gebhart/patrepeval huggingface dataset:
Human cytomegalovirus terminase as a target for antiviral chemotherapy (2002)

Herpesviral DNA packaging is a complex process involving binding and cleavage of DNA containing the specific DNA-packaging motifs, pac1 and pac2, and packaging of the resulting unit-length genomes into preformed procapsids. This process is believed to be mediated by two packaging proteins, the terminase subunits. In the case of human cytomegalovirus the terminase consists of the proteins pUL56 and pUL89. While pUL56 (i) mediates the specific binding to pac sequences on the concatamers, (ii) provides energy for the translocation of the DNA to the procapsids and (iii) associates itself with the capsid for enabling the entry of the DNA into the procapsid, pUL89 is mainly required to effect DNA cleavage. Based on the limited efficacy of the current drugs ganciclovir, cidofovir and foscarnet, new antiviral therapeutics appear to be in demand. Inhibitors targeting pUL56 and/or pUL89 may offer an attractive alternative since mammalian cell DNA replication does not involve cleavage of concatameric DNA. Drugs targeted to terminase-like proteins should therefore be safe and highly selective.
Use of Exogenous Electric Current in the Treatment of Delayed Lesions in Peripheral Nerves (1988)

A commonly observed clinical problem following nerve injury is the incomplete recovery of function associated with the formation of a neuroma in continuity. In the present study, exogenous direct electric current was tested for its ability to promote growth of axons through a neuroma-like lesion. Neuroma-like structures were created by crushing rat sciatic nerves at two sites 4 mm apart and applying phenol to the intermediate region. A bulbous axonally impenetrable structure is formed 3 weeks later. At that time, silicone cuffs were sewn onto the nerve proximal to the phenol application site and 7 mm distally. In experimental groups, cuffs were attached to wires leading to a subcutaneously implanted Traxon power source, the distal cuff being cathodal. In control groups, cuffs were not electrically connected. In electrically active groups, substantial numbers of myelinated axons were seen distal to the cathode 3 weeks after implantation. Four times fewer fibers were observed in control groups. Footprint patterns from electrically active animals revealed a significant improvement over control neuroma preparations, as quantitated using the Sciatic Functional Index.
Monoclonal antibody‐coated magnetite particles as contrast agents in magnetic resonance imaging of tumors (1989)

A highly specific and powerful magnetic resonance imaging contrast agent has been prepared by coating magnetite (Fe3O4) particles with monoclonal antibodies directed against a tumor antigen. The preparation maintains both the immunoreactivity of the monoclonal antibody and the full relaxing capability of the magnetite particle. MRI image contrast by spin-echo methods can be easily induced in a concentration range of 1-10 nM of the antibody-coated magnetite particles.
<title>General stereo image matching using symmetric complex wavelets</title> (1996)

General stereo image matching provides an adequate but hard problem with sufficient complexity, with which the potential of wavelets may be exploited to a full extend. An ideal stereo image matching algorithm is supposed to be invariant to the scale, translation, rotation, and partial correspondence between two given stereo images. While the multi-resolution of wavelets is good at scale adaptivity, we also require the wavelet transform and pyramids to be translation- and rotation-invariant. This paper is intended to serve for three purposes: (1) To present the general problem of stereo image matching in a sufficient depth and extent, so that pure wavelet mathematicians could think on adequate and efficient solutions, (2) To present a complete algorithm for top-down image matching including surface reconstruction by using wavelet pyramids, (3) To search for a wavelet family optimal for image matching. It is expected that a family of adequately designed wavelets could provide a generic and robust solution to the stereo image matching problem, which could be an important breakthrough in computer vision, photogrammetry, and pattern recognition.
Laboratory and Field Evaluations of Transgenic Soybean Exhibiting High-Dose Expression of a Synthetic Bacillus thuringiensis cry1A Gene for Control of Lepidoptera (2005)

Transgenic lines of soybean, Glycine max (L.) Merrill, expressing a synthetic cry1A gene (tic107) from Bacillus thuringiensis (Bt), were evaluated in screenhouse and conventional field trials for efficacy against lepidopteran pests. In screenhouse trials, Bt soybean and negative checks (isogenic segregants and parental lines) were evaluated against Anticarsia gemmatalis Hübner and Pseudoplusia includens (Walker) in the United States and against A. gemmatalis, Epinotia aporema (Walsingham), Rachiplusia nu (Guenée), and Spilosoma virginica (F.) in Argentina. Bt soybean exhibited virtually complete efficacy against each of these pests, whereas negative checks suffered significant damage. Bt soybean and negative checks also were evaluated in conventional trials against native populations of A. gemmatalis and P. includens in the southeastern United States. Each of these insects caused significant damage to negative checks in one or more locations, whereas Bt soybean exhibited virtually complete efficacy against these pests. In the laboratory, lyophilized leaf tissues from Bt soybean incorporated in artificial diet at a concentration representing a 25-fold dilution of fresh tissue caused complete mortality of A. gemmatalis and near complete mortality of P. includens neonates after 11 d, whereas mortality on negative checks did not exceed 10% for either insect. Average TIC107 expression approached or exceeded 50 microg/g fresh weight at V3 stage of growth and 200 microg/g by R6 stage of growth. These results demonstrate that expression of TIC107 in soybean can not only achieve highly efficacious control of several lepidopterans under field conditions but also provide a high dose for effective insect resistance management.
Metastatic Properties of the Human Prostatic Cell Line, PPC-1, In Athymic Nude Mice (1991)

Limitation in the number of human prostatic cell lines has created a gap in knowledge regarding the in-vivo progression of this common cancer. The recently isolated primary prostatic carcinoma cell line, PPC-1, has been shown to be tumorigenic in athymic nude mice. These cells are now shown to form metastases to secondary sites in 10 of 12 animals in this initial study. Metastases were localized to lung and lymph nodes, and the tumor histology closely resembled that of the undifferentiated, rapidly dividing primary tumors. This is the first report describing the metastatic properties of a primary prostatic cancer cell line. PPC-1 cells are therefore likely to represent a good model system for the study of human prostate cancer progression.
Noninvasive Prenatal Testing and Incidental Detection of Occult Maternal Malignancies (2015)

In this preliminary study, a small number of cases of occult malignancy were subsequently diagnosed among pregnant women whose noninvasive prenatal testing results showed discordance with the fetal karyotype. The clinical importance of these findings will require further research.
Cleavage properties of an oligonuclotide containing a bridged internucleotide 5′-phosphorothioate RNA linkage (1995)

An oligonucleotide has been synthesized that contains a single bridging 5'-phosphorothioate at an RNA linkage (5'-ApCpGpGpTpCpTprCpsApCpGpApGpC-3'). This new phosphodiester linkage is found to be particularly susceptible to cleavage when compared with the corresponding oxo, deoxy and thiodeoxy derivatives. Divalent metal cations were observed to dramatically increase the cleavage rate. The products of the cleavage under a variety of conditions are a 5'-thiol-containing fragment (6mer) and a 2',3'-cyclic phosphate-containing fragment (8mer). The pseudo-first order rate constant, kobs, for cleavage at pH 7.5 (50 mM Tris-HCI) in the presence of 5 mM EDTA is 1.5 x 10(-4)/min. In the presence of 5 mM metal dichloride and 50 mM Tris-HCI, pH 7.5, the relative cleavage rate enhancements are 10, 24, 71, 98, 370 and 3400 for Mg2+, Ca2+, Mn2+, Co2+, Zn2+ and Cd2+ respectively. The rate enhancements correlate well with Pearson's HSAB principle, suggesting that cleavage is mediated in part by coordination of the metal to the 5'-mercapto leaving group. RNA linkages containing bridging 5'-phosphorothioates should prove valuable for studying the mechanistic details of a variety of RNA cleaving agents, such as ribozymes.
Phosphorylation of a UDP-glucuronosyltransferase regulates substrate specificity (2005)

UDP-glucuronosyltransferase (UGT) isozymes catalyze detoxification of numerous chemical toxins present in our daily diet and environment by conjugation to glucuronic acid. The special properties and enzymatic mechanism(s) that enable endoplasmic reticulum-bound UGT isozymes to convert innumerable structurally diverse lipophiles to excretable glucuronides are unknown. Inhibition of cellular UGT1A7 and UGT1A10 activities and of [33P]orthophosphate incorporation into immunoprecipitable proteins after exposure to curcumin or calphostin-C indicated that the isozymes are phosphorylated. Furthermore, inhibition of UGT phosphorylation and activity by treatment with PKCepsilon-specific inhibitor peptide supported PKC involvement. Co-immunoprecipitation, colocalization by means of immunofluorescence, and cross-linking studies of PKCepsilon and UGT1A7His revealed that the proteins reside within 11.4 angstroms of each other. Moreover, mutation of three PKC sites in each UGT isozyme demonstrated that T73A/G and T202A/G caused null activity, whereas S432G-UGT1A7 caused a major shift of its pH-8.5 optimum to 6.4 with new substrate selections, including 17beta-estradiol. S432G-UGT1A10 exhibited a minor pH shift without substrate alterations. PKCepsilon involvement was confirmed by the demonstration that PKCepsilon overexpression enhanced activity of UGT1A7 but not of its S432 mutant and the conversion of 17beta-[14C]estradiol by S432G-UGT1A7 but not by UGT1A7. Consistent with these observations, treatment of UGT1A7-transfected cells with PKCepsilon-specific inhibitor peptide or general PKC inhibitors increased 17beta-estradiol catalysis between 5- and 11-fold, with parallel decreases in phosphoserine-432. Here, we report a mechanism involving PKC-mediated phosphorylation of UGT such that phosphoserine/threonine regulates substrate specificity in response to chemical exposures, which possibly confers survival benefit.
Memory of tolerance and induction of regulatory T cells by erythrocyte-targeted antigens (2015)

New approaches based on induction of antigen-specific immunological tolerance are being explored for treatment of autoimmunity and prevention of immunity to protein drugs. Antigens associated with apoptotic debris are known to be processed tolerogenically in vivo. Our group is exploring an approach toward antigen-specific tolerization using erythrocyte-binding antigens, based on the premise that as the erythrocytes circulate, age and are cleared, the erythrocyte surface-bound antigen payload will be cleared tolerogenically along with the eryptotic debris. Here, we characterized the phenotypic signatures of CD8+ T cells undergoing tolerance in response to soluble and erythrocyte-targeted antigen. Signaling through programmed death-1/programmed death ligand-1 (PD-1/PD-L1), but not through cytotoxic T lymphocyte antigen 4 (CTLA4), was shown to be required for antigen-specific T cell deletion, anergy and expression of regulatory markers. Generation of CD25+FOXP3+ regulatory T cells in response to erythrocyte-targeted antigens but not soluble antigen at an equimolar dose was observed, and these cells were required for long-term maintenance of immune tolerance in both the CD4+ and CD8+ T cell compartments. Evidence of infectious tolerance was observed, in that tolerance to a one antigenic epitope was able to regulate responses to other epitopes in the same protein antigen.
Reliability issues of flash memory cells (1993)

Reliability issues for flash electrically erasable programmable read-only memories are reviewed. The reliability of both the source-erase type (ETOX) flash memory and the NAND structure EEPROM are discussed. Disturbs during programming, write/erase endurance, charge loss of both devices are reviewed, and the reliability of the tunnel oxide and the interpoly dielectric are described. It is shown that bipolarity F-N programming/erase, which is used in the NAND EEPROM, improves the charge to breakdown and decreases the stress-induced leakage current.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Identification of a Porphyromonas gingivalis Receptor for the Streptococcus gordonii SspB Protein (2000)

Colonization of the plaque biofilm by the oral pathogen Porphyromonas gingivalis is favored by the presence of antecedent organisms such as Streptococcus gordonii. Coadhesion between P. gingivalis and S. gordonii can be mediated by the SspB protein of S. gordonii; however, the P. gingivalis cognate receptor for this protein has not been identified. In this study, we identified a surface protein of P. gingivalis that interacts with the SspB protein. Coprecipitation between P. gingivalis outer membrane proteins and purified SspB protein demonstrated that a 100-kDa P. gingivalis protein bound to SspB. The 100-kDa protein also bound to an engineered strain of Enterococcus faecalis that expresses the SspB protein on the cell surface. Monospecific polyclonal antibodies to the 100-kDa protein inhibited the binding between P. gingivalis and S. gordonii in a dose-dependent manner up to 86%. Amino acid sequencing of the 100-kDa protein showed homology to a protein previously identified as the P. gingivalis minor fimbria. The minor fimbrial protein may exist as a complex with a hemagglutinin-like protein since the genes encoding these proteins are adjacent on the chromosome and are cotranscribed. Thus, the P. gingivalis receptor for S. gordonii SspB is a 100-kDa protein that structurally may be a minor fimbria-protein complex and functionally effectuates coadhesion.
A naturally processed peptide presented by HLA-A*0201 is expressed at low abundance and recognized by an alloreactive CD8+ cytotoxic T cell with apparent high affinity (1997)

In contrast to T cells that respond to peptides presented by self MHC molecules, alloreactive T cells recognize determinants expressed on nonself MHC molecules. Because current positive selection models suggest that T cell affinity toward a nonself MHC molecule would be lower than that toward a self MHC molecule, we previously proposed that vigorous alloreactive responses would be generated preferentially toward those antigenic peptide complexes presented at the highest density on the cell surface. The high abundance of two class I MHC-associated peptides that have been identified as allo- or xenoantigens is consistent with this hypothesis. We report here the identification of a naturally processed peptide YLDPAQQNL that is presented by HLA-A*0201 and recognized by an alloreactive T cell clone. This peptide appears to originate from an unknown member of the zinc finger proteins. Quantitation by mass spectrometry indicates that this peptide is present on the surface at 85 to 125 copies per cell, comparable with the density of several other epitopes presented by HLA-A*0201 to self MHC-restricted T cells. In addition, based on the affinity of the peptide for HLA-A*0201 and the half-maximal peptide concentration required for T cell sensitization, this alloreactive T cell appears to have an affinity similar to or higher than that of many self MHC-restricted T cells. These data suggest that allogeneic responses can be directed against antigenic determinants of low abundance and that recognition of alloreactive peptides is not limited by a lower affinity of T cells for nonself MHC molecules.
Immune responses to Streptococcus sobrinus surface protein antigen A expressed by recombinant Salmonella typhimurium (1993)

In this study, we used a vaccine strain of Salmonella typhimurium to express antigenic determinants of the SpaA antigen of Streptococcus sobrinus, which is involved in the caries-forming process. We cloned either a single repeat (pYA2901) or three tandem repeats (pYA2905) of the 0.48-kb fragment of the spaA gene, which codes for an important component of the SpaA protein, plus a 1.2-kb minor antigenic determinant and measured the resulting immune responses to SpaA in orally immunized BALB/c mice. The single or triple repeat of the spaA gene fragment was inserted into the Asd+ vector pYA292 and was transformed into the S. typhimurium delta cya delta crp vaccine strain chi 4072 containing delta asd in the chromosome. Female BALB/c mice were then orally immunized with two doses of the S. typhimurium containing either of the two SpaA constructs, and the immune responses to the expressed SpaA protein were assessed. Significant serum immunoglobulin G (IgG) anti-SpaA titers were detected in mice immunized with chi 4072(pYA2905) but not chi 4072(pYA2901). Salivary anti-SpaA IgA titers were minimal and were only detected in mice immunized with S. typhimurium expressing the SpaA encoded by pYA2905. Intestinal anti-SpaA IgA titers, however, were detected in both groups of mice, particularly in mice immunized with chi 4072(pYA2905). An oral booster 26 weeks after the initial series of immunizations resulted in increased serum IgG titers in both chi 4072(pYA2901)- and chi 4072(pYA2905)-immunized animals, particularly in the chi 4072(pYA2905)-immunized animals. No anamnestic IgA response was detected in the saliva following the booster immunization.
Description of a real-time system to extract the fetal electrocardiogram (1989)

An overview is given of the FEMME-project (Fetal Electrocardiogram Measuring Method and Equipment). The project started in 1981 and is, at the moment, close to producing a prototype personal computer-based system. This records simultaneously a number of cutaneous potential signals and derives from this set one or more maternal electrocardiogram-free fetal heart signals, by combining linearly the recorded signals. An on-line adaptive algorithm based on the Singular Value Decomposition (SVD) has been designed to compute the coefficients in these linear combinations. This algorithm will be implemented on a DSP board that can be plugged into the real-time recording system. The system will be very useful in studies of the fetal electrocardiogram during pregnancy, but also in all other studies such as fetal heart rate variability, fetal movements, etc., where a precise trigger of the electrical signal from the fetal heart is required.
Increased Expression of Interleukin (IL)‐35 and IL‐17, But Not IL‐27, in Gingival Tissues With Chronic Periodontitis (2014)

IL-35 and IL-17, but not IL-27, may play important roles in the pathogenesis of periodontitis.
Formation ofβ-Sheet Assemblage with a View to Developing an Amyloid Model (2000)

Amphiphilic molecules that contain a tripeptide moiety form an aggregate not only in water but also in organic solvents. The aggregate possesses fibrous morphology and involves a rich amount of parallel β-sheet structure of peptides, which is similar to a β-amyloid peptide called an amyloid fibril. The dynamic properties of the aggregate of the tripeptide-containing amphiphiles were also similar to those of the amyloid. These similarities suggest that the tripeptide-containing amphiphiles are suitable for an amyloid model.
Faecal alpha 1 antitrypsin as a marker of gastrointestinal disease in HIV antibody positive individuals. (1996)

Hypoalbuminaemia and diarrhoea are common complications of HIV infection and substantial causes of morbidity, but the specific intestinal pathologies that cause enteric protein loss have not been clearly defined. Two hundred and twenty stool samples from patients with a variety of HIV related conditions were analysed for faecal alpha 1 antitrypsin. Patients with intestinal Kaposi's sarcoma had a significantly raised faecal alpha 1 antitrypsin value and hypoalbuminaemia. A faecal alpha 1 antitrypsin value of greater than 0.3 mg/g wet stool has a sensitivity of 94% and a specificity of 76% for the diagnosis of intestinal Kaposi's sarcoma in HIV positive individuals. Patients with cytomegalovirus and bacterial enteritis had raised faecal alpha 1 antitrypsin values but levels were normal for all other intestinal pathologies compared with pathogen negative stool. The combination of faecal alpha 1 antitrypsin concentration greater than 0.2 mg/g, a negative stool culture for enteric bacteria, and the absence of palatal Kaposi's sarcoma has a sensitivity of 55% and specificity of 88% for the diagnosis of enteric cytomegalovirus infection.
Reassortant rotaviruses as potential live rotavirus vaccine candidates (1985)

A series of reassortants was isolated from coinfection of cell cultures with a wild-type animal rotavirus and a "noncultivatable" human rotavirus. Wild-type bovine rotavirus (UK strain) was reassorted with human rotavirus strains D, DS-1, and P; wild-type rhesus rotavirus was reassorted with human rotavirus strains D and DS-1. The D, DS-1, and P strains represent human rotavirus serotypes 1, 2, and 3, respectively. Monospecific antiserum (to bovine rotavirus, NCDV strain) or a set of monoclonal antibodies to the major outer capsid neutralization glycoprotein, VP7 (of the rhesus rotavirus), was used to select for reassortants with human rotavirus neutralization specificity. This selection technique yielded many reassortants which received only the gene segment coding for the major neutralization protein from the human rotavirus parent, whereas the remaining genes were derived from the animal rotavirus parent. Single human rotavirus gene substitution reassortants of this sort represent potential live vaccine strains.
OCT4: A Sensitive and Specific Immunohistochemical Marker for Metastatic Germ Cell Tumors (2006)

Octamer-binding transcription factor 4 (OCT4) is a transcription factor normally expressed in embryonic stem cells and germ cells. Recent investigations have shown OCT4 to be a sensitive and specific immunohistochemical marker of gonadal germ cell tumors, specifically seminoma and embryonal carcinoma. Expanding on these previous studies, a recent report by Cheng evaluated the diagnostic utility of OCT4 immunohistochemistry in the identification of germ cell tumors in the metastatic setting. In this context, OCT4 was observed to be a highly reliable marker for metastatic germ cell tumors that contained components of seminoma or embryonal carcinoma. The results of this study indicate that OCT4 immunohistochemistry is a useful diagnostic tool for establishing the germ cell origin of a metastatic tumor and suggest a potential role for OCT4 in the immunohistochemical assessment of carcinomas of unknown primary origin.