gebhart/patrepeval huggingface dataset:
Methylation of Drosophila histones at proline, lysine, and arginine residues during heat shock. (1988)

Heat shock or arsenite treatment alter the pattern of histone methylation in Drosophila cells. Both types of stress induce a rapid increase in the methylation level of histone H2B. The methylated amino acid residue of H2B has been identified by thin layer chromatography and electrophoresis as methylproline and is located at the N-terminal end of H2B. Heat shock also induces a decrease in the level of methylation of histone H3. Under normal growth temperature conditions, histone H3 is shown to be methylated on lysine residues. However under heat shock conditions, there is a decrease in the extent of methylation of lysine residues and the appearance of new methylation on arginine residues in H3. These new heat shock-induced methylated residues have been identified as the symmetrical and asymmetrical forms of dimethylarginine. The methylated amino acid residue of histone H4 is lysine with mono-, di-, and trimethyl forms found in both control and heat or chemically stressed cells. These stress-induced changes in the methylation level of the N-terminal proline residue of histone H2B and shift in the methylation sites of histone H3 may be involved in the restructuration of chromatin accompanying the inactivation of normal genes in response to stress. Moreover, we suggest that the hypermethylation of H2B may also be involved in its protection from increased ubiquitin-mediated proteolytic activity under these conditions of cellular stress.
Single-Step Synthesis of Pyrimidine Derivatives (2006)

We describe a single-step conversion of various N-vinyl and N-aryl amides to the corresponding pyrimidine and quinazoline derivatives, respectively. The process involves amide activation with 2-chloropyridine and trifluoromethanesulfonic anhydride followed by nitrile addition into the reactive intermediate and cycloisomerization. In situ nitrile generation from primary amides allows for their use as nitrile surrogates. The use of this chemistry with sensitive N-vinyl amides and epimerizable substrates in addition to a wide range of functional groups is noteworthy.
Spin-Orbit Coupled Weakly Interacting Bose-Einstein Condensates in Harmonic Traps (2012)

We investigate theoretically the phase diagram of a spin-orbit coupled Bose gas in two-dimensional harmonic traps. We show that at strong spin-orbit coupling the single-particle spectrum decomposes into different manifolds separated by ℏω{⊥}, where ω{⊥} is the trapping frequency. For a weakly interacting gas, quantum states with Skyrmion lattice patterns emerge spontaneously and preserve either parity symmetry or combined parity-time-reversal symmetry. These phases can be readily observed in a spin-orbit coupled gas of ^{87}Rb atoms in a highly oblate trap.
Physical and chemical properties of randomly interesterified blends of soybean oil and tallow for use as margarine oils (1983)

Abstract Refined, unhydrogenated soybean oil and edible beef tallow were interesterified with sodium methoxide. This was done as an alternative to hydrogenation for the production of plastic fats for use as margarine oils. Using 0.5% sodium methoxide at 80 C, interesterifi‐cation was complete in 30 min as determined by lipase hydrolysis. A blend of 60% soybean oil and 40% edible beef tallow was found to have physical characteristics (melting point, solid fat index) similar to those of commercial tub margarine oils. The level of poly‐unsaturated fatty acids was slightly lower and the level of saturated fatty acids slightly higher than the commercial margarine oils. Iodine value and trans fatty acid determinations indicated no dis‐cernible effect on the degree of unsaturation or the level of isomeric fatty acids by the interesterification process. The interesterified blend did contain 3.0% trans fatty acids which were originally present in the tallow. Oxidative stability of the interesterified oils was estimated by peroxide value determinations over several days on samples stored at 60 C. Experimental blends treated with 0.1% citric acid had poorer stability than the partially hydrogenated margarine oils; however, 0.01% BHA significantly delayed oxidation of the experimental samples.
Fruitful Adrenergic α2C-Agonism/α2A-Antagonism Combination to Prevent and Contrast Morphine Tolerance and Dependence, (2010)

The functional in vitro study of the enantiomers of imidazolines 4-7 highlighted the role played by the nature of the ortho phenyl substituent in determining the preferred α(2C)-AR configuration. Indeed, the (S) enantiomers of 4-6 or (R) enantiomer of 7 behave as eutomers and activate this subtype as full agonists; the corresponding distomers are partial agonists. Because in clinical pain management with opioids α(2C)-AR agonists, devoid of the α(2A)-AR-mediated side effects, may represent an improvement over current therapies with clonidine like drugs, 4 and its enantiomers, showing α(2C)-agonism/α(2A)-antagonism, have been studied in vivo. The data suggest that partial α(2C)-activation is compatible with effective enhancement of morphine analgesia and reduction both of morphine tolerance acquisition and morphine dependence acquisition and expression. On the contrary, full α(2C)-activation appears advantageous in reducing morphine tolerance expression. Interestingly, the biological profile displayed by 4 (allyphenyline) and its eutomer (S)-(+)-4 has been found to be very unusual.
Catalytic asymmetric synthesis (2001)

Asymmetric Hydrogenation (T. Ohkuma, et al.). Asymmetric Hydrosilylation and Related Reactions (H. Nishiyama & K. Itoh). Asymmetric Isomerization of Allylamines (S. Akutagawa, et al.). Asymmetric Carbometallations (E. Negishi). Asymmetric Addition and Insertion Reactions of Catalytically-Generated Metal Carbenes (M. Doyle). Asymmetric Oxidations and Related Reactions (R. Johnson, et al.). Asymmetric Carbonylations (K. Nozaki & I. Ojima). Asymmetric Carbon-Carbon Bond-Forming Reactions (K. Maruoka, et al.). Asymmetric Amplification and Autocatalysis (K. Soai & T. Shibata). Asymmetric Phase-Transfer Reactions (M. O'Donnell). Asymmetric Polymerization (Y. Okamoto & T. Nakano). Epilogue. Appendix. Index.
Activating mutation of D835 within the activation loop of FLT3 in human hematologic malignancies (2001)

Mutations of receptor tyrosine kinases are implicated in the constitutive activation and development of human malignancy. An internal tandem duplication (ITD) of the juxtamembrane (JM) domain-coding sequence of the FLT3 gene (FLT3/ITD) is found in 20% of patients with acute myeloid leukemia (AML) and is strongly associated with leukocytosis and a poor prognosis. On the other hand, mutations of the c-KIT gene, which have been found in mast cell leukemia and AML, are clustered in 2 distinct regions, the JM domain and D816 within the activation loop. This study was designed to analyze the mutation of D835 of FLT3, which corresponds to D816 of c-KIT, in a large series of human hematologic malignancies. Several kinds of missense mutations were found in 30 of the 429 (7.0%) AML cases, 1 of the 29 (3.4%) myelodysplastic syndrome (MDS) cases, and 1 of the 36 (2.8%) acute lymphocytic leukemia patients. The D835Y mutation was most frequently found (22 of the 32 D835 mutations), followed by the D835V (5), and D835H (1), D835E (1), and D835N (1) mutations. Of note is that D835 mutations occurred independently of FLT3/ITD. An analysis in the 201 patients newly diagnosed with AML (excluding M3) revealed that, in contrast to the FLT3/ITD mutation (n = 46), D835 mutations (n = 8) were not significantly related to the leukocytosis, but tended to worsen disease-free survival. All D835-mutant FLT3 were constitutively tyrosine-phosphorylated and transformed 32D cells, suggesting these mutations were constitutively active. These results demonstrate that the FLT3 gene is the target most frequently mutated to become constitutively active in AML.
Role of the Stable Signal Peptide and Cytoplasmic Domain of G2 in Regulating Intracellular Transport of the Junin Virus Envelope Glycoprotein Complex (2006)

Enveloped viruses utilize the membranous compartments of the host cell for the assembly and budding of new virion particles. In this report, we have investigated the biogenesis and trafficking of the envelope glycoprotein (GP-C) of the Junín arenavirus. The mature GP-C complex is unusual in that it retains a stable signal peptide (SSP) as an essential component in association with the typical receptor-binding (G1) and transmembrane fusion (G2) subunits. We demonstrate that, in the absence of SSP, the G1-G2 precursor is restricted to the endoplasmic reticulum (ER). This constraint is relieved by coexpression of SSP in trans, allowing transit of the assembled GP-C complex through the Golgi and to the cell surface, the site of arenavirus budding. Transport of a chimeric CD4 glycoprotein bearing the transmembrane and cytoplasmic domains of G2 is similarly regulated by SSP association. Truncations to the cytoplasmic domain of G2 abrogate SSP association yet now permit transport of the G1-G2 precursor to the cell surface. Thus, the cytoplasmic domain of G2 is an important determinant for both ER localization and its control through SSP binding. Alanine mutations to either of two dibasic amino acid motifs in the G2 cytoplasmic domain can also mobilize the G1-G2 precursor for transit through the Golgi. Taken together, our results suggest that SSP binding masks endogenous ER localization signals in the cytoplasmic domain of G2 to ensure that only the fully assembled, tripartite GP-C complex is transported for virion assembly. This quality control process points to an important role of SSP in the structure and function of the arenavirus envelope glycoprotein.
An Allosamizoline/Glucosamine Hybrid NAGase Inhibitor (1997)

The glucosamine isothiourea derivative 7, which resembles the aminocyclitol isourea portion of the chitinase inhibitor allosamidin (5), inhibits jack bean NAGase with K i=160 μM.
High periostin expression correlates with aggressiveness in papillary thyroid carcinomas (2008)

Periostin is a mesenchyme-specific gene product, which acts as an adhesion molecule during bone formation and supports osteoblastic cell line attachment and spreading. However, periostin expression is activated in a large variety of epithelial human tumors and correlates with their aggressiveness. Knowledge of expression of periostin in thyroid tumors is still scanty. The aim of the present work was to investigate periostin expression in differentiated neoplasms of the thyroid and to correlate it with several clinical and molecular features of these tumors. Periostin expression was evaluated by quantitative PCR and immunohistochemistry in normal thyroid tissues, papillary thyroid carcinomas (PTCs), follicular thyroid carcinomas (FTCs), and follicular adenomas (FAs). Periostin mRNA levels were also evaluated in several thyroid tumor cell lines. PTCs show mean periostin mRNA levels significantly higher than corresponding normal tissues. In five PTCs, periostin mRNA values were at least 30-fold higher than corresponding normal tissues. Conversely, mean periostin mRNA levels of FTCs and FAs were similar to those of normal tissues. Consistent with mRNA studies, periostin was detectable by immunohistochemistry in cancerous epithelial cells only in several cases of PTCs but not in normal tissue, FTCs, and FAs. In PTCs, periostin mRNA levels positively correlate with extrathyroidal invasion, distant metastasis, and higher grade staging. A negative correlation between periostin and expression of some markers of the thyroid-differentiated phenotype (thyroglobulin, thyrotropin receptor) was also present in the PTCs. These results indicate that an increase in periostin gene expression is present in several PTCs, in which it appears as a marker of aggressiveness. Experiments in thyroid tumor cell lines indicate that high levels of periostin mRNA are due, at least in part, to the increase in periostin promoter activity.
Bone Tissue Fluorescence Reduction for Visible Laser Raman Spectroscopy (2002)

We report the successful reduction of background fluorescence in bone tissue by photo-irradiation with green laser light. Irradiation of bone tissue with intense green light has been shown to be nondestructive and to reduce permanently over 70% of the fluorescence background. The laser power dependence of the fluorescence reduction was found to be nonlinear.
Single-strand conformation polymorphism analysis of PCR-amplified ribosomal DNA internal transcribed spacers to differentiate species of Aspergillus section Flavi (1996)

A novel genetic approach for classifying the species of Aspergillus Section Flavi is described here. This approach consists of PCR amplification of the 5.8S ribosomal DNA-intervening internal transcribed spacer regions (ITS I-5.8S-ITS II) with universal primers and of analysis of the PCR product by the principle of single-strand conformation polymorphism (SSCP). The approximately 570- to 590-bp PCR products were denatured and subjected to electrophoresis on a polyacrylamide gel supplemented with 20% formamide. The SSCP patterns of these species became more distinct by the addition of formamide to the gel and by visualization with ethidium bromide staining. A little interspecific length polymorphism among amplified ribosomal DNAs was enhanced to be detected by PCR-SSCP analysis. This analysis was capable of classifying 67 of the 68 Aspergillus Section Flavi strains tested into the following four groups, regardless of origin: A. flavus/A. oryzae, A. parasiticus/A. sojae, A. tamarii, and A. nomius. The results of restriction fragment length polymorphism analysis with PCR products of the ITS regions were consistent with those of PCR-SSCP analysis, except for A. nomius, which was not clearly differentiated from A. parasiticus/A. sojae. Nonradiolabelled PCR-SSCP analysis is inexpensive and practical to perform without special apparatus or skill and should assist in fungal morphological identification.
Spray-Drying of Air–Liquid Interface Sensitive Recombinant Human Growth Hormone (1998)

□ Spray-drying is an attractive method for preparing fine recombinant human growth hormone (rhGH) powders if the detrimental effect of protein degradation at the air–liquid interface on the protein can be minimized. In this study, we demonstrated that rhGH degradation (insoluble and soluble aggregate formation), as the consequence of air–liquid interfacial degradation, could be prevented using the appropriate formulation. Adding polysorbate-20 surfactant into the liquid feed (with no presence of sugar protectant) significantly reduced the formation of insoluble protein aggregates, while adding the divalent metal zinc ion effectively suppressed the formation of soluble protein aggregates. The combination of the two yielded a spray-dried rhGH powder having insignificant protein degradation. Our data suggest that the two components might protect the protein through different mechanisms. Polysorbate molecules occupy the air–liquid interface of spray droplets, thereby reducing the chance for rhGH to form insoluble aggregates by surface denaturation. Two zinc ions associate with two rhGH molecules to form a dimer complex that can resist the formation of soluble protein aggregates. Characterization of spray-dried powders by scanning electron microscopy suggests that both formulation and drying conditions have a strong influence on particle morphology and shape. Overall, spherical rhGH powders of smooth surface and good biochemical quality can be prepared by spray-drying using this formulation with no addition of sugar protectant.
Evaluation of the Tissue Response to the Wear Products of the Hip Joint Endo-Arthroprosthesis (1979)

The causes of tissue reaction surrounding heterogeneous materials are: cell-mediated hypersensitivity due to an implant material; infection; post-surgery hematoma, following lysis of red cells and deposition of hemosiderin; "True" implant reaction, i.e., tissue modifications produced by wear particles of components of the prosthetic devices used. The stages of inflammation due to wear particles are: phagocytosis of particles by newly formed fibrous capsule cells; lymphatic drainage of particles through the newly formed joint capsule; granulation tissue reaction in the internal surface of the joint capsule which stores non-removed particles from inadequate drainage; necrosis of granulation tissue in contacting the artificial joint surface; formation of free masses of necrotic tissue in the joint cavity; formation of new granulation tissue due to these necrotic masses and by wear particles liberated from them (the beginning of a vicious cycle); insufficient storage by granulation tissue; formation of "auxiliary" granulation tissue in the fibrous layer of the bone-cement interfaces and in the R.E.S. of the bone-marrow; bone resorption and its replacement by granulation tissue; loosening of the prosthesis.
OKT3E, AN ANTI-CD3 ANTIBODY THAT DOES NOT ELICIT SIDE EFFECTS OR ANTIIDIOTYPE RESPONSES IN CHIMPANZEES (1991)

Chimpanzees were injected with OKT3 and two other anti-CD3 antibodies, OKT3D and OKT3E. Both of the new antibodies were of the mouse IgG2b isotype. Administration of the antibodies was identical to the clinical regimen used for OKT3 in humans: 5 mg i.v., daily for 10 consecutive days. All animals were monitored for fever during administration of the antibodies, and blood samples were taken throughout the treatment period for monitoring the effects of the antibodies on peripheral lymphocyte subsets and the appearance of circulating cytokines. OKT3 produced similar clinical effects to those observed in humans; fever (2/3), as well as elevations in cytokines were observed. As in humans, peripheral T cells were cleared with the first dose and remained absent or modulated of their T cell receptor molecules throughout treatment. OKT3D, IgG2b also produced fevers (2/3) and elevations of cytokines. Although it also cleared circulating T cells with the first dose and T cell counts remained low throughout treatment, remaining circulating T cells were coated with administered antibody and were able to reexpress the CD3 antigen. OKT3E, IgG2b produced no temperature elevations and no elevations in cytokines. Although it cleared the circulation of T cells with the first does, cells reappeared during treatment, modulated of their CD3 antigens or coated with the administered antibody. All three antibodies raised antimouse antibodies, and OKT3 and OKT3D also produced blocking antiidiotype antibodies. OKT3E treatment did not result in anti-OKT3E blocking antibodies.
Proteins from the FLOWERING LOCUS T‐like subclade of the PEBP family act antagonistically to regulate floral initiation in tobacco (2012)

Flowering is an important agronomic trait that often depends on the integration of photoperiod, vernalization, gibberellin and/or autonomous signaling pathways by regulatory proteins such as FLOWERING LOCUS T (FT), a member of the phosphatidylethanolamine-binding protein (PEBP) family. Six PEBP family proteins control flowering in the model plant Arabidopsis thaliana, and their regulatory functions are well established, but variation in the number and structural diversity of PEBPs in different species means their precise functions must be determined on a case-by-case basis. We isolated four novel FT-like genes from Nicotiana tabacum (tobacco), and determined their expression profiles in wild-type plants and their overexpression phenotypes in transgenic plants. We found that all four genes were expressed in leaves under short-day conditions, and at least NtFT3 expression was restricted to phloem companion cells. We also found that the NtFT1, NtFT2 and NtFT3 proteins are floral inhibitors (atypical for FT-like proteins), whereas only NtFT4 is a floral inducer. We were unable to detect the expression of these genes under long-day conditions, suggesting that all four tobacco FT-like proteins may control flowering in response to short days. Phylogenetic analysis of PEBP family proteins and their functions in different solanaceous species confirmed that gene duplication and divergence within the FT-like clade has led to the evolution of antagonistic regulators that may help to fine-tune floral initiation in response to environmental cues.
High level expression of heterologous proteins in methylotrophic yeast Pichia pastoris (1988)

Expression of human tumor necrosis factor-alpha (TNF) and four different TNF analogs has been studied in Pichia pastoris by utilizing the alcohol oxidase gene promoter. TNF expression level in certain transformants accounted for as much as 36% of the soluble protein. TNF expression was stably maintained during high cell density fermentation (100 g dry cell weight/liter) resulting in a TNF production level of 6-10 g/liter. TNF contained in P. pastoris cell lysates was biologically active as determined by its cytotoxic effect on murine L-929 fibroblast cells and the bioactivity was retained for at least 6 months in the lysates stored frozen at -20 degrees C in the presence of protease inhibitor PMSF. TNF expressed in P. pastoris was recognized by monoclonal antibodies prepared against recombinant Escherichia coli derived TNF. TNF purified from P. pastoris has the expected N-terminal amino acid sequence and specific activity of 10(7) units/mg protein. TNF analogs were also expressed at levels comparable to that of native TNF. Three of the four analogs were insoluble when produced in P. pastoris.
Alteration in Expression Profiles of a Series of Diabetes-Related Genes in db/db Mice Following Treatment With Thiazolidinediones (2000)

We studied the effect of pioglitazone on the transcription of 42 genes associated with diabetes to examine the relationship between the antidiabetic action of thiazolidinediones (TZDs) and their ability to modulate transcription through their peroxisome proliferater-activated receptor (PPAR)-agonistic activity. Diabetic (db/db) mice were orally administered with pioglitazone for two weeks. Total RNA was prepared from liver, muscle and adipocytes and the quantity of mRNA was determined by comparative RT-PCR. The expression of diabetes-related genes was compared between lean and untreated db/db mice and between untreated and drug-treated db/db mice. The onset of diabetes was associated with a considerable alteration in the expression of a large number of diabetes-related genes. Treatment of db/db mice with pioglitazone modulated the expression of genes involved in the metabolism of glucose, lipids and lipoproteins. This included genes for phosphoenolpyruvate carboxykinase, beta-oxidation enzymes, lipoprotein lipase, apolipoprotein AI and uncoupling proteins. Most of the genes responsible for insulin signaling were unaffected. Administration of pioglitazone was also shown to induce PPARgamma expression in liver and muscle. It is therefore possible to hypothesize that TZDs may ameliorate diabetes through a mechanism of action involving a direct decrease in plasma glucose and triglyceride levels and improvements in free fatty acid-induced insulin resistance.
FAD, a Powerful and Simple Database Language (1987)

FAD is a powerful and simple language designed for a highly parallel database machine. The basic concepts of the language are its data structures (which we call objects) and its programs (defined in terms of operators and predicates). The primary features of the language are (i) the support of complex objects with built-in notion of object identity; (ii) an abstract data type capability; (iii) a persistent object space; and (iv) the efficient support of iteration, conditionals, and set operations. FAD is functional and uses low level operators and operator constructors. This provides for the opportunity of dataflow execution in a parallel architecture. FAD has been successfully implemented in (i) an interpreter working on a main memory database and (ii) integrated in a prototype of a database machine.