gebhart/patrepeval huggingface dataset:
EXPLORATION ON SCALABILITY OF DATABASE BULK INSERTION WITH MULTITHREADING (2011)

The advancement of database engine and multi-core processors technologies have enable database insertion to be implemented concurrently via multithreading programming. The objective of this work is to evaluate the performance of using multithreading technique to perform database insertion of large data set with known size to enhance the performance of data access layer (DAL) particularly on the bulk-insertion operation. The performance evaluation includes techniques such as using single database connection, multithreads the insertion process with respective database connections, single threaded bulk insertion and multithreaded bulk insertion. MySQL 5.2 and SQL Server 2008 were used and the experimental results show that the performance of databases do not scale linearly with the number of threads. This work justifies our intention in developing a smart data access layer that autonomously decides the number of threads to spawn in order to improve the performance of the
<scp>l</scp>-carnosine (<i>β</i>-alanyl-<scp>l</scp>-histidine) and carcinine (<i>β</i>-alanylhistamine) act as natural antioxidants with hydroxyl-radical-scavenging and lipid-peroxidase activities (1994)

Carnosine (beta-alanyl-L-histidine) and carcinine (beta-alanylhistamine) are natural imidazole-containing compounds found in the non-protein fraction of mammalian tissues. Carcinine was synthesized by an original procedure and characterized. Both carnosine and carcinine (10-25 mM) are capable of inhibiting the catalysis of linoleic acid and phosphatidylcholine liposomal peroxidation (LPO) by the O2(-.)-dependent iron-ascorbate and lipid-peroxyl-radical-generating linoleic acid 13-monohydroperoxide (LOOH)-activated haemoglobin systems, as measured by thiobarbituric-acid-reactive substance. Carcinine and carnosine are good scavengers of OH. radicals, as detected by iron-dependent radical damage to the sugar deoxyribose. This suggests that carnosine and carcinine are able to scavenge free radicals or donate hydrogen ions. The iodometric, conjugated diene and t.l.c. assessments of lipid hydroperoxides (13-monohydroperoxide linoleic acid and phosphatidylcholine hydroperoxide) showed their efficient reduction and deactivation by carnosine and carcinine (10-25 mM) in the liberated and bound-to-artificial-bilayer states. This suggests that the peroxidase activity exceeded that susceptible to direct reduction with glutathione peroxidase. Imidazole, solutions of beta-alanine, or their mixtures with peptide moieties did not show antioxidant potential. Free L-histidine and especially histamine stimulated iron (II) salt-dependent LPO. Due to the combination of weak metal chelating (abolished by EDTA), OH. and lipid peroxyl radicals scavenging, reducing activities to liberated fatty acid and phospholipid hydroperoxides, carnosine and carcinine appear to be physiological antioxidants able to efficiently protect the lipid phase of biological membranes and aqueous environments.
Mutation of a putative ADP‐ribosylation motif in the <i>Pasteurella multocida</i> toxin does not affect mitogenic activity (1994)

Pasteurella multocida toxin (PMT) is a potent mitogen for Swiss 3T3 fibroblasts and cytotoxic to embryonic bovine lung cells. Site-directed mutagenesis was used to investigate the functional significance of a three amino acid motif in PMT that is present in five other bacterial protein toxins which exhibit ADP-ribosyl transferase activity. Crude lysates of mutant clones were fully cytotoxic for embryonic bovine lung cells. Purified mutant toxin was also as effective at stimulating inositol phosphate turnover and nucleic acid synthesis as wild type toxin. We conclude that this motif has no functional significance in Pasteurella multocida toxin.
T2-Weighted 4D Magnetic Resonance Imaging for Application in Magnetic Resonance–Guided Radiotherapy Treatment Planning (2017)

A methodology to obtain 4D-T2w MRI that retrospectively applies the motion information from 4D-T1w MRI to 3-dimensional T2w MRI was developed and verified. Four-dimensional T2w MRI can assist clinicians in delineating mobile lesions that are difficult to define on 4D-T1w MRI, because of poor tumor-tissue contrast.
AN ANALYSIS OF THE ASSOCIATION FOR COMPUTING MACHINERY (ACM) CODE OF ETHICS (2003)

As the Association for Computing Machinery (ACM) Code of Ethics has an important guiding role in embedding ethics into computing practice, both in the United States and around the globe, its content is important. This paper considers a way of analyzing the Code into ethical categories, inspired by a soft systems 'rich picture' Information Systems (IS) framework. A list of seven stakeholder categories, together with the major components of applied ethical theory, are used to map the elements of the ACM Code. While such an analysis is imprecise due to human interpretation, so also is the art of applied ethics. Yet, by framing the ACM Code according to stakeholder roles and basic ethical analysis tools, the ACM Code of Ethics becomes more useful in various ways. Overlaps and gaps can be identified, various interpretations of word meanings can be more easily identified and debated, and, perhaps, most importantly in the global ethical arena, a better comparison of the ACM with other codes of ethics is facilitated.
On Trees, Chains and Fast Transactions in the Blockchain. (2016)

A fundamental open problem in the area of blockchain protocols is whether the Bitcoin protocol is the only solution for building a secure transaction ledger. A recently proposed and widely considered alternative is the \GHOST protocol which, notably, was proposed to be at the core of Ethereum as well as other recent proposals for improved Bitcoin-like systems. % The \GHOST variant is touted as offering superior performance compared to Bitcoin (potentially offering block production speed up by a factor of more than 40) without a security loss. Motivated by this, in this work, we study from a provable security point of view the \GHOST protocol.<br/><br/>We introduce a new formal framework for the analysis of blockchain protocols that relies on trees (rather than chains) and we showcase the power of the framework by providing a unified description of the \GHOST and Bitcoin protocols, the former of which we extract and formally describe. We then prove that \GHOST implements a ``robust transaction ledger'' (i.e., possesses liveness and persistence) and hence it is a provably secure alternative to Bitcoin; moreover, our bound for the liveness parameter is superior to that proven for the bitcoin backbone in line with the original expectation for \GHOST. Our proof follows a novel methodology for establishing that \GHOST is a robust transaction ledger compared to previous works, which may be of independent interest and can be applicable to other blockchain variants.
Stream Processor Architecture (2001)

Stream Processor Architecture presents the architecture of the Imagine streaming media processor, which delivers a peak performance of 20 billion floating-point operations per second. Imagine efficiently supports 48 arithmetic units with a three-tiered data bandwidth hierarchy. At the base of the hierarchy, the streaming memory system employs memory access scheduling to maximize the sustained bandwidth of external DRAM. At the center of the hierarchy, the global stream register file enables streams of data to be recirculated directly from one computation kernel to the next without returning data to memory. Finally, local distributed register files that directly feed the arithmetic units enable temporary data to be stored locally so that it does not need to consume costly global register bandwidth. The bandwidth hierarchy enables Imagine to achieve up to 96% of the performance of a stream processor with infinite bandwidth from memory and the global register file.
High stability of self‐assembled peptide nanowires against thermal, chemical, and proteolytic attacks (2009)

Understanding the self-assembly of peptides into ordered nanostructures is recently getting much attention since it can provide an alternative route for fabricating novel bio-inspired materials. In order to realize the potential of the peptide-based nanofabrication technology, however, more information is needed regarding the integrity or stability of peptide nanostructures under the process conditions encountered in their applications. In this study, we investigated the stability of self-assembled peptide nanowires (PNWs) and nanotubes (PNTs) against thermal, chemical, proteolytic attacks, and their conformational changes upon heat treatment. PNWs and PNTs were grown by the self-assembly of diphenylalanine (Phe-Phe), a peptide building block, on solid substrates at different chemical atmospheres and temperatures. The incubation of diphenylalanine under aniline vapor at 150 degrees C led to the formation of PNWs, while its incubation with water vapor at 25 degrees C produced PNTs. We analyzed the stability of peptide nanostructures using multiple tools, such as electron microscopy, thermal analysis tools, circular dichroism, and Fourier-transform infrared spectroscopy. Our results show that PNWs are highly stable up to 200 degrees C and remain unchanged when incubated in aqueous solutions (from pH 1 to 14) or in various chemical solvents (from polar to non-polar). In contrast, PNTs started to disintegrate even at 100 degrees C and underwent a conformational change at an elevated temperature. When we further studied their resistance to a proteolytic environment, we discovered that PNWs kept their initial structure while PNTs fully disintegrated. We found that the high stability of PNWs originates from their predominant beta-sheet conformation and the conformational change of diphenylalanine nanostructures. Our study suggests that self-assembled PNWs are suitable for future nano-scale applications requiring harsh processing conditions.
Reactive Oxygen and Reactive Nitrogen Metabolites as Effector Molecules against Infectious Pathogens (2014)

This chapter focuses on the sources, the regulation, the spectrum of activities, and the viral and microbial targets of reactive oxygen intermediates (ROIs) and reactive nitrogen intermediates (RNIs) generated by mammalian host cells. With respect to the control of infectious agents, the two most important oxygen-dependent pathways for the generation of antiviral or antimicrobial effector molecules are the phagocyte NADPH oxidase (Phox) and the inducible nitric oxide synthase (iNOS) pathways. One of the most intriguing discoveries in the field of ROIs in recent years was the observation by Wentworth and colleagues that antibodies, independent of their source or antigen specificity, can catalyze the generation of ROIs. Members of all groups of infectious pathogens (viruses, bacteria, protozoa, helminths, and fungi) were found to be controlled by RNIs. The significant improvement of certain infectious diseases after inhibition or genetic deletion of iNOS, which was without negative effects on the pathogen clearance, was unexpected. It can be explained by the inhibition of T-cell proliferation or induction of T-cell apoptosis via iNOS-positive suppressor cells (macrophages and dendritic cells) or by the tissue-damaging properties of RNIs. Transgenic mouse models have been extremely helpful to elucidate the relative contributions of ROIs and RNIs for the control of infectious pathogens. Viruses, bacteria, parasites, and fungi have developed multiple strategies to evade killing by oxygen-dependent effector mechanisms. Current research projects aim at the development of ROI or RNI precursors that enter only certain types of host cells and are activated by the infectious pathogens themselves.
Raised interleukin-10 is an indicator of poor outcome and enhanced systemic inflammation in patients with acute coronary syndrome (2007)

In contrast with some previous reports, we conclude that IL-10 reflects a proinflammatory state in patients with ACS and we therefore suggest that IL-10 is as effective a biomarker for the risk prediction of future cardiovascular events as other markers of systemic inflammation.
Impact Analysis of SARS-CoV2 on Signaling Pathways during COVID19 Pathogenesis using Codon Usage Assisted Host-Viral Protein Interactions (2020)

Abstract Understanding the molecular mechanism of COVID19 disease pathogenesis helps in the rapid development of therapeutic targets. Usually, viral protein targets host proteins in an organized fashion. The pathogen may target cell signaling pathways to disrupt the pathway genes’ regular activities, resulting in disease. Understanding the interaction mechanism of viral and host proteins involved in different signaling pathways may help decipher the attacking mechanism on the signal transmission during diseases, followed by discovering appropriate therapeutic solutions. The expression of any viral gene depends mostly on the host translational machinery. Recent studies report the great significance of codon usage biases in establishing host-viral protein-protein interactions (PPI). Exploiting the codon usage patterns between a pair of co-evolved host and viral proteins may present novel insight into the host-viral protein interactomes during disease pathogenesis. Leveraging the codon usage pattern similarity (and dissimilarity), we propose a computational scheme to recreate the hostviral protein interaction network (HVPPI). We use seventeen (17) essential signaling pathways for our current work and study the possible targeting mechanism of SARS-CoV2 viral proteins on such pathway proteins. We infer both negatively and positively interacting edges in the network. We can find a relationship where one host protein may target by more than one viral protein. Extensive analysis performed to understand the network topologically and the attacking behavior of the viral proteins. Our study reveals that viral proteins, mostly utilize codons, rare in the targeted host proteins (negatively correlated interaction). Among non-structural proteins, NSP3 and structural protein, Spike (S) protein, are the most influential proteins in interacting multiple host proteins. In ranking the most affected pathways, MAPK pathways observe to be worst affected during the COVID-19 disease. A good number of targeted proteins are highly central in host protein interaction networks. Proteins participating in multiple pathways are also highly connected in their own PPI and mostly targeted by multiple viral proteins.
Evidence for stereospecific collision complexes of cyclo(tri‐<scp>L</scp>‐prolyl) with benzene (1972)

Abstract NMR spectra of cyclo(tri‐ L ‐prolyl), c‐(P) 3 , show large shifts of the H α resonance on adding C 6 D 6 to a solution of c‐(P) 3 in CD 2 Cl 2 . CPK models and observed coupling constants indicate a rigid c‐(P) 3 conformation, independent of solvent composition, suggesting that these shifts result from formation of stereospecific C 6 D 6 –c‐(P) 3 collision complexes in which the c‐(P) 3 H α lie near the face of the aromatic ring. The temperature dependence of the H α shifts and the solvent dependent shifts observed on adding toluene‐ d 8 or nitrobenzene‐ d 5 to the c‐(P) 3 solution suggest that preferred C 6 D 6 –c‐(P) 3 orientations result from attractive interactions between the electron‐rich aromatic ring and the electropositive H α 's and/or δ + nitrogen atoms in the peptide backbone. Reports of such interactions in increasingly diverse peptide model systems suggest that they may play a role in stabilizing protein structures.
Sensor Validation using Bayesian Networks (2018)

One of NASA’s key mission requirements is robust state estimation. Sensing, using a wide range of sensors and sensor fusion approaches, plays a central role in robust state estimation, and there is a need to diagnose sensor failure as well as component failure. Sensor validation techniques address this problem: given a vector of sensor readings, decide whether sensors have failed, therefore producing bad data. We take in this paper a probabilistic approach, using Bayesian networks, to diagnosis and sensor validation, and investigate several relevant but slightly different Bayesian network queries. We emphasize that onboard inference can be performed on a compiled model, giving fast and predictable execution times. Our results are illustrated using an electrical power system, and we show that a Bayesian network with over 400 nodes can be compiled into an arithmetic circuit that can correctly answer queries in less than 500 microseconds on average.
Evidence of Dislocation Jogs in Deformed Silicon (1958)

Trails extending from dislocations in plastically deformed silicon have been observed by decoration and also by an etching technique which develops channels on a {111} plane. The trails extending from screws tend to follow parallel &lt;110&gt; directions; those from mixed edge and screw dislocations are generally not crystallographic. Cusps occur where the trails are joined to the dislocations. A type of work hardening is found wherein trails from one turn of a Frank-Read spiral obstruct the motion of subsequent turns. Trails are sometimes segmented or zig-zag and appear to be composed of small discrete sections. Reversal of the direction of motion of a dislocation when the applied stress is removed is indicated by inversion of cusps. The main features of these trails can be accounted for on the basis of nonconservative motion of jogs which inject vacancies or interstitial atoms into their paths.
Heat transfer in foam insulation (1983)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1983.
N-terminal truncation mutagenesis of equinatoxin II, a pore-forming protein from the sea anemone Actinia equina (1997)

The role of the N-terminal segment 1-33 of equinatoxin II, a 20 kDa pore-forming protein from the sea anemone Actinia equina, was studied by N-truncation mutagenesis. A part of this segment was classified as being amphiphilic and membrane seeking. Wild-type equinatoxin II and its mutants lacking 5, 10 and 33 amino acid residues, respectively, were produced in Escherichia coli using T7 RNA polymerase-based expression vector. Soluble recombinant proteins were isolated from bacterial lysates and assayed for their inhibition by sphingomyelin, binding to red blood cells and hemolytic activity. The N-terminal deletion of 33 amino acids resulted in an insoluble protein, while mutants lacking 5 and 10 residues expressed increased relative avidity for sphingomyelin and red blood cell membranes. Their specific hemolytic activity was decreased, however, with increasing truncation. The results suggest that the N-terminus, which has been found to be conserved in sea anemone pore-forming toxins, contributes to the solubility of the equinatoxin II, but it is not essential for binding to lipid membranes. It is very likely that the N-terminus play a role in the formation of functional pores.
Caspase 3 inhibition attenuates hydrogen peroxide‐induced DNA fragmentation but not cell death in neuronal PC12 cells (2001)

Exposure of neurons to H(2)O(2) results in both necrosis and apoptosis. Caspases play a pivotal role in apoptosis, but exactly how they are involved in H(2)O(2)-mediated cell death is unknown. We examined H(2)O(2)-induced toxicity in neuronal PC12 cells and the effects of inducible overexpression of the H(2)O(2)-scavenging enzyme catalase on this process. H(2)O(2) caused cell death in a time- and concentration-dependent manner. Cell death induced by H(2)O(2) was found to be mediated in part through an apoptotic pathway as H(2)O(2)-treated cells exhibited cell shrinkage, nuclear condensation and marked DNA fragmentation. H(2)O(2) also triggered activation of caspase 3. Genetic up-regulation of catalase not only significantly reduced cell death but also suppressed caspase 3 activity and DNA fragmentation. While the caspase 3 inhibitor DEVD inhibited both caspase 3 activity and DNA fragmentation induced by H(2)O(2) it did not prevent cell death. Treatment with the general caspase inhibitor ZVAD, however, resulted in complete attenuation of H(2)O(2)-mediated cellular toxicity. These results suggest that DNA fragmentation induced by H(2)O(2) is attributable to caspase 3 activation and that H(2)O(2) may be critical for signaling leading to apoptosis. However, unlike inducibly increased catalase expression and general caspase inhibition both of which protect cells from cytotoxicity, caspase 3 inhibition alone did not improve cell survival suggesting that prevention of DNA fragmentation is insufficient to prevent H(2)O(2)-mediated cell death.
Studies on overwintering of bluetongue viruses in insects (2005)

Bluetongue viruses (BTVs) are economically important arboviruses that affect sheep and cattle. The overwintering mechanism of BTVs in temperate climates has eluded researchers for many years. Many arboviruses overwinter in their invertebrate vectors. To test the hypothesis that BTVs overwinter in their vertically infected insect vectors, Culicoides sonorensis larvae were collected from long-term study sites in northern Colorado, USA, and assayed for the presence of BTV RNA by nested RT-PCR. Sequences from BTV RNA segment 7 were detected in 30 % (17/56) of pools composed of larvae and pupae collected in 1998 and in 10 % (31/319) of pools composed of adults reared from larvae collected in 1996. BTV was not isolated from the insects. Additionally, Culicoides cell-culture lines derived from material collected at one of the sites, or derived from insect samples collected during a BTV outbreak, contained BTV RNA segment 7. In contrast, segment 2 RNA was detected at half the rate of segment 7 RNA in the field-collected larvae and was only detected in the Culicoides cell lines with one of two primer sets. These data suggest that BTVs could overwinter in the insect vector and that there is reduced expression of the outer capsid genes during persistent infection.
Ectopic production of intact parathyroid hormone by a squamous cell lung carcinoma in vivo and in vitro. (1996)

Ectopic tumoral production of intact parathyroid hormone (PTH) is rare. The PTH-related protein is the common cause of hypercalcemia in most solid tumors, particularly squamous and renal carcinomas. We report the case of a 71-yr-old man with a PTH-producing squamous cell lung carcinoma. Immunocytochemical analysis of the tumor tissue as well as of cultured tumor cells revealed PTH positive staining. Cultured tumor cells released PTH and were calcium sensitive, producing 122 +/- 16 pg/microgram DNA of intact PTH (mean +/- SEM) at 0.5 mmol/L calcium compared with 26 +/- 2 pg/microgram DNA at 3.0 mmol/L calcium. Somatostatin analogues have been used in the treatment of humoral hypercalcemia of malignancy (HHM). However, we found that somatostatin (0.1 microgram/L) in cultured tumor cells increased the release of intact PTH (123 +/- 19 versus 82 +/- 1 pg/microgram DNA, P < 0.05) and thus might have a negative effect on the HHM. This report is the first to describe a true ectopic PTH-producing squamous cell lung carcinoma associated with HHM.