gebhart/patrepeval huggingface dataset:
Cellobiohydrolase A (CbhA) from the cellulolytic bacterium Cellulomonas fimi is a β‐1,4‐exoceilobiohydrolase analogous to Trichoderma reesei CBH II (1994)

The gene cbhA from the cellulolytic bacterium Cellulomonas fimi encodes a protein of 872 amino acids designated cellobiohydrolase A (CbhA). Mature CbhA contains 832 amino acid residues and has a predicted molecular mass of 85,349 Da. It is composed of five domains: an N-terminal catalytic domain, three repeated sequences of 95 amino acids, and a C-terminal cellulose-binding domain typical of other C. fimi glycanases. The structure and enzymatic activities of the CbhA catalytic domain are closely related to those of CBH II, an exocellobiohydrolase in the glycosyl hydrolase family B from the fungus Trichoderma reesei. CbhA is the first such enzyme to be characterized in bacteria. The data support the proposal that extended loops around the active site distinguish exohydrolases from endohydrolases in this enzyme family.
Development of a multicomponent candidate vaccine for HIV-1 (1997)

Nucleic acid or DNA immunization represents a novel approach to both vaccine and immune therapeutic development. DNA vaccination induces antigen-specific cellular and humoral immune responses through the delivery of non-replicating transcription units which drive the synthesis of specific foreign proteins within the inoculated host. We have previously reported on the potential use of DNA immunization as a novel vaccine strategy for HIV-1. We found that both antigen-specific cellular and humoral immune responses could be induced in vivo with various DNA vaccine constructs against different antigenic targets within HIV-1. In order to enhance the DNA vaccine's ability to elicit cell-mediated immune responses, we co-delivered plasmids encoding costimulatory molecule B7 and interleukin-12 genes with DNA vaccine for HIV-1. We observed a dramatic increase in both antigen-specific T helper cell proliferation and CTL response. Eventual development of successful vaccines for HIV-1 would likely involve targeting multiple antigenic components of the virus to direct and empower the immune system to protect the host from viral infection. We present here the utility of multicomponent DNA immunization to elicit specific humoral and cell-mediated immune responses against different antigenic targets of HIV-1 as well as the ability of this immunization strategy to achieve significant enhancements of antigen-specific cellular immune responses.
Effects of common polymorphisms on the properties of recombinant human methylenetetrahydrofolate reductase (2001)

Methylenetetrahydrofolate reductase (MTHFR) catalyzes the conversion of methylenetetrahydrofolate to methyltetrahydrofolate, the major methyl donor for the conversion of homocysteine to methionine. Two common polymorphisms of the human enzyme have been identified: 677C>T, which leads to the substitution of Ala-222 by valine, and 1298A>C, which leads to the replacement of Glu-429 by alanine; the former polymorphism is the most frequent genetic cause of mild hyperhomocysteinemia, a risk factor for cardiovascular disease. By using a baculovirus expression system, recombinant human MTHFR has been expressed at high levels and purified to homogeneity in quantities suitable for biochemical characterization. The Glu429Ala protein has biochemical properties that are indistinguishable from the wild-type enzyme. The Ala222Val MTHFR, however, has an enhanced propensity to dissociate into monomers and to lose its FAD cofactor on dilution; the resulting loss of activity is slowed in the presence of methyltetrahydrofolate or adenosylmethionine. This biochemical phenotype is in good agreement with predictions made on the basis of studies comparing wild-type Escherichia coli MTHFR with a mutant, Ala177Val, homologous to the Ala222Val mutant human enzyme [Guenther, B. D., et al. (1999) Nat. Struct. Biol. 6, 359-365].
Antimicrobial Spectrum of Triclosan, a Broad-Spectrum Antimicrobial Agent for Topical Application (1979)

The antimicrobial activity of 5-chloro-2(2,4-dichlorophenoxy) phenol (triclosan, one of the active ingredients of Logamel, Ciba-Geigy) was compared in vitro with that of other antimicrobials exclusively or occasionally used as topical agents in dermatology: hexachlorophene, clioquinol, chlorquinaldol. gentamicin, neomycin, nystatin, econazole, clotrimazole and salicylic acid. Upon determination of the MICs for 53 strains of aerobic and anaerobic bacteria, yeasts and fungi, triclosan was found to display a high degree of activity against most of the test organisms and to have the broadest spectrum of chemotherapeutically significant antimicrobial activity of the substances tested.
Coupling on‐chip solid‐phase extraction to electrospray mass spectrometry through an integrated electrospray tip (2005)

We report the integration of solid-phase extraction (SPE) with mass spectrometry (MS) through an on-chip electrospray tip for sample precleaning and preconcentration. An in situ polymerized alkylacrylate-based monolithic column was used as the stationary phase for the on-chip SPE. Each microchip consists of two sets of microchannels and their respective integrated electrospray tips, with a common gold electrode. After the microchip was fabricated from cycloolefin polymer by hot embossing, thermal bonding, and annealing steps, a mixture of monomers and porogenic solvents was pumped into the microchannels and certain areas of the main microchannels were exposed to UV irradiation through a mask. The resulting porous monolithic beds that were polymerized from different compositions of the mixture were characterized by scanning electron microscopy. The microchip containing the monolithic column was then interfaced to an ion trap (IT) mass spectrometer by modifying a commercially available interfacing system. Makeup solution from the side channel was infused concurrently with the solution flowing into the main channel, and the mixture of these two solutions was sprayed into the MS orifice. Both the adsorption and elution of a pharmaceutical test compound, imipramine, to and from the on-chip SPE columns were monitored by MS. The potential application of this device for sample cleanup was demonstrated by pretreatment of urine samples spiked with imipramine.
Identification of differentially expressed root genes upon rhizomania disease (2008)

Rhizomania is one of the most devastating sugar beet diseases. It is caused by Beet necrotic yellow vein virus (BNYVV), which induces abnormal rootlet proliferation. To understand better the physiological and molecular basis of the disorder, transcriptome analysis was performed by restriction fragment differential display polymerase chain reaction (RFDD-PCR), which provided differential gene expression profiles between non-infected and infected sugar beet roots. Two distinct viral isolates were used to detect specific or general virus-induced genes. Differentially expressed genes were selected and identified by sequence analysis, followed by reverse Northern and reverse transcriptase PCR experiments. These latter analyses of different plants (Beta vulgaris and Beta macrocarpa) infected under distinct standardized conditions revealed specific and variable expressions. Candidate genes were linked to cell development, metabolism, defence signalling and oxidative stress. In addition, the expression of already characterized genes linked to defence response (pathogenesis-related protein genes), auxin signalling and cell elongation was also studied to further examine some aspects of the disease. Differential expression was retrieved in both B. vulgaris and B. macrocarpa. However, some candidate genes were found to be deregulated in only one plant species, suggesting differential response to BNYVV or specific responses to the BNYVV vector.
Movements of truncated kinesin fragments with a short or an artificial flexible neck (1997)

To investigate the role of the neck domain of kinesin, we used optical trapping nanometry to perform high-resolution measurements of the movements and forces produced by recombinant kinesin fragments in which the neck domains were shortened or replaced by an artificial random coil. Truncated kinesin fragments (K351) that contain a motor domain consisting of approximately 340 aa and a short neck domain consisting of approximately 11 aa showed fast movement (800 nm/s) and 8-nm steps. Such behavior was similar to that of recombinant fragments containing the full-length neck domain (K411) and to that of native kinesin. Kinesin fragments lacking the short neck domain (K340), however, showed very slow movement (<50 nm/s), as previously reported. Joining an artificial 11-aa sequence that was expected to form a flexible random chain to the motor domain (K340-chain) produced normal fast ( approximately 700 nm/s) and stepwise movement. The results suggest that the neck domain does not act as a rigid lever arm to magnify the structural change at the catalytic domain as has been believed for myosin, but it does act as a flexible joint to guarantee the mobility of the motor domain.
Hepatic artery in liver transplantation. (1987)

Advances in surgical techniques have contributed to the improved results of orthotopic liver transplantation (OLTX) that have been realized over the last few years.1 Examples include better understanding of anomalies of the hepatic arterial supply, development of methods of reconstructing them, and the use of vascular grafts and other innovative techniques of revascularization. Nonetheless, ∼10% of liver grafts still are lost from arterial complications.2 In this report, we describe our experience with the management and complications of the hepatic artery (HA) in the donors and recipients of 231 liver grafts procured and transplanted at the University of Pittsburgh.
Chitin Whiskers: An Overview (2011)

Chitin is the second most abundant semicrystalline polysaccharide. Like cellulose, the amorphous domains of chitin can also be removed under certain conditions such as acidolysis to give rise to crystallites in nanoscale, which are the so-called chitin nanocrystals or chitin whiskers (CHWs). CHW together with other organic nanoparticles such as cellulose whisker (CW) and starch nanocrystal show many advantages over traditional inorganic nanoparticles such as easy availability, nontoxicity, biodegradability, low density, and easy modification. They have been widely used as substitutes for inorganic nanoparticles in reinforcing polymer nanocomposites. The research and development of CHW related areas are much slower than those of CW. However, CHWs are still of strategic importance in the resource scarcity periods because of their abundant availability and special properties. During the past decade, increasing studies have been done on preparation of CHWs and their application in reinforcing polymer nanocomposites. Some other applications such as being used as feedstock to prepare chitosan nanoscaffolds have also been investigated. This Article is to review the recent development on CHW related studies.
Graphical Approach for Evaluating Performance Limitations in Externally Modulated Analog Photonic Links (2008)

We present a novel graphical approach for evaluating the performance of analog photonic links employing an external intensity modulator biased at quadrature. A single graph is sufficient to grasp the engineering tradeoffs among noise figure, third-order spurious-free dynamic range, and RF gain for various values of half-wave voltage and dc photocurrent.
Chemical Components of Four Essential Oils in Aromatherapy Recipe (2015)

This study focused on characterization of the chemical components of an aromatherapy recipe. The formulation consisted of four blended essential oils; rosemary oil, eucalyptus oil, pine oil and lime oil (volume ratio 6 : 2 : 1 : 1). The single and combination essential oils were identified by gas chromatography-mass spectrometry (GC-MS). The analysis of GC-MS data revealed that several components exist in the mixture. The five most important components of the blended essential oils were 1,8-cineole (35.6 %), α-pinene (11.1%), limonene (9.6%), camphor (8.4%), and camphene (6.6%). The main components of rosemary oil were 1,8-cineole (37.3%), α-pinene (19.3%), camphor (14.7%), camphene (8.8%), and β-pinene (5.5%); of eucalyptus oil 1,8-cineole (82.6%) followed by limonene (7.4%), o-cymene (4.3%), γ-terpinene (2.7%), and α-pinene (1.5%); of pine oil terpinolene (26.7%), α-terpineol (20.50%), 1-terpineol (10.8%), α-pinene (6.0%), and γ-terpineol (5.3%); and of lime oil limonene (62.9%), γ-terpinene (11.5%), α-terpineol (7.6%), terpinolene (6.0%), and α-terpinene (2.8%). The present study provided a theoretical basis for the potential application of blended essential oils to be used as an aromatherapy essential oil recipe. GC-MS serves as a suitable and reliable method for the quality control of the chemical markers.
Lack of CD47 on nonhematopoietic cells induces split macrophage tolerance to CD47nullcells (2007)

Macrophages recognize CD47 as a marker of "self" and phagocytose CD47(null) hematopoietic cells. Using CD47 chimera models, here, we show that the phagocytic activity of macrophages against CD47(null) hematopoietic cells is conferred by CD47 expression on nonhematopoietic cells, and this "education" process is hematopoietic cell-independent. Macrophages in the chimeras where nonhematopoietic cells express CD47 phagocytose CD47(null) cells, whereas those in the chimeras lacking CD47 on nonhematopoietic cells are tolerant to CD47(null) cells. However, macrophages in the latter chimeras retain phagocytic activity against CD47(null) RBCs, demonstrating a split macrophage tolerance to CD47(null) hematopoietic cells. The findings highlight the potential importance of nonhematopoietic cells in the regulation of macrophage function, and suggest a previously uncharacterized mechanism of macrophage tolerance.
Charge Transfer and the Mobility of H-Ions in Atomic Hydrogen (1956)

The energies of interaction of H- and H are calculated over a wide range of nuclear separations using molecular wave functions based upon various forms of atomic orbitals and these energies used for the calculation of the charge transfer and diffusion cross sections of H- ions in atomic hydrogen by the perturbed stationary state method. The charge transfer cross sections decrease from 2 × 10-14 cm2 at an impact energy of 1 eV to 0.3 × 10-14 cm2 at 1000 eV and the diffusion cross sections lead to values of the mobility of H- ions in atomic hydrogen decreasing from 3.5 cm2 volt-1 sec-1 at 100°K to 1.8 cm2 volt-1 sec-1 at 600°K.
Palladium-Catalyzed Cross-Coupling Reaction of Aryl or Vinylic Triflates with Organoboron Compounds (1990)

The palladium-catalyzed coupling reactions of aryl or 1-alkenyl triflates with alkyl-, aryl-, and 1-alkenylboron compounds in the presence of potassium phosphate take place readily in high yield under mild conditions. The reaction provides a simple method for the preparation of alkenes, 1,3-alkadienes, aryl-alkenes, and biaryls.
Agrobacterium tumefaciens -mediated transformation of an elite Australian barley cultivar with virus resistance and reporter genes (2001)

Efficient transformation of barley cv. Schooner was achieved using Agrobacterium delivery, hygromycin or bialaphos selection and embryogenic callus. Using this system, transgenic plants were generated that contained either the green fluorescent protein gene, or transgenes derived from barley yellow dwarf (BYDV) and cereal yellow dwarf (CYDV) viruses. Many of these plants contained 1–3 transgene copies that were inherited in a simple Mendelian manner. Some plants containing BYDV and/or CYDV derived transgenes showed reduced virus symptoms and rates of viral replication when challenged with the appropriate virus. The ability to transform Schooner is a significant advance for the Australian barley industry, as this elite malting variety is, and has for the last 15 years been, the most widely grown barley variety in eastern Australia.
Arabidopsis gene co-expression network and its functional modules (2009)

This study reveals new insight into the topological properties of biological networks. The preferential hub-hub connections might be necessary for the formation of modular structure in gene co-expression networks. The study also reveals new insight into the organization of gene functional modules.
Hybridization triggered cross-linking of deoxyoligonucleotides (1986)

This paper reports details of the synthesis of oligodeoxynucleotides containing the modified base 5-methyl-N4,N4-ethanocytosine (Ce). The 9-fluorenylmethoxycarbonyl group is used as a protecting group for the exocyclic amines of dA and dC. This group can be removed rapidly under very mild conditions. Oligomers containing the Ce base form a cross-link when hybridized to their complementary deoxyoligonucleotides. Some of the scope and limitations of these cross-link forming oligonucleotides are reported.
BANNING US FOREIGN BRIBERY: DO US FIRMS WIN? (2013)

I document a striking stock market underperformance of US firms in industries engaged in international trade during the period March 1976 to December 1977. I argue that a suitable candidate for explaining it is the US unilateral banning of foreign bribery that takes place in this period of time. I conduct a long-run event-study to analyse the stock market performance of firms differing in exposure to this policy. The results show that the cumulative abnormal returns of companies in industries most opened to international trade start to fall precisely the day banning foreign bribery is introduced in the political debate, and keep falling until it becomes law. I also show that the patternsobserved are also evident when considering simply raw returns. Results are robust to different specifications and alternative explanations, such as oil prices or the exchange rate. I also disregard the influence of global shocks by performing the analysis for a country not subject to the policy. I conclude that the evidence points in the direction that the US unilateral banning of foreign bribery had a significant negative effect on the market value of firms most exposed to this policy.
Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. (1992)

Detailed knowledge of gene maps or even complete nucleotide sequences for small genomes leads to the feasibility of evolutionary inference based on the macrostructure of entire genomes, rather than on the traditional comparison of homologous versions of a single gene in different organisms. The mathematical modeling of evolution at the genomic level, however, and the associated inferential apparatus are qualitatively different from the usual sequence comparison theory developed to study evolution at the level of individual gene sequences. We describe the construction of a database of 16 mitochondrial gene orders from fungi and other eukaryotes by using complete or nearly complete genomic sequences; propose a measure of gene order rearrangement based on the minimal set of chromosomal inversions, transpositions, insertions, and deletions necessary to convert the order in one genome to that of the other; report on algorithm design and the development of the DERANGE software for the calculation of this measure; and present the results of analyzing the mitochondrial data with the aid of this tool.
A Simple and Generic Belief Tracking Mechanism for the Dialog State Tracking Challenge: On the believability of observed information (2013)

This paper presents a generic dialogue state tracker that maintains beliefs over user goals based on a few simple domainindependent rules, using basic probability operations. The rules apply to observed system actions and partially observable user acts, without using any knowledge obtained from external resources (i.e. without requiring training data). The core insight is to maximise the amount of information directly gainable from an errorprone dialogue itself, so as to better lowerbound one’s expectations on the performance of more advanced statistical techniques for the task. The proposed method is evaluated in the Dialog State Tracking Challenge, where it achieves comparable performance in hypothesis accuracy to machine learning based systems. Consequently, with respect to different scenarios for the belief tracking problem, the potential superiority and weakness of machine learning approaches in general are investigated. 1
Characterization of the pcaR regulatory gene from Pseudomonas putida, which is required for the complete degradation of p-hydroxybenzoate (1994)

The pca branch of the beta-ketoadipate pathway in Pseudomonas putida is responsible for the complete degradation of p-hydroxybenzoate through ortho cleavage of the initial pathway metabolite, protocatechuate. The pcaR regulatory locus has been found to be required for both induction of all of the genes within the pca regulon (pcaBDC, pcaIJ, and pcaF) and the chemotactic response of the bacteria to aromatic compounds. Insertional inactivation mutagenesis, using Tn5 and mini-Tn5 transposons, was used to locate, clone, and sequence this pcaR regulatory gene. The pcaR gene product, when overexpressed in Escherichia coli, possessed a specific affinity for the pcaIJ promoter region and demonstrated that the entire PcaR protein was required for this function. The deduced amino acid sequence of the PcaR regulatory peptide bears little resemblance to its counterpart in the other branch of the pathway, CatR, but exhibits significant homology to its regulatory antecedent, PobR, which regulates the initial breakdown of p-hydroxybenzoate into protocatechuate. Comparisons of the pcaIJ and pcaR promoter regions revealed conservation of a 15-bp sequence centered around the -10 region in both sequences. This, together with previously defined deletional studies with the pcaIJ promoter region, suggests that PcaR exerts its regulatory effect through protein-DNA interactions within this region, which would be unusually close to the transcriptional start site of pcaIJ for a positive regulator.