gebhart/patrepeval huggingface dataset:
Mutation detection using a novel plant endonuclease (1998)

We have discovered a useful new reagent for mutation detection, a novel nuclease CEL I from celery. It is specific for DNA distortions and mismatches from pH 6 to 9. Incision is on the 3'-side of the mismatch site in one of the two DNA strands in a heteroduplex. CEL I-like nucleases are found in many plants. We report here that a simple method of enzyme mutation detection using CEL I can efficiently identify mutations and polymorphisms. To illustrate the efficacy of this approach, the exons of the BRCA1 gene were amplified by PCR using primers 5'-labeled with fluorescent dyes of two colors. The PCR products were annealed to form heteroduplexes and subjected to CEL I incision. In GeneScan analyses with a PE Applied Biosystems automated DNA sequencer, two independent incision events, one in each strand, produce truncated fragments of two colors that complement each other to confirm the position of the mismatch. CEL I can detect 100% of the sequence variants present, including deletions, insertions and missense alterations. Our results indicate that CEL I mutation detection is a highly sensitive method for detecting both polymorphisms and disease-causing mutations in DNA fragments as long as 1120 bp in length.
Structure‐Function Relationships of the Luteinizing Hormone Receptor (2005)

Of the 800-900 genes in the human genome that appear to encode G-protein-coupled receptors (GPCRs), two are known to encode receptors that bind the three heterodimeric human gonadotropins, luteinizing hormone (LH), chorionic gonadotropin (CG), and follicle-stimulating hormone (FSH). LH and CG bind to a common receptor, LHR, and FSH binds to a paralogous receptor. These GPCRs contain a relatively large ectodomain (ECD), responsible for high-affinity ligand binding, and a transmembrane portion, as in the other GPCRs. The ECD contains nine leucine-rich repeats capped by N-terminal and C-terminal cysteine-rich regions. The overall goal of this research is to elucidate the molecular mechanisms by which CG and LH bind to and activate LHR and the latter, in turn, activates Gs alpha. A combination of molecular modeling and site-directed mutagenesis, coupled with binding and signaling studies in transiently transfected HEK 293 cells expressing wild-type and mutant forms of LHR, has been used to develop and test models for the LHR ECD, the CG-LHR ECD complex, and the structural changes in the transmembrane helices and intracellular loops, particularly loop 2, that accompany receptor activation. In addition, a single-chain CG-LHR complex was designed in which a fusion protein of the two subunits of human CG was linked to full-length LHR. This ligand-receptor complex was shown to be constitutively active in cellular models and in transgenic mice, the latter of which exhibit precocious puberty. From a combination of molecular modeling, site-directed mutagenesis, genetic/protein engineering, and receptor characterization in cellular and animal models, considerable insight is being developed on the mechanisms of normal and aberrant activation of LHR.
The rat vault RNA gene contains a unique RNA polymerase III promoter composed of both external and internal elements that function synergistically. (1994)

A novel gene transcribed by RNA polymerase (pol) III has been recently identified that produces an RNA component of a large cytoplasmic ribonucleoprotein complex (Kickhoefer, V. A., Searles, R. P., Kedersha, N. L., Garber, M. E., Johnson, D. L., and Rome, L. H. (1993) J. Biol. Chem. 268, 7868-7873). Since sequence analysis revealed that this gene contains promoter elements from two different classes of RNA pol III gene promoters, we examined the function of the 5'-flanking type-3 and internal type-2 sequences on transcription activity and the production of stable transcription complexes. We find that the vRNA gene contains a novel RNA pol III promoter, where both the external and internal sequences are essential for template activity and for the productive interaction of TFIIIC with the internal elements. Thus, the vRNA gene represents the first example of a template that requires both type-2 and type-3 promoter elements that appear to function synergistically in the formation of productive transcription complexes. We have further examined the function of the unique arrangement of an internal A box and two B box elements. We find that at least one B element is required for template activity. In the absence of the 5'-flanking sequence the presence of both B elements inhibits transcription and the binding of TFIIIC. The formation of active complexes is restored when either the B2 element is inactivated or the distance separating the two B elements is increased. Therefore, the B2 element appears to negatively regulate template activity in the absence of the upstream sequences. This unique RNA pol III promoter arrangement may provide a novel mechanism for the regulation of vRNA gene activity.
The α‐gal epitope and the anti‐Gal antibody in xenotransplantation and in cancer immunotherapy (2005)

The alpha-gal epitope (Galalpha1-3Galbeta1-(3)4GlcNAc-R) is abundantly synthesized on glycolipids and glycoproteins of non-primate mammals and New World monkeys by the glycosylation enzyme alpha1,3galactosyltransferase (alpha1,3GT). In humans, apes and Old World monkeys, this epitope is absent because the alpha1,3GT gene was inactivated in ancestral Old World primates. Instead, humans, apes and Old World monkeys produce the anti-Gal antibody, which specifically interacts with alpha-gal epitopes and which constitutes approximately 1% of circulating immunoglobulins. Anti-Gal has functioned as an immunological barrier, preventing the transplantation of pig organs into humans, because anti-Gal binds to the alpha-gal epitopes expressed on pig cells. The recent generation of alpha1,3GT knockout pigs that lack alpha-gal epitopes has resulted in the elimination of this immunological barrier. Anti-Gal can be exploited for clinical use in cancer immunotherapy by targeting autologous tumour vaccines to APC, thereby increasing their immunogenicity. Autologous intact tumour cells from haematological malignancies, or autologous tumour cell membranes from solid tumours are processed to express alpha-gal epitopes by incubation with neuraminidase, recombinant alpha1,3GT and with uridine diphosphate galactose. Subsequent immunization with such autologous tumour vaccines results in in vivo opsonization by anti-Gal IgG binding to these alpha-gal epitopes. The interaction of the Fc portion of the vaccine-bound anti-Gal with Fcgamma receptors of APC induces effective uptake of the vaccinating tumour cell membranes by the APC, followed by effective transport of the vaccinating tumour membranes to the regional lymph nodes, and processing and presentation of the tumour-associated antigen (TAA) peptides. Activation of tumour-specific T cells within the lymph nodes by autologous TAA peptides may elicit an immune response that in some patients will be potent enough to eradicate the residual tumour cells that remain after completion of standard therapy. A similar expression of alpha-gal epitopes can be achieved by transduction of tumour cells with an adenovirus vector (or other vectors) containing the alpha1,3GT gene, thus enabling anti-Gal-mediated targeting of the vaccinating transduced cells to APC. Intratumoral delivery of the alpha1,3GT gene by various vectors results in the expression of alpha-gal epitopes. Such expression of the xenograft carbohydrate phenotype is likely to induce anti-Gal-mediated destruction of the tumour lesion, similar to rejection of xenografts by this antibody. Opsonization of the destroyed tumour cell membranes by anti-Gal IgG further targets them to APC, thus converting the tumour lesion, treated by the alpha1,3GT gene, into an in situ autologous tumour vaccine.
Reamed Nailing of Open Tibial Fractures: Does the Antibiotic Bead Pouch Reduce the Deep Infection Rate? (1996)

Eighty-one open tibial fractures were treated by reamed intramedullary nailing. There were 38 type II, 23 type IIIa and 20 type IIIb injuries. At the end of the nailing procedure the first 26 fractures (15 type II, five type IIIa, and six type IIIb) had antibiotic prophylaxis and delayed closure of the open wound. The subsequent 55 fractures (23 type II, 18 type IIIa, and 14 type IIIb) had identical management but in addition had an antibiotic bead pouch inserted into the open wound following debridement. Three amputations were performed: one (3.8%) in the group treated without a bead pouch and two (3.6%) in the bead pouch group in patients with grade IIIb fractures and severe crushing injuries. Of the remainder, there were four deep infections (16%) in the 25 fractures treated prior to the use of the bead pouch and two (4%) deep infections in the 53 fractures following introduction of the bead pouch. Addition of the bead pouch to the wound management protocol was associated with a worthwhile reduction of deep infection.
Titration Behavior and Spectral Transitions of Water-Soluble Polythiophene Carboxylic Acids (1999)

Water-soluble poly(3-thiophene acetic acid) (P3TAA) and its copolymers with 3-n-methylthiophene or with 3-n-octadecylthiophene were synthesized. The solution properties of these water-soluble polythiophene carboxylic acids were studied by potentiometric titration, viscosity measurements, and UV−visible spectroscopy. We have found that the Henderson−Hasselbach plot of the titration curve showed an inflection of the slope around pH = 5−6. The reduced viscosity and electronic spectra of the P3TAA aqueous solution also showed an abrupt change at this pH region. These results are quite different from that of a common flexible polyelectrolyte, such as poly(acrylic acid) (PAA) and strongly suggest that the pH-induced abrupt conformational changes occurred from the aggregated state to the extended state of the polymer main chain. The observed results are explained in terms of the rigid hydrophobic main chain and the nature of the conjugated polymer.
Characteristics of an Albumin Cobalt Binding Test for Assessment of Acute Coronary Syndrome Patients: A Multicenter Study (2001)

Abstract Background: The ability of the N-terminal region of human albumin to bind cobalt is diminished by myocardial ischemia. The characteristics of an assay based on albumin cobalt binding were assessed in suspected acute coronary syndrome patients and in a control reference population. The ability of the Albumin Cobalt Binding (ACBTM) Test measurement at presentation to predict troponin-positive or -negative results 6–24 h later was also examined. Methods: We enrolled 256 acute coronary syndrome patients at four medical centers. Blood specimens were collected at presentation and then 6–24 h later. The dichotomous decision limit and performance characteristics of the ACB Test for predicting troponin-positive or -negative status 6 h-24 h later were determined using ROC curve analysis. Results for 32 patients could not be used because the time of onset of ischemia appeared to have been &amp;gt;3 h before presentation or was uncertain. The reference interval was determined by parametric analysis to estimate the upper 95th percentile of a reference population (n = 109) of ostensibly healthy individuals. Results: Increased cTnI was found in 35 of 224 patients. The ROC curve area for the ACB Test was 0.78 [95% confidence interval (CI), 0.70–0.86]. At the optimum decision point of 75 units/mL, the sensitivity and specificity of the ACB Test were 83% (95% CI, 66–93%) and 69% (95% CI, 62–76%). The negative predictive value was 96% (95% CI, 91–98%), and the positive predictive value was 33% (95% CI, 24–44%). The within-run CV of the ACB Test was 7.3%. Results for the reference population were normally distributed; the one-sided parametric 95th percentile was 80.2 units/mL. Conclusions: This exploratory study suggests that the ACB Test has high negative predictive value and sensitivity in the presentation sample for predicting troponin-negative or -positive results 6–24 h later.
Treatment of transplanted murine tumors with an oncolytic virus and cyclophosphamide. (1978)

Effective treatment of transplanted murine mammary tumors with an oncolytic virus and cyclophosphamide is reported. The oncolytic virus was cultured initially from a murine ascites tumor that had undergone "spontaneous" regression. This virus used alone causes rapid lysis of ascites tumors, but successful treatment of solid tumors requires the addition of cyclophosphamide. The virus must be injected directly into the tumor. The virus causes no detectable disease in mice even when administered in conjunction with cyclophosphamide. Fluorescent antibody techniques revealed that all A/S stock mice have antibody against cells infected with this virus.
Purification and Comparative Properties of the Delta and Sigma Subunits of RNA Polymerase from Bacillus subtilis (1977)

Bacillus subtilis delta protein is a 21 500-Mr polypeptide that can be isolated in association with RNA polymerase holoenzyme from uninfected bacteria and with modified forms of RNA polymerase from cells infected with phage SP01 [Pero, J., Nelson, J. and Fox, T. (1975) Proc. Natl Acad. Sci. U.S.A. 72,1589]. Although no function has been assigned to delta protein in uninfected cells, this host polypeptide enhances the specificity of transcription by phage-modified forms of RNA polymerase that contain SP01-coded regulatory subunits. This report describes the purification of delta and sigma proteins from uninfected B. subtilis and examines the comparative effects of these polypeptides on transcription by core RNA polymerase. Purified sigma polypeptide was found to stimulate the transcription of phage DNA while having little effect on RNA synthesis with the synthetic DNA poly(dA-dT) as template. In contrast, purified delta protein markedly depressed the transcription of poly(dA-dT) while having little effect on enzyme activity with phage DNA as template. The inhibitory effect of delta protein on poly (dA-dT) transcription was strongly dependent on the presence of KC1 in the RNA synthesis reaction mixture.
A phase I/II trial of hydroxychloroquine in conjunction with radiation therapy and concurrent and adjuvant temozolomide in patients with newly diagnosed glioblastoma multiforme (2014)

Preclinical studies indicate autophagy inhibition with hydroxychloroquine (HCQ) can augment the efficacy of DNA-damaging therapy. The primary objective of this trial was to determine the maximum tolerated dose (MTD) and efficacy of HCQ in combination with radiation therapy (RT) and temozolomide (TMZ) for newly diagnosed glioblastoma (GB). A 3 + 3 phase I trial design followed by a noncomparative phase II study was conducted in GB patients after initial resection. Patients received HCQ (200 to 800 mg oral daily) with RT and concurrent and adjuvant TMZ. Quantitative electron microscopy and immunoblotting were used to assess changes in autophagic vacuoles (AVs) in peripheral blood mononuclear cells (PBMC). Population pharmacokinetic (PK) modeling enabled PK-pharmacodynamic correlations. Sixteen phase I subjects were evaluable for dose-limiting toxicities. At 800 mg HCQ/d, 3/3 subjects experienced Grade 3 and 4 neutropenia and thrombocytopenia, 1 with sepsis. HCQ 600 mg/d was found to be the MTD in this combination. The phase II cohort (n = 76) had a median survival of 15.6 mos with survival rates at 12, 18, and 24 mo of 70%, 36%, and 25%. PK analysis indicated dose-proportional exposure for HCQ. Significant therapy-associated increases in AV and LC3-II were observed in PBMC and correlated with higher HCQ exposure. These data establish that autophagy inhibition is achievable with HCQ, but dose-limiting toxicity prevented escalation to higher doses of HCQ. At HCQ 600 mg/d, autophagy inhibition was not consistently achieved in patients treated with this regimen, and no significant improvement in overall survival was observed. Therefore, a definitive test of the role of autophagy inhibition in the adjuvant setting for glioma patients awaits the development of lower-toxicity compounds that can achieve more consistent inhibition of autophagy than HCQ.
Discovery of 2-{4-[(3S)-Piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide (MK-4827): A Novel Oral Poly(ADP-ribose)polymerase (PARP) Inhibitor Efficacious in BRCA-1 and -2 Mutant Tumors (2009)

We disclose the development of a novel series of 2-phenyl-2H-indazole-7-carboxamides as poly(ADP-ribose)polymerase (PARP) 1 and 2 inhibitors. This series was optimized to improve enzyme and cellular activity, and the resulting PARP inhibitors display antiproliferation activities against BRCA-1 and BRCA-2 deficient cancer cells, with high selectivity over BRCA proficient cells. Extrahepatic oxidation by CYP450 1A1 and 1A2 was identified as a metabolic concern, and strategies to improve pharmacokinetic properties are reported. These efforts culminated in the identification of 2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide 56 (MK-4827), which displays good pharmacokinetic properties and is currently in phase I clinical trials. This compound displays excellent PARP 1 and 2 inhibition with IC(50) = 3.8 and 2.1 nM, respectively, and in a whole cell assay, it inhibited PARP activity with EC(50) = 4 nM and inhibited proliferation of cancer cells with mutant BRCA-1 and BRCA-2 with CC(50) in the 10-100 nM range. Compound 56 was well tolerated in vivo and demonstrated efficacy as a single agent in a xenograft model of BRCA-1 deficient cancer.
Trimeric Membrane-anchored gp41 Inhibits HIV Membrane Fusion (2004)

The HIV-1 envelope glycoprotein is composed of a receptor binding subunit, gp120 that is non-covalently linked to the membrane-anchored fusion protein, gp41. Triggered by cellular receptor binding, the trimeric envelope complex mediates the fusion of viral and cellular membranes through the rearrangement of the fusion protein subunit into a six-helical bundle core structure. Here we describe the biophysical and functional properties of a membrane-anchored fragment of gp41 (gp41ctm) that includes the complete C-terminal heptad repeat region 2, the connecting part, and the transmembrane region. We show that the transmembrane domain of the envelope glycoprotein is sufficient for trimerization in vitro, contributing most of the alpha-helical content of gp41ctm. Trimeric gp41ctm is protease-resistant and recognizes neutralizing antibodies 2F5 and 4E10. However, gp41ctm and gp41ctm proteoliposomes elicit no clear neutralizing immune responses in preliminary mouse studies. We further show that gp41ctm and surprisingly also gp41ctm proteoliposomes have potent anti-viral activity. Our data suggest that liposome-anchored gp41ctm exerts its inhibitory action outside of the initial fusion contact site, and its implications for the fusion reaction are discussed.
Integrating multiple knowledge sources for detection and correction of repairs in human-computer dialog (1992)

We have analyzed 607 sentences of spontaneous human-computer speech data containing repairs, drawn from a total corpus of 10,718 sentences. We present here criteria and techniques for automatically detecting the presence of a repair, its location, and making the appropriate correction. The criteria involve integration of knowledge from several sources: pattern matching, syntactic and semantic analysis, and acoustics.
Purification and Properties of d-Glycerate 3-Kinase from Escherichia coli (1966)

Abstract The adaptive d-glycerate 3-kinase from glycerate-adapted Escherichia coli has been purified 4200-fold in 37% yield and has been crystallized. The procedure, starting with the crude, cell-free extract, consisted of treatment with protamine sulfate, ammonium sulfate, passage through a diethylaminoethyl Sephadex column, and precipitation with ethanol. The reaction product, 3-phosphoglycerate, has been identified by paper chromatography and specific enzymatic assay. Some characteristics of the enzyme which show clearly its differences from other glycerate kinases are described.
Virulence factors (aerobactin and mucoid phenotype) inKlebsiella pneumoniaeandEscherichia coliblood culture isolates (1995)

We examined the presence of two virulence factors in 241 blood isolates of Klebsiella pneumoniae from patients hospitalized during 1989 and 1990 in 7 French hospitals, and 125 blood isolates of Escherichia coli from one hospital. Aerobactin was scored phenotypically and genotypically with an intragenic DNA probe of 2 kb. The mucoid phenotype was assessed by culture on trypticase soy agar and by genotypic analysis (intragenic DNA probe of 235 bp). Only 6%K. pneumoniae isolates were aerobactin-positive with no significant variation according to geographical location while 20% of K. pneumoniae isolates displayed the mucoid phenotype, with a significant variation according to hospital. Aerobactin was always associated with the mucoid phenotype. The frequency of aerobactin production but not mucoid phenotype (14%) was higher among E. coli isolates (48%). They harbored two types of large plasmids. Intraperitoneal injection into mice of 103 cfu of K. pneumoniae producing both virulence factors demonstrated that capsular serotype K2 was the more virulent K23 and K28.
B7-Dc, a New Dendritic Cell Molecule with Potent Costimulatory Properties for T Cells (2001)

Dendritic cells (DCs), unique antigen-presenting cells (APCs) with potent T cell stimulatory capacity, direct the activation and differentiation of T cells by providing costimulatory signals. As such, they are critical regulators of both natural and vaccine-induced immune responses. A new B7 family member, B7-DC, whose expression is highly restricted to DCs, was identified among a library of genes differentially expressed between DCs and activated macrophages. B7-DC fails to bind the B7.1/2 receptors CD28 and cytotoxic T lymphocyte-associated antigen (CTLA)-4, but does bind PD-1, a receptor for B7-H1/PD-L1. B7-DC costimulates T cell proliferation more efficiently than B7.1 and induces a distinct pattern of lymphokine secretion. In particular, B7-DC strongly costimulates interferon gamma but not interleukin (IL)-4 or IL-10 production from isolated naive T cells. These properties of B7-DC may account for some of the unique activity of DCs, such as their ability to initiate potent T helper cell type 1 responses.
Development and characterization ofin vivoflexible electrodes compatible with large tissue displacements (2009)

Electrical activity is the ultimate functional measure of neuronal tissue and recording that activity remains a key technical challenge in neuroscience. The mechanical mismatch between rigid electrodes and compliant brain tissue is a critical limitation in applications where movement is an inherent component. An electrode that permits recording of neural activity, while minimizing tissue disruption, is beneficial for applications that encompass both normal physiological movements and those which require consistent recording during large tissue displacements. In order to test the extreme of this range of movement, flexible electrodes were developed to record activity during and immediately following cortical impact in the rat. Photolithography techniques were used to fabricate flexible electrodes that were readily insertable into the brain using a parylene C base and gold conduction lines and contact pads, permitting custom geometry. We found that this electrode configuration retained mechanical and electrical integrity following both durability studies and large movements within the cortex. This novel flexible electrode configuration provides a novel platform for experimentally examining neuronal activity during a range of brain movements.