gebhart/patrepeval huggingface dataset:
The cyclin encoded by Kaposi's sarcoma-associated herpesvirus stimulates cdk6 to phosphorylate the retinoblastoma protein and histone H1 (1997)

Kaposi's sarcoma-associated herpesvirus (KSHV or human herpesvirus 8) is a novel gammaherpesvirus implicated in the cause of Kaposi's sarcoma and certain malignancies of lymphatic origin. One of the candidate genes possibly involved in promoting tumor development is an open reading frame (ORF) with sequence similarity to human type D cyclin genes. This cyclin-like gene, when expressed in tissue culture cells, promotes phosphorylation and inactivation of the retinoblastoma tumor suppressor protein and thereby may result in deregulation of cell division control. We report here the biochemical characterization of this cyclin (KSHV-cyc) and the kinase activity that it elicits upon expression in tissue culture cells. We demonstrate that the kinase activity associated with KSHV-cyc is sensitive to the cdk inhibitor p27 (KIP) and due to activation of cdk6. However, in contrast to cdk6 activated by cellular type D cyclins, the cdk6 activated by KSHV-cyc is capable of phosphorylating not only the retinoblastoma protein but also histone H1. This finding implies that activation by KSHV-cyc alters the substrate preference of this cdk. This may have important physiological consequences in that the kinase activity triggered by this viral cyclin may abrogate cell cycle checkpoints in addition to those targeted by cellular cyclin D-cdk6 kinase.
Surface and Defect Excitations in Covalently Bonded Solids (1992)

Abstract : This bibliography lists the following reports: Optimized pseudopotentials, Ab-initio materials science and engineering using the molecular dynamics methods for total energy pseudopotential calculations, Oxygen complexes in Si, The enchanting properties of oxygen atoms in silicon, The electronic structure of oxygen in silicon as revealed by volume visualization of ab-initio calculations, Photonic bound states in periodic dielectric materials, Precise and efficient ab-initio molecular dynamics, Donor and acceptor modes in photonic band structures.
Demand Is Very Elastic! (2011)

Demand-Side Management (DSM) has been on the agendas of many state public utility commissions (SPUCs) since the first oil embargo in 1974. Many utilities bought meters and control devices with the large communication infrastructure to comply with SPUC orders to implement or to test DSM. Many of the devices never left the warehouse as the energy crisis dissipated.
Exploiting the Chemical Shielding Anisotropy to Probe Structure and Disorder in Ceramics: 89Y MAS NMR and First-Principles Calculations (2012)

The local structure and cation disorder in Y2(Sn,Ti)2O7 pyrochlores, materials proposed for the encapsulation of lanthanide- and actinide-bearing radioactive waste, is investigated using 89Y (I = 1/2) NMR spectroscopy and, in particular, measurement of the 89Y anisotropic shielding. Although known to be a good probe of the local environment, information on the anisotropy of the shielding interaction is removed under magic angle spinning (MAS). Here, we consider the feasibility of experimental measurement of the 89Y anisotropic shielding interaction using two-dimensional CSA-amplified PASS experiments, implemented for 89Y for the first time. Despite the challenges associated with the study of low-γ nuclei, and those resulting from long T1 relaxation times, the successful implementation of these experiments is demonstrated for the end member pyrochlores, Y2Sn2O7 and Y2Ti2O7. The accuracy and robustness of the measurement to various experimental parameters is also considered, before the approach is then applied to the disordered materials in the solid solution. The anisotropies extracted for each of the sideband manifolds are compared to those obtained using periodic first-principles calculations, and provide strong support for the assignment of the spectral resonances. The value of the span, Ω, is shown to be a sensitive probe of the next nearest neighbor (NNN) environment, i.e., the number of Sn and Ti on the six surrounding “B” (i.e., six-coordinate) sites, and also provides information on the local geometry directly, through a correlation with the average Y–O8b distance (where 8b indicates the Wyckoff position of the oxygen).
MATCHA: Speeding Up Decentralized SGD via Matching Decomposition Sampling (2019)

This paper studies the problem of error-runtime trade-off, typically encountered in decentralized training based on stochastic gradient descent (SGD) using a given network. While a denser (sparser) network topology results in faster (slower) error convergence in terms of iterations, it incurs more (less) communication time/delay per iteration. In this paper, we propose MATCHA, an algorithm that can achieve a win-win in this error-runtime trade-off for any arbitrary network topology. The main idea of MATCHA is to parallelize inter-node communication by decomposing the topology into matchings. To preserve fast error convergence speed, it identifies and communicates more frequently over critical links, and saves communication time by using other links less frequently. Experiments on a suite of datasets and deep neural networks validate the theoretical analyses and demonstrate that MATCHA takes up to $5\times$ less time than vanilla decentralized SGD to reach the same training loss.
Statistics, philosophy, and health: the SMAC 2021 webconference (2022)

SMAC 2021 was a webconference organized in June 2021. The aim of this conference was to bring together data scientists, (bio)statisticians, philosophers, and any person interested in the questions of causality and Bayesian statistics, ranging from technical to philosophical aspects. This webconference consisted of keynote speakers and contributed speakers, and closed with a round-table organized in an unusual fashion. Indeed, organisers asked world renowned scientists to prepare two videos: a short video presenting a question of interest to them and a longer one presenting their point of view on the question. The first video served as a "teaser" for the conference and the second were presented during the conference as an introduction to the round-table. These videos and this round-table generated original scientific insights and discussion worthy of being shared with the community which we do by means of this paper.
Supplementary Table S1, S2, S3, S4 from <i>Paired Box 5</i> Methylation Detection by Droplet Digital PCR for Ultra-Sensitive Deep Surgical Margins Analysis of Head and Neck Squamous Cell Carcinoma (2023)

&lt;p&gt;Supplementary Table S1: List of primers and probes used for QMSP and ddQMSP Supplementary Table S2: Analysis of clinicopathological and molecular factors in association with clinical outcomes of imprint cases Supplementary Table S3: Analysis of clinicopathological and molecular factors in association with clinical outcomes of tissue cases Supplementary Table S4: QMSP assay of 6 HNSCC surgical margin tissues which were histologically cancer-positive&lt;/p&gt;
4H-SiC Planar MESFET for Microwave Power Device Applications (2005)

4H-SiC planar MESFETs were fabricated using ion-implantation on semi-insulating substrate without recess gate etching. A modified RCA method was used to clean the substrate before each procedure. A thin, thermal oxide layer was grown to passivate the surface and then a thick field oxide was deposited by CVD. The fabricated MESFET showed good contact properties and DC/RF performances. The maximum oscillation frequency of 34 GHz and the cut-off frequency of 9.3 GHz were obtained. The power gain was 10.1 dB and the output power of 1.4 W was obtained for 1 mm-gate length device at 2 GHz. The fabricated MESFETs showed the charge trapping-free characteristics and were characterized by the extracted small-signal equivalent circuit parameters.
ICSM 2000: Over Twenty-Five Years of Synthetic Metals (2000)

The International Conference on the Science and Technology of Synthetic Metals (ICSM), its impact on the scientific community, and the rapid progress that has occurred throughout this broad field of materials science are reflected upon. These meetings are held in beautiful and stimulating locations around the world as exemplified by the Figure.
Three low-mass companions around aged stars discovered by TESS (2022)

We report the discovery of three transiting low-mass companions to aged stars: a brown dwarf (TOI-2336b) and two objects near the hydrogen burning mass limit (TOI-1608b and TOI-2521b). These three systems were first identified using data from the Transiting Exoplanet Survey Satellite (TESS). TOI-2336b has a radius of $1.05\pm 0.04\ R_J$, a mass of $69.9\pm 2.3\ M_J$ and an orbital period of 7.71 days. TOI-1608b has a radius of $1.21\pm 0.06\ R_J$, a mass of $90.7\pm 3.7\ M_J$ and an orbital period of 2.47 days. TOI-2521b has a radius of $1.01\pm 0.04\ R_J$, a mass of $77.5\pm 3.3\ M_J$ and an orbital period of 5.56 days. We found all these low-mass companions are inflated. We fitted a relation between radius, mass and incident flux using the sample of known transiting brown dwarfs and low-mass M dwarfs. We found a positive correlation between the flux and the radius for brown dwarfs and for low-mass stars that is weaker than the correlation observed for giant planets. We also found that TOI-1608 and TOI-2521 are very likely to be spin-orbit synchronized, leading to the unusually rapid rotation of the primary stars considering their evolutionary stages. Our estimates indicate that both systems have much shorter spin-orbit synchronization timescales compared to their ages. These systems provide valuable insights into the evolution of stellar systems with brown dwarf and low-mass stellar companions influenced by tidal effects.
Riluzole metabolism and CYP1A1/2 polymorphisms in patients with ALS (2007)

Riluzole is the only FDA approved drug for the treatment of amyotrophic lateral sclerosis. Riluzole is assumed to be mainly metabolized by the liver cytochrome CYP1A2 and by the extra-hepatic cytochrome CYP1A1. CYP1A2 and CYP1A1 genetic polymorphisms are known, but their relationship to riluzole metabolism in ALS patients has not been investigated. The aim of this study was to determine whether the polymorphisms of the CYP1A2 and the CYP1A1 genes in ALS patients are associated with riluzole metabolic profiles. Thirty-two patients with a diagnosis of probable or definite ALS and who were on riluzole, participated in the study. Trough and peak plasma riluzole levels were measured using analytical chromatography-mass spectrometry methods. Association of the genotypes of the SNPs spanning the CYP1A1 and CYP1A2 genes (including one SNP in the intergenic region) with mean riluzole peak and trough levels was studied using ANOVA and Tukey's HSD. The mean peak riluzole level was 202+/-111 ng/ml and mean trough level 54.3+/-37.5 ng/ml. Our data do not support any association of the four CYP1A1 and CYP1A2 polymorphisms with the riluzole metabolic profile. In conclusion, genetic variations in CYP1A1 and CYP1A2 genes do not seem to influence riluzole levels. Further work is needed to better understand the genetic regulation of CYP1A enzymes and their role in riluzole metabolism.
<title>Dynamic scanpaths: eye movement analysis methods</title> (1999)

An eye movements sequence, or scanpath, during viewing of a stationary stimulus has been described as a set of fixations onto regions-of-interest, ROIs, and the saccades or transitions between them. Such scanpaths have high similarity for the same subject and stimulus both in the spatial loci of the ROIs and their sequence; scanpaths also take place during recollection of a previously viewed stimulus, suggesting that they play a similar role in visual memory and recall.
Value of CRP in coronary risk determination. (2009)

Initial studies showed that C-reactive protein (CRP) may have a role in the genesis of atherosclerotic lesions and as a novel biomarkers of patients at risk of developing coronary heart disease (CHD) events. Most of these studies had methodologic limitations, and recent data contradict these findings and suggest that inflammatory markers, such as CRP, have limited usefulness in the prediction of CHD events over and above conventional risk factors. Its low predictive value creates difficulty in interpreting the CRP data in an individual patient. Current scientific literature does not support measurement of CRP in individual patients in clinical medicine. In this review, we critically appraise role of CRP in cardiovascular medicine.
High Performance Full Chip Device Profiling and DOE selection for Physical and Parametric Yield Monitoring (2019)

Products today can contain tens of billions of devices with hundreds of millions of unique layout contexts. The electrical performance of these transistors (e.g. Idsat, Vth, etc.) are highly sensitive to Layout Dependent Effects (LDE). This paper describes a novel and high-performance flow to identify a representative sampling of devices for LDE parameter extraction and simulation. Common and outlier devices can be chosen for process control monitoring. This can reduce the gap between models and silicon.
A 1V 14b self-timed zero-crossing-based incremental &#x0394;&#x03A3; ADC (2013)

This paper introduces a clock-free self-timed incremental ΔΣ ADC. Unlike conventional ΔΣ ADCs, it does not require a dedicated clock signal, thus saving energy and reducing system complexity. As such, it has similar advantages as self-timed (or asynchronous) SAR ADCs [1]. It is particularly suited for use in energy-constrained sensor applications, in which conversions of a quasistatic input signal are triggered by infrequent and possibly irregular external events. As it autonomously powers down upon completion of a conversion, it can adapt to a wide range of conversion rates in an energy-efficient way.
The Survey for Ventilation Systems of Weaned Pig House in Korea (2014)

This survey was conducted to give the basic information for ventilation systems of weaned pig house to establish the acceptable ventilation system in Korea. A total of 11 farms were surveyed in this study and 1 more farm in each province was regionally selected. The general information, inlet and outlet ventilation system, alley in house, space allowance of weaned pigs and manure management were surveyed. Space allowance of weaned pig in 82% of surveyed farms met the legal standard. Side wall inlet and outlet ventilation system were 82% and 73% of surveyed farms, respectively. Moreover, 73% farms have alley in the pig house to control temperature of inlet air. In this survey, both planar slot and circular duct inlet system and side wall fan outlet system could be a favorable ventilation system in weaned pig house.
Reversible Competitive α-Ketoheterocycle Inhibitors of Fatty Acid Amide Hydrolase Containing Additional Conformational Constraints in the Acyl Side Chain: Orally Active, Long-Acting Analgesics (2011)

A series of α-ketooxazoles containing conformational constraints in the C2 acyl side chain of 2 (OL-135) were examined as inhibitors of fatty acid amide hydrolase (FAAH). Only one of the two possible enantiomers displayed potent FAAH inhibition (S vs R enantiomer), and their potency is comparable or improved relative to 2, indicating that the conformational restriction in the C2 acyl side chain is achievable. A cocrystal X-ray structure of the α-ketoheterocycle 12 bound to a humanized variant of rat FAAH revealed its binding details, confirmed that the (S)-enantiomer is the bound active inhibitor, shed light on the origin of the enantiomeric selectivity, and confirmed that the catalytic Ser241 is covalently bound to the electrophilic carbonyl as a deprotonated hemiketal. Preliminary in vivo characterization of the inhibitors 12 and 14 is reported demonstrating that they raise brain anandamide levels following either intraperitoneal (ip) or oral (po) administration indicative of effective in vivo FAAH inhibition. Significantly, the oral administration of 12 caused dramatic accumulation of anandamide in the brain, with peak levels achieved between 1.5 and 3 h, and these elevations were maintained over 9 h. Additional studies of these two representative members of the series (12 and 14) in models of thermal hyperalgesia and neuropathic pain are reported, including the demonstration that 12 administered orally significantly attenuated mechanical (>6 h) and cold (>9 h) allodynia for sustained periods consistent with its long-acting effects in raising the endogenous concentration of anandamide.
Distinct interacting cortical networks for stimulus-response and repetition-suppression (2022)

Non-invasive studies consider the initial neural stimulus response (SR) and repetition suppression (RS) - the decreased response to repeated sensory stimuli - as engaging the same neurons. That is, RS is a suppression of the SR. We challenge this conjecture using electrocorticographic (ECoG) recordings with high spatial resolution in ten patients listening to task-irrelevant trains of auditory stimuli. SR and RS were indexed by high-frequency activity (HFA) across temporal, parietal, and frontal cortices. HFA<sub>SR</sub> and HFA<sub>RS</sub> were temporally and spatially distinct, with HFA<sub>RS</sub> emerging later than HFA<sub>SR</sub> and showing only a limited spatial intersection with HFA<sub>SR</sub>: most HFA<sub>SR</sub> sites did not demonstrate HFA<sub>RS</sub>, and HFA<sub>RS</sub> was found where no HFA<sub>SR</sub> could be recorded. β activity was enhanced in HFA<sub>RS</sub> compared to HFA<sub>SR</sub> cortical sites. θ activity was enhanced in HFA<sub>SR</sub> compared to HFA<sub>RS</sub> sites. Furthermore, HFA<sub>SR</sub> sites propagated information to HFA<sub>RS</sub> sites via transient θ:β phase-phase coupling. In contrast to predictive coding (PC) accounts our results indicate that HFA<sub>SR</sub> and HFA<sub>RS</sub> are functionally linked but have minimal spatial overlap. HFA<sub>SR</sub> might enable stable and rapid perception of environmental stimuli across extended temporal intervals. In contrast HFA<sub>RS</sub> might support efficient generation of an internal model based on stimulus history.
Low Temperature Electronics workshop (2002)

Interest in cool and cold electronics has increased markedly over the last five years. The benefits of low temperature operation have long been known, but until recently, efforts to commercialize moderate to high volume applications, such as high performance computing, employing high capacity chilling systems have universally failed. Powerful and simple cooling approaches combined with an increasing need for speed have reawakened interest in low temperature applications. The SEMITHERM Low Temperature Electronics workshop addresses the critical areas of cost effective cooling and issues associated with the application of chilling within high performance computers. Detailed discussions of below-ambient cooling of two commercially available computers, an enterprise server and a 1 GHz personal computer clearly overview the state-of-the-art. Efforts underway to develop smaller and colder cooling systems are also overviewed.
Surface Transitions by Shear Modulation Force Microscopy (2001)

With the increasing importance of thin film in various applications, there is a need for new techniques with high surface sensitivity to measure physical properties. In this paper, we report results using a recently developed technique based on atomic force microscopy, temperature-dependent shear modulation force microscopy (SMFM), to investigate the surface glass transition. We test the effects of pressure under the tip, modulation frequency, and driving amplitude, which have been the subject of some controversy. The glass transition measurements on polystyrene and poly(methyl methacrylate) with different sample geometries demonstrate that the active volume probed by this technique has lateral dimensions on the order of the tip−sample contact radius. Applications to thin film glass transition measurements and surface segregation in long-chain/short-chain blends demonstrate the general utility of this technique.
A Research Agenda for Helminth Diseases of Humans: Intervention for Control and Elimination (2012)

Recognising the burden helminth infections impose on human populations, and particularly the poor, major intervention programmes have been launched to control onchocerciasis, lymphatic filariasis, soil-transmitted helminthiases, schistosomiasis, and cysticercosis. The Disease Reference Group on Helminth Infections (DRG4), established in 2009 by the Special Programme for Research and Training in Tropical Diseases (TDR), was given the mandate to review helminthiases research and identify research priorities and gaps. A summary of current helminth control initiatives is presented and available tools are described. Most of these programmes are highly dependent on mass drug administration (MDA) of anthelmintic drugs (donated or available at low cost) and require annual or biannual treatment of large numbers of at-risk populations, over prolonged periods of time. The continuation of prolonged MDA with a limited number of anthelmintics greatly increases the probability that drug resistance will develop, which would raise serious problems for continuation of control and the achievement of elimination. Most initiatives have focussed on a single type of helminth infection, but recognition of co-endemicity and polyparasitism is leading to more integration of control. An understanding of the implications of control integration for implementation, treatment coverage, combination of pharmaceuticals, and monitoring is needed. To achieve the goals of morbidity reduction or elimination of infection, novel tools need to be developed, including more efficacious drugs, vaccines, and/or antivectorial agents, new diagnostics for infection and assessment of drug efficacy, and markers for possible anthelmintic resistance. In addition, there is a need for the development of new formulations of some existing anthelmintics (e.g., paediatric formulations). To achieve ultimate elimination of helminth parasites, treatments for the above mentioned helminthiases, and for taeniasis and food-borne trematodiases, will need to be integrated with monitoring, education, sanitation, access to health services, and where appropriate, vector control or reduction of the parasite reservoir in alternative hosts. Based on an analysis of current knowledge gaps and identification of priorities, a research and development agenda for intervention tools considered necessary for control and elimination of human helminthiases is presented, and the challenges to be confronted are discussed.
Jointly Attacking Graph Neural Network and its Explanations (2023)

Graph Neural Networks (GNNs) have boosted the performance for many graph-related tasks. Despite the great success, recent studies have shown that GNNs are still vulnerable to adversarial attacks, where adversaries can mislead the GNNs' prediction by modifying graphs. On the other hand, the explanation of GNNs (GnnExplainer for short) provides a better understanding of a trained GNN model by generating a small subgraph and features that are most influential for its prediction. In this paper, we first perform empirical studies to validate that GnnExplainer can act as an inspection tool and have the potential to detect the adversarial perturbations for graphs. This finding motivates us to further investigate a new problem: Whether a graph neural network and its explanations can be jointly attacked by modifying graphs with malicious desires? It is challenging to answer this question since the goals of adversarial attack and bypassing the GnnExplainer essentially contradict with each other. In this work, we give a confirmative answer for this question by proposing a novel attack framework (GEAttack) for graphs, which can attack both a GNN model and its explanations by exploiting their vulnerabilities simultaneously. To the best of our knowledge, this is the very first effort to attack both GNNs and explanations on graph-structured data for the trustworthiness of GNNs. Comprehensive experiments on various real-world datasets demonstrate the effectiveness of the proposed method.