bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of and risk factors for abnormal ankle–brachial index in patients with type 2 diabetes
Authors: LI Xiang , WANG Yu‐zheng , YANG Xiao‐ping , XU Zhang‐rong 
Published: November 2011

AbstractBackground:  The aim of the present study was to examine abnormalities in the ankle–brachial index (ABI) and related risk factors in patients with type 2 diabetes.Methods:  Between September 2003 and June 2010, the ABI was determined in 3924 outpatients attending the Diabetes Center of the People’s Liberation Army 306th Hospital. In addition, demographic and laboratory data were collected. The risk factors for an abnormal ABI were determined using univariate and stepwise logistic regression analysis.Results:  The ABI was normal (0.91–1.3) in 93.1% of patients, low (<0.9) in 5.2%, and high (>1.3) in 1.7%. The prevalence of abnormal lower ABI was greater in elderly (≥ 65 years) patients (12.2%) than in younger (< 65 years) patients (3.6%). Using normal ABI as the reference, low ABI in younger patients was found to be independently associated with HbA1c, the urinary albumin:creatinine ratio, diabetic peripheral neuropathy, diabetic retinopathy, and cerebrovascular disease. A low ABI in elderly patients was found to be independently associated with age, smoking, HbA1c, uric acid, total cholesterol, diabetic peripheral neuropathy, diabetic retinopathy, diabetic nephropathy and cerebrovascular disease. A high ABI in younger patients was associated with being male.Conclusions:  The prevalence of an abnormal ABI was high in patients with type 2 diabetes, especially elderly patients. Early identification and intensive treatment are needed to improve the quality of life and overall prognosis of patients with type 2 diabetes.
Quantifying individual variation in reaction norms: how study design affects the accuracy, precision and power of random regression models
Authors: van de Pol Martijn 
Published: November 2011

Summary1. Quantifying individual heterogeneity in plasticity is becoming common in studies of evolutionary ecology, climate change ecology and animal personality. Individual variation in reaction norms is typically quantified using random effects in a mixed modelling framework. However, little is known about what sampling effort and design provide sufficient accuracy, precision and power.2. I developed ‘odprism’, an easy‐to‐use software package for the statistical language R, which can be used to investigate the accuracy, precision and power of random regression models for various types of data structures. Moreover, I conducted simulations to derive rules‐of‐thumb for four design decisions that biologists often face.3. First, I investigated the trade‐off between sampling many individuals a few times versus sampling few individuals often. Generally, at least 40 individuals should be sampled with a total sample size of at least 1000 to obtain accurate and precise estimates of individual variation in elevation and slopes of linear reaction norms and their correlation. Contrasting a previous recommendation, it is worthwhile to bias the ratio of number of individuals over replicates towards sampling more individuals.4. Second, I considered how the range of environmental conditions over which individuals are sampled affects the optimal sampling strategy. I show that when all individuals experience the same conditions during a sampling event, sampling each individual only twice should be strictly avoided.5. Third, I examined the case where the number of replicates per individual is constrained by their lifespan, as is common when sampling annual traits in the wild. I show that for a given sampling effort, it is much easier to detect individual variation in reaction norms for long‐lived than for short‐lived species.6. Fourth, I investigated the performance of random regression models when studying traits under selection. Reassuringly, directional viability selection barely caused any bias in estimates of variance components.7. Random regression models are inherently data hungry, and reviewing the literature shows that particularly behavioural studies have low sampling effort. Therefore, the software and rules‐of‐thumbs I identified for designing reaction‐norm studies should help researchers make more informed choices, which likely improve the reliability and interpretation of plasticity studies.
Factors Driving Potential Ammonia Oxidation in Canadian Arctic Ecosystems: Does Spatial Scale Matter?
Authors: Banerjee Samiran , Siciliano Steven D. 
Published: November 2011

ABSTRACT

Ammonia oxidation is a major process in nitrogen cycling, and it plays a key role in nitrogen limited soil ecosystems such as those in the arctic. Although mm-scale spatial dependency of ammonia oxidizers has been investigated, little is known about the field-scale spatial dependency of aerobic ammonia oxidation processes and ammonia-oxidizing archaeal and bacterial communities, particularly in arctic soils. The purpose of this study was to explore the drivers of ammonia oxidation at the field scale in cryosols (soils with permafrost within 1 m of the surface). We measured aerobic ammonia oxidation potential (both autotrophic and heterotrophic) and functional gene abundance (bacterial
amoA
and archaeal
amoA
) in 279 soil samples collected from three arctic ecosystems. The variability associated with quantifying genes was substantially less than the spatial variability observed in these soils, suggesting that molecular methods can be used reliably evaluate spatial dependency in arctic ecosystems. Ammonia-oxidizing archaeal and bacterial communities and aerobic ammonia oxidation were spatially autocorrelated. Gene abundances were spatially structured within 4 m, whereas biochemical processes were structured within 40 m. Ammonia oxidation was driven at small scales (<1m) by moisture and total organic carbon, whereas gene abundance and other edaphic factors drove ammonia oxidation at medium (1 to 10 m) and large (10 to 100 m) scales. In these arctic soils heterotrophs contributed between 29 and 47% of total ammonia oxidation potential. The spatial scale for aerobic ammonia oxidation genes differed from potential ammonia oxidation, suggesting that in arctic ecosystems edaphic, rather than genetic, factors are an important control on ammonia oxidation.
Differential Protection of Cry1Fa Toxin against Spodoptera frugiperda Larval Gut Proteases by Cadherin Orthologs Correlates with Increased Synergism
Authors: Rahman Khalidur , Abdullah Mohd Amir F. , Ambati Suresh , Taylor Milton D. , Adang Michael J. 
Published: November 2011

ABSTRACTThe Cry proteins produced byBacillus thuringiensis(Bt) are the most widely used biopesticides effective against a range of crop pests and disease vectors. Like chemical pesticides, development of resistance is the primary threat to the long-term efficacy of Bt toxins. Recently discovered cadherin-based Bt Cry synergists showed the potential to augment resistance management by improving efficacy of Cry toxins. However, the mode of action of Bt Cry synergists is thus far unclear. Here we elucidate the mechanism of cadherin-based Cry toxin synergism utilizing two cadherin peptides,Spodoptera frugiperdaCad (SfCad) andManduca sextaCad (MsCad), which differentially enhance Cry1Fa toxicity toSpodoptera frugiperdaneonates. We show that differential SfCad- and MsCad-mediated protection of Cry1Fa toxin in theSpodoptera frugiperdamidgut correlates with differential Cry1Fa toxicity enhancement. Both peptides exhibited high affinity for Cry1Fa toxin and an increased rate of Cry1Fa-induced pore formation inS. frugiperda. However, only SfCad bound theS. frugiperdabrush border membrane vesicle and more effectively prolonged the stability of Cry1Fa toxin in the gut, explaining higher Cry1Fa enhancement by this peptide. This study shows that cadherin fragments may enhanceB. thuringiensistoxicity by at least two different mechanisms or a combination thereof: (i) protection of Cry toxin from protease degradation in the insect midgut and (ii) enhancement of pore-forming ability of Cry toxin.
Cow Teat Skin, a Potential Source of Diverse Microbial Populations for Cheese Production
Authors: Verdier-Metz Isabelle , Gagne Geneviève , Bornes Stéphanie , Monsallier Françoise , Veisseire Philippe , Delbès-Paus Céline , Montel Marie-Christine 
Published: November 2011

ABSTRACT

The diversity of the microbial community on cow teat skin was evaluated using a culture-dependent method based on the use of different dairy-specific media, followed by the identification of isolates by 16S rRNA gene sequencing. This was combined with a direct molecular approach by cloning and 16S rRNA gene sequencing. This study highlighted the large diversity of the bacterial community that may be found on teat skin, where 79.8% of clones corresponded to various unidentified species as well as 66 identified species, mainly belonging to those commonly found in raw milk (
Enterococcus
,
Pediococcus
,
Enterobacter
,
Pantoea
,
Aerococcus
, and
Staphylococcus
). Several of them, such as nonstarter lactic acid bacteria (NSLAB),
Staphylococcus
, and
Actinobacteria
, may contribute to the development of the sensory characteristics of cheese during ripening. Therefore, teat skin could be an interesting source or vector of biodiversity for milk. Variations of microbial counts and diversity between the farms studied have been observed. Moreover,
Staphylococcus auricularis
,
Staphylococcus devriesei
,
Staphylococcus arlettae
,
Streptococcus bovis
,
Streptococcus equinus
,
Clavibacter michiganensis
,
Coprococcus catus
, or
Arthrobacter gandavensis
commensal bacteria of teat skin and teat canal, as well as human skin, are not common in milk, suggesting that there is a breakdown of microbial flow from animal to milk. It would then be interesting to thoroughly study this microbial flow from teat to milk.
Distinct Transcriptional Profiles and Phenotypes Exhibited by Escherichia coli O157:H7 Isolates Related to the 2006 Spinach-Associated Outbreak
Authors: Parker Craig T. , Kyle Jennifer L. , Huynh Steven , Carter Michelle Q. , Brandl Maria T. , Mandrell Robert E. 
Published: November 2011

ABSTRACT

In 2006, a large outbreak of
Escherichia coli
O157:H7 was linked to the consumption of ready-to-eat bagged baby spinach in the United States. The likely sources of preharvest spinach contamination were soil and water that became contaminated via cattle or feral pigs in the proximity of the spinach fields. In this study, we compared the transcriptional profiles of 12
E. coli
O157:H7 isolates that possess the same two-enzyme pulsed-field gel electrophoresis (PFGE) profile and are related temporally or geographically to the above outbreak. These
E. coli
O157:H7 isolates included three clinical isolates, five isolates from separate bags of spinach, and single isolates from pasture soil, river water, cow feces, and a feral pig. The three clinical isolates and two spinach bag isolates grown in cultures to stationary phase showed decreased expression of many σ
S
-regulated genes, including
gadA
,
osmE
,
osmY
, and
katE
, compared with the soil, water, cow, feral pig, and the other three spinach bag isolates. The decreased expression of these σ
S
-regulated genes was correlated with the decreased resistance of the isolates to acid stress, osmotic stress, and oxidative stress but increases in scavenging ability. We also observed that intraisolate variability was much more pronounced among the clinical and spinach isolates than among the environmental isolates. Together, the transcriptional and phenotypic differences of the spinach outbreak isolates of
E. coli
O157:H7 support the hypothesis that some variants within the spinach bag retained characteristics of the preharvest isolates, whereas other variants with altered gene expression and phenotypes infected the human host.
Metagenomic Analysis of Stress Genes in Microbial Mat Communities from Antarctica and the High Arctic
Authors: Varin Thibault , Lovejoy Connie , Jungblut Anne D. , Vincent Warwick F. , Corbeil Jacques 
Published: November 2011

ABSTRACTPolar and alpine microbial communities experience a variety of environmental stresses, including perennial cold and freezing; however, knowledge of genomic responses to such conditions is still rudimentary. We analyzed the metagenomes of cyanobacterial mats from Arctic and Antarctic ice shelves, using high-throughput pyrosequencing to test the hypotheses that consortia from these extreme polar habitats were similar in terms of major phyla and subphyla and consequently in their potential responses to environmental stresses. Statistical comparisons of the protein-coding genes showed similarities between the mats from the two poles, with the majority of genes derived fromProteobacteriaandCyanobacteria; however, the relative proportions differed, with cyanobacterial genes more prevalent in the Antarctic mat metagenome. Other differences included a higher representation ofActinobacteriaandAlphaproteobacteriain the Arctic metagenomes, which may reflect the greater access to diasporas from both adjacent ice-free lands and the open ocean. Genes coding for functional responses to environmental stress (exopolysaccharides, cold shock proteins, and membrane modifications) were found in all of the metagenomes. However, in keeping with the greater exposure of the Arctic to long-range pollutants, sequences assigned to copper homeostasis genes were statistically (30%) more abundant in the Arctic samples. In contrast, more reads matching the sigma B genes were identified in the Antarctic mat, likely reflecting the more severe osmotic stress during freeze-up of the Antarctic ponds. This study underscores the presence of diverse mechanisms of adaptation to cold and other stresses in polar mats, consistent with the proportional representation of major bacterial groups.
Functions of the Duplicated
hik31
Operons in Central Metabolism and Responses to Light, Dark, and Carbon Sources in Synechocystis sp. Strain PCC 6803
Authors: Nagarajan Sowmya , Sherman Debra M. , Shaw Isaac , Sherman Louis A. 
Published: November 2011

ABSTRACT

There are two closely related
hik31
operons involved in signal transduction on the chromosome and the pSYSX plasmid in the cyanobacterium
Synechocystis
sp. strain PCC 6803. We studied the growth, cell morphology, and gene expression in operon and
hik
mutants for both copies, under different growth conditions, to examine whether the duplicated copies have the same or different functions and gene targets and whether they are similarly regulated. Phenotype analysis suggested that both operons regulated common and separate targets in the light and the dark. The chromosomal operon was involved in the negative control of autotrophic events, whereas the plasmid operon was involved in the positive control of heterotrophic events. Both the plasmid and double operon mutant cells were larger and had division defects. The growth data also showed a regulatory role for the chromosomal
hik
gene under high-CO
2
conditions and the plasmid operon under low-O
2
conditions. Metal stress experiments indicated a role for the chromosomal
hik
gene and operon in mediating Zn and Cd tolerance, the plasmid operon in Co tolerance, and the chromosomal operon and plasmid
hik
gene in Ni tolerance. We conclude that both operons are differentially and temporally regulated. We suggest that the chromosomal operon is the primarily expressed copy and the plasmid operon acts as a backup to maintain appropriate gene dosages. Both operons share an integrated regulatory relationship and are induced in high light, in glucose, and in active cell growth. Additionally, the plasmid operon is induced in the dark with or without glucose.
E622, a Miniature, Virulence-Associated Mobile Element
Authors: Stavrinides John , Kirzinger Morgan W. B. , Beasley Federico C. , Guttman David S. 
Published: November 2011

ABSTRACT

Miniature inverted terminal repeat elements (MITEs) are nonautonomous mobile elements that have a significant impact on bacterial evolution. Here we characterize E622, a 611-bp virulence-associated MITE from
Pseudomonas syringae
, which contains no coding region but has almost perfect 168-bp inverted repeats. Using an antibiotic coupling assay, we show that E622 is transposable and can mobilize an antibiotic resistance gene contained between its borders. Its predicted parent element, designated Tn
E622
, has a typical transposon structure with a three-gene operon, consisting of resolvase, integrase, and
exeA
-like genes, which is bounded by the same terminal inverted repeats as E622. A broader genome level survey of the E622/Tn
E622
inverted repeats identified homologs in
Pseudomonas
,
Salmonella
,
Shewanella
,
Erwinia
,
Pantoea
, and the cyanobacteria
Nostoc
and
Cyanothece
, many of which appear to encompass known virulence genes, including genes encoding toxins, enzymes, and type III secreted effectors. Its association with niche-specific genetic determinants, along with its persistence and evolutionary diversification, indicates that this mobile element family has played a prominent role in the evolution of many agriculturally and clinically relevant pathogenic bacteria.
Evidence that the Folate-Dependent Proteins YgfZ and MnmEG Have Opposing Effects on Growth and on Activity of the Iron-Sulfur Enzyme MiaB
Authors: Waller Jeffrey C. , Ellens Kenneth W. , Hasnain Ghulam , Alvarez Sophie , Rocca James R. , Hanson Andrew D. 
Published: November 2011

ABSTRACT

The folate-dependent protein YgfZ of
Escherichia coli
participates in the synthesis and repair of iron-sulfur (Fe-S) clusters; it belongs to a family of enzymes that use folate to capture formaldehyde units. Ablation of
ygfZ
is known to reduce growth, to increase sensitivity to oxidative stress, and to lower the activities of MiaB and other Fe-S enzymes. It has been reported that the growth phenotype can be suppressed by disrupting the tRNA modification gene
mnmE
. We first confirmed the latter observation using deletions in a simpler, more defined genetic background. We then showed that deleting
mnmE
substantially restores MiaB activity in
ygfZ
deletant cells and that overexpressing MnmE with its partner MnmG exacerbates the growth and MiaB activity phenotypes of the
ygfZ
deletant. MnmE, with MnmG, normally mediates a folate-dependent transfer of a formaldehyde unit to tRNA, and the MnmEG-mediated effects on the phenotypes of the Δ
ygfZ
mutant apparently require folate, as evidenced by the effect of eliminating all folates by deleting
folE
. The expression of YgfZ was unaffected by deleting
mnmE
or overexpressing MnmEG or by folate status. Since formaldehyde transfer is a potential link between MnmEG and YgfZ, we inactivated formaldehyde detoxification by deleting
frmA
. This deletion had little effect on growth or MiaB activity in the Δ
ygfZ
strain in the presence of formaldehyde, making it unlikely that formaldehyde alone connects the actions of MnmEG and YgfZ. A more plausible explanation is that MnmEG erroneously transfers a folate-bound formaldehyde unit to MiaB and that YgfZ reverses this.
Current and long-term spousal caregiving and onset of cardiovascular disease
Authors: Capistrant Beatrix Davoli , Moon J Robin , Berkman Lisa F , Glymour M Maria 
Published: November 2011

BackgroundPrior evidence suggests that caregiving may increase risk of cardiovascular disease (CVD) onset. This association has never been examined in a nationally (USA) representative sample, and prior studies could not fully control for socioeconomic confounders. This paper seeks to estimate the association between spousal caregiving and incident CVD in older Americans.MethodsMarried, CVD-free Health and Retirement Study respondents aged 50+ years (n=8472) were followed up to 8 years (1669 new stroke or heart disease diagnoses). Current caregiving exposure was defined as assisting a spouse with basic or instrumental activities of daily living ≥14 h/week according to the care recipients' report in the most recent prior biennial survey; we define providing ≥14 h/week of care at two consecutive biennial surveys as ‘long-term caregiving’. Inverse probability weighted discrete-time hazard models with time-updated exposure and covariate information (including socioeconomic and cardiovascular risk factors) were used to estimate the effect of caregiving on incident CVD.ResultsCaregiving significantly predicted CVD incidence (HR=1.35, 95% CI 1.06 to 1.68) in the population overall. Long-term caregiving was associated with double the risk of CVD onset (HR=1.95, 95% CI 1.19 to 3.18). This association for long-term care givers varied significantly by race (p<0.01): caregiving predicted CVD onset for white (HR=2.37, 95% CI 1.43 to 3.92) but not for non-white (HR=0.28, 95% CI 0.06 to 1.28).ConclusionsSpousal caregiving independently predicted risk of CVD in a large sample of US adults. There was significant evidence that the effect for long-term care givers differs for non-whites and white.
Metabolomic NMR Fingerprinting to Identify and Predict Survival of Patients with Metastatic Colorectal Cancer
Authors: Bertini Ivano , Cacciatore Stefano , Jensen Benny V. , Schou Jakob V. , Johansen Julia S. , Kruhøffer Mogens , Luchinat Claudio , Nielsen Dorte L. , Turano Paola 
Published: November 2011

Abstract
Earlier detection of patients with metastatic colorectal cancer (mCRC) might improve their treatment and survival outcomes. In this study, we used proton nuclear magnetic resonance (1H-NMR) to profile the serum metabolome in patients with mCRC and determine whether a disease signature may exist that is strong enough to predict overall survival (OS). In 153 patients with mCRC and 139 healthy subjects from three Danish hospitals, we profiled two independent sets of serum samples in a prospective phase II study. In the training set, 1H-NMR metabolomic profiling could discriminate patients with mCRC from healthy subjects with a cross-validated accuracy of 100%. In the validation set, 96.7% of subjects were correctly classified. Patients from the training set with maximally divergent OS were chosen to construct an OS predictor. After validation, patients predicted to have short OS had significantly reduced survival (HR, 3.4; 95% confidence interval, 2.06–5.50; P = 1.33 × 10−6). A number of metabolites concurred with the 1H-NMR fingerprint of mCRC, offering insights into mCRC metabolic pathways. Our findings establish that 1H-NMR profiling of patient serum can provide a strong metabolomic signature of mCRC and that analysis of this signature may offer an independent tool to predict OS. Cancer Res; 72(1); 356–64. ©2011 AACR.