gebhart/patrepeval huggingface dataset:
Evaluation and reporting of enzyme immunoassay determinations of antibody to herpes simplex virus in sera and cerebrospinal fluid (1982)

Several methods for evaluating and reporting enzyme immunoassay (EIA) determinations of antibody to herpes simplex virus derived from one dilution of single serum samples were studied. An EIA ratio method for serological evidence of current infection from paired serum samples was also evaluated. Optical density (OD) of the reaction at a 1:100 serum dilution and estimated titers obtained by reference of the OD of the serum dilution to a standard curve were compared to the corresponding plotted EIA titer obtained by titration to endpoint. Neither the OD per se nor the estimated titer was completely predictive of the plotted titer (correlation coefficient [r] of 0.824 and 0.817, respectively), and they provided only a semiquantitative measurement of antibody concentration. For an antibody status report, however, OD would be sufficient if related to the cutoff value as an EIA index (OD of sample divided by cutoff OD for positive specimens). The OD of the EIA reaction at a single dilution (1:5) of cerebrospinal fluid, on the other hand, correlated quite well with the titer obtained by titration (r = 0.950). For serological diagnosis of current infection, the OD ratio of convalescence-phase/acute-phase sera was determined at several dilutions. A ratio of greater than or equal to 1.54 was calculated as a reliable index for a significant rise in antibody concentration and compatible with current infection. By determining the convalescent-phase/acute-phase serum ratio at two dilutions, 1:100 and 1:1,000, the EIA ratio method appeared to be a sensitive as or more sensitive than, complement fixation in diagnosing current infection.
Nucleotide sequence of equine erythropoietin and characterization of region-specific antibodies (2004)

Abstract Objective —To determine the full-length complementary DNA (cDNA) sequence of equine erythropoietin (EPO) and to develop region-specific antibodies to differentiate equine EPO (eEPO) and human EPO (hEPO). Sample Population —RNA and lysate extracted from renal tissues of an adult Thoroughbred. Procedure —Full-length cDNA was determined by use of a reverse transcriptase-polymerase chain reaction assay and a rapid amplification of cDNA ends method. The deduced amino acid sequence was compared with sequences of EPO reported for other species. Furthermore, 4 synthetic peptides were designed in 2 distinctive parts of the eEPO and hEPO amino acid sequences to obtain antibodies specific for eEPO and hEPO. Specificity of the antibodies was tested against supernatant of homogenized equine kidney and recombinant hEPO (rhEPO) by use of western immunoblotting techniques. Results —Analysis of the 1,181 bp in the nucleotide sequence revealed that eEPO was a residue of 192 amino acids. Similarity of eEPO with amino acid sequences of EPO from other species was 81.0% to 90.6%. Antibodies were specifically recognized by eEPO or rhEPO molecules. Anti-hEPO (161 to 165) antibody specifically recognized rhEPO. In contrast, anti-eEPO (133 to 144) antibody reacted with the equine kidney lysate. Conclusions and Clinical Relevance —We determined the cDNA and amino acid sequence of eEPO and developed region-specific antibodies that specifically recognized eEPO or rhEPO. These antibodies may be useful in distinguishing rhEPO from eEPO in a test to detect the misuse of rhEPO in racehorses. ( Am J Vet Res2004;65:15–19)
Lossless scalable video coding with H.264 compliant base layer (2005)

This paper proposes a two-layered SNR scalable video coding scheme having a lossless enhancement layer. The base bitstream is fully compliant with the H.264 standard, and the enhancement bitstream is derived from the orthogonal transform coefficients of H.264. In enhance bitstream coding, grid points that cannot be used by the original signal are eliminated to optimize the coding efficiency. We also utilize the numerical relationships between the coefficients to accelerate the process. Computer simulation confirms that the intra coding efficiency of proposed method is comparable to that of motion JPEG2000 reversible mode, while inter coding was achieved with bit reductions of 25 to 50%. A base layer optimization strategy is also described that is shown to yield reasonable overall performance.
Gabapentin Treatment for Alcohol Dependence (2013)

clinicaltrials.gov Identifier: NCT00391716.
Phase 2a Clinical Trial of Mitochondrial Protection (Elamipretide) During Stent Revascularization in Patients With Atherosclerotic Renal Artery Stenosis (2017)

URL: https://www.clinicaltrials.gov. Unique identifier: NCT01755858.
A Survey About Prediction-Based Data Reduction in Wireless Sensor Networks (2016)

One of the main characteristics of Wireless Sensor Networks (WSNs) is the constrained energy resources of their wireless sensor nodes. Although this issue has been addressed in several works and received much attention over the years, the most recent advances pointed out that the energy harvesting and wireless charging techniques may offer means to overcome such a limitation. Consequently, an issue that had been put in second place now emerges: the low availability of spectrum resources. Because of it, the incorporation of the WSNs into the Internet of Things and the exponential growth of the latter may be hindered if no control over the data generation is taken. Alternatively, part of the sensed data can be predicted without triggering transmissions that could congest the wireless medium. In this work, we analyze and categorize existing prediction-based data reduction mechanisms that have been designed for WSNs. Our main contribution is a systematic procedure for selecting a scheme to make predictions in WSNs, based on WSNs’ constraints, characteristics of prediction methods, and monitored data. Finally, we conclude the article with a discussion about future challenges and open research directions in the use of prediction methods to support the WSNs’ growth.
The structure of melittin (1988)

The conformation of the 26-residue polypeptide melittin has been studied using 1H-NMR spectroscopy in methanolic solution. The 1H-NMR spectrum of melittin has been assigned using two-dimensional NMR techniques and the secondary structure has been calculated from nuclear Overhauser enhancement data using distance geometry and restrained molecular dynamics analyses. The structure is found to be mainly helical, and similar to that found in crystals from diffraction data: residues 2-11 and 13-26 form regular alpha-helices joined by a 'hinge' between residues 11-12. The structure in this hinge region is shown to be significantly different from that in the crystal structure, leading to a smaller angle between the two helices. The possible significance of the proline residues in this and similar membrane-spanning peptides is discussed.
Structure of the Dominant Negative S17N Mutant of Ras<sup>,</sup> (2010)

The use of the dominant negative mutant of Ras has been crucial in elucidating the cellular signaling of Ras in response to the activation of various membrane-bound receptors. Although several point mutants of Ras exhibit a dominant negative effect, the asparagine to serine mutation at position 17 (S17N) remains the most popular and the most effective at inhibiting the activation of endogenous Ras. It is now widely accepted that the dominant negative effect is due to the ability of the mutant to sequester upstream activators and its inability to activate downstream effectors. Here, we present the crystal structure of RasS17N in the GDP-bound form. In the three molecules that populate the asymmetric unit, the Mg(2+) ion that normally coordinates the beta-phosphate is absent because of steric hindrance from the Asn17 side chain. Instead, a Ca(2+) ion is coordinating the alpha-phosphate. Also absent from one molecule is electron density for Phe28, a conserved residue that normally stabilizes the nucleotide's guanine base. Except for Phe28, the nucleotide makes conserved interactions with Ras. Combined, the inability of Phe28 to stabilize the guanine base and the absence of a Mg(2+) ion to neutralize the negative charges on the phosphates explain the weaker affinity of GDP for Ras. Our data suggest that the absence of the Mg(2+) should also dramatically affect GTP binding to Ras and the proper positioning of Thr35 necessary for the activation of switch 1 and the binding to downstream effectors, a prerequisite for the triggering of signaling pathways.
Side effects and emotional distress during cancer chemotherapy (1989)

Chemotherapy side effects, patient distress, and patient-practitioner communication were evaluated in an inception sample of 238 patients with breast cancer or malignant lymphoma. Participants were interviewed at five points during their first six cycles of therapy, and a subsample kept brief daily symptom diaries. Nausea, hair loss, and tiredness were each experienced by more than 80% of patients. By cycle 6, 46% of patients had thoughts about quitting therapy, but only a few had told medical staff. Patients' ratings of the objective difficulty of treatment increased over time, varied by treatment regimen, and were predicted by the experience of side effects, with the number of different side effects serving as the best predictor. In contrast, emotional distress was less sensitive to the directly assessable characteristics of treatment. Communication between patient and practitioner was found to be inadequate in a number of respects (i.e., patients did not fully anticipate the toxicities of treatment and did not report their concerns to medical staff). Communication may be impeded by inaccuracies in a patient's recall of treatment difficulties and by a patient's inability or unwillingness to attend to all presented information. More frequent opportunities for patient-practitioner discussion are necessary.
Openhole Log Analysis and Formation Evaluation (2012)

Since the first edition of Openhole Log Analysis and Formation Evaluation , which was published in 1985, the science and art of formation evaluation has seen many innovations. Measurements of formation resistivity have advanced, advances have been made in the design of sonic tools and in the processing of their recorded signals, and new methods of looking at the distribution of pore sizes, their fluid content, and formation flow potential have become widely used. This revised and updated second edition will prepare the reader for a fuller understanding of modern formation evaluation data-gathering methods, as well as illuminate advanced analysis techniques. The book is divided into sections that address a number of formation evaluation themes, including Methods of Gathering Formation Evaluation Data, Methods of Analysis and Application of Results, Openhole Logging Measurements, Analysis of Logs and Cores, and Formation Testing. Errata ( http://go.spe.org/OPLAerrata )
Pseudomonas aeruginosa virulence and therapy: Evolving translational strategies* (2009)

Adjuvant therapies directed against virulence factors have the potential to improve outcomes in P. aeruginosa infections.
Survival of patients with glioblastoma multiforme has not improved between 1993 and 2004: analysis of 625 cases (2007)

Glioblastoma is the most common primary brain tumour. The aim of this study was to determine trends in survival over a 12-year period. Survival data were collected retrospectively for 625 patients who had surgery for histologically-confirmed glioblastoma between 1993 and 2004 in a single centre. Data including age, sex, preoperative Karnofsky performance score, tumour site, date of surgery, and type of surgical and adjuvant treatment were collected. Overall median survival was 189 days; there was no significant change in survival over 12 years. Multivariate analysis identified the following independent positive prognostic factors: age <60 years (p < 0.0005), Karnofsky score > or = 70 (p < 0.0001), tumour debulking, rather than biopsy (p < 0.001), right-sided lesion (p < 0.05), unilateral tumour (p < 0.05) and radiotherapy (p < 0.0001). Despite neurosurgical advances, the survival of patients with glioblastoma has not changed for more than a decade. Although, overall, glioblastoma has a short survival, our data show that individual patient survival is heterogeneous.
On-chip stimulated Brillouin scattering (2011)

We demonstrate on-chip stimulated Brillouin scattering (SBS) in an As2S3 chalcogenide rib waveguide. SBS was characterized in a cm long waveguide with a cross-section 4 μm x 850 nm using the backscattered signal and pump-probe technique. The measured Brillouin shift and its full-width at half-maximum (FWHM) linewidth were ~7.7 GHz and 34 MHz, respectively. Probe vs. pump power measurements at the Brillouin shift were used to obtain the gain coefficient from an exponential fit. The Brillouin gain coefficient obtained was 0.715 x 10(-9) m/W. A probe gain of 16 dB was obtained for a CW pump power of ~300 mW.
Reliable Method for Eliminating Stacking Fault on 3C-SiC(001) (2012)

A reliable method for reducing the stacking faults (SFs) is demonstrated on the 3C-SiC (001) surface. It is a practical method based on Monte Carlo (MC) simulations of SF propagation during 3C-SiC epitaxial growth, which showed that introducing some discontinuity on the (001) surface enhanced SF reduction. The method is implemented by patterning on the 3C-SiC (001) surface and subsequent homo-epitaxial growth, and this sufficiently reduced the SF density to less than 400 cm -1 . A yield of 97.4 % was estimated for a device-ready area of 10 mm 2 by statistical measurements of SF density on the entire epitaxial layer surface.
Antibacterial Effect of Crude Drugs on Bacteria Associated with Periodontitis. (1997)

本研究の目的は, 中医薬に用いられる生薬の抗菌効果が, 成人性歯周炎の局所治療に有効であるかどうかを検討することである。これまで, 生薬の抗菌効果については, 黄色ブドウ球菌などごく一部の細菌に対してのみ検討されてきた。したがって, 歯周病関連細菌などに対する生薬の抗菌効果を検討した報告はほとんどなされていない。そこで, 炎症性患者に適応されている中医薬の処方中の構成生薬より, 10種類の生薬を選択し, 抗生剤の抗菌効果の判定の標準法として用いられている微量液体培地法による抗菌効果を検討したところ, 黄連, 黄苓, 黄柏は他の生薬として比較して, 培地中の生薬濃度1mg/mlで明らかな抗菌効果を示した。本報告ではさらに, それら生薬の抗菌活性の背景をberberineに求め, 今回は上に黄連抽出液を薄層クロマトグラフィーによって分画し, 各分画の抗菌活性を測定したところberberine, coptisineに相当する分画の抽出液の抗菌活性を認めた。これらの結果より, 従来から中医学において「清熱剤」として用いられてきた抗炎症剤の構成生薬に, 抗菌活性が認められることが示唆された。
Enhanced RSTD for scalable bandwidth of OTDOA positioning in 3GPP LTE (2013)

We study the reference signal time difference (RSTD) performance and implementation of scalable positioning reference signal (PRS) bandwidth in long term evolution (LTE). Limited number of reference signal symbols for performing RSTD measurements reduces the quality of the timing and position estimations. To overcome this limitation, we propose to share the PRS transmit port with one of the cell-specific reference signals (CRS) transmit ports, named C-PRS scheme. To get over 10% performance enhancements for small bandwidth cases, we pay an extra complexity from 3 CRS symbols. In order to reduce the overhead of large PRS bandwidth subframes, PRSs keep only in odd slots and data can be transmitted in even slots. The C-PRS scheme may transmit extra 3~4 symbols per one PRS subframe with the negligible losses of performance in the large PRS bandwidth cases. We also discuss the implementation of RSTD measurements which compute the cross-correlation of scalable bandwidth signals by dynamic or fixed FFT/IFFT size algorithms. The fixed FFT/IFFT size algorithm can balance the computation efficiency and the size of local memories.
Hyaluronic Acid or TNF-α Plus Fibronectin Triggers Granulocyte Macrophage-Colony-Stimulating Factor mRNA Stabilization in Eosinophils Yet Engages Differential Intracellular Pathways and mRNA Binding Proteins (2003)

Eosinophils (Eos) accumulate in airways and lung parenchyma of active asthmatics. GM-CSF is a potent inhibitor of Eos apoptosis both in vitro and in vivo and is produced by activated fibroblasts, mast cells, T lymphocytes as well as Eos. Cytokine release by Eos is preceded by GM-CSF mRNA stabilization induced by TNF-alpha plus fibronectin. Hyaluronic acid (HA) is a major extracellular matrix proteoglycan, which also accumulates in the lung during asthma exacerbations. In this study we have analyzed the effects of HA on Eos survival and GM-CSF expression. We demonstrate that like TNF-alpha plus fibronectin, HA stabilizes GM-CSF mRNA, increases GM-CSF secretion, and prolongs in vitro Eos survival. GM-CSF mRNA stabilization accounts for most of the observed GM-CSF mRNA accumulation and protein production. Unlike TNF-alpha plus fibronectin, GM-CSF mRNA stabilization induction by HA requires continuous extracellular signal-regulated kinase phosphorylation. Finally, to identify potential protein regulators responsible for GM-CSF mRNA stabilization, immunoprecipitation-RT-PCR studies revealed increased GM-CSF mRNA associated with YB-1, HuR, and heterogeneous nuclear ribonucleoprotein (hnRNP) C after TNF-alpha plus fibronectin but only hnRNP C after HA. Thus, our data suggest that both TNF-alpha plus fibronectin and HA, which are relevant physiological effectors in asthma, contributes to long-term Eos survival in vivo by enhancing GM-CSF production through two different posttranscriptional regulatory pathways involving extracellular signal-regulated kinase phosphorylation and RNA binding proteins YB-1, HuR, and hnRNP C.
Rheological and microcalorimetric studies of a model alkali-soluble associative polymer (HASE) in nonionic surfactant solutions (2000)

Rheological experiments were carried out on a 1 wt % hydrophobically modified alkali-soluble emulsion (HASE) solutions at pH ∼ 9 in the presence of nonionic polyoxyethylene ether type surfactant (C12EO23). The low shear viscosity and dynamic moduli increases at c > cmc until they reach a maximum at a critical concentration, cm of approximately 1 mM (∼17 times the cmc of free surfactant) and then decrease. The dominant mechanism at cmc < c < cm is an increase in the number of intermolecular hydrophobic junctions and a strengthening of the overall associative network structure. Above cm, the disruption of the associative network causes a reduction in the number of junctions and strength of the overall network structure. The influence of C12EO23 on HASE before cmc could not be detected macroscopically by the rheological technique. However, isothermal titration calorimetry enables the determination of complex binding of surfactant to the polymer. Isothermal titration of C12EO23 into 0.1 wt % HASE indicates that the C12EO23 aggregation in water and 0.1 wt % HASE polymer solutions is entropically driven. A reduction in the critical aggregation concentration (cac) confirms the existence of polymer–surfactant interactions. The hydrophobic micellar junctions cause a decrease in the ΔH and ΔS of aggregation of the nonionic surfactant. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 2019–2032, 2000
Extra-Binomial Variation in Logistic Linear Models (1982)

SUMMARY The logistic-linear model, and its maximum likelihood estimation by iterated reweighted least squares, can be simply modified to incorporate a component of extra-binomial variation. The modifications are very easily effected if the GLIM program is used.
The polysaccharide fucoidan inhibits microvascular thrombus formation independently from P‐ and <scp>l</scp>‐selectin function <i>in vivo</i> (2000)

Taken together, our novel findings suggest that fucoidan effectively prevents microvascular thrombus formation induced by endothelial damage in arterioles and venules in vivo. This protective effect of fucoidan is not attributable to inhibition of P- and L-selectin function but may instead be related to the anticoagulative capacity of fucoidan.
Fidelity of Escherichia coli DNA Polymerase IV (2002)

Escherichia coli DNA polymerase IV (pol IV), a member of the error-prone Y family, predominantly generates 1 frameshifts when copying DNA in vitro. T 3 G transversions and T 3 C transitions are the most frequent base substitutions observed. The in vitro data agree with mutational spectra obtained when pol IV is overexpressed in vivo. Single base deletion and base substitution rates measured in the lacZ gene in vitro are, on average, 2 10 4 and 5 10 5 , respectively. The range of misincorporation and mismatch extension efficiencies determined kinetically are 10 3 to 10 5 . The presence of sliding clamp and -complex clamp loading proteins strongly enhance pol IV processivity but have no discernible influence on fidelity. By analyzing changes in fluorescence of a 2-aminopurine template base undergoing replication in real time, we show that a "dNTP-stabilized" misalignment mechanism is responsible for making 1 frameshift mutations on undamaged DNA. In this mechanism, a dNTP substrate is paired "correctly" opposite a downstream template base, on a "looped out" template strand instead of mispairing opposite a next available template base. By using the same mechanism, pol IV "skips" past an abasic template lesion to generate a 1 frameshift. A crystal structure depicting dNTP-stabilized misalignment was reported recently for Sulfolubus solfataricus Dpo4, a Y family homolog of Escherichia coli pol IV.
Low Power Embedded Speech Enhancement System Based on a Fixed-Point DSP (2009)

In this paper, we introduce a practical real-time speech enhancement system based on the TI TMS320VC5509A digital signal processor (DSP). A stereo audio codec is used as the analog input/output (I/O). The algorithm for noise reduction is an improved and optimized spectral-subtraction method. The detailed design of the hardware and software is described and the experiments show an improved performance. Low power consumption and high efficiency make the whole system suitable for portable devices.
<title>Fabrication of microrelief surfaces using a one-step lithography process</title> (1997)

To fabricate arbitrarily shaped microrelief surfaces you should be able to design and control beside the X- and Y- direction also the Z-direction. With common micromachining technologies this could not be obtained. The surface micro machining technology, with sacrificial layer etching as a key process, is a planar technology, which offers no degree of freedom to design the surface in Z-direction. The bulk micro machining technology, with anisotropic KOH etching of silicon as a key process, offers only restricted possibilities for 3D design. To overcome this limitation binary optical elements have been fabricated using multi-mask processes or multidose e-beam or laser writing. For refractive optical lenses resist melting is a good compromise. This paper reports on a new methodology to fabricate the above discussed arbitrarily shaped structures using a one step lithography process. This technique is called one-level gray-tone lithography, which is common to standard IC manufacturing processes, supplemented by some processes like spincoating and developing of thick resist layer, electroplating of thick metal layers and dry etching. This group of processes has been collected into a new technology category with free design capabilities in Z- direction up to 20 micrometer: relief micro machining. Particular emphasis is put on the design of the halftone transmission masks. The algorithms to transfer an initial height profile into a design representation in the common data format GDSII are discussed. The great data amount of a reticle layout is reduced significantly by a first order data compaction. The specific parameters for the mask making and the resist process are determined. Several components like shaped gratings or lenses are shown in resist up to 15 micrometers thick. In the field of transferring the pattern into a substrate material like silicon or glass, a dry etching process is evaluated.
Hybrid D.C. squid fabrication and characterization (1983)

Early practical SQUID sensors have used point contact junctions. Ultimately all thin-film SQUIDs are desirable to permit integration of superconductive electronic circuitry. We report on hybrid D.C. SQUIDs using Nb/αSi/Nb thin film junctions and a toroidal canister. SQUIDs having white flux noise levels of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10^{-5}\phi_{0}/\sqrt{Hz}</tex> are routinely produced.