gebhart/patrepeval huggingface dataset:
Power reduction through measurement and modeling of users and CPUs (2007)

Dynamic Voltage and Frequency Scaling (DVFS) is one of the most commonly used power reduction techniques in high-performance processors. DVFS varies the frequency and voltage of a microprocessor in real-time according to processing needs. Although there are different versions of DVFS, at its core DVFS adapts power consumption and performance to the current workload of the CPU. Specifically, existing DVFS techniques in high-performance processors select an operating point (CPU frequency and voltage) based on the utilization of the processor. This approach integrates OS-level control, but such control is pessimistic. Existing DVFS techniques are pessimistic about the user. Indeed, they ignore the user, assuming that CPU utilization or the OS events prompting it are sufficient proxies. A high CPU utilization simply leads to a high frequency and high voltage, regardless of the user’s satisfaction or expectation of performance. Existing DVFS techniques are pessimistic about the CPU. They assume worst-case manufacturing process variation and operating temperature by basing their policies on loose worstcase bounds given by the processor manufacturer. A voltage level for a given frequency is set such that even the worst shipped processor of a given generation will be stable at the highest specified temperature. In response to these observations, we have developed, implemented, and evaluated the following two new power management techniques that can be readily employed independently or together. We elaborate on these techniques in detail elsewhere [4].
Chimeric Antigen Receptor–Modified T Cells in CLL (2011)

Porter et al. describe the treatment of a patient with autologous T cells that were genetically modified to recognize the B-cell antigen CD19.This article confirms many findings of our December 2010 article, 1 which described a patient with advanced follicular lymphoma whom we treated with chemotherapy followed by an infusion of T cells expressing an anti-CD19 chimeric antigen receptor (CART19).A dramatic partial remission lasting 10 months was achieved in our patient.He was retreated on our protocol and was in an ongoing partial remission 26 months after the original treatment.In addition, both normal and malignant Blineage cells were completely eradicated from the blood and bone marrow in our patient for 36 weeks.Similarly to the patient described by Porter and coworkers, hypogammaglobulinemia developed in our patient.We have treated a total of 11 patients in two different clinical trials of CART19.][3][4]
GTPase-mediated activation of ATP sulfurylase. (1992)

GTP stimulates the synthesis of APS (adenosine 5'-phosphosulfate) by the enzyme ATP sulfurylase (ATP:sulfate adenylyltransferase, EC 2.7.7.4) via a GTPase mechanism. The activation of the enzyme, purified from Escherichia coli, is titratable with GTP. The initial rate of APS formation is increased 116-fold at a saturating concentration of GTP. The enzyme exhibits a GTPase activity that is stimulated by ATP and further enhanced by SO4; however, SO4 alone does not significantly stimulate GTP hydrolysis. The larger subunit of ATP sulfurylase, encoded by cysN, contains a GTP-binding consensus sequence common to other known GTP-binding proteins. This is the first evidence that the sulfate activation pathway is a metabolic target for regulation by a GTPase.
Peak temperature control and leakage reduction during binding in high level synthesis (2005)

Temperature is becoming a first rate design criterion in ASICs due to its negative impact on leakage power, reliability, performance, and packaging cost. Incorporating awareness of such lower level physical phenomenon in high level synthesis algorithms will help to achieve better designs. In this work, we developed a temperature aware binding algorithm. Switching power of a module correlates with its operating temperature. The goal of our binding algorithm is to distribute the activity evenly across functional units. This approach avoids steep temperature differences between modules on a chip, hence, the occurrence of hot spots. Starting with a switching optimal binding solution, our algorithm iteratively minimizes the maximum temperature reached by the hottest functional unit. Our algorithm does not change the number of resources used in the original binding. We have used HotSpot, a temperature modeling tool, to simulate temperature of a number ASIC designs. Our binding algorithm reduces temperature reached by the hottest resource by 12.21°C on average. Reducing the peak temperature has a positive impact on leakage as well. Our binding technique improves leakage power by 11.89%, and overall power by 3.32% on average at 130nm technology node compared to a switching optimal binding
Transport effects in the oxygen reduction reaction on nanostructured, planar glassy carbon supported Pt/GC model electrodes (2008)

The role of transport and re-adsorption processes on the oxygen reduction reaction (ORR), and in particular on its selectivity was studied using nanostructured model electrodes consisting of arrays of Pt nanostructures of well-defined size and separation on a planar glassy carbon (GC) substrate. The electrochemical measurements were performed under controlled transport conditions in a double-disk electrode thin-layer flow-cell configuration; the model electrodes were fabricated by colloidal lithography techniques, yielding Pt nanostructures of well defined and controlled size and density (diameter: 140 or 85 nm, height: 20 or 10 nm, separation: from 1-2 to more than 10 diameters). The nanostructured model electrodes were characterized by scanning electron microscopy and electrochemical probing of the active surface area (via the hydrogen adsorption charge). The electrocatalytic measurements revealed a pronounced variation of the hydrogen peroxide yield, which increases by up to two orders of magnitude with increasing separation and decreasing size of the Pt nanostructures. Similar, though less pronounced effects were observed upon varying the electrolyte flow and thus the mass transport characteristics. These effects are discussed in a reaction model which includes (i) direct reduction to H(2)O on the Pt surface and (ii) additional H(2)O(2) formation and desorption on both Pt and carbon surfaces and subsequent partial re-adsorption and further reduction of the H(2)O(2) molecules on the Pt surface.
Ceria‐Based Solid Catalysts for Organic Chemistry (2010)

Ceria has been the subject of thorough investigations, mainly because of its use as an active component of catalytic converters for the treatment of exhaust gases. However, ceria-based catalysts have also been developed for different applications in organic chemistry. The redox and acid-base properties of ceria, either alone or in the presence of transition metals, are important parameters that allow to activate complex organic molecules and to selectively orient their transformation. Pure ceria is used in several organic reactions, such as the dehydration of alcohols, the alkylation of aromatic compounds, ketone formation, and aldolization, and in redox reactions. Ceria-supported metal catalysts allow the hydrogenation of many unsaturated compounds. They can also be used for coupling or ring-opening reactions. Cerium atoms can be added as dopants to catalytic system or impregnated onto zeolites and mesoporous catalyst materials to improve their performances. This Review demonstrates that the exceptional surface (and sometimes bulk) properties of ceria make cerium-based catalysts very effective for a broad range of organic reactions.
Origin of Smooth Muscle Progenitor Cells: Different Conclusions From Different Models (2003)

We read with interest the recent article by Hu et al 1 who investigated the origin of smooth muscle cells (SMCs) in transplant atherosclerotic lesions.][4] We are concerned that such opposite conclusions are drawn using different experimental systems to test the hypothesis.Hu et al 1 used a novel mouse model of arterial transplantation.The authors grafted a donor aorta to a recipient carotid artery using the cuff technique in the absence of immunosuppressants.The pathophysiology of vasculopathy in the authors' model may differ from that of arteriosclerosis observed in immunosuppressed cardiac allografts, as many studies have suggested that immunosuppressants potentially affect the pathogenesis of transplant arteriosclerosis.By inducing 3 distinct types of mechanical vascular injuries to a single mouse, we found that recruitment of bone marrow-derived cells to vascular lesions depends largely on the type of model used (K.Tanaka and M. Sata, unpublished observation, 2002).We detected a robust contribution of bone marrow-derived cells after mechanical endovascular injury, whereas there were only a few marker-positive cells in the neointima after ligation of the common carotid artery.We seldom found bone marrow-derived cells in the lesion induced by perivascular cuff replacement.These results suggest that in certain types of models, we may underestimate the potential contribution of bone marrow cells in vascular remodeling.Furthermore, Hu et al 1 used a transgenic mouse that expresses LacZ in vascular SMCs under the transcriptional control of the SM22 promoter.Human vascular SMCs are quite heterogeneous in the expression of differentiation markers, although ␣-actin is abundantly expressed in all SMCs. 5 Thus, some ␣-actin-positive cells may not express LacZ in the transgenic mouse.Consequently, although the transgenic mice are useful to identify SMCs, they may not be adequate to identify "SMC-like cells" in the neointima.Finally, we are aware that irradiation and bone marrow transplantation have tremendous effects on many tissues, even when the blood system appears to have been reconstituted.Therefore, Hu et al 1 might have underestimated the potential contribution of bone marrow cells to graft vasculopathy.We also believe that there are other sources of smooth muscle progenitors.We suggest caution before extrapolating the conclusions provided by Hu et al to the pathogenesis of graft vasculopathy.
Population pharmacokinetic data analysis of three phase I studies of matuzumab, a humanised anti-EGFR monoclonal antibody in clinical cancer development (2008)

A population pharmacokinetic model based on data from three phase I studies was to be developed including a covariate analysis to describe the concentration-time profiles of matuzumab, a novel humanised monoclonal antibody. Matuzumab was administered as multiple 1 h i.v. infusions with 11 different dosing regimens ranging from 400 to 2000 mg, q1w-q3w. For analysis, 90 patients with 1256 serum concentration-time data were simultaneously fitted using the software NONMEM. Data were best described using a two-compartment model with the parameters central (V1) and peripheral distribution volume (V2), intercompartmental (Q) and linear (CLL) clearance and an additional nonlinear elimination pathway (Km, Vmax). Structural parameters were in agreement with immunoglobulin characteristics. In total, interindividual variability on Vmax, CLL, V1 and V2 and interoccasion variability on CLL was 22-62% CV. A covariate analysis identified weight having an influence on V1 (+0.44% per kg) and CLL (+0.87% per kg). All parameters were estimated with good precision (RSE<39%). A robust population pharmacokinetic model for matuzumab was developed, including a nonlinear pharmacokinetic process. In addition, relevant and plausible covariates were identified and incorporated into the model. When correlated to efficacy, this model could serve as a tool to guide dose selection for this 'targeted' cancer therapy.
Single stranded DNA translocation through a nanopore: A master equation approach (2003)

We study voltage driven translocation of a single stranded DNA through a membrane channel. Our model, based on a master equation approach, investigates the probability density function of the translocation times, and shows that it can be either double peaked or mono peaked, depending on the system parameters. We show that the most probable translocation time is proportional to the polymer length, and inversely proportional to the first or second power of the voltage, depending on the initial conditions. The model recovers experimental observations on hetropolymers when using their properties inside the pore, such as stiffness and polymer-pore interaction.
Separation of Gases by Pressure Swin (1991)

Abstract The recent status of pressure swing adsorption (PSA) as a process for separating multicomponent gas mixtures is reviewed. The applications of a new generation of adsorbents, such as zeolites, carbon molecular sieves, and, more recently, pore engineered molecular sieves, are described in detail. The more important theories of adsorption from gas mixtures as well as those of the PSA process are described briefly. The commercial applications of PSA the process-present and potential-are discussed at length.
Using recent infection testing algorithm tests in clinical practice (2012)

There are major epidemiological and public health advantages in using RITA testing but there are also advantages to using the RITA test on an individual basis, provided that it is used appropriately.
Insights into Mechanisms Used by Staphylococcus aureus to Avoid Destruction by Human Neutrophils (2005)

Polymorphonuclear leukocytes (PMNs, or neutrophils) are critical for human innate immunity and kill most invading bacteria. However, pathogens such as Staphylococcus aureus avoid destruction by PMNs to survive, thereby causing human infections. The molecular mechanisms used by pathogens to circumvent killing by the immune system remain largely undefined. To that end, we studied S. aureus pathogenesis and bacteria-PMN interactions using strains originally isolated from individuals with community-acquired (CA) and hospital-acquired infections. Compared with strains from hospital infections (COL and MRSA252), strain MW2 and a methicillin-susceptible relative, MnCop, were significantly more virulent in a mouse model of S. aureus infection, and caused the greatest level of pathology in major vital organs. Although phagocytosis of each strain triggered production of reactive oxygen species and granule-phagosome fusion, those from CA infections were significantly more resistant to killing by human PMNs and caused greater host cell lysis. Microarray analysis of the strains during neutrophil phagocytosis identified genes comprising a global S. aureus response to human innate host defense. Genes involved in capsule synthesis, gene regulation, oxidative stress, and virulence, were up-regulated following ingestion of the pathogen. Notably, phagocytosis of strains from CA infections induced changes in gene expression not observed in the other strains, including up-regulation of genes encoding virulence factors and hypothetical proteins. Our studies reveal a gene transcription program in a prominent human pathogen that likely contributes to evasion of innate host defense.
Vibration minimized access control for disk drives (1996)

A new access control method called SMART (Structural Vibration Minimized Acceleration Trajectory) has been developed for hard disk drives. The access formula is derived from a minimum-jerk cost function. The closed loop of access mode is based on velocity control and the target velocity to keep minimum-jerk is easily calculated as a function of position by a DSP controller. With SMART control the high harmonics of the actuator acceleration are suppressed in comparison with conventional control. Residual vibration after the access operation and spacing fluctuation of the head slider are both greatly decreased.
Nucleoside Phosphorothioates (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNucleoside PhosphorothioatesFritz EcksteinCite this: J. Am. Chem. Soc. 1966, 88, 18, 4292–4294Publication Date (Print):September 1, 1966Publication History Published online1 May 2002Published inissue 1 September 1966https://pubs.acs.org/doi/10.1021/ja00970a054https://doi.org/10.1021/ja00970a054research-articleACS PublicationsRequest reuse permissionsArticle Views509Altmetric-Citations96LEARN 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
Susceptibility of Human Metabolic Phenotypes to Dietary Modulation (2006)

Dietary composition has been shown to influence metabolism and to impact on the prevalence and risk for certain diseases, but hitherto, there have been no systematic studies on the effects of dietary modulation of human metabolic phenotype (metabotype). Here, we have applied 1H NMR spectroscopy in combination with multivariate statistical analysis to characterize the effects of three diets: "vegetarian", "low meat", and "high meat" on the metabotype signature of human participants. Twelve healthy male participants (age range of 25-74 years) consumed each of these diets, in a randomized order, for continuous 15-day-periods with an intervening washout period between each diet of 7 days duration. Each participant provided three consecutive 24-hour urine collections on days 13, 14, and 15 of each dietary period, and 1H NMR spectra were acquired on all samples. Pattern recognition analysis allowed differentiation of the characteristic metabolic signatures of the diets with creatine, carnitine, acetylcarnitine, and trimethylamine-N-oxide (TMAO) being elevated in the high-meat consumption period. Application of orthogonal projection to latent structure discriminant analysis (O-PLS-DA) allowed the low-meat diet and vegetarian diet signatures to be characterized, and p-hydroxyphenylacetate (a microbial mammalian cometabolite) was higher in the vegetarian than meat diet samples, signaling an alteration of the bacterial composition or metabolism in response to diet. This work shows the potential for the routine use of metabonomics in nutritional and epidemiological studies, in characterizing and predicting the metabolic effects and the influence of diet on human metabotypes.
Comparative Sequencing in the Genus Lycopersicon: Implications for the Evolution of Fruit Size in the Domestication of Cultivated Tomatoes (2002)

Sequence variation was sampled in cultivated and related wild forms of tomato at fw2.2--a fruit weight QTL key to the evolution of domesticated tomatoes. Variation at fw2.2 was contrasted with variation at four other loci not involved in fruit weight determination. Several conclusions could be reached: (1) Fruit weight variation attributable to fw2.2 is not caused by variation in the FW2.2 protein sequence; more likely, it is due to transcriptional variation associated with one or more of eight nucleotide changes unique to the promoter of large-fruit alleles; (2) fw2.2 and loci not involved in fruit weight have not evolved at distinguishably different rates in cultivated and wild tomatoes, despite the fact that fw2.2 was likely a target of selection during domestication; (3) molecular-clock-based estimates suggest that the large-fruit allele of fw2.2, now fixed in most cultivated tomatoes, arose in tomato germplasm long before domestication; (4) extant accessions of L. esculentum var. cerasiforme, the subspecies thought to be the most likely wild ancestor of domesticated tomatoes, appear to be an admixture of wild and cultivated tomatoes rather than a transitional step from wild to domesticated tomatoes; and (5) despite the fact that cerasiforme accessions are polymorphic for large- and small-fruit alleles at fw2.2, no significant association was detected between fruit size and fw2.2 genotypes in the subspecies--as tested by association genetic studies in the relatively small sample studied--suggesting the role of other fruit weight QTL in fruit weight variation in cerasiforme.
Characterization of cDNA clones encoding rabbit and human serum paraoxonase: the mature protein retains its signal sequence (1991)

Serum paraoxonase hydrolyzes the toxic metabolites of a variety of organophosphorus insecticides. High serum paraoxonase levels appear to protect against the neurotoxic effects of organophosphorus substrates of this enzyme [Costa et al. (1990) Toxicol. Appl. Pharmacol. 103, 66-76]. The amino acid sequence accounting for 42% of rabbit paraoxonase was determined by (1) gas-phase sequencing of the intact protein and (2) peptide fragments from lysine and arginine digests. From these data, two oligonucleotide probes were synthesized and used to screen a rabbit liver cDNA library. A clone was isolated and sequenced, and contained a 1294-bp insert encoding an open reading frame of 359 amino acids. Northern blot hybridization with RNA isolated from various rabbit tissues indicated that paraoxonase mRNA is synthesized predominately, if not exclusively, in the liver. Southern blot experiments suggested that rabbit paraoxonase is coded by a single gene and is not a family member of closely related genes. Human paraoxonase clones were isolated from a liver cDNA library by using the rabbit cDNA as a hybridization probe. Inserts from three of the longest clones were sequenced, and one full-length clone contained an open reading frame encoding 355 amino acids, four less than the rabbit paraoxonase protein. Each of the human clones appeared to be polyadenylated at a different site, consistent with the absence of the canonical polyadenylation signal sequence. Of potential significance with respect to the paraoxonase polymorphism, the derived amino acid sequence from one of the partial human cDNA clones differed at two positions from the full-length clone. Amino-terminal sequences derived from purified rabbit and human paraoxonase proteins suggested that the signal sequence is retained, with the exception of the initiator methionine residue [Furlong et al. (1991) Biochemistry (preceding paper in this issue)]. Characterization of the rabbit and human paraoxonase cDNA clones confirms that the signal sequences are not processed, except for the N-terminal methionine residue. The rabbit and human cDNA clones demonstrate striking nucleotide and deduced amino acid similarities (greater than 85%), suggesting an important metabolic role and constraints on the evolution of this protein.
Comparative Study on Overexpression of HER2/neu and HER3 in Gastric Cancer (2009)

The selective overexpression of HER2 and HER3 in the two histologic types of gastric cancer is strongly associated with a poor prognosis. Being an important member of the HER family, HER3 may become another candidate for molecular-targeted therapy in gastric cancer, especially for the diffuse histologic type.
A rat model for studying effects of sacral neuromodulation on the contractile activity of a chronically inflamed bladder (2004)

The results show that this animal model is suitable for studying the effects and mechanisms of sacral neuromodulation on a chronic hyperactive urinary bladder.