gebhart/patrepeval huggingface dataset:
Development of necrosis and activation of disease resistance in transgenic tobacco plants with severely reduced catalase levels (1997)

Numerous studies argue that salicylic acid (SA) is an important component of the plant signal transduction pathway(s) leading to disease resistance. The discovery that the SA-binding protein is a catalase, whose activity is blocked by SA, led to the proposal that one of SA's modes of action is to inhibit this H2O2-degrading enzyme and thus elevate H2O2 levels. To test this model, an attempt was made to mimic the action of SA by reducing the synthesis of catalase using antisense RNA technology. Analyses of transgenic tobacco plants that expressed the tobacco catalase 1 (cat1) or catalase 2 (cat2) gene in an antisense orientation indicate that there is no correlation between modest to high levels of reduction in catalase activity and activation of plant defenses such as pathogenesis-related (PR)-1 protein synthesis. However, three independent antisense catalase transgenic plants (ASCAT1 Nos 16, 17, and 28), which exhibited the most severe reduction in catalase activity (approximately 90% or more), developed chlorosis or necrosis on some of their lower leaves. These same leaves accumulated very high levels of PR-1 proteins and showed enhanced resistance to tobacco mosaic virus. Necrosis and elevated SA, which appear to result from severe depression of catalase levels, may be responsible for the induction of these defense responses.
Redesigning protein pKavalues (2006)

The ability to re-engineer enzymatic pH-activity profiles is of importance for industrial applications of enzymes. We theoretically explore the feasibility of re-engineering enzymatic pH-activity profiles by changing active site pK(a) values using point mutations. We calculate the maximum achievable DeltapK(a) values for 141 target titratable groups in seven enzymes by introducing conservative net-charge altering point mutations. We examine the importance of the number of mutations introduced, their distance from the target titratable group, and the characteristics of the target group itself. The results show that multiple mutations at 10A can change pK(a) values up to two units, but that the introduction of a requirement to keep other pK(a) values constant reduces the magnitude of the achievable DeltapK(a). The algorithm presented shows a good correlation with existing experimental data and is available for download and via a web server at http://enzyme.ucd.ie/pKD.
Expression of the mRNA and Protein of LOX-1 Induced by Oxidized LDL (2004)

ObjectsOxidized LDL plays an important role in pathogenesis and development of atherosclerosis. In this study, whether the mRNA and protein of LOX-1(lectin-like oxidized LDL receptor) can be induced by oxidized LDL was observed. MethodsHuman umbilical vein endothelial cells were incubated with different concentration (20, 40, 60, 80 mg/L) of oxidized LDL for 24 h or with 40 mg/L oxidized LDL for different periods (0, 3, 6, 12, 24 h). LOX-1 mRNA was detected by quantitative reverse transcription polymerase chain reaction and LOX-1 protein was examined by cell-based enzyme linked immunosorbant assay.Results The levels of mRNA and protein of LOX-1 increased after cells were incubated with 20 mg/L oxidized LDL (P0.01) and reached the maximum at 40 mg/L oxidized LDL, and then declined. Otherwise in the same concentration of 40 (mg/L) oxidized LDL the expression of both mRNA and protein of LOX-1 were progressively increased with the incubation time from 0h to 24h (P0.01).ConclusionsOxidized LDL upregulates the expression of the mRNA and protein of LOX-1 in a concentration- and time-dependent manner and LOX-1 is likely to play an important role in pathogenesis and development of atherosclerosis.
A prospective longitudinal population‐based study of clinical miscarriage in an urban Swedish population (2007)

Clinical miscarriage constituted 12% of all pregnancies, and one in four women who had been pregnant up to 39 years of age had experienced a miscarriage. Three or more miscarriages were experienced by 7.4%. The occurrence of a miscarriage was not influenced by the order of the pregnancy.
MicroRNA-124a Regulates Foxa2 Expression and Intracellular Signaling in Pancreatic β-Cell Lines (2007)

MicroRNAs (miRNAs) are short non-coding RNAs that have been implicated in fine-tuning gene regulation, although the precise roles of many are still unknown. Pancreatic development is characterized by the complex sequential expression of a gamut of transcription factors. We have performed miRNA expression profiling at two key stages of mouse embryonic pancreas development, e14.5 and e18.5. miR-124a2 expression was strikingly increased at e18.5 compared with e14.5, suggesting a possible role in differentiated beta-cells. Among the potential miR-124a gene targets identified by biocomputation, Foxa2 is known to play a role in beta-cell differentiation. To evaluate the impact of miR-124a2 on gene expression, we overexpressed or down-regulated miR-124a2 in MIN6 beta-cells. As predicted, miR-124a2 regulated Foxa2 gene expression, and that of its downstream target, pancreatic duodenum homeobox-1 (Pdx-1). Foxa2 has been described as a master regulator of pancreatic development and also of genes involved in glucose metabolism and insulin secretion, including the ATP-sensitive K(+) (K(ATP)) channel subunits, Kir6.2 and Sur-1. Correspondingly, miR-124a2 overexpression decreased, and anti-miR-124a2 increased Kir6.2 and Sur-1 mRNA levels. Moreover, miR-124a2 modified basal and glucose- or KCl-stimulated intracellular free Ca(2+) concentrations in single MIN6 and INS-1 (832/13) beta-cells, without affecting the secretion of insulin or co-transfected human growth hormone, consistent with an altered sensitivity of the beta-cell exocytotic machinery to Ca(2+). In conclusion, whereas the precise role of microRNA-124a2 in pancreatic development remains to be deciphered, we identify it as a regulator of a key transcriptional protein network in beta-cells responsible for modulating intracellular signaling.
Natural Product Chemistry: A mechanistic, biosynthetic and ecological approach (1997)

Chemical ecology carbohydrates and primary metabolites the shikimic acid pathway the polyketide pathway the mevalonic acid pathway the terpenes amino acids, peptides and proteins the alkaloids N-hetroaromatics answers to problems.
Chemical reduction of 3-oxo and unsaturated groups in fatty acids of diphosphoryl lipid A from the lipopolysaccharide of Rhodopseudomonas sphaeroides. Comparison of biological properties before and after reduction. (1991)

Unlike the diphosphoryl lipid A (DPLA) derived from toxic lipopolysaccharide of Escherichia coli and Salmonella strains, the DPLA from nontoxic lipopolysaccharide of Rhodopseudomonas sphaeroides ATCC 17023 is biologically inactive. This could be due to the presence of 3-oxotetradecanoic and delta 7-tetradecenoic acids. These two fatty acids in R. sphaeroides DPLA were catalytically reduced in platinum oxide/H2 to the 3-hydroxy and saturated fatty acids, respectively. The biologically active E. coli DPLA was also treated with platinum oxide/H2, but as expected, the reduction step did not change the structure. These two preparations were then compared with the untreated samples for biological activity in three select in vitro assays. Over a range of 0.01-100 ng/ml, both normal and reduced DPLA from R. sphaeroides were inactive in priming phorbol myristate acetate-stimulated superoxide anion release in human alveolar macrophages. Over a range of 10-10(3) ng/ml, both samples failed to induce tumor necrosis factor in the RAW 264.7 murine macrophage cell line. The reduced DPLA marginally activated 70Z/3 pre-B cells at concentrations of 0.1-30 micrograms/ml. In every case, both normal and platinum oxide/H2-treated E. coli DPLA were biologically active. These results indicate that the lack of biological activity of R. sphaeroides DPLA is not due to the presence of 3-oxo and unsaturated fatty acids, but rather to one or more of the following: (i) presence of only five fatty acyl groups (compared to six in active lipid A); (ii) presence of 3-hydroxydecanoic acids (rather than 3-hydroxytetradecanoic, in active lipid A); (iii) greater variation in size of the fatty acids.
Gellan gum as a substitute for agar in leptospiral media (1986)

An albumin polysorbate semisolid medium (Ellinghausen McCullough Johnson Harris medium) gelled with gellan gum (Gelrite; Kelco Div., Merck & Co., Inc.) compared favorably with conventional agar media for the cultivation of both pathogenic and saprophytic leptospires. The gellan gum medium supported the growth of all 18 leptospiral strains studied which included an array of serovars with various fastidious growth characteristics. Gellan gum medium was also used advantageously as a long-term maintenance medium; 9- to 12-month-old cultures still contained viable organisms. The colonial growth in gellan gum plating medium of six representative strains was consistent with previously described colonial growth on agar plating media. In addition, gellan gum medium appeared to be an excellent medium for the recovery of leptospires from the blood, liver, and kidneys of hamsters experimentally infected with a virulent Leptospira interrogans serovar bataviae strain. As few as 1 to 10 organisms in the infective tissue could be recovered in semisolid Ellinghausen McCullough Johnson Harris-gellan gum medium. The antigenicity did not appear to be affected by growth in gellan gum medium. The hamster-virulent strain of L. interrogans serovar bataviae isolated from a moribund hamster maintained its virulence after 10 sequential passages in gellan gum medium. Gellan gum medium can be a valuable adjunct to currently used cultural procedures.
A Small In Vitro Fermentation Model for Screening the Gut Microbiota Effects of Different Fiber Preparations (2019)

The development of prebiotic fibers requires fast high-throughput screening of their effects on the gut microbiota. We demonstrated the applicability of a mictotiter plate in the in vitro fermentation models for the screening of potentially-prebiotic dietary fibers. The effects of seven rye bran-, oat- and linseed-derived fiber preparations on the human fecal microbiota composition and short-chain fatty acid production were studied. The model was also used to study whether fibers can alleviate the harmful effects of amoxicillin-clavulanate on the microbiota. The antibiotic induced a shift in the bacterial community in the absence of fibers by decreasing the relative amounts of Bifidobacteriaceae, Bacteroidaceae, Prevotellaceae, Lachnospiraceae and Ruminococcaceae, and increasing proteobacterial Sutterilaceae levels from 1% to 11% of the total microbiota. The fermentation of rye bran, enzymatically treated rye bran, its insoluble fraction, soluble oat fiber and a mixture of rye fiber:soluble oat fiber:linseed resulted in a significant increase in butyrate production and a bifidogenic effect in the absence of the antibiotic. These fibers were also able to counteract the negative effects of the antibiotic and prevent the decrease in the relative amount of bifidobacteria. Insoluble and soluble rye bran fractions and soluble oat fiber were the best for controlling the level of proteobacteria at the level below 2%.
A simple method for extraction of fungal genomic DNA (2000)

We have developed a new, simple and effective method for extraction of fungal genomic DNA. The initial steps involved suspension of freeze-dried mycelium in buffer containing sodium dodecyl sulphate, detachment of DNA from polysaccharides by mild shearing, NaCl precipitation of polysaccharides and protein, chloroform extraction and ethanol precipitation. The ethanol precipitate was then subjected to a second round of mild shearing, NaCl precipitation, chloroform extraction and ethanol precipitation. The procedure required approximately 1 h to perform. The method yielded 8-32 microg of high molecular weight DNA per 30 mg of freeze-dried mycelium when tested on six fungal species: Aspergillus niger, A. flavus, Fusarium graminarum, Neotyphodium lolii, Penicillium citrinum and Rhizopus nigricanes. The DNA was digestible with EcoRI, HindIII, SalI and BamHI. For the slow-growing N. lolii, a modification of the method was developed that removed the agar residue from colonies grown on agar plates by centrifugation at 13 000 rev min(-1) in the presence of CsCl. The modified method yielded 1.5-2 microg of high molecular weight DNA per colony.
Thymus-independent expression of a truncated T cell receptor-alpha mRNA in murine kidney (1992)

During studies on gene expression in the kidney, we unexpectedly observed that murine kidney expresses a truncated form of TCR-alpha mRNA (1.3-1.4 kb). This transcript was not associated with the presence of complete TCR-alpha mRNA (1.7 kb) or detectable TCR-beta or -delta transcripts, thus indicating that the truncated TCR-alpha mRNA could not be attributed to blood contamination of the kidney RNA preparation. The truncated TCR-alpha message appeared to contain at least the C alpha region, as suggested by hybridization with an intra-C alpha 24 oligonucleotide probe, by amplification of the C alpha region with the polymerase chain reaction from total kidney mRNA, and by sequencing of, and hybridization with, the amplified products. In situ hybridization of kidney sections indicated that the transcript was expressed in interstitial cells. Northern blots of cortex and medulla RNA showed that the cells expressing the truncated TCR-alpha mRNA were predominantly located in the medulla. To investigate the possibility that the transcript was not produced by T cells or NK cells, fractionation of renal cell suspensions were performed. The truncated TCR-alpha mRNA was detected in a fraction containing large (low buoyant density) cells in which no expression of CD3, Thy 1, or NK-1.1 was detected, indicating that these cells are not mature T cells, do not express a functional TCR, and are not NK cells. The cells expressing the truncated TCR-alpha mRNA were radiosensitive, and were not thymus dependent, because this transcript was as abundant in nude mice as in normal mice. The transcript was not detected in bone marrow. Expression of the truncated TCR-alpha mRNA was not dependent on an intact recombinase activity as its expression was not affected by the severe combined immunodeficiency mutation. Our results show that murine kidney contains a population of radiosensitive thymus-independent large interstitial cells that express a truncated TCR-alpha mRNA that is not associated with surface expression of functional TCR. These cells may have attempted to rearrange TCR-alpha genes, suggesting that they may be related to the lymphoid lineage.
Enhanced invasion and tumor growth of fibroblast growth factor 8b-overexpressing MCF-7 human breast cancer cells. (2001)

Fibroblast growth factor 8 (FGF-8) is a secreted heparin-binding protein, which has mitogenic and transforming activity. Increased expression of FGF-8 has been found in human breast cancer, and it has a potential autocrine role in its progression. Human FGF-8 is alternatively spliced to generate four protein isoforms (a, b, e, and f). Isoform b has been shown to be the most transforming. In this work, we studied the role of FGF-8b in the growth (in vitro and in vivo) of MCF-7 human breast cancer cells, which proliferate in an estrogen-dependent manner. Constitutive overexpression of FGF-8b in MCF-7 cells down-regulated FGF-8b-binding receptors FGF receptor (FGFR) 1IIIc, FGFR2IIIc, and FGFR4 found to be expressed in these cells. FGF-8b overexpression led to an increase in the anchorage-independent proliferation rate in suspension culture and colony formation in soft agar, when MCF-7 cells were cultured with or without estradiol. FGF-8b also provided an additional growth advantage for cells stimulated with estradiol. In addition, FGF-8b-transfected cells invaded more actively through Matrigel than did control cells. This was possibly due to the increased secretion of matrix metalloproteinase 9. In vivo, FGF-8b-transfected MCF-7 cells formed faster growing tumors than vector-only-transfected cells when xenografted into nude mice. The tumors formed by FGF-8b-transfected cells were more vascular than the tumors formed by vector-only-transfected cells. In conclusion, FGF-8b expression confers a growth advantage to MCF-7 breast carcinoma cells, both in vitro and in vivo. In addition to stimulation of proliferation, this growth advantage probably arises from increased invasion and tumor vascularization induced by FGF-8b. The results suggest that FGF-8b signaling may be an important factor in the regulation of tumorigenesis and progression of human breast cancer.
Investigation of Polymer Adsorption on Rock Surface of Highly Saline Reservoirs (2002)

Blocking or reducing water production from oil wells is a serious problem in oil industry. Two types of polymers, namely, polyacrylamide (PAA) and polysaccharides (xanthan) have been investigated in this paper. The viscosity of both polymer solutions was first evaluated at different salinities, shear rates and concentrations. Afterwards, the solutions were injected into core samples to examine the adsorption on the rock surface by calculating the resistance factor as well as the residual resistance factor. Also, the effect of the injection rate of the polymer solutions has been studied. The results show that xanthan solution is tolerant of high salinity (20 %), while PAA solution is very sensitive to salt. Both polymer solutions show a pseudoplastic flow as a function of the shear rate. The core sample experiments show that both polymer solutions suffer a reduction in the adsorption rate with salinity increase. However, xanthan shows acceptable values even with a salinity up to 20 % and a temperature of 60 °C. Therefore, xanthan can be recommended to shut off water in high salinity and high temperature reservoirs. It was also found that the lower the injection rate the higher the adsorption on the rock surface.
Novel antipsychotics: comparison of weight gain liabilities. (1999)

Clozapine and olanzapine caused the most weight gain, risperidone was intermediate, and sertindole had less associated weight gain than haloperidol. The relative receptor affinities of the novel antipsychotics for histamine H1 appear to be the most robust correlate of these clinical findings.
SOD Therapeutics: Latest Insights into Their Structure-Activity Relationships and Impact on the Cellular Redox-Based Signaling Pathways (2013)

Mechanistic explorations of single and combined therapeutic strategies, along with studies of bioavailability and translational aspects, will comprise future work in optimizing redox-active drugs.
Durable Cancer Regression Off-Treatment and Effective Reinduction Therapy with an Anti-PD-1 Antibody (2012)

These data represent the most prolonged observation to date of patients with solid tumors responding to anti-PD-1 immunotherapy and the first report of successful reinduction therapy following delayed tumor progression. They underscore the potential for immune checkpoint blockade with anti-PD-1 to reset the equilibrium between tumor and the host immune system.
Do Allelic Variants in α 2A and α 2C Adrenergic Receptors Predispose to Hypertension in Blacks? (2006)

Sequence variations in the human alpha2 adrenergic receptor genes (ADRA2A and ADRA2C) have been implicated as a cause of hypertension in blacks. Although certain alleles are selectively enriched in blacks, their association with hypertension is based on small convenience samples and has not been evaluated in larger populations. From a stratified random population sample of 3398 individuals (52% blacks), we obtained DNA samples together with an in-home health interview, 10 in-home measurements of blood pressure, and cardiac MRI. We tested for associations among hypertension, untreated blood pressure, and parameters of hypertensive heart disease with 2 alleles, a DraI restriction fragment length polymorphism in the ADRA2A gene and a deletion of residues 322 to 325 in the ADRA2C gene. Although both alleles were selectively enriched in this black population, we found no association of either allele with hypertension, untreated blood pressure, or any of the cardiac function parameters. In a logistic model that controlled for age, body mass index, diabetes, and smoking, the adjusted odds ratio (OR) for hypertension was 1.0 (95% CI, 0.8 to 1.2), and 1.0 (95% CI, 0.9 to 1.2) for ADRA2A and ADRA2C variant alleles. In subjects not receiving prescription blood pressure medication, neither of these alleles, alone or in combination, was predictive of blood pressure, heart rate, left ventricular mass, cardiac output, systemic vascular resistance, or aortic compliance. Both the DraI restriction fragment length polymorphism in ADRA2A and the ADRA2C (Del 322 to 325) can be excluded as major candidate alleles for hypertension in blacks.
Broad Spectral Response Using Carbon Nanotube/Organic Semiconductor/C60 Photodetectors (2009)

We demonstrate that photogenerated excitons in semiconducting carbon nanotubes (CNTs) can be efficiently dissociated by forming a planar heterojunction between CNTs wrapped in semiconducting polymers and the electron acceptor, C(60). Illumination of the CNTs at their near-infrared optical band gap results in the generation of a short-circuit photocurrent with peak external and internal quantum efficiencies of 2.3% and 44%, respectively. Using soft CNT-hybrid materials systems combining semiconducting small molecules and polymers, we have fabricated broad-band photodetectors with a specific detectivity >10(10) cm Hz(1/2) W(1-) from lambda = 400 to 1450 nm and a response time of tau = 7.2 +/- 0.2 ns.
Characteristics of Hepatic IGF-II Expression and Monitored Levels of Circulating IGF-II mRNA in Metastasis of Hepatocellular Carcinoma (2010)

The prognosis of hepatocellular carcinoma (HCC) remains dismal. Insulin-like growth factor II (IGF-II), a fetal growth factor, is highly expressed during HCC development. We examined serum IGF-II levels and circulating IGF-II messenger RNA (mRNA) expression and analyzed the clinicopathologic characteristics in patients with liver diseases. The higher IGF-II level in the serum of patients with HCC could be correlated with hepatitis B virus infection but not with patient sex, age, tumor size, or α-fetoprotein (AFP) level. Total RNAs were extracted from liver tissues or peripheral blood mononuclear cells, and IGF-II complementary DNA (cDNA) and AFP cDNA were synthesized through random primers and reverse transcriptase; gene fragments were amplified by nested polymerase chain reaction and confirmed by sequencing. The incidence of the hepatic IGF-II gene was 100% in HCC, 54.3% in paracancerous tissues, and none in noncancerous tissues. The incidence rates for circulating IGF-II and AFP genes were 34.3% and 52.7%, respectively, and for both, 61.6% in patients with HCC. They were 100% in cases with extrahepatic metastasis. The IGF-II abnormality associates with HCC, and circulating IGF-II and IGF-II mRNA are useful molecular markers for HCC differential diagnosis and hematogenous metastasis.
A Drosophila mutation that eliminates a calcium-dependent potassium current. (1986)

A mutation of Drosophila, slowpoke (slo), specifically abolishes a Ca2+-dependent K+ current, IC, from dorsal longitudinal flight muscles of adult flies. Other K+ currents remain normal, providing evidence that IC is mediated by a molecularly distinguishable set of channels. The pharmacological properties of IC are similar to those of Ca2+-dependent currents in some vertebrate cells. The muscle action potential was significantly lengthened in slo flies, indicating that IC plays the major role in its repolarization.