gebhart/patrepeval huggingface dataset:
Identification and analysis of a matrix‐attachment region 5′ of the rat glutamate‐dehydrogenase‐encoding gene (1993)

Eukaryotic chromatin is thought to be organized into independently regulated loop domains by interaction of matrix-attachment regions (MAR) of the DNA to the nuclear matrix. To define the borders of the chromatin loop containing the glutamate dehydrogenase (GDH) gene, we screened the GDH gene and flanking regions for the presence of MAR sequences. We here report identification, mapping and sequencing of an (A + T)-rich MAR located 2010-1397 bp upstream of the transcription initiation site of GDH, that mediates strong binding to the nuclear matrix. Smaller regions can also confer binding capacity, although at a lower affinity. This (A + T)-rich MAR contained 11 bp and 12 bp (A + T)-rich direct repeats, but not any of the sequences previously described to be associated with MAR activity. We here show that the presence of (A + T)-rich domains of DNA is not sufficient to confer binding capacity, since (A + T)-rich sequences located downstream of the identified MAR did not bind to the nuclear matrix. Moreover, a consensus topoisomerase-II-binding site located downstream of the MAR was found to be insufficient to mediate substantial binding. The number of binding sites in the nuclear matrix for MAR-containing fragments was shown to be approximately 15,000/nucleus. Since organization of the entire rat genome in loops with an average loop size of 100 kbp would require 60,000 binding sites, this suggests that only part of the genome is organized in loops. Alternatively, we might have underestimated the number of binding sites. The GDH MAR, and MAR-containing fragments derived from other species, were found to bind to the same binding sites in the nuclear matrix, although the affinity varied.
[Clinical study on the effect of shuxuening tablet in treatment of coronary heart disease]. (1996)

Shuxuening was made of extract of Folium Ginkgo, the Shuxuening tablet No. 2 was a pure extract and No. 1 was a crude extract. Forty-six coronary heart disease patients were divided randomly into two groups according to the ratio of 2:1, Shuxuening tablet No. 1 and No. 2 were given to the two groups respectively. Results showed that both of them could alleviate the symptom of angina, the total effective rate of 2 groups were 60.00% and 83.87%, there was no significant difference between the two groups. But for the angina of middle and severe degree, the total effective rate of No. 2 was 83.33%, while that of No. 1 was 33.33%, the difference was significant (P < 0.01). They could also improve the abnormal electrocardiogram, the total effective rate of two groups were 60.00% and 74.19%, no significant difference between them was found. The two drugs could decrease the blood lipid as well.
Deepwater Pipelaying Method With A New Welding Technique And J-Curved Pipestring (1979)

ABSTRACT Extensive studies have shown that the J-method of offshore pipelaying can substantially increase the water depth capability for 20 inch pipe to about 3, 000 m (9,850 ft) or for 40 inch pipe to 1,200 m (3,950 ft). This achievement is not presently possible with conventional S-method pipelaying. This method was rendered feasible by the development of a fast, new flash butt welding technique. The entire J-pipe system is described and the technical practicability and potentialities for pipelaying are reported. Extensive welding tests have been performed and more are in progress. The tests have shown that the improved flash butt welding technique can produce quality welds meeting the requirements of offshore laying. The prototype welding machine is almost complete and further test series are scheduled. INTRODUCTION In the first half of the seventies there has been a substantial increase in efforts toward finding technically and economically acceptable solutions for deep water pipelaying. On one hand there are drilling activities in deeper and deeper waters. In 1974/75 drillers reached water depths of 600 to 700 m (2,000 to 2,300 ft). Pipelaying techniques are still relatively undeveloped for those water depths. In spite of decreased drilling activities in deep water, development is continuing. The 2,000 m (6,500ft) mark is forthcoming. On the other hand the problem of transporting oil and gas across deepwater areas exists. Best examples are pipelines for the Norwegian Trench and the Mediterranian Sea. The utilization of that gas found offshore or onshore - without a pipeline is possible only by shipping the gas to consumers in a processed condition, as methanol, LNG, etc. In 1975 a group of German companies commenced a deepwater pipelaying research and development programme. Many concepts for deepwater pipelining were assembled and evaluated. Special attention was paid to economic aspects, to the state of art, to experience with various pipelay techniques, and to the availability of essential technology in consideration of risks and time for research and development. The most promising method J-pipelaying with flash butt welding - was singled out and further developed. This paper describes results from this development programme. ARGUMENTS FOR J-CURVED PIPESTRING LAYING Offshore pipelaying methods differ in the procedure for lowering the pipestring and in the method of connecting new sections. If the pipeline is lowered from the surface, the suspended pipe span forms a J-curve or an S-curve. If a pipestring is constructed by the bottom tow method, there is no such curve. The last method requires an on-bottom connection, the first and second mentioned methods can be performed by (1) an on-bottom, (2) a floating (i. e. between bottom and surface) or (3) a surface connection Many technical limits of the pipelay methods refer to these aspects. Other limits are economic ones.
Intrinsic bioconjugation for site-specific protein PEGylation at N-terminal serine (2014)

Recently developed chemical ligation protocols were elaborated for rapid N-terminal protein PEGylation. We introduce a PEG-salicylaldehyde ester and demonstrate its site-specific ligation to the N-terminus of the RNase S protein and to the therapeutic polypeptide PTH (1-34).
Thermodynamic limits of extractable energy by pressure retarded osmosis (2014)

The maximum specific energy obtainable in pressure retarded osmosis and the corresponding optimal operating conditions are analytically determined for three different operation modes: an ideal reversible process, and constant-pressure systems with either co-current flow or counter-current flow in a membrane module.
Multi-disciplinary ontological geo-analytical incident modeling (2015)

Cultural patterns and representations of crime areas are important in geo-analytics. We discuss a multi-disciplinary ontology that provides an analytical, architectural framework to apply a broad spectrum of analytical capabilities to changes the world faces on a daily basis to determine an optimal allocation of resources for continuous enrichment of Foundation GEOINT content. All of these changes such as food shortages, weather, environmental hazards, traffic congestion, economic crises, political unrest, un-employment, and specifically crime, pose a constant struggle in societies to maintain status quo. What has always been difficult to predict is change to status quo, or predicting regions at risk or undergoing stress. We propose taking knowledge of a location and society, and marrying that with modern analytical capabilities, including linear game theory, to pit forces of maintaining status quo against forces within society that desire to force a drastic change. The result is a probabilistic output of potential outcomes that can be further analyzed to predict most likely and most dangerous outcomes. Our solution is based on analytical environment to support ingestion of many data sources and integration of analytical algorithms such as feature extraction, crowd source analysis, open source data mining, trends, pattern analysis and linear game theory optimization. Our framework consists of a hierarchy of data, space, time and knowledge entities. We exploit such crime statistics to predict crime activity based on past observations. We also show simulations based on minimum mean squared error (mmse) and pseudo estimators of crime activity.
High quality narrow GaInAs/InP quantum wells grown by atmospheric organometallic vapor phase epitaxy (1986)

A series of GaInAs/InP quantum wells from 10 to 135 Å has been grown by atmospheric organometallic vapor phase epitaxy using pressure balancing techniques. These wells exhibit strong exciton peaks at 4 K and have quantized energy shifts of up to 326 meV. These energy shifts are compared with two simple finite well models (Kronig–Penney and envelope function approximation) using a conduction-band offset of Vc≊40% ΔEg(GaInAs) and are in close agreement with the latter model. The full width half-maximum linewidths indicate an average interface roughness of ≊1 monolayer.
Effects of perfluorooctane sulfonate and its alternatives on long-term potentiation in the hippocampus CA1 region of adult rats in vivo (2016)

With the limited but ongoing usage of perfluorooctane sulfonate (PFOS), the health effects of both PFOS and its alternatives are far from being understood. Long-term potentiation (LTP) was evaluated in rats after exposure to PFOS and its alternatives, aiming to provide some evidence about their potential to affect cognitive ability. Different dosages of PFOS and alternative chemicals, including perfluorohexane sulfonate (PFHxS), perfluorobutane sulfonate (PFBS) and chlorinated polyfluorinated ether sulfonate (Cl-PFAES), were given to rats <i>via</i> acute intracerebroventricular injection. The field excitatory postsynaptic potential (fEPSP) amplitude of the input/output functions, paired-pulse facilitations, and LTP <i>in vivo</i> were recorded. PFOS and its alternatives inhibited LTP in varying degrees, without significant effects on the normal synaptic transmission. In addition, PFHxS and Cl-PFAES exhibited comparable potential to PFOS in disturbing LTP. The results suggested that acute exposure to PFOS and its alternatives impaired the synaptic plasticity by a postsynaptic rather than a presynaptic mechanism. Besides, the fEPSP amplitude of the baseline was reduced by Cl-PFAES but not by other compounds, indicating that Cl-PFAES might act in a different mode. Providing some electrophysiological evidence and the potential mechanism of the neurotoxicity induced by PFOS and its alternatives, the present study addresses further evaluation of their safety and health risks.
Modulation of the action of the recBC enzyme of Escherichia coli K-12 by Ca2+. (1979)

The various activities of the recBC enzyme of Escherichia coli are differentially sensitive to reaction conditions. Although spermidine up to 50 mM and putrescine up to 40 mM in the presence of Mg/sup 2 +/ produce no significant alteration in the activities of the enzyme, low concentrations of Ca/sup 2 +/ have a dramatic effect. In the presence of 1 mM Ca/sup 2 +/, 1 mM Mg/sup 2 +/, and 5 mM ATP, the DNA-dependent ATPase is unaffected, but the double strand DNA exonuclease and the single strand DNA exonuclease and endonuclease activities are completely inhibited. Duplex phage T7 DNA which has been exposed to enzyme under these conditions remains wholly duplex and full length, although about 5 nicks are made randomly in each duplex. When DNA binding protein from E. coli is included in the reaction with enzyme and DNA, the products are, at early stages of the reaction, duplex DNA molecules with one or two single-stranded tails at a terminus; after prolonged incubation, solely single-stranded fragments of 5000 to 35,000 nucleotides are found. (Full length strands are roughly 40,000 nucleotides long.) These products can be rationalized by a model in which the enzyme binds initially to the terminusmore » of a duplex DNA molecule and then tracks along the DNA, unwinding the strands of the helix as it moves. This denaturation would be transient and localized around the enzyme molecule so that the DNA would renature after the enzyme has passed through a particular region. However, the renaturation can be prevented by the presence of DNA binding protein during the reaction. During the passage of an enzyme molecule through a DNA molecule, a limited number of nicks are randomly introduced in a manner essentially unaffected by binding protein. This mode of action is distinct from that observed for the degradation of duplex DNA with Mg/sup 2 +/ but not Ca/sup 2 +/ present.« less
Current-Induced Domain Wall Motion in a Compensated Ferrimagnet (2018)

Owing to the difficulty in detecting and manipulating the magnetic states of antiferromagnetic materials, studying their switching dynamics using electrical methods remains a challenging task. By employing heavy-metal-rare-earth-transition-metal alloy bilayers, we experimentally study current-induced domain wall dynamics in an antiferromagnetically coupled system. We show that the current-induced domain wall mobility reaches a maximum at the angular momentum compensation point. With experiment and modeling, we further reveal the internal structures of domain walls and the underlying mechanisms for their fast motion. We show that the chirality of the ferrimagnetic domain walls remains the same across the compensation points, suggesting that spin orientations of specific sublattices rather than net magnetization determine Dzyaloshinskii-Moriya interaction in heavy-metal-ferrimagnet bilayers. The high current-induced domain wall mobility and the robust domain wall chirality in compensated ferrimagnetic material opens new opportunities for high-speed spintronic devices.
Pattern spectrum and multiscale shape representation (1989)

The results of a study on multiscale shape description, smoothing and representation are reported. Multiscale nonlinear smoothing filters are first developed, using morphological opening and closings. G. Matheron (1975) used openings and closings to obtain probabilistic size distributions of Euclidean-space sets (continuous binary images). These distributions are used to develop a concept of pattern spectrum (a shape-size descriptor). A pattern spectrum is introduced for continuous graytone images and arbitrary multilevel signals, as well as for discrete images, by developing a discrete-size family of patterns. Large jumps in the pattern spectrum at a certain scale indicate the existence of major (protruding or intruding) substructures of the signal at the scale. An entropy-like shape-size complexity measure is also developed based on the pattern spectrum. For shape representation, a reduced morphological skeleton transform is introduced for discrete binary and graytone images. This transform is a sequence of skeleton components (sparse images) which represent the original shape at various scales. It is shown that the partially reconstructed images from the inverse transform on subsequences of skeleton components are the openings of the image at a scale determined by the number of eliminated components; in addition, two-way correspondences are established among the degree of shape smoothing via multiscale openings or closings, the pattern spectrum zero values, and the elimination or nonexistence of skeleton components at certain scales.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Surface Tension and Its Temperature Coefficient for Liquid Metals (2005)

Temperature-dependent surface tension gamma(lv)(T) and its temperature coefficient (T) [=dgamma(lv)(T)/dT] for liquid metals are thermodynamically determined on the basis of an established model for surface energy of crystals. The model predictions correspond to the available experimental or theoretical results. It is found that for metallic liquids gamma(lv)(T(m)) proportional, variant H(v)/V(m)(2/3), gamma(lv)(T) proportional, variant T, and (T) proportional, variant T over a certain temperature range (including T < T(m) and T >/= T(m)), where H(v) and V(m) are the liquid-vapor transition enthalpy at boiling temperature T(b) and the atomic volume at melting temperature T(m), respectively. Furthermore, T(m)(T(m))/gamma(lv)(T(m)) almost remains constant, which gives a way to estimates of (T(m)) values when T(m) and gamma(lv)(T(m)) are known.
EPHA2 Blockade Overcomes Acquired Resistance to EGFR Kinase Inhibitors in Lung Cancer (2016)

Despite the success of treating EGFR-mutant lung cancer patients with EGFR tyrosine kinase inhibitors (TKI), all patients eventually acquire resistance to these therapies. Although various resistance mechanisms have been described, there are currently no FDA-approved therapies that target alternative mechanisms to treat lung tumors with acquired resistance to first-line EGFR TKI agents. Here we found that EPHA2 is overexpressed in EGFR TKI-resistant tumor cells. Loss of EPHA2 reduced the viability of erlotinib-resistant tumor cells harboring EGFR(T790M) mutations in vitro and inhibited tumor growth and progression in an inducible EGFR(L858R+T790M)-mutant lung cancer model in vivo. Targeting EPHA2 in erlotinib-resistant cells decreased S6K1-mediated phosphorylation of cell death agonist BAD, resulting in reduced tumor cell proliferation and increased apoptosis. Furthermore, pharmacologic inhibition of EPHA2 by the small-molecule inhibitor ALW-II-41-27 decreased both survival and proliferation of erlotinib-resistant tumor cells and inhibited tumor growth in vivo. ALW-II-41-27 was also effective in decreasing viability of cells with acquired resistance to the third-generation EGFR TKI AZD9291. Collectively, these data define a role for EPHA2 in the maintenance of cell survival of TKI-resistant, EGFR-mutant lung cancer and indicate that EPHA2 may serve as a useful therapeutic target in TKI-resistant tumors.
Synthesis, characterization, and biodegradation of copolymers of unsaturated and saturated poly(ester amide)s (2007)

Abstract A new family of biodegradable copolymers of unsaturated poly(ester amide)s (UPEAs) and saturated poly(ester amide)s (SPEAs) based on L ‐phenylalanine, aliphatic dicarboxylic acids, and aliphatic dialcohols was synthesized by solution polycondensation and characterized. These unsaturated/saturated poly(ester amide) copolymers (USPEAs) were obtained in fairly good yields with N,N ‐dimethylacetamide as the solvent. The molecular weights ( M n and M w ) of the USPEAs measured by GPC ranged from 15 to 60 kg/mol with a molecular weight distribution of 1.07–1.63. The chemical structures of the USPEAs were confirmed by both IR and NMR spectra. The USPEA copolymers had glass transition temperatures lower than that of pure UPEA but higher than that of pure SPEA. An increase in the unsaturated component in the USPEA copolymers led to an increase in their glass transition temperatures. The solubility of the copolymers was good in N,N ‐dimethylacetamide and dimethyl sulfoxide but poor in water, acetone, methanol, and ethyl acetate. The preliminary in vitro biodegradation properties of the USPEA copolymers were investigated in both pure phosphate buffered saline (PBS) buffer and α‐chymotrypsin solutions. The copolymers showed significantly faster weight loss in an enzyme solution than in a pure PBS buffer. Upon the adjustment of the unsaturated‐to‐saturated diester monomer feed ratio, the obtained USPEA copolymers could have controlled chemical and physical properties, such as glass transition temperatures, solubility, and biodegradability, which could easily extend their applications to biomedical and pharmaceutical areas. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 1595–1606, 2007
Functional impacts of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine at a single hemi-modified CpG dinucleotide in a gene promoter (2017)

Enzymatic oxidation of 5-methylcytosine (5-mC) in the CpG dinucleotides to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxycytosine (5-caC) has central role in the process of active DNA demethylation and epigenetic reprogramming in mammals. However, it is not known whether the 5-mC oxidation products have autonomous epigenetic or regulatory functions in the genome. We used an artificial upstream promoter constituted of one cAMP response element (CRE) to measure the impact of 5-mC in a hemi-methylated CpG on the promoter activity and further explored the consequences of 5-hmC, 5-fC, and 5-caC in the same system. All modifications induced mild impairment of the CREB transcription factor binding to the consensus 5'-TGACGTCA-3' CRE sequence. The decrease of the gene expression by 5-mC or 5-hmC was proportional to the impairment of CREB binding and had a steady character over at least 48 h. In contrast, promoters containing single 5-fC or 5-caC underwent further progressive loss of activity, up to an almost complete repression. This decline was dependent on the thymine-DNA glycosylase (TDG). The results thus indicate that 5-fC and 5-caC can provide a signal for perpetuation and enhancement of the repressed transcriptional state by a mechanism that requires base excision repair.
[1H magnetic resonance spectroscopy in the evaluation of high intensity focused ultrasound ablation for primary liver cancer]. (2011)

To investigate the clinical value of 1H magnetic resonance spectroscopy (1H MRS) in the evaluation of high intensity focused ultrasound (HIFU) ablation for primary liver cancer. Routine magnetic resonance sequences, contrast-enhanced magnetic resonance imaging and respiratory-triggered single voxel point resolved spectroscopy sequence (PRESS) were performed on 24 patients with primary liver cancer before and after HIFU ablation. A respiratory-triggered axial T2 weighted imaging (T2WI) was used as localizer for PRESS. Spectroscopy data was transmitted to a personal computer and was post-processed with a custom software (Saker, provided by Ning Jing, an engineer in GE Healthcare). It would be considered "technical success" if the baselines of spectra were stable and main metabolites were without overlapping and could be identified. Integral areas of choline (Cho) peak at 3.2 parts per million (ppm) and lipid (Lip) peak at 1.3 ppm were measured, and the choline to lipid (Cho/Lip) ratios were calculated. The differences of areas of Cho, Lip peak and Cho/Lip ratios before and after HIFU ablation were compared by using paired samples t test, and a P value of less than 0.05 was considered statistically significant. The technical success rate of 1H-MRS was 87.50% (42/48). Integral areas of Cho peak and Lip peak of 20 patients with satisfied spectra were measured, and the Cho/Lip ratios were calculated. The Integral area of Cho peak decreased from 34 597+/-6 802 before HIFU ablation to 6 372+/-2 466 after HIFU ablation (t = 18.02, P less than 0.01). The Integral area of Lip peak increased from 147 948+/-16 317 before HIFU ablation to 149 069+/-16 345 after HIFU ablation (t = -15.11, P less than 0.01). The Cho/Lip ratio decreased from 0.23+/-0.03 before HIFU ablation to 0.04+/-0.02 after HIFU ablation (t = 25.32, P less than 0.01). 1H-MRS could provide information of metabolites changes of primary liver cancer after HIFU ablation and could be used as a complementary sequence to other magnetic resonance sequences to evaluate all around primary liver cancer after HIFU ablation.