bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantification of Bacterial Indicators and Zoonotic Pathogens in Dairy Wastewater Ponds
Authors: Dungan Robert S. , Klein Marcus , Leytem April B. 
Published: September 2012

ABSTRACT

Zoonotic pathogens in land-applied dairy wastewaters are a potential health risk. The occurrence and abundance of 10 pathogens and 3 fecal indicators were determined by quantitative real-time PCR (qPCR) in samples from 30 dairy wastewaters from southern Idaho. Samples tested positive for
Campylobacter jejuni
,
stx
1
- and
eaeA
-positive
Escherichia coli
,
Listeria monocytogenes
,
Mycobacterium avium
subsp.
paratuberculosis
, and
Salmonella enterica
, with mean recoveries of genomic DNA corresponding to 10
2
to 10
4
cells ml
−1
wastewater. The most predominant organisms were
C. jejuni
and
M. avium
, being detected in samples from up to 21 and 29 of 30 wastewater ponds, respectively. The qPCR detection limits for the putative pathogens in the wastewaters ranged from 16 cells ml
−1
for
M. avium
to 1,689 oocysts ml
−1
for
Cryptosporidium. Cryptosporidium
and
Giardia
spp.,
Yersinia pseudotuberculosis
, and pathogenic
Leptospira
spp. were not detected by qPCR.
Stable Transfection of the Diplomonad Parasite Spironucleus salmonicida
Authors: Jerlström-Hultqvist Jon , Einarsson Elin , Svärd Staffan G. 
Published: September 2012

ABSTRACT

Eukaryotic microbes are highly diverse, and many lineages remain poorly studied. One such lineage, the diplomonads, a group of binucleate heterotrophic flagellates, has been studied mainly due to the impact of
Giardia intestinalis
, an intestinal, diarrhea-causing parasite in humans and animals. Here we describe the development of a stable transfection system for use in
Spironucleus salmonicida
, a diplomonad that causes systemic spironucleosis in salmonid fish. We designed vectors in cassette format carrying epitope tags for localization (3×HA [where HA is hemagglutinin], 2×
Escherichia coli
OmpF linker and mouse langerin fusion sequence [2×OLLAS], 3×MYC) and purification of proteins (2× Strep-Tag II–FLAG tandem-affinity purification tag or streptavidin binding peptide–glutathione
S
-transferase [SBP-GST]) under the control of native or constitutive promoters. Three selectable gene markers, puromycin acetyltransferase (
pac
), blasticidin
S
-deaminase (
bsr
), and neomycin phosphotransferase (
nptII
), were successfully applied for the generation of stable transfectants. Site-specific integration on the
S. salmonicida
chromosome was shown to be possible using the
bsr
resistance gene. We epitope tagged six proteins and confirmed their expression by Western blotting. Next, we demonstrated the utility of these vectors by recording the subcellular localizations of the six proteins by laser scanning confocal microscopy. Finally, we described the creation of an
S. salmonicida
double transfectant suitable for colocalization studies. The transfection system described herein and the imminent completion of the
S. salmonicida
genome will make it possible to use comparative genomics as an investigative tool to explore specific, as well as general, diplomonad traits, benefiting research on both
Giardia
and
Spironucleu
s.
Transposon Mutagenesis Identifies Uropathogenic Escherichia coli Biofilm Factors
Authors: Hadjifrangiskou Maria , Gu Alice P. , Pinkner Jerome S. , Kostakioti Maria , Zhang Ellisa W. , Greene Sarah E. , Hultgren Scott J. 
Published: September 2012

ABSTRACTUropathogenicEscherichia coli(UPEC), which accounts for 85% of urinary tract infections (UTI), assembles biofilms in diverse environments, including the host. Besides forming biofilms on biotic surfaces and catheters, UPEC has evolved an intracellular pathogenic cascade that culminates in the formation of biofilm-like intracellular bacterial communities (IBCs) within bladder epithelial cells. Rapid bacterial replication during IBC formation augments a build-up in bacterial numbers and persistence within the host. Relatively little is known about factors mediating UPEC biofilm formation and how these overlap with IBC formation. To address this gap, we screened a UPEC transposon mutant library in threein vitrobiofilm conditions: Luria broth (LB)-polyvinyl chloride (PVC), YESCA (yeast extract-Casamino Acids)-PVC, and YESCA-pellicle that are dependent on type 1 pili (LB) and curli (YESCA), respectively. Flagella are important in all three conditions. Mutants were identified that had biofilm defects in all three conditions but had no significant effects on the expression of type 1 pili, curli, or flagella. Thus, this approach uncovered a comprehensive inventory of novel effectors and regulators that are involved in UPEC biofilm formation under multiple conditions. A subset of these mutants was found to be dramatically attenuated and unable to form IBCs in a murine model of UTI. Collectively, this study expands our insights into UPEC multicellular behavior that may provide insights into IBC formation and virulence.
Course setting and selected biomechanical variables related to injury risk in alpine ski racing: an explorative case study
Authors: Spörri Jörg , Kröll Josef , Schwameder Hermann , Schiefermüller Christian , Müller Erich 
Published: September 2012

BackgroundCourse setting has often been discussed as a potential preventative measure in the World Cup ski-racing community. However, there is limited understanding of how it is related to injury risk.ObjectiveThis study was undertaken to investigate the effect of increased horizontal gate distance on energy-related and injury mechanism-related variables.MethodsDuring a video-based three-dimensional (3D)-kinematic field measurement, a top world-class racer performed giant slalom runs at two course settings with different horizontal gate distances. A full-body segment model was reconstructed in 3D and selected biomechanical parameters were calculated.ResultsFor the analysed turn, no significant differences were found in turn speed for increased horizontal gate distance. However, a large effect size was observed for speed reduction towards the end of the turn. Turn forces were by tendency higher at the beginning and significantly higher towards the end of the turn. Additionally, significant differences were found in higher inward leaning, and large effect sizes were observed for a decreased fore/aft position after gate passage.ConclusionsOn the basis of the data of this study, no final conclusion can be made about whether, for a section of consecutive turns, increasing horizontal gate distance is an effective tool for speed reduction. However, this study pointed out two major drawbacks of this course setting modification: (1) it may increase fatigue as a consequence of loading forces acting over a longer duration; (2) it may increase the risk of out-of-balance situations by forcing the athlete to exhaust his backward and inward leaning spectrum.
Identifying early warning signs for diagnostic errors in primary care: a qualitative study
Authors: Balla John , Heneghan Carl , Goyder Clare , Thompson Matthew 
Published: September 2012

ObjectiveWe investigate the mechanisms of diagnostic error in primary care consultations to detect warning signs for possible error. We aim to identify places in the diagnostic reasoning process associated with major risk indicators.DesignA qualitative study using semistructured interviews with open-ended questions.SettingA 2-month study in primary care conducted in Oxfordshire, UK.ParticipantsWe approached about 25 experienced general practitioners by email or word of mouth, 15 volunteered for the interviews and were available at a convenient time.InterventionInterview transcripts provided 45 cases of error. Three researchers searched these independently for underlying themes in relation to our conceptual framework.Outcome measuresLocating steps in the diagnostic reasoning process associated with major risk of error and detecting warning signs that can alert clinicians to increased risk of error.ResultsInitiation and closure of the cognitive process are most exposed to risk of error. Cognitive biases developed early in the process lead to errors at the end. These warning signs can be used to alert clinicians to the increased risk of diagnostic error. Ignoring red flags or critical cues was related to processes being biased through the initial frame, but equally well, it could be explained by knowledge gaps.ConclusionsCognitive biases developed at the initial framing of the problem relate to errors at the end of the process. We refer to these biases as warning signs that can alert clinicians to the increased risk of diagnostic error. We conclude that lack of knowledge is likely to be an important factor in diagnostic error. Reducing diagnostic errors in primary care should focus on early and systematic recognition of errors including near misses, and a continuing professional development environment that promotes reflection in action to highlight possible causes of process bias and of knowledge gaps.
FINITE GROUPS WITH NON-CYCLIC 2-SUBGROUPS WHICH ARE SUBNORMAL OR HAVE SMALL INDICES IN THEIR NORMALIZERS
Authors: SHI JIANGTAO , ZHANG CUI 
Published: September 2012

A new criteria for the solvability of finite groups is obtained. It is proven that a finite group G is always solvable if (i) H is subnormal in G or |NG(H) : H| ≤ 2 for every non-cyclic 2-subgroup H of G that is not a subgroup of Z(G), or (ii) H is subnormal in G or G is A4-free and |NG(H) : H| ≤ 6 for every non-cyclic 2-subgroup H of G that is not a subgroup of Z(G). Moreover, some new criteria for a finite group being p-nilpotent are also obtained.
Predictors of Survival in Never-Smokers with Non–Small Cell Lung Cancer: A Large-Scale, Two-Phase Genetic Study
Authors: Pu Xia , Ye Yuanqing , Spitz Margaret R. , Wang Liang , Gu Jian , Lippman Scott M. , Hildebrandt Michelle A.T. , Hong Waun Ki , Minna John D. , Roth Jack A. , Yang Ping , Wu Xifeng 
Published: September 2012

Abstract
Purpose: Lung cancer in never-smokers (LCINS) is increasingly recognized as a distinct disease from that in ever-smokers owing to substantial differences in etiology, clinical characteristics, and prognosis. Therefore, we aimed to identify prognostic markers specific for LCINS.
Experimental Design: First, 11,930 single-nucleotide polymorphisms (SNP) in 904 inflammation-related genes were genotyped, and their associations with overall survival in 411 patients with LCINS at MD Anderson Cancer Center were analyzed. Next, validation of the top 27 SNPs in 311 patients with LCINS at Mayo Clinic was conducted.
Results: Three SNPs (IL17RA:rs879576, BMP8A:rs698141, and STY:rs290229) were validated (P &lt; 0.05), and two SNPs (CD74:rs1056400 and CD38:rs10805347) reached borderline significance (P = 0.08) in the Mayo Clinic population. We validated a survival-tree created in the MD Anderson population exploring gene–gene interactions in the Mayo Clinic population. This survival-tree stratified patients into subsets with significantly different risks of death: patients with the rs1056400_GG/rs698141_GA + AA genotype had significantly higher risk of death in both MD Anderson (HR:2.32, 95%CI: 1.58–3.41) and Mayo (HR:1.97, 95%CI: 1.11–3.50) populations compared with those with the rs1056400_GG/rs698141_GG or rs1056400_GA + AA genotype. We evaluated these five SNPs in 996 ever-smokers from MD Anderson and found no significant associations.
Conclusions: Our study provides strong evidence that inflammation-related genetic variations can affect clinical outcomes in LCINS, which may lead to significant biologic insight into these outcomes. Clin Cancer Res; 18(21); 5983–91. ©2012 AACR.
Genotype-Dependent Impairment of Hemoglobin Clearance Increases Oxidative and Inflammatory Response in Human Diabetic Atherosclerosis
Authors: Purushothaman Meerarani , Krishnan Prakash , Purushothaman K-Raman , Baber Usman , Tarricone Arthur , Perez Juan S. , Wiley Jose , Kini Annapoorna , Sharma Samin K. , Fuster Valentin , Moreno Pedro R. 
Published: September 2012

Objective—
Haptoglobin (Hp) protein is responsible for hemoglobin clearance after intra-plaque hemorrhage. Hp gene exists as Hp-1 and Hp-2 alleles and the phenotypes show important molecular heterogeneity. We tested the hypothesis that hemoglobin clearance may be deficient in diabetic atheroma from patients with Hp2-2, triggering increased oxidative, inflammatory, and angiogenic patterns compared with controls.

Methods and Results—

Forty patients with diabetes mellitus were genotyped and their peripheral plaques compared after atherectomy. Plaque hemorrhage, iron content, hemoglobin-binding protein CD163, and heme-oxygenase-1 were quantified. Oxidative, inflammatory, and angiogenic patterns were evaluated by measuring myeloperoxidase, interleukin-10, macrophages, vascular cell adhesion molecule-1, smooth muscle actin, and plaque neovascularization (CD34/CD31). Plaques with Hp2-2 (n=7) had increased hemorrhage (
P
<0.005), iron content (
P
<0.001), and reduced CD163 expression (
P
<0.002) compared with controls (n=14). Hp2-2 plaques had increased heme-oxygenase-1 protein (
P
<0.02), myeloperoxidase gene (
P
<0.05), and protein (
P
<0.0001). Anti-inflammatory interleukin-10 gene (
P
<0.04), and protein expressions (
P
<0.0001) were decreased in Hp2-2. Finally, macrophage (
P
<0.0001), vascular cell adhesion molecule-1 (
P
=0.001), smooth muscle actin (
P
=0.002) scores, and neovessels density (
P
<0.0001) were increased in Hp2-2.

Conclusion—
Genotype-dependent impairment of hemoglobin clearance after intra-plaque hemorrhage is associated with increased oxidative, inflammatory, and angiogenic response in human diabetic atherosclerosis.
Associations Among Vascular Risk Factors, Carotid Atherosclerosis, and Cortical Volume and Thickness in Older Adults
Authors: Cardenas Valerie A. , Reed Bruce , Chao Linda L. , Chui Helena , Sanossian Nerses , DeCarli Charles C. , Mack Wendy , Kramer Joel , Hodis Howard N. , Yan Mingzhu , Buonocore Michael H. , Carmichael Owen , Jagust William J. , Weiner Michael W. 
Published: September 2012

Background and Purpose—
The purpose of this study was to investigate whether the Framingham Cardiovascular Risk Profile and carotid artery intima-media thickness are associated with cortical volume and thickness.

Methods—

Consecutive subjects participating in a prospective cohort study of aging and mild cognitive impairment enriched for vascular risk factors for atherosclerosis underwent structural MRI scans at 3-T and 4-T MRI at 3 sites. Freesurfer (Version 5.1) was used to obtain regional measures of neocortical volumes (mm
3
) and thickness (mm). Multiple linear regression was used to determine the association of Framingham Cardiovascular Risk Profile and carotid artery intima-media thickness with cortical volume and thickness.

Results—

One hundred fifty-two subjects (82 men) were aged 78 (±7) years, 94 had a clinical dementia rating of 0, 58 had a clinical dementia rating of 0.5, and the mean Mini-Mental State Examination was 28 ± 2. Framingham Cardiovascular Risk Profile score was inversely associated with total gray matter volume and parietal and temporal gray matter volume (adjusted
P
<0.04). Framingham Cardiovascular Risk Profile was inversely associated with parietal and total cerebral gray matter thickness (adjusted
P
<0.03). Carotid artery ntima-media thickness was inversely associated with thickness of parietal gray matter only (adjusted
P
=0.04). Including history of myocardial infarction or stroke and radiological evidence of brain infarction, or apolipoprotein E genotype did not alter relationships with Framingham Cardiovascular Risk Profile or carotid artery intima-media thickness.

Conclusions—
Increased cardiovascular risk was associated with reduced gray matter volume and thickness in regions also affected by Alzheimer disease independent of infarcts and apolipoprotein E genotype. These results suggest a “double hit” toward developing dementia when someone with incipient Alzheimer disease also has high cardiovascular risk.
What Causes Disability After Transient Ischemic Attack and Minor Stroke?
Authors: Coutts Shelagh B. , Modi Jayesh , Patel Shiel K. , Aram Heidi , Demchuk Andrew M. , Goyal Mayank , Hill Michael D. 
Published: September 2012

Background and Purpose—
Minor stroke and transient ischemic attack portend a significant risk of disability. Three possible mechanisms for this include disability not captured by the National Institutes of Health Stroke Scale, symptom progression, or recurrent stroke. We sought to assess the relative impact of these mechanisms on disability in a population of patients with transient ischemic attack and minor stroke.

Methods—
Five hundred ten consecutive minor stroke (National Institutes of Health Stroke Scale <4) or patients with transient ischemic attack who were previously not disabled and had a CT/CT angiography completed within 24 hours of symptom onset were prospectively enrolled. Disability was assessed at 90 days using the modified Rankin Scale. Predictors of disability (modified Rankin Scale ≥2) and the relative impact of the initial event versus recurrent events were assessed.

Results—

Seventy-four of 499 (15%; 95% CI, 12%–18%) patients had a disabled outcome. Baseline factors predicting disability were: age ≥60 years, diabetes mellitus, premorbid modified Rankin Scale 1, ongoing symptoms, baseline National Institutes of Health Stroke Scale, CT/CT angiography-positive metric, and diffusion-weighted imaging positivity. In the multivariable analysis ongoing symptoms (OR, 2.4; 95% CI, 1.3–4.4;
P
=0.004), diabetes mellitus (OR, 2.3; 95% CI, 1.2–4.3;
P
=0.009), female sex (OR, 1.8; 95% CI, 1.1–3;
P
=0.025), and CT/CT angiography-positive metric (OR, 2.4; 95% CI, 1.4–4;
P
=0.001) predicted disability. Of the 463 patients who did not have a recurrent event, 55 were disabled (12%). By contrast 19 of 36 (53%) patients were disabled after a recurrent event (risk ratio, 4.4; 95% CI, 3–6.6;
P
<0.0001).

Conclusions—
We found that a substantial proportion of patients with transient ischemic attack and minor stroke become disabled. In terms of absolute numbers, most patients have disability as a result of their presenting event; however, recurrent events have the largest relative impact on outcome.
Conjugate Eye Deviation in Acute Intracerebral Hemorrhage
Authors: Sato Shoichiro , Koga Masatoshi , Yamagami Hiroshi , Okuda Satoshi , Okada Yasushi , Kimura Kazumi , Shiokawa Yoshiaki , Nakagawara Jyoji , Furui Eisuke , Hasegawa Yasuhiro , Kario Kazuomi , Arihiro Shoji , Nagatsuka Kazuyuki , Minematsu Kazuo , Toyoda Kazunori 
Published: September 2012

Background and Purpose—
Conjugate eye deviation (CED) occurs frequently in patients with acute stroke. The purpose of this study was to elucidate the factors that correlate with CED as well as the relationship between CED and outcomes in patients with acute intracerebral hemorrhage.

Methods—
A total of 211 patients with acute supratentorial intracerebral hemorrhage were recruited in a multicenter, prospective study. CED was assessed with a National Institutes of Health Stroke Scale “best gaze” subscore of ≥1. Hematoma location and volume were assessed on CT.

Results—
Forty-five percent of the patients had CED. On multivariable analysis, right-sided lesion (OR, 2.36; 95% CI, 1.18–4.93), hematoma volume (OR, 1.07; 95% CI, 1.04–1.10 per 1 mL), and baseline Glasgow Coma Scale score (OR, 0.66; 95% CI, 0.53–0.80 per 1 point) were independently associated with CED. After adjusting for sex, age, intraventricular extension of the hematoma, baseline Glasgow Coma Scale score, and hematoma volume, the presence of CED both on admission and 72 hours later was an independent predictor of death or dependency at 3 months poststroke (OR, 5.77; 95% CI, 2.27–16.94). The optimal cutoff volume of hematoma related to CED was ≥13.5 mL for patients with putaminal hemorrhage (sensitivity, 76%; specificity, 72%) and ≥7.7 mL for patients with thalamic hemorrhage (sensitivity, 82%; specificity, 83%).

Conclusions—
The persistence of CED was a significant predictor of death or dependency after acute supratentorial intracerebral hemorrhage even after adjusting for initial severity and hematoma volume. CED can be evoked by a relatively smaller thalamic hematoma than a putaminal hematoma.
Pacific Ocean Contribution to the Asymmetry in Eastern Indian Ocean Variability
Authors: Ummenhofer Caroline C. , Schwarzkopf Franziska U. , Meyers Gary , Behrens Erik , Biastoch Arne , Böning Claus W. 
Published: September 2012

Abstract
Variations in eastern Indian Ocean upper-ocean thermal properties are assessed for the period 1970–2004, with a particular focus on asymmetric features related to opposite phases of Indian Ocean dipole events, using high-resolution ocean model hindcasts. Sensitivity experiments, where interannual atmospheric forcing variability is restricted to the Indian or Pacific Ocean only, support the interpretation of forcing mechanisms for large-scale asymmetric behavior in eastern Indian Ocean variability. Years are classified according to eastern Indian Ocean subsurface heat content (HC) as proxy of thermocline variations. Years characterized by an anomalous low HC feature a zonal gradient in upper-ocean properties near the equator, while high events have a meridional gradient from the tropics into the subtropics. The spatial and temporal characteristics of the seasonal evolution of HC anomalies for the two cases is distinct, as is the relative contribution from Indian Ocean atmospheric forcing versus remote influences from Pacific wind forcing: low events develop rapidly during austral winter/spring in response to Indian Ocean wind forcing associated with an enhanced southeasterly monsoon driving coastal upwelling and a shoaling thermocline in the east; in contrast, formation of an anomalous high eastern Indian Ocean HC is more gradual, with anomalies earlier in the year expanding from the Indonesian Throughflow (ITF) region, initiated by remote Pacific wind forcing, and transmitted through the ITF via coastal wave dynamics. Implications for seasonal predictions arise with high HC events offering extended lead times for predicting thermocline variations and upper-ocean properties across the eastern Indian Ocean.
CMIP3 Subtropical Stratocumulus Cloud Feedback Interpreted through a Mixed-Layer Model
Authors: Caldwell Peter M. , Zhang Yunyan , Klein Stephen A. 
Published: September 2012

Abstract
Large-scale conditions over subtropical marine stratocumulus areas are extracted from global climate models (GCMs) participating in phase 3 of the Coupled Model Intercomparison Project (CMIP3) and used to drive an atmospheric mixed-layer model (MLM) for current and future climate scenarios. Cloud fraction is computed as the fraction of days where GCM forcings produce a cloudy equilibrium MLM state. This model is a good predictor of cloud fraction and its temporal variations on time scales longer than 1 week but overpredicts liquid water path and entrainment.
GCM cloud fraction compares poorly with observations of mean state, variability, and correlation with estimated inversion strength (EIS). MLM cloud fraction driven by these same GCMs, however, agrees well with observations, suggesting that poor GCM low cloud fraction is due to deficiencies in cloud parameterizations rather than large-scale conditions. However, replacing the various GCM cloud parameterizations with a single physics package (the MLM) does not reduce intermodel spread in low-cloud feedback because the MLM is more sensitive than the GCMs to existent intermodel variations in large-scale forcing. This suggests that improving GCM low cloud physics will not by itself reduce intermodel spread in predicted stratocumulus cloud feedback.
Differences in EIS and EIS change between GCMs are found to be a good predictor of current-climate MLM cloud amount and future cloud change. CMIP3 GCMs predict a robust increase of 0.5–1 K in EIS over the next century, resulting in a 2.3%–4.5% increase in MLM cloudiness. If EIS increases are real, subtropical stratocumulus may damp global warming in a way not captured by the GCMs studied.