gebhart/patrepeval huggingface dataset:
All-angle negative refraction in a three-dimensionally periodic photonic crystal (2002)

We introduce a photonic crystal that has a large range of effective negative refractive index in three dimensions (3D) and demonstrate its negative-refraction property by numerical simulations. With slight modifications, our design is also amenable to layer-by-layer fabrication. This work should enable experimental observation of negative refraction and related phenomena in 3D at optical frequencies.
Embodiment of the warm white-light-emitting diodes by using a Ba2+ codoped Sr3SiO5:Eu phosphor (2006)

The shifts of the emission band to longer wavelength (yellow-orange) of the Sr3SiO5:Eu yellow phosphor under the 450–470 nm excitation range have been achieved by adding the codoping element (Ba2+) in the host. In order to apply to white-light-emitting diodes (LEDs) with warm white and high color rendering index, we have fabricated white LEDs through the integration of the InGaN blue LED chip and the two phosphor blends (Sr2SiO4:Eu yellow phosphor +Ba2+ co-doped Sr3SiO5:Eu yellow-orange phosphor) into a single package. By employing two phosphors, covering a red region, the white LEDs show a warm white in the range of 2500–5000 K correlated color temperature and a good color rendering of over 85.
Shape memory and superelasticity in polycrystalline Cu–Al–Ni microwires (2009)

We report a strategy to significantly improve the ductility and achieve large superelastic and shape memory strains in polycrystalline Cu–Al–Ni shape memory alloys that are normally brittle. We use a liquid-phase (Taylor) wire forming process to obtain microwires of 10–150 μm diameter with a bamboo grain structure. The reduction of grain boundary area, removal of triple junctions, and introduction of a high specific surface area in the wire decrease constraints on the martensitic transformation, and permit both superelasticity and stress-assisted two-way shape memory with recoverable strains as high as 6.8%.
Expression of the Smooth Muscle Cell Calponin Gene Marks the Early Cardiac and Smooth Muscle Cell Lineages during Mouse Embryogenesis (1996)

Although several genes are considered markers for vascular smooth muscle cell (SMC) differentiation, few have been rigorously tested for SMC specificity in mammals, particularly during development where considerable overlap exists between different muscle gene programs. Here we describe the temporospatial expression pattern of the SMC calponin gene (formerly h1 or basic calponin) during mouse embryogenesis and in adult mouse tissues and cell lines. Whereas SMC calponin mRNA expression is restricted exclusively to SMCs in adult tissues, during early embryogenesis, SMC calponin transcripts are expressed throughout the developing cardiac tube as well as in differentiating SMCs. Transcription of the SMC calponin gene initiates at two closely juxtaposed sites in the absence of a consensus TATAA or initiator element. Transient transfection assays in cultured SMC demonstrated that high level SMC calponin promoter activity required no more than 549 nucleotides of 5 sequence. In contrast to the strict cell type-specificity of SMC calponin mRNA expression, the SMC calponin promoter showed activity in several cell lines that do not express the endogenous SMC calponin gene. These results demonstrate that SMC calponin responds to cardiac and smooth muscle gene regulatory programs and suggest that the cardiac and smooth muscle cell lineages may share a common gene regulatory program early in embryogenesis, which diverges as the heart matures. The finding that the isolated SMC calponin promoter is active in a wider range of cells than the endogenous SMC calponin gene also suggests that long-range repression or higher order regulatory mechanism(s) are involved in cell-specific regulation of SMC calponin expression.
CVP chemotherapy plus rituximab compared with CVP as first-line treatment for advanced follicular lymphoma (2004)

The combination of cyclophosphamide, vincristine, and prednisone (CVP) is one of several standard treatment options for advanced follicular lymphoma. This, like similar chemotherapeutic regimens, induces response rates of 60% to 80%, with a median response duration of under 2 years. Rituximab, a chimeric monoclonal antibody against CD20, is active in follicular lymphoma, both as monotherapy and in combination with chemotherapy. Previously untreated patients with stages III to IV follicular lymphoma were randomly assigned to receive either 8 cycles of CVP plus rituximab (R-CVP; n = 162) or CVP (n = 159). Overall and complete response rates were 81% and 41% in the R-CVP arm versus 57% and 10% in the CVP arm, respectively (P < .0001). At a median follow-up of 30 months, patients treated with R-CVP had a very significantly prolonged time to progression (median 32 months versus 15 months for CVP; P < .0001). Median time to treatment failure was 27 months in patients receiving R-CVP and 7 months in the CVP arm (P < .0001). Rituximab did not add significantly to the toxicity of CVP. The addition of rituximab to the CVP regimen significantly improves the clinical outcome in patients with previously untreated advanced follicular lymphoma, without increased toxicity.
Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury (2015)

We have developed a novel plasma protein analysis platform with optimized sample preparation, chromatography, and MS analysis protocols. The workflow, which utilizes chemical isobaric mass tag labeling for relative quantification of plasma proteins, achieves far greater depth of proteome detection and quantification while simultaneously having increased sample throughput than prior methods. We applied the new workflow to a time series of plasma samples from patients undergoing a therapeutic, "planned" myocardial infarction for hypertrophic cardiomyopathy, a unique human model in which each person serves as their own biologic control. Over 5300 proteins were confidently identified in our experiments with an average of 4600 proteins identified per sample (with two or more distinct peptides identified per protein) using iTRAQ four-plex labeling. Nearly 3400 proteins were quantified in common across all 16 patient samples. Compared with a previously published label-free approach, the new method quantified almost fivefold more proteins/sample and provided a six- to nine-fold increase in sample analysis throughput. Moreover, this study provides the largest high-confidence plasma proteome dataset available to date. The reliability of relative quantification was also greatly improved relative to the label-free approach, with measured iTRAQ ratios and temporal trends correlating well with results from a 23-plex immunoMRM (iMRM) assay containing a subset of the candidate proteins applied to the same patient samples. The functional importance of improved detection and quantification was reflected in a markedly expanded list of significantly regulated proteins that provided many new candidate biomarker proteins. Preliminary evaluation of plasma sample labeling with TMT six-plex and ten-plex reagents suggests that even further increases in multiplexing of plasma analysis are practically achievable without significant losses in depth of detection relative to iTRAQ four-plex. These results obtained with our novel platform provide clear demonstration of the value of using isobaric mass tag reagents in plasma-based biomarker discovery experiments.
Increased incorporation of adenosine into adenine nucleotide pools in serum-deprived mammalian cells. (1978)

The effects of serum deprivation on the incorporation of adenosine into the intracellular adenine nucleotide pools by several mamalian cell lines were studied. Cells arrested in the G1 phase of the cell cycle showed increased incorporation of exogenous adenosine into their adenine nucleotide pools as compared with growing cells. This phenomenon is unexpected because salvage pathways from all other preformed nucleosides and bases as well as the de novo synthesis of adenine nucleotides is decreased after arrest of growth by serum deprivation. The incorporation of adenosine into adenine nucleotides may serve as an intracellular signal in the regulation of growth in mammalian cells.
Mast cell tryptase causes airway smooth muscle hyperresponsiveness in dogs. (1989)

Supernatants obtained by degranulation of dog mastocytoma cells greatly increased the sensitivity and the magnitude of the contractile response of isolated dog bronchial smooth muscle to histamine. The enhanced contractile response was reversed completely by H1-receptor antagonists and was prevented by an inhibitor of tryptase (a major protease released with histamine from secretory granules of mast cells). The potentiation of histamine-induced contractions was reproduced by active tryptase in pure form. The contractions due to the combination of histamine and purified tryptase were abolished by the Ca2+ channel blockers nifedipine and verapamil. The bronchoconstricting effects of KCl and serotonin, which, like histamine, contract airway smooth muscle by a mechanism predominantly involving membrane potential-dependent Ca2+ transport, were also potentiated by tryptase. However, the contractile effects of acetylcholine, which contracts dog airway smooth muscle by a mechanism independent of Ca2+ channels, were unaffected by tryptase. These findings show a striking promotion of agonist-induced bronchial smooth muscle contraction by mast cell tryptase, via direct or indirect effects on Ca2+ channels, and the findings therefore suggest a novel potential mechanism of hyperresponsiveness in dog bronchi.
Effect of concentration of D,L-2-difluoromethylornithine on murine mammary carcinogenesis. (1985)

The appearance of chemically induced mammary gland carcinomas in virgin female Sprague-Dawley rats was blocked by the administration of D,L-2-difluoromethylornithine (DFMO) in drinking water during the stage of tumor promotion. Rats were given injections s.c. at 50 days of age with either 35 mg of 1-methyl-1-nitrosourea (MNU) per kg of body weight or the 0.9% NaCl solution in which the carcinogen was dissolved. At 57 days of age, the rats were each randomly allocated to one of 14 treatment groups. Ten groups (five solvent treated and five MNU treated) were assigned to treatments consisting of 0.00, 0.0625, 0.125, 0.25, or 0.50% (w/v) solution of DFMO in their drinking water; two MNU-treated groups were placed on or removed from DFMO treatment (0.5%; w/v) at 90 days post-carcinogen exposure; and two carcinogen-treated groups received either putrescine (0.5-g/kg diet) or putrescine and DFMO (0.5%; w/v) throughout the experiment. The study was terminated 183 days after carcinogen treatment. All doses of DFMO exerted a protective effect against the induction of mammary cancer; however, only the feeding of the 0.125% and the 0.5% solutions of DFMO resulted in a significant reduction in cancer incidence. The average number of cancers per rat was reduced, and cancer-free time was extended at all concentrations of DFMO. The protective effect of DFMO was sustained following withdrawal of treatment at 90 days post-MNU injection. Feeding putrescine in conjunction with DFMO treatment partially blocked the inhibitory activity of DFMO. DFMO treatment did not affect food or water intake; body weight gain; the weight of ovaries, uterus, adrenal glands, liver, kidney, or spleen; or the periodicity of the estrous cycle. These data provide evidence of an inhibitory effect of DFMO against mammary cancer induced by MNU which cannot be attributed to a systemic toxic effect of this compound.
Molecular Genetic Methods for Mapping Disease Genes (1994)

Recent technological enhancements in molecular genetics have significantly improved our ability to locate disease genes by linkage analysis. Despite the introduction of molecular methods such as PCR and the discovery of highly polymorphic SSRs, genotyping is still rate-limiting for localizing disease genes by linkage. These methods have been, until recently, highly technical, time-consuming, and expensive. The challenge of mapping the major genes that render one susceptible to environmentally initiated lung disorders such as asthma will require efficient and highly accurate methods of genotyping. We have shown that genotyping by semi-automated fluorescence-based techniques is both highly accurate and efficient. These methods may improve productivity by more than an order of magnitude and can be easily adapted to most linkage studies.
Construction, purification, and characterization of new interferon gamma (IFN gamma) inhibitor proteins. Three IFN gamma receptor-immunoglobulin hybrid molecules. (1992)

Three efficient mouse interferon y (MoIFNy) inhibitors were constructed, which consist of the MoIFNy receptor (MoIFNyR) extracellular portion and constant domains of immunoglobulin (Ig) molecules.These are: 1) the constant domain of the mouse K chain, 2) the hinge region and the constant domains 2 and 3 of the mouse y2a chain, and 3) the hinge region and the constant domains 2 and 3 of the human y 3 chain.The hybrid molecules were expressed in the mouse myeloma cell line J558L and recovered from the supernatants of cell cultures in one purification step.The proteins MoIFNyR-My2a and MoIFNyR-Hr3 form homodimers, whereas MoIFNyR-MK is a monomer.All three constructs inhibit the binding of radiolabeled MoIFNy to its receptor on L1210 cells.They are biologically active in vitro, neutralizing the action of MoIFNy in an antiviral activity assay.The fusions of Ig regions to the soluble MoIFNyR do not decrease the affinity of the binding site for the ligand.MoIFNrR-MK has about the same affinity as the soluble MoIFNyR and the cell surface receptor of L1210 cells in situ, which are also monomers, whereas the dimers MoIFNyR-My2a and MoIFNyR-Hy3 display a 5-10-fold higher affinity for MoIFNy than the monomeric molecules.This is best documented in the efficacy of the inhibitors to antagonize the antiviral activity of MoIFNy, as the dimeric constructs are about 10 times more active than MoIFNrR-MK and the soluble MoIFNrR.The hybrid constructs can be used as high efficiency MoIFNy inhibitors in mouse models of several pathological states in humans, where IFNy is thought to play a diseasepromoting role.y interferon (IFNy)' is a lymphokine almost exclusively produced by T lymphocytes (1-3) and natural killer cells (4).IFNy acts as a potent immunomodulator (5).It facilitates the proliferation of T cells, enhances the maturation of cytotoxic T cells (6, 7) and the development of T helper cells from their precursors (8), and inhibits the generation of some suppressor * The costs of publication of this article were defrayed in part by the payment of page charges.
Growth patterns and metastatic behavior of human tumors growing in athymic mice. (1978)

The growth characteristics and metastatic behavior of human tumors growing in athymic nude mice were studied. Human tumor cell lines HEp-2 (carcinoma or larynx) and SW480 (colon carcinoma) were transplanted into athymic nude mice of BALB/c origin. Tumor cells (1 x 10(6) and 2 x 10(7)) were given either s.c. or i.p. Following s.c. injection tumors developed rapidly to become easily palpable with 2 weeks forming a s.c. tumor focus surrounded by a thick fibrous capsule. Animals with s.c. transplants were little affected by the growing tumor. At the time they were sacrificed at Day 34 (HEp-2) and 62 (SW480), a large part of the tumor was necrotic. Capsular infiltration and invasion of lymphatic vessels and perineural and perivascular lymphatic spaces were observed. Metastases to regional lymph nodes were seen in animals kept alive for up to 6 months. Following i.p. transplantation, tumors spread widely in the peritoneal cavity, invaded intraabdominal organs, and metastasized to mediastinal lymph nodes and lungs. Fifteen of 26 animals (60%) developed metastases. Necrosis of the i.p. growing tumors was minimal. All animals in this group died as a result of tumor growth.
Carbonic anhydrase is an ancient enzyme widespread in prokaryotes (1999)

Carbonic anhydrases catalyze the reversible hydration of CO(2) and are ubiquitous in highly evolved eukaryotes. The recent identification of a third class of carbonic anhydrase (gamma class) in a methanoarchaeon and our present finding that the beta class also extends into thermophilic species from the Archaea domain led us to initiate a systematic search for these enzymes in metabolically and phylogenetically diverse prokaryotes. Here we show that carbonic anhydrase is widespread in the Archaea and Bacteria domains, and is an ancient enzyme. The occurrence in chemolithoautotrophic species occupying deep branches of the universal phylogenetic tree suggests a role for this enzyme in the proposed autotrophic origin of life. The presence of the beta and gamma classes in metabolically diverse species spanning the Archaea and Bacteria domains demonstrates that carbonic anhydrases have a far more extensive and fundamental role in prokaryotic biology than previously recognized.
Advances in sepsis-associated liver dysfunction (2014)

Recent studies have revealed liver dysfunction as an early event in sepsis. Sepsis-associated liver dysfunction is mainly resulted from systemic or microcirculatory disturbances, spillovers of bacteria and endotoxin (lipopolysaccharide, LPS), and subsequent activation of inflammatory cytokines as well as mediators. Three main cell types of the liver which contribute to the hepatic response in sepsis are Kupffer cells (KCs), hepatocytes and liver sinusoidal endothelial cells (LSECs). In addition, activated neutrophils, which are also recruited to the liver and produce potentially destructive enzymes and oxygen-free radicals, may further enhance acute liver injury. The clinical manifestations of sepsis-associated liver dysfunction can roughly be divided into two categories: Hypoxic hepatitis and jaundice. The latter is much more frequent in the context of sepsis. Hepatic failure is traditionally considered as a late manifestation of sepsis-induced multiple organ dysfunction syndrome. To date, no specific therapeutics for sepsis-associated liver dysfunction are available. Treatment measure is mainly focused on eradication of the underlying infection and management for severe sepsis. A better understanding of the pathophysiology of liver response in sepsis may lead to further increase in survival rates.
Efficient expression of small RNA polymerase III genes from a novel Simian virus 40 vector and their effect on viral gene expression (1989)

In the past, simian virus 40 (SV40) has been used as a cloning vehicle to clone foreign genes by substituting portions of the viral genome vital for viral replication. Propagation of these defective viruses required a helper virus and the recombinant viruses obtained could be grown only as a mixture. In this study, we describe a novel nondefective SV40 vector to clone small RNA polymerase III genes. Two small RNA polymerase III genes, an amber suppressor human serine tRNA gene and the adenovirus (Ad) VAI RNA gene, were cloned in the intron region of the large-T antigen gene of SV40 after deleting DNA sequences coding for the small-t polypeptide. The recombinant viruses grew to wild type levels and showed no growth defects. When CV-1p cells were infected with these viruses, the cloned RNA polymerase III genes were expressed at high levels at late times. Interestingly, large amounts VAI RNA in CV-1p cells infected with SV40-VA recombinant virus, did not enhance translation of viral mRNAs significantly but did lead to a 3 to 4 fold increase in the steady state levels of large-T mRNA suggesting a novel function for VAI RNA in SV40 infected monkey cells. Furthermore, VAI mutants which fail to function in Ad infected human cells also failed to enhance the levels of large-T mRNAs in monkey cells infected with SV40. The simple SV40 vector described here may be useful to study the structure and function of small RNA polymerase III genes in the context of a eucaryotic chromosome. In addition, the nondefective recombinant SV40 which expresses the suppressor tRNA gene at high levels may provide a useful helper system to propagate animal viruses with amber mutations in essential genes.
Melanoma cells present high levels of <scp>HLA</scp>‐<scp>A</scp>2‐tyrosinase in association with instability and aberrant intracellular processing of tyrosinase (2012)

Short-lived protein translation products are proposed to be a major source of substrates for major histocompatibility complex (MHC) class I antigen processing and presentation; however, a direct link between protein stability and the presentation level of MHC class I-peptide complexes has not been made. We have recently discovered that the peptide Tyr((369-377)) , derived from the tyrosinase protein is highly presented by HLA-A2 on the surface of melanoma cells. To examine the molecular mechanisms responsible for this presentation, we compared characteristics of tyrosinase in melanoma cells lines that present high or low levels of HLA-A2-Tyr((369-377)) complexes. We found no correlation between mRNA levels and the levels of HLA-A2-Tyr((369-377)) presentation. Co-localization experiments revealed that, in cell lines presenting low levels of HLA-A2-Tyr((369-377)) complexes, tyrosinase co-localizes with LAMP-1, a melanosome marker, whereas in cell lines presenting high HLA-A2-Tyr((369-377)) levels, tyrosinase localizes to the endoplasmic reticulum. We also observed differences in tyrosinase molecular weight and glycosylation composition as well as major differences in protein stability (t(1/2) ). By stabilizing the tyrosinase protein, we observed a dramatic decrease in HLA-A2-tyrosinase presentation. Our findings suggest that aberrant processing and instability of tyrosinase are responsible for the high presentation of HLA-A2-Tyr((369-377)) complexes and thus shed new light on the relationship between intracellular processing, stability of proteins, and MHC-restricted peptide presentation.
Shelf-life of a 2.5% sodium hypochlorite solution as determined by arrhenius equation (2009)

Accelerated stability tests are indicated to assess, within a short time, the degree of chemical degradation that may affect an active substance, either alone or in a formula, under normal storage conditions. This method is based on increased stress conditions to accelerate the rate of chemical degradation. Based on the equation of the straight line obtained as a function of the reaction order (at 50 and 70 degrees C) and using Arrhenius equation, the speed of the reaction was calculated for the temperature of 20 degrees C (normal storage conditions). This model of accelerated stability test makes it possible to predict the chemical stability of any active substance at any given moment, as long as the method to quantify the chemical substance is available. As an example of the applicability of Arrhenius equation in accelerated stability tests, a 2.5% sodium hypochlorite solution was analyzed due to its chemical instability. Iodometric titration was used to quantify free residual chlorine in the solutions. Based on data obtained keeping this solution at 50 and 70 degrees C, using Arrhenius equation and considering 2.0% of free residual chlorine as the minimum acceptable threshold, the shelf-life was equal to 166 days at 20 degrees C. This model, however, makes it possible to calculate shelf-life at any other given temperature.