gebhart/patrepeval huggingface dataset:
Temperature Effect on Supramolecular Chirality Induction in Bis(zinc porphyrin) (2000)

The achiral syn folded conformer (face-to-face) of the ethane-bridged bis(Zn porphyrin) gradually transforms into the chiral extended anti form in the presence of enantiopure guest molecules (alcohols or amines) upon lowering the temperature from 293 to 183 K. The mechanism of the supramolecular chirality induction is based upon the formation of right- or left-handed screw diastereomers of the anti form. The split absorption maxima which are caused by the exciton coupling of the corresponding B transitions match the bisigned Cotton effects. The amplitude of the CD bands is found to be dependent on the bulk and ligation strength of the chiral guest, while the sign of the couplets is observed to be determined by the absolute configuration of the external ligand. The formation of the screw structure in the anti conformation is also confirmed by 1H NMR.
GLUT1 Glucose Transporter Expression in Benign and Malignant Thyroid Nodules (1997)

Malignant cells exhibit increased rates of glycolysis and glucose uptake, the latter of which is mediated by glucose transport proteins. Because several types of cancer have been shown to express high levels of the GLUT1 glucose transporter isoform, we hypothesized that expression of GLUT1 might distinguish malignant from benign thyroid tissue. Archival thyroid tissue obtained at surgery was immunostained for GLUT1 protein. There were 38 benign cases (24 follicular adenoma, 1 Hürthle cell adenoma, 8 nodular goiter, 3 Hashimoto's thyroiditis, 2 Graves' disease) and 28 cases of thyroid cancer (17 papillary and its follicular variant, 6 follicular, 1 Hurthle cell, 2 anaplastic, 2 medullary). Normal thyroid tissue adjacent to nodules showed no thyrocyte staining in any case. No GLUT1 staining was seen in thyrocytes in benign nodular tissue, except for a single case of Hashimoto's thyroiditis in which a few Hurthle cells showed weak staining. Among the thyroid cancers, 13 of 28 (46%) showed tumor cell GLUT1 staining in at least some areas. This included 9 of 17 cases of papillary carcinoma and its follicular variant, 2 of 6 cases of follicular carcinoma and 2 of 2 cases of anaplastic carcinoma. Tumor cell GLUT1 staining was seen in two patterns: circumferential plasma membrane staining focally within the tumor, or asymmetric staining of the basilar aspect of tumor cells adjacent to stroma in some cases of papillary carcinoma. We conclude that GLUT1 expression is frequently detectable by immunostaining in thyroid cancer, but not in benign nodules or normal thyroid. GLUT1 expression may be a clinically useful molecular marker for thyroid cancer.
Effect of Fluorine on the Photovoltaic Properties of Amorphous Silicon Prepared by DC Glow Discharge (1981)

Amorphous Si–F–H films were prepared by DC glow discharge in an atmosphere of SiF 4 +H 2 . The electrical and optical properties have been described. Infrared spectra of amorphous Si–F–H have been studied for various deposition pressures. In the n-type doping characteristics, the maximum conductivity obtained is 10.0 (Ω cm) -1 with the addition of 500 vppm PH 3 . The Schottky barrier a · Si–F–H solar cell shows an efficiency of 3.5% under AM1, 100 mW/cm 2 insolation.
Consumers of 4-chloro-2-methylphenoxyacetic acid from agricultural soil and drilosphere harbor<i>cadA</i>,<i>r/sdpA</i>, and<i>tfdA</i>-like gene encoding oxygenases (2013)

Microbial degradation of 2-methyl-4-chlorophenoxyacetic acid (MCPA) in soil is enhanced by earthworms and initiated by tfdA-like, cadA and r/sdpA gene encoding oxygenases. Copy numbers of such genes increased during MCPA degradation in soil, and MCPA stimulated transcription of tfdA-like and r/sdpA genes up to 4×. Transcription of cadA was detected in the presence of MCPA only. DNA stable isotope probing after consumption of 0.6-0.8 mg 13C-MCPA gdw -1 in oxic microcosms indicated diverse labeled oxygenase genes in bulk soil, burrow walls, and cast. 9, 6, and 3 operational taxonomic units of tfdA-like, cadA, and r/sdpA genes, respectively, were labeled and affiliated with group 2 Alphaproteobacteria including Bradyrhizobia and group 1 class III Betaproteobacteria. New genes encoding putative MCPA degrading oxygenases were identified. Diversity of labeled OTUs tended to be lower for cast than for bulk soil. The collective data indicate (1) hitherto unknown active MCPA degraders and/or oxygenase genes in soil; (2) that multiple oxygenases are associated with MCPA degradation in soil at the same time; (3) that earthworms impact the capability of MCPA degraders in soil to respond to MCPA; and (4) the collective data enable a more in-depth analysis of MCPA degrader communities in soil by future structural gene-based experimental strategies.
Wettability Alteration of Heavy-Oil/Bitumen Containing Carbonates Using Solvents, high pH Solutions and Nano/Ionic Liquids (2015)

Abstract Capillary imbibition tests are commonly applied to measure wettability alteration potential of chemicals. However, these tests are exhaustive, time-consuming, expensive, and the underlying physics of the alteration process from a surface chemistry point of view is often limited and/or unexplained. Contact angle measurement is a quicker and more feasible screening tool to assess the emerging wettability modifiers. They also provide visual data on the mechanics of the wettability alteration process. This paper focuses on contact angle measurements as a mean to evaluate the wettability alteration on mineral plates and porous rock samples. Imidazolium ionic liquids were tested at different concentrations. To study the effect of pH on the wettability, sodium chloride and sodium borate were used at different concentrations. The composition of divalent ions was varied due to their possible use with low/high salinity water as wettability alteration agent. Unmodified and surface modified silica, zirconium, and alumina nanoparticles were also tested. Contact angle measurements were performed initially on mica, marble, and calcite plates. Experiments were repeated on polished surfaces of Berea sandstone, Indiana limestone, and -cleaned- Grosmont carbonate cores. Oils (pure and solvent mixed crude oils) with different viscosities and densities were used to test the effect of oil type on the process. The images were obtained by an SLR camera at different temperatures ranging from 25 to 80°C. By testing with different concentrations, the optimum chemicals were found for different mineral plates/porous rock systems. Then, the results were cross-checked with the imbibition tests performed on the same samples to validate the contact angle measurement observations. Thermal stability tests were also performed in case of their use during or after a thermal method. For the thermal stability tests, contact angle experiments were conducted in a high pressure and high temperature (up to 200°C) cell. It was shown that certain ionic liquids and nanofluids are stable at high temperatures and can be efficiently used at low concentrations.
M1 Protein Allows Group A Streptococcal Survival in Phagocyte Extracellular Traps through Cathelicidin Inhibition (2009)

M1 protein contributes to Group A Streptococcus (GAS) systemic virulence by interfering with phagocytosis and through proinflammatory activities when released from the cell surface. Here we identify a novel role of M1 protein in the stimulation of neutrophil and mast cell extracellular trap formation, yet also subsequent survival of the pathogen within these DNA-based innate defense structures. Targeted mutagenesis and heterologous expression studies demonstrate M1 protein promotes resistance to the human cathelicidin antimicrobial peptide LL-37, an important effector of bacterial killing within such phagocyte extracellular traps. Studies with purified recombinant protein fragments mapped the inhibition of cathelicidin killing to the M1 hypervariable N-terminal domain. A survey of GAS clinical isolates found that strains from patients with necrotizing fasciitis or toxic shock syndrome were significantly more likely to be resistant to cathelicidin than GAS M types not associated with invasive disease; M1 isolates were uniformly resistant. We conclude increased resistance to host cathelicidin and killing within phagocyte extracellular traps contribute to the propensity of M1 GAS strains to produce invasive infections.
Effect of retroreflection on a Fizeau phase-shifting interferometer (1993)

Phase errors in a Fizeau phase-shifting interferometer caused by multiple-reflected beams from a retroreflective optics, such as a corner cube and a right-angle prism, are studied. Single- and double-pass configurations are presented, and their measurement results are compared. An attenuator is not needed in a double-pass configuration because light is reflected by the retroreflective optics twice and the reference surface once and hence the intensities match. It is more accurate to test a corner cube or a right-angle prism in a double-pass configuration than in a single-pass configuration. Simulations and experimental results are presented.
OPTION PRICING METHODOLOGY (1998)

AbstractThe following sections are included:EQUILIBRIUM AND ARBITRAGEBASIC OPTION TERMINOLOGYTHE BLACK-SCHOLES OPTION PRICING MODELPRICING OPTIONS USING THE ARBITRAGE-FREE ARGUMENTSOLVING PARTIAL DIFFERENTIAL EQUATIONSRISK-NEUTRAL VALUATION RELATIONSHIPMONTE CARLO SIMULATIONSLATTICE- AND TREE-BASED METHODMETHOD USED IN THIS BOOKQUESTIONS AND EXERCISES
Label-free electrical detection of pyrophosphate generated from DNA polymerase reactions on field-effect devices (2012)

We introduce a label-free approach for sensing polymerase reactions on deoxyribonucleic acid (DNA) using a chelator-modified silicon-on-insulator field-effect transistor (SOI-FET) that exhibits selective and reversible electrical response to pyrophosphate anions. The chemical modification of the sensor surface was designed to include rolling-circle amplification (RCA) DNA colonies for locally enhanced pyrophosphate (PPi) signal generation and sensors with immobilized chelators for capture and surface-sensitive detection of diffusible reaction by-products. While detecting arrays of enzymatic base incorporation reactions is typically accomplished using optical fluorescence or chemiluminescence techniques, our results suggest that it is possible to develop scalable and portable PPi-specific sensors and platforms for broad biomedical applications such as DNA sequencing and microbe detection using surface-sensitive electrical readout techniques.
Application of "Honeypot "Technique in Computer -based Network Security (2005)

This paper analyzes and compares tra ditional firewall technique used fo r protecting the computer -based network security and thehoneypottechnique developed currently,and holds that the latter,which shakes o ff the passivity of the former in dealing with the atta cks,possesses the strategies of dealing with various attacks actively a nd resist various attacks connecting with the forms of the evidence obtaining for the computer crimes,having broader developi ng prospect.
Endoscopic coronary artery bypass graft (ECABG) procedure with robotic assistance. (1999)

The use of robotic assistance during an ECABG procedure on a cadaver model is feasible. This study is a necessary and useful progression from the use of robotics in the animal lab to the use of robotics in the human operating room.
Cellulase Activity of <i>Leishmania major</i> in the Sandfly Vector and in Culture (1997)

The secretion of cellulose-degrading enzymes by Leishmania promastigotes in culture and in the sandfly vector was demonstrated. Two types of activity of cellulase enzyme-complexes were measured: endoglucanases, which randomly cleave cellulose chains and cellobioydrolases, which remove cellobiose from the nonreducing end of the molecule. The assays demonstrated that enzymes with these activities were secreted into the culture medium by Leishmania major, L. donovani, and L. braziliensis. These activities were also found in cultures of Sauroleishmania agamae, Leptomonas seymouri, Herpetomonas muscarum, Crithidia fasciculata and Trypanosoma brucei brucei that had a relatively low endoglucanase activity. Both endoglucanase and cellobiohydrolase activities were found in the gut of L. major-infected Phlebotomus papatasi, while gut preparations of uninfected sandflies had only cellobiohydrolase activity. The similar growth of L. major parasites in medium supplemented with either cellulose or glucose suggests these parasites can utilize cellulose.
Serine 187 is a crucial residue for allosteric regulation of<i>Corynebacterium glutamicum</i>3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (2001)

Corynebacterium glutamicum 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase is sensitive to feedback inhibition by tyrosine. One feedback-insensitive mutant was obtained by in vitro chemical mutagenesis and the mutation was identified as a C-->G mutation at nucleotide 560 causing a Ser(187) to Cys(187) substitution. Replacing Ser(187) with cysteine, tyrosine or phenylalanine by site-directed mutagenesis not only reduced the enzymatic activity but also relieved its feedback inhibition by tyrosine, while Ser(187)Ala exhibited a comparable activity to that of wild-type enzyme and sensitized to allosteric regulation. The His(6)-tagged enzymes were expressed in Escherichia coli and purified to homogeneity by immobilized nickel-ion affinity chromatography. Kinetic analysis showed that tyrosine is a competitive inhibitor of phosphoenol pyruvate, one of the precursors for DAHP biosynthesis.
GRASP and Path Relinking for 2-Layer Straight Line Crossing Minimization (1999)

In this article, we develop a greedy randomized adaptive search procedure (GRASP) for the problem of minimizing straight line crossings in a 2-layer graph. The procedure is fast and is particularly appealing when dealing with low-density graphs. When a modest increase in computational time is allowed, the procedure may be coupled with a path relinking strategy to search for improved outcomes. Although the principles of path relinking have appeared in the tabu search literature, this search strategy has not been fully implemented and tested. We perform extensive computational experiments with more than 3,000 graph instances to first study the effect of changes in critical search parameters and then to compare the efficiency of alternative solution procedures. Our results indicate that graph density is a major influential factor on the performance of a solution procedure.
Nonisotropic attenuation in SPECT: phantom tests of quantitative effects and compensation techniques. (1987)

A quantitative study of nonisotropic attenuation in SPECT imaging is presented. The study includes a case where the spatial distribution of the attenuation coefficient is nonuniform, as well as a case where the photon path length in the attenuating medium is variable as a function of direction. The effects are studied using phantoms with known source activity and density distributions. Reconstructed images of the phantoms with and without attenuation compensation are compared with the source distribution. Three methods are used to provide partial attenuation compensation, using effective attenuation coefficients. These coefficients include some of the effects of photon scatter, but scatter is not explicitly treated. One attenuation compensation method involves a multiplicative postprocessing correction using an assumed constant attenuation coefficient. A modification of this technique is implemented using the correct nonuniform attenuation map to determine the multiplication factors. A single-iteration technique is used to provide a more complete compensation. The results indicate that nonuniform attenuation can produce significant distortion in line spread functions and in larger distributed sources. This distortion can alter volume determinations, quantitation measurements, and the shape of small objects, and can cause misplacement of counts into regions of low density. The distortion cannot be eliminated by the multiplicative postprocessing correction, but the single-iteration technique can significantly decrease the distortion.
Prediction of process parameters for intelligent control of freezing tunnels using simulation (2002)

Various analytical and empirical methods assuming the existence of steady state and requiring homogenous properties of the product have been used with limited success in estimating freezing times in the food processing industry. Irrespective of the method adopted for estimating freezing time requirements, a critical process issue that needs to be considered is that of system control. Simulation models suggest that a feedforward control strategy, as discussed in this paper, can be used to control a freezing tunnel and obtain considerable energy savings while ensuring 'appropriate' freezing of all products. The control strategy discussed in this paper, involves the continuous monitoring of product input and controlling either or both of the refrigerant flow and conveyor speed. The primary objective of this paper is to demonstrate the use of simulation to predict process parameters for 'intelligent control' of freezing tunnels, and provide an estimate of potential energy savings.
CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model (2013)

Thousands of novel transcripts have been identified using deep transcriptome sequencing. This discovery of large and 'hidden' transcriptome rejuvenates the demand for methods that can rapidly distinguish between coding and noncoding RNA. Here, we present a novel alignment-free method, Coding Potential Assessment Tool (CPAT), which rapidly recognizes coding and noncoding transcripts from a large pool of candidates. To this end, CPAT uses a logistic regression model built with four sequence features: open reading frame size, open reading frame coverage, Fickett TESTCODE statistic and hexamer usage bias. CPAT software outperformed (sensitivity: 0.96, specificity: 0.97) other state-of-the-art alignment-based software such as Coding-Potential Calculator (sensitivity: 0.99, specificity: 0.74) and Phylo Codon Substitution Frequencies (sensitivity: 0.90, specificity: 0.63). In addition to high accuracy, CPAT is approximately four orders of magnitude faster than Coding-Potential Calculator and Phylo Codon Substitution Frequencies, enabling its users to process thousands of transcripts within seconds. The software accepts input sequences in either FASTA- or BED-formatted data files. We also developed a web interface for CPAT that allows users to submit sequences and receive the prediction results almost instantly.
Expression of antisense SnRK1 protein kinase sequence causes abnormal pollen development and male sterility in transgenic barley (2001)

A chimaeric gene was constructed comprising a wheat high molecular weight glutenin subunit gene promoter, a 304-bp sucrose non-fermenting-1-related (SnRK1) protein kinase sequence in the antisense orientation, and the cauliflower mosaic virus 35S RNA gene terminator. Transgenic barley plants containing the antisense SnRK1 chimaeric gene were produced by particle bombardment of barley immature embryos with the aim of obtaining plants expressing the antisense SnRK1 sequence in the seeds. Despite the fact that the promoter was expected to be active only in seeds, two independent transgenic lines were found to fail to transmit the transgene to the T1 generation. These T0 plants had matured and died before this was discovered, but subsequently four other independent transgenic lines were found to be affected in the same way. Cytological analysis of the pollen grains in these lines showed that about 50% were normal but the rest had arrested at the binucleate stage of development, were small, pear-shaped, contained little or no starch and were non-functional. The presence of antisense SnRK1 transcripts was detected in the anthers of the four lines analyzed and a ubiquitin promoter/UidA (Gus) gene, one of the marker genes codelivered with the antisense gene, was found to be expressed only in the abnormal pollen. Expression analyses confirmed that SnRK1 is expressed in barley anthers and that expression of one class of SnRK1 transcripts (SnRK1b) was reduced in the abnormal lines. All of the abnormal lines showed approximately 50% seed set, and none of the transgenes were detected in the T1 generation.
The efficiency of refuse collection services in Spanish municipalities: do non-controllable variables matter? (2001)

espanolEl proposito de este trabajo es analizar la eficiencia tecnica y de coste de los servicios de recogida de basuras situados en 73 municipios de Cataluna. El analisis se ha llevado a cabo utilizando una modificacion del modelo DEA en tres fases desarrolladas por Fried y Lovell (1996), que permite tener en cuenta la influencia de esos factores que el productor no puede controlar (variables no controlables). Los resultados parecen confirmar la hipotesis de que las variables no controlables no afectan en mucho la provision de los servicios, con la excepcion de algunos municipios. EnglishThe aim of this article is to analyse the technical efficiency and costefficiency of the refuse collection services in 73 municipalities located in Catalonia, Spain. The analysis has been carried out using a modification of the DEA model in three stages developed by Fried and Lovell (1996), that allows to take into account the influence of those factors that the producer cannot control (non-controllable variables). The results seem to back the hypothesis that non-controllable variables do not affect very much the ease of provision of the service, with the exception of few municipalities.
Fate of the Two-Component Lantibiotic Lacticin 3147 in the Gastrointestinal Tract (2007)

The component peptides of lacticin 3147 were degraded by alpha-chymotrypsin in vitro with a resultant loss of antimicrobial activity. Activity was also lost in ileum digesta. Following oral ingestion, neither of the lacticin 3147 peptides was detected in the gastric, jejunum, or ileum digesta of pigs, and no lacticin 3147 activity was found in the feces. These observations suggest that lacticin 3147 ingestion is unlikely to have adverse effects, since it is probably inactivated during intestinal transit.
Teaching top-down design using VHDL and CPLD (2002)

The paper presents a teaching experience in using VHDL and CPLD in the senior digital design course. The course focuses on teaching the top-down design methodology through hands-on experiments. The industrially available tools-Maxplus2, made possible through Altera's University Program, provide students with a smooth transition from academic concepts to industrial practice. VHDL, the industrial standard language (IEEE-1076), is used as the design entry. Thus the students are forced to learn the practical aspect of writing a synthesizable VHDL code. The hands-on weekly projects are exercised on the integrated CPLD design tool which has VHDL, compiler, logic synthesizer, functional and timing simulator, floor plan editor and programmer. With the help of programmable devices, students can bypass the timing period for IC fabrication and obtain ASIC designs after the devices have been programmed. The VHDL design entry in Maxplus2 is ideal for teaching top-down design methodology. Translating from a given algorithmic state machine (ASM) chart to a synthesizable and efficient VHDL code is presented. Exploiting the VHDL constructs to make a design reusable is demonstrated through examples. In this course, students learn how to partition a complex design into small components and focus on higher level of abstraction and hierarchy in design description which have become desirable to digital systems designers.