responses of diverse bacterial taxa to two widely used ENPs, nano-TiO
2
and nano-ZnO, at various doses (0, 0.5, 1.0, and 2.0 mg g
−1
soil for TiO
2
; 0.05, 0.1, and 0.5 mg g
−1
soil for ZnO) in incubated soil microcosms. These ENPs significantly altered the bacterial communities in a dose-dependent manner, with some taxa increasing as a proportion of the community, but more taxa decreasing, indicating that effects mostly reduced diversity. Some of the declining taxa are known to be associated with nitrogen fixation (
Rhizobiales
,
Bradyrhizobiaceae
, and
Bradyrhizobium
) and methane oxidation (
Methylobacteriaceae
), while some positively impacted taxa are known to be associated with the decomposition of recalcitrant organic pollutants (
Sphingomonadaceae
) and biopolymers including protein (
Streptomycetaceae
and
Streptomyces
), indicating potential consequences to ecosystem-scale processes. The latter was suggested by a positive correlation between protease activity and the relative abundance of
Streptomycetaceae
(
R
= 0.49,
P
= 0.000) and
Streptomyces
(
R
= 0.47,
P
= 0.000). Our results demonstrate that some metal oxide nanoparticles could affect soil bacterial communities and associated processes through effects on susceptible, narrow-function bacterial taxa.
Proximity-Dependent Inhibition of Growth of Mannheimia haemolytica by Pasteurella multocida
Authors: Bavananthasivam Jegarubee , Dassanayake Rohana P. , Kugadas Abirami , Shanthalingam Sudarvili , Call Douglas R. , Knowles Donald P. , Srikumaran Subramaniam 
Published: July 2012

ABSTRACT

Mannheimia haemolytica
,
Pasteurella multocida
, and
Bibersteinia trehalosi
have been identified in the lungs of pneumonic bighorn sheep (BHS;
Ovis canadensis
). Of these pathogens,
M. haemolytica
has been shown to consistently cause fatal pneumonia in BHS under experimental conditions. However,
M. haemolytica
has been isolated by culture less frequently than the other bacteria. We hypothesized that the growth of
M. haemolytica
is inhibited by other bacteria in the lungs of BHS. The objective of this study was to determine whether
P. multocida
inhibits the growth of
M. haemolytica
. Although in monoculture both bacteria exhibited similar growth characteristics, in coculture with
P. multocida
there was a clear inhibition of growth of
M. haemolytica
. The inhibition was detected at mid-log phase and continued through the stationary phase. When cultured in the same medium, the growth of
M. haemolytica
was inhibited when both bacteria were separated by a membrane that allowed contact (pore size, 8.0 μm) but not when they were separated by a membrane that limited contact (pore size, 0.4 μm). Lytic bacteriophages or bactericidal compounds could not be detected in the culture supernatant fluid from monocultures of
P. multocida
or from
P. multocida
-
M. haemolytica
cocultures. These results indicate that
P. multocida
inhibits the growth of
M. haemolytica
by a contact- or proximity-dependent mechanism. If the inhibition of growth of
M. haemolytica
by
P. multocida
occurs
in vivo
as well, it could explain the inconsistent isolation of
M. haemolytica
from the lungs of pneumonic BHS.
Characterization of Staphylococcus aureus Strains Associated with Food Poisoning in Shenzhen, China
Authors: Yan Xiaomei , Wang Bing , Tao Xiaoxia , Hu Qinghua , Cui Zhigang , Zhang Jianzhong , Lin Yiman , You Yuanhai , Shi Xiaolu , Grundmann Hajo 
Published: July 2012

ABSTRACT

To characterize isolates of
Staphylococcus aureus
that were associated with staphylococcal food poisoning between 2006 and 2009 in Shenzhen, Southern China, a total of 52
Staphylococcus aureus
isolates from 11 outbreaks were analyzed by using multilocus sequence typing (MLST),
spa
typing, and pulsed-field gel electrophoresis (PFGE). PCR analysis was used to analyze the staphylococcal enterotoxin (SE) genes
sea
to
sei
, and antimicrobial susceptibility testing was also performed. ST6 was the most dominant sequence type (ST), constituting 63.5% (34/52) of all of the isolates in 7 outbreaks. The next most common ST was ST943, which constituted 23.1% (12/52) of the isolates that were collected from 3 outbreaks. t701, t091, and t2360 were the most predominant
spa
types, constituting 67.3% (35/52) of the isolates that were collected from 11 outbreaks. Three PFGE types, (types A, B, and C) were the most frequently observed types, constituting 84.6% (44/52) of all of the isolates. The enterotoxin gene that we detected most frequently was
sea
(45/52; 86.5%). Four SE gene profiles were observed, including
sea
(
n
= 45),
sec-seh
(
n
= 3),
seb
(
n
= 2), and
seg-sei
(
n
= 2). With respect to antibiotic resistance, penicillin resistance was the most common (96.2%; 50/52), followed by resistance to tetracycline (28.8%; 15/52). Approximately 30.8% (16/52) of the isolates were resistant to at least two antibiotics, and 7.7% (4/52) of the isolates were resistant to three or more drugs. The two predominant
S. aureus
lineages, (i) PFGE types A and B with ST6 and (ii) PFGE type C with ST943, were identified in the outbreaks.
Proteomic Analysis of Survival of Rhodococcus jostii RHA1 during Carbon Starvation
Authors: Patrauchan Marianna A. , Miyazawa Daisuke , LeBlanc Justin C. , Aiga Carol , Florizone Christine , Dosanjh Manisha , Davies Julian , Eltis Lindsay D. , Mohn William W. 
Published: July 2012

ABSTRACT

Rhodococcus jostii
RHA1, a catabolically diverse soil actinomycete, is highly resistant to long-term nutrient starvation. After 2 years of carbon starvation, 10% of the bacterial culture remained viable. To study the molecular basis of such resistance, we monitored the abundance of about 1,600 cytosolic proteins during a 2-week period of carbon source (benzoate) starvation. Hierarchical cluster analysis elucidated 17 major protein clusters and showed that most changes occurred during transition to stationary phase. We identified 196 proteins. A decrease in benzoate catabolic enzymes correlated with benzoate depletion, as did induction of catabolism of alternative substrates, both endogenous (lipids, carbohydrates, and proteins) and exogenous. Thus, we detected a transient 5-fold abundance increase for phthalate, phthalate ester, biphenyl, and ethyl benzene catabolic enzymes, which coincided with at least 4-fold increases in phthalate and biphenyl catabolic activities. Stationary-phase cells demonstrated an ∼250-fold increase in carbon monoxide dehydrogenase (CODH) concurrent with a 130-fold increase in CODH activity, suggesting a switch to CO or CO
2
utilization. We observed two phases of stress response: an initial response occurred during the transition to stationary phase, and a second response occurred after the cells had attained stationary phase. Although SigG synthesis was induced during starvation, a Δ
sigG
deletion mutant showed only minor changes in cell survival. Stationary-phase cells underwent reductive cell division. The extreme capacity of RHA1 to survive starvation does not appear to involve novel mechanisms; rather, it seems to be due to the coordinated combination of earlier-described mechanisms.
Toxigenic Clostridium difficile PCR Ribotypes from Wastewater Treatment Plants in Southern Switzerland
Authors: Romano Vincenza , Pasquale Vincenzo , Krovacek Karel , Mauri Federica , Demarta Antonella , Dumontet Stefano 
Published: July 2012

ABSTRACT

The occurrence of
Clostridium difficile
in nine wastewater treatment plants in the Ticino Canton (southern Switzerland) was investigated. The samples were collected from raw sewage influents and from treated effluents. Forty-seven out of 55 characterized
C. difficile
strains belonged to 13 different reference PCR ribotypes (009, 010, 014, 015, 039, 052, 053, 066, 070, 078, 101, 106, and 117), whereas 8 strains did not match any of those available in our libraries. The most frequently isolated ribotype (40%) was 078, isolated from six wastewater treatment plants, whereas ribotype 066, a toxigenic emerging ribotype isolated from patients admitted to hospitals in Europe and Switzerland, was isolated from the outgoing effluent of one plant. The majority of the isolates (85%) were toxigenic. Forty-nine percent of them produced toxin A, toxin B, and the binary toxin (toxigenic profile A
+
B
+
CDT
+
), whereas 51% showed the profile A
+
B
+
CDT
−
. Interestingly, eight ribotypes (010, 014, 015, 039, 066, 078, 101, and 106) were among the riboprofiles isolated from symptomatic patients admitted to the hospitals of the Ticino Canton in 2010. Despite the limitation of sampling, this study highlights that toxigenic ribotypes of
C. difficile
involved in human infections may occur in both incoming and outgoing biological wastewater treatment plants. Such a finding raises concern about the possible contamination of water bodies that receive wastewater treatment plant effluents and about the safe reuse of treated wastewater.
Identification of a
p
-Coumarate Degradation Regulon in Rhodopseudomonas palustris by Xpression, an Integrated Tool for Prokaryotic RNA-Seq Data Processing
Authors: Phattarasukol Somsak , Radey Matthew C. , Lappala Colin R. , Oda Yasuhiro , Hirakawa Hidetada , Brittnacher Mitchell J. , Harwood Caroline S. 
Published: July 2012

ABSTRACT

High-throughput sequencing of cDNA prepared from RNA, an approach known as RNA-seq, is coming into increasing use as a method for transcriptome analysis. Despite its many advantages, widespread adoption of the technique has been hampered by a lack of easy-to-use, integrated, open-source tools for analyzing the nucleotide sequence data that are generated. Here we describe Xpression, an integrated tool for processing prokaryotic RNA-seq data. The tool is easy to use and is fully automated. It performs all essential processing tasks, including nucleotide sequence extraction, alignment, quantification, normalization, and visualization. Importantly, Xpression processes multiplexed and strand-specific nucleotide sequence data. It extracts and trims specific sequences from files and separately quantifies sense and antisense reads in the final results. Outputs from the tool can also be conveniently used in downstream analysis. In this paper, we show the utility of Xpression to process strand-specific RNA-seq data to identify genes regulated by CouR, a transcription factor that controls
p
-coumarate degradation by the bacterium
Rhodopseudomonas palustris
.
Changes in Bowel Microbiota Induced by Feeding Weanlings Resistant Starch Stimulate Transcriptomic and Physiological Responses
Authors: Young Wayne , Roy Nicole C. , Lee Julian , Lawley Blair , Otter Don , Henderson Gemma , McCann Mark J. , Tannock Gerald W. 
Published: July 2012

ABSTRACT

The ability to predictably engineer the composition of bowel microbial communities (microbiota) using dietary components is important because of the reported associations of altered microbiota composition with medical conditions. In a synecological study, weanling conventional Sprague-Dawley rats (21 days old) were fed a basal diet (BD) or a diet supplemented with resistant starch (RS) at 5%, 2.5%, or 1.25% for 28 days. Pyrosequencing of 16S rRNA genes and temporal temperature gradient electrophoresis (TTGE) profiles in the colonic digesta showed that rats fed RS had altered microbiota compositions due to blooms of
Bacteroidetes
and
Actinobacteria
. The altered microbiota was associated with changes in colonic short-chain fatty acid (SCFA) concentrations, colonic-tissue gene expression (
Gsta2
and
Ela1
), and host physiology (serum metabolite profiles and colonic goblet cell numbers). Comparisons between germ-free and conventional rats showed that transcriptional and serum metabolite differences were mediated by the microbiota and were not the direct result of diet composition. Altered transcriptomic and physiological responses may reflect the young host's attempts to maintain homeostasis as a consequence of exposure to a new collection of bacteria and their associated biochemistry.
Bioremediation and Tolerance of Humans to Heavy Metals through Microbial Processes: a Potential Role for Probiotics?
Authors: Monachese Marc , Burton Jeremy P. , Reid Gregor 
Published: July 2012

ABSTRACTThe food and water we consume are often contaminated with a range of chemicals and heavy metals, such as lead, cadmium, arsenic, chromium, and mercury, that are associated with numerous diseases. Although heavy-metal exposure and contamination are not a recent phenomenon, the concentration of metals and the exposure to populations remain major issues despite efforts at remediation. The ability to prevent and manage this problem is still a subject of much debate, with many technologies ineffective and others too expensive for practical large-scale use, especially for developing nations where major pollution occurs. This has led researchers to seek alternative solutions for decontaminating environmental sites and humans themselves. A number of environmental microorganisms have long been known for their ability to bind metals, but less well appreciated are human gastrointestinal bacteria. Species such asLactobacillus, present in the human mouth, gut, and vagina and in fermented foods, have the ability to bind and detoxify some of these substances. This review examines the current understanding of detoxication mechanisms of lactobacilli and how, in the future, humans and animals might benefit from these organisms in remediating environmental contamination of food.
Intestinal Origin of Sourdough
Lactobacillus reuteri
Isolates as Revealed by Phylogenetic, Genetic, and Physiological Analysis
Authors: Su Marcia Shu-Wei , Oh Phaik Lyn , Walter Jens , Gänzle Michael G. 
Published: July 2012

ABSTRACT

Lactobacillus reuteri
is both a gut symbiont and a stable member of sourdough microbiota. This study employed multilocus sequence analysis and an analysis of host-specific physiological and genetic traits to assign five sourdough isolates to rodent- or human-specific lineages. Comparative genome hybridization revealed that the model sourdough isolate LTH2584 had a genome content very similar to that of the model rodent isolate 100-23. These results demonstrate that sourdough isolates of
L. reuteri
are of intestinal origin.