gebhart/patrepeval huggingface dataset:
Virtual private caches (2007)

Virtual Private Machines (VPM) provide a framework for Quality of Service (QoS) in CMP-based computer systems. VPMs incorporate microarchitecture mechanisms that allow shares of hardware resources to be allocated to executing threads, thus providing applications with an upper bound on execution time regardless of other thread activity. Virtual Private Caches (VPCs) are an important element of VPMs. VPC hardware consists of two major components: the VPC Arbiter, which manages shared cache bandwidth, and the VPC Capacity Manager, which manages the cache storage. Both the VPC Arbiter and VPC Capacity Manager provide minimum service guarantees that, when combined, achieve QoS for the cache subsystem. Simulation-based evaluation shows that conventional cache bandwidth management policies allow concurrently executing threads to affect each other significantly in an uncontrollable manner. The evaluation targets cache bandwidth because the effects of cache capacity sharing have been studied elsewhere. In contrast with the conventional policies, the VPC Arbiter meets its QoS performance objectives on all workloads studied and over a range of allocated bandwidth levels. The VPC Arbiter’s fairness policy, which distributes leftover bandwidth, mitigates the effects of cache preemption latencies, thus ensuring threads a high-degree of performance isolation. Furthermore, the VPC Arbiter eliminates negative bandwidth interference which can improve aggregate throughput and resource utilization.
Gene Expression Profiling of Cultured Human Bronchial Epithelial and Lung Carcinoma Cells (2001)

Lung cancer is a complex collection of diseases that is thought to begin with single mutated progenitor cells and culminates in any of several clinically described pathologies. Our knowledge of the molecular events that lead to different lung cancer types--small cell carcinoma, squamous cell carcinoma, adenocarcinoma, and large cell carcinoma--is incomplete. Nonetheless, it is evident that genetic changes that impact multiple molecular networks are involved in the generation of each specific phenotype. Due to the obvious complexity of these processes, the simultaneous quantitative monitoring of changes in the expression of genes that define these networks can provide mechanistic information to increase our understanding of the molecular basis for human pulmonary carcinogenesis. To this end, we have employed a commercially available human cDNA array (Atlas Human Array, Clontech Laboratories) to systematically screen for alterations in the expression of 600 genes in normal human bronchial epithelial (NHBE) cells as well as in several lung carcinoma lines. Studies on the reproducibility and variability of array results indicate that a 2-fold or greater difference in the expression of a particular gene could be considered a real difference in transcript abundance. Accuracy of gene expression as measured in the array was verified by comparing mRNA levels of the proto-oncogene c-myc in the array with results obtained by traditional Northern blot analysis and by quantitative RT-PCR. Gene expression profiles were compared within and among cell types. The differential expression of 17 genes, including downregulation of MRP8 and MRP14 and upregulation of CYP1B1, was observed in all four carcinoma lines compared to NHBE cells. The direction of all 17 gene expression differences, either upregulation or downregulation relative to NHBE cells, was the same for all four carcinoma lines, underscoring their common molecular features. Each lung tumor line also exhibited a number of unique differences compared to both normal cells and the other tumor cell lines. These differences may be due to differences in the cellular origin and/or pathology of the cell lines studied.
Management of Androgen-Independent Prostate Cancer (2004)

Secondary hormone therapy, chemotherapy, and bisphosphonate therapy may provide benefits for selected patients. Correlation of disease stage with biologic characteristics of the tumor and host facilitates proper choices of interventions. Docetaxel-based chemotherapy regimens should be considered for first-line treatment of patients with progressive metastatic AIPC.
Genetics of Clusterin Isoform Expression and Alzheimer's Disease Risk (2012)

The minor allele of rs11136000 within CLU is strongly associated with reduced Alzheimer's disease (AD) risk. The mechanism underlying this association is unclear. Here, we report that CLU1 and CLU2 are the two primary CLU isoforms in human brain; CLU1 and CLU2 share exons 2-9 but differ in exon 1 and proximal promoters. The expression of both CLU1 and CLU2 was increased in individuals with significant AD neuropathology. However, only CLU1 was associated with the rs11136000 genotype, with the minor "protective" rs11136000T allele being associated with increased CLU1 expression. Since CLU1 and CLU2 are predicted to encode intracellular and secreted proteins, respectively, we compared their expression; for both CLU1 and CLU2 transfected cells, clusterin is present in the secretory pathway, accumulates in the extracellular media, and is similar in size to clusterin in human brain. Overall, we interpret these results as indicating that the AD-protective minor rs11136000T allele is associated with increased CLU1 expression. Since CLU1 and CLU2 appear to produce similar proteins and are increased in AD, the AD-protection afforded by the rs11136000T allele may reflect increased soluble clusterin throughout life.
A deep learning genome-mining strategy for biosynthetic gene cluster prediction (2019)

Natural products represent a rich reservoir of small molecule drug candidates utilized as antimicrobial drugs, anticancer therapies, and immunomodulatory agents. These molecules are microbial secondary metabolites synthesized by co-localized genes termed Biosynthetic Gene Clusters (BGCs). The increase in full microbial genomes and similar resources has led to development of BGC prediction algorithms, although their precision and ability to identify novel BGC classes could be improved. Here we present a deep learning strategy (DeepBGC) that offers reduced false positive rates in BGC identification and an improved ability to extrapolate and identify novel BGC classes compared to existing machine-learning tools. We supplemented this with random forest classifiers that accurately predicted BGC product classes and potential chemical activity. Application of DeepBGC to bacterial genomes uncovered previously undetectable putative BGCs that may code for natural products with novel biologic activities. The improved accuracy and classification ability of DeepBGC represents a major addition to in-silico BGC identification.
Radical and Concerted Mechanisms in Oxidations of Amines, Sulfides, and Alkenes by Peroxynitrite, Peroxynitrous Acid, and the Peroxynitrite−CO<sub>2</sub> Adduct:  Density Functional Theory Transition Structures and Energetics (1996)

The mechanisms of oxidations of amines, sulfides, and alkenes by peroxynitrous acid, as well as the mechanism for the conversion of peroxynitrous acid to nitric acid, have been investigated with density functional theory methods using the Becke3LYP functional and the 6-31G* basis set. Theoretical evidence is obtained for the mechanisms and transition states of oxidations by peroxynitrous acid both by one- and two-electron processes. Transition structures for two-electron oxidations of amines, sulfides, and alkenes are reported. An activated form of peroxynitrous acid, HOONO*, is often invoked to account for the potent oxidative chemistry of peroxynitrous acid and derivatives; a structure with the appropriate characteristics has been located. The structure of the CO2 adduct of peroxynitrite is also explored, and a mechanistic scheme is proposed for the acceleration of peroxynitrite oxidations in the presence of CO2. Energetics are described in detail for each of these species and oxidation transition structures.
Analysis of Inhibition Rate Enhancement by Covalent Linkage of Antithrombin to Heparin as a Potential Predictor of Reaction Mechanism (2006)

Antithrombin (AT) inhibition of coagulation enzymes is catalyzed by unfractionated heparin (UFH) and other heparinoids. Reaction proceeds either via conformational activation of the inhibitor or template-mediated binding of both inhibitor and protease. We investigated if the relative inhibition rates of AT + UFH and covalent AT-heparin conjugate (ATH) with coagulation factors might be indicative of the mechanism involved. Rates were determined by discontinuous assay and mechanisms were probed by a variety of binding studies with UFH or ATH heparin chains. Rates were increased more than 2-fold with ATH over AT + UFH in reactions with thrombin, factor (F) VIIa + tissue factor + Ca2+ + lipid, FIXa and FXIa, but not with FXa or FXIIa. In comparison, UFH or ATH heparin binding (evidence of a template mechanism) was only observed with thrombin, tissue factor, FIXa and FXIa. Thus, inhibition rate enhancement by conjugation of AT with heparin were predictive of inhibitor.enzyme template bridging by heparin. Rationales behind this novel concept are discussed.
Are alterations of skeletal muscle ultrastructure in patients with heart failure reversible under treatment with ACE-inhibitors? (1993)

In patients with chronic heart failure, exercise capacity and clinical symptoms correlate poorly, if at all with the degree of left ventricular dysfunction. These observations might indicate that peripheral alterations (e.g. reduced perfusion of the exercising muscle) contribute to the functional state and exercise capacity of patients with chronic heart failure. Acute improvements in hemodynamics by means of therapy with vasodilators or positive inotropes, however, could not be translated into an enhanced oxygen consumption. These studies have prompted the hypothesis that in the setting of heart failure, intrinsic abnormalities of the exercising muscle develop that prevent acute improvement in peak VO2. Indeed, ultrastructural analysis of a large cohort of patients with chronic heart failure revealed that volume density of mitochondria and surface density of mitochondrial cristae (both are parameters for the oxidative capacity of skeletal muscle) were reduced by more than 20% as compared to healthy control subjects. In contrast to left ventricular contractility parameters, ultrastructural changes of the skeletal muscle correlated closely with peak oxygen consumption, indicating that abnormalities of the exercising muscle contribute to a decreased exercise capacity in this patient group. Chronic but not acute treatment with angiotensin converting enzyme (ACE) inhibitors increases blood flow to the exercising muscle and improves peak oxygen consumption. These protracted effects of ACE-inhibitors might be due to an inhibitory effect on the vascular renin angiotensin system leading to a beneficial remodelling of the vessel wall. Forearm vessels of patients with heart failure do not respond adequately to acetylcholine and reactive hyperemia, indicating an impaired endothelial function.(ABSTRACT TRUNCATED AT 250 WORDS)
A competitive modular connectionist architecture (1990)

We describe a multi-network, or modular, connectionist architecture that captures that fact that many tasks have structure at a level of granularity intermediate to that assumed by local and global function approximation schemes. The main innovation of the architecture is that it combines associative and competitive learning in order to learn task decompositions. A task decomposition is discovered by forcing the networks comprising the architecture to compete to learn the training patterns. As a result of the competition, different networks learn different training patterns and, thus, learn to partition the input space. The performance of the architecture on a &quot;what &quot; and &quot;where &quot; vision task and on a multi-payload robotics task are presented. 1
Performance of a PCR Assay for Detection of <i>Pneumocystis carinii</i> from Respiratory Specimens (1998)

ABSTRACT This study evaluates the performance of a PCR assay for the detection of Pneumocystis carinii from respiratory specimens that has been designed for use in the clinical microbiology laboratory. The test includes a simple method for nucleic acid extraction and amplification, a colorimetric probe hybridization technique for detection of amplicons, and an internal control to evaluate for the presence of inhibitors of amplification. Two hundred thirty-two clinical specimens (120 induced-sputum [IS] and 112 bronchoalveolar lavage [BAL] specimens) from 168 patients were tested by both immunofluorescent (direct fluorescent-antibody [DFA]) staining and PCR. Of the 112 BAL specimens, 17 were positive for P. carinii by DFA staining and PCR. An additional two specimens were DFA negative and PCR positive. For BAL specimens, the sensitivity and specificity of PCR compared to DFA were 100 and 98%, respectively. Eighteen IS specimens were positive for P. carinii by DFA, and 27 were positive by PCR. One of the 18 DFA-positive IS specimens was negative by PCR; this patient had just completed therapy for P. carinii pneumonia. Of the 10 specimens that were PCR positive and DFA negative, 4 were from patients who had a subsequent BAL specimen that was positive by DFA and PCR. For IS specimens, the sensitivity of DFA and PCR was 82 and 95%, respectively. The specificity of PCR for IS specimens was 94%. Due to the high sensitivity of PCR for the detection of P. carinii from IS specimens, a PCR-based diagnostic test may be a useful screening test and may alleviate the need for bronchoscopy in some patients.
Orthogonal Arrays of Index Unity (1952)

In this paper we shall proceed to generalize the notion of a set of orthogonal Latin squares, and we term this extension an orthogonal array of index unity. In Section 2 we secure bounds for the number of constraints which are the counterpart of the familiar theorem which states that the number of mutually orthogonal Latin squares of side $s$ is bounded above by $s - 1$. Curiously, our bound depends upon whether $s$ is odd or even. In Section 3 we give a method of constructing these arrays by considering a class of polynomials with coefficients in the finite Galois field $GF(s)$, where $s$ is a prime or a power of a prime. In the concluding section we give a brief discussion of designs based on these arrays.
From Consumer Likes and Dislikes to a Consumer Behaviour Theory (1992)

Discusses the results of a consumer survey on the likes and dislikes of consumers towards breakfast cereals. Suggests a possible model of consumer behaviour to explain their preferences. The perceived risks and risk‐reducing strategies used by consumers are empirically investigated. Discusses the results in a way that highlights their usefulness to the industry′s marketers.
Introduction (2018)

ONE of the most important manuscript witnesses to polyphonic music in the Middle Ages resides in the library of Montpellier's historic medical school. The so-called Montpellier codex (Bibliothèque interuniversitaire, Bibliothèque universitaire de médecine, H. 196, hereafter Mo) is modest in dimensions, but it contains the largest medieval motet collection in existence, and is packed with gorgeous gold-leaf illuminations, historiated initials, decorative borders, and exquisite music calligraphy. Unsurprisingly, this comprehensive and beautiful manuscript has long attracted scholarly attention and the details of its production are, in the main, well established and widely accepted. It seems that the earliest layer of the book – commonly referred to as Mo's 'old corpus' – was produced in Paris in the late 1270s or 1280s. This old corpus comprises four internal fascicles (numbers 2–6), discrete sections of the manuscript usually devoted to certain musical genres or stylistic types, with the opening of each new fascicle clearly signaled by a historiated initial. Mo's old corpus was later bookended by two additional fascicles (numbers 1 and 7), probably in the 1290s. But the last stage in Mo's compilation, and the status of its final fascicle – number 8, containing forty-three three-voice compositions – remains mysterious and contested. Most scholars agree that the forty-eight folios appended to the end of Mo must be chronologically later than the rest of the codex, but just how much later is still in question. Intriguingly, the contents of fascicle 8 straddle a crucial historiographical juncture: alongside examples of the established thirteenth-century motet tradition represented by the earlier parts of Mo, fascicle 8 features musical and notational techniques conventionally associated with newer practices. Why and at what date was fascicle 8 produced? Was it intended to be part of Mo from the outset? And how and why might this eclectic collection of different types of compositions – some perceptibly outmoded, others noticeably innovative – have come about? The essays in this volume engage with these fundamental questions, challenging and undercutting a still pervasive historiographical division between the thirteenth and fourteenth centuries in the study of medieval music.
Building Workflow Engines for Commerce Logic Automation (2000)

Literally speaking, workflow means flow of work, which requires the coordination of potentially complex sequences of tasks among many agents. Coordination of tasks involves modeling of the process linking the tasks,
Through-polymer-via for 3D heterogeneous integration and packaging (2015)

Microelectronics industry is moving towards three dimensional stacking, packaging and integration of chips to answer to the need for increased functionality, miniaturization and cost reduction of smart systems. Their increasing complexity require novel and more robust approaches for the fabrication of vertical-interconnections (vias) to connect chips, devices, interconnection layers and wafers in out of plane direction. However, due to significant technology difficulties and high production costs, existing 3D technologies have limited usages. This paper describes the development of a new and robust fabrication method for dense high-aspect-ratio conductive through-polymer-vias for three-dimensional stacking, packaging and heterogeneous integration of semiconductor dies and wafers. Our approach relies on patterning micro-pillars in a 350 μm thick layer of photo resist on a carrier wafer or substrate. The pillars are conformal coated with a metal film and subsequently encapsulated inside an epoxy molding compound, resulting in vertical through-polymer interconnect vias (TPV). For subsequent interconnect processing, a clean and free of epoxy top surface of the pillars is crucial which was achieved by using foil assisted transfer molding technology. Even for very thin pillars with extreme aspect ratios of >15 clean connection surfaces are obtained. Advantages of this technology are: pillars are more easily exposed and wetted by the plating solution, faster metallization than bottom-up plating, no voiding nor trapping of plating chemicals, suitable for parallel fabrication, lithographically defined, enabling layout variations and extremely accurate positioning of the vias. The technology is promising for low-cost, large-scale parallel fabrication of micro-vias for 3D heterogeneous integration and packaging.
Photosensitized oxidation of dialkyl disulfides (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotosensitized oxidation of dialkyl disulfidesRobert W. Murray and Sohan L. JindalCite this: J. Org. Chem. 1972, 37, 22, 3516–3520Publication Date (Print):November 1, 1972Publication History Published online1 May 2002Published inissue 1 November 1972https://pubs.acs.org/doi/10.1021/jo00795a027https://doi.org/10.1021/jo00795a027research-articleACS PublicationsRequest reuse permissionsArticle Views168Altmetric-Citations39LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
An optical multichannel detection system for modulation spectroscopy (1977)

A measurement system using a silicon target vidicon is described, which can greatly improve signal-to-noise ratio compared with the commonly used photomultiplier. Contrary to the photomultiplier, however, a relatively high light level is required because of the higher dark current level of the vidicon. Originally developed for Stark modulation spectroscopy, the system should also be suitable for other modulation-type experiments.
<scp>d</scp>‐Serine Regulates Proliferation and Neuronal Differentiation of Neural Stem Cells from Postnatal Mouse Forebrain (2012)

Our findings demonstrate for the first time that NSCs can synthesize D-serine and, thereby, promote themselves proliferation and neuronal differentiation, which may afford a novel therapeutic strategy for the neurological disorders that require nerve cell replenishment, such as neurodegenerative diseases and stroke.
Efficacy of a new needleless insulin delivery system monitoring of blood glucose fluctuations and free insulin levels (1989)

A new insulin delivery system Vitajet has been invented which involves a high-pressure spring and obviates the use of needle injections. To study its efficacy we compared blood glucose fluctuations, integrated glycemia, free insulin and total free insulin concentrations in six insulin-dependent diabetics. After obtaining a steady state of carbohydrate metabolism overnight by feedback control through the artificial endocrine pancreas (AEP) Biostator, the patients received their usual morning and evening doses of insulin by either conventional injection or Vitajet in random order. Blood glucose levels were significantly lower after Vitajet than conventional injections (p less than 0.04) between 10 a.m. and 4 p.m., but the difference disappeared from 4 p.m. onwards. The areas under the curve (AUCs) of glucose fluctuations were lower after Vitajet (28036 +/- 4655 vs 31086 +/- 2310 mg. min% mean +/- SEM, p less than 0.01). AUCs for free insulin concentrations (microU.min/ml) were close: 39286 +/- 4510 (Vitajet) vs 30597 +/- 3575 (conventional). It is concluded that Vitajet constitutes an efficient needleless route for administering insulin pulses.
Automatische Überwachung des Stanzvorganges durch Auswertung prozeßbedingten Körperschalls/ Automatic control of punch processes by using structure born sound (1985)

Article Automatische Überwachung des Stanzvorganges durch Auswertung prozeßbedingten Körperschalls/ Automatic control of punch processes by using structure born sound was published on November 1, 1985 in the journal tm - Technisches Messen (volume 52, issue 11).
Annexin V used for measuring apoptosis in the early events of cellular cytotoxicity (1999)

This rapid and novel assay permits the discrimination of the cell death mechanisms occurring during a cytotoxic response and to precisely evaluate the contribution of apoptosis in the early phases of cell-mediated cytotoxicity.