gebhart/patrepeval huggingface dataset:
Identifying scalability bottlenecks for large-scale parallel programs with graph analysis (2020)

Scaling a parallel program to modern supercomputers is challenging due to inter-process communication, code serialization, and resource contention. Performance analysis tools for finding such scaling bottlenecks either base on profiling or tracing. Profiling incurs lower overheads but does not capture detailed dependencies needed for root-cause analyses. Tracing collects all information at prohibitive overheads. In this work, we develop ScalAna that uses static analysis techniques to achieve the best of both worlds---it enables the analyzability of traces at a cost similar to profiling. We leverage compiler and runtime lightweight techniques to generate performance graph and perform graph analysis algorithm to detect the root cause of scaling issues. We evaluate ScalAna with real applications on the Tianhe-2 supercomputer. Results show that our approach can effectively locate the root cause of scalability bottlenecks for real applications and incur less than 6.38% overhead (1.89% on average) for up to 2,048 processes.
Monte Carlo simulation of mercury cadmium telluride (1994)

Mercury Cadmium Telluride (MCT) has a very large electron mobility and exhibits a non-ohmic behavior in relatively small electric fields. The goal of this project was to reach the understanding of electron transport properties of narrow band gap semiconductors, with emphasis on high-field behavior. Even though the primary material of interest was Mercury Cadmium Telluride (MCT), but we also investigated Indium Antimonide. Researchers derived expressions for scattering rates for electrons in Mercury Cadmium Telluride which accounted for correct wave functions for narrow band gap materials, and performed the Monte- Carlo simulation of Hg(0.205)Cd(0.795)Te at 77K for different doping levels.
Chalcopyrite dissolution in cupric chloride solutions (2009)

Hydrometallurgical technology offers the possibility of processing low-grade or small copper ore bodies and concentrates economically. Chloride solutions have become of great interest, having high leaching kinetics and no passivation of sulfide minerals. This thesis presents an investigation of chalcopyrite (CuFeS2) dissolution in cupric chloride solutions. Firstly, the formation and composition of reaction product layers formed on chalcopyrite were studied. Secondly, the rate-controlling step in chalcopyrite dissolution was defined and thirdly, the prevailing cupric and cuprous species were observed. Electrochemical methods, such as anodic and cathodic polarization, potentiostatic measurements, redox measurements, and electrochemical impedance spectroscopy (EIS) were applied. In addition, stereo-optical microscopy and scanning electron microscopy (SEM) as well as thermodynamic software HSC 5.11/6.1 were used. The solution used had sodium chloride concentrations in the range 250 - 280 g/l, cupric ion concentrations were 0.9 - 40 g/l. The temperature was set to be 70 - 95 °C and the pH values were in the range of 1 - 3. &#13;\n The thesis focuses on studying the reaction product layer on chalcopyrite. Color, thickness and the resistance of reaction product layers in the solid - solution interface were determined as a function of time from 0 to 22 hours at pHs 1, 2 and 3. The results suggested that sulfur was present at all times and pHs in the reaction product layers. At pH 1, elemental sulfur was the main phase forming the reaction product layer. This gray colored, porous, and easily removable layer grew to a thickness of 9 µm within 22 hours. The elemental sulfur layer appeared to decrease the rate of the chemical dissolution reaction. By increasing the pH from 1 to 3 and by increasing the dissolution time, the formation of FeOOH became more dominant. At pH 2, the formation of FeOOH was observed after 3 hours and at pH 3 at all leaching times. The co-precipitation of FeOOH was favorable for chalcopyrite dissolution, shifting the dissolution equilibrium to the right. It was determined that the dissolution of a stationary chalcopyrite sample was controlled by diffusion in the reaction product layer at pH 3, changing to chemical rate control at pH 1. FeOOH formation, in addition to the elemental sulfur, favored chalcopyrite dissolution. &#13;\n In concentrated cupric chloride solutions, cupric ions were assumed to be at least partially not in a chloro-complex form, whereas cuprous ions readily form complexes in chloride solutions. However, cuprous ions were determined not to be chloro-complexed at significantly low cuprous concentrations, in the order of 10-13 - 10-17 mol/m³. This was based on the determined Eo value of 0.158 V ± 0.121 V vs. SHE, which is typical for redox couples having cuprous ion not in a chloro-complex form.
Personalized Privacy-Preserving Data Aggregation for Histogram Estimation (2015)

Histogram estimation is one of the fundamental tasks in crowdsourcing data aggregation. Since contributing data reveal more or less information about individuals' identifications and activities, participants need to preserve privacy of data according to their own levels of privacy concern. However, most of the existing work only aggregates data with an identical privacy level. In this paper, we propose an aggregation scheme for histogram estimation, wherein participants can publish their data at personalized differential-privacy levels. The aggregator also benefits from potential wider engagement or more honest data. Specially, since privacy levels under personalized privacy policy are sensitive information for participants, our scheme permits participants to keep their privacy levels secret even from the aggregator. We also show how to further optimize the estimation accuracy under given privacy levels by choosing specific randomization strategies.
Document-Level N-ary Relation Extraction with Multiscale Representation Learning (2019)

Robin Jia, Cliff Wong, Hoifung Poon. Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long and Short Papers). 2019.
Radiotracers and Drug Registration (2006)

This chapter outlines studies to determine a drug’s metabolism which are conducted separately from the clinical studies. It presents the timing of drug metabolism studies. The use of radiotracers is only one tool of many used by the pharmaceuticals industry in the science-driven drug registration process. Before embarking on the subject of radiotracers, however, it is worth setting the scene with a general overview of the various stages of drug registration. How radiotracers are applied to this process can be placed into context. Without radiotracers, the elucidation of many biochemical pathways would have been extremely difficult, if not impossible. Radiotracers are used to follow the metabolic fate of a drug through a test system where otherwise it would be difficult or impossible to distinguish the drug from its surroundings. For convenience, regulatory drug testing programs that utilize radiotracers can be divided into two groups: standard studies and explorative studies.
Joint Learning of Vessel Segmentation and Artery/Vein Classification with Post-processing (2020)

Retinal imaging serves as a valuable tool for diagnosis of various diseases. However, reading retinal images is a difficult and time-consuming task even for experienced specialists. The fundamental step towards automated retinal image analysis is vessel segmentation and artery/vein classification, which provide various information on potential disorders. To improve the performance of the existing automated methods for retinal image analysis, we propose a two-step vessel classification. We adopt a UNet-based model, SeqNet, to accurately segment vessels from the background and make prediction on the vessel type. Our model does segmentation and classification sequentially, which alleviates the problem of label distribution bias and facilitates training. To further refine classification results, we post-process them considering the structural information among vessels to propagate highly confident prediction to surrounding vessels. Our experiments show that our method improves AUC to 0.98 for segmentation and the accuracy to 0.92 in classification over DRIVE dataset.
Roaming Dynamics in Formaldehyde-d2 Dissociation (2009)

State-resolved photodissociation dynamics of formaldehyde-d(2), i.e., D(2)CO, at energies slightly above the deuterium atom elimination channel have been studied both experimentally and theoretically. The results showed a clear bimodal distribution of energy into molecular photofragments. Substantial translational excitation of products at high rotational levels of CO was observed together with the D(2) cofragment in moderately excited vibrational levels, whereas rather small translational energy release of CO in low rotational levels was matched by a large degree of vibrational excitation in the D(2) molecule. An analogous distribution of energy in two distinct channels has been recently observed under similar conditions in H(2)CO photolysis and attributed to two different dissociation pathways, namely, a pathway via the conventional transition state geometry and the previously unobserved pathway, deemed "roaming". Our experimental and theoretical data indicated that the same two dissociation pathways were responsible for the bimodal energy distribution into the molecular fragments resulting from the photolysis of D(2)CO. Energy partitioning into molecular products was compared between photolysis of H(2)CO and D(2)CO at energies slightly above the H/D atom abstraction threshold.
Proteomics Analysis of CA1 Region of the Hippocampus in Pre-, Progression and Pathological Stages in a Mouse Model of the Alzheimer’s Disease (2019)

We conclude that CA1 region-specific proteomic analysis of hippocampal degeneration may be useful in identifying the earliest as well as progressional changes that are associated with Alzheimer's disease.
Subspace-based estimation of multipath channel parameters for CDMA communication systems (2002)

Considers the estimation of multipath channel parameters to exploit time diversity in asynchronous code division multiple access communication systems. The multiuser channel estimation problem is decomposed into a series of single user problems through a subspace-based approach using the sample correlation matrix of the received signal. The authors estimate the channel impulse response associated with a given user by choosing filter coefficients that minimize the projection of the filtered spreading waveform into the estimated noise subspace. They then perform a least-squares fit of a parametric channel model to this unconstrained estimate to extract the desired channel coefficients. This method requires no training sequence, is near-far resistant, and is robust to changing channel conditions.
An Investigation into the Influence of Counterion on the Properties of Some Amorphous Organic Salts (2008)

Amorphous solids and crystalline salts are both of interest as a means of improving the dissolution characteristics and apparent solubility of poorly water soluble active pharmaceutical ingredients which have low bioavailability in humans. The theory and selection of both crystalline drug substance salt forms and amorphous products have been extensively studied. However, less is known about the impact of different counterions on the properties of amorphous drug substance salts. In this study, several salts of either nicardipine or propranolol were prepared and characterized with respect to glass transition temperature, crystallization tendency and moisture sorption behavior. Although the moisture sorption behavior and crystallization tendency varied depending on the counterion used, no trends were readily apparent. The glass transition temperature was found to be dependent on the counterion used to form the salt, and was higher in all instances for the salts than for the neutral compound. Several molecular descriptors were calculated for the various counterions, and multivariate analysis was used to build a model that successfully correlated Tg with a number of these parameters. Important parameters which influenced Tg included counterion pKa and electrophilicity index. In conclusion, it is apparent that, as for crystalline salts, the counterion has an effect on the properties of amorphous materials.
Mitogen-induced changes in Ca2+ permeability are not mediated by voltage-gated K+ channels. (1986)

Binding of mitogenic lectins to T lymphocytes results in elevated cytoplasmic Ca2+ concentrations ([Ca2+]i). This change in [Ca2+]i is thought to be essential for cellular proliferation. In addition, the lectins increase the conductance to K+ through voltage-sensitive channels. Based on the inhibitory effect of K+ channel blockers on lectin-induced mitogenesis, it has been suggested that Ca2+ could enter the cells through these activated K+ channels (Chandy, K. G., De Coursey, T. E., Cahalan, M. D., McLaughlin, C., and Gupta, S. (1984) J. Exp. Med. 160, 369-385; Chandy, K. G., De Coursey, T. E., Cahalan, M. D., and Gupta, S. (1985) J. Clin. Immunol. 5, 1-5). This hypothesis was tested experimentally by measuring the effect of activation or blockade of K+ channels on [Ca2+]i using quin-2 and indo-1 and by determining the effect of K+ channel blockers on lectin-induced proliferation. We found that: depolarization of the membrane, which is expected to open the K+ channels, failed to increase [Ca2+]i, K+ channel blockers such as tetraethylammonium and 4-aminopyridine had only a marginal effect on the lectin-induced increase in [Ca2+]i, and the inhibitory effect of K+ channel blockers on proliferation was found to be nonspecific, occurring also when proliferation was triggered by phorbol esters under conditions where [Ca2+]i is not elevated. It is concluded that the lectin-induced changes in [Ca2+]i are not mediated by the opening of voltage-gated K+ channels.
Controlling opioid receptor functional selectivity by targeting distinct subpockets of the orthosteric site (2021)

Controlling receptor functional selectivity profiles for opioid receptors is a promising approach for discovering safer analgesics; however, the structural determinants conferring functional selectivity are not well understood. Here, we used crystal structures of opioid receptors, including the recently solved active state kappa opioid complex with <b>MP1104</b>, to rationally design novel mixed mu (MOR) and kappa (KOR) opioid receptor agonists with reduced arrestin signaling. Analysis of structure-activity relationships for new <b>MP1104</b> analogs points to a region between transmembrane 5 (TM5) and extracellular loop (ECL2) as key for modulation of arrestin recruitment to both MOR and KOR. The lead compounds, <b>MP1207 and MP1208,</b> displayed MOR/KOR Gi-partial agonism with diminished arrestin signaling, showed efficient analgesia with attenuated liabilities, including respiratory depression and conditioned place preference and aversion in mice. The findings validate a novel structure-inspired paradigm for achieving beneficial in vivo profiles for analgesia through different mechanisms that include bias, partial agonism, and dual MOR/KOR agonism.
Comment on “Characterizing the N-Terminal Processing Motif of MHC Class I Ligands” (2008)

In a recent article, Schatz et al. ([1][1]) characterized the N-terminal processing motif of MHC class I ligands. They demonstrated that this motif comprised approximately seven residues that matched the known preferences of proteasome and TAP, consistent with the view that these peptide ligands are
Anticonvulsant Action of GABA in the High Potassium–Low Magnesium Model of Ictogenesis in the Neonatal Rat Hippocampus In Vivo and In Vitro (2005)

Previous developmental studies in vitro suggested that the inhibitory neurotransmitter GABA exerts depolarizing and excitatory actions on the immature neurons and that depolarizing GABA is causally linked to ictal activity during the first weeks of postnatal life. However, remarkably little is known on the role of GABA in the generation of neonatal seizures in vivo. Here, using extracellular recordings from CA3 hippocampus, we studied the effects of GABA(A)-acting drugs on electrographic seizures induced by local intrahippocampal injection of the epileptogenic agents (high K(+)/low Mg(2+)) in the nonanesthetized rats in vivo and in the hippocampal slices in vitro during the second postnatal week (postnatal days P8-12). We found that in vivo, the induction of ictal-like events was facilitated by co-infusion of high-K(+)/low Mg(2+) together with the GABA(A) antagonist bicuculline or gabazine. Moreover, the infusion of bicuculline alone caused ictal-like activity in approximately 30% of cases. Co-infusion of the GABA(A) receptor agonist isoguvacine or the GABA(A)-positive allosteric modulator diazepam completely prevented high-K(+)/low Mg(2+)-induced seizures. In in vitro studies using hippocampal slices, we also found that high-K(+)/low Mg(2+) produced ictal activity that was exacerbated by bicuculline and gabazine and reduced by isoguvacine. Thus in the model of high-K(+)/low Mg(2+)-induced seizures both in in vivo and in vitro conditions, GABA, acting via GABA(A) receptors, has an anticonvulsant effect during the critical developmental period of enhanced excitability.
Enhancing the Performance and Fairness of Shared DRAM Systems with Parallelism-Aware Batch Scheduling (2008)

In a chip-multiprocessor (CMP) system, the DRAM system is shared among cores. In a shared DRAM system, requests from a thread can not only delay requests from other threads by causing bank/bus/row-buffer conflicts but they can also destroy other threads ’ DRAM-bank-level parallelism. Requests whose latencies would otherwise have been overlapped could effectively become serialized. As a result both fairness and system throughput degrade, and some threads can starve for long time periods. This paper proposes a fundamentally new approach to designing a shared DRAM controller that provides quality of service to threads, while also improving system throughput. Our parallelism-aware batch scheduler (PAR-BS) design is based on two key ideas. First, PAR-BS processes DRAM requests in batches to provide fairness and to avoid starvation of requests. Second, to optimize system throughput, PAR-BS employs a parallelism-aware DRAM scheduling policy that aims to process requests from a thread in parallel in the DRAM banks, thereby reducing the memory-related stall-time experienced by the thread. PAR-BS seamlessly incorporates support for system-level thread priorities and can provide different service levels, including purely opportunistic service, to threads with different priorities. We evaluate the design trade-offs involved in PAR-BS and compare it to four previously proposed DRAM scheduler designs on 4-, 8-, and 16-core systems. Our evaluations show that, averaged over 100 4-core workloads, PAR-BS improves fairness by 1.11X and system throughput by 8.3 % compared to the best previous scheduling technique, Stall-Time Fair Memory (STFM) scheduling. Based on simple request prioritization rules, PAR-BS is also simpler to implement than STFM. 1.
Severity of neurological signs and degree of inflammatory lesions in the brains of rats with Borna disease correlate with the induction of nitric oxide synthase (1993)

The putative role of nitric oxide in the neuropathogenesis of Borna disease was investigated by determining changes in the expression of inducible nitric oxide synthase (iNOS) mRNA and constitutively expressed NOS (cNOS) mRNA in brains of Borna disease virus (BDV)-infected rats. iNOS mRNA was not detected in normal rat brain but was identified in BDV-infected brain at 14 days postinfection (p.i.), reaching maximum levels at 21 days p.i., when neurological signs and inflammatory reactions in the brain were also at a peak. cNOS mRNA was expressed in both normal brain and infected brain, increasing markedly at 17 days p.i. and reaching a peak at 21 days p.i. In situ hybridization analysis revealed iNOS mRNA in some, but not all, BDV-infected regions of the brain, particularly in the basolateral cortex and the hippocampus. iNOS-positive cells, as identified immunohistologically, were preferentially localized in perivascular areas of the hippocampus and in outer cortical layers. These iNOS-positive cells resembled monocytes/macrophages in morphology and distribution pattern but were significantly fewer. The correlation of iNOS and cNOS mRNA expression with the development of neurological disease, as well as the enhanced expression of iNOS within brain regions with inflammatory lesions, strongly suggests that NO may contribute to pathogenesis of Borna disease.
Stable and High‐Efficiency Methylammonium‐Free Perovskite Solar Cells (2020)

Organic-inorganic metal halide perovskite solar cells (PSCs) have achieved certified power conversion efficiency (PCE) of 25.2% with complex compositional and bandgap engineering. However, the thermal instability of methylammonium (MA) cation can cause the degradation of the perovskite film, remaining a risk for the long-term stability of the devices. Herein, a unique method is demonstrated to fabricate highly phase-stable perovskite film without MA by introducing cesium chloride (CsCl) in the double cation (Cs, formamidinium) perovskite precursor. Moreover, due to the suboptimal bandgap of bromide (Br<sup>-</sup> ), the amount of Br<sup>-</sup> is regulated, leading to high power conversion efficiency. As a result, MA-free perovskite solar cells achieve remarkable long-term stability and a PCE of 20.50%, which is one of the best results for MA-free PSCs. Moreover, the unencapsulated device retains about 80% of the original efficiencies after a 1000 h aging study. These results provide a feasible approach to enhance solar cell stability and performance simultaneously, paving the way for commercializing PSCs.
Hierarchical analysis of options for lunar-surface power (1994)

A decision analysis study was conducted to evaluate potential habitat power concepts for manned lunar-surface operations. The objectives of the study were to rank alternative lunar-surface power systems for the first lunar outpost (FLO). The six alternative power concepts evaluated are the following: photovoltaic with regenerative fuel cell (RFC) storage, solar dynamic with RFC storage, TOPAZ 2 and SP-100 space reactor systems, dynamic isotope power system (DIPS), and laser-beamed power. The analytical hierarchy decision-making process was used for the decision-making methodology. The process provides a systematic approach to managing complex decisions that involve numerous tradeoffs between alternative concepts and evaluation criteria. Safety, risk, performance, lifetime, supportability, special factors, and versatility were selected as the major evaluation criteria. Based on the available information, DIPS was the power system of choice for a 45-day, 12-kWe FLO mission because of its favorable combination of ranking and cost. When launch costs were not considered, the photovoltaic system with RFC storage ranked first. The results of this study reflect the best judgments of the working group, given the set of requirements, the agreed-on set of selection criteria, and the best available concept information. 7 refs.