gebhart/patrepeval huggingface dataset:
Beta-endorphin and islet hormone release in type-2 diabetes mellitus the effects of normoglycemia, enkephalin, naloxone and somatostatin. (1988)

The present study was aimed at characterizing the effects of beta-endorphin on plasma glucose, insulin and glucagon plasma levels in subjects with type-2 diabetes mellitus. Infusion of 0.5 mg/h human beta-endorphin produced significant and simultaneous increments in both insulin and glucagon concentrations and decreased plasma glucose levels (-18 +/- 4 mg/dl, 60 min level, p less than 0.01). When the same diabetics were rendered euglycemic by an insulin infusion (1 mU/kg/min), beta-endorphin did not produce the expected decrease in plasma glucose concentrations nor raise plasma insulin levels; only the response of glucagon was preserved. Normal subjects were rendered hyperglycemic by an intravenous glucose infusion to match the plasma glucose levels of diabetic subjects. In this condition, beta-endorphin produced a significant increase of insulin concentrations, whereas glucagon remained suppressed. The intravenous administration of the long-acting met-enkephalin analogue DAMME (0.25 mg) blunted the hormonal responses to the subsequent beta-endorphin infusion in diabetic patients, although the inhibition was short-lived (30-40 min). Naloxone (5 mg), an opiate antagonist, did not produce any significant change in the insulin and glucagon responses to beta-endorphin, while somatostatin (0.25 mg/h) completely abolished the hormonal responses to the opioid.(ABSTRACT TRUNCATED AT 250 WORDS)
The translocation (6;9), associated with a specific subtype of acute myeloid leukemia, results in the fusion of two genes, dek and can, and the expression of a chimeric, leukemia-specific dek-can mRNA. (1992)

The translocation (6;9) is associated with a specific subtype of acute myeloid leukemia (AML). Previously, it was found that breakpoints on chromosome 9 are clustered in one of the introns of a large gene named Cain (can). cDNA probes derived from the 3' part of can detect an aberrant, leukemia-specific 5.5-kb transcript in bone marrow cells from t(6;9) AML patients. cDNA cloning of this mRNA revealed that it is a fusion of sequences encoded on chromosome 6 and 3' can. A novel gene on chromosome 6 which was named dek was isolated. In dek the t(6;9) breakpoints also occur in one intron. As a result the dek-can fusion gene, present in t(6;9) AML, encodes an invariable dek-can transcript. Sequence analysis of the dek-can cDNA showed that dek and can are merged without disruption of the original open reading frames and therefore the fusion mRNA encodes a chimeric DEK-CAN protein of 165 kDa. The predicted DEK and CAN proteins have molecular masses of 43 and 220 kDa, respectively. Sequence comparison with the EMBL data base failed to show consistent homology with any known protein sequences.
Precise and programmable C:G to G:C base editing in genomic DNA (2020)

Abstract Many genetic diseases are caused by single-nucleotide polymorphisms (SNPs). Base editors can correct SNPs at single-nucleotide resolution, but until recently, only allowed for C:G to T:A and A:T to G:C transition edits, addressing four out of twelve possible DNA base substitutions. Here we developed a novel class of C:G to G:C Base Editors (CGBEs) to create single-base genomic transversions in human cells. Our CGBEs consist of a nickase CRISPR-Cas9 (nCas9) fused to a cytosine deaminase and base excision repair (BER) proteins. Characterization of &gt;30 CGBE candidates and 27 guide RNAs (gRNAs) revealed that CGBEs predominantly perform C:G to G:C editing (up to 90% purity), with rAPOBEC-nCas9-rXRCC1 being the most efficient (mean C:G to G:C edits at 15% and up to 37%). CGBEs target cytosine in WCW, ACC or GCT sequence contexts and within a precise two-nucleotide window of the target protospacer. We further targeted genes linked to dyslipidemia, hypertrophic cardiomyopathy, and deafness, showing the therapeutic potential of CGBE in interrogating and correcting human genetic diseases.
Manufacture of Gene-Modified Human T-Cells with a Memory Stem/Central Memory Phenotype (2014)

Advances in genetic engineering have made it possible to generate human T-cell products that carry desired functionalities, such as the ability to recognize cancer cells. The currently used strategies for the generation of gene-modified T-cell products lead to highly differentiated cells within the infusion product, and on the basis of data obtained in preclinical models, this is likely to impact the efficacy of these products. We set out to develop a good manufacturing practice (GMP) protocol that yields T-cell receptor (TCR) gene-modified T-cells with more favorable properties for clinical application. Here, we show the robust clinical-scale production of human peripheral blood T-cells with an early memory phenotype that express a MART-1-specific TCR. By combining selection and stimulation using anti-CD3/CD28 beads for retroviral transduction, followed by expansion in the presence of IL-7 and IL-15, production of a well-defined clinical-scale TCR gene-modified T-cell product could be achieved. A major fraction of the T-cells generated in this fashion were shown to coexpress CD62L and CD45RA, and express CD27 and CD28, indicating a central memory or memory stemlike phenotype. Furthermore, these cells produced IFNγ, TNFα, and IL-2 and displayed cytolytic activity against target cells expressing the relevant antigen. The T-cell products manufactured by this robust and validated GMP production process are now undergoing testing in a phase I/IIa clinical trial in HLA-A*02:01 MART-1-positive advanced stage melanoma patients. To our knowledge, this is the first clinical trial protocol in which the combination of IL-7 and IL-15 has been applied for the generation of gene-modified T-cell products.
Neurons produce FGF2 and VEGF and secrete them at least in part by shedding extracellular vesicles (2007)

We previously found that neurons are able to affect the ability of brain capillary endothelial cells to form in vitro a monolayer with properties resembling the blood-brain barrier. We then looked, by immunofluorescence and western analysis, for factors, produced by neurons, with the potential to influence growth and differentiation of endothelial cells. In the present paper, we report that neurons produce both vascular endothelial growth factor and fibroblast growth factor 2, two well-known angiogenic factors. More interestingly, we gained evidence that both factors are released by neurons, at least in part, by shedding of extracellular vesicles, that contain beta1 integrin, a membrane protein already known to be part of extracellular vesicles released by tumour cells. Shedding of extracellular vesicles by neurons was also confirmed by scanner electron microscopy.
The protein tyrosine kinase inhibitor SU5614 inhibits FLT3 and induces growth arrest and apoptosis in AML-derived cell lines expressing a constitutively activated FLT3 (2003)

Activating mutations of the protein tyrosine kinase (PTK) FLT3 can be found in approximately 30% of patients with acute myeloid leukemia (AML), thereby representing the most frequent single genetic alteration in AML. These mutations occur in the juxtamembrane (FLT3 length mutations; FLT3-LMs) and the second tyrosine kinase domain of FLT3-TKD and confer interleukin 3 (IL-3)-independent growth to Ba/F3 cells. In the mouse bone marrow transplantation model, FLT3-LMs induce a myeloproliferative syndrome stressing their transforming activity in vivo. In this study, we analyzed the pro-proliferative and antiapoptotic potential of FLT3 in FLT3-LM/TKD-mutation-transformed Ba/F3 cells and AML-derived cell lines. The PTK inhibitor SU5614 has inhibitory activity for FLT3 and selectively induces growth arrest, apoptosis, and cell cycle arrest in Ba/F3 and AML cell lines expressing a constitutively activated FLT3. In addition, the compound reverts the antiapoptotic and pro-proliferative activity of FLT3 ligand (FL) in FL-dependent cells. No cytotoxic activity of SU5614 was found in leukemic cell lines that express a nonactivated FLT3 or no FLT3 protein. At the biochemical level, SU5614 down-regulated the activity of the hyperphosphorylated FLT3 receptor and its downstream targets, signal transducer and activator of (STAT) 3, STAT5, and mitogen-activated protein kinase (MAPK), and the STAT5 target genes BCL-X(L) and p21. Our results show that SU5614 is a PTK inhibitor of FLT3 and has antiproliferative and proapoptotic activity in AML-derived cell lines that endogenously express an activated FLT3 receptor. The selective and potent cytotoxicity of FLT3 PTK inhibitors support a clinical strategy of targeting FLT3 as a new molecular treatment option for patients with FLT3-LM/TKD-mutation(+) AML.
ALK5- and TGFBR2-independent role of ALK1 in the pathogenesis of hereditary hemorrhagic telangiectasia type 2 (2007)

ALK1 belongs to the type I receptor family for transforming growth factor-beta family ligands. Heterozygous ALK1 mutations cause hereditary hemorrhagic telangiectasia type 2 (HHT2), a multisystemic vascular disorder. Based largely on in vitro studies, TGF-beta1 has been considered as the most likely ALK1 ligand related to HHT, yet the identity of the physiologic ALK1 ligand remains controversial. In cultured endothelial cells, ALK1 and another TGF-beta type I receptor, ALK5, regulate angiogenesis by controlling TGF-beta signal transduction, and ALK5 is required for ALK1 signaling. However, the extent to which such interactions between these 2 receptors play a role in pathogenesis of HHT is unknown. We directly addressed these issues in vivo by comparing the phenotypes of mice in which the Alk1, Alk5, or Tgfbr2 gene was conditionally deleted in restricted vascular endothelia using a novel endothelial Cre transgenic line. Alk1-conditional deletion resulted in severe vascular malformations mimicking all pathologic features of HHT. Yet Alk5- or Tgfbr2-conditional deletion in mice, or Alk5 inhibition in zebrafish, did not affect vessel morphogenesis. These data indicate that neither ALK5 nor TGFBR2 is required for ALK1 signaling pertinent to the pathogenesis of HHT and suggest that HHT might not be a TGF-beta subfamily disease.
A new computer program for Rietveld analysis of X-ray powder diffraction patterns (1981)

The Rietveld [J. Appl. Cryst. (1969), 2, 65–71] method of structure refinement from powder diffraction patterns is widely used with neutron data and increasingly so with X-ray data. A computer program for the application of the method with X-ray data, or with neutron nuclear scattering data, has been written ab initio in an effort to make it versatile, user oriented, portable, convenient, and largely self-contained yet reasonably comprehensive. It is of modular construction to facilitate user-desired modifications, one of which may be additions to the choice of four profile functions now included. The program accommodates either one or two wavelengths (e.g. α1 and α2 or λ and λ/2). It permits simultaneous refinement of the structures of two phases and the background.
Synthesis and Characterization of Elastin−Mimetic Hybrid Polymers with Multiblock, Alternating Molecular Architecture and Elastomeric Properties (2009)

We are interested in developing elastin-mimetic hybrid polymers (EMHPs) that capture the multiblock molecular architecture of tropoelastin as well as the remarkable elasticity of mature elastin. In this study, multiblock EMHPs containing flexible synthetic segments based on poly(ethylene glycol) (PEG) alternating with alanine-rich, lysine-containing peptides were synthesized by step-growth polymerization using α,ω-azido-PEG and alkyne-terminated AKA(3)KA (K = lysine, A = alanine) peptide, employing orthogonal click chemistry. The resulting EMHPs contain an estimated three to five repeats of PEG and AKA(3)KA and have an average molecular weight of 34 kDa. While the peptide alone exhibited α-helical structures at high pH, the fractional helicity for EMHPs was reduced. Covalent cross-linking of EMHPs with hexamethylene diisocyanate (HMDI) through the lysine residue in the peptide domain afforded an elastomeric hydrogel (xEMHP) with a compressive modulus of 0.12 MPa when hydrated. The mechanical properties of xEMHP are comparable to a commercial polyurethane elastomer (Tecoflex SG80A) under the same conditions. In vitro toxicity studies showed that while the soluble EMHPs inhibited the growth of primary porcine vocal fold fibroblasts (PVFFs) at concentrations ≥0.2 mg/mL, the cross-linked hybrid elastomers did not leach out any toxic reagents and allowed PVFFs to grow and proliferate normally. The hybrid and modular approach provides a new strategy for developing elastomeric scaffolds for tissue engineering.
Neuroexcitatory Amino Acids and Their Relation to Infarct Size and Neurological Deficit in Ischemic Stroke (1996)

Our results support the excitotoxic activity of glutamate and glycine in patients with cerebral infarction.
A Decision Support System for Finding Research Topic based on Paper Recommendation (2013)

Finding a good research topic is very crucial for a researcher, especially a new researcher, such as PhD student. Generally, a PhD student’s research interest in the beginning is not clear, and he have to spend much time reading a lot of research literatures, step by step, his research preference will become clearer and clearer, and easier to find an advanced research topic in which he is really interested. So, reading a certain number of research literatures is critical for a PhD student to find final research topic. But, which literature should be selected to read? How to quickly clear user preference and determine final research topic by reading fewest literatures? As far as we known, there is no system used to support the user to find research topic. In the paper, a research topic decision support system is originally proposed and creatively developed to help a user to quickly find potential research topic based on iteratively paper recommendation. Starting from user’s initial unclear research preference, through continuous recommending appropriate literatures to the user, then the user read and critiques them by rating until he find final research topic. During the process, since the user read the most appropriate literature in each round, he can quickly find the research topic while spending minimal time.
Characterization of the interactions between MHC class I subunits: a systematic approach for the engineering of higher affinity variants of beta 2-microglobulin. (1998)

Human beta 2m (h beta 2m) binds to murine MHC I molecules with higher affinity than does murine beta2m and therefore can be used as a model system to define and dissect the interactions between beta2m and MHC I heavy chains that promote the stability of the complex. In the present study we compare three-dimensional crystal structures of human and murine MHC I molecules and use functional studies of chimeric human:murine beta 2m variants to define a region of beta2m that is involved in the higher affinity of h beta 2m for murine MHC I heavy chains. Further examination of the three-dimensional structure in this region revealed conformational differences between human and murine beta2m that affect the ability of an aspartic acid residue at position 53 (D53) conserved in both beta 2ms to form an ionic bond with arginine residues at positions 35 and 48 of the heavy chain. Mutation of residue D53 to either asparagine (D53N) or valine (D53V) largely abrogated the stabilizing effects of h beta 2m on murine MHC I expression in a predictable manner. Based on this observation a variant of h beta 2m was engineered to create an ionic bond between the heavy chain and beta 2m. This variant stabilizes cell surface H-2Dd heavy chains to a greater extent than wild-type h beta 2m. Studying these interactions in light of the growing database of MHC I crystal structures should allow the rational design of higher affinity h beta 2m variants for use in novel peptide-based vaccines capable of inducing cell-mediated immune responses to viruses and tumors.
Typhoid fever vaccines: a meta-analysis of studies on efficacy and toxicity (1998)

Whole cell vaccines are more effective than the Ty21a and Vi vaccines but are more frequently associated with adverse events. Whether the added efficacy of the whole cell vaccines outweighs their toxicity will depend on the setting in which vaccination is used.
Ionisation behaviour and solution properties of the potassium‐channel blocker ShK toxin (1998)

The effects of pH, temperature and polypeptide concentration on the solution structure and side chain interactions of ShK toxin, a potassium-channel-blocking polypeptide from the sea anemone Stichodactyla helianthus, have been investigated by means of one-dimensional and two-dimensional 1H-NMR spectroscopy. Resonance assignments have been obtained for most protons in the molecule, and for the alpha and beta carbon atoms. The lack of concentration dependence of the 1H chemical shifts and linewidths indicates that self-association is not significant and cannot account for the sheet-like structure near the N terminus. The structure is stable to high temperature, showing little change even at 353 K. This stability allowed backbone-amide temperature coefficients to be interpreted, and the correlation of these values with hydrogen bonds observed in the structures and with solvent exchange rates is discussed. pKa values have been measured for Asp5, His19 and Tyr23, and the contributions to these pKa values from other residues investigated using the analogues R11Q (denoting substitution of Argll with Gln), R11E, H19K, K22A, Y23A and K30A. These results show that Asp5 (pKa 2.8) makes an electrostatic interaction with Lys30, which may be partially responsible for the importance of these side chains in the folding of synthetic toxin. The phenolic pKa of Tyr23 is reduced to 8.7 in the native toxin, as a result of interactions with the positively charged side chains of Arg11 and to a lesser extent Lys22. Several hydrogen bonds between the Arg11 guanidino group and the Tyr23 phenolic group are found in the solution structures. As these three residues are implicated in the tight binding of ShK toxin to the T-lymphocyte voltage-gated potassium channel Kv1.3, their close interactions should be taken into account in models of binding of this toxin to the pore and vestibule of this and other potassium channels.
Phase I Clinical Trial of Oral Curcumin (2004)

Curcumin, a polyphenolic antioxidant derived from a dietary spice, exhibits anticancer activity in rodents and in humans. Its efficacy appears to be related to induction of glutathione S-transferase enzymes, inhibition of prostaglandin E(2) (PGE(2)) production, or suppression of oxidative DNA adduct (M(1)G) formation. We designed a dose-escalation study to explore the pharmacology of curcumin in humans. Fifteen patients with advanced colorectal cancer refractory to standard chemotherapies consumed capsules compatible with curcumin doses between 0.45 and 3.6 g daily for up to 4 months. Levels of curcumin and its metabolites in plasma, urine, and feces were analyzed by high-pressure liquid chromatography and mass spectrometry. Three biomarkers of the potential activity of curcumin were translated from preclinical models and measured in patient blood leukocytes: glutathione S-transferase activity, levels of M(1)G, and PGE(2) production induced ex vivo. Dose-limiting toxicity was not observed. Curcumin and its glucuronide and sulfate metabolites were detected in plasma in the 10 nmol/L range and in urine. A daily dose of 3.6 g curcumin engendered 62% and 57% decreases in inducible PGE(2) production in blood samples taken 1 hour after dose on days 1 and 29, respectively, of treatment compared with levels observed immediately predose (P < 0.05). A daily oral dose of 3.6 g of curcumin is advocated for Phase II evaluation in the prevention or treatment of cancers outside the gastrointestinal tract. PGE(2) production in blood and target tissue may indicate biological activity. Levels of curcumin and its metabolites in the urine can be used to assess general compliance.
PROTEIN DISPERSIBILITY OF SPRAY‐DRIED WHOLE SOYBEAN MILK BASE: EFFECT OF PROCESSING VARIABLES (1977)

ABSTRACT A full‐fat soybean milk base was produced by grinding blanched soybean cotyledons with water, heating, and homogenizing the resulting slurry (Nelson et al., JFS 41(1): 57, 1976). The soy milk base was spray dried using a Necro‐Niro portable spray drier. The protein dispersibility index (PDI) of the spray dried powder was altered by changing the processing conditions used during manufacture or spray drying. The PDI of the spray‐dried soy milk base was higher when ammonium bicarbonate rather than sodium bicarbonate was used for blanching the cotyledons. The PDI of the spraydried powder increased when the soybean slurry was homogenized at high pressures and when sodium bisulfite was added to the soy milk base before drying. Sodium bisulfite was the most effective single treatment for increasing PDI. Increasing the pH of the soy milk base to 9 before spray drying increased the PDI of the soy powder. Desludging the soy milk base did not increase the PDI. The best PDI obtained was 72.
A noise-reduction GWAS analysis implicates altered regulation of neurite outgrowth and guidance in autism (2011)

As statistical noise is likely to particularly affect studies of complex disorders, where genetic heterogeneity or interaction between genes may confound the ability to detect association, GWAS-NR offers a powerful method for prioritizing regions for follow-up studies. Applying this method to autism datasets, GWAS-NR analysis indicates that a large subset of genes involved in the outgrowth and guidance of axons and dendrites is implicated in the aetiology of autism.
Garden Water Use in Utah (2002)

The goal of garden irrigation is to maintain yield and quality by replacing water lost to the atmosphere from the soil by evaporation, and from leaf surfaces by transpiration. The combination of evaporation and transpiration is referred to as evapotranspiration (Et), or simply water use. Garden water use is presented in units of inches of water per day, week or month.
Application of quadrature mirror filters to split band voice coding schemes (2005)

This paper deals with applications of Quadrature Mirror Filters (QMF) to coding of voice signal in sub-bands. Use of QMF's enables to avoid the aliasing effects due to samples decimation when signal is split into sub-bands. Each sub-band is then coded independently with use of Block Companded PCM (BCPCM) quantizers. Then a variable number of bits is allocated to each sub-band quantizer in order to take advantage of the relative perceptual effect of the quantizing error. The paper is organized as follows: - First, splitting in two sub-bands with QMF's is analysed. -Then, a general description of a splitband voice coding scheme using QMF's is made. -Finally, two coding schemes are considered, operating respectively at 16 KBps and 32 KBps. Averaged values of S/N performances are given when encoding both male and female voices. Comparisons are made with conventional BCPCM and CCITT A-Law. Taped results will be played at the conference.
Paracoccus seriniphilus sp. nov., an l-serine-dehydratase-producing coccus isolated from the marine bryozoan Bugula plumosa (2003)

A novel marine Gram-negative, non-motile, non-spore-forming, aerobic bacterium, associated with the bryozoan Bugula plumosa, was isolated in a screening programme for strains containing enzymes able to convert the amino acid L-serine. Strain MBT-A4T produced L-serine dehydratase and was able to grow on L-serine as the sole carbon and nitrogen source. The nearest phylogenetic neighbour was Paracoccus marcusii, as determined by 16S rDNA sequence analysis (97.8% similarity). The DNA-DNA reassociation value obtained for Paracoccus marcusii DSM11574T and MBT-A4T was 32.6%. The major ubiquinone was 0-10. Based on genotypic, chemotaxonomic and physiological characteristics, a new species of the genus Paracoccus is proposed, Paracoccus seriniphilus sp. nov., the type strain being strain MBT-A4T (=DSM 14827T =CIP 107400T).