gebhart/patrepeval huggingface dataset:
Treating non-compatibility problem from matter element analysis to extenics (1997)

Cai Wen's land mark article "Extension Set and Non-compatible Problems" was published in 1983, and thus proclaimed the birth of extenics. Its objectives were to study contradictory (non-compromising and non-compatible) problems in the real world. Its theoretical foundations are matter element theory and extension set theory. Extension control, extension information, extension system, extension logic, etc. , are part of this theoretical system. Its practical methodology includes extension engineering methods which further includes the concepts of extension characteristic analysis, transforming bridge, extension cognition, extension decision, extension forecast, etc. Basically, the theoretical system and the practical methodology of extenics are introduced in this article.
The CLDN5 locus may be involved in the vulnerability to schizophrenia (2004)

The present study was designed to detect three single nucleotide polymorphisms (SNPs) located on 22q11 that was thought as being of particularly importance for genetic research into schizophrenia. We recruited a total of 176 Chinese family trios of Han descent, consisting of mothers, fathers and affected offspring with schizophrenia for the genetic analysis. The transmission disequilibrium test (TDT) showed that of three SNPs, rs10314 in the 3'-untranslated region of the CLDN5 locus was associated with schizophrenia (chi(2) = 4.75, P = 0.029). The other two SNPs, rs1548359 present in the CDC45L locus centromeric of rs10314 and rs739371 in the 5'-flanking region of the CLDN5 locus, did not show such an association. The global chi-square (chi(2)) test showed that the 3-SNP haplotype system was not associated with schizophrenia although the 1-df test for individual haplotypes showed that the rs1548359(C)-rs10314(G)-rs739371(C) haplotype was excessively non-transmitted (chi(2) = 5.32, P = 0.02). Because the claudin proteins are a major component for barrier-forming tight junctions that could play a crucial role in response to changing natural, physiological and pathological conditions, the CLDN5 association with schizophrenia may be an important clue leading to look into a meeting point of genetic and environmental factors.
MOLECULAR AND FUNCTIONAL DIVERSITY OF K+ CHANNELS (1995)

1. Amino acid sequences encoding K+ channels belong to several subfamilies of the voltage-gated ion channel superfamily which includes Na2+-, Ca2+-, and cyclic nucleotide gated channels. The Kv family is the largest group, and encodes delayed rectifier, A-type, and large conductance Ca2+ activated K+ channels. 2. The alpha-subunits of Kv channels form as tetramers of four independent subunits. Each subunit has six membrane spanning regions and a pore forming 'P' region. Subunits belong to subfamilies (Kv1-4, BK, Eag) comprising multiple members, each of which has distinct properties resembling each of the major types of native Kv channel when expressed as homomultimers in heterologous systems. 3. Enormous diversity of Kv channel function arises from the multiplicity of subunits, the formation of heteromultimers within subfamilies and from association with intracellular beta-subunit proteins. 4. In the absence of direct structural information, mutational analyses have provided considerable insights into the structure of the voltage-sensor, pore-forming region and the sites of action of drugs, toxins and associated proteins. 5. Another subfamily, the inwardly rectifying, or KIR, family, appears to have arisen from a deletion of the first four membrane spanning regions of ancient Kv channels, changing gating properties from outward to inward rectification. These include the G-protein gated inward rectifiers and KATP channels.
Cytotoxic activity of purified guinea pig lymphotoxin against various cell lines. (1976)

Cytotoxic activity of the purified guinea pig lymphotoxin (GLT) was tested on various blood cells and various cultured cell lines. GLT was generally ineffective on erythrocytes and lymphocytes, but it was somewhat effective on peritoneal exudate cells indicating GLT might play an important role in the regulatory mechanism of the cellular immunity. Considerable difference in target cell sensitivity was observed among the cultured cell lines tested. The sensitivity of L cells to GLT was significantly lowered by the trypsin treatment of the cells. Furthermore, porcine thyroglobulin glycopeptide exerted weak but definite inhibitory activity against GLT. These results suggest that the cytotoxicity of GLT might be triggered by the binding of GLT to the receptor sites of glycoprotein nature on the cell surface.
A novel general framework for evolutionary optimization: Adaptive fuzzy fitness granulation (2007)

Computational complexity is a major challenge in evolutionary algorithms due to their need for repeated fitness function evaluations. Here, we aim to reduce number of fitness function evaluations by the use of fitness granulation via an adaptive fuzzy similarity analysis. In the proposed algorithm, an individual’s fitness is only computed if it has insufficient similarity to a queue of fuzzy granules whose fitness has already been computed. If an individual is sufficiently similar to a known fuzzy granule, then that granule’s fitness is used instead as a crude estimate. Otherwise, that individual is added to the queue as a new fuzzy granule. The queue size as well as each granule’s radius of influence is adaptive and will grow/shrink depending on the population fitness and the number of dissimilar granules. The proposed technique is applied to a set of 6 traditional optimization benchmarks that are for their various characteristics. In comparison with standard application of evolutionary algorithms, statistical analysis reveals that the proposed method will significantly decrease the number of fitness function evaluations while finding equally good or better solutions.
A green approach for assembling graphene films on different carbon-based substrates and their electrocatalysis toward nitrite (2015)

A green strategy for assembling graphene films on various carbon-based substrates and its significant electrocatalytic activity toward nitrite oxidation.
<title>Laser-induced fluorescence endoscopic imaging for detection of colonic dysplasia</title> (1995)

We are studying the use of the laser-induced fluorescence (LIF) endoscopic images of colonic mucosa for detection of pre-malignant lesions. LIF images were collected through a fiber optic colonoscope, and adenomatous polyps were used as a model of dysplasia. A total of 12 tissue samples containing 29 adenomas, obtained from colectomy specimens from 3 familial adenomatous polyposis patients, were studied. Regions of colonic mucosa were illuminated by a quartz optical fiber with near-UV light from an argon-ion laser. Autofluorescence between 400 and 700 nm was detected by means of an intensified CID camera. In the LIF images, adenomatous polyps appeared lower in intensity than normal mucosa by about a factor of 2. The LIF images were processed by dividing the raw image by a spatially averaged one to correct for differences in the distance to the tissue and in the light collection efficiency of the optics. Relative intensity thresholds were set at values varying between 55% and 90% compared to the spatial average to determine likely areas of disease. The results were compared to histology taken at 2 mm intervals along several transverse cross-sections of the specimens. At a threshold of 75%, 26 true positives, 256 true negatives, 22 false positives, and 3 false negatives were identified, resulting in a sensitivity, specificity, positive predictive value and percentage of correct determinations of 90%, 92%, 54%, and 92%, respectively. These values are comparable to results of independent diagnoses by two pathologists, demonstrating the potential of LIF to guide biopsy.
Thermally activated switching of perpendicular magnet by spin-orbit spin torque (2014)

We theoretically investigate the threshold current for thermally activated switching of a perpendicular magnet by spin-orbit spin torque. Based on the Fokker-Planck equation, we obtain an analytic expression of the switching current, in agreement with numerical result. We find that thermal energy barrier exhibits a quasi-linear dependence on the current, resulting in an almost linear dependence of switching current on the log-scaled current pulse-width even below 10 ns. This is in stark contrast to standard spin torque switching, where thermal energy barrier has a quadratic dependence on the current and the switching current rapidly increases at short pulses. Our results will serve as a guideline to design and interpret switching experiments based on spin-orbit spin torque.
In vitro attachment of glycosyl-inositolphospholipid anchor structures to mouse Thy-1 antigen and human decay-accelerating factor. (1989)

Glycosyl-inositolphospholipid (GPL) anchoring structures are incorporated into GPL-anchored proteins immediately posttranslationally in the rough endoplasmic reticulum, but the biochemical and cellular constituents involved in this "glypiation" process are unknown. To establish whether glypiation could be achieved in vitro, mRNAs generated by transcription of cDNAs encoding two GPL-anchored proteins, murine Thy-1 antigen and human decay-accelerating factor (DAF), and a conventionally anchored control protein, polymeric-immunoglobulin receptor (IgR), were translated in a rabbit reticulocyte lysate. Upon addition of dog pancreatic rough microsomes, nascent polypeptides generated from the three mRNAs translocated into vesicles. Dispersal of the vesicles with Triton X-114 detergent and incubation of the hydrophobic phase with phosphatidylinositol-specific phospholipases C and D, enzymes specific for GPL-anchor structures, released Thy-1 and DAF but not IgR protein into the aqueous phase. The selective incorporation of phospholipase-sensitive anchoring moieties into Thy-1 and DAF but not IgR translation products during in vitro translocation indicates that rough microsomes are able to support and regulate glypiation.
Heat shock proteins: Stress proteins with Janus-like properties in cancer (2008)

Heat shock proteins (HSPs) were first identified as stress proteins that confer resistance to physical stresses such as elevated temperatures in all cellular organisms. HSPs are rapidly elevated after stress and confer a temperature resistant phenotype. Temperature resistance is dependent on the ability of HSPs to function as molecular chaperones and prevent aggregation and on the capacity of Hsp27 and Hsp70 to act as wide spectrum inhibitors of the cell death pathways. HSP expression becomes deregulated in cancer leading to elevated expression. Elevated HSP expression promotes cancer by inhibiting programmed cell death (Hsp27, Hsp70) and by promoting autonomous growth (Hsp90) and leads to resistance to chemotherapy and hyperthermia. Tumor HSPs have another property that can be exploited in therapy. They are immunogenic and can be used to form the basis of anticancer vaccines. Elevation in HSP levels may thus have competing effects in tumor growth, being required for tumor cell survival but conferring a hazard for cancer cells due to their immunogenic properties. This dichotomy is also reflected by the approaches used to target HSP in therapy. Pharmacological approaches are being employed to inhibit activity or expression of tumor HSP. Immunological approaches aim at increasing HSP levels in cells and tissues with the aim of increasing tumor antigen presentation to the immune system.
SOx/NOx Removal from Flue Gas Streams by Solid Adsorbents: A Review of Current Challenges and Future Directions (2015)

One of the main challenges in the power and chemical industries is to remove generated toxic or environmentally harmful gases before atmospheric emission. To comply with stringent environmental and pollutant emissions control regulations, coal-fired power plants must be equipped with new technologies that are efficient and less energy-intensive than status quo technologies for flue gas cleanup. While conventional sulfur oxide (SOx) and nitrogen oxide (NOx) removal technologies benefit from their large-scale implementation and maturity, they are quite energy-intensive. In view of this, the development of lower-cost, less energy-intensive technologies could offer an advantage. Significant energy and cost savings can potentially be realized by using advanced adsorbent materials. One of the major barriers to the development of such technologies remains the development of materials that are efficient and productive in removing flue gas contaminants. In this review, adsorption-based removal of SOx/NOx impurities from flue gas is discussed, with a focus on important attributes of the solid adsorbent materials as well as implementation of the materials in conventional and emerging acid gas removal technologies. The requirements for effective adsorbents are noted with respect to their performance, key limitations, and suggested future research directions. The final section includes some key areas for future research and provides a possible roadmap for the development of technologies for the removal of flue gas impurities that are more efficient and cost-effective than status quo approaches.
Biofertilizers from Algal Treatment of Dairy and Swine Manure Effluents (2007)

Abstract An alternative practice to land spreading of manure effluents is to grow crops of algae on the nitrogen (N) and phosphorus (P) present in these liquid slurries. The overall environmental and economic values of this approach depend, in part, on the use and value of the resulting algal byproduct. Among the potential uses of algal biomass from such systems is its use as a slow release fertilizer. The objective of this study was to evaluate the fertilizer value of algae that had been grown in laboratory (indoor) and pilot scale (outdoor) algal turf scrubbers using raw dairy manure effluent, anaerobically digested dairy manure effluent and raw swine manure effluent for vegetable production. Results from a multifactorial N-mineralization experiment using soil amended with eight algal biomass treatments showed that approximately 5% of total algal N was present as plant available N at day 0. After 21 and 63 days, the total algal N present as mineral N increased to 25–29% and 36–41%, respectively. Approximately 40% of total algal P was present as Mehlich-3 extractable P throughout the 63-day incubations. Results from plant growth experiments showed that 17 day-old corn (Zea mays L.) seedlings grown in algae-amended potting mixes were equivalent to those grown with comparable levels of fertilizer-amended potting mixes with respect to shoot dry weight and nutrient content. There were no differences in the fertilizer value of different batches of algae at the low rate amendment (-47 kg of available N·ha−1). However, at the high rate amendment (-93 kg of available N·ha−1) shoot biomass, and shoot N and P contents were greatest for treatments containing algae grown using indoor laboratory scale algal turf scrubbers (ATS) units and least for treatments with algae grown outdoors using pilot scale ATS units. Longer term field studies are needed to assess the effect of algal biomass amendment on corn and vegetable yields under a range of growth conditions.
Intermediate Q from Soluble Methane Monooxygenase Hydroxylates the Mechanistic Substrate Probe Norcarane:  Evidence for a Stepwise Reaction (2001)

Norcarane is a valuable mechanistic probe for enzyme-catalyzed hydrocarbon oxidation reactions because different products or product distributions result from concerted, radical, and cation based reactions. Soluble methane monooxygenase (sMMO) from Methylosinus trichosporium OB3b catalyzes the oxidation of norcarane to afford 3-hydroxymethylcyclohexene and 3-cycloheptenol, compounds characteristic of radical and cationic intermediates, respectively, in addition to 2- and 3-norcaranols. Past single turnover transient kinetic studies have identified several optically distinct intermediates from the catalytic cycle of the hydroxylase component of sMMO. Thus, the reaction between norcarane and key reaction intermediates can be directly monitored. The presence of norcarane increases the rate of decay of only one intermediate, the high-valent bis-mu-oxo Fe(IV)(2) cluster-containing species compound Q, showing that it is responsible for the majority of the oxidation chemistry. The observation of products from both radical and cationic intermediates from norcarane oxidation catalyzed by sMMO is consistent with a mechanism in which an initial substrate radical intermediate is formed by hydrogen atom abstraction. This intermediate then undergoes either oxygen rebound, intramolecular rearrangement followed by oxygen rebound, or loss of a second electron to yield a cationic intermediate to which OH(-) is transferred. The estimated lower limit of 20 ps for the lifetime of the putative radical intermediate is in accord with values determined from previous studies of sterically hindered sMMO probes.
Synthesis and reactivity of [18F]-N-fluorobenzenesulfonimide (2007)

A novel [18F]NF reagent and two novel radiochemical transformations have been developed: [18F]NFSi has been prepared from sodium dibenzenesulfonimide and reacted in the presence of silyl enol ethers and allylsilanes to deliver labelled fluorinated ketones and allylic fluorides respectively; the radiosynthesis of the fluorinated A ring of vitamin D3 has also been completed with success.
[Netropsin, distamycin A, bis-netropsins as selective inhibitors of restrictases and DNAse I]. (1987)

The simultaneous analysis of DNAase I "footprinting" data and restriction endonucleases inhibition data was performed on the same DNA end-labelled fragment. The inhibition induced by netropsin, a number of bis-netropsins and distamycin A was investigated. These experiments led us to the following conclusions. The restriction endonucleases inhibition by the ligands is caused by the ligand molecules binding in the close vicinity to the restriction endonuclease recognition sequence. The zone of +/- 4 bp from the center of the restriction endonuclease recognition sequence can be defined as the zone of the influence of the bounded ligand on the restriction endonuclease. But in this case the intersection of recognition sequence and the binding site occupied by a single ligand molecule is not sufficient for the inhibition to occur. Restriction endonuclease cutting sites protected by netropsin can be predicted basing upon known nucleotide sequence specificity of netropsin. Netropsin and bis-netropsins show different nucleotide sequence specificity. This fact can be used for selective inhibition of restriction endonucleases.
Bent helical structure in kinetoplast DNA (1982)

We have investigated the unusual physical properties of a restriction fragment of Leishmania tarentolae kinetoplast DNA. A gel-purified fragment comprising slightly more than half of a minicircle was determined by Maxam-Gilbert sequence determination to be 490 base pairs (bp) in length. This fragment has dramatically anomalous electrophoretic behavior; it has an apparent size of 450 bp on a 1% agarose gel but migrates as 1,380 bp on a 12% polyacrylamide gel. However, in gel filtration on Sephacryl S-500, the fragment elutes with an apparent size of 375 bp. Finally, it behaves anomalously in electric dichroism experiments. Field-free rotational relaxation times from transient electric dichroism studies are highly sensitive to effective molecular dimensions. The rotational relaxation time of the kinetoplast fragment is smaller than that of a 309-bp control fragment from pBR322. Because rigorous control experiments rule out the possibility that this fragment is modified, these anomalous properties must be dictated by the sequence itself. Fragment behavior indicates that it has an unusually compact configuration; we propose that this molecule contains a region of systematically bent B-DNA. This model accounts for the fragment's difficulty in snaking through the pores of a polyacrylamide gel, its ease in diffusing into Sephacryl beads, and its smaller rotational relaxation time. Bending of this molecule may be caused by periodicities in the DNA sequence.
Positive and Negative Regulation of Phosphoinositide 3-Kinase-Dependent Signaling Pathways by Three Different Gene Products of the p85α Regulatory Subunit (2000)

Phosphoinositide (PI) 3-kinase is a key mediator of insulin-dependent metabolic actions, including stimulation of glucose transport and glycogen synthesis. The gene for the p85alpha regulatory subunit yields three splicing variants, p85alpha, AS53/p55alpha, and p50alpha. All three have (i) a C-terminal structure consisting of two Src homology 2 domains flanking the p110 catalytic subunit-binding domain and (ii) a unique N-terminal region of 304, 34, and 6 amino acids, respectively. To determine if these regulatory subunits differ in their effects on enzyme activity and signal transduction from insulin receptor substrate (IRS) proteins under physiological conditions, we expressed each regulatory subunit in fully differentiated L6 myotubes using adenovirus-mediated gene transfer with or without coexpression of the p110alpha catalytic subunit. PI 3-kinase activity associated with p50alpha was greater than that associated with p85alpha or AS53. Increasing the level of p85alpha or AS53, but not p50alpha, inhibited both phosphotyrosine-associated and p110-associated PI 3-kinase activities. Expression of a p85alpha mutant lacking the p110-binding site (Deltap85) also inhibited phosphotyrosine-associated PI 3-kinase activity but not p110-associated activity. Insulin stimulation of two kinases downstream from PI-3 kinase, Akt and p70 S6 kinase (p70(S6K)), was decreased in cells expressing p85alpha or AS53 but not in cells expressing p50alpha. Similar inhibition of PI 3-kinase, Akt, and p70(S6K) was observed, even when p110alpha was coexpressed with p85alpha or AS53. Expression of p110alpha alone dramatically increased glucose transport but decreased glycogen synthase activity. This effect was reduced when p110alpha was coexpressed with any of the three regulatory subunits. Thus, the three different isoforms of regulatory subunit can relay the signal from IRS proteins to the p110 catalytic subunit with different efficiencies. They also negatively modulate the PI 3-kinase catalytic activity but to different extents, dependent on the unique N-terminal structure of each isoform. These data also suggest the existence of a mechanism by which regulatory subunits modulate the PI 3-kinase-mediated signals, independent of the kinase activity, possibly through subcellular localization of the catalytic subunit or interaction with additional signaling molecules.