Miracle-dz/UniFAR-FTUs huggingface dataset:
Targeted proteomics of myofilament phosphorylation and other protein posttranslational modifications

Global cardiac myofilament protein phosphorylation levels, and their site‐specific stoichiometry, are physiologically and clinically relevant for heart function. Unlike myofilament phosphorylation, other PTMs such as O‐GlcNAcylation are just beginning to gain attention due to their potential physiological and clinical implications. This review will focus on what is currently known about cardiac troponin I phosphorylation, and on the potential physiological and clinical impact of targeted proteomics including new findings on cardiac troponin I sites and stoichiometry. We will then discuss the increasing recognition of other myofilament PTMs functional relevance and the potential of targeted MS approaches, particularly MRM, for accelerating their systematic characterization. In addition, we will broadly discuss the development and application of MRM to quantitatively assess site‐specific PTMs. Finally, we will give an overview of expert's consensus on MRM methods design/validation and best practices to develop MRM assays intended to reach clinical application. The unique ability of MRM and similar methods to identify and quantify cardiac myofilament PTMs is likely to become central in answering important biological questions in the field of cardiac integrative physiology.
High efficiency thermophotovoltaic microgenerators

We proposed, designed, and demonstrated a first-of-a-kind millimeter-scale thermophotovoltaic (TPV) system using a metallic microburner, photonic crystal (PhC) emitter, and low bandgap TPV cells. Many technologies (fuel cells, Stirling, thermoelectric, etc.) that potentially enable a portable millimeter-scale hydrocarbon microgenerator are under active investigation because conventional fuels offer energy densities fifty times that of batteries. In a TPV system, combustion heats an emitter to incandescence and the resulting thermal radiation is converted to electricity by photovoltaic cells. Our approach uses a moderate temperature (1000–1200◦C) microburner coupled to a high emissivity, high selectivity PhC selective emitter and low bandgap TPV cells. The PhC emitter and low bandgap cells minimize total microgenerator mass by enabling simultaneous high efficiency and high power density, even at moderate temperatures which allow efficient coupling to the combustion process by reducing undesired heat loss mechanisms. This approach is predicted to be capable of up to 30% efficient fuel-to-electricity conversion within a millimeter-scale form factor. Although considerable technological barriers need to be overcome to reach full performance, we have performed a robust experimental demonstration that validates the theoretical framework and the key system components. We first demonstrated a first-of-a-kind TPV system built from a 10×10 mm catalytic silicon MEMS microburner with a Si/SiO2 1D PhC matched to the InGaAsSb (Eg = 0.55 eV) cells which achieved 2.7% fuel-to-electricity efficiency, a millimeter-scale record, at a power of 344 mWe. We then proposed, designed, and demonstrated a highly robust metallic platform comprised of a 20×20 mm Inconel microburner and a higher performance 2D tantalum PhC emitter. With the new system, we experimentally demonstrated a similar efficiency but can achieve 5% with simple mechanical improvements. These two experimental demonstrations will pave the way for a lightweight, high energy density TPV microgenerator. We modeled a complete microgenerator based on the experimental system and found an energy density of 850 Wh/kg and power density of 40 W/kg are achievable. Thesis Supervisor: Dr. Ivan Celanovic Title: Principal Research Scientist
The metabolic syndrome in children and adolescents – an IDF consensus report

Zimmet P, Alberti K George MM, Kaufman F, Tajima N, Silink M, Arslanian S, Wong G, Bennett P, Shaw J, Caprio S; IDF Consensus Group. The metabolic syndrome in children and adolescents – an IDF consensus report. Pediatric Diabetes 2007: 8: 299–306. Paul Zimmet, K George MM Alberti, Francine Kaufman, Naoko Tajima, Martin Silink, Silva Arslanian, Gary Wong, Peter Bennett, Jonathan Shaw and Sonia Caprio; IDF Consensus Group International Diabetes Institute, Melbourne, Victoria, Australia; Department of Endocrinology and Metabolic Medicine, St Mary’s Hospital, London, UK; Center for Diabetes, Endocrinology and Metabolism, Children’s Hospital, Los Angeles, CA, USA; Division of Diabetes, Metabolism and Endocrinology, Jikei University School of Medicine, Tokyo, Japan; Institute of Endocrinology and Diabetes, The Children’s Hospital at Westmead, Sydney, New South Wales, Australia; Division of Endocrinology, Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA; Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong; Phoenix Epidemiology and Clinical Research Branch, NIDDK, National Institutes of Health, Phoenix, AZ, USA; and Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
Design of pseudo-random bit sequence generator with adjustable sinusoidal jitter

In this paper, a 27-1 pseudo-random bit sequence (PRBS) generator with built-in clock is designed in 0.18-μm CMOS technology. The MOS current mode logic (CML) is used in the PRBS generator for high-speed operation. The clock circuit is realized using a three-stage ring voltage controlled oscillator (VCO). The frequency of the clock can be from 3.3 to 2.7 GHz, while the controlled voltage of the VCO is varied from 0 to 1.1 V. The periodic jitter of the clock can be also controlled, while a sinusoidal wave is added in the controlled voltage of the VCO. The maximum sinusoidal jitter amplitude of our 3-Gb/s PRBS signal can be adjusted to about 0.9-UI.
Pattern-Based Accuracy Assessment of an Urban Footprint Classification Using TerraSAR-X Data

Assessing the accuracy of land-cover classifications is a major challenge in remote sensing. This is mostly due to the absence of geometrically and thematically highly resolved, reliable, area wide, and up-to-date reference data. This study focuses on a multifaceted accuracy assessment of an urban footprint classification derived from a single-polarized TerraSAR-X image in stripmap mode for the city of Padang in Indonesia. For this purpose, a pixel-based approach was used to identify the urbanized and nonurbanized areas. As reference, a geometrically and thematically highly resolved, accurate, and detailed 3-D city model is available. Based on this data, the classification result is assessed by basic methodologies-square measures and error matrix. Beyond that, the accuracy of the urban footprint classification is analyzed in dependence of the physical structure of the complex urban landscape-defined by built-up density and building volumes. Results reveal that the accuracy of classification results varies in dependence of the structural characteristics of the particular urban environment. Furthermore, the study shows what is thematically mapped by an urban footprint classification.
Relationship between RUNX 3 methylation and hepatocellular carcinoma in Asian populations : a systematic review

Runt-related transcription factor 3 (RUNX3) is a potential tumor suppressor that is frequently hypermethylated in hepatocellular carcinoma (HCC). The present meta-analysis of case-control studies was carried out to determine whether RUNX3 hypermethylation is associated with HCC. The PubMed, Embase, and Chinese National Knowledge Infrastructure databases were searched for all relevant studies published between May 2000 and May 2012. A total of 11 studies were identified, and 8 studies involving 491 patients with HCC and 409 patients without tumors were found to satisfy the inclusion criteria for the meta-analysis. All tissue samples were from Asian populations. There was significant heterogeneity between the studies. Over the entire sample, the odds ratio (OR) of RUNX3 promoter methylation was 18.5 [95% confidence interval
Reduced alpha- and beta-catenin expression predicts shortened survival in local prostate cancer.

UNLABELLED The aim of this study was to determine the prognostic value of alpha- and beta-catenin expressions in local prostate cancer (PC). MATERIALS AND METHODS One hundred and eighty-one PC patients treated with radical prostatectomy were followed-up for a mean of 7.3 years. The alpha- and beta-catenin expression were analysed by immunohistochemistry TMT (tissue microarray technique) and light microscopy. RESULTS Strong a-catenin expression was related to low Gleason grade (p < 0.001), cancer-free seminal vesicles (p = 0.04) and low preoperative PSA (p = 0.02). Strong beta-catenin expression was related to low Gleason grade (p < 0.001) and cancer-free seminal vesicle status (p = 0.03). Absence of nuclear beta-catenin expression was related to local disease (pT1-T2) (p = 0.05). alpha-catenin (p = 0.06), beta-catenin (p = 0.05), Gleason grade (p = 0.03) and capsular invasion (p = 0.01) were related to PSA recurrence in patients who reached PSA zero postoperatively. PSA recurrence-free survival (RFS) was significantly related to Gleason grade (p < 0.001), capsule invasion (p = 0.01), perineural growth (p = 0.05) and preoperative PSA (p = 0.05). In Cox's analysis, independent predictors of PSA RFS were Gleason grade (p < 0.001) and capsular invasion (p = 0.006). Low expressions of alpha- (p = 0.06) and beta-catenin (p = 0.05) were related to shortened PSA RFS. Survival was related to low alpha- (p = 0.011) and beta-catenin (p = 0.016) expressions. Independent predictors of shortened survival were seminal vesicle invasion (p = 0.016) and low alpha-catenin expression (p = 0.049). CONCLUSION Reduced alpha- or beta-catenin expressions are related to malignant phenotype in local prostate cancer and predict PSA failure as well as shortened survival.
Specific in vitro guanylylation of a 43-kilodalton membrane-associated protein of Streptomyces coelicolor

Incubation of [alpha-32P]GTP with cellular extracts or membranes of Streptomyces coelicolor labels a protein of 43 kDa, which was also labeled with [8,5'-3H]GTP but not with [alpha-32P]ATP or [gamma-32P]GTP. Radioactivity remained associated with this protein after boiling in 0.1 N NaOH, but it was dissociated after incubation in 0.1 N HCl or hydroxylamine. Chromatographic analysis of the HCl-dissociated compound showed that GMP was the covalently bound nucleotide. Furthermore, guanylylation appeared to be reversible and to take place by a pyrophosphorylytic mechanism. Guanylylation was more efficient at low temperatures. Several Streptomyces species showed a guanylylated protein with a similar molecular mass.
A 16-bit 250-kHz delta-sigma modulator and decimation filter

This paper describes a delta-sigma analog-to-digital converter (ADC) capable of converting input frequencies up to 250 kHz. It consists of a fifth-order switched-capacitor delta-sigma modulator and a decimation filter. Various design optimizations in the modulator are presented. The decimation filter consists of a comb filter followed by a novel, highly efficient and scalable finite impulse response filter. The ADC was implemented in 0.6-/spl mu/m CMOS technology. It achieves a dynamic range of 94 db.
A method of progressive constraints for nonholonomic motion planning

Presents a general method for nonholonomic motion planning (NMP), that is able to solve problems for systems with high-dimensional configuration spaces. The original NMP problem is replaced by a series of progressively constrained ones that are solved successively, and whose solution path converges towards a solution of the original problem. The nonholonomic constraints are introduced progressively in an iterative algorithm. Each iteration consists of exploring a neighborhood of the path obtained from the previous iteration, searching for a path that satisfies more accurate constraints. The explorations proceed according to a dynamic programming procedure able to deal with optimization criteria.
Threonine 79 Is a Hinge Residue That Governs the Fidelity of DNA Polymerase β by Helping to Position the DNA within the Active Site*

DNA polymerase β (pol β) is an ideal system for studying the role of its different amino acid residues in the fidelity of DNA synthesis. In this study, the T79S variant of pol β was identified using an in vivo genetic screen. T79S is located in the N-terminal 8-kDa domain of pol β and has no contact with either the DNA template or the incoming dNTP substrate. The T79S protein produced 8-fold more multiple mutations in the herpes simplex virus type 1-thymidine kinase assay than wild-type pol β. Surprisingly, T79S is a misincorporation mutator only when using a 3′-recessed primer-template. In the presence of a single nucleotide-gapped DNA substrate, T79S displays an antimutator phenotype when catalyzing DNA synthesis opposite template C and has similar fidelity as wild type opposite templates A, G, or T. Threonine 79 is located directly between two helix-hairpin-helix motifs located within the 8-kDa and thumb domains of pol β. As the pol β enzyme closes into its active form, the helix-hairpin-helix motifs appear to assist in the production and stabilization of a 90o bend of the DNA. The function of the bent DNA is to present the templating base to the incoming nucleotide substrate. We propose that Thr-79 is part of a hydrogen bonding network within the helix-hairpin-helix motifs that is important for positioning the DNA within the active site. We suggest that alteration of Thr-79 to Ser disrupts this hydrogen bonding network and results in an enzyme that is unable to bend the DNA into the proper geometry for accurate DNA synthesis.
Therapeutic Communities : The International Journal of Therapeutic Communities Emerald Article : Therapeutic communities for drug addicts in Israel : comparing addicts born in the Former Soviet Union and in Israel

Purpose – The purpose of this paper is to focus on comparing background characteristics, self-efficacy, and family support of immigrants from the Former Soviet Union (FSU) and of veteran Israelis who join therapeutic communities in Israel, and their adjustment to these communities. The aim of this research was to examine whether therapeutic communities are an appropriate rehabilitative setting for immigrants who come from a different cultural background. Design/methodology/approach – The study sample consisted of 213 people with addictions, who were being treated in therapeutic communities in Israel: 110 were Israeli-born and 103 were immigrants from the FSU. The data in the present study are based on questionnaires, which the participants completed upon their arrival into the communities: socio-demographic data; perceived self-efficacy in resisting the temptation of drugs; and family support. The dropout rates from the therapeutic communities were also examined. Findings – The findings indicate that the addicts who immigrated from the FSU had lower self-efficacy in resisting high-risk drug situations as well as lower levels of family support, whereas the dropout rate from the treatment program was considerably higher among the Israeli-born participants. Originality/value – The findings suggest that the therapeutic community is an appropriate setting for addicts from the FSU, and that they had a lower dropout rate than did the Israeli-born addicts. Thus, the main value of this research is that it suggests that the communities are an appropriate rehabilitative setting for the immigrants.
Mutation mapping of the 2B5 ecdysone locus in Drosophila melanogaster reveals a long-distance controlling element

Mutations at the Broad-Complex, a key gene triggering metamorphosis in Drosophila melanogaster, were mapped at the DNA level. The Broad-Complex includes two mutually complementing allelic classes, br and l(1)2Bc, both of which can associate to insertions at the same intron. Alterations spreading over 50 kilobases upstream from the transcription unit also disrupt br but not l(1)2Bc function.
Overview of recent advances in innovative electrical machines — With particular reference to magnetically geared switched flux machines

Electrical machines have been widely used for many applications, ranging from electric and hybrid electric vehicles, renewable energy including wind power generators, more electric aircrafts, industrial drives, automations, to domestic appliances etc. This paper overviews the recent developments in innovative electrical machines, with particular emphasis on recent advances in doubly salient switched flux machines and magnetically geared machines. Their unique relationships will be systematically revealed, resulting in recent development of a new class of magnetically geared switched flux machines, i.e. partitioned stator switched flux machines, which will be illustrated by examples.
Dietary fructo-oligosaccharides improve insulin sensitivity along with the suppression of adipocytokine secretion from mesenteric fat cells in rats

Short-chain fructo-oligosaccharides (FOS) are known to have beneficial effects on health. However, the effects of FOS on insulin resistance have not been fully clarified. We observed the effects of FOS feeding on insulin sensitivity and adipocytokine release from abdominal adipocytes in weaning rats. Male Sprague–Dawley rats, 3 weeks old, were divided into three groups and fed a sucrose-based American Institute of Nutrition (AIN)-93 growth diet (control), the control diet containing 5 % FOS for 5 weeks (FOS-5wk) or the control diet for 2 weeks followed by the 5 % FOS diet for 3 weeks (FOS-3wk). Tail blood was collected after fasting for 9 h on day 33 of feeding, and glucose and insulin levels were measured. On the last day, rats were anaesthetised and killed after the collection of aortic blood. Small- and large-intestinal mesenteric fat tissues were immediately excised, and the release of adiponectin, leptin and TNF-α was evaluated from the subsequently isolated adipocytes. The weight of the large-intestinal mesenteric fat, fasting blood insulin level and homeostatic model assessment for insulin resistance decreased in a time-dependent manner, and were much lower in the FOS-5wk group than in the control group. These values were correlated with aortic blood leptin levels. The secretion rate of leptin from the isolated mesenteric adipocytes in the small intestine, but not in the large intestine, was lower in the FOS-fed groups than in the control group. In conclusion, FOS feeding improved insulin sensitivity accompanied by the reduction in large-intestinal fat mass and leptin secretion from the mesenteric adipocytes of the small intestine.
Duplicate Maize Wrinkled 1 Transcription Factors Activate Target Genes Involved in Seed Oil Biosynthesis 1 [ C ] [ W ]

Université de Lyon, Ecole Normale Supérieure de Lyon, Université Lyon 1, IFR128 BioSciences Lyon Gerland, Unité Reproduction et Développement des Plantes, F–69364 Lyon, France (B.P., V.V., V.M., C.P., G.G., P.M.R.); INRA, UMR879 Reproduction et Développement des Plantes, F–69364 Lyon, France (B.P., V.V., V.M., C.P., G.G., P.M.R.); CNRS, UMR5667 Reproduction et Développement des Plantes, F–69364 Lyon, France (B.P., V.V., V.M., C.P., G.G., P.M.R.); INRA, UMR1318 Institut Jean-Pierre Bourgin, F–78026 Versailles, France (S.B.); and Biogemma SAS, Laboratoire de Biologie Cellulaire et Moléculaire, F–63028 Clermont-Ferrand, France (J.-P.P., J.R., W.P.)
Controlling the Stormram 2: An MRI-compatible robotic system for breast biopsy

Breast cancer is the most frequently life-threatening diagnosed type of cancer among women. Early and accurate diagnosis by acquiring a tissue sample using biopsy techniques is essential. However, small lesions only visible by MRI are often missed in standard methods, indicating the need for a robotic-assisted biopsy system that is MRI-compatible. Existing proof-of-concepts are difficult to employ due to large sizes and/or actuation complexities. Therefore, a compact pneumatically-actuated 5 DOF MRI-compatible robot was further developed and controlled by a computerized valve manifold. Accuracy and efficiency measurements have been performed using two different PVC breast phantoms with embedded fish oil capsules (mimicking lesions) inside a 0.25T MRI scanner. Preliminary results show that the end-effector was able to hit the targeted capsules, and that the position accuracy is in the range of 4.7–7.3 mm. The developed robotic system has potential to perform MRI-guided breast biopsies accurately and improve the clinical workflow.
Regression calibration with more surrogates than mismeasured variables

In a recent paper (Weller EA, Milton DK, Eisen EA, Spiegelman D. Regression calibration for logistic regression with multiple surrogates for one exposure. Journal of Statistical Planning and Inference 2007; 137: 449‐461), the authors discussed fitting logistic regression models when a scalar main explanatory variable is measured with error by several surrogates, that is, a situation with more surrogates than variables measured with error. They compared two methods of adjusting for measurement error using a regression calibration approximate model as if it were exact. One is the standard regression calibration approach consisting of substituting an estimated conditional expectation of the true covariate given observed data in the logistic regression. The other is a novel two‐stage approach when the logistic regression is fitted to multiple surrogates, and then a linear combination of estimated slopes is formed as the estimate of interest. Applying estimated asymptotic variances for both methods in a single data set with some sensitivity analysis, the authors asserted superiority of their two‐stage approach. We investigate this claim in some detail. A troubling aspect of the proposed two‐stage method is that, unlike standard regression calibration and a natural form of maximum likelihood, the resulting estimates are not invariant to reparameterization of nuisance parameters in the model. We show, however, that, under the regression calibration approximation, the two‐stage method is asymptotically equivalent to a maximum likelihood formulation, and is therefore in theory superior to standard regression calibration. However, our extensive finite‐sample simulations in the practically important parameter space where the regression calibration model provides a good approximation failed to uncover such superiority of the two‐stage method. We also discuss extensions to different data structures. Copyright © 2012 John Wiley & Sons, Ltd.