gebhart/patrepeval huggingface dataset:
The half-life of c-myc mRNA in growing and serum-stimulated cells: influence of the coding and 3' untranslated regions and role of ribosome translocation. (1994)

c-myc mRNA contains at least two discrete sequence elements that account for its short half-life, one in the 3' untranslated region and the other in the carboxy-terminal coding region (coding-region determinant). To investigate the function of each determinant, one or both were fused in frame to portions of a gene encoding long-lived beta-globin mRNA. Each chimeric gene was stably transfected into HeLa and NIH 3T3 cells and was transcribed from a constitutive cytomegalovirus promoter or from a serum-regulated c-fos promoter, respectively. The steady-state levels of the chimeric mRNAs in exponentially growing HeLa cells were compared, and their half-lives were measured by two independent methods: (i) in actinomycin D-treated HeLa cells and (ii) after serum addition to starved 3T3 cells. By each method, mRNAs containing either instability determinant were less stable than beta-globin mRNA. mRNA containing only the c-myc 3' untranslated region was not significantly more stable than mRNA with both determinants. In a cell-free mRNA decay system containing polysomes from transfected HeLa cells, mRNA containing the coding-region determinant was destabilized by addition of a specific RNA competitor, whereas mRNA containing only the 3' untranslated region was unaffected. When a stop codon was inserted upstream of the coding-region determinant, the chimeric mRNA was stabilized approximately twofold. These and other data suggest that degradation involving the coding-region determinant occurs most efficiently when ribosomes are translating the determinant.
Circulating Antibody against Tumor Necrosis Factor–Alpha Protects Rat Brain from Reperfusion Injury (1998)

The role of tumor necrosis factor-alpha (TNF alpha) in brain injury is controversial. We studied the effect of anti-TNF-alpha antibody in a rat model of reversible middle cerebral artery occlusion. During focal ischemia and early reperfusion, TNF-alpha was rapidly and transiently released into circulation. Pretreatment with intravenous anti-TNF-alpha antibody reduced cortical (71%, P < 0.015) and subcortical (58%, P < 0.007) injury, enhanced the cerebral blood flow during reperfusion, and improved the neurologic outcome. This further supports the contention that TNF-alpha is a deleterious cytokine in stroke, whereas circulating antibody against TNF-alpha may protect brain from reperfusion injury.
Effect of krestin (PSK) as adjuvant treatment on the prognosis after radical radiotherapy in patients with non-small cell lung cancer. (1994)

From 1976 to 1985, 185 patients with non-small cell lung cancer at stages I-III were treated with definitive radiotherapy in Gunma University Hospital. As a result of analyzing the long-term survivors treated with radiotherapy, suitable conditions of the patients for radical radiotherapy were as follows; 1) stage I or II, and some stage III, 2) as regards the histologic type epidermoid carcinoma or well-differentiated adenocarcinoma, 3) as regards the primary sites, the upper lobe and the superior segment of the lower lobe, 4) the optimum dose was 60-70Gy, 5) the size of the radiation fields given > 40Gy was 100 cm2 or less, and 6) the host condition was satisfactory (BRM combined use). In particular, as a result of administering PSK as adjuvant treatment to patients with epidermoid carcinoma of the lung showing satisfactory tumour shrinkage after radiotherapy, the five year survival rate of the patients with stages I or II disease, as well as stage III was 39% and 22% respectively, compared with the non-administered group's 16% and 5%. These differences are statistically significant. Although an improvement in the results of treatment with the combined use of appropriate BRMs is anticipated in the future, when clinical trials for combined BRM and radiotherapy are planned, the subjects should be patients with satisfactory tumour regression after radiotherapy.
Measurements of scattered light on a microchip flow cytometer with integrated polymer based optical elements (2004)

Flow cytometry is widely used for analyzing microparticles, such as cells and bacteria. In this paper, we report an innovative microsystem, in which several different optical elements (waveguides, lens and fiber-to-waveguide couplers) are integrated with microfluidic channels to form a complete microchip flow cytometer. All the optical elements, the microfluidic system, and the fiber-to-waveguide couplers were defined in one layer of polymer (SU-8, negative photoresist) by standard photolithography. With only a single mask procedure required, all the fabrication and packaging processes can be finished in one day. Polystyrene beads were measured in the microchip flow cytometer, and three signals (forward scattering, large angle scattering and extinction) were measured simultaneously for each bead. To our knowledge this is the first time forward scattered light and incident light extinction were measured in a microsystem using integrated optics. The microsystem can be applied for analyzing different kinds of particles and cells, and can easily be integrated with other microfluidic components.
Genetic ablation of root cap cells inArabidopsis (1999)

The root cap is increasingly appreciated as a complex and dynamic plant organ. Root caps sense and transmit environmental signals, synthesize and secrete small molecules and macromolecules, and in some species shed metabolically active cells. However, it is not known whether root caps are essential for normal shoot and root development. We report the identification of a root cap-specific promoter and describe its use to genetically ablate root caps by directing root cap-specific expression of a diphtheria toxin A-chain gene. Transgenic toxin-expressing plants are viable and have normal aerial parts but agravitropic roots, implying loss of root cap function. Several cell layers are missing from the transgenic root caps, and the remaining cells are abnormal. Although the radial organization of the roots is normal in toxin-expressing plants, the root tips have fewer cytoplasmically dense cells than do wild-type root tips, suggesting that root meristematic activity is lower in transgenic than in wild-type plants. The roots of transgenic plants have more lateral roots and these are, in turn, more highly branched than those of wild-type plants. Thus, root cap ablation alters root architecture both by inhibiting root meristematic activity and by stimulating lateral root initiation. These observations imply that the root caps contain essential components of the signaling system that determines root architecture.
Modular Approaches to Star and Miktoarm Star Polymers by ATRP of Cross‐Linkers (2010)

Abstract The topologies and site‐specific functionalities of a variety of star and miktoarm star copolymers can be easily manipulated by copolymerization of monomers and cross‐linkers using the ATRP technique. The polymerization of monomer prior to addition of cross‐linker produced core cross‐linked star polymers with initiating sites in the core, while polymerization of cross‐linker before monomer led to the core cross‐linked star polymers with initiating sites on the star periphery. When a mixture of linear macroinitiator and/or macromonomer was cross‐linked in a one‐pot reaction, miktoarm star copolymers with freely‐varied arm compositions and ratios were obtained.
3-Phosphoglycerate Phosphatase in Plants (1971)

A particulate form of 3-phosphoglycerate phosphatase represents about 20% of this activity in spinach (Spinacia oleracea var. Longstanding Bloomsdale) leaves. By differential and isopycnic sucrose density gradient centrifugation, all the particulate activity was found in starch grains that pelleted through 2.5 m sucrose. This particulate phosphatase was extremely stable, had a pH optimum of 5.8, and an apparent Michaelis constant (3-phosphoglycerate) of 9 x 10(-4)m. No cation requirement for activity could be demonstrated, and the enzyme was inhibited by 0.5 mm Zn(2+) or Cu(2+). The enzyme was most active in catalyzing the hydrolysis of 3-phospho-d-glycerate, but it was not substrate specific. The phosphatase from the starch grains could not be removed by washing, dialysis, homogenization, or treatment with a French pressure cell, but it was solubilized by prolonged sonication or by addition of 0.25 m MgCl(2), when the particles were suspended in 0.8 m sucrose. The solubilized enzyme was partially purified. The properties of the enzyme on the particles or after solubilization were similar to those previously described for the cytosol form of this phosphatase. It is conjectured that the phosphatase of the starch grain regulates glucan synthesis by controlling a 3-phosphoglycerate pool which is an effector for ADP-glucose pyrophosphorylase.
Analyzing Memory Accesses in x86 Binary Executables (2003)

This paper concerns static analysis algorithms for analyzing x86 executables. The aim of the work is to recover intermediate representations that are similar to those that can be created for a program written in a high-level language. Our goal is to perform this task for programs such as plugins, mobile code, worms, and virus-infected code. For such programs, symbol-table and debugging information is either entirely absent, or cannot be relied upon if present; hence, the technique described in the paper makes no use of symbol-table/debugging information. Instead, an analysis is carried out to recover information about the contents of memory locations and how they are manipulated. The analysis, called value-set analysis, tracks address-valued and integer-valued quantities simultaneously.
Effect of Composition of Substrate-Modifying Random Copolymers on the Orientation of Symmetric and Asymmetric Diblock Copolymer Domains (2008)

The ability of random copolymer brushes and cross-linked mats to induce the vertical orientation of domains in overlying films of lamellae- and cylinder-forming block copolymers was investigated as a function of the composition. The substrate-modifying layers consisted of styrene and methyl methacrylate random copolymers and contained either a terminal hydroxyl group or a third polar comonomer of 2-hydroxyethyl methacrylate (HEMA) for grafting brushes to silicon oxide surfaces or glycidyl methacrylate (GMA) for cross-linking the random copolymer into a mat. Polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) lamellae- and cylinder-forming block copolymers (both PS and PMMA minority block copolymers) were deposited and annealed on the modified surfaces. In all cases the vertical orientation of domains was observed for a range of random copolymer composition, but the ranges of composition were different for each combination of surface layer and block copolymer. The cylindrical domains of PS exhibited vertical structures for a very narrow range of compositions compared to cylindrical domains of PMMA or lamellae. As expected, the incorporation of polar HEMA or GMA monomers in the surface layers shifted the composition range for the perpendicular orientation of domains to higher fractions of styrene. The results are discussed in terms of the equilibration of the films in the presence of the chemically modified surfaces.
Evidence of Chromosomal Instability in Prostate Cancer Determined by Spectral Karyotyping (SKY) and Interphase FISH Analysis (2001)

The way in which cytogenetic aberrations develop in prostate cancer (CaP) is poorly understood. Spectral karyotype (SKY) analysis of CaP cell lines has shown that they have unstable karyotypes and also have features associated with chromosomal instability (CIN). To accurately determine the incidence of de novo structural and numerical aberrations in vitro in CaP, we performed SKY analysis of three independent clones derived from one representative cell line, DU145. The frequent generation of new chromosomal rearrangements and a wide variation in the number of structural aberrations within two to five passages suggested that this cell line exhibited some of the features associated with a CIN phenotype. To study numerical cell-to-cell variation, chromosome 8 aneusomy was assessed in the LNCaP, DU145, and PC-3 cell lines and a patient cohort of 15 CaP primary tumors by interphase fluorescence in situ hybridization (FISH). This analysis showed that a high frequency of numerical alteration affecting chromosome 8 was present in both in vitro and in CaP tissues. In comparison to normal controls, the patient cohort had a statistically significant (P<.05), greater frequency of cells with one and three centromere 8 copies. These data suggest that a CIN-like process may be contributing towards the generation of de novo numerical and structural chromosome abnormalities in CaP.
Substituted thiazolamide coupled to a redox delivery system: a new γ-secretase inhibitor with enhanced pharmacokinetic profile (2005)

Inhibition of gamma-secretase, one of the enzymes responsible for the cleavage of the amyloid precursor protein (APP) to produce pathogenic A beta peptides, is an attractive approach for the treatment of Alzheimer's disease. We have designed a new gamma-secretase thiazolamide inhibitor bearing a dihydronicotinoyl moiety as Redox Delivery System which allows specific delivery of the drug to the brain. Through, on the one hand, A beta peptide production measurements by specific in vitro assays (gamma-secretase Cell Free assay and Cell Based assay on HEK 293 APP transfected cells) and, on the other hand, pharmacokinetic studies on animal models, the new inhibitor shows a good pharmacokinetic profile as well as a potent gamma-secretase inhibitory activity in vitro. From the obtained results, it is expected that drug will be mainly delivered to the CNS with low diffusion in the peripheral tissues. Consequently the side effects of this gamma-secretase inhibitor on the immune cells could be reduced.
Mouse beta 2-microglobulin cDNA clones: a screening procedure for cDNA clones corresponding to rare mRNAs. (1981)

We have isolated three cDNA clones for beta 2-microglobulin, the small subunit of the major histocompatibility antigens. beta 2-Microglobulin makes up less than 0.1% of mouse liver protein, and its mRNA is approximately 0.03% of liver poly(A)+ mRNA. The cDNA clones were identified by screening 1400 cDNA clones made from 9--10S mouse liver poly(A)+ mRNA. The procedure for screening the cDNA clones involved binding pooled plasmid DNA to nitrocellulose filters and testing the ability of each filter to select beta 2-microglobulin mRNA. The filter-selected mRNAs were assayed for their ability to direct the synthesis of beta 2-microglobulin in translation reactions in vitro. The isolated clones were shown by nucleotide sequence analysis to encode beta 2-microglobulin. The positive-selection--hybridization assay has been modified to facilitate the screening of large numbers of cDNA clones, and the modified assay should allow the isolation of cDNAs corresponding to any mRNA whose in vitro translation products can be immunoprecipitated. These modifications are of particular value in the isolation of cDNA clones corresponding to rare species of mRNA.
Fixation Precision in High-Speed Noncontact Eye-Gaze Tracking (2008)

The precision of point-of-gaze (POG) estimation during a fixation is an important factor in determining the usability of a noncontact eye-gaze tracking system for real-time applications. The objective of this paper is to define and measure POG fixation precision, propose methods for increasing the fixation precision, and examine the improvements when the methods are applied to two POG estimation approaches. To achieve these objectives, techniques for high-speed image processing that allow POG sampling rates of over 400 Hz are presented. With these high-speed POG sampling rates, the fixation precision can be improved by filtering while maintaining an acceptable real-time latency. The high-speed sampling and digital filtering techniques developed were applied to two POG estimation techniques, i.e., the high-speed pupil-corneal reflection (HS P-CR) vector method and a 3-D model-based method allowing free head motion. Evaluation on the subjects has shown that when operating at 407 frames per second (fps) with filtering, the fixation precision for the HS P-CR POG estimation method was improved by a factor of 5.8 to 0.035 degrees (1.6 screen pixels) compared to the unfiltered operation at 30 fps. For the 3-D POG estimation method, the fixation precision was improved by a factor of 11 to 0.050 degrees (2.3 screen pixels) compared to the unfiltered operation at 30 fps.
A Study of Stereoselective Hydrolysis of Symmetrical Diesters with Pig Liver Esterase (1983)

Abstract Pig liver esterase‐(PLE) catalyzed hydrolysis of dimethyl esters of symmetrical dicarboxylic acids, including meso ‐diacids, cis ‐1,2‐cycloalkanedicarboxylic acids, and diacids with a prochiral center, was studied with 14 substrates. The products of these stereoselective hydrolyses are chiral monoesters of dicarboxylic acids, with an enantiomeric excess (e.e.) from 10% to 100%. Some of these optically active monoesters are valuable synthons in natural products synthesis. An additivity pattern of α‐ and β‐substituents with the glutaric esters on the stereoselectivity of enzymatic hydrolysis was observed. Analysis of the experimental results leads to a model of enzyme stereoselectivity of diester hydrolysis in which the substitution pattern at α‐ and β‐C‐atoms is found to determine the absolute configuration of the resulting monoester.
Carrier recombination at silicon–silicon nitride interfaces fabricated by plasma-enhanced chemical vapor deposition (1999)

Using the light-biased microwave-detected photoconductance decay method, injection level dependent measurements of the effective surface recombination velocity Seff at silicon surfaces passivated by plasma-enhanced chemical vapor deposited (PECVD) silicon nitride (SiNx) films are performed on monocrystalline silicon wafers of different resistivities and doping types. In order to theoretically simulate the measured dependences of Seff on the bulk injection level Δn, the extended Shockley-Read-Hall formalism is used. Simulation input parameters are the energy dependent interface state densities and capture cross sections of the involved interface defects as well as the positive insulator charge density Qf. The energy dependent properties of the interface defects are experimentally determined by means of small-pulse deep-level transient spectroscopy. These measurements reveal the existence of three “deep” silicon dangling bond defects at the Si-SiNx interface with similar interface state densities but very different capture cross sections and hence recombination rates. Another defect is found very close (⩽0.1 eV) to the edge of the silicon conduction band. This defect is identified with the K+ center which is responsible for the large positive Qf values (∼1012 cm−2) at Si-SiNx interfaces obtained from standard dark capacitance-voltage measurements. In order to get a good agreement between measured and calculated Seff(Δn) dependences, a reduction of Qf by one order of magnitude is found to be necessary. The explanation for this reduction is the capture of electrons from the silicon conduction band into the K+ centers. The comparison of Si-SiNx interfaces fabricated by different PECVD techniques shows that the dominant interface defect is produced by the ion bombardment during the SiNx deposition. Thus, avoidance of the ion bombardment leads to a strongly reduced interface recombination and hence a better surface passivation quality.
Prosthesis-Guided Training For Practical Use Of Pattern Recognition Control Of Prostheses (2011)

The potential for pattern recognition to improve powered prosthesis control has been discussed for many years. One remaining barrier to at-home use of these techniques is that practical methods of user prompting during system training are lacking. Most research and development of pattern recognition systems for prosthesis control has relied on on-screen cues to prompt the prosthesis wearer during signal collection; therefore most systems require connection to a computer or external device. We have developed a method called Prosthesis-Guided Training (PGT) to address this issue. In PGT, the prosthesis itself moves through a pre-programmed sequence of motions to prompt the wearer to elicit the appropriate muscle contractions. PGT requires no extra hardware and allows wearers to retrain, refresh, or recalibrate the controller in many locations and situations. Training via PGT is self-initiated and requires only about 1 minute of the wearer’s time. Furthermore, PGT provides a practical mechanism for overcoming malfunctioning or changing inputs, addresses differences in routine donning, and results in acquisition of myoelectric signals representative of those elicited during functional use. Qualitative and quantitative data acquired to investigate the efficacy of PGT suggest that it is an intuitive, effective, and clinically viable method of training pattern recognition–controlled prostheses.
Metabolic imaging of untreated prostate cancer by positron emission tomography with 18fluorine-labeled deoxyglucose. (1996)

18F-deoxyglucose PET does not allow for metabolic labeling in the majority of untreated primary prostate cancers. BPH and primary prostate cancer cannot be reliably differentiated on the basis of PET. Increased 18F-deoxyglucose accumulation occurs in some primary prostate tumors and in metastatic deposits of prostate cancer.
Development of Artificial Antigen Presenting Cells for Prostate Cancer Immunotherapy (2004)

Abstract : A major goal in cancer immunotherapy is to generate an effective anti-tumor immune response. Adoptive immunotherapy involves stimulation of tumor-specific T cells, ex vivo (outside the body), followed by transfer of expanded numbers of activated T cells back into patients. While adoptive immunotherapy holds promise as a treatment for cancer, development of adoptive immunotherapy has been impeded by the lack of a reproducible and economically viable method for generating therapeutic numbers of antigen-specific CTL. The work proposed in this application will enable advances in adoptive immunotherapy. Most prostate cancers express prostate specific molecules. These molecules, including PSA and PMSA, can serve as potential targets for immune-based treatments. Studies on immune recognition of these molecules have already identified potential target regions within these proteins and are the basis of a variety of different experimental immunotherapies for treatment of prostate cancer. In this study we propose to study the ability to use HLA-Ig based aAPC as a viable method for induction, expansion and activation of prostate specific T cells for immunotherapy for prostate cancer. These studies will serve as precursor ones for induction and expansion of prostate specific CTL from patients with disease for initiation of adoptive immunotherapy phase I clinical studies.