gebhart/patrepeval huggingface dataset:
Molecular biology of human serum cholinesterase. (1986)

More than 90% of the amino acid sequence of purified human serum cholinesterase has been determined in our laboratory. Purified enzyme was digested with several proteolytic enzymes; the resulting polypeptides were then separated, purified, and sequenced. Optimal sequence regions were identified and used as the basis for the synthesis of three 17-mer oligonucleotide probes. In addition, one long peptide of 58 amino acid residues was selected for construction of two unique sequence oligonucleotide probes of 39-mer and 53-mer; the peptide regions corresponding to the latter are six amino acids apart. The probes have been used to screen a human liver cDNA library and a human genomic library. Several positive clones to both types of probes have been identified. These are being characterized, and some of them have been or are now being sequenced. A high degree of homology in the amino acid sequence of the active center of human serum cholinesterase and that of acetylcholinesterase from the Torpedo fish has been noted. It appears that this region of cholinesterases has been conserved during evolution, and there may be an important, still unrecognized role for serum nonspecific cholinesterase in mammalian metabolism.
Effect of the Attenuating Deletion and of Sequence Alterations Evolving In Vivo on Simian Immunodeficiency Virus C8-Nef Function (1999)

ABSTRACT The simian immunodeficiency virus macC8 (SIVmacC8) variant has been used in a European Community Concerted Action project to study the efficacy and safety of live attenuated SIV vaccines in a large number of macaques. The attenuating deletion in the SIVmacC8 nef -long terminal repeat region encompasses only 12 bp and is “repaired” in a subset of infected animals. It is unknown whether C8-Nef retains some activity. Since it seems important to use only well-characterized deletion mutants in live attenuated vaccine studies, we analyzed the relevance of the deletion, and the duplications and point mutations selected in infected macaques for Nef function in vitro. The deletion, affecting amino acids 143 to 146 (DMYL), resulted in a dramatic decrease in Nef stability and function. The initial 12-bp duplication resulted in efficient Nef expression and an intermediate phenotype in infectivity assays, but it did not significantly restore the ability of Nef to stimulate viral replication and to downmodulate CD4 and class I major histocompatibility complex cell surface expression. The additional substitutions however, which subsequently evolved in vivo, gradually restored these Nef functions. It was noteworthy that coinfection experiments in the T-lymphoid 221 cell line revealed that even SIVmac nef variants carrying the original 12-bp deletion readily outgrew an otherwise isogenic virus containing a 182-bp deletion in the nef gene. Thus, although C8-Nef is unstable and severely impaired in in vitro assays, it maintains some residual activity to stimulate viral replication.
Ultrastructural Localization of Collagen IV, Fibronectin, and Laminin in the Trabecular Meshwork of Normal and Glaucomatous Eyes (2001)

The ultrastructural characteristics and immunogold labeling of basement membranes were similar in normal and glaucomatous eyes; no additional structures were labeled in POAG eyes that were not also labeled in normal eyes. Label of the patches of amorphous fibrogranular material within the juxtacanalicular tissue suggests it is basement membrane in origin, while the sheath material which is known to accumulate in POAG was not heavily labeled and does not appear to be basement membrane in origin.
Spectratype/Immunoscope Analysis of the Expressed TCR Repertoire (2000)

Measuring the diversity of TCRs utilized by specific primary and memory T cell responses is critical to the fundamental understanding of regulation of the immune system. This unit describes the Spectratype/Immunoscope technique which permits an in depth analysis of the TCR repertoire present in a variety of biological samples from mice to humans. Spectratype analysis takes advantage of PCR technology to amplify template cDNA corresponding to rearranged transcripts with different CDR3 lengths from specific TCR variable region genes in a competitive manner. The PCR products are then resolved on polyacrylamide sequencing gels to reveal precise sizes in nucleotide base pairs. The unit also includes protocols that have been optimized to process and produce the starting materials required for spectratype analysis.
Action of a mammalian AP-endonuclease on DNAs of defined sequences (1989)

An apurinic/apyrimidinic (AP) specific endonuclease from mouse plasmacytoma cells (line MPC-11), was observed to cleave apurinic sites in oligonucleotides 9, 11, 12, 39 and 40 nucleotides in length. However, the enzyme failed to cleave AP-sites in two oligonucleotides 7 nucleotides in length. The maximum rates of digestion observed on these short single-stranded DNA (ssDNA) fragments were approximately 1/30 of the rates observed on double-stranded DNA (dsDNA). In studies using the Maxam-Gilbert DNA sequencing analysis, apurinic sites in purine-rich regions were preferentially cleaved in dsDNA but not in ssDNA, indicating that the enzyme has a sequence preference on dsDNA. These results suggest that some sites on DNA might be more efficiently repaired than others.
Efficient Photoacids Based upon Triarylamine Dialkylsulfonium Salts (2002)

New triarylamine dialkylsulfonium salts that are photosensitive in the near-ultraviolet have been prepared. The quantum yields of photoacid generation were found to be approximately 0.5 and are independent of the counterion. On the other hand, the efficiencies of the sulfonium salts toward the photopolymerization of cyclohexene oxide depend on the counterion and the sulfonium substituents. Photopolymerization kinetic studies demonstrate that these triphenylamine sulfonium salts are highly efficient cationic photoinitiators.
Active capture (2003)

The Active Capture demonstration is part of a new computational media production paradigm that transforms media production from a manual mechanical process into an automated computational one that can produce mass customized and personalized media integrating video of non-actors. Active Capture leverages media production knowledge, computer vision and audition, and user interaction design to automate direction and cinematography and thus enables the automatic production of annotated, high quality, reusable media assets. The implemented system automates the process of capturing a non-actor performing two simple reusable actions ("screaming" and "turning her head to look at the camera") and automatically integrates those shots into various commercials and movie trailers.
Antirheumatic Agents. I. Novel Methotrexate Derivatives Bearing an Indoline Moiety. (1996)

Various novel methotrexate (MTX) derivatives bearing an indoline moiety were synthesized and tested for biological activities using human peripheral blood mononuclear cell (hPBMC) and human synovial cells (hSC) derived from patients with rheumatoid arthritis (RA). Compounds having potent activity in vitro were further evaluated using an adjuvant arthritis model in vivo. N-[1-(2,4-Diamino-6-pteridinylmethyl)indoline-5-carbonyl]-L-glutam ic acid 2f showed more potent activities than MTX in vitro and in vivo, and N-[1-(2,4-diamino-6-pteridinylmethyl)-indoline-5-carbonyl]-L-2-ami noadipic acid 2d exhibited fairly good activities in vitro and considerable activity in vivo. Compound 2d was, as expected, not sensitive to folyl-polyglutamate synthetase (FPGS) and did not undergo polyglutamation, a process which may be responsible for a side-effect during MTX therapy.
Chemokine Signaling and Functional Responses: The Role of Receptor Dimerization and TK Pathway Activation (2001)

A broad array of biological responses, including cell polarization, movement, immune and inflammatory responses, and prevention of HIV-1 infection, are triggered by the chemokines, a family of structurally related chemoattractant proteins that bind to specific seven-transmembrane receptors linked to G proteins. Here we discuss one of the early signaling pathways activated by chemokines, the JAK/STAT pathway. Through this pathway, and possibly in conjunction with other signaling pathways, the chemokines promote changes in cellular morphology, collectively known as polarization, required for chemotactic responses. The polarized cell expresses the chemokine receptors at the leading cell edge, to which they are conveyed by rafts, a cholesterol-enriched membrane fraction fundamental to the lateral organization of the plasma membrane. Finally, the mechanisms through which the chemokines promote their effect are discussed in the context of the prevention of HIV-1 infection.
Branches of the Tibial Nerve: Anatomic Variations (1995)

Anatomic variations in tibial nerve branches may help explain discrepancies between clinical examination and electrophysiologic tests as to the location of neuronal lesions. Dissection of 20 cadaveric feet (10 pair) along the course of the tibial nerve and its branches confirmed that it bifurcates within 2 cm of the medio-malleolar-calcaneal axis in 90% (18/20) and that it gives off frequent small branches with its accompanying vascular structures. Unlike other studies, however, we found that 60% had multiple calcaneal branches off the tibial nerve and that 20% evidenced previously undescribed accessory innervation to the abductor hallucis muscle from other than the medial plantar nerve.
Long‐term follow‐up of cervical intraepithelial neoplasia treated with minimal conization by carbon dioxide laser (1997)

Background and Objective Minimal conization with carbon dioxide laser (CO2) for safe diagnosis and treatment of cervical intraepithelial neoplasia (CIN) 1–3 has been utilized for 15 years. To evaluate the results of 15 years' follow-up. Study Design/Materials and Methods: Clinical prospective study: 2,903 non-pregnant women whose cervicovaginal smear revealed CIN 1–3, confirmed by colposcopy, were referred for minimal conization treatment (LMC). This outpatient free-hand excision is performed under local anesthesia with a 60-W continuous laser beam focused to a 0.1-mm spot size, giving a power density of 165,000 W/cm2. Adjuvant cervical curettage is done routinely. Results Complications after the procedure were insignificant. Histopathological investigation revealed invasive carcinoma in 1.2% of the minicones. The primary cure rate was 96.1%. In the life table analysis of the patients the cumulative risk of recurrence for all forms of CIN was 0.89% at year 5, 1.36% at year 10, and 3.02% at year 15. There was no sudden onset carcinoma during the follow-up period. Conclusion Minimal conization is a safe, effective treatment for CIN and early forms of microinvasive carcinoma. Invasive carcinoma can be detected early and should be treated without delay. The cumulative risk of developing new CIN is 3.02% at year 15 and there is no risk of sudden-onset invasive carcinoma following this procedure. Lasers Surg. Med. 20:461–466, 1997. © 1997 Wiley-Liss, Inc.
Boosting Vaccine for Tuberculosis (2001)

An effective new vaccine for the control of tuberculosis is badly needed. While current research attempts to improve vaccination are concentrating on new prophylactic or immunotherapeutic vaccines, virtually no emphasis has been placed on boosting individuals already inoculated with Mycobacterium bovis BCG. It is shown here that mice vaccinated with BCG gradually lose their capacity to resist an aerosol challenge infection as they age. However, if these mice are inoculated with the 30-kDa mycolyl transferase A protein in midlife, after challenge when aged they express levels of protection in the lungs comparable to those of young mice, associated with minimal pathological damage.
The Annealing Mechanism of HIV-1 Reverse Transcription Primer onto the Viral Genome (2004)

Reverse transcription of human immunodeficiency virus-1 viral RNA uses human tRNA(3)(Lys) as a primer. The first step of viral replication is, thus, the annealing of the primer tRNA onto the primer binding site located in the 5' leader region of the viral RNA. This involves large rearrangements of both RNA structures and requires the chaperone activity of the viral nucleocapsid protein. We have developed a novel approach to analyze dynamically such RNA refolding events using heteronuclear NMR spectroscopy of mixtures of (15)N-labeled and unlabeled large RNA fragments (up to 50 kDa). We have thus been able to characterize the detailed mechanisms of both heat- and nucleocapsid-mediated annealing and to identify previously unknown key steps. The role played by the nucleocapsid is 2-fold; it facilitates strand exchange at the level of the tRNA acceptor stem, presumably via its basic N- and C-terminal extensions, and it unlocks the highly stable tertiary interactions at the level of the T Psi C loop, most likely by specific interactions involving its two zinc knuckles.
Point mutations in the dystrophin gene: Evidence for frequent use of cryptic splice sites as a result of splicing defects (1999)

Ten different mutations have been identified in patients with Becker (n = 1) or Duchenne (n = 9) muscular dystrophy using reverse transcription of total RNA, polymerase chain reaction amplification of the whole coding region of the gene and protein truncation test (PTT) analysis. Seven mutations had not been reported previously, and these consist in three nonsense mutations (Q2522X, E2726X, R3381X), three frameshifting deletions (3686–3687delGT, 5126delA, 5759delC), and four splicing defects of which the effects on the muscle dystrophin mRNA transcripts have been analyzed. In one case, a 3′ splice-site mutation (IVS74-2A→G) resulted in a complex pattern of exon skipping involving exons of the C-terminal domain. In the three other cases, nucleotide substitutions in splice donor (IVS26+2T→A, IVS65+1G→A) or acceptor (IVS8-15A→G) recognition sequences led to the use of cryptic splice sites, with consequent insertions of intronic sequences in the processed mRNA. Up to 34% (70/203) of the point mutations reported to date in the dystrophin database (http://www.dmd.nl) affect splice sites of the dystrophin gene. However, altered mRNA splicing has been confirmed experimentally in only 23% of cases (16/70). Combined with PTT, the transcript analysis protocol defined in this study permits direct determination of the impact of intronic variations on the structure of dystrophin mRNA and of the resulting consequences on the translational reading frame. We present evidence for a frequent use of cryptic splice sites as a result of splicing defects. Hum Mutat 14:359–368, 1999. © 1999 Wiley-Liss, Inc.
High performance multidimensional analysis of large datasets (1998)

Summary information from data in large databases is used to auswer queries in On-Line Analytical Processing (OLAP) systems and to build decision support systems over them. The Data Cube is used to calculate and store summary information on a variety of dimensions, which is computed only partially if the number of dimensions is large. Queries posed on such systems are quite complex and require different views of data. These may either be auswered from a materialized cube in the data cube or calculated on the fly. Further, data mining for associations can be performed on the data cube. Analytical models need to capture the multidimensionality of the underlying data, a task for which multidimensional databases are well suited. Multidimensional databases store data in multidimensional structure on which analytical operations are performed. A challenge for these systems is how to handle large data sets in a large number of dimensions. This paper presents q parallel OLAP h&structure for multidimensional databases integrated with association rule mining. Scheduling optimisations for parallel computation of wmplete data cubes are presented. We propose left aud right schedules for partial data cubes for m-way mining of association rules. Our implementation on the IBM SP-2, a shared-nothing parallel machine, cau handle large data sets and a large number of dimensions by using disk I/O in our algorithms.
Preservatives in Nebulizer Solutions: Risks without Benefit (1998)

Edetate disodium (EDTA) and benzalkonium chloride (BAC) are often present as preservative or stabilizing agents in nebulizer solutions used to treat asthma and chronic obstructive pulmonary disease. Benzalkonium chloride is a potent bronchoconstrictor when inhaled in concentrations similar to those in which it is present in these solutions. Inclusion of BAC (together with EDTA) in the ipratropium bromide (Atrovent) nebulizer solution resulted in paradoxic bronchoconstriction in some asthmatic patients and an overall reduction in bronchodilator efficacy. The presence of BAC in albuterol nebulizer solutions does not affect the short-term bronchodilator response to a single dose, although case reports suggest that its repeated use in patients with severe asthma may result in paradoxic bronchoconstriction. When inhaled by asthmatic subjects, EDTA also causes dose-dependent bronchoconstriction, although it is less potent than BAC. The use of preservative-free bronchodilator nebulizer solutions does not result in clinically significant bacterial contamination if they are dispensed in sterile unit-dose vials, in volumes and concentrations that do not require modification by the user. Despite this evidence, in the United States a number of solutions, including some preparations of albuterol, contain either BAC or EDTA. Current regulations do not require that the concentration of preservatives be documented on the product; however, considerably different doses of BAC are delivered with different products. For example, a standard 2.5-mg dose of albuterol nebulizer solution contains 50 microg of BAC when administered from the multidose dropper bottle and 300 microg from the unit-dose screw-cap product. Furthermore, it is legal for pharmacists to substitute or compound solutions containing high concentrations of BAC when the physician has prescribed a preservative-free product. We recommend that the United States follow the practice of most Western countries and withdraw bronchodilator nebulizer solutions that contain preservatives such as BAC. We further recommend that the solutions should be prepared under sterile conditions, formulated preservative free, and made available in unit-dose vials.
The impact of eye gaze on communication using humanoid avatars (2001)

In this paper we describe an experiment designed to investigate the importance of eye gaze in humanoid avatar's representing people engaged in conversation. We compare responses to dyadic conversations in four mediated conditions: video, audio-only, and two avatar conditions. The avatar conditions differed only in their treatment of eye gaze. In the random-gaze condition the avatars head and eye animations were unrelated to conversational flow. In the informed-gaze condition, they were related to turn-taking during the conversation. The head animations were tracked and the eye animations were inferred from the audio stream. Our comparative analysis of 100 post-experiment questionnaires showed that the random-gaze avatar did not improve on audio-only communication. The informed-gaze avatar significantly outperformed the random-gaze model and also outperformed audio-only on several response measures. We conclude that an avatar whose gaze behaviour is related to the conversation provides a marked improvement on an avatar that merely exhibits liveliness.
The Role of Blood from HLA-Homozygous Donors in Fatal Transfusion-Associated Graft-versus-Host Disease after Open-Heart Surgery (1989)

Acute graft-versus-host disease has been described in immunocompromised patients receiving nonirradiated blood products.1 2 3 In addition to the involvement of the skin, liver, and gut typically seen in graft-versus-host disease after bone marrow transplantation,4 these patients have bone marrow involvement that results in pancytopenia. The aplasia observed in graft-versus-host disease is presumably due to recognition by the donor's immune-reactive cells of histoincompatible antigens on the host's hematopoietic precursor cells. Transfusion-associated graft-versus-host disease carries a high mortality rate; most patients succumb to infection.2 Because the onset of transfusion-associated graft-versus-host disease is delayed and because its symptoms are similar to those seen in . . .
Rotifers from high altitude crater-lakes at Nevado de Toluca Volcano, México. (1997)

A survey on the high-altitude lakes El Sol and La Luna located in the crater of the volcano Nevado de Toluca, was carried out for rotifer fauna. Samples were taken with a mesh of 60 um from the littoral and limnetic zones of both lagoons in 1994. Results include 34 specific taxa representing 10 families and 16 genera. In total 11 species are new records to the fauna of Mexico viz. Aspelta lestes, Cephalodella tenuiseta, Dicranophorus forcipatus, Lecane inopinata, Lecane scutata, Lepadella rhomboides, Notommata glyphura, Taphrocampa annulosa, Testudinella emarginula, Trichocerca bidens and Trichocerca collaris. The fauna found emphasizes the transition between neartics and neotropics of the Mexican altiplano.
Fc Site-Specific Labeling of Immunoglobulins with Calf Intestinal Alkaline Phosphatase (1994)

A strategy is described for the site-specific conjugation of alkaline phosphatase to the Fc region of immunoglobulins. Mild oxidation of immunoglobulins by sodium periodate followed by reductive amination with excess cystamine and sodium cyanoborohydride covalently attaches cystamine specifically to the oligosaccharide chains of the antibody's Fc region. The disulfide bonds of the conjugated cystamine moieties are then reduced to free thiols with a low concentration of dithiothreitol. The thiol-modified antibodies (typically containing three to four thiols per Fc region) are then brought into contact with maleimide-functionalized alkaline phosphatase to form antibody-alkaline phosphatase conjugates. The Fc site-specific conjugation methodology was optimized and successfully applied to a number of different monoclonal and polyclonal antibodies. The conjugates prepared show assay performances superior to those prepared by more conventional means. Evidence obtained indicates that this superior conjugate performance results from total retention of the antibody's antigen binding activity following the Fc site-specific conjugation procedure.
Quantifying the Memory Effects of Power Amplifiers: EVM Closed-Form Derivations of Multicarrier Signals (2016)

This letter deals with the analysis of the memory effects of the power amplifier (PA) on multicarrier signals. We analytically derive the expressions of the error vector magnitude (EVM) of amplified signals jointly considering a memory polynomial PA model and clipping effects. We provide analytical EVM expressions that depend on the PA coefficients, PA order, and memory depth as well as the clipping threshold of the input signal. These analytical expressions are new general formulas which allow to predict in-band distortions at the PA output.