bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hole-Pattern and Honeycomb Seal Rotordynamic Forces: Validation of CFD-Based Prediction Techniques
Authors: Krogh Nielsen Kenny , Jønck Kasper , Underbakke Harald 
Published: December 2013

This paper deals with modeling of hole-pattern and honeycomb seals. These are frequently used as balance piston seals in high pressure centrifugal compressor applications as they have the potential to facilitate superior rotordynamic damping characteristics while providing good leakage control. On the other hand it is also well-established that the rotordynamic performance of hole-pattern and honeycomb seals is very sensitive to convergence and divergence in the streamwise direction.
The ISOTSEAL bulk-flow code has shown difficulties in predicting the rotordynamic coefficients for convergent seal geometries or in cases with negative preswirl. This has lead to increased interest in CFD-based analysis of seal dynamics. CFD-based models generally have less assumptions and are applicable for complex geometries or operating ranges not covered by bulk-flow codes.
The CFD-based Instationary Perturbation Model (IPM) is utilized for the analysis of the hole-pattern and honeycomb seals. The rotordynamic forces are obtained by means of a time-dependent perturbation of the rotor position with respect to the stator. A sequence of perturbation frequencies is utilized to obtain the frequency dependence of the rotordynamic seal force coefficients.
A strong effort has been put into validating the CFD-based perturbation modeling techniques against published experimental seal test data and the paper describes selected validation cases. A constant-clearance hole-pattern seal and a convergent honeycomb seal are analyzed and the results are compared to experimental results. The frequency dependence of the rotordynamic stiffness and damping characteristics of the seals is very well-captured for both types of seals.
Finally the IPM method was applied to a convergent hole-pattern seal to investigate the effects of eccentricity on the rotordynamic coefficients. The results are consistent with available experimental data.
Corrosion of Iron by Sulfate-Reducing Bacteria: New Views of an Old Problem
Authors: Enning Dennis , Garrelfs Julia 
Published: December 2013

ABSTRACT

About a century ago, researchers first recognized a connection between the activity of environmental microorganisms and cases of anaerobic iron corrosion. Since then, such microbially influenced corrosion (MIC) has gained prominence and its technical and economic implications are now widely recognized. Under anoxic conditions (e.g., in oil and gas pipelines), sulfate-reducing bacteria (SRB) are commonly considered the main culprits of MIC. This perception largely stems from three recurrent observations. First, anoxic sulfate-rich environments (e.g., anoxic seawater) are particularly corrosive. Second, SRB and their characteristic corrosion product iron sulfide are ubiquitously associated with anaerobic corrosion damage, and third, no other physiological group produces comparably severe corrosion damage in laboratory-grown pure cultures. However, there remain many open questions as to the underlying mechanisms and their relative contributions to corrosion. On the one hand, SRB damage iron constructions indirectly through a corrosive chemical agent, hydrogen sulfide, formed by the organisms as a dissimilatory product from sulfate reduction with organic compounds or hydrogen (“chemical microbially influenced corrosion”; CMIC). On the other hand, certain SRB can also attack iron via withdrawal of electrons (“electrical microbially influenced corrosion”; EMIC),
viz
., directly by metabolic coupling. Corrosion of iron by SRB is typically associated with the formation of iron sulfides (FeS) which, paradoxically, may reduce corrosion in some cases while they increase it in others. This brief review traces the historical twists in the perception of SRB-induced corrosion, considering the presently most plausible explanations as well as possible early misconceptions in the understanding of severe corrosion in anoxic, sulfate-rich environments.
Measurement of Ice Nucleation-Active Bacteria on Plants and in Precipitation by Quantitative PCR
Authors: Hill Thomas C. J. , Moffett Bruce F. , DeMott Paul J. , Georgakopoulos Dimitrios G. , Stump William L. , Franc Gary D. 
Published: December 2013

ABSTRACT

Ice nucleation-active (INA) bacteria may function as high-temperature ice-nucleating particles (INP) in clouds, but their effective contribution to atmospheric processes, i.e., their potential to trigger glaciation and precipitation, remains uncertain. We know little about their abundance on natural vegetation, factors that trigger their release, or persistence of their ice nucleation activity once airborne. To facilitate these investigations, we developed two quantitative PCR (qPCR) tests of the
ina
gene to directly count INA bacteria in environmental samples. Each of two primer pairs amplified most alleles of the
ina
gene and, taken together, they should amplify all known alleles. To aid primer design, we collected many new INA isolates. Alignment of their partial
ina
sequences revealed new and deeply branching clades, including sequences from
Pseudomonas syringae
pv.
atropurpurea
,
Ps. viridiflava
,
Pantoea agglomerans
,
Xanthomonas campestris
, and possibly
Ps. putida
,
Ps. auricularis
, and
Ps. poae
. qPCR of leaf washings recorded ∼10
8
ina
genes g
−1
fresh weight of foliage on cereals and 10
5
to 10
7
g
−1
on broadleaf crops. Much lower populations were found on most naturally occurring vegetation. In fresh snow,
ina
genes from various INA bacteria were detected in about half the samples but at abundances that could have accounted for only a minor proportion of INP at −10°C (assuming one
ina
gene per INA bacterium). Despite this, an apparent biological source contributed an average of ∼85% of INP active at −10°C in snow samples. In contrast, a thunderstorm hail sample contained 0.3 INA bacteria per INP active at −10°C, suggesting a significant contribution to this sample.
Replicon-Dependent Differentiation of Symbiosis-Related Genes in Sinorhizobium Strains Nodulating Glycine max
Authors: Guo Hui Juan , Wang En Tao , Zhang Xing Xing , Li Qin Qin , Zhang Yan Ming , Tian Chang Fu , Chen Wen Xin 
Published: December 2013

ABSTRACT

In order to investigate the genetic differentiation of
Sinorhizobium
strains nodulating
Glycine max
and related microevolutionary mechanisms, three housekeeping genes (
SMc00019
,
truA
, and
thrA
) and 16 symbiosis-related genes on the chromosome (7 genes), pSymA (6 genes), and pSymB (3 genes) were analyzed. Five distinct species were identified among the test strains by calculating the average nucleotide identity (ANI) of
SMc00019-truA-thrA
:
Sinorhizobium fredii
,
Sinorhizobium sojae
,
Sinorhizobium
sp. I,
Sinorhizobium
sp. II, and
Sinorhizobium
sp. III. These species assignments were also supported by population genetics and phylogenetic analyses of housekeeping genes and symbiosis-related genes on the chromosome and pSymB. Different levels of genetic differentiation were observed among these species or different replicons.
S. sojae
was the most divergent from the other test species and was characterized by its low intraspecies diversity and limited geographic distribution. Intergenic recombination dominated the evolution of 19 genes from different replicons. Intraspecies recombination happened frequently in housekeeping genes and symbiosis-related genes on the chromosome and pSymB, whereas pSymA genes showed a clear pattern of lateral-transfer events between different species. Moreover, pSymA genes were characterized by a lower level of polymorphism and recombination than those on the chromosome and pSymB. Taken together, genes from different replicons of rhizobia might be involved in the establishment of symbiosis with legumes, but these symbiosis-related genes might have evolved differently according to their corresponding replicons.
Revealing the Genetic Basis of Natural Bacterial Phenotypic Divergence
Authors: Freddolino Lydia , Goodarzi Hani , Tavazoie Saeed 
Published: December 2013

ABSTRACT

Divergent phenotypes for distantly related strains of bacteria, such as differing antibiotic resistances or organic solvent tolerances, are of keen interest both from an evolutionary perspective and for the engineering of novel microbial organisms and consortia in synthetic biology applications. A prerequisite for any practical application of this phenotypic diversity is knowledge of the genetic determinants for each trait of interest. Sequence divergence between strains is often so extensive as to make brute-force approaches to identifying the loci contributing to a given trait impractical. Here we describe a global linkage analysis approach, GLINT, for rapid discovery of the causal genetic variants underlying phenotypic divergence between distantly related strains of
Escherichia coli
. This general strategy will also be usable, with minor modifications, for revealing genotype-phenotype associations between naturally occurring strains of other bacterial species.
The Uptake Hydrogenase in the Unicellular Diazotrophic Cyanobacterium Cyanothece sp. Strain PCC 7822 Protects Nitrogenase from Oxygen Toxicity
Authors: Zhang Xiaohui , Sherman Debra M. , Sherman Louis A. 
Published: December 2013

ABSTRACT

Cyanothece
sp. strain PCC 7822 is a unicellular, diazotrophic cyanobacterium that can produce large quantities of H
2
when grown diazotrophically. This strain is also capable of genetic manipulations and can represent a good model for improving H
2
production from cyanobacteria. To this end, a knockout mutation was made in the
hupL
gene (Δ
hupL
), and we determined how this would affect the amount of H
2
produced. The Δ
hupL
mutant demonstrated virtually no nitrogenase activity or H
2
production when grown under N
2
-fixing conditions. To ensure that this mutation only affected the
hupL
gene, a complementation strain was constructed readily with wild-type properties; this indicated that the original insertion was only in
hupL
. The mutant had no uptake hydrogenase activity but had increased bidirectional hydrogenase (Hox) activity. Western blotting and immunocytochemistry under the electron microscope indicated that the mutant had neither HupL nor NifHDK, although the
nif
genes were transcribed. Interestingly, biochemical analysis demonstrated that both HupL and NifH could be membrane associated. The results indicated that the
nif
genes were transcribed but that NifHDK was either not translated or was translated but rapidly degraded. We hypothesized that the Nif proteins were made but were unusually susceptible to O
2
damage. Thus, we grew the mutant cells under anaerobic conditions and found that they grew well under N
2
-fixing conditions. We conclude that in unicellular diazotrophs, like
Cyanothece
sp. strain PCC 7822, the HupLS complex helps remove oxygen from the nitrogenase, and that this is a more important function than merely oxidizing the H
2
produced by the nitrogenase.
Ozone air pollution and ischaemic stroke occurrence: a case-crossover study in Nice, France
Authors: Suissa Laurent , Fortier Mikael , Lachaud Sylvain , Staccini Pascal , Mahagne Marie-Hélène 
Published: December 2013

ObjectivesRelationship between low-level air pollution and stroke is conflicting. This study was conducted to document the relationship between outdoor air pollution and ischaemic stroke occurrence.DesignTime-stratified case-crossover analysis.SettingUniversity Hospital of Nice, France.ParticipantsAll consecutive patients with ischaemic stroke living in Nice admitted in the University Hospital of Nice (France) between January 2007 and December 2011.Main outcome measureAssociation (adjusted OR) between daily levels of outdoor pollutants (ozone (O3), nitrogen dioxide (NO2), particulate matter (PM10) and sulfur dioxide (SO2)) and ischaemic stroke occurrence.Results1729 patients with ischaemic stroke (mean age: 76.1±14.0 years; men: 46.7%) were enrolled. No significant association was found between stroke occurrence and short-term effects of all pollutants tested. In stratified analysis, we observed significant associations only between recurrent (n=280) and large artery ischaemic stroke (n=578) onset and short-term effect of O3exposure. For an increase of 10 µg/m3of O3level, recurrent stroke risk (mean D-1, D-2 and D-3 lag) was increased by 12.1% (95% CI 1.5% to 23.9%) and large artery stroke risk (mean D-3 and D-4 lag) was increased by 8% (95% CI 2.0% to 16.6%). Linear dose–response relationship for both subgroups was found.ConclusionsOur results confirm the relationship between low-level O3exposure and ischaemic stroke in high vascular risk subgroup with linear exposure–response relation, independently of other pollutants and meteorological parameters. The physiopathological processes underlying this association between ischaemic stroke and O3exposure remain to be investigated.
Associations between race, lifecourse socioeconomic position and prevalence of diabetes among US women and men: results from a population-based panel study
Authors: Insaf T Z , Strogatz D S , Yucel R M , Chasan-Taber L , Shaw B A 
Published: December 2013

BackgroundFew studies have examined the degree to which racial disparities in the development of diabetes are accounted by differences in lifecourse socioeconomic position (SEP). We assessed the association between race, lifecourse SEP measures and prevalence of diabetes in a representative US sample of black and white adults.MethodsA generalised estimating equations approach was used with a sample of 3497 adults from the Americans’ Changing Lives study. Sex-specific models were calculated to compute prevalence ratios (PR) for associations of race and SEP with self-reported diagnoses of diabetes.ResultsFor men, childhood and adult SEP were unrelated to diabetes, and adjustment for lifecourse SEP had little effect on the excess diabetes in blacks (PR=1.56, 95% CI 1.11 to 2.21). Adjustment for measures of lifecourse SEP reduced the PR for the association between race and diabetes in women from 1.96 (95% CI 1.52 to 2.54) to 1.40 (95% CI 1.04 to 1.87) with the respondent's education responsible for most of the reduction in the association. However, diabetes was also inversely associated with father's education, and low SEP throughout the lifecourse was associated with a nearly threefold increase in diabetes (PR=2.89, 95% CI 2.10 to 3.99).ConclusionsRacial disparities in diabetes existed among both men and women, but lifecourse SEP was related to diabetes only among women. The pathway and cumulative hypotheses for lifecourse SEP effects on diabetes may be especially salient for women.
Deep Sequence Analysis of Gene Expression Identifies Osteopontin as a Downstream Effector of Integrin-Linked Kinase (ILK) in Cardiac-Specific ILK Knockout Mice
Authors: Dai Jing , Matsui Takashi , Abel E. Dale , Dedhar Shoukat , Gerszten Robert E. , Seidman Christine E. , Seidman J.G. , Rosenzweig Anthony 
Published: December 2013

Background—
Integrin-linked kinase (ILK) is a serine/threonine kinase that has been linked to human and experimental heart failure, but its role in the heart is not fully understood.

Methods and Results—

To define the role of cardiomyocyte ILK, we generated cardiac-specific ILK knockout mice using α-myosin heavy chain–driven Cre expression. Cardiac-specific ILK knockout mice spontaneously developed lethal dilated cardiomyopathy and heart failure with an early increase in apoptosis, fibrosis, and cardiac inflammation. To identify downstream effectors, we used deep sequence analysis of gene expression to compare comprehensive transcriptional profiles of cardiac-specific ILK knockout and wild-type hearts from 10-day-old mice before the development of cardiac dysfunction. Approximately 2×10
6
cDNA clones from each genotype were sequenced, corresponding to 33 274 independent transcripts. A total of 93 genes were altered, using nominal thresholds of >1.4-fold change and
P
<0.001. The most highly upregulated gene was osteopontin (47-fold increase;
P
=9.6×10
−45
), an inflammatory chemokine implicated in heart failure pathophysiology. ILK also regulated osteopontin expression in cardiomyocytes in vitro. Importantly, blocking antibodies to osteopontin mitigated but did not fully rescue the functional decline in cardiac-specific ILK knockout mice.

Conclusions—
Cardiomyocyte-specific ILK deletion leads to a lethal cardiomyopathy characterized by cardiomyocyte death, fibrosis, and inflammation. Comprehensive profiling identifies ILK-dependent transcriptional effects and implicates osteopontin as a contributor to these phenotypes.
The relationship between working status and symptoms, quality of life and self-esteem in patients with schizophrenia in Turkey
Authors: Hacioglu Yildirim Munevver , Alantar Zeynep , Yildirim Ejder A 
Published: December 2013

Background: Schizophrenia is a severe mental disorder with substantial socioeconomic burden associated with poorer psychosocial functioning during the course of illness. In schizophrenia patients, multiple factors play a role in occupational functioning. Aim: It was aimed to investigate the relationship between different working conditions and quality of life and self-esteem on patients with schizophrenia in Turkey. Methods: A total of 100 patients diagnosed as schizophrenic were divided into three groups: competitive working, supported working and unemployed. Results: The groups did not differ significantly with regard to psychotic symptoms, self-esteem and illness history. Working was associated with higher scores on quality of life subscales especially in supported working group, whereas unemployed patients had more depressive symptoms and autonomic drug side effects. Conclusion: Structured working programs which may improve social life of patients with schizophrenia in many aspects is warranted in Turkey.
Place of death and end-of-life transitions experienced by very old people with differing cognitive status: Retrospective analysis of a prospective population-based cohort aged 85 and over
Authors: Perrels Anouk J , Fleming Jane , Zhao Jun , Barclay Stephen , Farquhar Morag , Buiting Hilde M , Brayne Carol ,   The Cambridge City over-75s Cohort (CC75C) study collaboration
Published: December 2013

Background: Despite fast-growing ‘older old’ populations, ‘place of care’ trajectories for very old people approaching death with or without dementia are poorly described and understood. Aim: To explore end-of-life transitions of ‘older old’ people across the cognitive spectrum. Design: Population-based prospective cohort (United Kingdom) followed to death. Setting/participants: Mortality records linked to 283 Cambridge City over-75s Cohort participants’ cognitive assessments <1 year before dying aged ≥85 years. Results: Overall, 69% were community dwelling in the year before death; of those with severe cognitive impairment 39% were community dwelling. Only 6% subsequently changed their usual address. However, for 55% their usual address on death registration was not their place of death. Dying away from the ‘usual address’ was associated with cognition, overall fewer moving with increasing cognitive impairment – cognition intact 66%, mildly/moderately impaired 55% and severely impaired 42%, trend p = 0.003. This finding reflects transitions being far more common from the community than from institutions: 73% from the community and 28% from institutions did not die where last interviewed ( p < 0.001). However, severely cognitively impaired people living in the community were the most likely group of all to move: 80% (68%−93%). Hospitals were the most common place of death except for the most cognitively impaired, who mostly died in care homes. Conclusion: Most very old community-dwelling individuals, especially the severely cognitively impaired, died away from home. Findings also suggest that long-term care may play a role in avoidance of end-of-life hospital admissions. These results provide important information for planning end-of-life services for older people across the cognitive spectrum, with implications for policies aimed at supporting home deaths. MeSH Terms: Cognitive impairment, Dementia, Aged, 80 and over, Aged, frail elderly, Patient Transfer, Residential characteristics, Homes for the aged, Nursing Homes, Delivery of Health Care, Terminal care Other key phrases: Older old, Oldest old, Place of death, Place of care, End-of-life care.
Histogram analysis of apparent diffusion coefficient map of diffusion-weighted MRI in endometrial cancer: a preliminary correlation study with histological grade
Authors: Woo Sungmin , Cho Jeong Yeon , Kim Sang Youn , Kim Seung Hyup 
Published: December 2013

Background Until now, several investigators have explored the value of diffusion-weighted magnetic resonance imaging (DWI) for the preoperative tumor grading of endometrial cancer. However, the diagnostic value of DWI with quantitative analysis of apparent diffusion coefficient (ADC) has been controversial. Purpose To explore the role of histogram analysis of ADC maps based on entire tumor volume in determining the grade of endometrial cancer. Material and Methods This study was IRB-approved with waiver of informed consent. Thirty-three patients with endometrial cancer underwent DWI (b = 0, 600, 1000 s/mm2), and corresponding ADC maps were acquired. Regions of interest (ROIs) were drawn on all slices of the ADC map in which the tumor was visualized including areas of necrosis to derive volume-based histographic ADC data. Histogram parameters (5th–95th percentiles, mean, standard deviation, skewness, kurtosis) were correlated with histological grade using one-way ANOVA with Tukey-Kramer test for post hoc comparisons, and were compared between high (grade 3) and low (grades 1/2) grade using Student t-test. ROC curve analysis was performed to determine the optimum threshold value for each parameter, and their corresponding sensitivity and specificity. Results The standard deviation, quartile, 75th, 90th, and 95th percentiles of ADC showed significant differences between grades ( P ≤ 0.03 for all) and between high and low grades ( P ≤ 0.024 for all). There were no significant correlations between tumor grade and other parameters. ROC curve analysis yielded sensitivities and specificities of 75% and 96%, 62.5% and 92%, 100% and 52%, 100% and 72%, and 100% and 88%, using standard deviation, quartile, 75th, 90th, and 95th percentiles for determining high grade with corresponding areas under the curve (AUCs) of 0.787, 0.792, 0.765, 0.880, and 0.925, respectively. Conclusion Histogram analysis of ADC maps based on entire tumor volume can be useful for predicting the histological grade of endometrial cancer. The 90th and 95th percentiles of ADC were the most promising parameters for differentiating high from low grade.