gebhart/patrepeval huggingface dataset:
MonSTer: An Out-of-the-Box Monitoring Tool for High Performance Computing Systems (2020)

Understanding the status of high-performance computing platforms and correlating applications to resource usage provide insight into the interactions among platform components. A lot of efforts have been devoted into developing monitoring solutions; however, a large-scale HPC system usually requires a combination of methods/tools to successfully monitor all metrics, which will lead to a huge effort in configuration and monitoring. Besides, monitoring tools are often left behind in the procurement of large-scale HPC systems. These challenges have motivated the development of a next-generation out-of-the-box monitoring tool that can be easily deployed without losing informative metrics. In this work, we introduce MonSTer, an “out-of-the-box” monitoring tool for high-performance computing platforms. MonSTer uses the evolving specification Redfish to retrieve sensor data from Baseboard Management Controller (BMC), and resource management tools such as Univa Grid Engine (UGE) or Slurm to obtain application information and resource usage data. Additionally, it also uses a time-series database (e.g. InfluxDB) for data storage. MonSTer correlates applications to resource usage and reveals insightful knowledge without having additional overhead on the application and computing nodes. This paper presents the design and implementation of MonSTer, as well as experiences gained through real-world deployment on the 467-node Quanah cluster at Texas Tech University's High Performance Computing Center (HPCC) over the past year. In this work, we introduce MonSTer, an “out-of-the-box” monitoring tool for high-performance computing platforms. MonSTer uses the evolving specification Redfish to retrieve sensor data from Baseboard Management Controller (BMC), and resource management tools such as Univa Grid Engine (UGE) or Slurm to obtain application information and resource usage data. Additionally, it also uses a time-series database (e.g. InfluxDB) for data storage. MonSTer correlates applications to resource usage and reveals insightful knowledge without having additional overhead on the application and computing nodes. This paper presents the design and implementation of MonSTer, as well as experiences gained through real-world deployment on the 467-node Quanah cluster at Texas Tech University's High Performance Computing Center (HPCC) over the past year.
Supplemental Figure 5 from Diagnostic Distinction of Malignant Melanoma and Benign Nevi by a Gene Expression Signature and Correlation to Clinical Outcomes (2023)

&lt;p&gt;Supplemental Figure 5 shows a lesion from the back of a 43 year old female was classified as a superficial spreading melanoma arising within a pre-existing dysplastic nevus (Breslow thickness 1.6 mm, mitotic index 0/mm&lt;sup&gt;2&lt;/sup&gt;, ulceration absent). The lesion was completely excised. The score was +4.6. Metastases to the soft tissue and skin of the upper chest were detected 56 months after diagnosis.&lt;/p&gt;
<title>Microassembly technologies for MEMS</title> (1998)

Microassembly promises to extend MEMS beyond the confines of silicon micromachining. This paper surveys research in both serial and parallel microassembly. The former extends conventional `pick and place' assembly into the micro- domain, where surface forces play a dominant role. Parallel assembly involves the simultaneous precise organization of an ensemble of micro components. This can be achieved by microstructure transfer between aligned wafers or arrays of binding sites that trap an initially random collection of parts. Binding sites can be micromachined cavities or electrostatic traps; short-range attractive forces and random agitation of the parts serve to fill the sites. Microassembly strategies should furnish reliable mechanical bonds and electrical interconnection between the micropart and the target substrate or subassembly.
The Intermediate Filament Protein Vimentin Is a New Target for Epigallocatechin Gallate (2005)

Epigallocatechin gallate (EGCG) is the major active polyphenol in green tea. Protein interaction with EGCG is a critical step in the effects of EGCG on the regulation of various key proteins involved in signal transduction. We have identified a novel molecular target of EGCG using affinity chromatography, two-dimensional electrophoresis, and mass spectrometry for protein identification. Spots of interest were identified as the intermediate filament, vimentin. The identification was confirmed by Western blot analysis using an anti-vimentin antibody. Experiments using a pull-down assay with [3H]EGCG demonstrate binding of EGCG to vimentin with a Kd of 3.3 nm. EGCG inhibited phosphorylation of vimentin at serines 50 and 55 and phosphorylation of vimentin by cyclin-dependent kinase 2 and cAMP-dependent protein kinase. EGCG specifically inhibits cell proliferation by binding to vimentin. Because vimentin is important for maintaining cellular functions and is essential in maintaining the structure and mechanical integration of the cellular space, the inhibitory effect of EGCG on vimentin may further explain its anti-tumor-promoting effect.
Effect of cromakalim and glibenclamide on spontaneous and evoked motility of the guinea‐pig isolated renal pelvis and ureter (1994)

1. We have investigated the effect of the potassium (K) channel opener, cromakalim, on the spontaneous myogenic activity of the guinea-pig isolated renal pelvis and on myogenic contractions evoked by direct electrical stimulation of the guinea-pig isolated ureter. 2. In the presence of Bay K 8644 (1 microM), electrical stimulation of the guinea-pig ureter (10 Hz for 1 s, pulse width 5 ms, 60 V) produced regular tetrodotoxin-(1 microM) resistant phasic contractions which were suppressed by 3 microM cromakalim. Glibenclamide (0.1-3 microM), 4-aminopyridine (4-AP, 0.1-2 mM) and tetraethylammonium (TEA, 1-10 mM) produced a concentration-dependent inhibition of the effect of cromakalim with the rank order of potency (EC50 in parentheses): glibenclamide (0.64 microM) >> 4-AP (1.11 mM) > TEA (6.6 mM). Apamin (0.1-0.3 microM) was without effect. 3. Cromakalim (0.1-10 microM) produced concentration-dependent inhibition and suppression of spontaneous contractions of the guinea-pig isolated renal pelvis and of evoked contractions of the ureter with EC50 values of 0.71 and 0.47 microM, respectively. 4. Glibenclamide (1 microM) produced a rightward shift of the concentration-response curve to cromakalim in both the renal pelvis and ureter, without producing depression of the maximal inhibitory effect. Glibenclamide did not affect the spontaneous activity of the renal pelvis while it produced a slight enhancement (10-15% increase) of evoked contractions of the ureter. Glibenclamide did not affect the inhibitory action of the adenylate cyclase activator, forskolin, in the renal pelvis or ureter. 5. In electrophysiological experiments (sucrose gap), cromakalim (0.3 and 1 microM) produced hyperpolarization of ureter smooth muscle. Cromakalim also produced a transient suppression of action potentials and accompanying phasic contractions evoked by electrical stimulation. Before suppression of evoked contractions, a shortening of action potential duration was observed concomitant with the developing hyperpolarization produced by cromakalim. A lower concentration (0.1 MicroM) of cromakalim did not affect membrane potential but shortened action potential duration and reduced the evoked contraction.6. Glibenclamide (1 MicroM) inhibited the hyperpolarizing action of cromakalim and prevented its inhibitory action on evoked action potentials and contractions of the ureter. Glibenclamide also produced a slight prolongation of action potential duration and increased the amplitude and duration of the accompanying mechanical response.7. These findings demonstrate that activation of cromakalim- and glibenclamide-sensitive K channels produces a powerful mechanism for regulation of pyeloureteral motility and suppression of latent pacemakers of the ureter in guinea-pig. Glibenclamide-sensitive K channels take part in determining action potential shape and duration in the guinea-pig ureter.
Polyphosphazenes for Biology and Medicine: Current Status and Future Prospects (2008)

This chapter contains sections titled: References
Impact of Side‐Chain Hydrophilicity on Packing, Swelling, and Ion Interactions in Oxy‐Bithiophene Semiconductors (2022)

Exchanging hydrophobic alkyl-based side chains to hydrophilic glycol-based side chains is a widely adopted method for improving mixed-transport device performance, despite the impact on solid-state packing and polymer-electrolyte interactions being poorly understood. Presented here is a molecular dynamics (MD) force field for modeling alkoxylated and glycolated polythiophenes. The force field is validated against known packing motifs for their monomer crystals. MD simulations, coupled with X-ray diffraction (XRD), show that alkoxylated polythiophenes will pack with a "tilted stack" and straight interdigitating side chains, whilst their glycolated counterpart will pack with a "deflected stack" and an s-bend side-chain configuration. MD simulations reveal water penetration pathways into the alkoxylated and glycolated crystals-through the π-stack and through the lamellar stack respectively. Finally, the two distinct ways triethylene glycol polymers can bind to cations are revealed, showing the formation of a metastable single bound state, or an energetically deep double bound state, both with a strong side-chain length dependence. The minimum energy pathways for the formation of the chelates are identified, showing the physical process through which cations can bind to one or two side chains of a glycolated polythiophene, with consequences for ion transport in bithiophene semiconductors.
The WWOX Gene Modulates High-Density Lipoprotein and Lipid Metabolism (2014)

Our data indicate that WWOX disruption alters HDL and lipoprotein metabolism through several mechanisms and may account for the low-HDL phenotype observed in families expressing the WWOX variants. These findings thus describe a novel gene involved in cellular lipid homeostasis, which effects may impact atherosclerotic disease development.
P3Ka: A Driver of Tumor Metastasis? (2010)

Received: August 18, 2010 , Accepted: August 20, 2010 , Published: September 11, 2010 //
Al2O3 Passivation for Copper Plated 15.6x15.6 cm2 IBC Cells (2016)

Today, the silicon solar cells with the highest efficiency are interdigitated back contact solar cells. At imec, the cell concept for 15.6x15.6 cm2 IBC cells relies on a rear design with multiple busbars and a Cu plated rear metallization. Previously, we reported efficiencies up to 21.9% by introducing Cu plated contacts. Further developments in the rear design to overcome FF and Jsc losses were implemented and reported as well, showing IBC cells with 22.5% efficiency. In a next optimization round, the passivation quality at the rear of these IBC cells needed to be improved. To do so, we demonstrate in this paper the application of a rear Al2O3 based passivation stack on both emitter and BSF. A 10 nm ALD Al2O3 - PECVD SiOx stack was implemented and a thermal activation step (firing) post deposition was applied and optimized to guarantee a good passivation on both the emitter and the BSF. Best cells with this process showed an efficiency of 22.8% and Voc up to 688mV.
Activation of blood coagulation factor IX by gingipains R, arginine-specific cysteine proteinases from Porphyromonas gingivalis (2001)

The effect of two arginine-specific cysteine proteinases (gingipains R) from Porphyromonas gingivalis, an aetiological factor of adult periodontitis, on the activation of human factor IX was investigated in the presence of ethylene glycol, an activity enhancer of activated factor IX (factor IXa), with the use of a fluorogenic oligopeptide substrate. Each gingipain R rapidly activated factor IX but the 95 kDa proteinase complex (HRgpA) that contains both haemagglutinin/adhesion and catalytic domains was 2.4-fold more efficient than the single-chain 50 kDa gingipain R (RgpB), which has only a catalytic domain. SDS/PAGE and N-terminal sequence analysis of factor IX digestion fragments indicated that, like all endogenous activators, gingipains R also produce factor IXabeta via an IXa intermediate. Significantly, phospholipids augmented the activation of factor IX by HRgpA but not by RgpB in a Ca(2+)-dependent manner. In the presence of both cofactors the kinetic efficiency of HRgpA to activate factor IX (k(cat)/K(m)=1.9x10(6) M(-1).s(-1)) was 8.5-fold higher than that of RgpB (k(cat)/K(m)=2.3x10(5) M(-1).s(-1)) and double that of the factor VIIa-tissue factor complex, but 8-fold lower than that for factor XIa. A comparison of the relative activation rates of factor IX, factor X and prothrombin directly in plasma by HRgpA suggests a significant contribution for factor IX conversion in blood coagulation induced by gingipains R. Taken together, gingipains R are the first-reported activators of factor IX of bacterial origin. By this effect they could be involved in the production of thrombin as well as the subsequent generation of prostaglandins and interleukin 1, all of which have been found to be associated with the development and progression of periodontitis.
Automatic sleep scoring using patient-specific ensemble models and knowledge distillation for ear-EEG data (2022)

Human sleep can be described as a series of transitions between distinct states. This makes automatic sleep analysis (scoring) suitable for an automatic implementation using machine learning. However, the task becomes harder when data is sampled using more light-weight or mobile equipment, often chosen due to greater comfort for the patient. In this study we investigate the improvement in sleep scoring when multiple state-of-the-art neural networks are joined into an ensemble, and subsequently distilled into a single model of identical network architecture, but with improved predictive performance. In this study we investigate ensembles of up to 10 networks, and show that, on the same data, ensembles of neural networks perform better than each single subject model (improvement: 2.4%) and that this improvement can be transferred back into a single network using a combination of patient specific data and knowledge distillation. The study demonstrates both a way to further improve automatic sleep scoring from mobile devices, which in itself is interesting, but also highlights the great potential of the vast amounts of unlabeled personal data which will become available from personal recording devices.
Design efficiencies for indoor wireless (2002)

Summary form only given. This paper explores an emerging frontier for wireless communications: campus and indoor wireless coverage. Proper design of an indoor wireless solution involves RF performance, cost, specific customer requests, ease of installation and ease of maintenance. Tradeoffs exist in the selection of an indoor wireless system from the various types available, based on cost versus performance. Optimum placement for system components depends on objectives such as coverage with minimal use of antennas or cables, and disguise for minimum visual impact. Currently available service types for in-building wireless include indoor public voice and data service, wireless office service (WOS) and wireless LAN. Customization and archival issues based on user adoption and growth expectations impact the selection and design decisions for in-building systems. Finally, the paper highlights the involvement and support of IT staff in installation and deployment strategies for successful and efficient design of any indoor wireless solution.
Geiger-mode quad-cell array for adaptive optics (2008)

We report an array of Shack-Hartmann wavefront sensors using high-fill-factor Geiger-mode avalanche detector quad cells hybridized to all-digital CMOS counting circuits. The absence of readout noise facilitates fast wavefront sensing at low light levels.
Amplitude sampling (2016)

The theoretical basis for conventional acquisition of bandlimited signals typically relies on uniform time sampling and assumes infinite-precision amplitude values. In this paper, we explore signal representation and recovery based on uniform amplitude sampling with assumed infinite precision timing information. The approach is based on applying a one-level level-crossing detector to the result of adding a sawtooth waveform to the source signal. The source signal is then represented by the level-crossing times. For analysis purposes, the output of the level-crossing detector is interpreted as the result of applying a multi-level level crossing detector to the monotonic function consisting of the sum of the source signal and an appropriate linear ramp. This monotonic function is then uniformly sampled in amplitude with the source signal again represented by the level crossing times of the monotonic function. We refer to this technique as amplitude sampling. The approach can equivalently be viewed as nonuniform time sampling of the original source signal or uniform amplitude sampling of the monotonic function to which it is transformed. In this paper we explore this approach and, in particular, present duality and frequency-domain properties for the functions involved in the transformation and develop and compare two iterative algorithms for recovery of the source signal.
Studying Effects of Arc Discharge Surface Texturing on Stress Distribution in Adhesively Bonded Joints by Using Finite Element Modeling (2011)

This study investigates the potentiality of using atmospheric-pressure Direct Current (DC) plasma arc discharge as a surface treatment method of aluminum alloys in adhesively bonded joints in order to enhance adhesion. The surface morphology exposed to the arc for the current of 40 A (low intensity) and the plasma torch scanning speeds between 20 and 120 mm/s, exhibits a micro-scale surface roughness appropriate for adhesive bonding. The arc textured surfaces are characterized by using an optical profilometer. Additionally, the effect of modified surface on the stress distribution throughout the single-lap adhesively bonded joint in tension is explored by 2D FEM. The geometrical model for FE analysis of adhesively bonded structure is generated by including the surface texture coordinates obtained from the optical profilometer.
Evaluation of the prothrombin time for measuring rivaroxaban plasma concentrations using calibrators and controls (2012)

<h3>Background</h3> Rivaroxaban is widely used in clinical practice. Although routine coagulation monitoring is not required, quantitative determination of rivaroxaban might be valuable in certain clinical circumstances. Variation in response sensitivity of prothrombin time (PT) reagents to rivaroxaban is well described in the literature, and the conventional international normalised ratio cannot be used for rivaroxaban. <h3>Purpose</h3> This multicentre study assessed the intra and interlaboratory precision of measurements of rivaroxaban plasma concentrations using the PT assay together with rivaroxaban calibrators and controls. <h3>Materials and methods</h3> Participating laboratories (Europe and North America) were provided with rivaroxaban calibrators (0, 41, 219 and 430 ng/ml), rivaroxaban pooled human plasma controls (19, 160 and 643 ng/ml) and PT reagent. Evaluation was performed over 10 consecutive days by each laboratory using local PT reagents as well as the centrally provided PT reagent (STA Neoplastine CI Plus; Diagnostica Stago). A calibration curve was produced each day, and day-to-day precision was evaluated by testing three control plasma samples. The control was diluted and re-tested if the level was above the highest concentration of the calibration curve. <h3>Results</h3> Intralaboratory variations in PT were dependent on the sensitivity of the local PT reagents, regardless of the type of instrument used. A large inter-laboratory variation (in seconds) was observed with local PT reagents; the coefficient of variation (CV) was 13.6–29.7%. When the results were expressed as rivaroxaban concentration (ng/ml), the inter-reagent variations were reduced; less variation was found with both local reagents (CV: 5.1–15.5%) and the central reagent (CV: 2.2–7.5%). However, over-estimation was observed with both local and central reagents. The CV for the calibrator containing 41 ng/ml rivaroxaban was 5.8% when the central reagent was used. <h3>Conclusions</h3> The PT assay may be useful for measuring rivaroxaban peak plasma concentrations (2–3 h after drug intake) using rivaroxaban calibrators and controls.
Heart failure with preserved ejection fraction: from mechanisms to therapies (2018)

This review aims to provide a translational perspective on recent developments in heart failure with preserved ejection fraction (HFpEF), linking mechanistic insights to potential therapies. A key concept in this review is that HFpEF is a haemodynamic condition wherein the heart fails to keep up with the circulatory demands of the body, or does so at the expense of raised left ventricular filling pressures. We, therefore, propose that the 'final common pathway' for development of congestion, i.e. basic haemodynamic mechanisms of increased left ventricular end-diastolic pressure, left atrial hypertension, pulmonary venous congestion, and plasma volume expansion, represents important initial targets for therapy in HFpEF. Accordingly, we group this review into six mechanisms translating into potential therapies for HFpEF: beginning with three haemodynamic mechanisms (left atrial hypertension, pulmonary hypertension, and plasma volume expansion), and working backward to three potential molecular mechanisms [systemic microvascular inflammation, cardiometabolic functional abnormalities, and cellular (titin)/extracellular (fibrosis) structural abnormalities].
Efficient Laser Performance Using a Micro-Optic Based Pump Source (2004)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text T. S. Rose, J. S. Swenson, D. A. Hinkley, and R. A. Fields, "Efficient Laser Performance Using a Micro-Optic Based Pump Source," in Advanced Solid State Lasers, T. Fan and B. Chai, eds., Vol. 20 of OSA Proceedings Series (Optica Publishing Group, 1994), paper LT4. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article