gebhart/patrepeval huggingface dataset:
Human Papillomavirus Testing for Triage of Women With Cytologic Evidence of Low-Grade Squamous Intraepithelial Lesions: Baseline Data From a Randomized Trial (2000)

Because a very high percentage of women with an LSIL diagnosis from Pap smears are positive for HPV DNA by HCII testing, there is limited potential for this assay to direct decisions about the clinical management of women with LSIL. The role of HPV testing in the management of women with ASCUS is still under study.
Flavopiridol Synergizes with Sorafenib to Induce Cytotoxicity and Potentiate Antitumorigenic Activity in EGFR/HER-2 and Mutant RAS/RAF Breast Cancer Model Systems (2013)

Oncogenic receptor tyrosine kinase (RTK) signaling through the Ras-Raf-Mek-Erk (Ras-MAPK) pathway is implicated in a wide array of carcinomas, including those of the breast. The cyclin-dependent kinases (CDKs) are implicated in regulating proliferative and survival signaling downstream of this pathway. Here, we show that CDK inhibitors exhibit an order of magnitude greater cytotoxic potency than a suite of inhibitors targeting RTK and Ras-MAPK signaling in cell lines representative of clinically recognized breast cancer (BC) subtypes. Drug combination studies show that the pan-CDK inhibitor, flavopiridol (FPD), synergistically potentiated cytotoxicity induced by the Raf inhibitor, sorafenib (SFN). This synergy was most pronounced at sub-EC50 SFN concentrations in MDA-MB-231 (KRAS-G13D and BRAF-G464V mutations), MDA-MB-468 [epidermal growth factor receptor (EGFR) overexpression], and SKBR3 [ErbB2/EGFR2 (HER-2) overexpression] cells but not in hormone-dependent MCF-7 and T47D cells. Potentiation of SFN cytotoxicity by FPD correlated with enhanced apoptosis, suppression of retinoblastoma (Rb) signaling, and reduced Mcl-1 expression. SFN and FPD were also tested in an MDA-MB-231 mammary fat pad engraftment model of tumorigenesis. Mice treated with both drugs exhibited reduced primary tumor growth rates and metastatic tumor load in the lungs compared to treatment with either drug alone, and this correlated with greater reductions in Rb signaling and Mcl-1 expression in resected tumors. These findings support the development of CDK and Raf co-targeting strategies in EGFR/HER-2-overexpressing or RAS/RAF mutant BCs.
CD8 + Lymphocytes Can Control HIV Infection in Vitro by Suppressing Virus Replication (1986)

Lymphocytes bearing the CD8 marker were shown to suppress replication of human immunodeficiency virus (HIV) in peripheral blood mononuclear cells. The effect was dose-dependent and most apparent with autologous lymphocytes; it did not appear to be mediated by a cytotoxic response. This suppression of HIV replication could be demonstrated by the addition of CD8+ cells at the initiation of virus production as well as after several weeks of virus replication by cultured cells. The observations suggest a potential approach to therapy in which autologous CD8 lymphocytes could be administered to individuals to inhibit HIV replication and perhaps progression of disease.
An efficient method for multi-locus molecular haplotyping (2006)

Many methods exist for genotyping--revealing which alleles an individual carries at different genetic loci. A harder problem is haplotyping--determining which alleles lie on each of the two homologous chromosomes in a diploid individual. Conventional approaches to haplotyping require the use of several generations to reconstruct haplotypes within a pedigree, or use statistical methods to estimate the prevalence of different haplotypes in a population. Several molecular haplotyping methods have been proposed, but have been limited to small numbers of loci, usually over short distances. Here we demonstrate a method which allows rapid molecular haplotyping of many loci over long distances. The method requires no more genotypings than pedigree methods, but requires no family material. It relies on a procedure to identify and genotype single DNA molecules, and reconstruction of long haplotypes by a 'tiling' approach. We demonstrate this by resolving haplotypes in two regions of the human genome, harbouring 20 and 105 single-nucleotide polymorphisms, respectively. The method can be extended to reconstruct haplotypes of arbitrary complexity and length, and can make use of a variety of genotyping platforms. We also argue that this method is applicable in situations which are intractable to conventional approaches.
The type IV bundle‐forming pilus of enteropathogenic Escherichia coli undergoes dramatic alterations in structure associated with bacterial adherence, aggregation and dispersal (1999)

BFP, a plasmid-encoded type IV bundle-forming pilus produced by enteropathogenic Escherichia coli (EPEC), has recently been shown to be associated with the aggregation of bacteria and dispersal of bacteria from bacterial microcolonies. In standard 3 h HEp-2 cell assays, EPEC adhere in localized microcolonies; after 6 h, bacterial microcolonies are no longer present, indicating that bacterial aggregation and dispersal occurs in vitro during EPEC adhesion to cultured epithelial cells. To examine the role of BFP in EPEC aggregation and dispersal, we examined HEp-2 cell adhesion of strain E2348/69 and defined E2348/69 mutants by immunofluorescence and immunoelectron microscopy. BFP was expressed initially as approximately 40 nm diameter pilus bundles that promoted bacteria-bacteria interaction and microcolony formation. BFP subsequently underwent a striking alteration in structural organization with the formation of much longer and thicker ( approximately 100 nm diameter) pilus bundles, which frequently aggregated laterally to form even thicker bundles often arranged in a loose three-dimensional network; EPEC dispersal from bacterial microcolonies was associated with this transformation of BFP from thin to thick bundles. Bacterial dispersal and transformation of BFP from thin to thick bundles did not occur with a bfpF mutant of strain E2348/69. It is concluded that BFP promotes both the formation and the dispersal of EPEC microcolonies, that the dispersal phase requires BfpF and that dispersal is associated with dramatic alterations in the structure of BFP bundles.
Synthesis of heterocyclic compounds. XXXIX. Synthesis of 5‐cyano‐2‐phenyl‐4‐thioxo‐3,4‐dihydropyrimidines (1985)

Abstract The reaction of thiobenzamide with 3‐alkoxy‐3‐aryl(or alkyl)‐2‐cyanopropenenitriles 1 and sodium 2‐propoxide in 2‐propanol afforded after acidic treatment 6‐aryl(or alkyl)‐5‐cyano‐2‐phenyl‐4‐thioxo‐3,4‐dihydropyrimidines 3 through formation of the 3‐aryl(or alkyl)‐2‐cyano‐3‐thiobenzamidopropenenitrile 2 that has been isolated in one case ( 2a , R 1 = Ph).
Nonlinear optical studies of a fluorinated poled polyimide guest-host system (1994)

We report on poling of a low dielectric constant preimidized fluorinated fully aromatic guest-host polyimide nonlinear optical material including thermal stability of optical nonlinearities and waveguiding properties. We measured a second-harmonic coefficient (d33=4.9±0.5 pm/V at 1217 nm fundamental wavelength) which is accurately predicted by a thermodynamic model of poled polymers. The optical nonlinearity of a poled sample was thermally stable at 80 °C for over 300 h. Films were observed to have negative birefringence. Optical losses for slab waveguides in lowest order TE and TM modes were ≥7.7 dB/cm for doped waveguides at 800 nm wavelength and increased after poling.
Molecular basis for passive immunotherapy of Alzheimer's disease (2007)

Amyloid aggregates of the amyloid-beta (Abeta) peptide are implicated in the pathology of Alzheimer's disease. Anti-Abeta monoclonal antibodies (mAbs) have been shown to reduce amyloid plaques in vitro and in animal studies. Consequently, passive immunization is being considered for treating Alzheimer's, and anti-Abeta mAbs are now in phase II trials. We report the isolation of two mAbs (PFA1 and PFA2) that recognize Abeta monomers, protofibrils, and fibrils and the structures of their antigen binding fragments (Fabs) in complex with the Abeta(1-8) peptide DAEFRHDS. The immunodominant EFRHD sequence forms salt bridges, hydrogen bonds, and hydrophobic contacts, including interactions with a striking WWDDD motif of the antigen binding fragments. We also show that a similar sequence (AKFRHD) derived from the human protein GRIP1 is able to cross-react with both PFA1 and PFA2 and, when cocrystallized with PFA1, binds in an identical conformation to Abeta(1-8). Because such cross-reactivity has implications for potential side effects of immunotherapy, our structures provide a template for designing derivative mAbs that target Abeta with improved specificity and higher affinity.
N-Heterocyclic Carbene Catalyzed Ring Expansion of 4-Formyl-β-lactams:  Synthesis of Succinimide Derivatives (2007)

N-heterocyclic carbene (NHC) has been employed as an efficient catalyst for ring expansion of 4-formyl-beta-lactams, allowing the facile synthesis of succinimide derivatives. This organocatalytic process features readily availability of the catalyst, low catalyst loading, and mild reaction conditions.
Effects of local administration of GH and IGF-1 on longitudinal bone growth in rats (1986)

The effect of local administration of growth hormone (GH) and insulinlike growth factor 1 (IGF-1) on longitudinal bone growth was studied in the proximal tibia of hypophysectomized rats, by using the tetracycline method. Human GH (hGH) stimulated local bone growth when administered into the epiphysial growth plate, into the epiphysis through an implanted cannula, or into the knee joint intraarticularly. In contrast, hGH administration into the metaphysis did not cause such a stimulation. The effect of hGH was dose dependent, and the lowest daily dose of hGH that caused a stimulation was 50 ng. hGH produced by cloned bacteria was as effective as pituitary-derived hGH, excluding the possibility of a pituitary growth factor being the active compound. GH from other mammalian species (rat GH, ovine GH, and bacterially produced bovine GH) also stimulated local bone growth. Ovine prolactin (oPRL) stimulated local bone growth but the threshold dose of oPRL was approximately 100 times higher than that of hGH, suggesting that contamination of this preparation by GH may account for the stimulation. Reduced carboxymethylated human GH, that has a greatly reduced anabolic activity, did not stimulate local bone growth. Local administration of 5 micrograms of bacterially produced human IGF-1 per day produced a small but significant effect on unilateral bone growth. Simultaneous administration of hGH had no additive effect with, nor did it potentiate, the stimulatory effect of IGF-1. The present study confirms and extends earlier investigations, showing that local injection of GH at the site of the epiphysial growth plate stimulates unilateral bone growth. The study also shows that local administration of IGF-1 stimulates longitudinal bone growth.
New type of cyclization of .alpha.,.beta.,.chi.,.psi.-unsaturated dioic acid esters through tandem conjugate additions by using lithium N-benzyl-N-(trimethylsilyl)amide as a nitrogen nucleophile (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew type of cyclization of .alpha.,.beta.,.chi.,.psi.-unsaturated dioic acid esters through tandem conjugate additions by using lithium N-benzyl-N-(trimethylsilyl)amide as a nitrogen nucleophileTadao Uyehara, Naomi Shida, and Yoshinori YamamotoCite this: J. Org. Chem. 1992, 57, 11, 3139–3145Publication Date (Print):May 1, 1992Publication History Published online1 May 2002Published inissue 1 May 1992https://pubs.acs.org/doi/10.1021/jo00037a034https://doi.org/10.1021/jo00037a034research-articleACS PublicationsRequest reuse permissionsArticle Views319Altmetric-Citations57LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Semiconductor-surface restoration by valence-mending adsorbates: Application to Si(100):S and Si(100):Se (1991)

A set of criteria is proposed for choosing adsorbates that can lead to restoration of the ideal bulk-terminated geometry on semiconductor surfaces. Two systems, Si(100):S and Si(100):Se, which are likely to fulfill the surface-restoration criteria are investigated in detail through first-principles calculations. These restored surfaces are energetically stable against structural changes such as embedding the adsorbates in subsurface sites.
Genes encoding major light-harvesting polypeptides are clustered on the genome of the cyanobacterium Fremyella diplosiphon. (1986)

The polypeptide composition of the phycobilisome, the major light-harvesting complex of prokaryotic cyanobacteria and certain eukaryotic algae, can be modulated by different light qualities in cyanobacteria exhibiting chromatic adaptation. We have identified genomic fragments encoding a cluster of phycobilisome polypeptides (phycobiliproteins) from the chromatically adapting cyanobacterium Fremyella diplosiphon using previously characterized DNA fragments of phycobiliprotein genes from the eukaryotic alga Cyanophora paradoxa and from F. diplosiphon. Characterization of two lambda-EMBL3 clones containing overlapping genomic fragments indicates that three sets of phycobiliprotein genes--the alpha- and beta-allophycocyanin genes plus two sets of alpha- and beta-phycocyanin genes--are clustered within 13 kilobases on the cyanobacterial genome and transcribed off the same strand. The gene order (alpha-allophycocyanin followed by beta-allophycocyanin and beta-phycocyanin followed by alpha-phycocyanin) appears to be a conserved arrangement found previously in a eukaryotic alga and another cyanobacterium. We have reported that one set of phycocyanin genes is transcribed as two abundant red light-induced mRNAs (1600 and 3800 bases). We now present data showing that the allophycocyanin genes and a second set of phycocyanin genes are transcribed into major mRNAs of 1400 and 1600 bases, respectively. These transcripts are present in RNA isolated from cultures grown in red and green light, although lower levels of the 1600-base phycocyanin transcript are present in cells grown in green light. Furthermore, a larger transcript of 1750 bases hybridizes to the allophycocyanin genes and may be a precursor to the 1400-base species.
Modeling TCP throughput (1998)

In this paper we develop a simple analytic characterization of the steady state throughput, as a function of loss rate and round trip time for a bulk transfer TCP flow, i.e., a flow with an unlimited amount of data to send. Unlike the models in [6, 7, 10], our model captures not only the behavior of TCP's fast retransmit mechanism (which is also considered in [6, 7, 10]) but also the effect of TCP's timeout mechanism on throughput. Our measurements suggest that this latter behavior is important from a modeling perspective, as almost all of our TCP traces contained more time-out events than fast retransmit events. Our measurements demonstrate that our model is able to more accurately predict TCP throughput and is accurate over a wider range of loss rates.
Non-linear primary-multiple separation with directional curvelet frames (2007)

Predictive multiple suppression methods consist of two main steps: a prediction step, during which multiples are predicted from seismic data, and a primary-multiple separation step, during which the predicted multiples are 'matched' with the true multiples in the data and subsequently removed. This second separation step, which we will call the estimation step, is crucial in practice: an incorrect separation will cause residual multiple energy in the result or may lead to a distortion of the primaries, or both. To reduce these adverse effects, a new transformed-domain method is proposed where primaries and multiples are separated rather than matched. This separation is carried out on the basis of differences in the multiscale and multidirectional characteristics of these two signal components. Our method uses the curvelet transform, which maps multidimensional data volumes into almost orthogonal localized multidimensional prototype waveforms that vary in directional and spatio-temporal content. Primaries-only and multiples-only signal components are recovered from the total data volume by a non-linear optimization scheme that is stable under noisy input data. During the optimization, the two signal components are separated by enhancing sparseness (through weighted ℓ1-norms) in the transformed domain subject to fitting the observed data as the sum of the separated components to within a user-defined tolerance level. Whenever, during the optimization, the estimates for the primaries in the transformed domain correlate with the predictions for the multiples, the recovery of the coefficients for the estimated primaries will be suppressed while for regions where the correlation is small the method seeks the sparsest set of coefficients that represent the estimation for the primaries. Our algorithm does not seek a matched filter and as such it differs fundamentally from traditional adaptive subtraction methods. The method derives its stability from the sparseness obtained by a non-parametric (i.e. not depending on a parametrized physical model) multiscale and multidirectional overcomplete signal representation. This sparsity serves as prior information and allows for a Bayesian interpretation of our method during which the log-likelihood function is minimized while the two signal components are assumed to be given by a superposition of prototype waveforms, drawn independently from a probability function that is weighted by the predicted primaries and multiples. In this paper, the predictions are based on the data-driven surface-related multiple elimination method. Synthetic and field data examples show a clean separation leading to a considerable improvement in multiple suppression compared to the conventional method of adaptive matched filtering. This improved separation translates into an improved stack.
Fenofibrate for the treatment of type IV and V hyperlipoproteinemias: a double-blind, placebo-controlled multicenter US study. (1989)

The results of a randomized, double-blind, placebo-controlled multicenter trial of fenofibrate in the treatment of type IV/V hyperlipoproteinemia are reported. Ten study centers in the United States recruited 147 adults with a history of type IV or V hyperlipoproteinemia. After a six- to 12-week dietary stabilization period and a four-week placebo period, patients whose 12-hour fasting total plasma triglyceride levels ranged from 350 to 1,500 mg/dl were continued in the study; 55 patients with levels of 350 to 499 mg/dl were placed in group A and 92 with levels of 500 to 1,500 mg/dl in group B. Patients in each group were randomly assigned to receive 100 mg of fenofibrate or placebo three times daily for eight weeks. In both groups A and B fenofibrate-treated patients showed statistically significant reductions in levels of total cholesterol, very-low-density lipoprotein cholesterol, total triglycerides, and very-low-density lipoprotein triglycerides, and significant increases in high-density lipoprotein cholesterol; patients in group B also showed a significant increase in low-density lipoprotein cholesterol levels. Sixteen of the 75 fenofibrate-treated patients and 11 of the 72 placebo patients reported adverse events that were potentially drug related; most of these were gastrointestinal and a few reported musculoskeletal and skin reactions. It is concluded that fenofibrate is an effective and safe agent in the treatment of type IV/V hyperlipoproteinemia.
Percutaneous Radiofrequency Ablation of the Splanchnic Nerves in Patients with Chronic Pancreatitis: Results of Single and Repeated Procedures in 11 Patients (2013)

Radiofrequency ablation of the splanchnic nerves is a minimally invasive, effective procedure for pain relief. After the effect has subsided, RFSN can be successfully repeated. RFSN might become an alternative treatment in a selected group of CP patients. A larger, randomized trial is justified to substantiate these findings.
Effect of Ca2+ ions on plasmid transformation of Streptococcus lactis protoplasts (1985)

The effects of Mg2+ and Ca2+ ions on the efficiency of the plasmid transformation of lysozyme-treated Streptococcus lactis protoplasts were compared. A 33-megadalton plasmid, pLP712, coding for lactose fermentation and a 6.5-megadalton plasmid, pGB301, coding for erythromycin and chloramphenicol resistance were used as model plasmids, and S. lactis MG1614 was the recipient. Replacing Mg2+ with Ca2+ in the transformation buffer was found to increase transformant frequency more than 10-fold with both plasmids.
Expression and function of TRK-B and BDNF in human neuroblastomas. (1994)

There is considerable interest in the role of the TRK family of neuotrophin receptors in regulating growth and differentiation in normal and neoplastic nerve cells. A neuroblastoma is a common pediatric tumor derived from the neural crest, and the majority of favorable neuroblastomas express a high level of TRK-A mRNA. However, little is known about the expression or function of TRK-B in these tumors. TRK-B encodes a tyrosine kinase that binds to brain-derived neuotrophic factor (BDNF), as well as neurotrophin-3 (NT-3) and NT-4/5. We have studied the N-myc-amplified human neuroblastoma cell line, SMS-KCN, which expresses both TRK-B and BDNF. Exogenous BDNF induces tyrosine phosphorylation of TRK-B as well as phosphorylation of phospholipase C-gamma 1, the extracellular signal-regulated kinases 1 and 2, and phosphatidylinositol-3 kinase. BDNF also induces expression of the immediate-early genes c-FOS and NGFI-A but not NGFI-B or NGFI-C. In addition, BDNF appears to promote cell survival and neurite outgrowth. SMS-KCN cells also express TRK-A, which is phosphorylated in response to nerve growth factor. However, the downstream TRK-A signaling is apparently defective. Finally, we determined that in a series of 74 primary neuroblastomas, 36% express TRK-B mRNA, 68% express BDNF mRNA, and 31% express both. Truncated TRK-B appears to be preferentially expressed in more-differentiated tumors (ganglioneuromas and ganglioneuroblastomas), whereas full-length TRK-B is expressed almost exclusively in immature neuroblastomas with N-myc amplification. Our findings suggest that in TRK-B-expressing human neuroblastomas, BDNF promotes survival and induces neurite outgrowth in an autocrine or paracrine manner. The BDNF/TRK-B pathway may be particularly important for growth and differentiation of neuroblastomas with N-myc amplification.