bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic quantification of epicardial fat volume on non‐enhanced cardiac CT scans using a multi‐atlas segmentation approach
Authors: Shahzad Rahil , Bos Daniel , Metz Coert , Rossi Alexia , Kirişli Hortense , van der Lugt Aad , Klein Stefan , Witteman Jacqueline , de Feyter Pim , Niessen Wiro , van Vliet Lucas , van Walsum Theo 
Published: August 2013

Purpose:There is increasing evidence that epicardial fat (i.e., adipose tissue contained within the pericardium) plays an important role in the development of cardiovascular disease. Obtaining the epicardial fat volume from routinely performed non‐enhanced cardiac CT scans is therefore of clinical interest. The purpose of this work is to investigate the feasibility of automatic pericardium segmentation and subsequent quantification of epicardial fat on non‐enhanced cardiac CT scans.Methods:Imaging data of 98 randomly selected subjects belonging to a larger cohort of subjects who underwent a cardiac CT scan at our medical center were retrieved. The data were acquired on two different scanners. Automatic multi‐atlas based method for segmenting the pericardium and calculating the epicardial fat volume has been developed. The performance of the method was assessed by (1) comparing the automatically segmented pericardium to a manually annotated reference standard, (2) comparing the automatically obtained epicardial fat volumes to those obtained manually, and (3) comparing the accuracy of the automatic results to the inter‐observer variability.Results:Automatic segmentation of the pericardium was achieved with a Dice similarity index of 89.1 ± 2.6% with respect to Observer 1 and 89.2 ± 1.9% with respect to Observer 2. The correlation between the automatic method and the manual observers with respect to the epicardial fat volume computed as the Pearson's correlation coefficient (R) was 0.91 (P < 0.001) for both observers. The inter‐observer study resulted in a Dice similarity index of 89.0 ± 2.4% for segmenting the pericardium and a Pearson's correlation coefficient of 0.92 (P < 0.001) for computation of the epicardial fat volume.Conclusions:The authors developed a fully automatic method that is capable of segmenting the pericardium and quantifying epicardial fat on non‐enhanced cardiac CT scans. The authors demonstrated the feasibility of using this method to replace manual annotations by showing that the automatic method performs as good as manual annotation on a large dataset.
Mercury Methylation by the Methanogen Methanospirillum hungatei
Authors: Yu Ri-Qing , Reinfelder John R. , Hines Mark E. , Barkay Tamar 
Published: August 2013

ABSTRACT

Methylmercury (MeHg), a neurotoxic substance that accumulates in aquatic food chains and poses a risk to human health, is synthesized by anaerobic microorganisms in the environment. To date, mercury (Hg) methylation has been attributed to sulfate- and iron-reducing bacteria (SRB and IRB, respectively). Here we report that a methanogen,
Methanospirillum hungatei
JF-1, methylated Hg in a sulfide-free medium at comparable rates, but with higher yields, than those observed for some SRB and IRB. Phylogenetic analyses showed that the concatenated orthologs of the Hg methylation proteins HgcA and HgcB from
M. hungatei
are closely related to those from known SRB and IRB methylators and that they cluster together with proteins from eight other methanogens, suggesting that these methanogens may also methylate Hg. Because all nine methanogens with HgcA and HgcB orthologs belong to the class
Methanomicrobia
, constituting the late-evolving methanogenic lineage, methanogenic Hg methylation could not be considered an ancient metabolic trait. Our results identify methanogens as a new guild of Hg-methylating microbes with a potentially important role in mineral-poor (sulfate- and iron-limited) anoxic freshwater environments.
Novel Cultivation-Based Approach To Understanding the Miscellaneous Crenarchaeotic Group (MCG) Archaea from Sedimentary Ecosystems
Authors: Gagen Emma J. , Huber Harald , Meador Travis , Hinrichs Kai-Uwe , Thomm Michael 
Published: August 2013

ABSTRACT

The uncultured miscellaneous crenarchaeotic group (MCG) archaea comprise one of the most abundant microbial groups in the Earth's subsurface environment. However, very little information is available regarding the lifestyle, physiology, and factors controlling the distribution of members of this group. We established a novel method using both cultivation and molecular techniques, including a pre-PCR propidium monoazide treatment, to investigate viable members of the MCG
in vitro
. Enrichment cultures prepared from estuarine sediment were provided with one of a variety of carbon substrates or cultivation conditions and incubated for 3 weeks. Compared with the samples from time zero, there was an order-of-magnitude increase in the number of MCG 16S rRNA genes in almost all cultures, indicating that MCG archaea are amenable to
in vitro
cultivation. None of the tested substrates or conditions significantly stimulated growth of MCG archaea more than the basal medium alone; however, glycerol (0.02%) had a significantly inhibitory effect (
P
< 0.05). Diversity analysis of populations resulting from four culture treatments (basal medium, addition of amino acids, H
2
-CO
2
as the gas phase, or initial aerobic conditions) revealed that the majority of viable MCG archaea were affiliated with the MCG-8 and MCG-4 clusters. There were no significant differences in MCG diversity between these treatments, also indicating that some members of MCG-4 and MCG-8 are tolerant of initially oxic conditions. The methods outlined here will be useful for further investigation of MCG archaea and comparison of substrates and cultivation conditions that influence their growth
in vitro
.
Functional Identification of Rubber Oxygenase (RoxA) in Soil and Marine Myxobacteria
Authors: Birke Jakob , Röther Wolf , Schmitt Georg , Jendrossek Dieter 
Published: August 2013

ABSTRACT

The rubber oxygenase (RoxA) of
Xanthomonas
sp. strain 35Y (RoxA

Xsp

) is so far the only known extracellular
c
-type diheme cytochrome that is able to cleave poly(
cis
-1,4-isoprene). All other rubber-degrading bacteria described are Gram positive and employ a nonheme protein (latex-clearing protein [Lcp]) for the postulated primary attack of polyisoprene. Here, we identified RoxA orthologs in the genomes of
Haliangium ochraceum
,
Myxococcus fulvus
,
Corallococcus coralloides
, and
Chondromyces apiculatus
. The
roxA
orthologs of
H. ochraceum
(RoxA

Hoc

),
C. coralloides
BO35 (RoxA

Cco

), and
M. fulvus
(RoxA

Mfu

) were functionally expressed in a Δ
roxA Xanthomonas
sp. 35Y background. All RoxA orthologs oxidatively cleaved polyisoprene, as revealed by restoration of clearing-zone formation and detection of 12-oxo-4,8-dimethyltrideca-4,8-diene-1-al (ODTD) as a cleavage product. RoxA

Xsp

, RoxA

Mfu

, and RoxA

Cco

were purified and biochemically characterized. The optimal temperature of RoxA

Cco

and RoxA

Mfu

was between 22 and 30°C. All RoxA orthologs as isolated showed an oxidized UV-visible spectrum. Chemical reduction of RoxA

Cco

and RoxA

Mfu

indicated the presence of two slightly different heme centers with absorption maxima between 549 and 553 nm, similar to RoxA

Xsp

. Sequence analysis and modeling of the three-dimensional structures of the RoxA orthologs revealed a high degree of similarity to the recently solved RoxA

Xsp

structure and included several conserved residues, notably, W
302
, F
317
, and a MauG motif at about H
517
. Lcp-like sequences were not detected in the genomes of the
Xanthomonas
sp. 35Y,
H. ochraceum
,
M. fulvus
, and
C. coralloides
. No RoxA orthologs were found in Gram-positive bacteria, and this first description of functional RoxA in Gram-negative bacteria other than
Xanthomonas
proves that RoxA is more common among rubber degraders than was previously assumed.
Comparative Genomic and Transcriptomic Analyses Reveal Habitat Differentiation and Different Transcriptional Responses during Pectin Metabolism in Alishewanella Species
Authors: Jung Jaejoon , Park Woojun 
Published: August 2013

ABSTRACT

Alishewanella
species are expected to have high adaptability to diverse environments because they are isolated from different natural habitats. To investigate how the evolutionary history of
Alishewanella
species is reflected in their genomes, we performed comparative genomic and transcriptomic analyses of
A. jeotgali
,
A. aestuarii
, and
A. agri
, which were isolated from fermented seafood, tidal flat sediment, and soil, respectively. Genomic islands with variable GC contents indicated that invasion of prophage and transposition events occurred in
A. jeotgali
and
A. agri
but not in
A. aestuarii
. Habitat differentiation of
A. agri
from a marine environment to a terrestrial environment was proposed because the species-specific genes of
A. agri
were similar to those of soil bacteria, whereas those of
A. jeotgali
and
A. aestuarii
were more closely related to marine bacteria. Comparative transcriptomic analysis with pectin as a sole carbon source revealed different transcriptional responses in
Alishewanella
species, especially in oxidative stress-, methylglyoxal detoxification-, membrane maintenance-, and protease/chaperone activity-related genes. Transcriptomic and experimental data demonstrated that
A. agri
had a higher pectin degradation rate and more resistance to oxidative stress under pectin-amended conditions than the other 2
Alishewanella
species. However, expression patterns of genes in the pectin metabolic pathway and of glyoxylate bypass genes were similar among all 3
Alishewanella
species. Our comparative genomic and transcriptomic data revealed that
Alishewanella
species have evolved through horizontal gene transfer and habitat differentiation and that pectin degradation pathways in
Alishewanella
species are highly conserved, although stress responses of each
Alishewanella
species differed under pectin culture conditions.
Mapping of the SecA Signal Peptide Binding Site and Dimeric Interface by Using the Substituted Cysteine Accessibility Method
Authors: Bhanu Meera K. , Zhao Ping , Kendall Debra A. 
Published: August 2013

ABSTRACT

SecA is an ATPase nanomotor critical for bacterial secretory protein translocation. Secretory proteins carry an amino-terminal signal peptide that is recognized and bound by SecA followed by its transfer across the SecYEG translocon. While this process is crucial for the onset of translocation, exactly where the signal peptide interacts with SecA is unclear. SecA protomers also interact among themselves to form dimers in solution, yet the oligomeric interface and the residues involved in dimerization are unknown. To address these issues, we utilized the substituted cysteine accessibility method (SCAM); we generated a library of 23 monocysteine SecA mutants and probed for the accessibility of each mutant cysteine to maleimide-(polyethylene glycol)
2
-biotin (MPB), a sulfhydryl-labeling reagent, both in the presence and absence of a signal peptide. Dramatic differences in MPB labeling were observed, with a select few mutants located at the preprotein cross-linking domain (PPXD), the helical wing domain (HWD), and the helical scaffold domain (HSD), indicating that the signal peptide binds at the groove formed between these three domains. The exposure of this binding site is varied under different conditions and could therefore provide an ideal mechanism for preprotein transfer into the translocon. We also identified residues G793, A795, K797, and D798 located at the two-helix finger of the HSD to be involved in dimerization. Adenosine-5′-(γ-thio)-triphosphate (ATPγS) alone and, more extensively, in conjunction with lipids and signal peptides strongly favored dimer dissociation, while ADP supports dimerization. This study provides key insight into the structure-function relationships of SecA preprotein binding and dimer dissociation.
Characterization of IntA, a Bidirectional Site-Specific Recombinase Required for Conjugative Transfer of the Symbiotic Plasmid of Rhizobium etli CFN42
Authors: Hernández-Tamayo Rogelio , Sohlenkamp Christian , Puente José Luis , Brom Susana , Romero David 
Published: August 2013

ABSTRACT

Site-specific recombination occurs at short specific sequences, mediated by the cognate recombinases. IntA is a recombinase from
Rhizobium etli
CFN42 and belongs to the tyrosine recombinase family. It allows cointegration of plasmid p42a and the symbiotic plasmid via site-specific recombination between attachment regions (
attA
and
attD
) located in each replicon. Cointegration is needed for conjugative transfer of the symbiotic plasmid. To characterize this system, two plasmids harboring the corresponding attachment sites and
intA
were constructed. Introduction of these plasmids into
R. etli
revealed IntA-dependent recombination events occurring at high frequency. Interestingly, IntA promotes not only integration, but also excision events, albeit at a lower frequency. Thus,
R. etli
IntA appears to be a bidirectional recombinase. IntA was purified and used to set up electrophoretic mobility shift assays with linear fragments containing
attA
and
attD
. IntA-dependent retarded complexes were observed only with fragments containing either
attA
or
attD
. Specific retarded complexes, as well as normal
in vivo
recombination abilities, were seen even in derivatives harboring only a minimal attachment region (comprising the 5-bp central region flanked by 9- to 11-bp inverted repeats). DNase I-footprinting assays with IntA revealed specific protection of these zones. Mutations that disrupt the integrity of the 9- to 11-bp inverted repeats abolish both specific binding and recombination ability, while mutations in the 5-bp central region severely reduce both binding and recombination. These results show that IntA is a bidirectional recombinase that binds to
att
regions without requiring neighboring sequences as enhancers of recombination.
Structure-Function Analysis of MurJ Reveals a Solvent-Exposed Cavity Containing Residues Essential for Peptidoglycan Biogenesis in Escherichia coli
Authors: Butler Emily K. , Davis Rebecca M. , Bari Vase , Nicholson Paul A. , Ruiz Natividad 
Published: August 2013

ABSTRACT

Gram-negative bacteria such as
Escherichia coli
build a peptidoglycan (PG) cell wall in their periplasm using the precursor known as lipid II. Lipid II is a large amphipathic molecule composed of undecaprenyl diphosphate and a disaccharide-pentapeptide that PG-synthesizing enzymes use to build the PG sacculus. During PG biosynthesis, lipid II is synthesized at the cytoplasmic face of the inner membrane and then flipped across the membrane. This translocation of lipid II must be assisted by flippases thought to shield the disaccharide-pentapeptide as it crosses the hydrophobic core of the membrane. The inner membrane protein MurJ is essential for PG biogenesis and homologous to known and putative flippases of the MOP (
m
ultidrug/
o
ligo-saccharidyl-lipid/
p
olysaccharide) exporter superfamily, which includes flippases that translocate undecaprenyl diphosphate-linked oligosaccharides across the cytoplasmic membranes of bacteria. Consequently, MurJ has been proposed to function as the lipid II flippase in
E. coli
. Here, we present a three-dimensional structural model of MurJ generated by the I-TASSER server that suggests that MurJ contains a solvent-exposed cavity within the plane of the membrane. Using
in vivo
topological studies, we demonstrate that MurJ has 14 transmembrane domains and validate features of the MurJ structural model, including the presence of a solvent-exposed cavity within its transmembrane region. Furthermore, we present functional studies demonstrating that specific charged residues localized in the central cavity are essential for function. Together, our studies support the structural homology of MurJ to MOP exporter proteins, suggesting that MurJ might function as an essential transporter in PG biosynthesis.
Functionally Essential Interaction between Yersinia YscO and the T3S4 Domain of YscP
Authors: Mukerjea Romila , Ghosh Partho 
Published: August 2013

ABSTRACT

The type III secretion (T3S) system is essential to the virulence of a large number of Gram-negative bacterial pathogens, including
Yersinia
. YscO is required for T3S in
Yersinia
and is known to interact with several other T3S proteins, including the chaperone SycD and the needle length regulator YscP. To define which interactions of YscO are required for T3S, we pursued model-guided mutagenesis: three conserved and surface-exposed regions of modeled YscO were targeted for multiple alanine substitutions. Most of the mutations abrogated T3S and did so in a recessive manner, consistent with a loss of function. Both functional and nonfunctional YscO mutant proteins interacted with SycD, indicating that the mutations had not affected protein stability. Likewise, both functional and nonfunctional versions of YscO were exclusively intrabacterial. Functional and nonfunctional versions of YscO were, however, distinguishable with respect to interaction with YscP. This interaction was observed only for wild-type YscO and a T3S-proficient mutant of YscO but not for the several T3S-deficient mutants of YscO. Evidence is presented that the YscO-YscP interaction is direct and that the type III secretion substrate specificity switch (T3S4) domain of YscP is sufficient for this interaction. These results provide evidence that the interaction of YscO with YscP, and in particular the T3S4 domain of YscP, is essential to type III secretion.
A meta-analysis of cognitive-based behaviour change techniques as interventions to improve medication adherence
Authors: Easthall Claire , Song Fujian , Bhattacharya Debi 
Published: August 2013

ObjectiveTo describe and evaluate the use of cognitive-based behaviour change techniques as interventions to improve medication adherence.DesignSystematic review and meta-analysis of interventions to improve medication adherence.Data sourcesSearch of the MEDLINE, EMBASE, PsycINFO, CINAHL and The Cochrane Library databases from the earliest year to April 2013 without language restriction. References of included studies were also screened to identify further relevant articles.Review methodsWe used predefined criteria to select randomised controlled trials describing a medication adherence intervention that used Motivational Interviewing (MI) or other cognitive-based techniques. Data were extracted and risk of bias was assessed by two independent reviewers. We conducted the meta-analysis using a random effects model and Hedges’ g as the measure of effect size.ResultsWe included 26 studies (5216 participants) in the meta-analysis. Interventions most commonly used MI, but many used techniques such as aiming to increase the patient's confidence and sense of self-efficacy, encouraging support-seeking behaviours and challenging negative thoughts, which were not specifically categorised. Interventions were most commonly delivered from community-based settings by routine healthcare providers such as general practitioners and nurses. An effect size (95% CI) of 0.34 (0.23 to 0.46) was calculated and was statistically significant (p < 0.001). Heterogeneity was high with an I2value of 68%. Adjustment for publication bias generated a more conservative estimate of summary effect size of 0.21 (0.08 to 0.33). The majority of subgroup analyses produced statistically non-significant results.ConclusionsCognitive-based behaviour change techniques are effective interventions eliciting improvements in medication adherence that are likely to be greater than the behavioural and educational interventions largely used in current practice. Subgroup analyses suggest that these interventions are amenable to use across different populations and in differing manners without loss of efficacy. These factors may facilitate incorporation of these techniques into routine care.
Myocardial Fibrosis as a Key Determinant of Left Ventricular Remodeling in Idiopathic Dilated Cardiomyopathy
Authors: Masci Pier Giorgio , Schuurman Robert , Andrea Barison , Ripoli Andrea , Coceani Michele , Chiappino Sara , Todiere Giancarlo , Srebot Vera , Passino Claudio , Aquaro Giovanni Donato , Emdin Michele , Lombardi Massimo 
Published: August 2013

Background—
In idiopathic dilated cardiomyopathy, there are scarce data on the influence of late gadolinium enhancement (LGE) assessed by cardiovascular magnetic resonance on left ventricular (LV) remodeling.

Methods and Results—

Fifty-eight consecutive patients with idiopathic dilated cardiomyopathy underwent baseline clinical, biohumoral, and instrumental workup. Medical therapy was optimized after study enrollment. Cardiovascular magnetic resonance was used to assess ventricular volumes, function, and LGE extent at baseline and 24-month follow-up. LV reverse remodeling (RR) was defined as an increase in LV ejection fraction ≥10 U, combined with a decrease in LV end-diastolic volume ≥10% at follow-up. ΔLGE extent was the difference in LGE extent between follow-up and baseline. LV-RR was observed in 22 patients (38%). Multivariate regression analysis showed that the absence of LGE at baseline cardiovascular magnetic resonance was a strong predictor of LV-RR (odds ratio, 10.857 [95% confidence interval, 1.844–63.911];
P
=0.008) after correction for age, heart rate, New York Heart Association class, LV volumes, and LV and right ventricular ejection fractions. All patients with baseline LGE (n=26; 45%) demonstrated LGE at follow-up, and no patient without baseline LGE developed LGE at follow-up. In LGE-positive patients, there was an increase in LGE extent over time (
P
=0.034), which was inversely related to LV ejection fraction variation (Spearman ρ, −0.440;
P
=0.041). Five patients showed an increase in LGE extent >75th percentile of ΔLGE extent, and among these none experienced LV-RR and 4 had a decrease in LV ejection fraction ≥10 U at follow-up.

Conclusions—
In patients with idiopathic dilated cardiomyopathy, the absence of LGE at baseline is a strong independent predictor of LV-RR at 2-year follow-up, irrespective of the initial clinical status and the severity of ventricular dilatation and dysfunction. The increase in LGE extent during follow-up was associated with progressive LV dysfunction.
One-shot scleroembolization: a new technique for the treatment of varicose veins disease of lower extremities. Preliminary results
Authors: Viani Marco P , Viani Giacomo M , Sergenti Jessica 
Published: August 2013

Objective The aim of this article is to present a new technique for minimally invasive treatment of varicose veins disease of lower extremities. Methods One-shot scleroembolization is a new technique designed for the treatment of varicose veins of the lower extremities, which associates a mechanical interruption of the sapheno-femoral junction to classic sclerotherapy with no need for surgery or anesthesia. This is achieved with the combined use of a coil positioned in the terminal portion of the great saphenous vein and a foamed sclerosant drug. Results At three months’ follow-up no complications have been observed. The great saphenous vein was still occluded in all patients (nine out of nine). Conclusions One-shot scleroembolization seems to be an effective technique for the treatment of varicose veins disease in outpatients, with the advantage of causing little distress to the patient.