gebhart/patrepeval huggingface dataset:
Triage (2007)

Diagnosing production run failures is a challenging yet importanttask. Most previous work focuses on offsite diagnosis, i.e.development site diagnosis with the programmers present. This is insufficient for production-run failures as: (1) it is difficult to reproduce failures offsite for diagnosis; (2) offsite diagnosis cannot provide timely guidance for recovery or security purposes; (3)it is infeasible to provide a programmer to diagnose every production run failure; and (4) privacy concerns limit the release of information(e.g. coredumps) to programmers. To address production-run failures, we propose a system, called Triage , that automatically performs onsite software failure diagnosis at the very moment of failure. It provides a detailed diagnosis report, including the failure nature, triggering conditions, related code and variables, the fault propagation chain, and potential fixes. Triage achieves this by leveraging lightweight reexecution support to efficiently capture the failure environment and repeatedly replay the moment of failure, and dynamically--using different diagnosis techniques--analyze an occurring failure. Triage employs afailure diagnosis protocol that mimics the steps a human takes in debugging. This extensible protocol provides a framework to enable the use of various existing and new diagnosis techniques. We also propose a new failure diagnosis technique, delta analysis , to identify failure related conditions, code, and variables. We evaluate these ideas in real system experiments with 10 real software failures from 9 open source applications including four servers. Triage accurately diagnoses the evaluated failures, providing likely root causes and even the fault propagation chain, while keeping normal-run overhead to under 5%. Finally, our user study of the diagnosis and repair of real bugs shows that Triagesaves time (99.99% confidence), reducing the total time to fix by almost half.
Delivering Erythropoietin through Genetically Engineered Cells (2000)

Erythropoietin (Epo) is a glycoprotein hormone produced by genetic engineering. Many pathologic conditions could benefit from its administration, such as chronic renal failure or hemoglobinopathies. Epo secretion from genetically modified tissued could be proposed to patients only if the protocol is low cost and low risk. For that purpose, retroviral vectors and adeno-associated vectors expressing the Epo cDNA were developed. Gene transfer was performed into skeletal muscles. To avoid polycythemia, a tetracycline-regulated system was used to control the levels of protein secretion in vivo. beta-thalassemias are among diseases that could benefit from an Epo gene transfer. beta-thalassemias are attributable to deficient synthesis of beta-globin and accumulation of unpaired alpha-chains. Stimulation of fetal globin synthesis is one strategy to correct the globin chain imbalance. There is evidence that Epo could play this role. In a mouse model of beta-thalassemia, an adeno-associated vector expressing the Epo cDNA was injected intramuscularly. Epo was secreted continuously during at least 1 yr. Erythropoiesis was improved in those mice by increasing the synthesis of fetal hemoglobin.
16.3 A −246dB Jitter-FoM 2.4GHz Calibration-Free Ring-Oscillator PLL Achieving 9% Jitter Variation Over PVT (2019)

Low-jitter phase-locked loops (PLLs) are critical building blocks in various systems, including wireless and wireline communications and ADCs. LC oscillators exhibit low phase noise (PN) but suffer from large area, magnetic coupling, and small tuning range. While ring voltage-controlled oscillators (RVCO) are free from the above issues, their inferior PN performance restricts their applicability. The injection-locked clock multiplier (ILCM) attains a low PN through phase realignment. However, both the PN and the reference spur deteriorate when the injection instant drifts over PVT. Although the frequency-tracking loop (FTL) can calibrate the center frequency, its power consumption, converging speed, and accuracy limit the performance of the ILCM [1, 2]. The Type-I PLL performs wideband filtering [3], but its efficiency is 3dB lower than that of the ILCM [4]. A PLL with fast phase-error correction (FPEC) [4] realizes a PN filtering close to the ILCM and keeps a small reference spur. Nevertheless, both Type-I and FPEC PLLs rely on the closed-loop wideband filtering to achieve a low PN. The drifted loop gain over PVT significantly degrades jitter performance and even causes instability, implying a trade-off between wideband filtering and stability. Consequently, a loop-gain calibration [4] is necessary to maintain the stability and low PN.
Dielectric spectroscopy on alumina-epoxy composites towards the quantification of filler-particulate microstructure effects (2015)

Cylindrical ingots of epoxy resin composites containing alumina of various microstructure particulates were prepared and their dielectric properties were investigated by the parallel capacitance method in the frequency range 20 Hz – 1 MHz, as a function of depth below the surface. Nano-porous (90 Å), or non-porous alumina particulates, with sizes varying from 63 to 200 µm, were mixed as composite fillers at various contents (up to 5% wt). Sample-wafers were extracted from the cylindrical ingots to investigate the porosity induced effects on particulate mixing, dispersibility, precipitation, and relate filler concentration to the electrical response observed at various depths. According to the experimental results, the nano-pore induced effects dominate and reduce the effective relative dielectric constant compared to the non-porous alumina, while the dissipation factor values remain unaffected. Finally, the presence of nano-pores in the alumina particulates induces particle stratification effects and the filler particles with increased pore concentrations become stratified within the upper layer of the molded material.
The sequence of an embryonic myosin heavy chain gene and isolation of its corresponding cDNA. (1987)

The complete sequence of an embryonic chicken myosin heavy chain has been determined. Introns and exons were identified by comparison with the corresponding cDNA. The cDNA contains 5,962 bases, of which 85 bases constitute the poly(A) tail. The cDNA represents the entire mRNA transcript, except for 90 bases at the 5'-coding terminus and 101 bases of the 5'-untranslated region. The gene's coding region is split by 37 introns; two additional introns split the 101 base pairs which make up the 5'-untranslated region. The complete gene is approximately 23,000 base pairs and encodes a protein whose molecular weight is 222,559 and consists of 1,940 amino acids. Analysis of the protein and comparison with other myosin sequences reveal that certain regions have been conserved; those amino acids which have been postulated to participate in the ATPase and actin-binding activities of the molecule are highly homologous. These comparisons have allowed the identification of isolated regions within the myosin heavy chain that appear to be essential for the molecule's function.
Abstract 4190: miR-30 as a tumor suppressor connects EGF/Src signal to EMT and ERG. (2013)

Abstract Src tyrosine kinase (Src) is implicated in the development of bone metastasis and castration-resistance of prostate cancer. Src inhibitors are currently being tested in clinical trials for such diseases. Understanding the molecular and cellular actions of Src inhibitors holds the key to future improvement of this line of therapy. Here we describe the microRNA expression profiles modulated by two Src inhibitors and demonstrate that the miR-30 family members are the most prominently induced species. Consistent with its tumor suppressor role, miR-30 is downmodulated by oncogenic signals such as epidermal growth factor (EGF) and hepatocyte growth factor (HGF), and is generally underexpressed in prostate cancer specimens. A number of epithelial to mesenchymal transition (EMT)-associated genes are predicted targets of miR-30. Among these genes the Ets Related Gene (ERG) is the most frequently overexpressed-oncogene in prostate cancer activated by genomic fusion events between promoter upstream sequences of the TMPRSS2 and coding sequences of ERG. We showed by ERG 3’UTR-reporter and mutagenesis assays that ERG is a direct target of miR-30. Overexpression of miR-30 in prostate cancer cells suppresses EMT phenotypes and inhibits cell migration and invasion. It also inhibits the in vitro and in vivo growth of VCaP cells, which depends on TMPRSS2-ERG for proliferation. TMPRSS2-ERG is generally regulated by androgen at the transcriptional level. Our finding reveals a new post-transcriptional mechanism of TMPRSS2-ERG regulation by Src and growth signals via miR-30 providing a rationale for targeting ERG positive castration resistant tumors with Src inhibitors. Citation Format: Chiao-Jung Kao, Anthony Martiniez, Xu-Bao Shi, Albert Dobi, Ralph W. deVere White, Hsing-Jien Kung. miR-30 as a tumor suppressor connects EGF/Src signal to EMT and ERG. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4190. doi:10.1158/1538-7445.AM2013-4190
Assembly of the <scp>BclB</scp> glycoprotein into the exosporium and evidence for its role in the formation of the exosporium ‘cap’ structure in <i><scp>B</scp>acillus anthracis</i> (2012)

The outermost layer of the Bacillus anthracis spore consists of an exosporium comprised of an outer hair-like nap layer and an internal basal layer. A major component of the hair-like nap is the glycosylated collagen-like protein BclA. A second collagen-like protein, BclB, is also present in the exosporium. BclB possesses an N-terminal sequence that targets it to the exosporium and is similar in sequence to a cognate targeting region in BclA. BclB lacks, however, sequence similarity to the region of BclA thought to mediate attachment to the basal layer via covalent interactions with the basal layer protein BxpB. Here we demonstrate that BxpB is critical for correct localization of BclB during spore formation and that the N-terminal domains of the BclA and BclB proteins compete for BxpB-controlled assembly sites. We found that BclB is located principally in a region of the exosporium that excludes a short arc on one side of the exosporium (the so-called bottle-cap region). We also found that in bclB mutant spores, the distribution of exosporium proteins CotY and BxpB is altered, suggesting that BclB has roles in exosporium assembly. In bclB mutant spores, the distance between the exosporium and the coat, the interspace, is reduced.
MicroRNAs targeting Nicastrin regulate AÎ² production and are affected by target site polymorphisms (2014)

Despite the growing number of genome-wide association studies, the involvement of polymorphisms in microRNA target sites (polymiRTS) in Alzheimer's disease (AD) remains poorly investigated. Recently, we have shown that AD-associated single-nucleotide polymorphisms (SNPs) present in the 3' untranslated region (3'UTR) of amyloid precursor protein (APP) could directly affect miRNA function. In theory, loss of microRNA (miRNA) function could lead to risk for AD by increasing APP expression and Aβ peptide production. In this study, we tested the hypothesis that Nicastrin, a γ-secretase subunit involved in Aβ generation, could be regulated by miRNAs, and consequently affected by 3'UTR polymorphisms. Bioinformatic analysis identified 22 putative miRNA binding sites located in or near Nicastrin 3'UTR polymorphisms. From these miRNA candidates, six were previously shown to be expressed in human brain. We identified miR-24, miR-186, and miR-455 as regulators of Nicastrin expression, both in vitro and under physiological conditions in human cells, which resulted in altered Aβ secretion. Using luciferase-based assays, we further demonstrated that rs113810300 and rs141849450 SNPs affected miRNA-mediated repression of Nicastrin. Notably, rs141849450 completely abolished the miR-455-mediated repression of Nicastrin. Finally, the rs141849450 variant was identified in 1 out of 511 AD cases but not in 631 controls. These observations set the stage for future studies exploring the role of miRNAs and 3'UTR polymorphisms in AD.
Optimization techniques for concurrent STM-based implementations: A concurrent binary heap as a case study (2009)

Much research has been done in the area of software transactional memory (STM) as a new programming paradigm to help ease the implementation of parallel applications. While most research has been invested for answering the question of how STM should be implemented, there is less work about how to use STM efficiently. This paper is focused on the challenge of how to use STM for efficient and scalable implementations of non-trivial applications. We present a fine-grained STM-based concurrent binary heap, an application of STM for a data structure that is notoriously difficult to parallelize. We describe extensions to the basic STM approach and also the benefits of our proposal. Our results show that the fine-grained STM-based binary heap provides very good scalability compared to the naive approach. Nevertheless, we reach a point where the complexity of some fine-grained techniques do not justify its use for the increase in performance that can be obtained.
Microstructural studies of gluten and a hypothesis on dough formation (1991)

The transformation of a mixture of water and wheat flour into a viscoelastic dough was studied by light microscopy, scanning and transmission electron mi croscopy. In flour particles, gluten protein fills up the space between the starch granules forming a three- dimensional network. Dough formation is the result of the adhesion of the protein networks of individual flour particles to one another and their extension during kneading. In the course of the kneading process protein films form from the strands by bidirectional extension. The strands of the gluten network consist of randomly arranged protein threads which are twisted to form loops and knots in the unextended state. Bidirectional extension of the gluten pulls apart these knots to platelet- like forms .
The zirconium doped (Ba<sub>0.65</sub>Sr<sub>0.35</sub>)(Ti<sub>1−x</sub>Zr<sub>x</sub>)O<sub>3</sub> thin films for gbit-scale dynamic random access memory device applications (1999)

Abstract High dielectric constant (Ba0.65Sr0.35)(Ti1−xZrx)O3 (BSTZ) thin films with different Zr content were prepared on Pt/Ti/SiO2/Si substrates at 500°C by rf magnetron sputtering technique. The grain size, dielectric constant, and leakage current density of the 90 nm thick BSTZ films decreased with increasing Zr content. The dielectric constant and dissipation factor of BSTZ films with Zr content of 0.26 were 390 and 0.025 at an applied frequency of 100 kHz, respectively. The leakage current density of films was about 9.0 × 10−9 A/cm2 at 200 kV/cm. The decrease of leakage current density with increasing Zr content was due to increase of Schottky barrier height. The BSTZ films deposited by rf magnetron sputtering were attractive for semiconductor memory capacitor application. Key Words: BSTZDRAMSchottky barrier heightPt3Tirf-magnetron sputtering
Identification of a cys-ser substitution in the 5-HT{sub 2C} (HTR2C) receptor gene and allelic association to violent behavior and alcoholism (1994)

Several lines of evidence suggest that brain serotonergic functions, including behavioral and neurochemical responses to 5-HT{sub 2C} agonist, are abnormal in some individuals with alcoholism and aggressive behaviors. The aim of the present study was to identify coding sequence variants in the human 5-HT{sub 2C} receptor gene which may cause abnormal or variant function of this receptor. Using SSCP analysis, a non-conservative cys-ser substitution was found in the 5-HT{sub 2C} receptor (designated 5-HT{sub 2Ccys} and 5-HT{sub 2Cser}). The polymorphism was typed in CEPH families to genetically map the gene. To test for association of the variant to alcoholism, violent behavior and serotonin function, the 5-HT{sub 2C} genotypes of 151 non-related Finnish male alcoholic violent offenders and impulsive fire setters and 127 Finnish psychiatrically interviewed healthy male volunteers were determined. CSF 5-HIAA concentrations were available for 74 alcoholic violent offenders and 25 healthy volunteers. Linkage analysis placed the 5-HT{sub 2C} gene on Xq21, a region that has been previously shown to contain genes for several mental retardation syndromes. The 5-HT{sub 2Ccys}/5-HT{sub 2Cser} genotype frequencies in alcoholic violent offenders and controls differed significantly (0.90/0.10 and 0.82/0.18, respectively, P=0.048). The association was found to be strongest in the violent offenders who did notmore » fulfill the criteria for antisocial personality disorder (5-HT{sub 2Ccys}/5-HT{sub 2Cser} 0.93/0.07, p=0.021). No association was found between CSF 5-HIAA concentrations and 5-HT{sub 2C} genotype. These results implicate a 5-HT{sub 2C} receptor amino acid substitution in predisposition to alcohol abuse and violent behavior in a subgroup of alcoholics.« less
High angular resolution diffusion MRI (from local estimation to segmentation and tractography) (2008)

La résolution actuelle des IRM pondérées en diffusion suggère qu'il y a entre un et deux tiers des voxels de la matière blanche qui contiennent plusieurs faisceaux de fibres qui se croisent. L'IRM par tenseur de diffusion (DTI) classique est intrinsèquement limitée à ces endroits par son hypothèse de base qu'un seul faisceau traverse chaque voxel de l'image. Le but de cette thèse est donc de développer des techniques d'IRM à haute résolution angulaire (HARDI) pour pouvoir retrouver une ou plusieurs fibres et surmonter aux limites DTI. L'imagerie par q-ball (QBI) est une technique récente qui permet d'estimer la distribution d'orientation des fibres (ODF). La technique de QBI ainsi que l'ODF de diffusion des fibres permettent de retrouver plusieurs directions de fibres en chaque voxel de l'image. Ceux-ci joueront donc un rôle important tout au long de ce document. Cette thèse propose plusieurs contributions originales. D'abord, nous développons l'estimation robuste du signal HARDI en utilisant une base modifiée d'harmoniques sphériques et un terme de régularisation. Ensuite, nous proposons la modélisation du coefficient de diffusion apparent (ADC) pour étudier les mesures d'anisotropie HARDI et faire la classification des voxels contenant une distribution isotrope, une distribution d'une seule population de fibres et une distribution de plusieurs faisceaux fibres. Nous proposons de plus, le développement d'une solution analytique pour estimer l'ODF de diffusion en QBI ainsi qu'un nouvel algorithme de segmentation de ces images d'ODF obtenues par le QBI. Nous présentons également le calcul de l'ODF de fibres avec une nouvelle méthode de déconvolution sphérique à partir des données QBI. Enfin, nous développons de nouveaux algorithmes de suivi de fibres (tracking) déterministes et probabilistes à partir de l'ODF du q-ball et l'ODF de fibres. Finalement, tous ces nouveaux algorithmes sont testés et appliqués sur des données HARDI simulées, sur un fantôme biologique et sur des données réelles de plusieurs sujets dans des régions complexes avec plusieurs faisceaux qui se croisent. Nos résultats illustrent clairement la valeur ajoutée de nos méthodes HARDI sur la plupart des méthodes courantes en DTI qui négligent ces faisceaux complexes, ce qui peut amener à une mauvaise analyse et interprétation de l'anatomie et des fonctions cérébrales.
In situ optical backpropagation training of diffractive optical neural networks (2020)

Training an artificial neural network with backpropagation algorithms to perform advanced machine learning tasks requires an extensive computational process. This paper proposes to implement the backpropagation algorithm optically for in situ training of both linear and nonlinear diffractive optical neural networks, which enables the acceleration of training speed and improvement in energy efficiency on core computing modules. We demonstrate that the gradient of a loss function with respect to the weights of diffractive layers can be accurately calculated by measuring the forward and backward propagated optical fields based on light reciprocity and phase conjunction principles. The diffractive modulation weights are updated by programming a high-speed spatial light modulator to minimize the error between prediction and target output and perform inference tasks at the speed of light. We numerically validate the effectiveness of our approach on simulated networks for various applications. The proposed in situ optical learning architecture achieves accuracy comparable to in silico training with an electronic computer on the tasks of object classification and matrix-vector multiplication, which further allows the diffractive optical neural network to adapt to system imperfections. Also, the self-adaptive property of our approach facilitates the novel application of the network for all-optical imaging through scattering media. The proposed approach paves the way for robust implementation of large-scale diffractive neural networks to perform distinctive tasks all-optically.
A note on the budgeted maximization of submodular functions (2018)

Abstract: "Many set functions F in combinatorial optimization satisfy the diminishing returns property F(A [union of] X) - F(A) [> or =] F(A' [union of] X) - F(A') for A [element of] A'. Such functions are called submodular. A result from Nemhauser et.al. states that the problem of selecting k-element subsets maximizing a nondecreasing submodular function can be approximated with a constant factor (1 - 1/e) performance guarantee. Khuller et.al. showed that for the special submodular function involved in the MAX-COVER problem, this approximation result generalizes to a budgeted setting under linear nonnegative cost-functions. In this note, we extend this result to general submodular functions. Motivated by the problem of maximizing entropy in discrete graphical models, where the submodular objective cannot be evaluated exactly, we generalize our result to account for absolute errors."
Suppression of apolipoprotein B production during treatment of cholesteryl ester storage disease with lovastatin. Implications for regulation of apolipoprotein B synthesis. (1987)

Cholesteryl ester storage disease (CESD) is characterized by the deficient activity of lysosomal cholesteryl ester (CE) hydrolase, accumulation of LDL-derived CE in lysosomes, and hyperlipidemia. We studied the kinetics of VLDL and LDL apolipoprotein B (apoB), using 125I-VLDL and 131I-LDL, in a 9-yr-old female with CESD and elevated total cholesterol (TC) (271.0 +/- 4.4 mg/dl), triglyceride (TG) (150.0 +/- 7.8 mg/dl), and LDL cholesterol (184.7 +/- 3.4 mg/dl). These studies demonstrated a markedly elevated production rate (PR) of apoB, primarily in LDL, with normal fractional catabolism of apoB in VLDL and LDL. Urine mevalonate levels were elevated, indicative of increased synthesis of endogenous cholesterol. Treatment with lovastatin, a competitive inhibitor of hydroxymethylglutaryl coenzyme A reductase, resulted in significant reductions in TC (196.8 +/- 7.9 mg/dl), TG (100.8 +/- 20.6 mg/dl), and LDL cholesterol (102.0 +/- 10.9 mg/dl). Therapy reduced VLDL apoB PR (5.2 vs. 12.2 mg/kg per d pretreatment) and LDL apoB PR (12.7 vs. 24.2 mg/kg per d pretreatment). Urine mevalonate levels also decreased during therapy. These results indicate that, in CESD, the inability to release free cholesterol from lysosomal CE resulted in elevated synthesis of endogenous cholesterol and increased production of apoB-containing lipoproteins. Lovastatin reduced both the rate of cholesterol synthesis and the secretion of apoB-containing lipoproteins.
Comparison of flea control strategies using imidacloprid or lufenuron on cats in a controlled simulated home environment (1997)

Results from this experimental model suggest that flea populations within a home may be controlled by carefully timed on-host treatments with potent long-acting insecticides such as imidacloprid.