gebhart/patrepeval huggingface dataset:
Development of Deuterium Labeling Method Based on the Heterogeneous Platinum Group Metal-Catalyzed C-H Activation (2013)

Deuterium (D) labeled compounds are utilized in various scientific fields such as mechanistic elucidation of reactions, preparation of new functional materials, tracers for microanalysis, deuterium labeled heavy drugs and so on. Although the H-D exchange reaction is a straightforward method to produce deuterated organic compounds, many precedent methods require expensive deuterium gas and/or harsh reaction conditions. A part of our leading research agendas is intended to the development of novel and functional heterogeneous platinum-group catalysts and the reclamation of unknown functionalities of existing heterogeneous platinum-group catalysts. During the course of the study, benzylic positions of substrates were site-selectively deuterated under mild and palladium-on-carbon (Pd/C)-catalyzed hydrogenation conditions in heavy water (D2O). Heat conditions promoted the H-D exchange reactivity and facilitated the H-D exchange reaction at not only the benzylic sites but also inactive C-H bonds and heterocyclic nuclei. It is noteworthy that platinum-on-carbon (Pt/C) indicated a quite high affinity toward aromatic nuclei, and the H-D exchange reaction was strongly enhanced by the use of Pt/C as a catalyst under milder conditions. The mixed use of Pd/C and Pt/C was found to be more efficient in the H-D exchange reaction compared to the independent use of Pd/C or Pt/C. Furthermore, simple alkanes could also be efficiently deuterated under rhodium-on-carbon (Rh/C)-catalyzed conditions. The use of ruthenium-on-carbon (Ru/C) enabled the regiospecific and efficient deuterium incorporation at α-positions of alcohols and results were applied as a regio- and stereoselective multi-deuteration method of sugar derivatives.
Phosphorylation sites of the E2 transcriptional regulatory proteins of bovine papillomavirus type 1 (1989)

The E2 open reading frame of bovine papillomavirus type 1 (BPV-1) encodes three transcriptional regulatory proteins. The full-length open reading frame encodes a protein of 410 amino acids which functions as a transcriptional transactivator. Two transcriptional repressor proteins, E2-TR and E8/E2, contain the C-terminal 249 and 204 amino acids, respectively. We have expressed both the full-length E2 protein and the E2-TR repressor protein in insect cells, by using recombinant baculoviruses, and in mammalian COS-1 cells, by using a chimeric simian virus 40/BPV-1 virus. Analysis of the E2 proteins revealed that both the transactivator and repressor forms are phosphorylated predominately on serine residues at similar sites in both expression systems. By a combination of peptide mapping and site-directed mutagenesis techniques, the serine residues at positions 298 and 301 were determined to be the major phosphorylation sites of the BPV-1 E2 proteins.
Biochemical and antigenic characterization of the Mycobacterium tuberculosis 71 kD antigen, a member of the 70 kD heat‐shock protein family (1989)

A 71 kiloDalton antigen from Mycobacterium tuberculosis is recognized by antibodies and by T lymphocytes during infection (Britton et al., 1986a). Partial sequence analysis indicates a relationship between this antigen and the highly conserved family of 70-kiloDalton heat shock proteins (hsp70) (Young et al., 1988). Biochemical and serological characterization of the protein confirms its membership of the hsp70 gene family, and metabolic labelling demonstrates that it is a major component of the mycobacterial response to heat stress. The role of stress proteins as antigens during infection is discussed.
Efficacy of the farnesyltransferase inhibitor R115777 in a rat mammary tumor model: role of Ha-ras mutations and use of microarray analysis in identifying potential targets (2006)

Rats treated with the alkylating agent methylnitrosourea (MNU) develop multiple, hormonally dependent mammary tumors. Roughly 50% of the tumors have Ha-ras mutation, whereas 50% do not. The MNU-induced rat mammary tumor model was employed to examine the therapeutic efficacy of the farnesyltransferase inhibitor (FTI), R115777, and to examine the use of genomics in identifying susceptible tumors as well as identifying genes whose expression are modulated by FTI treatment. In animals bearing palpable mammary tumors (< 7 mm diameter), we performed a surgical biopsy, and 3 days following the biopsy, rats were treated with R115777 (50 mg/kg body wt/day) by gavage. Tumors with Ha-ras mutations underwent profound regression, with nearly 90% showing complete regressions within 4 weeks. In contrast, the non-Ha-ras mutation-bearing tumors yielded a more variable response, although roughly half of the non-Ha-ras mutation tumors underwent significant regression. These results show that although all tumors appear to respond to the FTI inhibitor the tumors with Ha-ras mutations were exquisitely sensitive. We employed a microarray approach to define potential targets and the mechanism of action of R115777 in Ha-ras mutant or wildtype tumors following treatment with FTI. In addition, we determined whether gene expression prior to FTI treatment can be used to differentiate highly sensitive tumors (Ha-ras mutant) and tumors with variable sensitivity (Ha-ras wildtype). Untreated or FTI-treated (4 days at 50 mg/kg body wt) tumors (Ha-ras mutant or wildtype) were examined using oligonucleotide arrays. A significant number of genes were differentially expressed in control rat mammary tumors with or without an activated Ha-ras mutation, suggesting that a microarray analysis might differentiate highly sensitive and variably sensitive tumors. Most of the genes whose expressions were modulated by FTI in tumors were independent of Ha-ras status and were presumably modulated by effects on farnesylation of proteins other than Ha-ras. However, treatment of Ha-ras-mutated mammary tumors with R155777 results in preferential modulation of genes involved in ras-MAP kinase signal transduction pathway and in decreased expression of many genes involved with cell proliferation. In contrast, several classes of genes are altered in rat mammary tumors without a mutated Ha-ras, suggesting that non-ras targets are involved. Ras pathway related genes, p53, WT1 and PCNA, were preferentially modulated in Ha-ras-mutated tumors, whereas modulation of genes in the G-protein pathway, various cytochrome p450s and RB1 are involved in Ha-ras wildtype tumors. Elucidation of gene expression changes in FTI-treated or control rat mammary adenocarcinomas will help in identifying potential pharmacodynamic markers of FTI treatment as well as potential molecular targets of R115777 and other FTIs.
Expanding the Use of Zymography by the Chemical Linkage of Small, Defined Substrates to the Gel Matrix (2003)

In the postgenomic era, the comprehensive proteomic analysis of metabolic and signaling pathways is inevitably faced with the challenge of large-scale identification and characterization of polypeptides with a particular enzymatic activity. Previous work has shown that a wide variety of enzymatic activities of microbial, plant, and animal origin can be assigned to individual polypeptides using in-gel activity staining (zymography). However, a number of limitations, such as special substrate requirements, the lack of a standard procedure, and difficulties in distinguishing enzymes with overlapping activities have precluded the widespread use of zymography as a routine laboratory method. Here we demonstrate that, by employing small-defined substrates that are covalently attached to the gel matrix, we can largely overcome the aforementioned problems and assay readily a number of different classes of enzymatic activities within gels after standard SDS-polyacrylamide electrophoresis. Moreover, this development is compatible with the two-dimensional separation of proteins and thus has great potential in the high-throughput screening and characterization of complex biological and clinical samples.
House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection (2013)

Exposure to dogs in early infancy has been shown to reduce the risk of childhood allergic disease development, and dog ownership is associated with a distinct house dust microbial exposure. Here, we demonstrate, using murine models, that exposure of mice to dog-associated house dust protects against ovalbumin or cockroach allergen-mediated airway pathology. Protected animals exhibited significant reduction in the total number of airway T cells, down-regulation of Th2-related airway responses, as well as mucin secretion. Following dog-associated dust exposure, the cecal microbiome of protected animals was extensively restructured with significant enrichment of, amongst others, Lactobacillus johnsonii. Supplementation of wild-type animals with L. johnsonii protected them against both airway allergen challenge or infection with respiratory syncytial virus. L. johnsonii-mediated protection was associated with significant reductions in the total number and proportion of activated CD11c(+)/CD11b(+) and CD11c(+)/CD8(+) cells, as well as significantly reduced airway Th2 cytokine expression. Our results reveal that exposure to dog-associated household dust results in protection against airway allergen challenge and a distinct gastrointestinal microbiome composition. Moreover, the study identifies L. johnsonii as a pivotal species within the gastrointestinal tract capable of influencing adaptive immunity at remote mucosal surfaces in a manner that is protective against a variety of respiratory insults.
ABCB1 Pharmacogenetics: Progress, Pitfalls, and Promise (2007)

In 1976, Juliano and Ling(1) reported expression of a 170 kDa protein in colchicine-resistant Chinese hamster ovary (CHO) cells that was absent in drug-sensitive cells. Because this protein altered cellular permeability to colchicine, the authors named it P-glycoprotein (P-gp).(1) P-gp overexpression was described in tumor samples and leukemic cells.(2) High homology with bacterial transporters suggested that P-gp was an efflux transporter, modulating intracellular xenobiotic concentrations.(3) In 1986, the gene encoding P-gp was discovered and designated MDR1 (HUGO name ABCB1).(4) Immunohistochemical studies demonstrated P-gp expression in tissues with secretory or excretory functions (liver, kidney, and gastrointestinal tract) and at blood-tissue barrier sites, such as the blood-brain barrier.(5) This pattern of expression indicated that P-gp may influence xenobiotic response and toxicity, either through pharmacokinetic or pharmacodynamic effects.(6)
Progressive development of the rat osteoblast phenotype in vitro: Reciprocal relationships in expression of genes associated with osteoblast proliferation and differentiation during formation of the bone extracellular matrix (1990)

The relationship of cell proliferation to the temporal expression of genes characterizing a developmental sequence associated with bone cell differentiation was examined in primary diploid cultures of fetal calvarial derived osteoblasts by the combined use of autoradiography, histochemistry, biochemistry, and mRNA assays of osteoblast cell growth and phenotypic genes. Modifications in gene expression define a developmental sequence that has 1) three principle periods--proliferation, extracellular matrix maturation, and mineralization--and 2) two restriction points to which the cells can progress but cannot pass without further signals--the first when proliferation is down-regulated and gene expression associated with extracellular matrix maturation is induced, and the second when mineralization occurs. Initially, actively proliferating cells, expressing cell cycle- and cell growth-regulated genes, produce a fibronectin/type I collagen extracellular matrix. A reciprocal and functionally coupled relationship between the decline in proliferative activity and the subsequent induction of genes associated with matrix maturation and mineralization is supported by 1) a temporal sequence of events in which there is an enhanced expression of alkaline phosphatase immediately following the proliferative period, and later, an increased expression of osteocalcin and osteopontin at the onset of mineralization; 2) increased expression of a specific subset of osteoblast phenotype markers, alkaline phosphatase and osteopontin, when proliferation is inhibited by hydroxyurea; and 3) enhanced levels of expression of the osteoblast markers as a function of ascorbic acid-induced collagen deposition, suggesting that the extracellular matrix contributes to both the shutdown of proliferation and the development of the osteoblast phenotype.
The effect of workload on the performance and availability of voting algorithms (2002)

Voting algorithms are a popular way to provide data consistency in replicated data systems. By maintaining multiple copies of data on distinct servers, they can increase the data's availability, as perceived by a user. Many models have been made to study the degree to which replication increases the availability of data, and some have been made to study the cost incurred in maintaining consistency. However, little work has been done to evaluate the time it takes to serve a request, accounting for server and network failures, or to determine the effect of workload on these measures. The effect of workload can be significant, since failures of system components are not important unless they are needed to deliver a service, and requests can force updates on data that would otherwise be outdated. In this paper, with the help of stochastic activity networks, we determine the availability and mean time to respond to write requests as a function of the number of replicated copies and workload offered to the system. The results illustrate that it is indeed possible to determine such measures analytically and that workload, as well as the number of copies, is an important determinant of availability and response time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The dual functions of Fas ligand in the regulation of peripheral CD8+and CD4+T cells (2000)

Although Fas ligand (FasL) is well characterized for its capacity to deliver a death signal through its receptor Fas, recent work demonstrates that FasL also can receive signals facilitating antigen (Ag)-specific proliferation of CD8(+) T cells. The fact that the gld mutation differentially influences the proliferative capacity of CD8(+) and CD4(+) T cells presented the intriguing possibility that a single molecule may play opposing roles in these two subpopulations. The present study focuses on how these positive and negative regulatory roles are balanced. We show that naive CD4(+) T cells are responsive to FasL-mediated costimulation on encounter with Ag when Fas-mediated death is prevented. Thus, the machinery responsible for transducing the FasL positive reverse signal operates in both CD4(+) and CD8(+) T cells. Instead, differential control of FasL expression distinguishes the role of FasL in these two T cell subpopulations. FasL costimulation occurs immediately on T cell receptor ligation and correlates with the up-regulation of FasL expression on CD8(+) and naive CD4(+) T cells, both of which are sensitive to the FasL costimulatory signal. Conversely, FasL-initiated death occurs late in an immune response when high levels of FasL expression are maintained on CD4(+) T cells that are sensitive to Fas-mediated death, but not on CD8(+) T cells that are relatively insensitive to this signal. This careful orchestration of FasL expression during times of susceptibility to costimulation and conversely, to death, endows FasL with the capacity to both positively and negatively regulate the peripheral T cell compartment.
Cascade regulation of terminal adipocyte differentiation by three members of the C/EBP family of leucine zipper proteins. (1995)

Terminal differentiation of cultured 3T3-L1 fibroblasts to the adipogenic phenotype is potently stimulated by dexamethasone (DEX) and methylisobutylxanthine (MIX). Previous studies have shown that these hormones induce the expression of genes encoding two members of the CCAAT/enhancer binding protein (C/EBP) family of transcription factors. In the absence of new protein synthesis DEX activates the gene encoding C/EBP delta. Likewise, MIX is a direct inducer of C/EBP beta gene expression. Optimal conditions for differentiation entail a 2-day period wherein confluent fibroblasts are exposed to DEX and MIX, followed by removal of the hormones and subsequent culture in the presence of insulin and fetal bovine serum. During the early phase of differentiation, high levels of C/EBP delta and C/EBP beta accumulate. These transcription factors diminish during the terminal phase of differentiation and come to be replaced by a third member of the C/EBP family, C/EBP alpha. Conclusive evidence has already shown that C/EBP alpha regulates terminal adipocyte differentiation, turning on the battery of fat-specific genes required for the synthesis, uptake, and storage of long chain fatty acids. Here we provide evidence that C/EBP delta and C/EBP beta play early catalytic roles in the differentiation pathway, relaying the effects of the hormonal stimulants DEX and MIX in a cascade-like fashion, leading to the activation of the gene encoding C/EBP alpha. Conditions facilitating the precocious expression of either C/EBP delta or C/EBP beta were observed to accelerate adipogenesis and, in the case of C/EBP beta, relieve dependence on the early hormonal stimulants. Likewise, conditions that prevented the expression of functional C/EBP beta effectively blocked terminal differentiation. Finally, we have discovered that ectopic expression of C/EBP beta in multipotential NIH-3T3 cells results in their conversion into committed adipoblasts capable, upon hormonal stimulation, of synchronous and uniform differentiation into fat-laden adipocytes.
Increased Plasma Concentrations of Cytoskeletal and Ca2+-Binding Proteins and Their Peptides in Psoriasis Patients (2008)

The identified increased concentrations of cytoskeletal proteins, their peptides, and calgranulins in psoriatic plasma, as well as the underlying altered protease activity, are proposed to be related to psoriasis pathogenesis.
On the Complexity of Positional Sequencing by Hybridization (2001)

In sequencing by hybridization (SBH), one has to reconstruct a sequence from its l-long substrings. SBH was proposed as an alternative to gel-based DNA sequencing approaches, but in its original form the method is not competitive. Positional SBH (PSBH) is a recently proposed enhancement of SBH in which one has additional information about the possible positions of each substring along the target sequence. We give a linear time algorithm for solving PSBH when each substring has at most two possible positions. On the other hand, we prove that the problem is NP-complete if each substring has at most three possible positions. We also show that PSBH is NP-complete if the set of allowed positions for each substring is an interval of length k and provide a fast algorithm for the latter problem when k is bounded.
Fault-Tolerant Linear Optical Quantum Computing with Small-Amplitude Coherent States (2008)

Quantum computing using two coherent states as a qubit basis is a proposed alternative architecture with lower overheads but has been questioned as a practical way of performing quantum computing due to the fragility of diagonal states with large coherent amplitudes. We show that using error correction only small amplitudes (alpha>1.2) are required for fault-tolerant quantum computing. We study fault tolerance under the effects of small amplitudes and loss using a Monte Carlo simulation. The first encoding level resources are orders of magnitude lower than the best single photon scheme.
THE PORPHYROPSIN VISUAL SYSTEM (1939)

1. In the rods of fresh-water and some anadromous fishes, rhodopsin is replaced by the purple photolabile pigment porphyropsin. This participates in a retinal cycle identical in form with that of rhodopsin, but in which new carotenoids replace retinene and vitamin A. 2. Porphyropsin possesses a broad absorption maximum at 522 +/- 2 mmicro, and perhaps a minimum at about 430 mmicro. The vitamin A-analogue, vitamin A(2), possesses a maximum in chloroform at 355 mmicro and yields with antimony trichloride a deep blue color due to a band at 696 mmicro. The retinene-analogue, retinene(2), absorbs maximally in chloroform at 405 mmicro and possesses an antimony chloride maximum at 706 mmicro. 3. Its non-diffusibility through a semi-permeable membrane, salting-out properties, and sensitivity to chemical denaturants and to heat, characterize porphyropsin as a conjugated carotenoid-protein. 4. The porphyropsin cycle may be formulated: porphyropsin See PDF for Structure. retinene(2)-protein ((2)) (-->) vitamin A(2)-protein ((3)) (-->) porphyropsin. Isolation of the retina cuts this cycle at (3); denaturation procedures or extraction of porphyropsin into aqueous solution eliminate in addition (1) and (2). 5. The primary difference between the rhodopsin and porphyropsin systems appears to be the possession by the latter of an added ethylenic group in the polyene chain.
Second harmonic generation in periodically-poled LiNbO_3 (1989)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text G. A. Magel, E. J. Lim, M. M. Fejer, and R. L. Byer, "Second harmonic generation in periodically-poled LiNbO3," Optics News 15(12), 20-21 (1989) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Sketch-based tree modeling using Markov random field (2008)

In this paper, we describe a new system for converting a user's freehand sketch of a tree into a full 3D model that is both complex and realistic-looking. Our system does this by probabilistic optimization based on parameters obtained from a database of tree models. The best matching model is selected by comparing its 2D projections with the sketch. Branch interaction is modeled by a Markov random field, subject to the constraint of 3D projection to sketch. Our system then uses the notion of self-similarity to add new branches before finally populating all branches with leaves of the user's choice. We show a variety of natural-looking tree models generated from freehand sketches with only a few strokes.
ANATASE - RUTIL TiO2 THIN FILMS DEPOSITED IN A D.C. MAGNETRON SPUTTERING SYSTEM ê (2008)

Anatase TiO2 thin films were deposited in a d.c. reactive magnetron sputtering system. It was found that there is a strong dependence between anatase-rutil structures of TiO2 films and the technological conditions, the most relevant parameter being the oxygen percentage from the argon and oxygen mixture. Our measurements carried out for electrical properties of d.c. magnetron sputtering TiO2 thin films revealed that it is possible to obtain TiO2 films with controllable structure and properties.
Novel soft-switching DC-DC converter with full ZVS-range and reduced filter requirement. II. Constant-input, variable-output applications (2001)

For pt.I see ibid., vol.16, no.2, p.184-92 (2001). The performance of the hybrid converter featuring zero-voltage-switching (ZVS) down to no-load and significant reduction in the filter requirement, proposed in Part I of this paper, is analyzed here for constant-input, variable-output applications. For these applications, the main drawback of the hybrid converter, namely the increased transformer rating is eliminated. The advantages of the hybrid configuration like the reduction in filter rating and full-load ZVS with negligible penalty on conduction loss, are retained. An extension of the basic hybrid converter-a combination of two full-bridges using six switches is proposed. This configuration is well suited for applications above a few kilowatts, and results in significant reduction in the ripple current rating of the input filter capacitor. Experimental results obtained from a 1 kW/100 kHz prototype are presented.