bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequence of Ralstonia pickettii DTP0602, a 2,4,6-Trichlorophenol Degrader
Authors: Ohtsubo Yoshiyuki , Fujita Nobuyuki , Nagata Yuji , Tsuda Masataka , Iwasaki Tomohiro , Hatta Takashi 
Published: November 2013

ABSTRACT

Ralstonia pickettii
strain DTP0602 utilizes 2,4,6-trichlorophenol as its sole carbon and energy source. Here, we report the complete genome sequence of strain DTP0602, which comprises three chromosomes and no plasmids. We also found that the two
had
gene clusters responsible for the degradation of 2,4,6-trichlorophenol are located on the 2.9-Mb chromosome 2.
Draft Genome Sequence of the Antibiotic-Producing Cystic Fibrosis Isolate Pantoea agglomerans Tx10
Authors: Smith Derek D. N. , Kirzinger Morgan W. B. , Stavrinides John 
Published: November 2013

ABSTRACT

Pantoea agglomerans
is an enteric bacterium that is capable of causing both plant and human disease. Here, we report the genome sequence of a cystic fibrosis isolate,
P. agglomerans
Tx10, which produces an antibiotic that is effective against
Staphylococcus aureus
.
The trends and the risk of type 1 diabetes over the past 40 years: an analysis by birth cohorts and by parental migration background in Sweden
Authors: Hussen Hozan Ismael , Persson Martina , Moradi Tahereh 
Published: November 2013

ObjectiveTo investigate the trends and the risk of developing type 1 diabetes in the offspring of Swedes and immigrants by specific parental migration background, age, sex and birth cohort.DesignRegistry-based cohort study.SettingUsing Swedish nationwide data we analysed the risk of developing type 1 diabetes in 3 457 486 female and 3 641 304 male offspring between 0 and 30 years of age, born to native Swedes or immigrants and born and living in Sweden between 1969 and 2009. We estimated incidence rate ratios (IRRs) with 95% CIs using Poisson regression models. We further calculated age-standardised rates (ASRs) of type 1 diabetes, using the world population as standard.ResultsWe observed a trend of increasing ASRs among offspring below 15 years of age born to native Swedes and a less evident increase among offspring of immigrants. We further observed a shift towards a younger age at diagnosis in younger birth cohorts in both groups of offspring.Compared with offspring of Swedes, children (0–14 years) and young adults (15–30 years) with one parent born abroad had an overall 30% and 15–20% lower IRR, respectively, after multivariable adjustment. The reduction in IRR was even greater among offspring of immigrants if both parents were born abroad. Analysis by specific parental region of birth revealed a 45–60% higher IRR among male and female offspring aged 0–30 years of Eastern Africa.ConclusionsParental country of birth and early exposures to environmental factors play an important role in the aetiology of type 1 diabetes.
Adherence to antiretroviral drug therapy in adult patients who are HIV-positive in Northwest Ethiopia: a study protocol
Authors: Bezabhe Woldesellassie M , Peterson Gregory M , Bereznicki Luke , Chalmers Leanne , Gee Peter 
Published: November 2013

IntroductionAchievement of optimal medication adherence and management of antiretroviral toxicity pose great challenges among Ethiopian patients with HIV/AIDS. There is currently a lack of long-term follow-up studies that identify the barriers to, and facilitators of, adherence to antiretroviral therapy (ART) in the Ethiopian setting. Therefore, we aim to investigate the level of adherence to ART and a wide range of potential influencing factors, including adverse drug reactions occurring with ART.Methods and analysisWe are conducting a 1-year prospective cohort study involving adult patients with HIV/AIDS starting on ART between December 2012 and March 2013. Data are being collected on patients’ appointment dates in the ART clinics. Adherence to ART is being measured using pill count, medication possession ratio and patient's self-report. The primary outcome of the study will be the proportion of patients who are adherent to their ART regimen at 3, 6 and 12 months using pill count. Taking 95% or more of the dispensed ART regimen using pill count at given points of time will be considered the optimal level of adherence in this study. Data will be analysed using descriptive and inferential statistical procedures.Ethics and disseminationEthics approval was obtained from the Tasmania Health and Medical Human Research Ethics Committee and Bahir-Dar University's Ethics Committee. The results of the study will be reported in peer-reviewed scientific journals, conferences and seminar presentations.
Estimation of net muscle volume in patients with muscular dystrophy using muscle CT for prospective muscle volume analysis: an observational study
Authors: Nakayama T , Kuru S , Okura M , Motoyoshi Y , Kawai M 
Published: November 2013

ObjectivesMuscle volume in patients with muscle disease is an index of disease progression. The aim of this study was to demonstrate a new method of muscle volumetry using CT of thigh muscles.DesignObservational study.Participants(1) For muscle volumetry using CT and dual-energy X-ray absorptiometry (DXA), 13 patients with muscle disease participated. (2) For prospective CT volumetry, 12 patients participated over 4 years.Primary and secondary outcome measuresTo establish the new CT volumetry, the results of which were correlated with the muscle mass calculated from DXA (primary outcome). To show the decrease in muscle volume using our method over 4 years (secondary outcome)Methods(1) Helical CT imaging of the thigh was performed. CT images were analysed by applying estimated functions, and the accumulation of outcomes resulted in muscle volumes. We refer to this method as ‘net muscle volumetry’. Simultaneously, DXA was performed in these patients, and the muscle mass of the thigh was calculated with vendor-provided software. (2) To evaluate longitudinal changes in muscle volume, net muscle volumetry at the 14 cm section of the middle part of the thigh was performed repeatedly over a 4-year period.Results(1) Volumes of the thigh muscle on one side were calculated to be 300–3400 cm3using CT. Muscle mass of the thigh was calculated from DXA to be 1100–5000 g. These results correspond closely, with a Pearson correlation coefficient of 0.993. (2) Thigh net muscle volumes of seven patients with gait disturbance decreased over the 4-year study period (p<0.01).ConclusionsA method of measuring net muscle volume using CT, which was validated by muscle mass calculated from DXA, was developed. Decrements in net muscle volume over 4 years support the reliability of this method. This less arbitrary method is suitable for assessment of muscle volume in patients with muscular dystrophy.
OX40 Is a Potent Immune-Stimulating Target in Late-Stage Cancer Patients
Authors: Curti Brendan D. , Kovacsovics-Bankowski Magdalena , Morris Nicholas , Walker Edwin , Chisholm Lana , Floyd Kevin , Walker Joshua , Gonzalez Iliana , Meeuwsen Tanisha , Fox Bernard A. , Moudgil Tarsem , Miller William , Haley Daniel , Coffey Todd , Fisher Brenda , Delanty-Miller Laurie , Rymarchyk Nicole , Kelly Tracy , Crocenzi Todd , Bernstein Eric , Sanborn Rachel , Urba Walter J. , Weinberg Andrew D. 
Published: November 2013

AbstractOX40 is a potent costimulatory receptor that can potentiate T-cell receptor signaling on the surface of T lymphocytes, leading to their activation by a specifically recognized antigen. In particular, OX40 engagement by ligands present on dendritic cells dramatically increases the proliferation, effector function, and survival of T cells. Preclinical studies have shown that OX40 agonists increase antitumor immunity and improve tumor-free survival. In this study, we performed a phase I clinical trial using a mouse monoclonal antibody (mAb) that agonizes human OX40 signaling in patients with advanced cancer. Patients treated with one course of the anti-OX40 mAb showed an acceptable toxicity profile and regression of at least one metastatic lesion in 12 of 30 patients. Mechanistically, this treatment increased T and B cell responses to reporter antigen immunizations, led to preferential upregulation of OX40 on CD4+ FoxP3+ regulatory T cells in tumor-infiltrating lymphocytes, and increased the antitumor reactivity of T and B cells in patients with melanoma. Our findings clinically validate OX40 as a potent immune-stimulating target for treatment in patients with cancer, providing a generalizable tool to favorably influence the antitumor properties of circulating T cells, B cells, and intratumoral regulatory T cells. Cancer Res; 73(24); 7189–98. ©2013 AACR.
Role of Soluble Endothelial Cell–Selective Adhesion Molecule Biomarker in Albuminuria and Kidney Function Changes in Patients With Coronary Artery Disease
Authors: Park Meyeon , Vittinghoff Eric , Ganz Peter , Peralta Carmen A. , Whooley Mary , Shlipak Michael G. 
Published: November 2013

Objective—
Endothelial dysfunction is a possible mechanism to explain the association between atherosclerosis and kidney disease. This study evaluated circulating soluble endothelial cell–selective adhesion molecule (sESAM), a marker of endothelial dysfunction, as a risk factor for kidney function decline and albuminuria.

Approach and Results—

In the Heart and Soul Study, we measured sESAM from baseline serum samples and defined elevated levels of sESAM by the highest quartile (quartile 4 [Q4]: >65.4 ng/mL). We evaluated the associations of high sESAM with baseline estimated glomerular filtration rate (eGFR) and ratio of urine albumin to creatinine (ACR), and with longitudinal changes in eGFR and ACR. Among 990 participants with sESAM measurements, median sESAM was 54.5 ng/mL (interquartile range, 45.3–65.8). After multivariable adjustment, elevated levels of sESAM were strongly and independently associated with baseline reduced eGFR <60 mL/min per 1.73 m
2
(odds ratio [OR], 11.44;
P
<0.0001) and ACR ≥30 mg/g (OR, 5.23;
P
<0.0001). Associations of sESAM (Q4 versus quartile 1 [Q1]) with change in ACR (β=54.47;
P
<0.0001) were also significant after full adjustment. The association with change in eGFR (1.56%;
P
=0.0049) was not statistically significant after application of the Bonferroni correction for multiple markers. In unadjusted models, sESAM was associated with rapid kidney function loss, defined as 3% annual eGFR decline (OR, 2.28;
P
=0.0003), although this was attenuated by adjustment (OR, 2.11;
P
=0.0095).

Conclusions—
sESAM is associated with albuminuria and reduced kidney function in both cross-sectional and longitudinal analyses. These findings implicate endothelial dysfunction as a potential contributor to the elevated kidney disease risk in persons with cardiovascular disease.
Modulation of Protein C Activation by Histones, Platelet Factor 4, and Heparinoids
Authors: Kowalska M. Anna , Zhao Guohua , Zhai Li , David George , Marcus Stephen , Krishnaswamy Sriram , Poncz Mortimer 
Published: November 2013

Objective—
Histones are detrimental in late sepsis. Both activated protein C (aPC) and heparin can reverse their effect. Here, we investigated whether histones can modulate aPC generation in a manner similar to another positively charged molecule, platelet factor 4, and how heparinoids (unfractionated heparin or oxygen-desulfated unfractionated heparin with marked decrease anticoagulant activity) may modulate this effect.

Approach and Results—
We measured in vitro and in vivo effects of histones, platelet factor 4, and heparinoids on aPC formation, activated partial thromboplastin time, and murine survival. In vitro, histones and platelet factor 4 both affect thrombin/thrombomodulin aPC generation following a bell-shaped curve, with a peak of >5-fold enhancement. Heparinoids shift these curves rightward. Murine aPC generation studies after infusions of histones, platelet factor 4, and heparinoids supported the in vitro data. Importantly, although unfractionated heparin and 2-O, 3-O desulfated heparin both reversed the lethality of high-dose histone infusions, only mice treated with 2-O, 3-O desulfated heparin demonstrated corrected activated partial thromboplastin times and had significant levels of aPC.

Conclusions—
Our data provide a new contextual model of how histones affect aPC generation, and how heparinoid therapy may be beneficial in sepsis. These studies provide new insights into the complex interactions controlling aPC formation and suggest a novel therapeutic interventional strategy.
Spectrum of Transient Visual Symptoms in a Transient Ischemic Attack Cohort
Authors: Lavallée Philippa C. , Cabrejo Lucie , Labreuche Julien , Mazighi Mikaël , Meseguer Elena , Guidoux Céline , Abboud Halim , Lapergue Bertrand , Klein Isabelle F. , Olivot Jean-Marc , Sirimarco Gaia , Gonzales-Valcarcel Jaime , Touboul Pierre-Jean , Amarenco Pierre 
Published: November 2013

Background and Purpose—
Transient visual symptoms (TVS) are common complaints. They can be related to transient ischemic attacks, but the nature of the symptoms often remains uncertain, and data on prognosis are scarce. We studied the prevalence, presentation, and effect of different types of TVS, paying particular attention to the association with high-risk pathology of embolism.

Methods—
A total of 2398 patients with suspected transient ischemic attack admitted to the SOS-TIA clinic between January 2003 and December 2008 underwent immediate evaluation and treatment.

Results—

Eight hundred twenty-six (34.5%) patients had TVS, including 422 (17.6%) patients with isolated TVS. Transient monocular blindness was the most frequent TVS (36.3%), followed by diplopia (13.4%), homonymous lateral hemianopia (12.3%), bilateral positive visual phenomena (10.8%), and lone bilateral blindness (4.5%). Positive diffusion-weighted imaging was found in 11.8%, 8.1%, 8.1%, and 5.0% of patients with homonymous lateral hemianopia, diplopia, lone bilateral blindness, and transient monocular blindness, respectively. Among 1850 patients (595 patients with TVS) with definite/possible transient ischemic attack or minor stroke, a major source of embolism of cardiac or arterial origin was found less frequently in patients with isolated or nonisolated TVS than in patients without TVS (19.6%; 19.7% versus 28.1%, respectively;
P
<0.001). However, we found a higher rate of atrial fibrillation in patients with homonymous lateral hemianopia (23.2%) than in patients with other TVS (4.0%; adjusted odds ratio, 6.71; 95% confidence interval, 2.99–15.06) or nonvisual symptoms (9.1%; adjusted odds ratio, 4.39; 95% confidence interval, 2.26–8.50).

Conclusions—
Approximately 20% of patients with TVS had a major source of embolism detected, requiring urgent management. Atrial fibrillation was particularly frequent in patients with transient homonymous lateral hemianopia.
Cerebral Microbleeds as a Predictor of 1-Year Outcome of Poststroke Depression
Authors: Tang Wai Kwong , Chen Yangkun , Liang Huajun , Chu Winnie Chiu Wing , Mok Vincent Chung Tong , Ungvari Gabor Sandor , Wong Ka Sing 
Published: November 2013

Background and Purpose—
Cerebral microbleeds (CMBs) are common in stroke survivors and community-dwelling elderly. The clinical significance of CMBs in the outcome of poststroke depression (PSD) is unknown. This study examined the association between the 1-year outcome of PSD and CMBs.

Methods—
The study population comprised 774 Chinese patients with acute ischemic stroke who were admitted to the acute stroke unit of a university-affiliated regional hospital in Hong Kong. Three and 15 months after the onset of the index stroke, a research assistant administered the locally validated 15-item Geriatric Depression Scale. PSD was defined as a Geriatric Depression Scale score of ≥7. Of the 213 patients with PSD at the 3-month follow-up, 135 (63.4%) attended the 15-month follow-up, at which time 89 (65.9%) patients remained depressed (nonremitters), and 46 (34.1%) had recovered (remitters). The presence and location of CMBs were evaluated with magnetic resonance imaging.

Results—

In comparison with the remitters, nonremitters were more likely to have lobar CMBs (18.4% versus 4.3%;
P
=0.024). Lobar CMBs remained an independent predictor of PSD in the multivariate analysis, with an odds ratio of 4.96 (
P
=0.039).

Conclusions—
The results suggest that lobar CMBs may influence the outcome of PSD. The importance of CMBs in the clinical course of depression in stroke survivors warrants further investigation.
Evolution of Computed Tomography Angiography Spot Sign Is Consistent With a Site of Active Hemorrhage in Acute Intracerebral Hemorrhage
Authors: Dowlatshahi Dar , Wasserman Jason K. , Momoli Franco , Petrcich William , Stotts Grant , Hogan Matthew , Sharma Mukul , Aviv Richard I. , Demchuk Andrew M. , Chakraborty Santanu 
Published: November 2013

Background and Purpose—
CT angiography spot sign predicts hematoma expansion in patients with acute intracerebral hemorrhage (ICH). The spot sign may represent a site of active extravasation, a locus of arrested hemorrhage forming fibrin globes, or represent associated epiphenomena such as hypertensive microaneurysms. We sought to describe the evolution of spot signs over 60 seconds in acute ICH using dynamic CT angiography and determine whether they grow and diffuse into the hematoma as would be expected with active extravasation.

Methods—
We prospectively identified consecutive patients presenting with spontaneous ICH <6 hours from symptom onset that completed dynamic CT angiography imaging over a 60-second acquisition protocol. We determined spot positivity, quantified spot volumes, and then used repeated-measures ANOVA to assess changes in spot volume over time.

Results—

We collected data on 35 patients; 13 of 35 (37%) patients were spot-positive. Spot-positive patients had larger median ICH volume compared with spot-negative patients (median 10.7 versus 49.2 mL;
P
=0.007). Maximal spot sign volumes ranged from 0.02 to 2.8 mL (median 0.17 mL). Spot sign volumes increased significantly with time (
P
<0.001) and seemed to disperse into the hematoma in all cases. Three of 13 (23%) spot-positive patients presented with 2 distinct spot signs, but the remaining patients either had only 1 spot sign or different contiguous components of an irregularly shaped spot sign.

Conclusions—
In this dynamic CT angiography study of ICH, spot signs evolve consistent with sites of active extravasation.
Bilateral Priming Accelerates Recovery of Upper Limb Function After Stroke
Authors: Stinear Cathy M. , Petoe Matthew A. , Anwar Samir , Barber Peter Alan , Byblow Winston D. 
Published: November 2013

Background and Purpose—
The ability to live independently after stroke depends on the recovery of upper limb function. We hypothesized that bilateral priming with active–passive movements before upper limb physiotherapy would promote rebalancing of corticomotor excitability and would accelerate upper limb recovery at the subacute stage.

Methods—
A single-center randomized controlled trial of bilateral priming was conducted with 57 patients randomized at the subacute stage after first-ever ischemic stroke. The PRIMED group made device-assisted mirror symmetrical bimanual movements before upper limb physiotherapy, every weekday for 4 weeks. The CONTROL group was given intermittent cutaneous electric stimulation of the paretic forearm before physiotherapy. Assessments were made at baseline, 6, 12, and 26 weeks. The primary end point was the proportion of patients who reached their plateau for upper limb function at 12 weeks, measured with the Action Research Arm Test.

Results—

Odds ratios indicated that PRIMED participants were 3× more likely than controls to reach their recovery plateau by 12 weeks. Intention-to-treat and per-protocol analyses showed a greater proportion of PRIMED participants achieved their plateau by 12 weeks (intention to treat, χ
2
=4.25;
P
=0.039 and per protocol, χ
2
=3.99;
P
=0.046). ANOVA of per-protocol data showed PRIMED participants had greater rebalancing of corticomotor excitability than controls at 12 and 26 weeks and interhemispheric inhibition at 26 weeks (all
P
<0.05).

Conclusions—
Bilateral priming accelerated recovery of upper limb function in the initial weeks after stroke.

Clinical Trial Registration—

URL:
http://www.anzctr.org.au
. Unique identifier: ANZCTR1260900046822.
Examining the Relationship between Drought Development and Rapid Changes in the Evaporative Stress Index
Authors: Otkin Jason A. , Anderson Martha C. , Hain Christopher , Svoboda Mark 
Published: November 2013

AbstractIn this study, the ability of a new drought metric based on thermal infrared remote sensing imagery to provide early warning of an elevated risk for drought intensification is assessed. This new metric, called the rapid change index (RCI), is designed to highlight areas undergoing rapid changes in moisture stress as inferred from weekly changes in the evaporative stress index (ESI) generated using the Atmosphere–Land Exchange Inverse (ALEXI) surface energy balance model. Two case study analyses across the central United States revealed that the initial appearance of negative RCI values indicative of rapid increases in moisture stress preceded the introduction of severe-to-exceptional drought in the U.S. Drought Monitor (USDM) by more than 4 weeks. Using data from 2000 to 2012, the probability of USDM intensification of at least one, two, or three categories over different time periods was computed as a function of the RCI magnitude. Compared to baseline probabilities, the RCI-derived probabilities often indicate a much higher risk for drought development that increases greatly as the RCI becomes more negative. When the RCI is strongly negative, many areas are characterized by intensification probabilities that are several times higher than the baseline climatology. The highest probabilities encompass much of the central and eastern United States, with the greatest increase over climatology within regions most susceptible to rapid drought development. These results show that the RCI provides useful drought early warning capabilities that could be used to alert stakeholders of an increased risk for drought development over subseasonal time scales.
Stokes Drift in Internal Equatorial Kelvin Waves: Continuous Stratification versus Two-Layer Models
Authors: Weber Jan Erik H. , Christensen Kai H. , Broström Göran 
Published: November 2013

Abstract
The Stokes drift in long internal equatorial Kelvin waves is investigated theoretically for an inviscid fluid of constant depth. While the Stokes drift in irrotational waves is positive everywhere in the fluid, that is, directed along the phase velocity, this is not always the case for internal Kelvin waves, which possess vorticity. For constant Brunt–Väisälä frequency, the Stokes drift in such waves is sinusoidal in the vertical with a negative value in the middle of the layer for the first baroclinic mode. For a pycnocline that is typical of the equatorial Pacific, this study finds for the first mode that the largest negative Stokes drift velocity occurs near the depth where the Brunt–Väisälä frequency has its maximum. Here, estimated drift values are found to be on the same order of magnitude as those observed in the Pacific Equatorial Undercurrent at the same level. In contrast, a two-layer model with constant density in each layer yields a positive Stokes drift in both layers. This contradicts the fact that, as shown in this paper, the vertically integrated Stokes drift (the Stokes flux) must be zero for arbitrary Brunt–Väisälä frequency.