gebhart/patrepeval huggingface dataset:
Comparative sequence analysis of American, European and Asian isolates of viruses in the genus Coltivirus. (1998)

In this study, the basis for the classification of virus isolates grouped within the genus Coltivirus, family Reoviridae, is discussed. Sequences of dsRNA segments from American (segments 9-12), European (segment 12) and Asian (segments 7-12) isolates were characterized and polythetic criteria were defined for their taxonomic classification. These criteria (including sequence analysis) permitted the different species to be distinguished and classified into two groups. In both groups, subgroups were defined according to the degree of homology between the genomic sequences. American and European isolates are classified within group A, which includes subgroups A1 (Colorado tick fever virus species) and A2 (Eyach virus species). Asian isolates are classified in group B, which includes subgroups B1 (JKT-7075 virus species) and B2 (JKT-6423 virus species). The proteins encoded by the sequenced genomic segments were analysed. This allowed the identification of dsRNA binding domains in the proteins encoded by segment 8 of subgroup B1 isolates and segment 12 of subgroup B2 isolates. A conserved pattern of amino acids in segment 7 of group B isolates matched sequences found in the catalytic domains of protein kinases.
Intercalating nucleic acids containing insertions of 1-O-(1-pyrenylmethyl)glycerol: stabilisation of dsDNA and discrimination of DNA over RNA (2002)

We have studied hybridisation affinities and fluorescence behaviour of intercalator-modified oligonucleotides. The phosphoramidite of (S)-1-O-(4, 4'-dimethoxytriphenylmethyl)-3-O-(1-pyrenylmethyl)glycerol, an intercalating pseudo-nucleotide (IPN), was synthesised and by standard methods inserted into 7mer and 13mer oligodeoxyribonucleotides (ODNs) to generate intercalating nucleic acids (INAs). INAs showed greatly increased affinity for complementary single-stranded DNA (ssDNA), as determined by a thermal stabilisation of the formed DNA/INA duplex of up to 10.9 degrees C per modification when the IPN was added as a dangling end and up to 6.7 degrees C per modification when the IPN was inserted as a bulge. There was a positive stabilisation effect of the formed DNA/INA duplex on introducing a second IPN in the INA strand, when the two IPNs were separated by at least 1 bp. The effect is more pronounced the larger the separation of the two IPNs. Contrary to the enhanced affinity for ssDNA, the IPNs lower the affinity for complementary single-stranded RNA (ssRNA), giving rise to a difference in melting temperature of up to 25.8 degrees C for two IPN insertions in an RNA/INA duplex when compared with the corresponding DNA/INA duplex. In this way INA is able to discriminate ssDNA over ssRNA with identical sequences. Fluorescence measurements show a stronger interaction of the pyrene moiety with DNA than with RNA, indicating intercalation as the stabilising factor in DNA/INA duplexes.
Peptide repeats in a mussel glue protein: theme and variations (1985)

The adhesive protein from Mytilus edulis contains 75-80 closely related, repeated peptide sequences in its primary structure. These peptides can be resolved following digestion with trypsin by reversed-phase high-pressure liquid chromatography. The most frequently repeated sequence is the decapeptide Ala-Lys-Pro-Ser-Tyr-Hyp-Hyp-Thr-Dopa-Lys (peptide E). Variations of this occur in peptides B with Hyp-3 and Dopa-5, C with Dopa-5, and D with Hyp-3, respectively. Lesser amounts of hexapeptides (A and B') that are lacking residues 4-7 also occur. Peptide A has the sequence Ala-Lys-Pro-Thr-Dopa-Lys, whereas B' contains Tyr instead of Dopa. 4-Hydroxyproline occurs at positions 3 and 7 and occasionally at position 6 of the decapeptide; 3-hydroxyproline occurs only at position 6. Adhesiveness of the protein may be related to the repetition of Dopa residues, the catecholic moiety of which has strong hydrogen-bonding and metal-liganding capabilities.
RNA Aptamer Therapy for Vaso-Occlusion in Sickle Cell Disease (2011)

Patients with sickle cell disease (SCD) often suffer painful vaso-occlusive episodes caused in part by the adhesion of sickle erythrocytes (SS-RBC) to the vascular endothelium. To investigate inhibition of SS-RBC adhesion as a possible treatment for vaso-occlusion, 2 adhesion molecules, α(v)β(3) and P-selectin, were targeted by high-affinity RNA aptamers. An in vitro flow chamber assay was used to test the antiadhesion activity of α(v)β(3) aptamer clone 17.16. Human SS-RBC were passed across a confluent monolayer of thrombin-stimulated human umbilical vein endothelial cells (HUVEC) at a constant rate. α(v)β(3) aptamer reduced SS-RBC adhesion to activated endothelial cells to the level seen with untreated HUVEC. An aptamer reactive with complement component 8 was used as a negative control and exerted no inhibition, confirming the specificity of α(v)β(3) aptamer (P=0.04). At 2 dyn/cm(2) shear stress, 30 nM α(v)β(3) aptamer showed maximal effect in decreasing SS-RBC adhesion to HUVEC. The antiadhesive activity of the P-selectin aptamer clone PF377 was also tested using HUVEC pretreated with IL-13 to upregulate expression of P-selectin as seen in activated endothelial cells. At 1 dyn/cm(2) shear stress, 60 nM of P-selectin aptamer had antiadhesion activity similar to heparin, a known inhibitor of SS-RBC adhesion to P-selectin. A negative control did not prevent adhesion (P=0.05). These data show the potential utility of aptamers to block endothelial adhesion molecules to prevent or treat vaso-occlusion in SCD.
A role for p75 neurotrophin receptor in the control of apoptosis‐driven hair follicle regression (2000)

To examine the mechanisms that underlie the neurotrophin-induced, apoptosis-driven hair follicle involution (catagen), the expression and function of p75 neurotrophin receptor (p75NTR), which is implicated in apoptosis control, were studied during spontaneous catagen development in murine skin. By RT-PCR, high steady-state p75NTR mRNA skin levels were found during the anagen-catagen transition of the hair follicle. By immunohistochemistry, p75NTR alone was strongly expressed in TUNEL+/Bcl2- keratinocytes of the regressing outer root sheath, but both p75NTR and TrkB and/or TrkC were expressed by the nonregressing TUNEL-/Bcl2+ secondary hair germ keratinocytes. To determine whether p75NTR is functionally involved in catagen control, spontaneous catagen development was compared in vivo between p75NTR knockout (-/-) and wild-type mice. There was significant catagen retardation in p75NTR knockout mice as compared to wild-type controls (P<0.05). Instead, transgenic mice-overexpressing NGF (promoter: K14) showed substantial acceleration of catagen (P<0.001). Although NGF, brain-derived neurotrophic factor (BDNF), and neurotrophin 3 (NT-3) accelerated catagen in the organ-cultured skin of C57BL/6 mice, these neurotrophins failed to promote catagen development in the organ-cultured p75NTR null skin. These findings suggest that p75NTR signaling is involved in the control of kerotinocyte apoptosis during catagen and that pharmacological manipulation of p75NTR signaling may prove useful for the treatment of hair disorders that display premature entry into catagen.
Flooding and Plant Growth (2002)

This Special Issue is based on the 7th Conference of the International Society for Plant Anaerobiosis (ISPA), held in
Integrated MEMS for pressure transponder (2002)

We propose the integrated MEMS technology for the purpose of pressure telemetry. This consists of the digitized pressure sensor, micro mechanical switch and interface circuit. The micro mechanical switch is used for the power saving, which is closed when external rf signal is applied. The digitized pressure sensor is a capacitive type sensor which has a sensing capacitor and 8 conversion capacitors and is read out by the interface circuit integrated on the same chip. The interface circuit contains the control clock generation circuit, weight making circuit and output stage. The integrated MEMS was fabricated and the fabricated micro mechanical switch has 43 V of threshold voltage and 100 /spl Omega/ of ON resistance.
Purification and properties of shikimate kinase II from Escherichia coli K-12 (1986)

Shikimate kinase II was purified to near homogeneity from an Escherichia coli strain which overproduced the enzyme. The apparent Km of this isoenzyme for shikimate was 200 microM, and for ATP it was 160 microM. The Km for shikimate is approximately 100-fold lower than the Km of shikimate kinase I, suggesting that shikimate kinase II is the isoenzyme normally functioning in aromatic biosynthesis. Shikimate kinase II is dependent on metal ions for activity.
Does rheumatoid arthritis remit during pregnancy and relapse postpartum?: Results from a nationwide study in the United Kingdom performed prospectively from late pregnancy (1999)

This, the largest prospective study of the influence of pregnancy on RA activity, has demonstrated widespread variability in disease response.
A limited set of SH2 domains binds BCR through a high-affinity phosphotyrosine-independent interaction. (1992)

SH2 (src homology region 2) domains are implicated in protein-protein interactions involved in signal transduction pathways. Isolated SH2 domains bind proteins that are tyrosine phosphorylated. A novel, phosphotyrosine-independent binding interaction between BCR, the Philadelphia chromosome breakpoint cluster region gene product, and the SH2 domain of its translocation partner c-ABL has recently been reported. We have examined the ability of additional SH2 domains to bind phosphotyrosine-free BCR and compared this with their ability to bind tyrosine-phosphorylated c-ABL 1b. Of 11 individual SH2 domains examined, 8 exhibited relatively high affinity for c-ABL 1b, whereas only 4 exhibited relatively high affinity for BCR. Binding of tyrosine-phosphorylated c-ABL 1b by the relatively high-affinity ABL and ARG SH2 domains was quantitatively analyzed, and equilibrium dissociation constants for both interactions were estimated to be in the range of 5 x 10(-7) M. The ABL SH2 domain exhibited relatively high affinity for phosphotyrosine-free BCR as well; however, this interaction appears to be about two orders of magnitude weaker than binding of tyrosine-phosphorylated c-ABL 1b. The ARG SH2 domain exhibited relatively weak affinity for BCR and was determined to bind about 10-fold less strongly than the ABL SH2 domain. The ABL and ARG SH2 domains differ by only 10 of 91 amino acids, and the substitution of ABL-specific amino acids into either the amino- or carboxy-terminal half of the ARG SH2 domain was found to increase its affinity for BCR. We discuss these results in terms of a model which has been proposed for peptide binding by class I histocompatibility glycoproteins.
Electroporation-Based Technologies for Medicine: Principles, Applications, and Challenges (2014)

When high-amplitude, short-duration pulsed electric fields are applied to cells and tissues, the permeability of the cell membranes and tissue is increased. This increase in permeability is currently explained by the temporary appearance of aqueous pores within the cell membrane, a phenomenon termed electroporation. During the past four decades, advances in fundamental and experimental electroporation research have allowed for the translation of electroporation-based technologies to the clinic. In this review, we describe the theory and current applications of electroporation in medicine and then discuss current challenges in electroporation research and barriers to a more extensive spread of these clinical applications.
Musculin/MyoR is expressed in kidney side population cells and can regulate their function (2005)

Musculin/MyoR is a new member of basic helix-loop-helix transcription factors, and its expression is limited to skeletal muscle precursors. Here, we report that musculin/MyoR is expressed in adult kidney side population (SP) cells and can regulate their function. SP phenotype can be used to purify stem cell-rich fractions. Microarray analysis clarified that musculin/MyoR was exclusively expressed in kidney SP cells, and the cells resided in the renal interstitial space. Musculin/MyoR-positive cells were decreased in acute renal failure, but infusion of kidney SP cells increased musculin/MyoR-positive cells and improved renal function. Kidney SP cells in reversible acute renal failure expressed a high level of renoprotective factors and leukemia inhibitory factor (LIF), but not in irreversible chronic renal failure. In cultured kidney SP cells, LIF stimulated gene expression of renoprotective factors, and down-regulation of musculin/MyoR augmented LIF-induced gene expression. Our results suggest that musculin/MyoR may play important roles not only in developmental processes but also in regenerative processes in adult tissue.
Effect of sodium butyrate on alkaline phosphatase in HRT-18, a human rectal cancer cell line. (1982)

Treatment of the human rectal cancer cell line HRT-18 with sodium butyrate caused a reversible elevation of alkaline phosphatase activity which was inhibited by cycloheximide and actinomycin D. The alkaline phosphatase in untreated cells was heat stable at neutral pH and inhibited by phenylalanine but not by homoarginine, and 80% of the enzyme activity was precipitated by antibody against human term-placental enzyme. Following butyrate treatment, the enzyme became more sensitive to all the inhibitors tested and more heat stable, compared to the enzyme in control cells. In addition, the butyrate-induced enzyme could be completely precipitated by anti-placental alkaline phosphatase antibody. The electrophoretic pattern of the butyrate-induced enzyme was different from that of control cells. Control HRT-18 cells contained a butyrate-insensitive heat-labile alkaline phosphatase component with an electrophoretic mobility similar to the enzyme from human colon cancer tissues. The alkaline phosphatase from four human colon cancer tissues was of the early placental form, while the enzyme from human normal mucosa was of the intestinal type.
Ciprofibrate increases paraoxonase activity in patients with metabolic syndrome (2006)

Three months of treatment with ciprofibrate favourably affected the lipid profile, increased LDL resistance to oxidation and improved antioxidant status by increasing serum paraoxonase activity in these patients.
Host-Pathogen Interactions (1981)

An elicitor of phytoalexin accumulation (endogenous elicitor) is solubilized from purified cell walls of soybean (Glycine max [L.] Merr., cv. Wayne) by extracting the walls with hot water or by subjecting the walls to partial acid hydrolysis. The endogenous elicitor obtained from soybean cell walls binds to an anion exchange resin. The elicitor-active material released from the resin contains oligosaccharides rich in galacturonic acid; small amounts of rhamnose and xylose are also present. The preponderance of galacturonic acid in the elicitor-active fragments suggests that the elicitor is, in fact, a fragment of a pectic polysaccharide. This possibility is supported by the observation that treatment of the wall fragments with a highly purified endopolygalacturonase destroys their ability to elicit phytoalexin accumulation. This observation, together with other evidence presented in this paper, suggests that galacturonic acid is an essential constituent of the elicitor-active wall fragments. Endogenous elicitors were also solubilized by partial hydrolysis from cell walls of suspension-cultured tobacco, sycamore, and wheat cells.
TauGene Mutation K257T Causes a Tauopathy Similar to Pick's Disease (2000)

Exonic and intronic mutations in Tau cause neurodegenerative syndromes characterized by frontotemporal dementia and filamentous tau protein deposits. Here we describe a K257T missense mutation in exon 9 of Tau. The proband, a 47-yr-old male, presented with severe personality changes followed by semantic memory loss. A diagnosis of Pick's disease was made. The symptoms progressed until death at age 51. The proband's brain showed a marked frontotemporal atrophy that was most pronounced in the temporal lobes. Numerous tau-immunoreactive Pick bodies were present in the neocortex and the hippocampal formation, as well as in some subcortical brain regions. Their appearance and staining characteristics were indistinguishable from those of sporadic Pick's disease. Diffuse staining for hyperphosphorylated tau was also observed in some nerve cell bodies. Immunoblot analysis of sarkosyl-insoluble tau showed 2 major bands of 60 and 64 kDa and 2 very minor bands of 68 and 72 kDa. Upon dephosphorylation, these bands resolved into 6 bands consisting of 3-repeat and 4-repeat tau isoforms, with an overall preponderance of 3-repeat tau. Isolated tau filaments were narrow, irregularly twisted ribbons. Biochemically, recombinant tau proteins with the K257T mutation showed a reduced ability to promote microtubule assembly, suggesting that this may be the primary effect of the mutation. In addition, the K257T mutation was found to stimulate heparin-induced assembly of 3-repeat tau into filaments. Taken together, the present findings indicate that the K257T mutation in Tau can cause a dementing condition similar to Pick's disease.
Year-round raspberry production (2013)

Raspberry is grown in many parts of the world with annual production estimated at 411,000 tonnes. A temperature sensitive fruit, most are produced in the cooler countries of Europe. However, raspberry production is increasing in warmer climates with year-round production in greenhouses.
Cyclooxygenase-2 Expression Inhibits Trophic Withdrawal Apoptosis in Nerve Growth Factor-differentiated PC12 Cells (2000)

Cyclooxygenase-2 (Cox-2), an enzyme responsible for catalyzing the committed step in prostanoid biosynthesis, is the product of an immediate early gene capable of being up-regulated by diverse stimuli. Significantly Cox-2 mRNA is absent from rat pheochromocytoma (PC12) cells, both basally and following stimulation with a range of agonists. Using PC12 cells engineered to stably express isopropyl-1-thio-beta-D-galactopyranoside-inducible Cox-2 (PCXII-4), we have investigated the putative effects of Cox-2 expression on differentiation, proliferation, and trophic withdrawal apoptosis. Cox-2 bioactivity had no effect on nerve growth factor-induced differentiation, epidermal growth factor-induced proliferation, or aromatic L-amino acid decarboxylase expression. However, trophic withdrawal apoptosis, induced by the removal of nerve growth factor following differentiation, was markedly reduced in the PCXII-4 when compared with control cells, as assessed by annexin V staining, DNA laddering, and Hoechst 33258 staining. The specificity of this effect was confirmed using two pharmacologically distinct nonsteroidal anti-inflammatory drugs, indomethacin and NS398. Investigations showed that the activity of the pro-apoptotic protease caspase-3 was reduced in PCXII cells. This study demonstrates that Cox-2-derived prostaglandins exert cytoprotective effects in trophic factor withdrawal apoptosis and provides evidence that this is, at least in part, due to suppression of caspase-3 activity.
Induction of tubuloreticular inclusions in human lymphoma cells (Raji line) related to S-phase treatment with halogenated pyrimidines. (1977)

Summary Formation of tubuloreticular inclusions (TRI) within the endoplasmic reticulum was initiated in human lymphoma cells (Raji line) by exposure of synchronized cultures to 5-bromo-2′-deoxyuridine (BUdR) for all or portions of a single S phase. The TRI were detected by electron microscopy as early as 36 hr after addition of 260 µm BUdR. By 72 hr, thin-section counts of TRI reached a maximum at circa 30% of cell cross-sections, which was estimated to represent no less than one TRI per two whole cells. Although the numbers of TRI depended upon the concentration of halogenated pyrimidine, cell division was not prerequisite to their appearance, and exposure of the cells to BUdR for repeated cycles of DNA synthesis did not increase the maximal level. These results were consistent with a unifilar dominance and modified regulation of gene expression, rather than transcription of an altered DNA. Raji cells exposed to equimolar thymidine as controls to each experiment, as well as untreated Raji cells, were uniformly negative for TRI. A relation of TRI induction to metabolism of BUdR was indicated by competitive inhibition with thymidine and lack of response in a subline selected for BUdR resistance. There was no evidence for previously postulated relationships of TRI to myxovirus infection or IgG production. In vitro induction of TRI can serve as an experimental model for further investigations into the significance of TRI found in lymphocytes of patients with systemic immune diseases or neoplasms.
ASCO 2009 Report: Lung Cancer (2009)

Adjuvant vs. Neoadjuvant Chemotherapy for Lung CancerDespite undergoing complete resection surgery, many patients with stage I and II non–small-cell
Synthesis and reactivity of 1,2,4‐triazolo[1,5‐c]quinazolines (1999)

Abstract The preparation of 1,2,4‐triazolo[1,5‐ c ]quinazolines 4a‐d , 5 , 8a‐d by cyclocondensation of 1a‐c with carboxylic acids and carboxylic anhydrides, respectively, is described. By different pathways, the 5‐thioxo‐5,6‐dihydro‐1,2,4‐triazolo[1,5‐ c ]quinazolines 4a‐d react with hydrazine hydrate or amines with the formation of 5‐substituted 1,2,4‐triazolo[1,5‐ c ]quinazolines 9 and 10a‐d . Cyclocondensation of 9 with carboxylic acids, carboxylic anhydrides, and nitrous acid, respectively, leads to the new anellated heterocycles bis‐1,2,4‐triazolo[4,3‐ a :1,5‐ c ]quinazoline 13 and tetrazolo [1,5‐ a ]‐1,2,4‐triazolo[1,5‐ c ]quinazoline ( 14 ).
Reversal of tumoral immune resistance by inhibition of tryptophan 2,3-dioxygenase (2012)

Tryptophan catabolism mediated by indoleamine 2,3-dioxygenase (IDO1) is an important mechanism of peripheral immune tolerance contributing to tumoral immune resistance, and IDO1 inhibition is an active area of drug development. Tryptophan 2,3-dioxygenase (TDO) is an unrelated hepatic enzyme that also degrades tryptophan along the kynurenine pathway. Here, we show that enzymatically active TDO is expressed in a significant proportion of human tumors. In a preclinical model, TDO expression by tumors prevented their rejection by immunized mice. We developed a TDO inhibitor, which, upon systemic treatment, restored the ability of mice to reject TDO-expressing tumors. Our results describe a mechanism of tumoral immune resistance based on TDO expression and establish proof-of-concept for the use of TDO inhibitors in cancer therapy.