Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation, nucleotide sequence analysis, and disruption of the MDH2 gene from Saccharomyces cerevisiae: evidence for three isozymes of yeast malate dehydrogenase

The major nonmitochondrial isozyme of malate dehydrogenase (MDH2) in Saccharomyces cerevisiae cells grown with acetate as a carbon source was purified and shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis to have a subunit molecular weight of approximately 42,000. Enzyme assays and an antiserum prepared against the purified protein were used to screen a collection of acetate-nonutilizing (acetate-) yeast mutants, resulting in identification of mutants in one complementation group that lack active or immunoreactive MDH2. Transformation and complementation of the acetate- growth phenotype was used to isolate a plasmid carrying the MDH2 gene from a yeast genomic DNA library. The amino acid sequence derived from complete nucleotide sequence analysis of the isolated gene was found to be extremely similar (49% residue identity) to that of yeast mitochondrial malate dehydrogenase (molecular weight, 33,500) despite the difference in sizes of the two proteins. Disruption of the MDH2 gene in a haploid yeast strain produced a mutant unable to grow on minimal medium with acetate or ethanol as a carbon source. Disruption of the MDH2 gene in a haploid strain also containing a disruption in the chromosomal MDH1 gene encoding the mitochondrial isozyme produced a strain unable to grow with acetate but capable of growth on rich medium with glycerol as a carbon source. The detection of residual malate dehydrogenase activity in the latter strain confirmed the existence of at least three isozymes in yeast cells.
Current error space vector based constant switching frequency hysteresis controller for VSI fed Induction Motor drives

A current error space vector based hysteresis controller for two-level voltage source inverter fed Induction Motor drives is proposed in this paper. All inherent advantages of conventional hysteresis controllers like fast dynamic response, simple implementation, switching in one phase at a time etc. are also retained in the proposed controller . The harmonic spectrum of phase voltage obtained using proposed controller is similar to that of constant switching frequency bus clamping space vector pulse width modulated voltage source inverter. In this proposed controller hysteresis boundary is computed online using estimated stator voltages along α and β axes. The current errors along alpha and beta axes and steady state model of induction motor are used for the estimation of stator voltages along α and β axes. Hysteresis boundary is computed and using that the vector selection logic is deduced in such a way that the vector switching pattern is exactly similar to that of bus clamping SVPWM technique. Extensive simulation of the proposed hysteresis controller based inverter fed drive scheme is carried out using SIMULINK toolbox of MATLAB for steady state performance.
Acute Coronary Syndrome Remodels the Protein Cargo and Functions of High-Density Lipoprotein Subfractions

Objectives This study examined alterations in the functions and proteome of high-density lipoprotein (HDL) subfractions (HDL2 and HDL3) isolated from patients with acute coronary syndrome (ACS) compared with control subjects. Methods We measured HDL subfraction cholesterol efflux capacity, inflammatory index (HII), paraoxonase-1 (PON1) activity, and lipid hydroperoxide (LOOH) levels in both male age-matched controls and the ACS group (n = 40/group). Additionally, proteomic analysis was used to monitor changes in the HDL subfraction proteome between controls and ACS subjects. Results Both HDL2 and HDL3 from ACS patients had greater HII and LOOH levels compared with controls (P<0.001); PON1 activity and cholesterol efflux capacity in both HDL2 and HDL3 from the ACS group were significantly less than those of controls (P<0.001). Using proteomic analysis, we demonstrated that, compared with the control group, nine proteins were selectively enriched in HDL3 from subjects with ACS, and ras-related protein Rab-7b was decreased in HDL3. Additionally, in the ACS subjects, 12 proteins were decreased in HDL2 and 4 proteins were increased in HDL2. Conclusions Functional HDL subfractions shifted to dysfunctional HDL subfractions during ACS, and the functional impairment was linked to remodeled protein cargo in HDL subfractions from ACS patients.
Strategies for Exercises

Abstract. Strategies specify how a wide range of exercises can be solved in-crementally, such as bringing a logic proposition to disjunctive normal form,reducing a matrix, or calculating with fractions. In this paper we introduce alanguage for specifying strategies for solving exercises. This language makesit easier to automatically calculate feedback, for example when a user makesan erroneous step in a calculation. We can automatically generate worked-outsolutions, track the progress of a student by inspecting submitted intermedi-ate answers, and report back suggestions in case the student deviates fromthe strategy. Thus it becomes less labor-intensive and less ad-hoc to specifynew exercise domains and exercises within that domain.A strategy describes valid sequences of transformation rules that solvethe exercise at hand, which turns tracking intermediate steps into a parsingproblem. This is a promising view at the problem because it allows us totake advantage of many years of experience in parsing sentences of context-free languages, and transfer this knowledge and technology to the domain ofstepwise solving exercises.In this paper we work out the similarities between parsing and solvingexercises incrementally, and we discuss the implementation of a recognizer forstrategies. We present a full implementation of such a recognizer, and discussa number of design choices we have made. In particular, we discuss the use ofa xed point combinator to deal with repetition, and labels to mark positionsin the strategy.
COCO: The Bi-objective Black Box Optimization Benchmarking (bbob-biobj) Test Suite

The bbob-biobj test suite contains 55 bi-objective functions in continuous domain which are derived from combining functions of the well-known single-objective noiseless bbob test suite. Besides giving the actual function definitions and presenting their (known) properties, this documentation also aims at giving the rationale behind our approach in terms of function groups, instances, and potential objective space normalization.
Prediction of 30-Year Risk for Cardiovascular Mortality by Fitness and Risk Factor Levels: The Cooper Center Longitudinal Study

Background—Fitness and traditional risk factors have well-known associations with cardiovascular disease (CVD) death in both short-term (10 years) and across the remaining lifespan. However, currently available short-term and long-term risk prediction tools do not incorporate measured fitness. Methods and Results—We included 16 533 participants from the Cooper Center Longitudinal Study (CCLS) without prior CVD. Fitness was measured using the Balke protocol. Sex-specific fitness levels were derived from the Balke treadmill times and categorized into low, intermediate, and high fit according to age- and sex-specific treadmill times. Sex-specific 30-year risk estimates for CVD death adjusted for competing risk of non-CVD death were estimated using the cause-specific hazards model and included age, body mass index, systolic blood pressure, fitness, diabetes mellitus, total cholesterol, and smoking. During a median follow-up period of 28 years, there were 1123 CVD deaths. The 30-year risk estimates for CVD mortality derived from the cause-specific hazards model demonstrated overall good calibration (Nam-D’Agostino &khgr;2 [men, P=0.286; women, P=0.664] and discrimination (c statistic; men, 0.81 [0.80–0.82] and women, 0.86 [0.82–0.91]). Across all risk factor strata, the presence of low fitness was associated with a greater 30-year risk for CVD death. Conclusions—Fitness represents an important additional covariate in 30-year risk prediction functions that may serve as a useful tool in clinical practice.
Versatile vision-based touch sensor for autonomous robots

Search robotics involves the use of autonomous systems which have to operate in unknown environments and interact with external objects or humans. Typically, these robots are equipped with sensors which are used to perceive the surrounding scenario and feed it back to the human operator. Besides the extensive research effort, a sensory system able to reproduce the human “sense of touch” is still missing and highly desirable. In this paper we propose a vision-based touch sensor mechanism for autonomous robots with the aim of improving robot's navigation in unsettled environments. Furthermore, we explore a new application area and describe how the sensory system can be embedded to a surveillance robot and used to perform human pat-down search.
Strassen's Algorithm for Tensor Contraction

Tensor contraction (TC) is an important computational kernel widely used in numerous applications. It is a multidimensional generalization of matrix multiplication (GEMM). While Strassen's algorithm for GEMM is well studied in theory and practice, extending it to accelerate TC has not been previously pursued. Thus, we believe this to be the first paper to demonstrate how one can in practice speed up TC with Strassen's algorithm. By adopting a block-scatter-matrix format, a novel matrix-centric tensor layout, we can conceptually view TC as GEMM for a general stride storage, with an implicit tensor-to-matrix transformation. This insight enables us to tailor a recent state-of-the-art implementation of Strassen's algorithm to a recent state-of-the-art TC, avoiding explicit transpositions (permutations) and extra workspace, and reducing the overhead of memory movement that is incurred. Performance benefits are demonstrated with a performance model as well as in practice on modern single core, multicore, and di.
Four-segment soft X-ray vacuum photodiode

A soft X-ray/XUV diode (XRD) is a powerful diagnostic tool for system alignment, among others, in capillary discharge experiments, which generate directional soft x-ray radiation, eventually a laser pulse. In our experimental devices (CAPEX and CAPEX-U) we usually used PIN diode or vacuum photodiode (one-segment). These diagnostics are not very suitable, mainly because many shots (more than 50) are necessary to find the optical axis. During last year we have designed and manufactured a four-segment soft X-ray vacuum diode with a golden photocathode, which detects the soft X-ray radiation emitted in the axial direction. This new diagnostic tool is capable to locate the axis of soft X-ray laser in a few capillary shots (less than 10). The description and the experimental measurement of the four-segment soft X-ray vacuum diode are a subject of this paper.
Plasma concentration of interleukin-6 and the risk of future myocardial infarction among apparently healthy men.

BACKGROUND Interleukin-6 (IL-6) plays a central role in inflammation and tissue injury. However, epidemiological data evaluating the role of IL-6 in atherogenesis are sparse. METHODS AND RESULTS In a prospective study involving 14 916 apparently healthy men, we measured baseline plasma concentration of IL-6 in 202 participants who subsequently developed myocardial infarction (MI) and in 202 study participants matched for age and smoking status who did not report vascular disease during a 6-year follow-up. Median concentrations of IL-6 at baseline were higher among men who subsequently had an MI than among those who did not (1.81 versus 1. 46 pg/mL; P=0.002). The risk of future MI increased with increasing quartiles of baseline IL-6 concentration (P for trend <0.001) such that men in the highest quartile at entry had a relative risk 2.3 times higher than those in the lowest quartile (95% CI 1.3 to 4.3, P=0.005); for each quartile increase in IL-6, there was a 38% increase in risk (P=0.001). This relationship remained significant after adjustment for other cardiovascular risk factors, was stable over long periods of follow-up, and was present in all low-risk subgroups, including nonsmokers. Although the strongest correlate of IL-6 in these data was C-reactive protein (r=0.43, P<0.001), the relationship of IL-6 with subsequent risk remained after control for this factor (P<0.001). CONCLUSIONS In apparently healthy men, elevated levels of IL-6 are associated with increased risk of future MI. These data thus support a role for cytokine-mediated inflammation in the early stages of atherogenesis.
A Markov Decision Process Approach for Optimal Data Backup Scheduling

The explosive growth of data generation and increasing reliance of business analysis on massive data make data loss more damaging than ever before. Nowadays many organizations start relying on cloud services for keeping their valuable data. It is a critical issue for cloud service provider to protect the data for individual users securely and effectively. To protect the data in a system with multiple data sources, backup schedule plays an important role for achieving the desired level of data protection while minimizing the impact on system operation. In this paper we investigate the use of Markov Decision Process (MDP) to guide the scheduling of data backup operation and propose a framework to automatically generate an MDP instance from system specifications and data protection requirements. We then demonstrate the benefits of the MDP approach.
Feasibility, accuracy, and performance of contact block reduction method for multi-band simulations of ballistic quantum transport

Numerical utilities of the contact block reduction (CBR) method in evaluating the retarded Green’s function are discussed for 3D multi-band open systems that are represented by the atomic tight-binding (TB) and continuum k·p (KP) band model. It is shown that the methodology to approximate solutions of open systems, which has been already reported for the single-band effective mass model, cannot be directly used for atomic TB systems, since the use of a set of zinc blende crystal grids makes the inter-coupling matrix non-invertible. We derive and test an alternative with which the CBR method can be still practical in solving TB systems. This multi-band CBR method is validated by a proof of principles on small systems and also shown to work excellent with the KP approach. Further detailed analysis on the accuracy, speed, and scalability on high performance computing clusters is performed with respect to the reference results obtained by the state-of-the-art recursive Green’s function and wavefunction algori.
MAGNETIC NESTED-WIND SCENARIOS FOR BIPOLAR OUTFLOWS: PREPLANETARY AND YSO NEBULAR SHAPING

We present results of a series of magnetohydrodynamic (MHD) and hydrodynamic (HD) 2.5 dimensional simulations of the morphology of outflows driven by nested wide-angle winds, i.e., winds that emanate from a central star as well as from an orbiting accretion disk. While our results are broadly relevant to nested-wind systems, we have tuned the parameters of the simulations to touch on issues in both young stellar objects and planetary nebula (PN) studies. In particular, our studies connect to open issues in the early evolution of PNs. We find that nested MHD winds exhibit marked morphological differences from the single MHD wind case along both dimensions of the flow. Nested HD winds, on the other hand, give rise mainly to geometric distortions of an outflow that is topologically similar to the flow arising from a single stellar HD wind. Our MHD results are insensitive to changes in ambient temperature between ionized and un-ionized circumstellar environments. The results are sensitive to the relative mass-loss rates and the relative speeds of the stellar and disk winds. We also present synthetic emission maps of both nested MHD and HD simulations. We find that nested MHD winds show knots of emission appearing on-axis that do not appear in the HD case.
The Interior of Enceladus

The internal structure of a planetary body provides essential clues about its origin and evolution. Based on its internal density structure, what is the likely composition of the materials from which the body formed (see the chapter in this volume by McKinnon et al.)? Did the interior become sufficiently warm to enable differentiation, with heavier components sinking toward the center? How quickly or slowly did the body form? What does the structure of the near surface and deeper interior tell us about the nature of the topography and the distribution of geologic provinces across the surface? The interior of Enceladus is of particular interest because of the complex tectonic structures that cover much of its unusually youthful surface (see chapter in this volume by Patterson et al.) and, most strikingly, because of the ongoing eruptions of water vapor and ice grains from its south polar region (see chapters in this volume by Postberg et al., Goldstein et al., and Spencer et al.). Are these eruptions sourced from a potentially habitable subsurface liquid water reservoir? If so, how deep is the reservoir beneath the icy surface? How thick is the icy crust? What is the structure of the crust and how does it support the surface topography? How is the liquid water, which is not buoyant with respect to the ice, transported to the surface? How does the interior respond to tidal stresses? What modulates the eruptive activity at the south pole? How large is the internal sea or ocean, and how does it keep from freezing solid? What is the composition and nature of the core, and what is its capacity for contributing to the heating of the interior? Although the internal structure cannot be observed directly, a variety of techniques are available for building a picture of the interior that can help to address many of these questions. Seismic imaging has proven to be the definitive technique for constraining the structure of Earth’s interior, and seismic stations placed on the Moon during the Apollo program have likewise helped to improve our understanding
Hypersonic: Model Analysis and Checking in the Cloud

Context: Modeling tools are traditionally delivered as monolithic desktop applications, optionally extended by plug-ins or special purpose central servers. This delivery model suffers from several drawbacks, ranging from poor scalability to dicult maintenance and the proliferation of \shelfware". Objective: In this paper we investigate the conceptual and technical feasibility of a new software architecture for modeling tools, where certain advanced features are factored out of the client and moved towards the Cloud. With this approach we plan to address the above mentioned drawbacks of existing modeling tools. Method: We base our approach on RESTful Web services. Using features implemented in the existing Model Analysis and Checking (MACH) tool, we create a RESTful Web service API oering model analysis facilities. We refer to it as the Hypersonic API. We provide a proof of concept implementation for the Hypersonic API using model clone detection as our example case. We also implement a sample Web application as a client for these Web services. Results: Our initial experiments with Hypersonic demonstrate the viability of our approach. By applying standards such as REST and JSON in combination with Prolog as an implementation language, we are able to transform MACH from a command line tool into the rst Web-based model clone detection service with remarkably little eort.
Hepatocyte-Specific Arid1a Deficiency Initiates Mouse Steatohepatitis and Hepatocellular Carcinoma

ARID1A, encoding a subunit of chromatin remodeling SWI/SNF complexes, has recently been considered as a new type of tumor suppressor gene for its somatic mutations frequently found in various human tumors, including hepatocellular carcinoma (HCC). However, the role and mechanism of inactivated ARID1A mutations in tumorigenesis remain unclear. To investigate the role of ARID1A inactivation in HCC pathogenesis, we generated hepatocyte-specific Arid1a knockout (Arid1a LKO) mice by crossing mice carrying loxP-flanked Arid1a exon 8 alleles (Arid1a f/f) with albumin promoter-Cre transgenic mice. Significantly, the hepatocyte-specific Arid1a deficiency results in mouse steatohepatitis and HCC development. In Arid1a LKO mice, we found that innate immune cells, including F4/80+ macrophages and CD11c+ neutrophil cells, infiltrate into the liver parenchyma, accompanied by the increased tumor necrosis factor (TNF)-α and interleukin (IL)-6, and activation of STAT3 and NF-κB pathways. In conclusion, hepatocyte-specific Arid1a deficiency could lead to mouse steatohepatitis and HCC development. This study provides an alternative mechanism by which Arid1a deficiency contributes to HCC tumorigenesis.
Analysis of an adaptive strategy for equitably approaching and joining human interactions

Since social, assistive and companion robots need to navigate within human crowds, understanding spatial social conventions while designing navigation solutions for such robots is an essential issue. This work presents analysis of an socially compliant robot motion strategy that could be employed by social robots such as humanoids, service robots or intelligent wheelchairs, for approaching and joining humans groups in interaction, and then become an equitable part of the interaction. Following our previous work that formalized the motion strategy, a detailed synthesis is presented here with experiments that validate the proposed system in the real world.
UVB radiation represses CYLD expression in melanocytes

CYLD lysine 63 deubiquitinase (CYLD) was originally identified as a tumor suppressor that is mutated in familial cylindromatosis. Unlike in cylindromatosis, downregulation of the deubiquitinase CYLD in melanoma, a highly aggressive tumor, is not caused by mutations in the CYLD gene, but rather by a constitutive and high expression of the snail family transcriptional repressor 1 (SNAIL1). A reduced CYLD level leads to B-cell lymphoma-3/p50/p52-dependent nuclear factor-κB activation, which in turn triggers the expression of genes such as cyclin D1 and N-cadherin. Elevated levels of cyclin D1 and N-cadherin promote melanoma proliferation and invasion. By analyzing the regulation of CYLD expression in melanocytes, the present study identified a signaling pathway that is regulated in response to ultraviolet B (UVB) radiation in melanocytes. UVB light leads to an extracellular signal-regulated kinase-mediated induction of SNAIL1 and subsequent downregulation of CYLD expression in normal human epithelial melanocytes. The UVB-mediated suppression of CYLD in melanocytes may have a key role in the reaction to UV stimuli, and may also potentially be involved in the early malignant transformation processes.
The fragile X syndrome–autism comorbidity: what do we really know?

Autism spectrum disorder (ASD) is a common comorbid condition in people with fragile X syndrome (FXS). It has been assumed that ASD symptoms reflect the same underlying psychological and neurobiological impairments in both FXS and non-syndromic ASD, which has led to the claim that targeted pharmaceutical treatments that are efficacious for core symptoms of FXS are likely to be beneficial for non-syndromic ASD as well. In contrast, we present evidence from a variety of sources suggesting that there are important differences in ASD symptoms, behavioral and psychiatric correlates, and developmental trajectories between individuals with comorbid FXS and ASD and those with non-syndromic ASD. We also present evidence suggesting that social impairments may not distinguish individuals with FXS with and without ASD. Finally, we present data that demonstrate that the neurobiological substrates of the behavioral impairments, including those reflecting core ASD symptoms, are different in FXS and non-syndromic ASD. Together, these data suggest that there are clinically important differences between FXS and non-syndromic ASD that are masked by reliance on the categorical diagnosis of ASD. We argue for use of a symptom-based approach in future research, including studies designed to evaluate treatment efficacy.