gebhart/patrepeval huggingface dataset:
EpiFactors: a comprehensive database of human epigenetic factors and complexes (2015)

Epigenetics refers to stable and long-term alterations of cellular traits that are not caused by changes in the DNA sequence per se. Rather, covalent modifications of DNA and histones affect gene expression and genome stability via proteins that recognize and act upon such modifications. Many enzymes that catalyse epigenetic modifications or are critical for enzymatic complexes have been discovered, and this is encouraging investigators to study the role of these proteins in diverse normal and pathological processes. Rapidly growing knowledge in the area has resulted in the need for a resource that compiles, organizes and presents curated information to the researchers in an easily accessible and user-friendly form. Here we present EpiFactors, a manually curated database providing information about epigenetic regulators, their complexes, targets and products. EpiFactors contains information on 815 proteins, including 95 histones and protamines. For 789 of these genes, we include expressions values across several samples, in particular a collection of 458 human primary cell samples (for approximately 200 cell types, in many cases from three individual donors), covering most mammalian cell steady states, 255 different cancer cell lines (representing approximately 150 cancer subtypes) and 134 human postmortem tissues. Expression values were obtained by the FANTOM5 consortium using Cap Analysis of Gene Expression technique. EpiFactors also contains information on 69 protein complexes that are involved in epigenetic regulation. The resource is practical for a wide range of users, including biologists, pharmacologists and clinicians.
Quality assessment of hydroponically stored watermelon and cucumber fruits. (2021)

Quality assessment of hydroponically stored water melon and cucumber were studied. Four set up were created. Oxo chlorate concentration chamber at 2.5 ml, Oxo chlorate concentration chamber at 5 ml, tap water chamber; water melon and cucumber fruits without a chamber served as control. The water melon and cucumber were suspended in a mesh over water at various Oxo chlorate concentrations and allowed for maximum of 36 days. The Relative Rumidity (RH), temperature, Oxygen (O2) and Carbon Dioxide (CO2) concentration were taken using RH meter and temperature logger. Vitamin A, C, Potassium, Calcium, Phosphorus elements and microbial load were accessed after storage periods. Results showed that the physical parameter, relative humidity, gaseous concentration, temperature favoured water melon and cucumber in hydroponic storage chambers. The nutritional content of mineral and vitamins were also highly favored except sodium mineral that was absent in all created chambers. Similarly, the microbial load in all the chambers for bacterial and fungi infestation reveal microbial loads within safety levels.
Novel quadrature branch-line coupler using CPW-to-microstrip transitions (2002)

This paper presents a new double-sided 3-dB branch-line coupler using CPW-to-microstrip via-hole transitions for multi-layers circuits. The coupler is designed using the even-odd mode method, and the circuit performance is calculated by the Finite Difference Time Domain (FDTD) method. The fabricated double-sided 3-dB branch-line coupler has /spl plusmn/0.5 dB maximum power imbalance and /spl plusmn/1/spl deg/ phase imbalance, 15 dB minimum isolation and 15 dB minimum return loss over a 24% bandwidth centered at 2 GHz. The high performance and the manufacturing compatibility can be effectively used for multi-layers circuits.
In Vitro Nucleotide Misinsertion Opposite the Oxidized Guanosine Lesions Spiroiminodihydantoin and Guanidinohydantoin and DNA Synthesis Past the Lesions Using <i>Escherichia coli</i> DNA Polymerase I (Klenow Fragment) (2002)

The low redox potential of 8-oxo-7,8-dihydroguanine (OG), a molecule regarded as a marker of oxidative damage in cells, makes it an easy target for further oxidation. Using a temperature-dependent method of synthesis, the oxidation products of OG, guanidinohydantoin (Gh) and/or its isomer iminoallantoin (Ia) as well as spiroiminodihydantoin (Sp), have been site-specifically incorporated into DNA oligomers. Single nucleotide insertion and primer extension experiments using Escherichia coli Kf exo(-) DNA polymerase were carried out under "standing start" and "running start" conditions in various sequence contexts. dAMP and dGMP were found to be inserted opposite these OG oxidation products. Steady-state kinetic studies show that the Gh/Ia.G base pair yields a lower K(m) value compared to the Sp.G pair or X.A (X = Gh/Ia or Sp). Running start experiments using oxidized and unoxidized OG-containing templates showed enhanced full extension in the presence of all four dNTPs. A sequence preference for efficiency of extension was found when Gh/Ia and Sp are present in the DNA template, possibly leading to primer misalignment. Full extension is more efficient for the templates containing two Gs immediately 3' to the lesions compared to two As. Although these lesions cause a significant block for DNA elongation, results show that they are more easily bypassed by the polymerase when situated in the appropriate sequence context. UV melting studies carried out on duplexes mimicking the template/primer systems were used to characterize thermal stability of the duplexes. These experiments suggest that both Gh/Ia and Sp destabilize the duplex to a much greater extent than OG, with Sp being most severe.
Nucleotide sequences of Bacillus subtilis flagellar biosynthetic genes fliP and fliQ and identification of a novel flagellar gene, fliZ (1992)

Three genes from the Bacillus subtilis major che-fla operon have been cloned and sequenced. Two of the genes encode proteins that are homologous to the Escherichia coli and Salmonella typhimurium flagellar biosynthetic proteins FliP and FliQ. The third gene, designated fliZ, encodes a 219-amino-acid protein with a predicted molecular mass of 24,872 Da. FliZ is not significantly homologous to any known proteins. Null mutants in fliP and fliZ do not have flagella; however, motility can be restored to the fliZ null mutant by expression of fliZ from a plasmid. FliZ has a conventional N-terminal signal sequence that does not direct secretion of the protein but appears to target the protein to the membrane. Two possible models of insertion of FliZ into the membrane are described.
The E-cadherin/catenin complex: an important gatekeeper in breast cancer tumorigenesis and malignant progression (2001)

E-cadherin is a cell-cell adhesion protein fulfilling a prominent role in epithelial differentiation. Data from model systems suggest that E-cadherin is a potent invasion/tumor suppressor of breast cancer. Consistent with this role in breast cancer progression, partial or complete loss of E-cadherin expression has been found to correlate with poor prognosis in breast cancer patients. The E-cadherin gene (CDH1) is located on human chromosome 16q22.1, a region frequently affected with loss of heterozygosity in sporadic breast cancer. Invasive lobular breast carcinomas, which are typically completely E-cadherin-negative, often show inactivating mutations in combination with loss of heterozygosity of the wild-type CDH1 allele. Mutations were found at early noninvasive stages, thus associating E-cadherin mutations with loss of cell growth control and defining CDH1 as the tumor suppressor for the lobular breast cancer subtype. Ductal breast cancers in general show heterogeneous loss of E-cadherin expression, associated with epigenetic transcriptional downregulation. It is proposed that the microenvironment at the invasive front is transiently downregulating E-cadherin transcription. This can be associated with induction of nonepithelial cadherins.
Thermostability of double-stranded deoxyribonucleic acids: the effects of covalent additions of a psoralen (1986)

We have carried out a thermodynamic study on the effects of covalent additions of the psoralen derivative HMT, 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen, on the stability of double-stranded deoxyoligonucleotides. This was done with two systems. The first was a double-stranded DNA formed by two non-self-complementary oligonucleotides, 5'-GAAGCTACGAGC-3' and 5'-GCTCGTAGCTTC-3', where we site specifically placed an HMT molecule on the thymidine residue in oligonucleotide 5'-GAAGCTACGAGC-3' as either a furan-side monoadduct or a pyrone-side monoadduct. The second was a double-stranded DNA formed by a self-complementary oligonucleotide, 5'-GGGTACCC-3', where we placed an HMT molecule on the thymidine residue of each strand as a furan-side monoadduct or cross-linked the two strands with an HMT molecule linked to the two thymidines. We found that HMT cross-linking of the two strands stabilizes the double helix formed by 5'-GGGTACCC-3', as one might expect. Less predictable results were that the monoaddition of a psoralen stabilizes the double helix formed by the two non-self-complementary oligonucleotides by as much as 1.3 kcal/mol as a furan-side monoadduct and 0.7 kcal/mol as a pyrone-side monoadduct at 25 degrees C in 50 mM NaCl. In contrast, the monoaddition of a psoralen on each of the two thymidines in the double helix formed by 5'-GGGTACCC-3' destabilizes the helix by 1.8 kcal/mol at 25 degrees C in 1 M NaCl. This destabilization arises from an unfavorable enthalpy change (8.6 kcal/mol) and a favorable entropy change (23 cal/K X mol) due to the two HMT molecules at the centers of each strand.(ABSTRACT TRUNCATED AT 250 WORDS)
Bovine cartilage types VI and IX collagens. Characterization of their forms <i>in vivo</i> (1989)

1. Collagens were extracted from bovine cartilage by 4 M-guanidinium chloride in the presence of proteinase inhibitors and identified by immunoblotting with specific anti-collagen sera. 2. The collagens retained their native conformations (shown by the resistance of their triple-helical domains to pepsin digestion), and the molecular masses of their component alpha-chains indicated that the chains were intact. 3. Type VI collagen was extracted as a large-molecular-mass disulphide-bonded aggregate composed of components of molecular mass 140 kDa and 200-240 kDa, and was therefore similar to type VI collagen identified in noncartilaginous tissues. Immunoblotting established the 200-240 kDa components as intact forms of the alpha 3(VI) chain. 4. Type IX collagen consisted of three clearly separable components of molecular mass 84 kDa, 72 kDa and 66 kDa, which were assigned to the alpha 1(IX)-, alpha 3(IX)- and alpha 2(IX)-chains respectively, and a large proportion of this collagen had no covalently bound glycosaminoglycan attached to the alpha 2(IX)-chain. 5. Differences between the type IX collagen extracted from bovine cartilage and that identified in biosynthetic studies on chick cartilage are discussed.
Sparse least squares Support Vector Machine classifiers. (2000)

. In least squares support vector machine (LS-SVM) classifiers the original SVM formulation of Vapnik is modified by considering equality constraints within a form of ridge regression instead of inequality constraints. As a result the solution follows from solving a set of linear equations instead of a quadratic programming problem. However, a drawback is that sparseness is lost in the LS-SVM case due to the choice of 2-norms. In this paper we propose a method for imposing sparseness to the LS-SVM solution. This is done by pruning the support value spectrum which is revealing the relative importance of the training data points and is immediately available as solution to the linear systems. Keywords. Support vector machines, classification, ridge regression, dual problem, sparse approximation, pruning. 1. Introduction Support vector machines (SVM&apos;s) have been successfully applied in classification and function estimation problems [2, 8] after its introduction by Vapnik withi...
Case Study on CRM: Detecting Likely Churners with Limited Information of Fixed-line Subscriber (2006)

Only with subscribers' contractual records and bill details in the investigated fixed-line services provider, we construct several churn prediction models, applying different data mining technologies. Comparing the models with predictors of duration of service use, payment type, amount and structure of monthly service fees and changes of the monthly service fees, we find that duration of service use is the most predictive variable. Then payment type and other predictors of amount and structure of monthly service fees, especially the predictors within the latest 3 months, are also effectual. We then build different decision tree models by reducing the amounts of monthly bill details for predicting, to find out how the prediction performance evolves. The result shows that with reduction of early monthly data, the model performance declines slightly. However, the processing data size and runtime of models decrease significantly. Thus, we suggest that using relatively fewer but latest monthly data to detect likely churner would be both effective and efficient
High-speed low-power ECL circuit with AC-coupled self-biased dynamic current source and active-pull-down emitter-follower stage (1992)

The design of an ECL circuit with AC-coupled self-biased dynamic current source and active-pull-down emitter-follower stage for low-power high-speed gate array applications is presented. The circuit features an AC-coupled dynamic current source to improve the power-delay of the logic stage (current switch). A self-biasing scheme for the dynamic current source and the active-pull-down transistor with no additional devices and power in the biasing circuit is described. Based on a 0.8- mu m double-poly, self-aligned bipolar technology at a power consumption of 1.0 mW/gate, the circuit offers 1.62* (1.90*) improvement in the speed (load driving capability) of a loaded gate compared with the conventional ECL circuit.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Deletions at the C-terminus of interferon <i>γ</i> reduce RNA binding and activation of double-stranded-RNA cleavage by bovine seminal ribonuclease (1995)

Recombinant interferon gamma (IFN-gamma) from three species activates the cleavage of double stranded (ds-) RNA by the dimeric RNAase isolated from bovine semen (BS-RNAase). Human and bovine IFN-gamma bind RNA tightly enough to inhibit cleavage by RNAase A [Schein, Haugg and Benner (1990) FEBS Lett. 270, 229-232]. Murine IFN-gamma and a proteolytic fragment of human IFN-gamma, both of which lack part of the positively charged C-terminus, bind RNA weakly and do not inhibit RNAase A. Their ability to activate BS-RNAase is proportional to their activity in the anti-viral assay. Two monoclonal antibodies that neutralize the anti-viral activity of human IFN-gamma inhibit the activation of BS-RNAase by both full-length and proteolysed human IFN-gamma. Our results demonstrate that the C-terminus of IFN-gamma contributes to RNA binding and activation of BS-RNAase, as well as to anti-viral activity.
Metallocene Polymers. XVIII. Poly(ferrocenylphosphine oxides) (1967)

Abstract The Lewis acid-catalyzed polycondensation of ferrocene with phenyldi-chlorophosphine is described. Under a variety of conditions, using melt and solution condensation conditions, followed by a mild postoxidation treatment, polymers composed of ferrocenylene units interconnected by phenylphosphoryl groups are obtained. The soluble, but largely infusible, products possess number-average molecular weights up to 3500 (6000 upon subfractionation). Elemental compositions vary with reaction conditions; optimal consistency with the ideal ferrocenylene(phenyl)phosphoryl recurring unit results from use of a moderate ferrocene excess and smallest possible solvent concentrations at temperatures not exceeding 105°. Much as in previously described polyacylations of ferrocene, a minor side reaction is observed which involves rupture of the metal-to-ring bond in ferrocene with subsequent incorporation of cyclopentylene groups into the polymer. This departure, however insignificant, from the purely aromatic poly-phosphine oxide composition results in thermal and oxidative stabilities not markedly superior to those of earlier ferrocenylene-methylene polymers.
Nanosized polyphenylene dendrimers based upon pentaphenylbenzene units (1997)

A facile divergent synthesis of monodisperse polyphenylene dendrimers having diameters of 21–55 Å is presented. These nanoparticles have been preparedvia a [2+4]cycloaddition–deprotection sequence using an excess of tetraphenylcyclopentadienone 1a as monomer and the tetraethynylbiphenyl 2 as core. Due to the dense packing of 22, 62 or 142 benzene rings in generations G 1 , G 2 and G 3 , respectively, the conformational freedom of the higher generations G 2 and G 3 is limited. Molecular mechanics calculations as well as molecular dynamics simulations are included in a discussion of the structure and the shape-persistence of G 2 . The calculations revealed that selected inner distances of the molecule varied only 5–10% during the molecular dynamics simulations, thus indicating that the overall shape of the molecule essentially did not change throughout the simulation time.
Small molecule inhibition of tumor necrosis factor gene processing during acute pancreatitis prevents cytokine cascade progression and attenuates pancreatitis severity. (1997)

The morbidity and mortality associated with acute pancreatitis are primarily a result of pancreatic parenchymal necrosis and the development of marked pulmonary dysfunction. Recent evidence suggests that both of these conditions are propagated by interleukin (IL)-1 beta and tumor necrosis factor (TNF)-alpha, which are produced in large quantities within these organs. Because the generation of these cytokines occurs in a predictable manner early in the development of acute pancreatitis, we aimed to determine whether cytokine gene processing could be inhibited in vivo and what effects this would have on pancreatitis severity. Mild [caerulein, 50 micrograms/kg/hour intraperitoneally (IP) x 4; n = 40] or severe (choline-deficient diet; n = 40) necrotizing pancreatitis was induced in NIH swiss mice. Animals were randomly given a novel small molecule (CNI-1493; 10 mg/kg IP) known to inhibit macrophage production of TNF and IL-1 in vitro by inhibiting translation of TNF mRNA into protein. Control animals received IP vehicle. All animals with acute pancreatitis showed dramatic up-regulation of the IL-1 beta and TNF-alpha genes. Those animals receiving CNI-1493 demonstrated attenuated production of both species of mRNA in pancreatic as well as pulmonary tissue (P < 0.01). Markers of pancreatitis severity such as serum amylase and lipase, as well as pancreatic necrosis, were decreased in animals treated with CNI-1493 (all P < 0.05). Posttranscriptional blockade of TNF production precludes induction of the proinflammatory cytokine cascade that normally occurs during acute pancreatitis. This lack of cytokine gene processing in the pancreas and lungs results in dramatic reductions in tissue damage and pancreatitis severity, which is not model dependent. This is the first time that a small molecule has been shown to influence this disease.
Raman spectroscopy for polymer characterization in an industrial environment (1999)

Abstract In this paper we discuss the use of Raman spectroscopy for characterising polymers both in the laboratory and also in‐situ at the production line. We show how polymer crystallinity can be followed during extrusion and drawing, and describe the compositional analysis of cross‐linked acrylic terpolymers in a polymerisation reactor. We also discuss problems which can arise such as sample fluorescence from moving polymers, distortion of relative band intensities due to chromatic aberration, and sampling difficulties with turbid solutions.
Thickness and growth-condition dependence of <i>in-situ</i> mobility and carrier density of epitaxial thin-film Bi2Se3 (2014)

Bismuth selenide Bi2Se3 was grown by molecular beam epitaxy, while carrier density and mobility were measured directly in situ as a function of film thickness. Carrier density shows high interface n-doping (1.5 × 1013 cm−2) at the onset of film conduction and bulk dopant density of ∼5 × 1011 cm−2 per quintuple-layer unit, roughly independent of growth temperature profile. Mobility depends more strongly on the growth temperature and is related to the crystalline quality of the samples quantified by ex-situ atomic force microscopy measurements. These results indicate that Bi2Se3 as prepared by widely employed parameters is n-doped before exposure to atmosphere, the doping is largely interfacial in origin, and dopants are not the limiting disorder in present Bi2Se3 films.
Whole Nerve Chorda Tympani Responses to Sweeteners in C57BL/6ByJ and 129P3/J Mice (2001)

The C57BL/6ByJ (B6) strain of mice exhibits higher preferences than does the 129P3/J (129) strain for a variety of sweet tasting compounds. We measured gustatory afferent responses of the whole chorda tympani nerve in these two strains using a broad array of sweeteners and other taste stimuli. Neural responses were greater in B6 than in 129 mice to the sugars sucrose and maltose, the polyol D-sorbitol and the non-caloric sweeteners Na saccharin, acesulfame-K, SC-45647 and sucralose. Lower neural response thresholds were also observed in the B6 strain for most of these stimuli. The strains did not differ in their neural responses to amino acids that are thought to taste sweet to mice, with the exception of L-proline, which evoked larger responses in the B6 strain. Aspartame and thaumatin, which taste sweet to humans but are not strongly preferred by B6 or 129 mice, did not evoke neural responses that exceeded threshold in either strain. The strains generally did not differ in their neural responses to NaCl, quinine and HCl. Thus, variation between the B6 and 129 strains in the peripheral gustatory system may contribute to differences in their consumption of many sweeteners.
Inflammation and Sex Hormone Metabolism (2006)

The incidence of autoimmune diseases is higher in females than in males. In both sexes, adrenal hormones, that is, glucocorticoids, dehydroepiandrosterone (DHEA), and androgens, are inadequately low in patients when compared to healthy controls. Hormonally active androgens are anti-inflammatory, whereas estrogens are pro-inflammatory. Therefore, the mechanisms responsible for the alterations of steroid profiles in inflammation are of major interest. The local metabolism of androgens and estrogens may determine whether a given steroid profile found in a subject's blood results in suppression or promotion of inflammation. The steroid metabolism in mixed synovial cells, fibroblasts, macrophages, and monocytes was assessed. Major focus was on cells from patients with rheumatoid arthritis (RA), while cells from patients with osteoarthritis served as controls. Enzymes directly or indirectly involved in local sex steroid metabolism in RA are: DHEA-sulfatase, 3beta-hydroxysteroid dehydrogenase, 17beta-hydroxysteroid dehydrogenase, and aromatase (CYP19), which are required for the synthesis of sex steroids from precursors, 5alpha-reductase and 16alpha-hydroxylase, which can be involved either in the generation of more active steroids or in the pathways leading to depletion of active hormones, and 3alpha-reductase and 7alpha-hydroxylase (CYP7B), which unidirectionally are involved in the depletion of active hormones. Androgens inhibit aromatization in synovial cells when their concentration is sufficiently high. As large amounts of estrogens are formed in synovial tissue, there may be a relative lack of androgens. Production of 5alpha-reduced androgens should increase the local anti-inflammatory activity; however, it also opens a pathway for the inactivation of androgens. The data discussed here suggest that therapy of RA patients may benefit from the use of nonaromatizable androgens and/or the use of aromatase inhibitors.