gebhart/patrepeval huggingface dataset:
Release of Hormones from Conjugates: Chloroplast Expression of β-Glucosidase Results in Elevated Phytohormone Levels Associated with Significant Increase in Biomass and Protection from Aphids or Whiteflies Conferred by Sucrose Esters (2010)

Transplastomic tobacco (Nicotiana tabacum) plants expressing β-glucosidase (Bgl-1) show modified development. They flower 1 month earlier with an increase in biomass (1.9-fold), height (1.5-fold), and leaf area (1.6-fold) than untransformed plants. Trichome density on the upper and lower leaf surfaces of BGL-1 plants increase by 10- and 7-fold, respectively, harboring 5-fold more glandular trichomes (as determined by rhodamine B staining), suggesting that BGL-1 lines produce more sugar esters than control plants. Gibberellin (GA) levels were investigated because it is a known regulator of flowering time, plant height, and trichome development. Both GA(1) and GA(4) levels are 2-fold higher in BGL-1 leaves than in untransformed plants but do not increase in other organs. In addition, elevated levels of other plant hormones, including zeatin and indole-3-acetic acid, are observed in BGL-1 lines. Protoplasts from BGL-1 lines divide and form calli without exogenous hormones. Cell division in protoplasts is enhanced 7-fold in the presence of exogenously applied zeatin-O-glucoside conjugate, indicating the release of active hormones from their conjugates. Whitefly (Bemisia tabaci) and aphid (Myzus persicae) populations in control plants are 18 and 15 times higher than in transplastomic lines, respectively. Lethal dose to kill 50% of the test population values of 26.3 and 39.2 μg per whitefly and 23.1 and 35.2 μg per aphid for BGL-1 and untransformed control exudates, respectively, confirm the enhanced toxicity of transplastomic exudates. These data indicate that increase in sugar ester levels in BGL-1 lines might function as an effective biopesticide. This study provides a novel strategy for designing plants for enhanced biomass production and insect control by releasing plant hormones or sugar esters from their conjugates stored within their chloroplasts.
Abstract 192: High Fat Diet Promotes Haplotype Dependent Differential Transcriptional Regulation of the Human Angiotensinogen Gene (2015)

Angiotensinogen (AGT) is the only known precursor to angiotensin II. Systemic renin angiotensin aldosterone system (RAAS) is activated in human and experimental models of obesity. RAAS activation in obesity is linked to the development of cardiovascular pathophysiologies. We have identified polymorphisms in 2.5 Kb promoter of human angiotensinogen gene (hAGT) that forms two haplotype (Hap) blocks: -6A/G (-1670A/G, -1562C/T, -1561T/C) and -217A/G (-532T/C, -793A/G, -1074T/C,& -1178G/A). Hap -6A/-217A (Hap -6A) is associated with human hypertension whereas, Hap -6G/-217G (Hap -6G) reduces cardiovascular risk. Here, we examine high fat diet-mediated allele-specific transcriptional regulation of the hAGT gene in adipose tissue, in vivo, in transgenic (TG) mice engineered with either haplotype of the hAGT gene. Twelve-week-old male TG mice with Hap –6A or –6G were fed normal diet (10% kcal as fat) and high fat diet (60% kcal as fat) for 10 weeks. Using Q - RT PCR and western blot we show increased hAGT expression in adipose tissue of the Hap -6A-TG mice after high fat diet than control diet (Hap -6A-0.68±0.04 vs. Hap -6G- 0.33±0.03 A.U., p<0.05). ChIP assay shows greater chromatin binding of GR, MR, CEBPβ and STAT3 transcriptional factors (Hap -6A- 0.80±0.04 vs. Hap -6G- 0.26±0.06 A.U., p<0.05) to the hAGT transgenes in Hap -6A TG mice after high fat diet. No significant change was observed in the endogenous mouse AGT gene. In addition, after high fat diet, change ([[Unable to Display Character: &#8710;]]) in inflammatory and redox markers was significantly (p<0.05) greater in TG mice with Hap I including, IL1 (4.6±0.8 vs. 2.1±0.49 fold), IL6 (4.0±0.69 vs. 2.1±0.2 fold) and NOX1 (8.3±0.4 vs. 2.5±0.6 fold). This is accompanied by reduction in levels of antioxidant defenses (SOD1: 0.97±0.0 vs. 1.4±0.1 fold; HO1: 0.77±0.1 vs. 1.3±0.2 fold) & activation of MAPK14 and ERK1/2 signaling. Taken together, our results show that SNPs in the hAGT Hap -6A favor high fat diet induced binding of transcriptional factors GR, MR, CEBP-β and STAT3 that lead to elevated expression of the hAGT in expanded mass of the adipose tissue. This also activates the RAAS with pathophysiological implications including, phosphorylation of kinases such as MAPK14 and ERK2, increase in tissue pro-inflammatory and oxidative stress molecules.
Treatment with Bazedoxifene, a Selective Estrogen Receptor Modulator, Causes Regression of Endometriosis in a Mouse Model (2011)

Endometriosis is a common estrogen-dependent disorder. Medical treatments currently consist of progestins or GnRH agonists; however, neither is fully effective and both entail significant side effects. Selective estrogen receptor (ER) modulators (SERM) have tissue-selective actions, acting as an ER agonist in some tissues and ER antagonist in others. The SERM bazedoxifene (BZA) effectively antagonizes estrogen-induced uterine endometrial stimulation without countering estrogenic effects in bone or central nervous system. These properties make it an attractive candidate for use in the treatment of endometriosis. Experimental endometriosis was created in reproductive-age CD-1 mice. After 8 wk, 10 animals received i.p. injections of BZA (3 mg/kg·d) for 8 wk, whereas 10 received vehicle control. Mice were killed, and implant size was assessed. The mean size of the implants after treatment was 60 mm(2) in the control group and 21 mm(2) in the BZA treatment group (P = 0.03). Quantitative PCR and immunohistochemical analysis were used to determine the effect on endometrial gene expression. PCNA, ERα, and LIF mRNA and protein expression were significantly decreased in endometrium of the treated group. Caspase 3 mRNA expression was increased. Expression of PR and Hoxa10 were not significantly altered by treatment. There was no evidence of ovarian enlargement or cyst formation. Decreased PCNA and ER expression demonstrated that the regression of endometriosis likely involved decreased estrogen-mediated cell proliferation. BZA may be an effective novel agent for the treatment of endometriosis due to greater endometrial-specific estrogen antagonism compared with other SERM.
Lookahead Optimizer: k steps forward, 1 step back (2019)

The vast majority of successful deep neural networks are trained using variants of stochastic gradient descent (SGD) algorithms. Recent attempts to improve SGD can be broadly categorized into two approaches: (1) adaptive learning rate schemes, such as AdaGrad and Adam, and (2) accelerated schemes, such as heavy-ball and Nesterov momentum. In this paper, we propose a new optimization algorithm, Lookahead, that is orthogonal to these previous approaches and iteratively updates two sets of weights. Intuitively, the algorithm chooses a search direction by looking ahead at the sequence of fast weights generated by another optimizer. We show that Lookahead improves the learning stability and lowers the variance of its inner optimizer with negligible computation and memory cost. We empirically demonstrate Lookahead can significantly improve the performance of SGD and Adam, even with their default hyperparameter settings on ImageNet, CIFAR-10/100, neural machine translation, and Penn Treebank.
Monitors for Usage Control (2007)

Distributed usage control is concerned with controlling how data may or may not be used after it has been given away. One strategy for enforcing usage control requirements is based on monitoring data usage and reacting to policy violations by imposing penalties. We show how to implement monitors for usage control requirements using runtime verification technology.
Definition of deadlock patterns for business processes workflow models (2003)

To support deadlock detection by computer, five patterns which cause deadlock are defined. In expressing the pattern of deadlock structures by control-node combinations only, it is difficult to express the connection properties, since these are decided by many complex combinations of control nodes. Therefore, two new concepts, "reachability" and "absolute transferability", which express connection properties between two control nodes, are introduced. With these concepts, the five deadlock patterns are expressed simply. It is demonstrated mathematically that all deadlock structures can be classified into these patterns and that deadlock occurs in business process workflow models which have one or more of these patterns.
Growth strain in the trunk and branches of Chamaecyparis formosensis and its influence on tree form (2005)

Distributions of growth strains in branches, straight trunks and basal sweeping trunks of Chamaecyparis formosensis Matsum. trees were measured with strain gauges. Microfibril angles (MFAs) of the S2 layer of the cell wall were measured by the iodine deposition method and their relationships with growth strain examined. The magnitude of the compressive stress on the lower side of trunks with a basal sweep was greater than that of the tensile stress at the surface of straight trunks. However, transverse compressive stress was similar around the trunk regardless of whether normal wood or compression wood was present. The released surface growth strains varied with MFA. At MFAs of 20-25 degrees , growth stress changed from tension to compression, and compressive stress increased dramatically in the compression wood region. Branches suffer bending stress due to self-loading. This stress is superimposed on the growth stress. Growth strains on the upper or lower sides of branches were larger than those in the trunks, suggesting that generation of growth stress on the lower sides of branches with extensive compression wood is affected by the gravitational bending stress due to self-loading. We conclude that branch form is affected by the interaction between the bending moment due to self-loading and that due to the asymmetric distribution of growth stress. Growth strain distribution in a branch differed depending on whether the branch was horizontal, upward bending or downward bending.
Phonons in semiconductor superlattices (1986)

Experimental results on phonons in semiconductor super-lattices are almost all from Raman scattering measurements. The superlattice system most studied is GaAs-Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</inf> Al <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</inf> As, and in the best-understood geometry the phonons are longitudinal modes with wave vectors perpendicular to the (001) interface planes. A linear-chain model then gives a good understanding of the results, which show folding of the acoustic modes and confinement of the optic modes into "phonon quantum wells." Modes propagating obliquely to the interfaces are either slab modes or interface modes. They have been less studied but can be explained using the dielectric model. A more thorough model is needed that takes into account both the coulomb interaction and the effects of the short-range interactions (spatial dispersion). Some results obtained on other semiconductor superlattices will also be discussed.
Discovery of <i>N</i>-(2-Aminophenyl)-4-[(4-pyridin-3-ylpyrimidin-2-ylamino)methyl]benzamide (MGCD0103), an Orally Active Histone Deacetylase Inhibitor (2008)

The design, synthesis, and biological evaluation of N-(2-aminophenyl)-4-[(4-pyridin-3-ylpyrimidin-2-ylamino)methyl]benzamide 8 (MGCD0103) is described. Compound 8 is an isotype-selective small molecule histone deacetylase (HDAC) inhibitor that selectively inhibits HDACs 1-3 and 11 at submicromolar concentrations in vitro. 8 blocks cancer cell proliferation and induces histone acetylation, p21 (cip/waf1) protein expression, cell-cycle arrest, and apoptosis. 8 is orally bioavailable, has significant antitumor activity in vivo, has entered clinical trials, and shows promise as an anticancer drug.
Infrared light scanning of the breast. (1986)

Transillumination and Infrared Light Scanning (I.L.S.) of the breast were evaluated in a high referral breast clinic over a 15-month period. Seven hundred (700) patients were examined and blindly transilluminated; 101 were biopsied, all had mammography. The study was conducted in two phases: Phase I evaluated transillumination without I.L.S. This included 22 biopsied patients out of 101, with eight carcinomas identified histologically, demonstrating 87 per cent sensitivity and 64 per cent specificity for transillumination, versus 87 per cent and 71 per cent for mammography, and 87 per cent and 57 per cent for examination. Phase II evaluated simple transillumination combined with I.L.S. This included 79 biopsied patients out of 101 with 26 carcinomas identified histologically, demonstrating 96 per cent sensitivity and 74 per cent specificity for transillumination combined with I.L.S. compared to 85 per cent and 72 per cent for mammography and 81 per cent and 73 per cent for examination. Of the 26 Phase II carcinomas identified, two were not felt by examination, and two were neither felt nor read correctly by mammography. I.L.S. of the breast has proven effective in the hands of trained personnel and should be used with routine breast examination or mammography to increase yield of breast pathology.
Tumor progression is accompanied by significant changes in the levels of expression of polyamine metabolism regulatory genes and clusterin (sulfated glycoprotein 2) in human prostate cancer specimens. (2000)

Using Northern blotting, the expression levels of the genes for polyamine metabolism regulatory proteins and clusterin have been measured in a series of 23 human prostate cancers (CaPs) dissected from radical prostatectomy specimens. Patient matched, nontumor tissue was dissected from benign areas of the gland. The results indicate that transcripts encoding ornithine decarboxylase (ODC), ODC antizyme, adenosylmethionine decarboxylase, and spermidine/spermine N1-acetyltransferase (SSAT) were significantly higher, whereas clusterin (sulfated glycoprotein 2) mRNA was significantly lower in tumors compared with the benign tissue. All mRNA levels were compared with those of histone H3 and growth arrest-specific gene 1, markers of cell proliferation and cell quiescence, respectively, and glyceraldehyde 3-phosphate dehydrogenase, a housekeeping gene. In poorly differentiated and locally invasive CaPs and in tumors with unfavorable prognosis or total prostate-specific antigen (PSA) levels > 10.0 ng/ml at diagnosis, an overall increase in the levels of H3 mRNA and a decrease in growth arrest-specific gene 1 mRNA was detected, indicative of higher proliferation activity, whereas the differences in expression levels for the polyamine metabolism and clusterin genes were higher. ODC and SSAT changes were positively correlated in normal tissue but not in high-grade cancer, whereas ODC antizyme and SSAT changes were positively correlated in more malignant CaPs but not in normal tissue. Tumor classification based on the changes in expression levels of all of the genes studied could be correlated to differentiation grade and local invasiveness classification systems in 72.2 and 83.3% of the cases, respectively. In a 1-year follow-up period, three patients whose CaPs ranked as less aggressive according to clinical staging, but classified as advanced cancers with the proposed molecular classification, showed increases in total PSA levels, indicative of tumor relapse. Thus, molecular classification, based on gene expression, may enhance the available prognostic tools for prostate tumors.
Hot-electron resistance device processing and design: a review (1989)

Continual reduction of MOS device size to optimize device performance and reduce die cost has led to reliability concerns. These are attributed to the ever increasing generation of hot electrons that accompany device size reduction. Hence, it is essential to thoroughly understand the relationships governing device performance, design, and reliability with respect to processing. Both the degradation rate and generation of hot electrons can be modified through processing and design. By reviewing various aspects of hot-electron resistance processing and fabrication techniques, guidelines are established which will prove useful in the design of a given process to reduce hot-electron degradation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Cyto‐ and genotoxic potential of <i>β</i>‐carotene and cleavage products under oxidative stress (2005)

Free radical attack on beta-carotene results in the formation of high amounts of cleavage products with prooxidant activities towards subcellular organelles such as mitochondria, a finding which could provide an explanation for the contradictory results obtained with beta-carotene in clinical efficacy and cancer prevention trials. Since primary hepatocytes proved to be very sensitive indicators for the genotoxic action of suspect mutagens/carcinogens we therefore investigated a beta-carotene cleavage products mixture (CP), apo-8'-beta-carotenal (apo-8') and beta-carotene in the primary rat hepatocyte assay in the presence and absence of oxidative stress provided by hypoxia/reoxygenation (Hy/re). The endpoints tested were: the mitotic indices, the percentages of necrotic and apoptotic cells, micronucleated cells (MN), chromosomal aberrations (CA) and sister chromatid exchanges (SCE). The results obtained indicate a genotoxic potential of both CP and apo-8' already in the concentration range of 100 nM and 1 microM, i.e. at physiologically relevant levels of beta-carotene and beta-carotene breakdown products. In contrast, no significant cytotoxic effects of these substances were observed, nor did beta-carotene induce significant cytotoxic or genotoxic effects at concentrations ranging from 0.01 up to 10 microM. However, when beta-carotene is supplemented during oxidative stress induced by hypoxia/reoxygenation, a dose-dependent increase of CP is observed accompanied by increasing genotoxicity. Furthermore, when beta-carotene cleavage products were supplied during oxidative stress significant additional increases of genotoxic effects were observed, the additional increases indicating an additive effect of both exposures. Summarizing, these results provide strong evidence that beta-carotene breakdown products are responsible for the occurrence of carcinogenic effects found in the Alpha-Tocopherol Beta-carotene-Cancer prevention (ATBC) study and the beta-CArotene and RETinol Efficacy (CARET) Trial.
Compression-based program characterization for improving cache memory performance (1997)

It is well known that compression and prediction are interrelated in that high compression implies good predictability, and vice versa. We use this correlation to find predictable properties of program behavior and apply them to appropriate cache management tasks. In particular, we look at two properties of program references: (1) Inter Reference Gaps: defined as the time interval between successive references to the same address by the processor, and (2) Cache Misses: references which access the next level of the memory hierarchy. Using compression, we show that these two properties are highly predictable and exploit them to improve Cache Replacement and Cache Prefetching, respectively. Using trace-driven simulations on SPEC and Dinero benchmarks, we demonstrate the performance of our predictive schemes, and compare them with other methods for doing the same. We show that, using our predictive replacement scheme, miss ratio in cache memories can be improved up to 43 percent over the well-known Least Recently Used (LRU) algorithm, which covers the gap between the LRU and the off-line optimal (MIN) miss ratios, by more than 84 percent. For cache prefetching, we show that our scheme eliminates up to 62 percent of the total misses in D-caches. An equivalent sequential prefetch scheme only removes up to 42 percent of the misses. For I-caches, our scheme performs almost the same as the sequential scheme and removes up to 78 percent of the misses.
[Possible etiological relations between Sjogren's syndrome and Epstein-Barr virus]. (1991)

Tissue biopsies from patients with Sjogren's syndrome (SS) and controls were detected by a monoclonal antibody (McAb) of gene engineering against Epstein-Barr virus (EBV) encoded early antigen (EA p138) and a 32p-labelled EBV DNA probe, and also B95-8 and K4 cells as antigens to detect reacting antibodies to EBV in patients' sera. As a result, cytoplasmic fluorescence staining of epithelial cells with the McAb as described above was noted in 15/33 labial and 7/7 renal biopsies from primary SS. The same McAb did not react with biopsies from secondary SS, non-SS connective tissue diseases, benign tumors and normal persons, nor with the other tissues detected from primary SS. By using McAbs against the EBV EA p54 and nuclear antigen (EBNA-1) and by using immunoblotting method, it was found that the reacting antigens in labial biopsies of primary SS had both a M. W. of 54,000 and a M. W. of 65,000, similar to the EA-D and EBNA-1 antigens found in lymphoblastoid cells lytically infected with EBV. Seven out of 21 labial and one out of two renal samples from primary SS patients contained EBV DNA detectable by dot blot hybridization with EBV Bam W probe. Serum levels of both antiviral capsid antigen antibodies and antinuclear antibodies were elevated in patients with primary SS. Our results demonstrated an elevated content of EBV in labial gland and kidney of patients with primary SS, where EBV has been of a lytic fate leading to active replication. It is concluded that EBV may play an important role in the pathogenesis of primary SS.
Clinical pharmacology and human antitumor activity of cytosine arabinoside (1967)

Cytosine arabinoside (ara-C) has been given to 89 patients with various types of neoplastic disease. Hematopoietic toxicity with megaloblastosis, leukopenia, and thrombocytopenia occurred frequently as did nausea and vomiting. Mucosal ulceration and CNS effects were rarely observed. Response in a variety of solid tumors has been disappointing, with only transient decrease in tumor masses being observed in seven of 62 patients treated. Responses in leukemia and lymphosarcoma were more frequent (four of four leukemias and 15 of 23 lymphomas), but these were only partial and of short duration. Experience with several dosage regimens indicated that large doses at seven-to-ten day intervals were less toxic and as effective as other regimens in treatment of lymphosarcomas. Biological assay of blood and urine for ara-C demonstrated disappearance of the drug from the blood within 15 min; only a small proportion appeared in the urine. Other investigators have reported that the major excretion product of ara-C is uracil arabinoside (ara-U), due to the presence of pyrimidine deaminases in human liver and kidney tissue. Further investigation of various dosage regimens in treatment of various human malignancies is recommended, as well as a search for agents which will prevent the rapid deamination of ara-C to ara-U.