gebhart/patrepeval huggingface dataset:
JARS (2016)

The enormous increase of data in RDF format calls for efficient storage and retrieval approaches. Being a highly connected data, RDF generates massive amounts of intermediate results during query processing. Many of the current RDF storage approaches involve large amounts of inter-node data movement even for simple selective query patterns. We propose JARS, a join-aware distributed RDF storage system with a dual-hash partitioning strategy coupled with two layered distributed clustered indexing and a rule-based query-execution approach. JARS eliminates the inter-node communication for star patterns and mitigates the communication cost for chain pattern SPARQL queries. Our experiments indicate that JARS achieves significant performance enhancement over the state-of-the-art RDF storage systems.
Change of Electrical Resistivity with Martensite Transformation of Ti-42 mass%Nb Alloy (2018)

The behavior of the martensite transformation of Ti-42 mass%Nb alloy was investigated by electrical resistivity measurement. The β phase was fully retained upon quenching from 1050°C. In the cooling and heating process below room temperature, hysteresis due to the martensite transformation was clearly observed, in contrast to previously reported behavior. The MS and Af temperatures of the sample prepared from the outer layer of a quenched plate were lower than those of the inner layer. Treatment of the solution under a low vacuum condition also lowered these temperatures and the hysteresis loop became much smaller. The effect of the solution temperature above β-transus on the transformation behavior was negligible. By heating to 400°C, the whole resistivity curve shifted upward, and the ωS temperature increased, but the hysteresis loop still appeared at a low temperature. In situ TEM observation revealed that acicular martensite was formed at a low temperature and disappeared with heating, and that the reflection intensities of ω and α” in the β matrix increased with cooling. However, such behavior was hardly observed in a region irradiated by an electron beam during cooling.
Model-based development for RTSJ platforms (2012)

The integration of real-time concepts into modeling tools and Java virtual machines and APIs are two problems addressed along last decade. Examples of standards addressing these problems are RTSJ (Real-Time Specification for Java) and MARTE (Modeling and Analysis of Real-time Embedded Systems). These standards, in general, have common fundaments (time predictability of software systems based on scheduling analysis methods and object-oriented languages).
BAG3: a multifaceted protein that regulates major cell pathways (2011)

Bcl2-associated athanogene 3 (BAG3) protein is a member of BAG family of co-chaperones that interacts with the ATPase domain of the heat shock protein (Hsp) 70 through BAG domain (110-124 amino acids). BAG3 is the only member of the family to be induced by stressful stimuli, mainly through the activity of heat shock factor 1 on bag3 gene promoter. In addition to the BAG domain, BAG3 contains also a WW domain and a proline-rich (PXXP) repeat, that mediate binding to partners different from Hsp70. These multifaceted interactions underlie BAG3 ability to modulate major biological processes, that is, apoptosis, development, cytoskeleton organization and autophagy, thereby mediating cell adaptive responses to stressful stimuli. In normal cells, BAG3 is constitutively present in a very few cell types, including cardiomyocytes and skeletal muscle cells, in which the protein appears to contribute to cell resistance to mechanical stress. A growing body of evidence indicate that BAG3 is instead expressed in several tumor types. In different tumor contexts, BAG3 protein was reported to sustain cell survival, resistance to therapy, and/or motility and metastatization. In some tumor types, down-modulation of BAG3 levels was shown, as a proof-of-principle, to inhibit neoplastic cell growth in animal models. This review attempts to outline the emerging mechanisms that can underlie some of the biological activities of the protein, focusing on implications in tumor progression.
Wall Teichoic Acid Function, Biosynthesis, and Inhibition (2009)

Off the wall: Wall teichoic acids (WTAs) are negatively charged glycopolymers found in dense arrays on the surface of Gram-positive bacteria. WTAs have profound effects on the physiology of Gram-positive organisms, and impact everything from cation homeostasis to antibiotic susceptibility to survival in a host. This review summarizes recent advances made toward understanding WTA function, biosynthesis and inhibition.
Stationary frame generalized integrators for current control of active power filters with zero steady state error for current harmonics of concern under unbalanced and distorted operation conditions (2002)

The paper proposes several concepts of integrators for sinusoidal signals. Parallel and series associations of the basic PI units using the stationary frame generalized integrators are used for current control of active power filters. Zero steady state error for the concerned current harmonics are realized, with reduced computation, under unbalanced utility or load conditions. Designing of the PI constants, digital realization of the generalized integrators, as well as compensation of the computation delay etc. are studied. Extensive test results from a 10 kW active power filter prototype are demonstrated.
Transforming Growth Factor β Activation of c-Abl Is Independent of Receptor Internalization and Regulated by Phosphatidylinositol 3-Kinase and PAK2 in Mesenchymal Cultures (2006)

Transforming growth factor beta (TGF-beta) modulates a number of cellular phenotypes as divergent as growth stimulation and growth inhibition. Although the Smad pathway is critical for many of these responses, recent evidence indicates that Smad-independent pathways may also have a critical role. One such protein previously shown to regulate TGF-beta action independent of the Smad proteins is the c-Abl nonreceptor tyrosine kinase. In the current study we determined that TGF-beta receptor signaling activates c-Abl kinase activity in a subset of fibroblast but not epithelial cultures. This cell type-specific response occurs in a membrane-proximal locale independent of receptor internalization and upstream of dynamin action. Although c-Abl activation by TGF-beta is independent of Smad2 or Smad3, it is prevented by inhibitors of phosphatidylinositol 3-kinase or PAK2. Thus, c-Abl represents a target downstream of phosphatidylinositol 3-kinase-activated PAK2, which differentiates TGF-beta signaling in fibroblasts and epithelial cell lines and integrates serine/threonine receptor kinases with tyrosine kinase pathways.
Deep-learning system to improve the quality and efficiency of volumetric heart segmentation for breast cancer (2021)

Although artificial intelligence algorithms are often developed and applied for narrow tasks, their implementation in other medical settings could help to improve patient care. Here we assess whether a deep-learning system for volumetric heart segmentation on computed tomography (CT) scans developed in cardiovascular radiology can optimize treatment planning in radiation oncology. The system was trained using multi-center data (n = 858) with manual heart segmentations provided by cardiovascular radiologists. Validation of the system was performed in an independent real-world dataset of 5677 breast cancer patients treated with radiation therapy at the Dana-Farber/Brigham and Women's Cancer Center between 2008-2018. In a subset of 20 patients, the performance of the system was compared to eight radiation oncology experts by assessing segmentation time, agreement between experts, and accuracy with and without deep-learning assistance. To compare the performance to segmentations used in the clinic, concordance and failures (defined as Dice < 0.85) of the system were evaluated in the entire dataset. The system was successfully applied without retraining. With deep-learning assistance, segmentation time significantly decreased (4.0 min [IQR 3.1-5.0] vs. 2.0 min [IQR 1.3-3.5]; p < 0.001), and agreement increased (Dice 0.95 [IQR = 0.02]; vs. 0.97 [IQR = 0.02], p < 0.001). Expert accuracy was similar with and without deep-learning assistance (Dice 0.92 [IQR = 0.02] vs. 0.92 [IQR = 0.02]; p = 0.48), and not significantly different from deep-learning-only segmentations (Dice 0.92 [IQR = 0.02]; p ≥ 0.1). In comparison to real-world data, the system showed high concordance (Dice 0.89 [IQR = 0.06]) across 5677 patients and a significantly lower failure rate (p < 0.001). These results suggest that deep-learning algorithms can successfully be applied across medical specialties and improve clinical care beyond the original field of interest.
High-efficiency power characteristics for WCDMA applications of SiGe HBT devices using a novel form of base-bias resistance (2003)

We present SiGe heterojunction bipolar transistor (HBT) devices that exhibit highly efficient and linear power characteristics comparable to those of GaAs HBTs under wide-band code-division multiple-access (WCDMA) modulation for the first time. Two resistors in series are inserted in the base-bias current path of the device. One only conducts envelope-frequency components of the base current while the other also conducts DC. By adjusting the resistance values, the adjacent channel power ratio (ACPR) was significantly reduced over a wide range of output power levels without loss of efficiency. An optimized device with a total emitter area of 3390 /spl mu/m/sup 2/ exhibited 44% power-added-efficiency (PAE) and 27.3-dBm output power with ACPR of less than -40 dBc under WCDMA modulation at 1.95 GHz and 3.4-V bias voltage.
Evolving Functional Symmetry in a Three Dimensional Model of an Elongated Organism (2008)

In evolutionary-developmental biology, it is well established that neural organization is coupled to a given organism's body-plan. Many theories attempt to underpin this coupling and the transitions involved during the organism's evolution, for example the transition from radial to bilateral symmetry. Before theoretically tackling these transitions however, we felt it essential to first address, in this paper, precisely why bilateral symmetry might be advantageous for a simple eel-like agent. We find that neural architectures affording the best motor-coordinated behavior (architectures that allow directional swimming of the agent), will readily emerge in a way that is functionally-bilaterally symmetric, suggesting therefore, that bilaterally symmetrical emergence for a long elongated creature can be essential if it needs to travel over some distance. © 2007 alifexi.org.
Synthesis and Reactions of 1,2-Dithiete and Related Compounds (1999)

Bis(methoxycarbonyl)-1,2-dithiete 1, the cyclic dimer 2, and the tetramer 3 were obtained by oxidation of titanocene dithiolene complex with sulfuryl chloride, and the crystal structures of 1 and 2 were determined by X-ray crystallographic analysis. Novel ring conversion reaction among the compounds was found under various conditions, such as in non-polar solvent, in polar solvent, and in the presence of silica-gel.
Voxel‐wise lesion mapping of self‐reported urinary incontinence in multiple sclerosis (2019)

Our voxel-wise analysis indicated associations between self-reported urinary incontinence and lesions in the left frontal white matter and right parahippocampal region. Thus, our data suggest that dysfunction of supraspinal bladder control due to cerebral lesions may contribute to the pathophysiology of urinary incontinence in MS.
Supplementary Table 4 from Identification of Differentially Regulated Splice Variants and Novel Exons in Glial Brain Tumors Using Exon Expression Arrays (2023)

Supplementary Table 4 from Identification of Differentially Regulated Splice Variants and Novel Exons in Glial Brain Tumors Using Exon Expression Arrays
Ground-state energy estimation of the water molecule on a trapped ion quantum computer (2019)

Quantum computing leverages the quantum resources of superposition and entanglement to efficiently solve computational problems considered intractable for classical computers. Examples include calculating molecular and nuclear structure, simulating strongly-interacting electron systems, and modeling aspects of material function. While substantial theoretical advances have been made in mapping these problems to quantum algorithms, there remains a large gap between the resource requirements for solving such problems and the capabilities of currently available quantum hardware. Bridging this gap will require a co-design approach, where the expression of algorithms is developed in conjunction with the hardware itself to optimize execution. Here, we describe a scalable co-design framework for solving chemistry problems on a trapped ion quantum computer, and apply it to compute the ground-state energy of the water molecule. The robust operation of the trapped ion quantum computer yields energy estimates with errors approaching the chemical accuracy, which is the target threshold necessary for predicting the rates of chemical reaction dynamics.
Monoamine oxidase A (MAO-A): a signature marker of alternatively activated monocytes/macrophages (2014)

Monocytes/macrophages are versatile cells centrally involved in host defense and immunity. Th1 cytokines induce a classical activation program in monocytes/macrophages leading to a proinflammatory M1 macrophage phenotype while Th2 cytokines IL-4 and IL-13 promote monocyte differentiation into an alternatively activated, anti-inflammatory M2 macrophage phenotype. Although monoamine oxidase A (MAO-A) is primarily known for its action in the nervous system, several recent studies have identified MAO-A as a signature marker of alternative activation of monocytes/macrophages. In this brief review we explore the signaling pathways/molecules that regulate MAO-A expression in alternatively activated monocytes/macrophages. We further discuss the contribution of MAO-A to the resolution of inflammation and identify potential therapeutic targets for controlling inflammation. Altogether this review provides deeper insight into the role of MAO-A in alternative activation of monocytes/macrophages and their participation in the inflammatory response.
The response and survival of children with recurrent diffuse intrinsic pontine glioma based on phase II study of antineoplastons A10 and AS2-1 in patients with brainstem glioma (2014)

The results suggest that ANP shows efficacy and acceptable tolerability profile in patients with RPDIPG.
Virtual Histology Evaluation of Atherosclerosis Regression During Atorvastatin and Ezetimibe Administration - HEAVEN Study - (2011)

Dual lipid-lowering therapy starts atherosclerosis regression, but does not lead to significant changes in plaque composition. The continuous shift in plaque from fibro and fibro-fatty to necrotic with calcification was present in both groups.
Assessment of liver fibrosis by a noninvasive method of transient elastography and biochemical markers (2006)

Our findings suggest that FibroScan can initially be used to assess LF as an alternative to a liver biopsy (LB) and serum diagnosis, because it is a safe method with comparable diagnostic accuracy regarding the existing LF markers.
A Level-Set Approach for Compressible, Multiphase Fluid Flows with Mass Transfer (2009)

In this work, a new level-set-based approach is presented and applied to compressible, multiphase flows. Using a species-mass-conservation-based level-set transport equation, several advantages over signed-distancefunction-based methods are demonstrated. Specific improvements include a ghost-fluid-free method for highly compressible problems, extensions to an arbitrary number of species, and finite-rate chemistry mass transfer modeling. While maintaining higher-order numerics, the approach is applicable to three-dimensional, time-accurate/steady, turbulent simulations. Herein, the method is applied to a flow solver that fully couples the mass, momentum, energy, and level-set transport equation; although the methods are equally applicable to segregated flow solvers. The methods are tested for ventilated supercavities, natural cavitation (incompressible, compressible, and thermal), and shock-induced boiling. Lastly, new reinitialization methods are developed specific to cavitating flows that decrease the interface diffusion where needed, while retaining an ability to admit subgrid-scale mixtures. Such an approach enables a more physical solution method for certain classes of multiphase flows. This formulation of the level-set approach is a general, valid, method that could easily be incorporated into any species-mass conservation solver.
Rheological properties of high molecular weight (HMW) syndiotactic poly(vinyl alcohol) (PVA)/HMW atactic PVA blend solutions (2006)

Abstract To identify the effect of blend ratios of syndiotacticity‐rich poly(vinyl alcohol) (s‐PVA)/atactic PVA (a‐PVA) having similar number‐average degrees of polymerization ( P n )s of 4000 and degrees of saponification (DS)s of 99.9% on the rheological properties of s‐PVA/a‐PVA/water solutions, water‐soluble s‐PVA and a‐PVA with different syndiotactic diad contents of 58.5 and 54.0%, respectively, were prepared by bulk copolymerization of vinyl pivalate and vinyl acetate (VAc) and solution polymerization of VAc, followed by saponifying the corresponding copoly(vinyl pivalate/vinyl acetate) and poly(vinyl acetate). The blend ratios played a significant role in rheological behavior. Over the frequency range of 10 −1 –10 2 rad/s, s‐PVA/a‐PVA blend solutions with larger s‐PVA content show more shear thinning at similar ( P n )s and (DS)s of polymer, suggesting that PVA molecules are more readily oriented as s‐PVA content increases. Yield stress is higher for s‐PVA/a‐PVA blend solutions with larger s‐PVA content at similar ( P n )s and (DS)s of polymer. This indicates that more domains with internal order are produced at larger s‐PVA content in s‐PVA/a‐PVA blend solutions. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 102: 3934–3939, 2006
An Ultra-Wideband Metal-Only Dipole Reflectarray Antenna (2018)

This paper presents a new ultra-wideband metalonly dipole reflectarray (MODRA) antenna, designed to operate over the frequency range of 10-19 GHz. The proposed structure offers many advantages over the legacy design. For instance, its simplicity and lightweight enable us to develop a large-size reflectarray (RA) antenna, which can be deployed on any platform including a satellite. The proposed MODRA antenna consists of dipole antennas with varying lengths, which is mechanically supported by a rectangular metallic ring and a short-circuited metal strip. Stainless-steel metal has been suggested as the material to use to fabricate the proposed structure. Normal incident simulation shows that at 10 GHz the MODRA antenna realizes 339° phase range when the dipole lengths vary from 1mm to 14mm; furthermore, it realizes a 298° phase range at 19 GHz for the same dipole-length variation. The maximum reflection loss is found to be 0.51 dB and 0.2 dB at 10 GHz and 19 GHz, respectively. Finally, metal-only multi-dipole reflectarray (MOMDRA) antenna is employed as a simple solution to overcome the phase shift limitation of the MODRA antenna. Simulations show that reflection phases of 345° and 657° are realized at 10 GHz and 18 GHz, respectively.
Supplementary Figure Legends from Lack of <i>p53</i> Augments Antitumor Functions in Cytolytic T Cells (2023)

&lt;p&gt;Details for comparative characterization of the phenotype, and anti-tumor function of p53-KO vs Wt T cells is included.&lt;/p&gt;
Robust Intermediate Read-Out for Deep Submicron Technology CMOS Image Sensors (2008)

In this paper, a CMOS image sensor featuring a novel spiking pixel design and a robust digital intermediate read-out is proposed for deep submicron CMOS technologies. The proposed read-out scheme exhibits a relative insensitivity to the ongoing aggressive scaling of the supply voltage. It is based on a novel compact spiking pixel circuit, which combines digitizing and memory functions. Illumination is encoded into a Gray code using a very simple yet robust Gray 8-bit counter memory. Circuit simulations and experiments demonstrate the successful operation of a 64 64 image sensor, implemented in a 0.35 CMOS technology. A scalability analysis is presented. It suggests that deep sub-0.18 will enable the full potential of the proposed Gray encoding spiking pixel. Potential applications include multiresolution imaging and motion detection.
Increase of Catecholamines in Mouse Brain by Systemic Administration of γ‐Glutamyl L‐3,4‐Dihydroxyphenylalanine (1987)

We investigated the effect of systemic administration of gamma-glutamyl L-3,4-dihydroxyphenylalanine (gamma-Glu-DOPA) on catecholamine contents in the brain. gamma-Glu-DOPA was transformed to dopamine (DA) in vitro with brain homogenate by the sequential action of gamma-glutamyl transpeptidase and aromatic L-amino acid decarboxylase. Intraperitoneal injection of gamma-Glu-DOPA to mice increased DA markedly and noradrenaline (NA) moderately in the brain. The increase of endogenous DA was followed by elevation of the main DA metabolites (3,4-dihydroxyphenyl-acetic acid and homovanillic acid). These increases were in a dose-dependent manner. The maximal elevation of DA was observed within 30 min after administration of gamma-Glu-DOPA, but a substantial increase of NA was observed 2 h after the administration. These results suggest that gamma-Glu-DOPA may be applicable to the treatment of Parkinson's disease.
PPI-Affinity: A Web Tool for the Prediction and Optimization of Protein–Peptide and Protein–Protein Binding Affinity (2022)

Virtual screening of protein-protein and protein-peptide interactions is a challenging task that directly impacts the processes of hit identification and hit-to-lead optimization in drug design projects involving peptide-based pharmaceuticals. Although several screening tools designed to predict the binding affinity of protein-protein complexes have been proposed, methods specifically developed to predict protein-peptide binding affinity are comparatively scarce. Frequently, predictors trained to score the affinity of small molecules are used for peptides indistinctively, despite the larger complexity and heterogeneity of interactions rendered by peptide binders. To address this issue, we introduce PPI-Affinity, a tool that leverages support vector machine (SVM) predictors of binding affinity to screen datasets of protein-protein and protein-peptide complexes, as well as to generate and rank mutants of a given structure. The performance of the SVM models was assessed on four benchmark datasets, which include protein-protein and protein-peptide binding affinity data. In addition, we evaluated our model on a set of mutants of EPI-X4, an endogenous peptide inhibitor of the chemokine receptor CXCR4, and on complexes of the serine proteases HTRA1 and HTRA3 with peptides. PPI-Affinity is freely accessible at https://protdcal.zmb.uni-due.de/PPIAffinity.
CMOS APS Image Sensor with Ultra-High-Linear-Dynamic-Range Utilizing Dual Output (1997)

We report a 64x64 element CMOS active pixel sensor (APS) with ultra-high-dynamic-range linear output. The chip features a new architecture enabling multiple samples per pixel per frame.