gebhart/patrepeval huggingface dataset:
Assesssing uncertainty in software reliability via quasi-monte carlo methods (2005)

The need of conducting uncertainty analysis in software reliability for the large and complexity system is demanding. The Monte Carlo method is used for reliability prediction and assessing uncertainty in software reliability. An important improvement of the convergence rate (and thus of speed) can be achieved by using quasi-Monte Carlo methods. These are variants of ordinary Monte Carlo methods, but use quasi-random (highly uniform) sequences instead of pseudorandom sequences. This enhanced uniformity leads to higher rates of convergence. Analysis of a simple problem in software reliability showed that quasi-Monte Carlo methods achieve the same or better parameter estimates as standard Monte Carlo, but have the potential to converge faster and so reduce the computational burden. The paper will explore the use of quasi-Monte Carlo methods to assessing uncertainty in software Reliability.
Esomeprazole once daily for 6 months is effective therapy for maintaining healed erosive esophagitis and for controlling gastroesophageal reflux disease symptoms: a randomized, double-blind, placebo-controlled study of efficacy and safety (2001)

Esomeprazole is effective and well tolerated in the maintenance of a healing erosive esophagitis. Esomeprazole 40 mg and 20 mg maintain healing in over 90% of patients while providing effective control of heartburn symptoms.
Vibrational spectroscopy of carboranes and parent boranes and its capabilities in carborane chemistry (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTVibrational spectroscopy of carboranes and parent boranes and its capabilities in carborane chemistryL. A. LeitesCite this: Chem. Rev. 1992, 92, 2, 279–323Publication Date (Print):March 1, 1992Publication History Published online1 May 2002Published inissue 1 March 1992https://pubs.acs.org/doi/10.1021/cr00010a006https://doi.org/10.1021/cr00010a006research-articleACS PublicationsRequest reuse permissionsArticle Views1289Altmetric-Citations194LEARN 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
Overlapped Message Passing for Quasi-Cyclic Low-Density Parity Check Codes (2004)

In this paper, a systematic approach is proposed to develop a high throughput decoder for quasi-cyclic low-density parity check (LDPC) codes, whose parity check matrix is constructed by circularly shifted identity matrices. Based on the properties of quasi-cyclic LDPC codes, the two stages of belief propagation decoding algorithm, namely, check node update and variable node update, could be overlapped and thus the overall decoding latency is reduced. To avoid the memory access conflict, the maximum concurrency of the two stages is explored by a novel scheduling algorithm. Consequently, the decoding throughput could be increased by about twice assuming dual-port memory is available.
Use of RhD Fusion Protein Expressed on K562 Cell Surface in the Study of Molecular Basis for D Antigenic Epitopes (1999)

The human D antigens, one of the most clinically important blood groups, are presented by RhD protein with a putative 12 transmembrane topology. To understand the molecular basis for the complex antigenic profile of RhD protein, we expressed a series of RhD fusion proteins using different portions of Duffy protein as a tag in erythroleukemic K562 cells. Because the reactivity of monoclonal anti-RhD antibody, LOR15C9, depends mainly on the sequence coded by exon 7 of RhD, we altered DNA sequence corresponding to the amino acid residues 323-331(A) and 350-354(B) in the exon 7. The mutation in region B resulted in a severe reduction in LOR15C9 binding by flow cytometry analysis, suggesting that region B may play an important role in constituting antigen epitopes recognized by LOR15C9. On the other hand, a slight decrease in the antibody binding was observed for the region A mutant, suggesting that the intracellularly located region A may elicit a long distance effect on the formation of exofacial antigen epitopes. In addition, using various monoclonal antibodies against RhD, we compared the antigenic profile of expressed RhD fusion protein with that of endogenous RhD in K562 cells as well as in erythrocytes.
Simulating and Designing Brillouin Gain Spectrum in Single-Mode Fibers (2004)

For many fiber applications, the Brillouin gain spectrum (BGS) contains important information including the Brillouin frequency shift, the Brillouin spontaneous linewidth, and the Brillouin gain coefficient. This paper is the first, to the best of our knowledge, to present an accurate numerical simulation of the BGS in single-mode fibers. The simulated and measured BGS were in good agreement. Through repeated numerical simulations, we revealed a tendency of the peak Brillouin gain coefficient that determines the stimulated Brillouin scattering threshold.
Automated parallel DNA sequencing on multiple channel microchips (2000)

We report automated DNA sequencing in 16-channel microchips. A microchip prefilled with sieving matrix is aligned on a heating plate affixed to a movable platform. Samples are loaded into sample reservoirs by using an eight-tip pipetting device, and the chip is docked with an array of electrodes in the focal plane of a four-color scanning detection system. Under computer control, high voltage is applied to the appropriate reservoirs in a programmed sequence that injects and separates the DNA samples. An integrated four-color confocal fluorescent detector automatically scans all 16 channels. The system routinely yields more than 450 bases in 15 min in all 16 channels. In the best case using an automated base-calling program, 543 bases have been called at an accuracy of >99%. Separations, including automated chip loading and sample injection, normally are completed in less than 18 min. The advantages of DNA sequencing on capillary electrophoresis chips include uniform signal intensity and tolerance of high DNA template concentration. To understand the fundamentals of these unique features we developed a theoretical treatment of cross-channel chip injection that we call the differential concentration effect. We present experimental evidence consistent with the predictions of the theory.
TEAPC: Temperature Adaptive Computing in a Real PC (2005)

TEAPC is an IBM/Intel-standard PC realization of a CPU temperature-adaptive feedback-control system. The control system adjusts the CPU frequency and/or voltage to maintain a constant set-point temperature. TEAPC dynamically adapts to changing CPU computation loads, as well as any other system phenomenon that affects the CPU temperature. For example, with the specific TEAPC hardware, should the CPU cooling fan fail, the control system detects the increase in CPU temperature and automatically reduces the CPU frequency and voltage to keep the CPU from overheating. In such a circumstance the system continues to operate. All of the adaptation is done dynamically, at runtime, on an unmodified standard operating system (Windows 2000) with a purely software-implemented feedback-control system.
Clinical and biologic implications of recurrent genomic aberrations in myeloma (2003)

Nonrandom recurrent chromosomal abnormalities are ubiquitous in multiple myeloma (MM) and include, among others, translocations of the immunoglobulin heavy chain locus (IgH). IgH translocations in MM result in the up-regulation of oncogenes, and include more commonly t(11;14)(q13;q32), t(4;14)(p16;q32), and t(14;16)(q32;q23). Based on the recurrent nature of these translocations and their finding since the early stages of the plasma cell (PC) disorders, we hypothesized that they would confer biologic and clinical variability. In addition, deletions of 13q14 and 17p13 have also been associated with a shortened survival. We used cytoplasmic Ig-enhanced interphase fluorescent in situ hybridization to detect deletions (13q14 and 17p13.1), and translocations involving IgH in 351 patients treated with conventional chemotherapy entered into the Eastern Cooperative Oncology Group clinical trial E9486/9487. Translocations were frequently unbalanced with loss of one of the derivative chromosomes. The presence of t(4; 14)(p16;q32) (n = 42; 26 vs 45 months, P <.001), t(14;16)(q32;q23) (n = 15; 16 vs 41 months, P =.003), - 17p13 (n = 37; 23 vs 44 months, P =.005), and - 13q14 (n = 176; 35 vs 51 months, P =.028) were associated with shorter survival. A stratification of patients into 3 distinct categories allowed for prognostication: poor prognosis group (t(4;14)(p16;q32), t(14; 16)(q32;q23), and - 17p13), intermediate prognosis (- 13q14), and good prognosis group (all others), with median survivals of 24.7, 42.3, and 50.5 months, respectively (P <.001). This molecular cytogenetic classification identifies patients into poor, intermediate, and good risk categories. More importantly it provides further compelling evidence that MM is composed of subgroups of patients categorized according to their underlying genomic aberrations.
Genetic analysis of a Chinese Han family with multiple endocrine neoplasia type 2A. (2013)

Multiple endocrine neoplasia type 2 (MEN2) is an autosomal dominant disorder that can be distinguished as three different syndromes: multiple endocrine neoplasia type 2A (MEN2A), MEN2B and familial medullary thyroid carcinoma (FMTC). This disorder is usually caused by the mutations of the rearranged during transfection protooncogene gene (RET) or the neurotrophic tyrosine kinase receptor type 1 gene (NTRK1). To investigate the genetic cause in a Chinese Han family with MEN2A and the genotype-phenotype correlations, nine members belonging to 3 generations of MEN2A family with 5 affected subjects underwent genetic analysis. Standard GTG-banded karyotype analysis and sequencing of the RET and NTRK1 genes were performed to identify the genetic cause of this family. A heterozygous mutation p.Cys634Arg in the RET gene was identified in 5 patients with MEN2A and one asymptomatic family member. The phenotype of patients was that of classic MEN2A, characterized by medullary thyroid carcinoma and phaeochromocytoma. The clinical features of all cases with RET mutations varied greatly, including onset age of clinical manifestations, severity and comorbidities. Thus, this study not only identified the hereditary nature of the MEN2A in the cases, but also discovered a family member harboring the same p.Cys634Arg mutation, who was unaware of his condition. These finding may provide new insights into the cause and diagnosis of MEN2A and have implications for genetic counseling.
Hypoxia up‐regulates expression of Eph receptors and ephrins in mouse skin (2005)

Eph receptor tyrosine kinases and their ligands (ephrins) are key players during the development of the embryonic vasculature; however, their role and regulation in adult angiogenesis remain to be defined. Both receptors and ligands have been shown to be up-regulated in a variety of tumors. To address the hypothesis that hypoxia is an important regulator of Ephs/ephrins expression, we developed a mouse skin flap model of hypoxia. We demonstrate that our model truly represents segmental skin hypoxia by applying four independent methods: continuous measurement of partial cutaneous oxygen tension, monitoring of tissue lactate/pyruvate ratio, time course of hypoxia-inducible factor-1alpha (HIF-1alpha) induction, and localization of stabilized HIF-1alpha by immunofluorescence in the hypoxic skin flap. Our experiments indicate that hypoxia up-regulates not only HIF-1alpha and vascular endothelial growth factor (VEGF) expression, but also Ephs and ephrins of both A and B subclasses in the skin. In addition, we show that in Hep3B and PC-3 cells, the hypoxia-induced up-regulation of Ephs and ephrins is abrogated by small interfering RNA-mediated down-regulation of HIF-1alpha. These novel findings shed light on the role of this versatile receptor/ligand family in adult angiogenesis. Furthermore, our model offers considerable potential for analyzing distinct mechanisms of neovascularization in gene-targeted mice.
Characterisation of a Protease from Escherichia coli Involved in Hydrogenase Maturation (1995)

The large subunits of nickel-containing hydrogenases are synthesised in a precursor form which, after nickel incorporation, is processed by proteolytic cleavage at the C-terminal end. The protease involved in processing of HycE, the large subunit of hydrogenase 3 from Escherichia coli, was purified by three chromatographic steps to apparent homogeneity. Its gene was identified by using a hybridisation probe generated by PCR with oligonucleotide primers the sequence of which was derived from the N-terminal and internal amino acid sequences. Determination of the nucleotide sequence showed that the gene is located distally and as a hitherto uncharacterised gene within the hyc operon, coding for hydrogenase 3 components. It was designated hycI. The HycI protease has a molecular mass of 17 kDa and is a monomer. Its cleavage reaction is not inhibited by conventional inhibitors of serine and metalloproteases, which correlates with the fact that the sequence does not contain signature motifs characteristic of serine-, metallo-, cysteine- or acid proteases. Homologous genes are present in other transcriptional units coding for hydrogenases.
Rayleigh and Mie scattering in polymer optical fibers (2006)

In this article, the influence of Rayleigh and Mie scattering, which are the main causes of mode mixing in polymer optical fibers (POFs), is investigated. Measurement results obtained from a variety of different POF types ranging from standard POF, high-temperature POF, up to custom-made POF are presented. These measurements are compared to theoretical results obtained from a simplified scattering model. By comparing both results, the contribution of the different scattering sources and mechanisms is characterized independently
Cocaine, Lidocaine, Tetracaine (1995)

The quality of nasal anesthesia obtained with three local anesthetic solutions (4% cocaine, 2% lidocaine in oxymetazoline, and 1% tetracaine in oxymetazoline) was evaluated in a randomized study.Each local anesthetic mixture was applied to the nasal septum of healthy volunteers using medication-soaked pledgets. Measurements of anesthetic effect (sensation threshold and pain perception) were made with Semmes-Weinstein monofilaments. Measurements were performed prior to local anesthetic application and 10 and 70 min after local anesthetic application. Subjects had greater increases in sensation threshold with tetracaine than with lidocaine or cocaine at both 10 and 70 min (P < 0.05). Subjects had greater decreases in pain perception with tetracaine than with lidocaine or cocaine at both time intervals (P < 0.05). Tetracaine mixed with oxymetazoline appears to be a superior topical anesthetic for nasal procedures. (Anesth Analg 1995;81:724-7)
Analysis for spectrum efficiency in single cell trunked and cellular mobile radio (1987)

Spectrum efficiencies for single-cell trunked and cellular mobile radio systems are analyzed, taking into consideration fading circumstances and call blocking probability. Two kinds of transmit power control methods are considered. One retains area mean power at the receiver constant and the other retains local mean power constant. For single-cell trunked systems, it has been shown how spectrum efficiency is limited by the required traffic quality or permitable adjacent channel interference. A narrower channel spaced system shows superiority to wide-band systems, if an adjacent channel interference protection ratio is lower than about -40 dB and a few percent interference probability is permitted. On comparing cellular systems, superiority in spectrum efficiency is determined by the product of protection ratio and channel spacing. Call blocking probability and interference have little effect on spectrum efficiency comparison. For both systems, the two kinds of transmit power control and the two interchannel interference criteria show no significant difference between their effects on spectrum efficiency.
Copolymer cell/scaffold constructs for bone tissue engineering: Co‐culture of low ratios of human endothelial and osteoblast‐like cells in a dynamic culture system (2012)

The aim of this study was to compare the effect of different ratios of human umbilical vein endothelial cells (HUVECs) on osteogenic activity of human osteoblast-like cells (HOB) and capillary-like structure (CLS), seeded into copolymer scaffolds in a dynamic culture system. HOB and HUVEC were co-cultured into poly(L-lactide)-co-(1,5-dioxepan-2-one) [poly(LLA-co-DXO)] scaffolds at ratios of 5:1 (5:1 group) and 2:1 (2:1 group). Samples were collected after 5, 15, and 25 days. Cross-sections were processed and the CLS from HUVEC was disclosed in both groups. Cell viability was determined by dsDNA assay. Cells seeded at the ratio of 5:1 had good viability. Total RNA was isolated and the reverse transcription reaction was performed. The influences on the expression of several osteogenic genes were various with regarding to different ratios of HUVEC demonstrated by the PCR array. The RT-PCR results was in consistent with the PCR array results that several osteogenesis related genes had higher expression in the 5:1 group than in the 2:1 group, especially at day 25, such as alkaline phosphatase, insulin-like growth factor 1 (IGF1), and so forth. ELISA showed that the production of IGF1 after 25 days of incubation were higher in cells co-cultured at the 5:1 ratio than at the 2:1 ratio. The results show that under dynamic culture conditions, co-culture of HOB with a low ratio of HUVEC in copolymer scaffolds results in CLS formation and significantly influenced the expression of osteogenic markers.
Progress towards ultra-rapid DNA sequencing with protein nanopores (2011)

The sequencing of individual DNA strands with nanopores is being developed as a rapid, low-cost platform in which bases are identified in order as a DNA strand is transported through a pore under an electrical potential. Several challenges remain and this thesis focuses on one major area, the base identification properties of the a-hemolysin (aHL) nanopore. Under the potentials required for threading, DNA translocates too fast for single bases to be identified. However, immobilization of the DNA within the pore increases the residence time and therefore improves the precision of the electrical current reading and allows for the small differences in current flow, associated with different sequences, to be observed. DNA molecules with a 3'-terminal biotin-tag were complexed with streptavidin. Streptavidin is too large to be transported through the aHL pore and therefore the DNA-btnestreptavidin complex is not fully translocated; thus, the DNA strand is immobilized within the pore. Using this approach the nucleobase recognition properties of the aHL pore were mapped. The data suggest that the transmembrane 13 barrel domain of the pore contains at least three nucleobase recognition sites, termed R1, R2 and R3. Additional sequence information can be gained when multiple recognition sites are employed within a single aHL pore, as compared to the simple case of a single recognition site. Recognition site R1, which is located near the central constriction, can be modified by site-directed mutagenesis of Met-113. It was observed that amino acids with related side chains produce similar patterns of nucleobase recognition. Amino acids that provide an energy barrier to ion flow (e.g. bulky or hydrophobic residues) strengthen base identification, while amino acids that lower the barrier, weaken identification. Deletion and site-directed mutagenesis were used to remove one recognition site and generate an αHL pore. With truncated β barrel domain that contains only two recognition sites.
Chemotransduction properties of nodose ganglion cardiac afferent neurons in guinea pigs (2000)

To determine the chemotransduction characteristics of ventricular sensory neurites associated with nodose ganglion afferent neurons, various chemicals were applied individually to epicardial sensory neurites associated with individual afferent neurons in anesthetized guinea pigs. The following ion channel-modifying agents were tested: barium chloride, cadmium chloride, calcium chloride, the chelating agent EGTA, nickel chloride, potassium chloride, tetraethylammonium chloride, and veratridine. An acidic solution (pH 6.0) and oxygen-derived free radicals (H(2)O(2)) were tested. The following chemicals were also tested: adenosine, alpha- and beta-adrenergic agonists, angiotensin II, bradykinin, calcitonin gene-related peptide (CGRP), histamine, nicotine, the nitric oxide donor nitroprusside, substance P, and vasoactive intestinal peptide. A total of 102 cardiac afferent neurons was identified, of which approximately 66% were sensitive to mechanical stimuli applied to their epicardial sensory fields. Application of individual ion channel-modifying agents to epicardial sensory fields modified most associated afferent neurons, with barium chloride affecting each neuron studied. Ventricular sensory neurites associated with most identified neurons were also responsive to the other tested chemicals, with hydrogen peroxide, adenosine, angiotensin II, bradykinin, CGRP, clonidine, and nicotine inducing responses from at least 75% of the neurons studied. It is concluded that 1) the ventricular sensory neurites associated with nodose ganglion afferent neurons transduce a much wider variety of chemical stimuli than considered previously, 2) these sensory neurites employ a variety of membrane ion channels in their transduction processes in situ, and 3) adrenergic agents influence on sensory neurites associated with cardiac afferent neurons suggests the presence of a cardiac feedback mechanism involving local catecholamine release by adjacent sympathetic efferent postganglionic nerve terminals.
Xylanases, xylanase families and extremophilic xylanases (2004)

Xylanases are hydrolytic enzymes which randomly cleave the beta 1,4 backbone of the complex plant cell wall polysaccharide xylan. Diverse forms of these enzymes exist, displaying varying folds, mechanisms of action, substrate specificities, hydrolytic activities (yields, rates and products) and physicochemical characteristics. Research has mainly focused on only two of the xylanase containing glycoside hydrolase families, namely families 10 and 11, yet enzymes with xylanase activity belonging to families 5, 7, 8 and 43 have also been identified and studied, albeit to a lesser extent. Driven by industrial demands for enzymes that can operate under process conditions, a number of extremophilic xylanases have been isolated, in particular those from thermophiles, alkaliphiles and acidiphiles, while little attention has been paid to cold-adapted xylanases. Here, the diverse physicochemical and functional characteristics, as well as the folds and mechanisms of action of all six xylanase containing families will be discussed. The adaptation strategies of the extremophilic xylanases isolated to date and the potential industrial applications of these enzymes will also be presented.