gebhart/patrepeval huggingface dataset:
Living ring-opening metathesis polymerization of bicyclo[3.2.0]heptene catalyzed by a ruthenium alkylidene complex (1993)

Living polymerizations using ring-opening metathesis&#13;\ncatalysts (ROMP) have allowed the synthesis of polymers&#13;\nwith controlled structure and properties. In the past&#13;\nfew years, efforts have been focused on developing novel&#13;\ntransition-metal alkylidene complexes that catalyze this&#13;\nreaction and provide either access to new product or easier&#13;\nsynthesis. All of the catalysts developed to date are high&#13;\noxidation state organometallic complexes, which exhibit&#13;\nlimited tolerance to polar functional groups, and only&#13;\ncatalyze the living polymerization of norbornene and its&#13;\nderivatives. Recently, we have synthesized a ruthenium&#13;\nalkylidene complex that exhibits exceptional tolerance to&#13;\na variety of polar functional groups and also catalyzes the&#13;\nliving ROMP of norbornene. Because we were interested&#13;\nin elucidating the details of this living polymerization,&#13;\nwe investigated the ROMP of highly reactive monomer&#13;\nbicyclo[3.2.0] heptene (I), catalyzed by the late-transitionmetal complex (PPh_3)_2(Cl)_2Ru(=CHCH=CPh_2) (II; eq 1). We hope that an investigation of this system will provide us with a better understanding of the mechanism&#13;\nof polymerization catalyzed by late-transition-metal alkylidene complexes and eventually allow us to control&#13;\nmolecular weight in the preparation of functionalized&#13;\npolymers with potential uses in biological applications.
Transfer of malignant trait to BRCA1 deficient human fibroblasts following exposure to serum of cancer patients (2016)

These data support the hypothesis that any human cells carrying a single oncosuppressor mutation is capable of integrating cancer factors carried in the blood and undergo complete malignant transformation. Oncosuppressor genes might protect the cell genome by impeding the integration inside the cells of these mutating factors.
An investigation of linguistic features and clustering algorithms for topical document clustering (2000)

We investigate four hierarchical clustering methods (single-link, complete-link, groupwise-average, and single-pass) and two linguistically motivated text features (noun phrase heads and proper names) in the context of document clustering. A statistical model for combining similarity information from multiple sources is described and applied to DARPA's Topic Detection and Tracking phase 2 (TDT2) data. This model, based on log-linear regression, alleviates the need for extensive search in order to determine optimal weights for combining input features. Through an extensive series of experiments with more than 40,000 documents from multiple news sources and modalities, we establish that both the choice of clustering algorithm and the introduction of the additional features have an impact on clustering performance. We apply our optimal combination of features to the TDT2 test data, obtaining partitions of the documents that compare favorably with the results obtained by participants in the official TDT2 competition.
Antitumor activity of magainin analogues against human lung cancer cell lines. (1992)

Magainin 1 and magainin 2, originally isolated from African clawed frog Xenopus laevis skin, inhibit the growth of bacteria and fungi. Synthetic magainin A (MAG A) and magainin G (MAG G) are more potent against bacteria and protozoa. In order to determine the antitumor activity of these analogues, we have tested these two analogues against six small cell lung cancer (SCLC) cell lines NCI-H82, NCI-H526, NCI-H678, NCI-H735, NCI-H841, and NCI-H889, which were known to differ by more than 10-fold in their sensitivity to different chemotherapeutic agents, and four normal human fibroblast cell lines. Semiautomated 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assays of the six SCLC cell lines revealed average concentrations producing 50% inhibition (IC50) values of 2.6 microM (range, 0.49-9.30 microM) for cisplatin, 2.5 microM (range, 0.39-6.00 microM) for etoposide, and 138.8 nM (range, 55.0-450.0 nM) for doxorubicin. The average IC50 of MAG A was 8.64 microM (range, 6.23-11.7 microM) and that of MAG G was 8.82 microM (range, 4.44-12.5 microM) against the SCLC cell lines. Despite a 10-fold difference in sensitivity to standard chemotherapeutic agents, the IC50 of MAG A and MAG G differs by less than 3-fold. The average IC50 against four normal human fibroblast cell lines was 21.1 microM (range, 12.7-25.6 microM) for MAG A and 29.2 microM (range, 21.3-34.8 microM) for MAG G. Combined exposure to the IC50 concentration of MAG A or MAG G plus IC50 of etoposide or cisplatin decreased the percentage of surviving SCLC cells to 29.0% (range, 26.1-31.7%). MAG A or MAG G had an additive effect when used with standard chemotherapeutic agents. These data suggest that MAG A and MAG G have in vitro antitumor activity against SCLC cell lines.
Pentamidine Inhibition of Group I Intron Splicing in Candida albicans Correlates with Growth Inhibition (2000)

We previously demonstrated that pentamidine, which has been clinically used against Pneumocystis carinii, inhibits in vitro a group I intron ribozyme from that organism. Another fungal pathogen, Candida albicans, also harbors a group I intron ribozyme (Ca.LSU) in the essential rRNA genes in almost half of the clinical isolates analyzed. To determine whether pentamidine inhibits Ca.LSU in vitro and in cells, phylogenetically closely related intron-containing (4-1) and intronless (62-1) strains were studied. Splicing in vitro of the Ca.LSU group I intron ribozyme was completely inhibited by pentamidine at 200 microM. On rich glucose medium, the intron-containing strain was more sensitive to growth inhibition by pentamidine than was the intronless strain, as measured by disk or broth microdilution assays. On rich glycerol medium, they were equally susceptible to pentamidine. At pentamidine levels selectively inhibiting the intron-containing strain (1 microM) in glucose liquid cultures, inhibition of splicing and rRNA maturation was detected by quantitative reverse transcription-PCR within 1 min with a 10- to 15-fold accumulation of precursor rRNA. No comparable effect was seen in the intronless strain. These results correlate the cellular splicing inhibition of Ca.LSU with the growth inhibition of strain 4-1 harboring Ca.LSU. Broth microdilution assays of 13 Candida strains showed that intron-containing strains were generally more susceptible to pentamidine than the intronless strains. Our data suggest that ribozymes found in pathogenic microorganisms but absent in mammals may be targets for antimicrobial therapy.
Patterns of DNA sequence polymorphism along chromosome 1 of maize ( Zea mays ssp. mays L.) (2001)

We measured sequence diversity in 21 loci distributed along chromosome 1 of maize (Zea mays ssp. mays L.). For each locus, we sequenced a common sample of 25 individuals representing 16 exotic landraces and nine U.S. inbred lines. The data indicated that maize has an average of one single nucleotide polymorphism (SNP) every 104 bp between two randomly sampled sequences, a level of diversity higher than that of either humans or Drosophila melanogaster. A comparison of genetic diversity between the landrace and inbred samples showed that inbreds retained 77% of the level of diversity of landraces, on average. In addition, Tajima's D values suggest that the frequency distribution of polymorphisms in inbreds was skewed toward fewer rare variants. Tests for selection were applied to all loci, and deviations from neutrality were detected in three loci. Sequence diversity was heterogeneous among loci, but there was no pattern of diversity along the genetic map of chromosome 1. Nonetheless, diversity was correlated (r = 0.65) with sequence-based estimates of the recombination rate. Recombination in our sample was sufficient to break down linkage disequilibrium among SNPs. Intragenic linkage disequilibrium declines within 100-200 bp on average, suggesting that genome-wide surveys for association analyses require SNPs every 100-200 bp.
Cation Exchange of Alkali Metal Hydroxides with Some Hydrothermally Synthesized Calcium Silicate Compounds (2004)

Crystalline calcium silicate hydrate compounds: xonotlite (6CaO.6SiO2.H2O) and gyrolite (4CaO.6SiO2.3H2O) synthesized at CaO/SiO2 mole ratios of 0.67 and 1.0 under hydrothermal conditions show cation exchange capacities amounting to 41.70 and 44.40 meq/100 g respectively. They also exhibit cation exchange properties toward alkalimetal ions such as Na+and K+ as hydroxides (MOH) with concentrations ranging from 0.005-0.10 mol/l. The uptake of M+ by the gyrolite solid was found to be larger than xonotlite. It also increases with the increase of MOH concentrations and/or the time of reaction. This uptake was reached the equilibrium after 24 hrs, and the amount of K+-ions entered into the crystal structure of the solids (mmol/ 100 g) was found to be larger than Na+-ions. The equilibrium amounts of alkali-metal ions incorporated into the mentioned solids (mmol/100 g) were found to be 40.96 for K+ and 39.97 for Na+ with gyrolite, 37.44 for K+ and 36.74 for Na+ with xonotlite at 0.1 M MOH after 24 hrs. The Ca2+⇔M+ ratio (M+/Ca2+) was found to be 1 at concentrations up to 0.025 mol/l MOH with a slight decrease of a value smaller than 1 at higher concentrations. The affinities of xonotlite and gyrolite for alkali metal ions can be used for their separation from solutions. The mechanism of the exchange reaction is discussed.
Parallel acquisition of PN sequences in DS/SS systems (1994)

The authors investigate methods for the parallel acquisition of a PN sequence in a baseband direct sequence spread spectrum system. Four different schemes are considered: the optimal estimation scheme, the maximum-likelihood estimation scheme, a hypothesis-testing scheme that searches over all shifts, and a locally optimum detection scheme. Approximate expressions for the probability of error are derived for the first and last of these schemes and compared with the actual error probabilities obtained via Monte Carlo simulation. Monte Carlo simulation is also used to obtain the error probabilities of the other two schemes and the results for all the schemes are compared. Since the obvious methods of implementing a parallel acquisition scheme require large amounts of hardware or excessive computation, they outline a technique that can be used to reduce the amount of computation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Debundling and Dissolution of Single-Walled Carbon Nanotubes in Amide Solvents (2004)

Wet chemical methods involving ultrasound and amide solvents were used to purify and separate large bundles of single-walled carbon nanotubes (SWNTs) into individual nanotubes that could then be transported to silicon or mica substrates. The SWNTs studied were produced by the arc-discharge process. Dry oxidation was used in an initial step to remove amorphous carbon. Subsequently, two acid purification schemes were investigated (HCl- and HNO(3)-reflux) to remove the metal growth catalyst (Ni-Y). Finally, ultrasonic dispersion of isolated tubes into either N,N-dimethylformamide (DMF) or N-methyl-2-pyrrolidone (NMP) was carried out. Raman scattering, atomic force microscopy (AFM), and electron microscopy were used to study the evolution of the products. Raman scattering was used to probe possible wall damage during the chemical processing. We found that both HCl and HNO(3) could be used to successfully remove the Ni-Y below approximately 1 wt %. However, the HNO(3)-reflux produced significant wall damage (that could be reversed by vacuum annealing at 1000 degrees C). In the dispersion step, both amide solvents (DMF and NMP) produced a high degree of isolated tubes in the final product, and no damage during this dispersion step was observed. HNO(3)-refluxed tubes were found to disperse the best into the amide solvents, perhaps because of significant wall functionalization. AFM was used to study the filament diameter and length distributions in the final product, and interesting differences in these distributions were observed, depending on the chemical processing route.
Transcription factor CHF1/Hey2 regulates EC coupling and heart failure in mice through regulation of FKBP12.6 (2012)

Heart failure is a leading cause of morbidity and mortality in Western society. The cardiovascular transcription factor CHF1/Hey2 has been linked to experimental heart failure in mice, but the mechanisms by which it regulates myocardial function remain incompletely understood. The objective of this study was to determine how CHF1/Hey2 affects development of heart failure through examination of contractility in a myocardial knockout mouse model. We generated myocardial-specific knockout mice. At baseline, cardiac function was normal, but, after aortic banding, the conditional knockout mice demonstrated a greater increase in ventricular weight-to-body weight ratio compared with control mice (5.526 vs. 4.664 mg/g) and a significantly decreased ejection fraction (47.8 vs. 72.0% control). Isolated cardiac myocytes from these mice showed decreased calcium transients and fractional shortening after electrical stimulation. To determine the molecular basis for these alterations in excitation-contraction coupling, we first measured total sarcoplasmic reticulum calcium stores and calcium-dependent force generation in isolated muscle fibers, which were normal, suggesting a defect in calcium cycling. Analysis of gene expression demonstrated normal expression of most genes known to be involved in myocardial calcium cycling, with the exception of the ryanodine receptor binding protein FKBP12.6, which was expressed at increased levels in the conditional knockout hearts. Treatment of the isolated knockout myocytes with FK506, which inhibits the association of FKBP12.6 with the ryanodine receptor, restored contractile function. These findings demonstrate that conditional deletion of CHF1/Hey2 in the myocardium leads to abnormalities in calcium handling mediated by FKBP12.6 that predispose to pressure overload-induced heart failure.
Chimaeric anti‐CD4 monoclonal antibody cross‐linked by monocyte Fcγ receptor mediates apoptosis of human CD4 lymphocytes (1993)

Previous studies have shown that murine anti-CD4 monoclonal antibody, cross-linked by rabbit anti-mouse immunoglobulin, could mediate apoptosis of murine CD4+ lymphocytes when they were stimulated by T cell receptor antibody. In this study, we have shown that the murine anti-CD4 monoclonal antibody, OKT4, can induce apoptosis in human CD4+ T cells stimulated by the recall antigen tuberculin purified protein derivative (PPD) only when cross-linked by rabbit anti-mouse immunoglobulin. The chimeric anti-CD4 monoclonal antibody, cM-T412 whose Fc fragment is human, was able to cause apoptosis without cross-linking by a second antibody. Similarly, abolition of PPD-induced proliferation of peripheral blood mononuclear cells by cM-T412 did not require cross-linking with rabbit anti-human immunoglobulin. Inhibition of proliferation by cM-T412 could be reduced by pre-treating monocytes with heat-aggregated human IgG. This suggested that monocyte Fc gamma receptors might be cross-linking the human Fc of cM-T412. Propidium iodide staining together with immunofluorescence showed that the apoptotic cells were indeed CD4+ lymphocytes. It is proposed that during treatment with cM-T412 in autoimmune disease such as rheumatoid arthritis, cM-T412-coated CD4 T cells, when they are subsequently stimulated by the unknown arthritogenic antigen, may undergo apoptotic cell death through cross-linking of cM-T412 on Fc gamma receptor-positive cells within the joint.
Skin cancers in chronic arsenic toxicity--a study of predictive value of some proliferative markers. (2004)

Prolonged exposure to arsenic contaminated water produces various clinical features, cutaneous features e.g. melanosis, keratosis and cancers being very common. Evaluation of such lesions by proliferative markers can provide useful information in regards to the biological behaviour of the lesions. Thus, cases with high proliferative status can be ominous sign for development of cancers. We studied skin biopsy of 42 cases. These were evaluated with AgNOR score and PCNA stain, in addition to H & E examination. Here, invasive cancer cases had mean AgNOR score of 3.56, those with severe dysplasia had 3.0, moderate and mild dysplasia scored 1.73, benign changes had mean score of 1.35 while normal control cases had 1.08. PCNA index in cancers was above 50, that of severe dysplasia 25-30, mild to moderate dysplasia 1.0-5.0, those with benign changes 0.5 -1.0 and normal control had LI of less than 0.5%. PCNA has the advantage of less chance of observer error over AgNOR stain.
Anti-Idiotype Monoclonal Antibody Carrying the Internal Image of Ganglioside GM3 (1990)

Murine anti-idiotype monoclonal antibodies were generated against a human IgM monoclonal antibody (L612) that recognizes ganglioside GM3 on human melanoma. Hybridomas secreting antibodies that bound specifically to L612 were selected by enzyme-linked immunosorbent assay using L612 and three negative control human IgMs, including monoclonal anti-GM2 and anti-GD2 antibodies, as well as purified serum IgM, as antigen sources. GM3-binding inhibition and cell-binding inhibition assays were used to identify seven anti-idiotype monoclonal antibodies that recognized determinants located within the antigen-combining sites of L612. To determine whether these anti-idiotype monoclonal antibodies possessed the internal image of the original antigen, we immunized syngeneic BALB/c mice with one of the anti-idiotype monoclonal antibodies, 4C10, coupled with keyhole limpet hemocyanin. Sera from the immunized mice reacted strongly with an antigen-positive M12 melanoma cell line and with purified GM3. Because L612 detects and kills melanoma tumor cells in vitro and in vivo in the presence of complement without affecting normal tissues, anti-idiotype monoclonal antibodies carrying the internal image of GM3 may be an effective tool for active specific immunotherapy in patients with melanoma.
Peripheral-Type Benzodiazepine Receptor Function in Cholesterol Transport. Identification of a Putative Cholesterol Recognition/Interaction Amino Acid Sequence and Consensus Pattern1 (1998)

In steroid-synthesizing cells, like the MA-10 mouse tumor Leydig cells, the peripheral-type benzodiazepine receptor (PBR) is an outer mitochondrial membrane protein involved in the regulation of cholesterol transport from the outer to the inner mitochondrial membrane, the rate-determining step in steroid biosynthesis. Expression of PBR in Escherichia coli DE3 cells, which have no PBR, no cholesterol, and do not make steroids, induced the ability to take up cholesterol in a time-dependent, temperature-sensitive, and energy-independent manner. These cells took up no other steroids tested. Addition of the high affinity PBR ligand PK 11195 to cholesterol-loaded membranes, obtained from cells transfected with PBR, resulted in the release of the uptaken cholesterol. Expression in DE3 cells of mutant PBRs demonstrated that deletions in the cytoplasmic carboxy-terminus dramatically reduced the cholesterol uptake function of PBR, although it retained full capacity to bind PK 11195. Site-directed mutagenesis in the carboxy-terminal region of PBR demonstrated that bacteria expressing the mutant PBR proteins PBR(Y153S) and PBR(R156L) do not accumulate cholesterol, suggesting that amino acids Y153 and R156 are involved in the interaction of the receptor with cholesterol. Considering these results, we postulate the existence of a common cholesterol recognition/interaction amino acid consensus pattern (-L/V-(X)(1-5)-Y-(X)(1-5)-R/K-). Indeed, we found this amino acid consensus pattern in all proteins shown to interact with cholesterol. In conclusion, these data suggest that the expression of PBR confers the ability to take up and release, upon ligand activation, cholesterol. Considering the widespread occurrence of this protein and its tissue and cell specific subcellular localization, these results suggest a more general role of PBR in intracellular cholesterol transport and compartmentalization.
Veins Theory (1998)

In this paper, we propose a generalization of Centering Theory (CT) (Grosz, Joshi, Weinstein (1995)) called Veins Theory (VT), which extends the applicability of centering rules from local to global discourse. A key facet of the theory involves the identification of «veins» over discourse structure trees such as those defined in RST, which delimit domains of referential accessibility for each unit in a discourse. Once identified, reference chains can be extended across segment boundaries, thus enabling the application of CT over the entire discourse. We describe the processes by which veins are defined over discourse structure trees and how CT can be applied to global discourse by using these chains. We also define a discourse «smoothness» index which can be used to compare different discourse structures and interpretations, and show how VT can be used to abstract a span of text in the context of the whole discourse. Finally, we validate our theory by analyzing examples from corpora of English, French, and Romanian.
Evidence of a Novel Mevalonate Pathway in Archaea (2014)

Isoprenoids make up a remarkably diverse class of more than 25000 biomolecules that include familiar compounds such as cholesterol, chlorophyll, vitamin A, ubiquinone, and natural rubber. The two essential building blocks of all isoprenoids, isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), are ubiquitous in the three domains of life. In most eukaryotes and archaea, IPP and DMAPP are generated through the mevalonate pathway. We have identified two novel enzymes, mevalonate-3-kinase and mevalonate-3-phosphate-5-kinase from Thermoplasma acidophilum, which act sequentially in a putative alternate mevalonate pathway. We propose that a yet unidentified ATP-independent decarboxylase acts upon mevalonate 3,5-bisphosphate, yielding isopentenyl phosphate, which is subsequently phosphorylated by the known isopentenyl phosphate kinase from T. acidophilum to generate the universal isoprenoid precursor, IPP.