Miracle-dz/UniFAR-FTUs huggingface dataset:
Single-nucleotide polymorphisms and genome diversity in Plasmodium vivax

The study of genetic variation in malaria parasites has practical significance for developing strategies to control the disease. Vaccines based on highly polymorphic antigens may be confounded by allelic restriction of the host immune response. In response to drug pressure, a highly plastic genome may generate resistant mutants more easily than a monomorphic one. Additionally, the study of the distribution of genomic polymorphisms may provide information leading to the identification of genes associated with traits such as parasite development and drug resistance. Indeed, the age and diversity of the human malaria parasite Plasmodium falciparum has been the subject of recent debate, because an ancient parasite with a complex genome is expected to present greater challenges for drug and vaccine development. The genome diversity of the important human pathogen Plasmodium vivax, however, remains essentially unknown. Here we analyze an ≈100-kb contiguous chromosome segment from five isolates, revealing 191 single-nucleotide polymorphisms (SNPs) and 44 size polymorphisms. The SNPs are not evenly distributed across the segment with blocks of high and low diversity. Whereas the majority (≈63%) of the SNPs are in intergenic regions, introns contain significantly less SNPs than intergenic sequences. Polymorphic tandem repeats are abundant and are more uniformly distributed at a frequency of about one polymorphic tandem repeat per 3 kb. These data show that P. vivax has a highly diverse genome, and provide useful information for further understanding the genome diversity of the parasite.
Potential of using GaN devices within air cooled bidirectional battery chargers for electric vehicles

This paper deals with the advantages of GaN devices for bidirectional battery chargers for plug-in hybrid electric vehicles and electric vehicles that are connected to the singlephase European ac grid. Compared to a charger with silicon devices a higher power density can be realized because of the lower switching losses of GaN devices that enable higher switching frequencies. A state-of-the-art battery charging systems will be described and the differences and advantages of fast switching GaN devices compared to standard silicon ones will be pointed out. The presented topology allows bidirectional power flow. Therefore, this charger can be used to stabilize the utility grid. An overview of the different components of the battery charger and their design aspects are presented in this paper.
Newton-Raphson version of stochastic approximation over discrete sets

This paper considers the problem of optimizing a complex stochastic system over a discrete set of feasible values of a parameter when the objective function can only be estimated through simulation. We propose a new gradient-based method that mimics the Newton-Raphson method and makes use of both the gradient and the Hessian of the objective function. The proposed algorithm is designed to give guidance on how to choose the sequence of gains which plays a critical role in the empirical performance of a gradient-based algorithm. In addition to the desired fast convergence in the first few steps of the procedure, the proposed algorithm converges to a local optimizer with probability one as n goes to infinity with rate 1/n where n is the number of iterations.
Mos is required for MAP kinase activation and is involved in microtubule organization during meiotic maturation in the mouse.

Mos is normally expressed during oocyte meiotic maturation in vertebrates. However, apart from its cytostatic factor (CSF) activity, its precise role during mouse meiosis is still unknown. First, we analyzed its role as a MAP kinase kinase kinase. Mos is synthesized concomitantly with the activation of MAP kinase in mouse oocytes. Moreover, MAP kinase is not activated during meiosis in oocytes from mos -/- mice. This result implies that Mos is necessary for MAP kinase activation in mouse oocytes. Raf-1, another MAP kinase kinase kinase, is already present in immature oocytes, but does not seem to be active when MAP kinase is activated. Moreover, the absence of MAP kinase activation in mos -/- oocytes demonstrates that Raf-1 cannot compensate for the lack of Mos. These results suggest that Raf-1 is not involved in MAP kinase activation. Second, we analyzed the organization of the microtubules and chromosomes in oocytes from mos -/- mice. We observed that during the transition between two meiotic M-phases, the microtubules and chromosomes evolve towards an interphase-like state in mos -/- oocytes, while in the control mos +/- oocytes they remain in an M-phase configuration, as in the wild type. Moreover, after spontaneous activation, the majority of mos -/- oocytes are arrested for at least 10 hours in a third meiotic M-phase where they exhibit monopolar half-spindles. These observations present the first evidence, in intact oocytes, of a role for the Mos/. /MAP kinase cascade in the control of microtubule and chromatin organization during meiosis.
NMR Diffusion Diffraction and Diffusion Interference from Cells

Pulsed field gradient spin-echo (PGSE) NMR spectroscopy is the definitive means for measuring translational motion of molecules in free solution and in heterogeneous systems. A unique ‘twist’ on the method is that in some systems in which diffusion is restricted the PGSE experiment yields information on the geometrical properties of the confining boundaries. When applied to red blood cells (RBCs) in suspensions, using intense magnetic field gradients (around 10 T m -1 ), the graph of normalized NMR-signal intensity versus the magnitude of the field gradients has the form of the diffraction and interference patterns that are seen in physical optics. We review here the nature of these so called q-space plots and discuss a data-processing method that adds objectivity to estimates of the mean RBC diameter. Convection potentially interferes with the veracity of these measurements so an experiment is reported in which a cell-free sample was deliberately made to flow. The very simple analysis of flow diffraction yielded estimates of flow that were in remarkable agreement with gravimetric measurements. Finally, in a theoretical study using a model of uniformly arrayed octagonal prisms that were ‘morphed’ in a systematic way, the dependence of the form of q-space plots on prism shape and packing density was obtained. This showed that elaborately shaped q-space plots can be obtained from simple periodic arrays of ‘cells’. The uniqueness or otherwise of shapes of q-space plots, and the prospect of generally solving the inverse problem whereby q-space analysis yields detailed information on packing arrangements is poised for further detailed investigations.
Transforming growth factor-beta 1 induces alpha-smooth muscle actin expression in granulation tissue myofibroblasts and in quiescent and growing cultured fibroblasts

Granulation tissue fibroblasts (myofibroblasts) develop several ultrastructural and biochemical features of smooth muscle (SM) cells, including the presence of microfilament bundles and the expression of alpha-SM actin, the actin isoform typical of vascular SM cells. Myofibroblasts have been proposed to play a role in wound contraction and in retractile phenomena observed during fibrotic diseases. We show here that the subcutaneous administration of transforming growth factor- beta 1 (TGF beta 1) to rats results in the formation of a granulation tissue in which alpha-SM actin expressing myofibroblasts are particularly abundant. Other cytokines and growth factors, such as platelet-derived growth factor and tumor necrosis factor-alpha, despite their profibrotic activity, do not induce alpha-SM actin in myofibroblasts. In situ hybridization with an alpha-SM actin probe shows a high level of alpha-SM actin mRNA expression in myofibroblasts of TGF beta 1-induced granulation tissue. Moreover, TGF beta 1 induces alpha-SM actin protein and mRNA expression in growing and quiescent cultured fibroblasts and preincubation of culture medium containing whole blood serum with neutralizing antibodies to TGF beta 1 results in a decrease of alpha-SM actin expression by fibroblasts in replicative and non-replicative conditions. These results suggest that TGF beta 1 plays an important role in myofibroblast differentiation during wound healing and fibrocontractive diseases by regulating the expression of alpha-SM actin in these cells.
Integrative prognostic risk score in acute myeloid leukemia with normal karyotype.

To integrate available clinical and molecular information for cytogenetically normal acute myeloid leukemia (CN-AML) patients into one risk score, 275 CN-AML patients from multicenter treatment trials AML SHG Hannover 0199 and 0295 and 131 patients from HOVON/SAKK protocols as external controls were evaluated for mutations/polymorphisms in NPM1, FLT3, CEBPA, MLL, NRAS, IDH1/2, and WT1. Transcript levels were quantified for BAALC, ERG, EVI1, ID1, MN1, PRAME, and WT1. Integrative prognostic risk score (IPRS) was modeled in 181 patients based on age, white blood cell count, mutation status of NPM1, FLT3-ITD, CEBPA, single nucleotide polymorphism rs16754, and expression levels of BAALC, ERG, MN1, and WT1 to represent low, intermediate, and high risk of death. Complete remission (P = .005), relapse-free survival (RFS, P < .001), and overall survival (OS, P < .001) were significantly different for the 3 risk groups. In 2 independent validation cohorts of 94 and 131 patients, the IPRS predicted different OS (P < .001) and RFS (P < .001). High-risk patients with related donors had longer OS (P = .016) and RFS (P = .026) compared with patients without related donors. In contrast, intermediate-risk group patients with related donors had shorter OS (P = .003) and RFS (P = .05). Donor availability had no impact on outcome of patients in the low-risk group. Thus, the IPRS may improve consolidation treatment stratification in CN-AML patients. Study registered at www.clinicaltrials. gov as #NCT00209833.
Up-regulation of the Sirtuin 1 (Sirt1) and Peroxisome Proliferator-activated Receptor γ Coactivator-1α (PGC-1α) Genes in White Adipose Tissue of Id1 Protein-deficient Mice

Background: Id1 is involved in diet-induced obesity by unknown mechanisms. Results: We show that Id1 ablation or ET2 expression protects the mice from obesity and glucose intolerance and stimulates Sirtuin1 and PGC-1α expression. Conclusion: E proteins control obesity by regulating the expression of regulators of energy metabolism. Significance: Sirt1 expression is for the first time linked to Id and E protein activities. Id1, a helix-loop-helix (HLH) protein that inhibits the function of basic HLH E protein transcription factors in lymphoid cells, has been implicated in diet- and age-induced obesity by unknown mechanisms. Here we show that Id1-deficient mice are resistant to a high fat diet- and age-induced obesity, as revealed by reduced weight gain and body fat, increased lipid oxidation, attenuated hepatosteatosis, lower levels of lipid droplets in brown adipose tissue, and smaller white adipocytes after a high fat diet feeding or in aged animals. Id1 deficiency improves glucose tolerance, lowers serum insulin levels, and reduces TNFα gene expression in white adipose tissue. Id1 deficiency also increased expression of Sirtuin 1 and peroxisome proliferator-activated receptor γ coactivator 1α, regulators of mitochondrial biogenesis and energy expenditure, in the white adipose tissue. This effect was accompanied by the elevation of several genes encoding proteins involved in oxidative phosphorylation and fatty acid oxidation, such as cytochrome c, medium-chain acyl-CoA dehydrogenase, and adipocyte protein 2. Moreover, the phenotype for Id1 deficiency was similar to that of mice expressing an E protein dominant-positive construct, ET2, suggesting that the balance between Id and E proteins plays a role in regulating lipid metabolism and insulin sensitivity.
Factor analysis invariant to linear transformations of data

Modeling data with Gaussian distributions is an important statistical problem. To obtain robust models one imposes constraints the means and covariances of these distributions [6, 4, 10, 8]. Constrained ML modeling implies the existence of optimal feature spaces where the constraints are more valid [2, 3]. This paper introduces one such constrained ML modeling technique called factor analysis invariant to linear transformations(FACILT)which is essentially factor analysis in optimal feature spaces. FACILT is a generalization of several existing methods for modeling covariances. This paper presents an EM algorithm for FACILT modeling.
Surveillance of Super-Extended Objects: Bimodal Approach

This paper describes an effective solution to the task of a remote monitoring of super-extended objects (oil and gas pipeline, railways, national frontier). The suggested solution is based on the principle of simultaneously monitoring of seismoacoustic and optical/infrared physical fields. The principle of simultaneous monitoring of those fields is not new but in contrast to the known solutions the suggested approach allows to control super-extended objects with very limited operational costs. So-called C-OTDR (Coherent Optical Time Domain Reflectometer) systems are used to monitor the seismoacoustic field. Far-CCTV systems are used to monitor the optical/infrared field. A simultaneous data processing provided by both systems allows effectively detecting and classifying target activities, which appear in the monitored objects vicinity. The results of practical usage had shown high effectiveness of the suggested approach. Keywords—Bimodal processing, C-OTDR monitoring system,
Dietary modulation of the human colonic microbiota: updating the concept of prebiotics

Prebiotics are non-digestible (by the host) food ingredients that have a beneficial effect through their selective metabolism in the intestinal tract. Key to this is the specificity of microbial changes. The present paper reviews the concept in terms of three criteria: (a) resistance to gastric acidity, hydrolysis by mammalian enzymes and gastrointestinal absorption; (b) fermentation by intestinal microflora; (c) selective stimulation of the growth and/or activity of intestinal bacteria associated with health and wellbeing. The conclusion is that prebiotics that currently fulfil these three criteria are fructo-oligosaccharides, galacto-oligosaccharides and lactulose, although promise does exist with several other dietary carbohydrates. Given the range of food vehicles that may be fortified by prebiotics, their ability to confer positive microflora changes and the health aspects that may accrue, it is important that robust technologies to assay functionality are used. This would include a molecular-based approach to determine flora changes. The future use of prebiotics may allow species-level changes in the microbiota, an extrapolation into genera other than the bifidobacteria and lactobacilli, and allow preferential use in disease-prone areas of the body.
Applications of parametric maxflow in computer vision

The maximum flow algorithm for minimizing energy functions of binary variables has become a standard tool in computer vision. In many cases, unary costs of the energy depend linearly on parameter lambda. In this paper we study vision applications for which it is important to solve the maxflow problem for different lambda's. An example is a weighting between data and regularization terms in image segmentation or stereo: it is desirable to vary it both during training (to learn lambda from ground truth data) and testing (to select best lambda using high-knowledge constraints, e.g. user input). We review algorithmic aspects of this parametric maximum flow problem previously unknown in vision, such as the ability to compute all breakpoints of lambda and corresponding optimal configurations infinite time. These results allow, in particular, to minimize the ratio of some geometric functional, such as flux of a vector field over length (or area). Previously, such functional were tackled with shortest path techniques applicable only in 2D. We give theoretical improvements for "PDE cuts" [5]. We present experimental results for image segmentation, 3D reconstruction, and the cosegmentation problem.
Environmental factors and soil properties effects

Introduction Conclusions References Tables Figures Back Close Full Screen / Esc Biogeosciences Discussions This discussion paper is/has been under review for the journal Biogeosciences (BG). Please refer to the corresponding final paper in BG if available. Abstract Introduction Conclusions References Tables Figures Back Close Full Screen / Esc Abstract Soil respiration rates were measured along different parts of a slope in (a) an evergreen forest with mature soil and (b) a deciduous forest with immature soil. The effects of soil temperature, soil moisture, and soil properties on soil respiration rates were estimated individually, and the magnitudes of these effects were compared between the decidu-5 ous and evergreen forests. In the evergreen forest with mature soil, soil properties had the greatest effect on soil respiration rates, followed by soil moisture and soil temperature. These results may be explained by different properties of soils that matured under different environments. Thus, we argue that the low soil respiration rates in Plot L of the evergreen forest resulted from soil properties and not from wet soil conditions. In 10 the deciduous forest, soil respiration rates were more strongly affected by soil moisture and soil temperature than by soil properties, which were likely due to the immaturity of the forest soil.
Precise Enforcement of Confidentiality for Reactive Systems

In the past years, researchers have been focusing on applying information flow security to web applications. These mechanisms should raise a minimum of false alarms in order to be applicable to millions of existing web pages. A promising technique to achieve this is secure multi-execution (SME). If a program is already secure, its secure multi- execution produces the same output events; otherwise, this correspondence is intentionally broken in order to preserve security. Thus, there is no way to know if unexpected results are due to bugs or due to semantics changes produced by SME. Moreover, SME provides no guarantees on the relative ordering of output events from different security levels. We argue that these shortcomings limit the applicability of SME. In this article, we propose a scheduler for secure multi- execution which makes it possible to preserve the order of output events. Using this scheduler, we introduce a novel com- bination between monitoring and SME, called multi-execution monitor, which raises alarms only for actions breaking the non-interference notion of ID-security for reactive systems. Additionally, we show that the monitor guarantees trans- parency even for CP-similarity, a progress-sensitive notion of observation.
Behavior Protocols for Software Components

In this paper, we propose a means to enhance an architecture description language with a description of component behavior. A notation used for this purpose should be able to express the "interplay" on the component's interfaces and reflect step-by-step refinement of the component's specification during its design. In addition, the notation should be easy to comprehend and allow for formal reasoning about the correctness of the specification refinement and also about the correctness of an implementation in terms of whether it adheres to the specification. Targeting all these requirements together, the paper proposes employing behavior protocols which are based on a notation similar to regular expressions. As proof of the concept, the behavior protocols are used in the SOFA architecture description language at three levels: interface, frame, and architecture. Key achievements of this paper include the definitions of bounded component behavior and protocol conformance relation. Using these concepts, the designer can verify the adherence of a component's implementation to its specification at runtime, while the correctness of refining the specification can be verified at design time.
Prevalence of GB Virus C/Hepatitis G Virus Infection among Various Populations in Surabaya, Indonesia, and Identification of Novel Groups of Sequence Variants

ABSTRACT A molecular epidemiological study was performed to investigate the prevalence of GB virus C/hepatitis G virus (GBV-C/HGV) infection among various populations in Surabaya, Indonesia. The prevalence of GBV-C/HGV RNA, determined by reverse transcription-PCR for a portion of the NS3 region of the viral genome, was 2.7% (4 of 150) among randomly collected blood donor sera, which were all negative for both hepatitis B virus surface antigen and antibodies against hepatitis C virus (HCV). On the other hand, the prevalence among anti-HCV-positive blood donors was 17.8% (13 of 73), with the ratio being significantly higher than that observed with the anti-HCV-negative blood donors (P < 0.001). A high prevalence of GBV-C/HGV infection was also observed among patients with chronic liver disease, such as chronic hepatitis (5.7%), liver cirrhosis (11.5%), and hepatocellular carcinoma (7.0%), and patients on maintenance hemodialysis (29.0%). No correlation was observed between GBV-C/HGV viremia and serum alanine aminotransferase levels in the populations tested, suggesting the possibility that GBV-C/HGV does not cause apparent liver injury. Phylogenetic analysis of sequences of a portion of the 5′ untranslated region and the E1 region of the viral genome identified, in addition to a previously reported then novel group of GBV-C/HGV variants (group 4), another novel group of variants (group 5). This result suggests that GBV-C/HGV can be classified into at least five genetic groups. GBV-C/HGV isolates of group 4 and group 5 were each shown to comprise approximately 40% of the total Indonesian isolates.
Chemotherapy as an Adjuvant to Surgery for Colorectal Cancer

A combined intraoperative and postoperative adjuvant program of 5 minus Fluorouracil (5 FU) for patients undergoing "curative" resection for adenocarcinoma of the colon and rectum was initiated as a randomized clinical trial in January 1968. Patients at the Medical College of Virginia and the University of Virginia were randomly assigned to an intraluminal 5 FU or intraluminal control (Saline) group and were so treated at the time of surgical resection if findings at operation indicated that all gross neoplastic disease could be resected. Patients with operative findings denoting incurability were eliminated from the study after surgical exploration. Those patients receiving intraluminal 5 FU (30mg/kg) received intravenous 5 FU (10mg/kg) on each of the two first postoperative days and 5 subsequent postoperative courses of oral 5FU (90 mg/kg in each 18 day course) over a one year period. By December 31, 1973 (6 years) 156 patients undergoing "curative" resection were entered into the study. SU therapy with the control or "No Treat" group reveal no significant benefit from this intensive adjuvant course of 5 FU thus far. Continued assessment of these patient groups and their subgroups will be required to develop confidence in these findings but the data thus far suggest no potential benefit from this particular adjuvant program.