julilili42/papers huggingface dataset:
Is the diagnostic yield of myocardial stress perfusion MRI impaired by three-vessel coronary artery disease?
2014-02-13

Background Three-vessel coronary artery disease (CAD) comes along with globally reduced myocardial perfusion potentially restricting the demarcation of regional hypoperfusion in stress perfusion cardiac magnetic resonance imaging (MRI). Purpose To evaluate whether stress perfusion cardiac MRI is capable of detecting myocardial hypoperfusion in patients with 3-vessel CAD reliably. Material and Methods Two hundred and five patients with symptoms of CAD were included. The examination protocol comprised imaging of myocardial perfusion at stress (0.14 mg/kg/min adenosine for 4 min) using a 2D saturation recovery gradient echo sequence after administration of gadobutrol (0.1 mmol/kg body weight). Perfusion sequences were assessed qualitatively by two experienced observers. Coronary angiography served as standard of reference. Results Sensitivity and specificity for hemodynamically relevant stenoses in patients with 0-, 1-, 2-, 3-vessel coronary artery disease were 100%/91%, 91%/73%, 90%/71%, 92%/64%; positive/negative predictive value, 67%/100%, 91%/73%, 83%/81%, 93%/58%; diagnostic accuracy, 93%/87%/83%/87%, respectively. The negative predictive value in patients with 3-vessel CAD was lower than in patients with 0- and 2-vessel CAD and the specificity lower than in patients with no CAD whereas the positive predictive value was higher than in patients with no CAD. The other proportions did not differ significantly between the groups. Conclusion The diagnostic value of stress perfusion cardiac MRI in patients with 3-vessel CAD is comparable to results in patients with 1- or 2-vessel CAD. In the rare event that stress perfusion images do not depict regional hypoperfusion in patients with severe 3-vessel CAD, myocardial ischemia could be identified by reduced semi-quantitative perfusion parameters.
Comparing manual and automatic segmentation of hippocampal volumes: Reliability and validity issues in younger and older brains
2014-02-14

Abstract We compared hippocampal volume measures obtained by manual tracing to automatic segmentation with FreeSurfer in 44 younger (20–30 years) and 47 older (60–70 years) adults, each measured with magnetic resonance imaging (MRI) over three successive time points, separated by four months. Retest correlations over time were very high for both manual and FreeSurfer segmentations. With FreeSurfer, correlations over time were significantly lower in the older than in the younger age group, which was not the case with manual segmentation. Pearson correlations between manual and FreeSurfer estimates were sufficiently high, numerically even higher in the younger group, whereas intra‐class correlation coefficient (ICC) estimates were lower in the younger than in the older group. FreeSurfer yielded higher volume estimates than manual segmentation, particularly in the younger age group. Importantly, FreeSurfer consistently overestimated hippocampal volumes independently of manually assessed volume in the younger age group, but overestimated larger volumes in the older age group to a less extent, introducing a systematic age bias in the data. Age differences in hippocampal volumes were significant with FreeSurfer, but not with manual tracing. Manual tracing resulted in a significant difference between left and right hippocampus (right &gt; left), whereas this asymmetry effect was considerably smaller with FreeSurfer estimates. We conclude that FreeSurfer constitutes a feasible method to assess differences in hippocampal volume in young adults. FreeSurfer estimates in older age groups should, however, be interpreted with care until the automatic segmentation pipeline has been further optimized to increase validity and reliability in this age group. Hum Brain Mapp 35:4236–4248, 2014 . © 2014 Wiley Periodicals, Inc .
Monocytic myeloid-derived suppressor cells in advanced melanoma patients
2014-02-14

The percentage of circulating CD14<sup>+</sup>CD11b<sup>+</sup>HLA-DR<sup>-/low</sup> myeloid-derived suppressor cells (MDSCs) inversely correlates with survival among advanced melanoma patients. High levels of MDSCs are associated with the absence of T lymphocytes specific for melanoma-derived antigens, implying a causal and clinically relevant interaction between these cell subsets. MDSCs might therefore represent prognostic markers as well as targets for the development of novel therapeutic interventions against melanoma.
Materialographic Examination of Three Different Types of Failed Dental Implants
2014-02-15

Abstract Focused on tissue interactions and the properties of the materials themselves, the causes of dental implant failure can be analysed successfully using methods developed within materials science. This will be exemplified by three failing implants. The implants represent a broad range of materials (titanium, PEEK, zirconium dioxide) and geometries (screw, cylindrical, disc). Materials and methods: Following appropriate specimen collection and preparation, EDX, ESEM, light microscopy and ultrasound examinations were performed. Since only the titanium implant exhibited osseointegration, the implant-bone interface of this implant was additionally analysed by FIB-TEM. Results: The absence of bone tissue residue on the zirconium dioxide and PEEK implants was confirmed by all imaging methods. Complete osseointegration is demonstrable only for a complete fragment of the titanium implant resected from the jaw bone, with a bone-to-metal contact of 82.5 %. Conclusion: A bioactive interaction with the target tissues was found only for the titanium implant. The loss of the titanium implant examined was due to a material failure. High-frequency ultrasonic microscopy has proven a suitable tool for the assessment of osseointegration. A reduced sample preparation effort and an ability to use ultrasound in situ would suggest that ultrasonic microscopy technology is a suitable technology for failure analysis.
Modeling circumbinary planets: The case of Kepler-38
2014-02-17

\\n Context. Recently, a number of planets orbiting binary stars have been discovered by the Kepler space telescope. In a few systems the planets reside close to the dynamical stability limit. Owing to the difficulty of forming planets in such close orbits, it is believed that they have formed farther out in the disk and migrated to their present locations.\\n Aims. Our goal is to construct more realistic models of planet migration in circumbinary disks and to determine the final position of these planets more accurately. In our work, we focus on the system <ext-link ext-link-type="aoi">Kepler-38</ext-link> where the planet is close to the stability limit. \\n Methods. The evolution of the circumbinary disk is studied using two-dimensional hydrodynamical simulations. We study locally isothermal disks as well as more realistic models that include full viscous heating, radiative cooling from the disk surfaces, and radiative diffusion in the disk midplane. After the disk has been brought into a quasi-equilibrium state, a 115 Earth-mass planet is embedded and its evolution is followed. \\n Results. In all cases the planets stop inward migration near the inner edge of the disk. In isothermal disks with a typical disk scale height of H/r = 0.05, the final outcome agrees very well with the observed location of planet Kepler-38b. For the radiative models, the disk thickness and location of the inner edge is determined by the mass in the system. For surface densities on the order of 3000 g/cm2 at 1 AU, the inner gap lies close to the binary and planets stop in the region between the 5:1 and 4:1 mean-motion resonances with the binary. A model with a disk with approximately a quarter of the mass yields a final position very close to the observed one. \\n Conclusions. For planets migrating in circumbinary disks, the final position is dictated by the structure of the disk. Knowing the observed orbits of circumbinary planets, radiative disk simulations with embedded planets can provide important information on the physical state of the system during the final stages of its evolution. \\n
Homeodomain leucine‐zipper proteins and their role in synchronizing growth and development with the environment
2014-02-17

Abstract The Arabidopsis ( Arabidopsis thaliana L.) genome encodes for four distinct classes of homeodomain leucine‐zipper (HD‐ZIP) transcription factors (HD‐ZIPI to HD‐ZIPIV), which are all organized in multi‐gene families. HD‐ZIP transcription factors act as sequence‐specific DNA‐binding proteins that are able to control the expression level of target genes. While HD‐ZIPI and HD‐ZIPII proteins are mainly associated with environmental responses, HD‐ZIPIII and HD‐ZIPIV are primarily known to act as patterning factors. Recent studies have challenged this view. It appears that several of the different HD‐ZIP families interact genetically to align both morphogenesis and environmental responses, most likely by modulating phytohormone‐signaling networks.
Hydrodynamic interactions induce anomalous diffusion under partial confinement
2014-02-17

Under partial confinement, the motion of colloidal particles is restricted to a plane or a line but their dynamics is influenced by hydrodynamic interactions mediated by the unconfined, three-dimensional flow of the embedding fluid. We demonstrate that this dimensionality mismatch induces a characteristic divergence in the collective diffusion coefficient of the colloidal subsystem. This result, independent of the specific interparticle forces in the colloid, is solely due to the kinematical constraint on the colloidal particles, and it is different from the known divergence of transport coefficients in purely one or two-dimensional fluids.
Necrotizing Enterocolitis and Focal Intestinal Perforation in Neonatal Intensive Care Units in the State of Baden-Wurttemberg, Germany
2014-02-17

In preterm infants with very low birth weight (VLBW) &lt;1500 g the most important acquired intestinal diseases are necrotising enterocolitis (NEC) and focal intestinal perforation (FIP). We analyzed data of the neonatology module of national external comparative quality assurance for inpatients in the state of Baden-Württemberg, Germany. Between 2010 and 2012, 59 of 3549 VLBW infants developed FIP (1.7%), 128 of them NEC (3.6%). In approximately 3% of infants with BW&lt;1000 g FIP was diagnosed, which was nearly 9 times more often than in infants with BW between 1250 and 1499 g (FIP frequency 0.36%). NEC frequency increased with decreasing BW and was more than 10 times higher in the smallest infants (BW&lt;750 g: 7.87%) compared to those with BW between 1250 and 1499 g (0.72%). The BW limit of 1250 g differentiates between groups of patients with distinguished risks for NEC and FIP.
On the Relation between the Mental Number Line and Arithmetic Competencies
2014-02-18

In this study, we aimed at investigating whether it is indeed the spatial magnitude representation that links number line estimation performance to other basic numerical and arithmetic competencies. Therefore, estimations of 45 fourth-graders in both a bounded and a new unbounded number line estimation task (with only a start-point and a unit given) were correlated with their performance in a variety of tasks including addition, subtraction, and number magnitude comparison. Assuming that both number line tasks assess the same underlying mental number line representation, unbounded number line estimation should also be associated with other basic numerical and arithmetic competencies. However, results indicated that children's estimation performance in the bounded but not the unbounded number line estimation task was correlated significantly with numerical and arithmetic competencies. We conclude that unbounded and bounded number line estimation tasks do not assess the same underlying spatial–numerical representation. Rather, the observed association between bounded number line estimation and numerical/arithmetic competencies may be driven by additional numerical processes (e.g., proportion judgement, addition/subtraction) recruited to solve the task.
Ha‐ras and β‐catenin oncoproteins orchestrate metabolic programs in mouse liver tumors
2014-02-18

The process of hepatocarcinogenesis in the diethylnitrosamine (DEN) initiation/phenobarbital (PB) promotion mouse model involves the selective clonal outgrowth of cells harboring oncogene mutations in Ctnnb1, while spontaneous or DEN‐only‐induced tumors are often Ha‐ras ‐ or B‐raf ‐mutated. The molecular mechanisms and pathways underlying these different tumor sub‐types are not well characterized. Their identification may help identify markers for xenobiotic promoted versus spontaneously occurring liver tumors. Here, we have characterized mouse liver tumors harboring either Ctnnb1 or Ha‐ras mutations via integrated molecular profiling at the transcriptional, translational and post‐translational levels. In addition, metabolites of the intermediary metabolism were quantified by high resolution 1 H magic angle nuclear magnetic resonance. We have identified tumor genotype‐specific differences in mRNA and miRNA expression, protein levels, post‐translational modifications, and metabolite levels that facilitate the molecular and biochemical stratification of tumor phenotypes. Bioinformatic integration of these data at the pathway level led to novel insights into tumor genotype‐specific aberrant cell signaling and in particular to a better understanding of alterations in pathways of the cell intermediary metabolism, which are driven by the constitutive activation of the β‐Catenin and Ha‐ras oncoproteins in tumors of the two genotypes.
Identification of a natural intergenotypic recombinant hepatitis delta virus genotype 1 and 2 in Vietnamese HBsAg‐positive patients
2014-02-18

Summary Hepatitis D virus ( HDV ) infection is acquired as a co‐ /superinfection of H epatitis B virus ( HBV ) and can modulate the pathophysiology of chronic hepatitis B and related liver diseases including hepatocellular carcinoma. Among the eight distinct HDV genotypes reported, relatively few studies have attempted to investigate the prevalence of HDV mixed genotypes and RNA recombination of HDV . With a recorded prevalence of 10–20% HBV infection in V ietnam, this study investigated the HDV variability, HDV genotypes and HDV recombination among twenty‐one HDV isolates in V ietnamese HB sAg‐positive patients. HDV subgenomic and full‐length genome sequences were obtained using newly established HDV ‐specific RT ‐ PCR techniques. The nucleotide homology was observed from 74.6% to 99.4% among the investigated full‐length genome of the HDV isolates. We observed HDV genotype 1 and HDV genotype 2 in the investigated V ietnamese patients. Although no HDV genotype mixtures were observed, we report here a newly identified recombinant of HDV genotypes ( HDV 1 and HDV 2). The identified recombinant HDV isolate C03 revealed sequence homology to both HDV genotype 1 (nt1 to nt907) and HDV genotype 2 (nt908 to nt1675; HDA g coding region) with a breakpoint at nt908. Our findings demonstrate the prevalence of intergenotypic recombination between HDV genotypes 1 and 2 in a V ietnamese HB sAg‐positive patient. Extended investigation on the distribution and prevalence of HDV , HDV mixed genotypes and recombinant HDV genotypes in a larger V ietnamese population offers vital insights into understanding of the micro‐epidemiology of HDV and subsequent pathophysiology in chronic HBV ‐ / HDV ‐related liver diseases.
User identification using raw sensor data from typing on interactive displays
2014-02-18

Personalized soft-keyboards which adapt to a user's individual typing behavior can reduce typing errors on interactive displays. In multi-user scenarios a personalized model has to be loaded for each participant. In this paper we describe a user identification technique that is based on raw sensor data from an optical touch screen. For classification of users we use a multi-class support vector machine that is trained with grayscale images from the optical sensor. Our implementation can identify a specific user from a set of 12 users with an average accuracy of 97.51% after one keystroke. It can be used to automatically select individual typing models during free-text entry. The resulting authentication process is completely implicit. We furthermore describe how the approach can be extended to automatic loading of personal information and settings.
Glutathione‐conjugated sulfanylalkanols are substrates for ABCC11 and γ‐glutamyl transferase 1: a potential new pathway for the formation of odorant precursors in the apocrine sweat gland
2014-02-18

Abstract We have previously shown that precursors of odorous components characteristic of axillary sweat are hardly detectable or undetectable in individuals carrying the 538G &gt; A SNP in the ABCC 11 transporter gene. However, it is unclear, whether ABCC 11 is directly involved in the transport of these compounds. To approach this question, transport of peptide‐conjugated potential precursors of 3‐methyl‐3‐sulfanylhexanol (3M3 SH ), a key determinant of axillary malodour, was measured using membrane vesicles of Sf9 insect cells overexpressing human ABCC 11. Whilst no ABCC 11‐mediated transport was detected for the dipeptide precursor Cys‐Gly‐3M3 SH , the glutathione conjugate of 3M3 SH ( SG ‐3M3 SH ) was robustly taken up by ABCC 11 at a transport rate of 0.47 pmol/mg/min. Collectively, these results illuminate SG ‐3M3 SH as a putative precursor of 3M3 SH , which then may undergo intra‐vesicular maturation to generate Cys‐Gly‐3M3 SH . Critically, the apocrine sweat gland was demonstrated to express γ ‐glutamyl transferase 1 ( GGT 1) protein, which is known to catalyse the deglutamylation of glutathionyl conjugates. Additionally, we provide evidence that recombinant and isolated hepatic human GGT 1 is capable of transforming SG ‐3M3 SH to Cys‐Gly‐3M3 SH in vitro . To sum up, we demonstrate that the functionality of ABCC 11 is likely to play an important role in the generation of axillary malodour. Furthermore, we identify GGT 1 as a key enzyme involved in the biosynthesis of Cys‐Gly‐3M3 SH .
Automated analysis of giant unilamellar vesicles using circular Hough transformation
2014-02-18

Abstract Motivation: In order to obtain statistically relevant results, the study of membrane effects at the single-vesicle level requires the analysis of several hundreds of giant unilamellar vesicles (GUVs), which becomes a very time-consuming task if carried out manually. Complete and user-friendly software for fast and bias-free automated analysis has not been reported yet. Results: We developed a framework for the automated detection, tracking and analysis of individual GUVs on digital microscopy images. Our tool is suited to quantify protein binding to membranes as well as several aspects of membrane permeabilization on single vesicles. We demonstrate the applicability of the approach by comparing alternative activation methods for Bax, a pore-forming protein involved in mitochondrial permeabilization during apoptosis. Availability and Implementation: The complete software is implemented in MATLAB (The MathWorks, Inc., USA) and available as a standalone as well as the full source code at http://www.ifib.uni-tuebingen.de/research/garcia-saez/guv-software.html. Contact: ana.garcia@uni-tuebingen.de Supplementary information: Supplementary data are available at Bioinformatics online.
GATA5 CpG island hypermethylation is an independent predictor for poor clinical outcome in renal cell carcinoma
2014-02-18

Transcriptional inactivation and CpG island (CGI) methylation of GATA transcription factor family members GATA3 and GATA5 have been reported for a few types of human cancer. Whether high-density CGI methylation of GATA3 or GATA5 is associated with the clinical course of patients with renal cell cancer (RCC) has not been clarified. Quantitative methylation-specific PCR assays were carried out to analyze 25 tumor cell lines including 6 RCC lines and 119 RCC and 87 adjacent normal tissues for the presence of densely methylated sequences. Methylation values were statistically compared with clinicopathological and recurrence-free survival (RFS) data for patients. Comparison of GATA3 and GATA5 methylation in different tumor cell lines revealed a marker-specific methylation characteristic with high and frequent signals for both methylation marks in RCC lines. GATA3 and GATA5 CGI relative methylation levels were found to be strongly associated with the state of metastasis (P=0.003 and P<0.001, respectively) and advanced disease (P=0.024 and P<0.001, respectively). Moreover, an independent decrease in RFS in Cox proportional hazard analysis was found for tumors exhibiting high GATA5 methylation (P<0.001, hazard ratio, 19.3; 95% confidence interval, 4.58-81.6). Epigenetic alterations in GATA family members may be associated with aggressive tumor phenotypes in RCC, and in the case of GATA5, may serve as a new independent molecular marker for aggressiveness and disease progression.
Randomized, Controlled, Assessor-Blind Clinical Trial To Assess the Efficacy of Single- versus Repeated-Dose Albendazole To Treat Ascaris lumbricoides, Trichuris trichiura, and Hookworm Infection
2014-02-19

ABSTRACT In many regions where soil-transmitted helminth infections are endemic, single-dose albendazole is used in mass drug administration programs to control infections. There are little data on the efficacy of the standard single-dose administration compared to that of alternative regimens. We conducted a randomized, controlled, assessor-blinded clinical trial to determine the efficacies of standard and extended albendazole treatment against soil-transmitted helminth infection in Gabon. A total of 175 children were included. Adequate cure rates and egg reduction rates above 85% were found with a single dose of albendazole for Ascaris infection, 85% (95% confidence interval [CI], 73, 96) and 93.8% (CI, 87.6, 100), respectively, while two doses were necessary for hookworm infestation (92% [CI, 78, 100] and 92% [CI, 78, 100], respectively). However, while a 3-day regimen was not sufficient to cure Trichuris (cure rate, 83% [CI, 73, 93]), this regimen reduced the number of eggs up to 90.6% (CI, 83.1, 100). The rate ratios of two- and three-dose regimens compared to a single-dose treatment were 1.7 (CI, 1.1, 2.5) and 2.1 (CI, 1.5, 2.9) for Trichuris and 1.7 (CI, 1.0, 2.9) and 1.7 (CI, 1.0, 2.9) for hookworm. Albendazole was safe and well tolerated in all regimens. A single-dose albendazole treatment considerably reduces Ascaris infection but has only a moderate effect on hookworm and Trichuris infections. The single-dose option may still be the preferred regimen because it balances efficacy, safety, and compliance during mass drug administration, keeping in mind that asymptomatic low-level helminth carriage may also have beneficial effects. (This study has been registered at ClinicalTrials.gov under registration number NCT01192802.)