gebhart/patrepeval huggingface dataset:
Design of logical topologies for wavelength-routed optical networks (1996)

The problem of designing a logical topology over a wavelength-routed all-optical network (AON) physical topology is studied. The physical topology consists of the nodes and fiber links in the network. On an AON physical topology, we can set up lightpaths between pairs of nodes, where a lightpath represents a direct optical connection without any intermediate electronics. The set of lightpaths along with the nodes constitutes the logical topology. For a given network physical topology and traffic pattern, our objective is to design the logical topology and the routing algorithm so as to minimize the network congestion while constraining the average delay seen by a source-destination pair and the amount of processing required at the nodes (degree of the logical topology). Ignoring the delay constraints can result in fairly convoluted logical topologies with very long delays. On the other hand, in all our examples, imposing it results in a minimal increase in congestion. While the number of wavelengths required to imbed the resulting logical topology on the physical all optical topology is also a constraint in general, we find that in many cases of interest this number can be quite small. We formulate the combined logical topology design and routing problem described above as a mixed integer linear programming problem which we then solve for a number of cases of a six-node network. This programming problem is split into two subproblems: logical topology design, and routing. We then compare the performance of several heuristic topology design algorithms against that of randomly generated topologies, as well as lower bounds.
Caspase-3 as a therapeutic target for heart failure (2013)

Although the underlying cause and the pathophysiological role of apoptosis remain elusive, antiapoptotic therapy has emerged as an enigma for heart failure. Caspases promote the progressive loss of contractile function in heart failure by facilitating the degradation of myofibrillar proteins. Selective inhibition of the proteolytic functions of caspase-3 may represent an attractive approach to attenuate or reverse heart failure.
Impedance coupling in content-targeted advertising (2005)

The current boom of the Web is associated with the revenues originated from on-line advertising. While search-based advertising is dominant, the association of ads with a Web page (during user navigation) is becoming increasingly important. In this work, we study the problem of associating ads with a Web page, referred to as content-targeted advertising, from a computer science perspective. We assume that we have access to the text of the Web page, the keywords declared by an advertiser, and a text associated with the advertiser's business. Using no other information and operating in fully automatic fashion, we propose ten strategies for solving the problem and evaluate their effectiveness. Our methods indicate that a matching strategy that takes into account the semantics of the problem (referred to as AAK for "ads and keywords") can yield gains in average precision figures of 60% compared to a trivial vector-based strategy. Further, a more sophisticated impedance coupling strategy, which expands the text of the Web page to reduce vocabulary impedance with regard to an advertisement, can yield extra gains in average precision of 50%. These are first results. They suggest that great accuracy in content-targeted advertising can be attained with appropriate algorithms.
Microtiter plate binding assay for cholinergic compounds utilizing the nicotinic acetylcholine receptor (1992)

A receptor-based binding assay for the determination of cholinergic compounds of the nicotinic acetylcholine receptor has been developed. By conducting the assay in a 96-well microtiter plate, the method is suitable for large-scale screening in drug development. Solid-phase extraction of the enzyme label significantly simplifies the assay protocol compared to earlier methods. The assay is based on immobilization of biotin-BSA on the microtiter which takes up avidin-labeled peroxidase due to avidin-biotin interaction. To perform the assay, a ligand (the analyte) and a biotin alpha-bungarotoxin conjugate (alpha Bgt-biotin) sequentially bind to a vesicle bound nicotinic acetylcholine receptor. This is done either in a test tube, assay I, or in a biotinylated microtiter well, assay II. Avidin-HRP is then added to this mixture; free alpha Bgt-biotin conjugate and immobilized biotin-BSA compete for the avidin sites. After the assay solution has been aspirated off, bound enzyme activity is determined which is directly related to the amount of alpha Bgt-biotin added. Dose-response curves of cholinergic compounds and Scatchard plots were generated to evaluate the apparent binding constants. Kinetic studies were conducted for the purpose of optimization. The final assay can be performed in under 4 h with a minimum of sample handling.
Genetic transmission of serum IgE levels (1981)

Genetic aspects of IgE levels were studied in three large pedigrees, many of whose members had atopic sensitivities to ragweed. Data on 184 persons (80 M, 104 F) were analyzed by the methods of Elston and Stewart after logarithmic transformation and appropriate adjustment for sex and age effects. Several modes of transmission were fitted to the data. The environmental model (of equal transmission frequency for all genotypes) clearly did not fit the data (chi 2 23.03, df 3); this suggested a strong hereditary involvement in IgE distribution. High IgE levels being determined by a dominant allele gave the best fit among the hypotheses examined in pooled data. Under a pure polygenic model, the estimated heritability was 49.5%. Using a mixed model of major gene and polygenic transmission (in an analysis which approximates, but is biased toward inflating the major gene component) polygenic inheritance was found to be 11%, but has no significant improvement over the major gene model. When families are analyzed separately, there was evidence of significant heterogeneity among families. The genetic picture was blurred, with one family favoring recessive inheritance of high IgE levels, one with no clear mode, and the third leaning slightly in favor of dominant inheritance. This suggests that the mechanism is not as simple as was thought and that there may be either two alleles or one gene involved in the determination of IgE levels. The findings are consistent with IgE levels being genetically determined with heritability estimated to be about 50%.
Video-Assisted Thoracoscopic Surgery Versus Open Thoracotomy for Anterior Thoracic Spinal Fusion (1998)

Thoracic interbody spinal fusions performed by thoracoscopy have demonstrated histologic, biomechanical, and radiographic equivalence to those performed by a thoracotomy approach. However, in the endoscopy group, intraoperative complications causing longer operative times, higher estimated blood loss, and increased animal morbidity indicated a substantial learning curve associated with the adoption of this surgical technique.
The novel transmembrane Escherichia coli proteins involved in the amino acid efflux (1999)

A novel gene of Escherichia coli, rhtB, has been characterized. Amplification of this gene provides resistance to homoserine and homoserine lactone. Another E. coli gene, rhtC, provides resistance to threonine. The homologues of RhtB are widely distributed among various eubacteria and archaea, from one to 12 copies of family members that differ in their primary structure were found in the genomes. Most of them are genes that encode hypothetical transmembrane proteins. Experimental data that indicate participation of the rhtB product in the excretion of homoserine have been obtained.
Soluble precursor of an integral membrane protein: synthesis of procoat protein in Escherichia coli infected with bacteriophage M13. (1979)

Prior to virus assembly, the major coat protein of coliphage M13 is an integral protein of the host cytoplasmic membrane. Coat protein synthesized in vitro is initially made with an NH2-terminal "leader peptide" of 23 amino acids and is termed "procoat." We now report that procoat is a biosynthetic precursor of coat protein in vivo. Conversion of procoat to coat occurs within 30 sec in cells infected with wild-type virus. This proteolytic processing is delayed in cells infected by M13 mutants (in genes 1, 5, or 7) that are defective in virus assembly. Pulse--chase experiments in combination with subcellular fractionation show that procoat is synthesized in a soluble form in the cytoplasm and is then incorporated into the cytoplasmic membrane, where it is converted to coat protein. This finding is supported by the observation that procoat is synthesized exclusively by polysomes that are not membrane bound. These results are interpreted in terms of the "membrane-triggered folding" hypothesis of membrane protein assembly.
The joints of the evolving foot. Part III. The fossil evidence. (1980)

The fossil record supports the conclusions derived from the study of extant species that the Primates evolved a unique suite of characters in the articulations of the foot. The tarsal bones of African Miocene apes show specializations characteristic of hominoid evolution and provide reasonable precursors for the morphology of Pan, Gorilla and even Pongo. The OH8 foot is essentially ape-like in it major features, with many close resemblances to Pan. Although fairly clearly from a bipedal primate, it lacked important functional specializations found in the human foot.
Characterization of the glutathione S-transferase GSTT1 deletion: discrimination of all genotypes by polymerase chain reaction indicates a trimodular genotype-phenotype correlation. (2000)

Glutathione S-transferase theta enzyme activity involved in the metabolism of toxic compounds is absent in approximately 20% of Caucasians due to a homozygous deletion of GSTT1 (*0/0). Because the exact manner of the GSTT1 deletion was unknown, current genotyping of GSTT1 was limited to detect the presence versus complete absence of the gene by a GSTT1-specific polymerase chain reaction (PCR). Thus, heterozygous (*A/0) and homozygous (*A/A) samples could not be discriminated. We have characterized the boundaries of the deletion of the human glutathione S-transferase theta (GSTT1) gene: PCR mapping and sequencing revealed a 54251 bp fragment including GSTT1 to be deleted from chromosome 22, most likely by a homologous recombination event between two highly homologous sequence stretches that flank GSTT1. Based on the knowledge of the GSTT1*0 region, a PCR assay was devised for unambiguous discrimination of homozygously deleted (*0/0), heterozygously (*A/0) and homozygously GSTT1 carrying (*A/A) individuals. Genotyping of 180 samples of a Caucasian population revealed that the deletion consists of one defined allele, whose distribution in the population fits the Hardy-Weinberg equilibrium with observed 20% *0/0, 46% *A/0 and 34% *A/A individuals. The number of GSTT1*A alleles detected by this procedure correlated highly significant with the enzyme activity in erythrocytes. Genotype-phenotype comparisons demonstrated a codominant type of inheritance by a gene-dose effect: samples with two active alleles expressed a statistically significant higher enzymatic activity compared to those with one null allele (P < 0.0001, ANOVA).
Protective Effects of PARP-1 Knockout on Dyslipidemia-Induced Autonomic and Vascular Dysfunction in ApoE−/− Mice: Effects on eNOS and Oxidative Stress (2009)

The aims of this study were to investigate the role of poly(ADP-ribose) polymerase (PARP)-1 in dyslipidemia-associated vascular dysfunction as well as autonomic nervous system dysregulation. Apolipoprotein (ApoE)(-/-) mice fed a high-fat diet were used as a model of atherosclerosis. Vascular and autonomic functions were measured in conscious mice using telemetry. The study revealed that PARP-1 plays an important role in dyslipidemia-associated vascular and autonomic dysfunction. Inhibition of this enzyme by gene knockout partially restored baroreflex sensitivity in ApoE(-/-) mice without affecting baseline heart-rate and arterial pressure, and also improved heart-rate responses following selective blockade of the autonomic nervous system. The protective effect of PARP-1 gene deletion against dyslipidemia-induced endothelial dysfunction was associated with preservation of eNOS activity. Dyslipidemia induced PARP-1 activation was accompanied by oxidative tissue damage, as evidenced by increased expression of iNOS and subsequent protein nitration. PARP-1 gene deletion reversed these effects, suggesting that PARP-1 may contribute to vascular and autonomic pathologies by promoting oxidative tissue injury. Further, inhibition of this oxidative damage may account for protective effects of PARP-1 gene deletion on vascular and autonomic functions. This study demonstrates that PARP-1 participates in dyslipidemia-mediated dysregulation of the autonomic nervous system and that PARP-1 gene deletion normalizes autonomic and vascular dysfunctions. Maintenance of eNOS activity may be associated with the protective effect of PARP-1 gene deletion against dyslipidemia-induced endothelial dysfunction.
Guidelines for the Management of Patients With Valvular Heart Disease (1998)

This executive summary and recommendations appears in the November 3, 1998, issue of Circulation. The guidelines in their entirety, including the ACC/AHA Class I, II, and III recommen
Blue Organic Electrophosphorescence Diodes using Diarylamino-substituted Heterocyclic Compounds as Host Material (2007)

Diarylamino-substituted heterocyclic compounds (DHCs), 2,6-dicarbazolo-1,5-pyridine (PYD2) and 2,4,6-tricarbazolo-1,3,5-pyrimidine (PYM3), possess a high triplet energy level (T1) of T1= 2.93 eV (PYD2) and T1= 2.89 eV (PYM3), respectively, in their solid state films. 6wt%-Iridium(III)bis[(4,6-di-fluorophenyl)-pyridinato-N,C2]picolinate (FIrpic):PYD2- and 6wt%- FIrpic:PYM3-doped films showed high photoluminescence (PL) efficiencies of ΦPL= 88±2 % and ΦPL= 80±1 %, indicating near perfect confinement of FIrpic triplet excitons. By increasing the FIrpic concentration in DHC hosts, lower driving voltage and higher external electroluminescence (EL) quantum efficiencies (ηEL) were observed, indicating enhancement of electron injection and transport (electron current) in these emitting layers
Nucleotide sequence of the genome of Pf3, an IncP-1 plasmid-specific filamentous bacteriophage of Pseudomonas aeruginosa (1985)

The circular, single-stranded DNA genome of the Pf3 bacteriophage was sequenced in its entirety by each of two methods, the M13-dideoxy chain termination method and the chemical degradation method. It consists of 5,833 nucleotides. With respect to both the DNA and the protein sequences, there is virtually no homology between Pf3 and the phages Ff (M13, f1, and fd) and IKe. However, similarities between these phages were noted with respect to their overall genome organizations. The gene for the single-stranded DNA-binding protein is followed by the gene for the major coat protein and then by a transcription termination signal. Open reading frames for seven other proteins were predicted, and their sizes and order show a fair correspondence to the sizes and order of the genes of the Ff phages and IKe. In addition, several regions have the potential to form stem and loop structures similar to those in the intergenic region of the Ff phage genome, but in Pf3 some are within open reading frames. Evolutionary relationships between Pf3 and the Ff phages and IKe are thus apparent through the correspondence of overall gene order rather than through primary sequence homologies.
Multi-Institutional Study of the Angiogenesis Inhibitor TNP-470 in Metastatic Renal Carcinoma (1999)

Long-term therapy with TNP-470 has manageable toxicities and is feasible in patients with metastatic renal cell carcinoma but does not lead to any significant objective responses. Further studies in this population using TNP-470 schedules that produce more prolonged drug levels and clinical trial end points other than objective tumor regression may be indicated.
Abolition of in vivo platelet thrombus formation in primates with monoclonal antibodies to the platelet GPIIb/IIIa receptor. Correlation with bleeding time, platelet aggregation, and blockade of GPIIb/IIIa receptors. (1989)

We studied the dose-response effects of the F(ab')2 fragments of murine monoclonal antibodies to the platelet GPIIb/IIIa receptor (7E3 and 10E5) on in vivo platelet thrombus formation in a well-characterized monkey model in which the carotid artery is stenosed and thrombus formation is provoked and augmented by intimal damage and the infusion of subaggregating doses of epinephrine. Both antibodies abolished thrombus formation with a mean dose of -0.2 mg/kg. Ex vivo platelet aggregation was not always abolished at doses that abolished thrombus formation; similarly, bleeding times were only moderately prolonged (9.1 +/- 1.4 minutes) at these doses. Increasing the dose above that required to abolish thrombus formation consistently produced abolition of ex vivo platelet aggregation, marked prolongation of the bleeding time (14.2 +/- 1.5 minutes), and nearly quantitative blockade of GPIIb/IIIa receptors. We conclude that in a significant percentage of animals, the extent of GPIIb/IIIa blockade required to prevent vasoocclusive thrombus formation in this model is less than that required for abolition of platelet aggregation, and that the preservation of only a minority of functional GPIIb/IIIa receptors might be adequate to maintain a nearly normal bleeding time.
Use of a temperature-sensitive, protoplast-forming Neurospora crassa strain for the detection of antifungal antibiotics (1983)

Protoplasts of the temperature-sensitive osmotic-1 mutant of Neurospora crassa grew and divided as cell wall-less cells when incubated under certain conditions at 37 degrees C. Each protoplast regenerated cell wall and formed a mycelium when the temperature was shifted to 22 degrees C. Cell wall regeneration, but not cell growth, was prevented by the inhibition of cell wall assembly functions. Thus, the inhibition of cell wall regeneration could serve as an indicator of the mode of action of antibiotic drugs. A method for detecting cell wall-inhibiting antifungal compounds with osmotic-1 protoplasts is described.
Mitochondrial FAD-linked Glycerol-3-phosphate Dehydrogenase: A Target for Cancer Therapeutics (2014)

Imbalances in cellular redox state are frequently observed in cancer cells, and contribute significantly to cancer progression and apoptotic resistance. Hydrogen peroxide (H2O2) is one reactive oxygen species (ROS) that is produced in excess within cancer cells. In this study, we investigated the mitochondrial glycerol-3-phosphate-dependent (GPD2) ROS production in PC-3 cells and demonstrated the importance of excessive H2O2 production on their survival. By exploiting the abnormal H2O2 production of PC-3 cells, we initiated a high-throughput screening of the Canadian Compound Collection, composed of 29,586 small molecules, targeting the glycerophosphate-dependent H2O2 formation in PC-3 cells. Eighteen compounds were identified to have significant inhibitory activity. These compounds have not been previously characterized as inhibitors of the enzyme. Six of these compounds were further analyzed in PC-3 cells and dose response studies displayed an inhibitory and anti-oxidative potency that ranged from 1 µM to 30 µM. The results presented here demonstrate that inhibitors of mitochondrial GPD2 activity elicit anti-proliferative effects on cancer cells.
Comparison of two radionuclide doses in melanoma imaging with anti P-97 monoclonal antibody (1985)

38 patients were included in phase I study of localization of melanoma with Indium-111 labeled P96.5 monoclonal antibody reactive to melanoma antigen P97. 21 patients were studied using 2.5 mCi of In-111 and 17 patients using 5 mCi of In-111. Results of the two doses of In-111 were compared with results of scans. In 9 pats. receiving doses of 2.5 mCi In-111/20 mg stable antibody, out of 54 evaluable sites of disease, 19 sites were seen on scans performed 48 to 72 h after injection (Sensitivity 35%). In 12 pats. studied with 5.0 mCi of In-111/20 mg stable antibody there were 43 known sites of disease of which 30 were identified giving a sensitivity of 70%. As there was a high percentage of lesions greater than 1 cm in diameter in the group receiving 5 mCi and since tumor size has been previously shown to be related to sensitivity of imaging, the data was reanalyzed after excluding lesions less than 1 cm. When only lesions > 2 cm in diameter were considered there were 17 out of 21 (81%) imaged with the 2.5 mCi tracer dose and 27 out of 29 (93%) with 5.0 mCi dose. These differences are significantmore » by chi square test with P < 0.05. Absorbed radiation dose from a 5 mCi dose of In-111 antibody has been calculated at 1.36 rads for the total body and 6.96 rads for the liver (critical organ). Although these doses could be lowered by using lower tracer dose, the results reported here suggest that the sensitivity would be significantly impaired at the smaller dose of 2.5 mCi. We conclude that the current maximum dose of 5.0 mCi should be used in evaluating In-111 labeled anti-P97 antibody imaging of melanoma.« less
High‐resolution capillary array electrophoretic sizing of multiplexed short tandem repeat loci using energy‐transfer fluorescent primers (1996)

Short tandem repeat regions (STRs) from the polymorphic loci VWFA, THO1, TPO and CSF were amplified by the multiplex polymerase chain reaction (PCR) and analyzed by capillary array electrophoresis with fluorescence detection of energy transfer (ET) labels. The fluorescent ET primers are labeled with one fluorescein at the 5' end and a second fluorescein at the position of the 7th or 9th (modified) base to produce fragments that fluoresce in the green (lambda max = 525 nm). M13 A-track sequencing fragments, used as an internal sizing standard, were generated with a universal primer that has a donor fluorescein at the 5' end and a rhodamine acceptor at the position of the 11th (modified) base to produce fragments fluorescing in the red (> 590 nm). The labeled DNA fragments were excited at 488 nm, and the fluorescence was detected with a two-color confocal fluorescence scanner. Separations were performed on arrays of hollow fused silica capillaries filled with denaturing and replaceable hydroxyethyl cellulose sieving matrices. Separations were complete in less than 50 min, and single base resolution as well as reproducible STR sizing was achieved. The relative standard deviation in sizing was below 0.6%. This work establishes the feasibility of high-resolution, high-speed and high-throughput STR typing of single-stranded DNA fragments using capillary array electrophoresis.