gebhart/patrepeval huggingface dataset:
Fault-tolerant computing with biased-noise superconducting qubits: a case study (2009)

We present a universal scheme of pulsed operations suitable for the IBM oscillator-stabilized flux qubit comprising the controlled-sigma(z) (CPHASE) gate, single-qubit preparations and measurements. Based on numerical simulations, we argue that the error rates for these operations can be as low as about 0.5% and that noise is highly biased, with phase errors being stronger than all other types of errors by a factor of nearly 10^3. In contrast, the design of a controlled σ(x) (CNOT) gate for this system with an error rate of less than about 1.2% seems extremely challenging. We propose a special encoding that exploits the noise bias allowing us to implement a logical CNOT gate where phase errors and all other types of errors have nearly balanced rates of about 0.4%. Our results illustrate how the design of an encoding scheme can be adjusted and optimized according to the available physical operations and the particular noise characteristics of experimental devices.
Efficacy of Azacytidine (5-AC) Given as Maintenance or Salvage Therapy for Patients (pts) with Acute Leukemia Post Allogeneic Stem Cell Transplantation (HSCT). (2007)

Abstract Background. Relapse is the most frequent cause of treatment failure in pts with refractory acute leukemia undergoing HSCT. Modifications of the preparative regimen using multiple combinations of chemotherapy and physical agents have failed to reduce the risk of relapse without an increase in non relapse mortality. 5-AC is a DNA hypomethylating agent that may induce leukemic cell differentiation and increased immunogenicity, therefore potentially increasing the graft-versus-leukemia effect. 5-AC, at low doses, through its hypomethylation effect has shown significant activity in pts with myelodysplastic syndromes. Furthermore, low doses are likely to be better tolerated after ASCT. Patients 5-AC was given as salvage therapy for post HSCT relapse in 7 pts with acute myeloid leukemia (AML) and as maintenance therapy in 5 (4 AML, 1 acute lymphocytic leukemia) with high-risk disease. Median age was 52 years (range, 29–67 years). At the time of HSCT, 8 pts were refractory and 4 pts (AML) were in second (n=2) and third complete remission (CR) (n=2). Four pts received and failed previous HSCT following ablative regimen. Donors were HLA-compatible related (n=2), unrelated (n=7; cord blood, n=2), or syngeneic (n=1). Conditioning regimen was gemtuzumab ozogamicin 2 mg/m2, fludarabine and melphalan 140 mg/m2 in 3 pts, fludarabine and melphalan 140 mg/m2 in 6, cyclophosphamide, fludarabine and low dose TBI in 2, and busulfan and cyclophosphamide in 1.GVHD prophylaxis was tacrolimus and mini-methotrexate. ATG was administered to recipients of unrelated donor transplants. Results. After HSCT all pts were in CR. 5-AC was administered at the time of relapse that occurred at a median of 11 months (range, 5–26), and at a median of 4 months (range, 1–12) post HSCT as a maintenance therapy. 5-AC was given at the dose of 16 mg/m2 daily × 5 repeated every 4 weeks (n=3) and 25 mg/m2 daily × 5 (n=9). A median of 7 cycles (range, 2–18 cycles) were delivered. Among 7 pts with relapsed disease [medullary relapse in 4 (median percentage of blasts, 39), extramedullary relapse in 3], 3 achieved a sustained CR for 7+ months, 2 had sustained partial remission for 3+ months, and 2 pts did not respond. All pts receiving 5 AC as maintenance therapy remain in CR for a median of 14+ months (4–28). There was no significant increase in the rates of GVHD. After a median follow-up of 14 months (range, 3–20 months) from the start of 5-AC therapy,11 out of 12 pts are alive, 9 in CR. The 12-month actuarial survival from HSCT is 91%. There were no extra-medullary toxicities and only grade I/II hematologic toxicities were noted. Conclusion. Low dose 5-AC may be effective in the post HSCT setting. Further follow-up and larger number of patients will be necessary to confirm these observations.
Mocvd process model for deposition of complex oxide ferroelectric thin films (2001)

Abstract Thin complex oxide films, such as ferroelectrics, pyroelectrics, waveguides, superconductors, MEMS/MOEMS and piezoelectrics are experiencing rapid growth in a wide variety of commercial markets. In particular, ferroelectrics as used in IC cards, embedded memories with micro-controllers, stand-alone memories, and other ASIC applications, require deposition by a technique that is compatible with deep sub-micron advanced geometry IC integration. Metal Organic Chemical Vapor Deposition (MOCVD) is the deposition method of choice for achieving conformal uniform (composition and thickness) contiguous pin hole free thin films over the challenging sub 0.2 micron geometry topology necessary for implementing advanced devices. MOCVD is free of the physical limitations that produce film defects associated with other liquid source and physical vapor deposition techniques. Of the different MOCVD approaches to complex oxide film deposition, we have found rotating disk reactor (RDR) MOCVD to be the most versatile and capable of producing uniform films efficiently. Using computational fluid dynamic methods, a process model for optimizing the multiple process parameters of RDR-MOCVD, single and multiple wafer production tools, has been developed. The models developed are compatible with plasma-assist, single or multiple precursor and graded composition deposition of films. The developed hardware and model have been combined to maximize thin oxide film properties. SMI modeled RDR MOCVD methodology and film results are presented.
Transfer of Several Phytopathogenic Pseudomonas Species to Acidovorax as Acidovorax avenae subsp. avenae subsp. nov., comb. nov., Acidovorax avenae subsp. citrulli, Acidovorax avenae subsp. cattleyae, and Acidovorax konjaci (1992)

DNA-rRNA hybridizations, DNA-DNA hybridizations, polyacrylamide gel electrophoresis of whole-cell proteins, and a numerical analysis of carbon assimilation tests were carried out to determine the relationships among the phylogenetically misnamed phytopathogenic taxa Pseudomonas avenae, Pseudomonas rubrilineans, "Pseudomonas setariae," Pseudomonas cattleyae, Pseudomonas pseudoalcaligenes subsp. citrulli, and Pseudomonas pseudoalcaligenes subsp. konjaci. These organisms are all members of the family Comamonadaceae, within which they constitute a separate rRNA branch. Only P. pseudoalcaligenes subsp. konjaci is situated on the lower part of this rRNA branch; all of the other taxa cluster very closely around the type strain of P. avenae. When they are compared phenotypically, all of the members of this rRNA branch can be differentiated from each other, and they are, as a group, most closely related to the genus Acidovorax. DNA-DNA hybridization experiments showed that these organisms constitute two genotypic groups. We propose that the generically misnamed phytopathogenic Pseudomonas species should be transferred to the genus Acidovorax as Acidovorax avenae and Acidovorax konjaci. Within Acidovorax avenae we distinguished the following three subspecies: Acidovorax avenae subsp. avenae, Acidovorax avenae subsp. cattleyae, and Acidovorax avenae subsp. citrulli. Emended descriptions of the new taxa are presented.
Wattch (2000)

Power dissipation and thermal issues are increasingly significant in modern processors. As a result, it is crucial that power/performance tradeoffs be made more visible to chip architects and even compiler writers, in addition to circuit designers. Most existing power analysis tools achieve high accuracy by calculating power estimates for designs only after layout or floorplanning are complete. In addition to being available only late in the design process, such tools are often quite slow, which compounds the difficulty of running them for a large space of design possibilities. This paper presents Wattch, a framework for analyzing and optimizing microprocessor power dissipation at the architecture-level. Wattch is 1000X or more faster than existing layout-level power tools, and yet maintains accuracy within 10% of their estimates as verified using industry tools on leading-edge designs. This paper presents several validations of Wattch's accuracy. In addition, we present three examples that demonstrate how architects or compiler writers might use Wattch to evaluate power consumption in their design process. We see Wattch as a complement to existing lower-level tools; it allows architects to explore and cull the design space early on, using faster, higher-level tools. It also opens up the field of power-efficient computing to a wider range of researchers by providing a power evaluation methodology within the portable and familiar SimpleScalar framework.
Effect of nano-CaCO3 on hydration of cement containing supplementary cementitious materials (2011)

The efficacy of the addition of nano-CaCO 3 in accelerating the hydration of ordinary Portland cement (OPC) delayed by the presence of high volumes of supplementary cementitious materials including fly ash and slag was investigated. The conduction calorimetry indicated that the early hydration of OPC was significantly accelerated by the addition of the nano-CaCO 3 and the higher the amount of CaCO 3 addition, the greater was the accelerating effect. The thermogravimetric analysis results showed that the amounts of added CaCO 3 became slightly lower as the hydration took place; however, any new reaction products were not detected by the X-ray diffractometry analysis. The engineering properties, including microhardness and modulus of elasticity, in the early stage of the hydration were remarkably improved by the addition of nano-CaCO 3 . It was suggested that the seeding effect of the nano-CaCO 3 particles and the nucleation of C–S–H caused the enhanced strength development.
Intrachain disulfide bond in the core hinge region of human IgG4 (1997)

IgG is a tetrameric protein composed of two copies each of the light and heavy chains. The four-chain structure is maintained by strong noncovalent interactions between the amino-terminal half of pairs of heavy-light chains and between the carboxyl-terminal regions of the two heavy chains. In addition, interchain disulfide bonds link each heavy-light chain and also link the paired heavy chains. An engineered human IgG4 specific for human tumor necrosis factor-alpha (CDP571) is similar to human myeloma IgG4 in that it is secreted as both disulfide bonded tetramers (approximately 75% of the total amount of IgG) and as tetramers composed of nondisulfide bonded half-IgG4 (heavy chain disulfide bonded to light chain) molecules. However, when CDP571 was genetically engineered with a proline at residue 229 of the core hinge region rather than serine, CDP571 (S229P), or with an IgG1 rather than IgG4 hinge region, CDP571(gamma 1), only trace amounts of nondisulfide bonded half-IgG tetramers were observed. Trypsin digest reversephase HPLC peptide mapping studies of CDP571 and CDP571(gamma 1) with on-line electrospray ionization mass spectroscopy supplemented with Edman sequencing identified the chemical factor preventing inter-heavy chain disulfide bond formation between half-IgG molecules: the two cysteines in the IgG4 and IgG1 core hinge region (CPSCP and CPPCP, respectively) are capable of forming an intrachain disulfide bond. Conformational modeling studies on cyclic disulfide bonded CPSCP and CPPCP peptides yielded energy ranges for the low-energy conformations of 31-33 kcal/mol and 40-42 kcal/mol, respectively. In addition, higher torsion and angle bending energies were observed for the CPPCP peptide due to backbone constraints caused by the extra proline. These modeling results suggest a reason why a larger fraction of intrachain bonds are observed in IgG4 rather than IgG1 molecules: the serine in the core hinge region of IgG4 allows more hinge region flexibility than the proline of IgG1 and thus may permit formation of a stable intrachain disulfide bond more readily.
Phase Ia-Ib trial of an anti-GD3 monoclonal antibody in combination with interferon-alpha in patients with malignant melanoma. (1990)

A phase Ia-Ib study was undertaken to treat melanoma patients with a constant dose of the anti-GD3 monoclonal antibody, R24, in combination with increasing dose levels of recombinant interferon-alpha (rHuIFN alpha-2a). Fifteen patients were treated on days 1-5 and 8-12 with a continuous 6-h i.v. infusion of R24 (8 mg/m2) and escalating i.m. doses of rHuIFN alpha-2a. Peripheral blood lymphocytes were obtained at multiple times before and during treatment and monitored for changes in lymphocyte subpopulations and changes in natural killer and antibody-dependent cellular toxicity functional activity. There were no consistent changes in most immune parameters; however, there was a decrease from pretreatment levels in the suppressor T cell (CD8+, CD11b+) subset and a dose-dependent decrease in the helper/inducer (CD4+, Leu-8+) T cell subset. The peak serum concentration of R24 was reached on day 5 of the study and was 9.4 micrograms/ml. During the second week of treatment, peak serum levels of R24 fell to less than 4 micrograms/ml. This finding was related to the development of human antimouse antibody, which would be detected as early as day 8 of the study. Binding of mouse Ig (R24) within the tumor bed was observed in 5 of 12 biopsy specimens. The maximal tolerated dose of the combination was dose level IV, in which patients received 8 mg/m2 of R24 and 50 x 10(6) units of rHuIFN alpha-2a on days 1-5 and 8-12 of treatment.
Circulating Irisin in Relation to Insulin Resistance and the Metabolic Syndrome (2013)

Irisin is associated with increased risk of MetS, cardiometabolic variables, and CVD in humans, indicating either increased secretion by adipose/muscle tissue and/or a compensatory increase of irisin to overcome an underlying irisin resistance in these subjects.
Breschini et al. (1988)

California Radiocarbon Dates . Fifth edition. Gary S. Breschini, Trudy Haversat, and Jon Erlandson, Compilers. Salinas: Coyote Press, 1988, vi -i- 119 pp., 30 figs., 1 table, $5.95 (paper).
The Role of Complement System in Septic Shock (2012)

Septic shock is a critical clinical condition with a high mortality rate. A better understanding of the underlying mechanisms is important to develop effective therapies. Basic and clinical studies suggest that activation of complements in the common cascade, for example, complement component 3 (C3) and C5, is involved in the development of septic shock. The involvement of three upstream complement pathways in septic shock is more complicated. Both the classical and alternative pathways appear to be activated in septic shock, but the alternative pathway may be activated earlier than the classical pathway. Activation of these two pathways is essential to clear endotoxin. Recent investigations have shed light on the role of lectin complement pathway in septic shock. Published reports suggest a protective role of mannose-binding lectin (MBL) against sepsis. Our preliminary study of MBL-associated serine protease-2 (MASP-2) in septic shock patients indicated that acute decrease of MASP-2 in the early phase of septic shock might correlate with in-hospital mortality. It is unknown whether excessive activation of these three upstream complement pathways may contribute to the detrimental effects in septic shock. This paper also discusses additional complement-related pathogenic mechanisms and intervention strategies for septic shock.
Dry-heat destruction of lipopolysaccharide: dry-heat destruction kinetics (1978)

Dry-heat destruction kinetics of lipopolysaccharides from Escherichia coli, Serratia marcescens, and Salmonella typhosa at 170 to 250 degrees C are described. The destruction rate seems to follow the second order and can be linearized by the equation, log y = a + b . -10cx. Because c is the slope, 1/c = D3. Both a and b are constant at a given temperature and are linear functions of temperature. The D(3)170, D(3)190, D(3)210, D(3)230, and D(3)250 values for E. coli lipopolysaccharide are 251, 99.4, 33.3, 12.3, and 4.99 min, respectively, with a z value of 46.4 min. The D values for lipopolysaccharides from S. marcescens and S. typhosa are not significantly different from those from E. coli lipopolysaccharide.
Performance of a Heat Exchanger Based on Enhanced Heat Diffusion in Fluids by Oscillation: Analysis (1990)

Fluid flow and heat transfer in capillary tubes (Stokes’ boundary-layer thickness nearly equal to the tube radius), subject to oscillatory flow from two reservoirs maintained at different temperatures, has been analyzed. Extension of existing analysis has been made by allowing for finite wall thickness and estimating the viscous dissipation. For a bundle of tubes connected to reservoirs of finite volume, analysis is also made of the oscillatory motion in the reservoirs (assuming a piston-type displacement within the reservoirs). The effects of various fluid and tube parameters on the heat transfer in a single tube are examined. The pathlines followed by fluid particles show that the extent of interaction between the fluid exiting the bundle and the fluid in the reservoirs (or the heat transfer surfaces in the reservoirs) depends strongly on the radial position of the exiting fluid particles. In a follow-up paper, these predictions are compared with some experimental results.
ENSEMBLE-BASED TIME SERIES DATA CLUSTERING FOR HIGH DIMENSIONAL DATA (2014)

The time series clustering analysis provides an effective way to discover the intrinsic structure. In most of the time, the series of data mining algorithms uses similarity search as the core subroutine, and hence the time taken for similarity search becomes complicated, due to the large data sets. In this paper, we have developed an approach for clustering the temporal data via the ensemble of cluster weight for multiple partitions developed by initial clustering analysis on two types of representations. Ini- tially, time series data sets are converted into representations in which each partition is used to reduce the dimension and subsequently, the clustering algorithm is applied. The different types of weight algorithms are applied to each of the representation. By consid- ering the weight and the representation matrix, we develop thenal clustering. Finally the experimentations are carried out on the time series data sets, and the simulation results demonstrate that our approach gives the desired results in clustering analysis of time series data. Keywords: Representations, Time series data, Representation clustered matrix, Wei- ghted consensus function, Fuzzy- C-means (FCM), Kernel function, Temporal data clus- tering
High-throughput carbohydrate microarray profiling of 27 antibodies demonstrates widespread specificity problems (2007)

Progress toward understanding the biological roles of carbohydrates has been remarkably slow, and efforts to exploit this class of biopolymers as diagnostic and therapeutic targets have proven extremely challenging. Both basic and clinical research rely heavily on identifying and monitoring expression levels of carbohydrates. Over the last 30 years, the majority of expression information has been derived from antibody- and lectin-binding studies. Using a carbohydrate microarray containing 80 different glycans and glycoproteins, the specificities of 27 antiglycan antibodies were evaluated, including antibodies to histo-blood group A, B, and H antigens (81FR2.2, CLCP-19B, B389, 92FR-A2, B480, B460, B376, and B393), Lewis antigens (7LE, 15C02, 28, ZC-18C, 121SLE, CA199.02, PR.5C5, 2-25LE, BR55, T174, T218, F3, A70-C/C8, FR4A5, and K21), and other tumor-associated antigens (B389, 1A4, B1.1, and 5B5). In total, evaluation of over 2000 individual carbohydrate-protein interactions was carried out. More than half of the antibodies considered to be specific for their designated antigen were found to cross-react with other glycans. The cross-reactive glycans could be mistaken for the designated antigen in biopsy samples or other biological samples, leading to inaccurate conclusions.
Achieving high performance web applications by service and database replications at edge servers (2009)

Edge server replication is an effective solution to achieve high performance in dynamic web applications, such as Web services. Many Web services involve frequent accesses to large-scale backend databases. Current database replication techniques are not directly applicable to edge server architectures. There is no algorithm to dynamically and automatically select the tables for replication. Also, most of the solutions do not consider the potentially limited disk sizes at the edge servers and the needs for them to serve many application sites. In this paper, we present a novel weighted table graph based database replication approach for edge servers to address these problems. Every step in our approach is based on quantitative computation, so it can generate an accurate result. Experimental studies show that our database replication approach significantly improves the performance of Web systems in terms of client response latency, Web application server off loading, and network bandwidth saving.
Influenza virus RNA polymerase PA subunit is a novel serine protease with Ser624 at the active site (2001)

These results constitute the demonstration of protease activity in PA subunit of the influenza virus RNA polymerase complexes.
Pulsatile pressure can prevent rapid baroreflex resetting (1990)

In a previous study [Am. J. Physiol. 255 (Heart Circ. Physiol. 24): H673-H678, 1988] we demonstrated that baroreflex responses decay (reset) to increased static sinus pressures, but with increased pulsatile pressure, responses are maintained. To determine more conclusively whether pulsatile pressure prevents rapid baroreflex resetting in this study we examined resetting as shifts of the baroreflex (sinus pressure-arterial pressure) curve. In seven anesthesized rabbits the left sinus was vascularly isolated and conditioned for 5 min to static or pulsatile pressures of 60, 100, or 140 mmHg mean pressure, 0 or 35-40 mmHg pulse pressure. The baroreflex curve was then determined by stepwise changing sinus pressure from 40 to 160 mmHg in 20-mmHg increments. Threshold, midpoint, and saturation sinus pressures shifted 25-39% with static conditioning pressures but did not shift significantly with pulsatile pressures. Also, the baroreflex responses to step increases in static sinus pressure decayed, as resetting occurred, but did not decay with pulsatile sinus pressure increases. Thus the baroreflex rapidly resets with static pressures, but there is minimal, if any, resetting with pulsatile pressures.
Molecular chaperone properties of serum amyloid P component (2000)

The selective binding of serum amyloid P component (SAP) to proteins in the pathological amyloid cross-beta fold suggests a possible chaperone role. Here we show that human SAP enhances the refolding yield of denatured lactate dehydrogenase and protects against enzyme inactivation during agitation of dilute solutions. These effects are independent of calcium ions and are not inhibited by compounds that block the amyloid recognition site on the B face of SAP, implicating the A face and/or the edges of the SAP pentamer. We discuss the possibility that the chaperone property of SAP, or its failure, may contribute to the pathogenesis of amyloidosis.