gebhart/patrepeval huggingface dataset:
Quality of rivers of the United States, 1975 water year; based on the National Stream Quality Accounting Network (NASQAN) (1977)

The National Stream Quality Accounting Network (NASQAN) was established by the U.S. Geological Survey to provide a nationally uniform basis for continuously assessing the quality of U.S. rivers. Stations generally are at the downstream end of hydrologic accounting units in order to measure the quantity and quality of water flowing from the units. The 1975 water year was the first year of operation of the network that represents essentially all of the accounting units and thereby describes the water- quality of the entire country. Data are available on a large number of water-quality constituents measured at 345 stations during the 1975 water year. Temperature data (usually continuous or daily measurements) from NASQAN stations were fitted to a first order harmonic equation and the parameters for the harmonic function are reported for each station. Mean temperatures generally range from 5°-10°C in the North to more than 20°C along the southern border of the continental United States and in Hawaii and Puerto Rico; means were less than 10°C at 63 stations and greater than 25°C at only 7 stations. Amplitudes of the temperature curves are greatest (greater than 12°C) for the streams at midlatitudes and in the Great and Central Plains, and they are smallest for the subtropical and cold-climate streams. Considering chemical and biological characteristics of U.S. streams as described by NASQAN data, water quality is best (by many standards) in the Northeast, Southeast, and Northwest. Waters there generally are low in dissolved solids and major and minor chemical constituents, generally are soft (except in Florida), and carry relatively small amounts of sediment. These conditions mainly reflect the geology of the regions and the relatively large amounts of precipitation. However, many of these waters show the effects of pollution and carry moderate or high levels of major nutrients and have correspondingly high populations of attached and floating plants. High counts of indicator bacteria also show signs of local pollution, particularly in regions of the country with large human and animal populations. In the Northeast, some heavy metals are at moderate levels, but not above most water-quality criteria.Rivers of most of the Mid-Continent and Southwest reflect the arid or semi-arid climate, erodible soils, and agricultural activities. They are characterized by moderate to high levels of dissolved major and minor constituents, sediment, major nutrients, and biota (floating and attached aquatic plants and indicator bacteria). In addition, the most incidences of pesticides in stream and bottom sediments were found in these regions. A special analysis was made to study the patterns of dissolved solids, major nutrients, phytoplankton, and zinc in the Mississippi River above Memphis, Tennessee. It was found that flow volume is an important factor in influencing river quality, and that stations with low concentration of major nutrients generally had low phytoplankton populations as well.
A GA-based dynamic personalized filtering for Internet search service on multi-search engine (2002)

This paper proposed a methodology based on the genetic algorithm (GA) to provide a novel way for searching via the Internet with a multi-search engine. The proposed system provides a WWW interface for users to enter the keyword. The system connects to the Octopus to get all links and contents. According to the user profile, the system dynamically trains the weights of each keyword by GA, and sorts all the links to adopt 10 best-fit to the user. When the user had browsed the first viewing page and gave the system some feedbacks, the system than utilizes the user's feedbacks to re-train the weights of each remaining keywords. After the training, it uses the new weight combination for the keywords set to determine the order of the remaining links to prepare the next viewing page, and so on. The experiments show that it is suitable for those people that want to collect comprehensive information via the Internet.
Intervening sequences divide the gene for the constant region of mouse immunoglobulin mu chains into segments, each encoding a domain. (1980)

To elucidate the structure of the gene for the constant region of immunoglobulin mu chains, we have cloned a 9.9-kilobase-pair fragment of mouse DNA bearing a gene for the constant region of the mu chain (C mu gene) from an IgM-secreting mouse plasmacytoma. The sequence around this gene has apparently undergone somatic rearrangement; the gene occurs in an EcoRI restriction endonuclease fragment of a different size from that in embryo or liver DNA and no C mu-bearing fragment of embryo size remains in the plasmacytoma. The cloned sequence lacks a variable region gene; hence, if this C mu gene is active, its position within the clone indicates that the gene for the variable region of a heavy chain (VH gene) must be more than 3.7 kilobase pairs away. The C mu gene is divided by three intervening sequences into four coding segments, each of which encodes one of the domains (homology units) of the polypeptide. The nucleotide sequence coding for amino acids near the V-C junction is not present within the C mu clone or clones bearing homologous embryonic VH genes. This suggests that an immunoglobulin heavy chain, in common with light chains, is encoded not only by a V and C gene, but also by an independent joining region (JH) gene.
Novel 2-substituted tetrahydro-3H-benz[e]indolamines: highly potent and selective agonists acting at the 5-HT1A receptor as possible anxiolytics and antidepressants (1993)

The synthesis of (+)-(R)-2-cyano-N,N-dipropyl-8-amino-6,7,8,9-tetrahydro-3H- benz[e]indole [(R)-14, U92016A], a potent 5-HT1A agonist, and related analogs is described. In vitro binding studies show that the (R)-enantiomers of this series possess the highest potency for the 5-HT1A receptor. In vivo hypothermia correlates with this, with the (R)-enantiomers causing a greater temperature drop than the (S)-enantiomers. The most active compound in 5-HT1A binding and in the in vivo models was (R)-14, which was found to be highly potent as an agonist in single cell firing studies, as well as potent and of very high intrinsic activity in mouse hypothermia and the sympathetic nerve discharge (SND) models. An in vivo duration of action study, following SND, showed (R)-14 to possess a long duration of action. The synthesis via a nitrene insertion, determination of absolute configuration, and biological activities of this series is described.
Evaluation of Downy Mildew (Peronospora farinosa f.sp. chenopodii) Resistance among Quinoa Genotypes and Investigation of P. farinosa Growth using Scanning Electron Microscopy (2008)

Quinoa (Chenopodium quinoa Willd.) is a pseudocereal native to the Andean region of South America and a staple crop for subsistence farmers in the altiplano of Bolivia and Peru. Downy mildew is the most significant disease of quinoa caused by the pathogen Peronospora farinosa f.sp. chenopodii Byford. This disease greatly impacts quinoa crops with yield losses up to 99%. As fungicides are expensive for farmers, the development of resistant cultivars appears to be the most efficient means for controlling downy mildew. The quinoa germplasm bank contains high amounts of genetic diversity, some of which exhibit mildew resistance. Methods for evaluating mildew severity are important for finding resistant genotypes that are useful in breeding programs. The main objectives of this study were to evaluate and investigate downy mildew resistance in quinoa through several different methods. A simple inoculation method was developed for downy mildew disease assessment by placing a damp piece of cheesecloth on a leaf, pipetting a known spore solution onto the cloth, and subjecting the plants to specific humidity cycles in a growth chamber. After inoculation of five quinoa-breeding lines in a growth chamber, accession 0654 was found to be the most resistant, while genotypes NL6 and Sayana showed moderate resistance. Each of these genotypes displayed some potential for resistance breeding programs. Investigation of the growth and development of P. farinosa through resistant and susceptible quinoa genotypes revealed fewer sporangiophores, hyphal strands, and haustoria among leaf tissues of accession 0654 than in the susceptible Chucapaca cultivar. Peronospora farinosa growth was detected in leaf, petiole, and stem tissues with polymerase chain reaction (PCR) using ITSP primers designed from the internal transcribed spacer (ITS) region of the pathogen. Scanning electron microscopy (SEM) also revealed that P. farinosa penetrated stomata via appressoria, secreted extracellular matrices during sporangia germination, grew intercellularly in leaf and petiole tissues, and exited leaf tissue through stomata. Future research requiring knowledge of resistant quinoa genotypes, P. farinosa growth and development, or inoculation methods for large numbers of small quinoa plants would benefit from this report.
A real-time PCR assay for DNA-methylation using methylation-specific blockers (2004)

DNA methylation-based biomarkers have been discovered that could potentially be used for the diagnosis of cancer by detection of circulating, tumor-derived DNA in bodily fluids. Any methylation detection assay that would be applied to these samples must be capable of detecting small amounts of tumor DNA in the presence of background normal DNA. We have developed a real-time PCR assay, called HeavyMethyl, that is well suited for this application. HeavyMethyl uses methylation-specific oligonucleotide blockers and a methylation-specific probe to achieve methylation-specific amplification and detection. We tested the assays on unmethylated and artificially methylated DNA in order to determine the limit of detection. After careful optimization, our glutathione-S-transferase pi1 and Calcitonin assays can amplify as little as 30 and 60 pg of methylated DNA, respectively, and neither assay amplifies unmethylated DNA. The Calcitonin assay showed a highly significant methylation difference between normal colon and colon adenocarcinomas, and methylation was also detected in serum DNA from colon cancer patients. These assays show that HeavyMethyl technology can be successfully employed for the analysis of very low concentrations of methylated DNA, e.g. in serum of patients with tumors.
The Choice of the Desired Impulse Response in Combined Linear-Viterbi Algorithm Equalizers (1978)

Equalizer structures using the Viterbi Algorithm achieve at least order of magnitude performance improvement over linear equalizers on some intersymbol interference channels. Using a linear equalizer to shape the original channel impulse response to some shorter desired impulse response (DIR) is a technique which reduces the complexity of the Viterbi Algorithm equalizer. This paper looks at three techniques for choosing a DIR. These are choosing the DIR by truncation, minimum mean square error and matching the power spectrum to that of the original channel. Using effective signal to noise ratio as the figure of merit for comparison, results are given for one particular channel.
Direct molecular cloning and expression of two distinct abrin A-chains. (1991)

The protein toxin abrin, which possesses an N-glycosylase activity toward eukaryotic 28 S rRNA, may have a potential in the deliberate eradication of certain cells. Here we report, by polymerase chain reaction technique, the isolation of genomic DNA sequences encoding two distinct abrin A-chains. A third sequence which encoded a part of a third type of A-chain was also isolated. The deduced amino acid sequences of the two full-length A-chains were about 84% similar. Addition of mRNA encoding the full-length A-chains to reticulocyte lysate strongly inhibited protein synthesis in the lysates, and a corresponding glycosylase activity on rRNA was observed. Addition of the same mRNA to toxin-resistant wheat germ extracts led to synthesis of the expected 30-kDa protein which could be precipitated with antibodies specific for abrin.
Induction of Hydroxycinnamic Acid Amides and Tryptophan by Jasmonic Acid, Abscisic Acid and Osmotic Stress in Barley Leaves (2001)

The effects of jasmonic acid (JA) and abscisic aid (ABA) on secondary metabolism in barley (Hordeum vulgare L.) were investigated. Treatment with JA at 100 microM for 48 h induced accumulation of four compounds in barley primary leaves. The accumulation of these compounds was also observed after treatment with ABA at 100 microM. The induced compounds were identified as p-coumaroylputrescine, p-coumaroylagmatine, p-coumaroyl-3-hydroxyagmatine and tryptophan by spectroscopic methods. The profiles of compounds induced by application of JA and ABA were different. JA exhibited stronger inducing activity for hydroxycinnamic acid amides than ABA, while ABA was more active in tryptophan accumulation. The major hydroxycinnamic acid amides in JA- and ABA-treated leaves were p-coumaroylagmatine and p-coumaroyl-3-hydroxyagmatine, respectively. These differences suggested that JA and ABA act in distinct modes. The induction of these compounds was also observed in leaf segments treated with 1 M sorbitol and glucose. These findings suggested that JA and ABA are involved in accumulation of hydroxycinnamic acid amides and tryptophan in response to osmotic stress in barley.
Therapeutic Mechanism and Efficacy of the Antibody–Drug Conjugate BAY 79-4620 Targeting Human Carbonic Anhydrase 9 (2011)

Carbonic anhydrase IX (CAIX) is a cell surface glycoprotein that is expressed in many different tumors and yet restricted in normal tissues to the gastrointestinal tract. It is upregulated by hypoxia and correlates with tumor grade and poor survival in several tumor indications. Monoclonal antibodies (mAb) with single digit nanomolar binding affinity for CAIX were derived by panning with the recombinant ectodomain of CAIX against the MorphoSys HUCAL Gold library of human Fabs. Highest affinity Fabs were converted to full-length IgGs and subjected to further characterization based upon their avidity and selectivity for CAIX, their capacity to undergo internalization in CAIX-expressing cell lines, and their selective localization to CAIX-positive human xenografted tumors when administered to mice as fluorescent conjugates. Through this selection process, the 3ee9 mAb was identified, which upon conjugation to monomethyl auristatin E through a self-immolative enzyme-cleavable linker yielded the potent and selective CAIX antibody-drug conjugate CAIX-ADC (BAY 79-4620). In preclinical human xenograft models in mice representing several tumor indications, BAY 79-4620 showed potent antitumor efficacy and in some models showed partial and complete tumor shrinkage even following a single dose. The mechanism of action was shown by histology to involve the sequelae of events typical of antitubulin agents. Efficacy in murine preclinical models correlated semiquantitatively, with CAIX expression levels as determined by immunohistochemistry and ELISA. These preclinical data collectively support the development of BAY 79-4620 for the treatment of cancer patients with CAIX overexpressing tumors.
LOXL4 as a selective molecular marker in primary and metastatic head/neck carcinoma. (2010)

Although both genes revealed a similar level of overexpression in the carcinoma samples, it was found that the a notably higher percentage of healthy mucosa tested positively for EGFR than LOXL4, indicating that LOXL4 may serve as a selective molecular marker in primary and metastatic head and neck carcinoma.
Gastric Inhibitory Polypeptide Enhanced Lipoprotein Lipase Activity in Cultured Preadipocytes (1979)

Fat feeding stimulated the release of gastric inhibitory polypeptide (GIP) without concomitant insulin secretion. Since antilipolytic effects of GIP have been demonstrated and the uptake of triglyceride fatty acid by adipose tissue postprandially is a process reciprocally regulated with lipolysis, a stimulatory role of GIP on adipose tissue lipoprotein lipase activity may be present. After cultured preadipocytes were incubated for 2 h with GIP, the release of lipoprotein lipase activity into the culture medium and the total cellular activity present in acetone-ether powders of cells were measured. GIP stimulated significant increases in the lipoprotein lipase activity released into the culture medium and in cells. A dose response relationship was strongest for the effect of GIP on the enzyme activity in extracts of acetone-ether powders of the cells. The increased lipoprotein lipase activity produced by GIP could provide a mechanisms for clearance of chylomicron triglyceride after feeding in man.
Cholesterol-dependent infection of Burkitt's lymphoma cell lines by Epstein–Barr virus (2003)

Epstein-Barr virus (EBV) infection is a multi-step process, first requiring virus binding to the host cell, followed by fusion of the viral envelope with the host cell plasma membrane. Efficient EBV entry into B cells requires, at the minimum, the interaction of the EBV-encoded glycoproteins gp350 with cellular CD21 and gp42 with MHC class II proteins. In this study, use of the cholesterol-binding drugs methyl-beta-cyclodextrin and nystatin efficiently inhibited EBV infection of target Burkitt's lymphoma B-cell lines, indicating an important role for cholesterol and suggesting the involvement of lipid rafts in EBV infection.
Complex Formation between Tap and p15 Affects Binding to FG-repeat Nucleoporins and Nucleocytoplasmic Shuttling (2002)

Mammalian Tap-p15 and yeast Mex67p-Mtr2p are conserved and essential mRNA export factor complexes that transport mRNPs through the nuclear pore. Here, we report that the small subunit p15 affects the binding of the large subunit Tap to repeat nucleoporins. BIAcore measurements revealed that recombinant Tap binds with high affinity (K(d) in the nm range) to repeat nucleoporins and dissociates from them very slowly. In contrast, when recombinant Tap was bound to p15, the derived heterodimeric complex exhibited a significant lower affinity to FG-repeat nucleoporins (K(d) in the microm range). Furthermore, when recombinant Tap lacking the N-terminal nuclear localization sequences (TapDeltaNLS) was microinjected in mammalian cells, it did not shuttle; however, TapDeltaNLS with bound p15 efficiently shuttles between nucleus and cytoplasm. We conclude that heterodimerization of Tap and p15 is required for shuttling of the functional Tap-p15 mRNA exporter complex.
Surface labeling of key residues during assembly of the transmembrane pore formed by staphylococcal α‐hemolysin (1994)

Structural changes in staphylococcal alpha-hemolysin (alpha HL) that occur during oligomerization and pore formation on membranes have been examined by using a simple gel-shift assay to determine the rate of modification of key single-cysteine mutants with the hydrophilic sulfhydryl reagent, 4-acetamido-4'-((iodoacetyl)amino)stilbene-2,2'-disulfonate (IASD). The central glycine-rich loop of alpha HL lines the lumen of the transmembrane channel. A residue in the loop remains accessible to IASD after assembly, in keeping with the ability of the pore to pass molecules of approximately 1000 Da. By contrast, residues near the N-terminus, which are critical for pore function, become deeply buried during oligomerization, while a residue at the extreme C-terminus increases in reactivity after assembly, consistent with a location in the part of the pore that projects from the surface of the lipid bilayer.
Regulation of oxysterol 7α-hydroxylase (CYP7B1) in primary cultures of rat hepatocytes (2002)

Conversion of cholesterol into 7alpha-hydroxylated bile acids is a principal pathway of cholesterol disposal. Cholesterol 7alpha-hydroxylase (CYP7A1) is the initial and rate-determining enzyme in the "classic" pathway of bile acid synthesis. An "alternative" pathway of bile acid synthesis is initiated by sterol 27-hydroxylase (CYP27) with subsequent 7alpha-hydroxylation of 27-hydroxycholesterol by oxysterol 7alpha-hydroxylase (CYP7B1). The regulation of CYP7B1, possibly a rate-determining enzyme in the alternative pathway, has not been thoroughly studied. The aims of this study were to (1) study the regulation of liver CYP7B1 by bile acids, cholesterol, adenosine 3', 5'-cyclic monophosphate (cAMP), and phorbol myristate acetate (PMA) in primary rat hepatocytes and (2) determine the effect of CYP7B1 overexpression on rates of bile acid synthesis. The effects of different bile acids (3-150 micromol/L), cAMP (50 micromol/L), PMA (100 nmol/L; protein kinase C stimulator), cholesterol (200 micromol/L), and squalestatin (1 micromol/L; cholesterol synthesis inhibitor) on CYP7B1 expression in primary rat hepatocytes were studied. Taurocholic acid and taurodeoxycholic acid decreased CYP7B1 activity by 45% +/- 10% and 36% +/- 7%, respectively. Tauroursodeoxycholic acid and taurochenodeoxycholic acid did not alter CYP7B1 activity. Inhibition of cholesterol synthesis with squalestatin decreased CYP7B1 activity by 35%, whereas addition of cholesterol increased activity by 39%. Both PMA and cAMP decreased CYP7B1 activity by 60% and 34%, respectively, in a time-dependent fashion. Changes in CYP7B1 messenger RNA (mRNA) levels correlated with changes in specific activities. Overexpression of CYP7B1 led to a marked increase in CYP7B1 mRNA levels and specific activity but no change in rates of bile acid synthesis. In conclusion, in the rat, CYP7B1 specific activity is highly regulated but does not seem to be rate limiting for bile acid synthesis.
Quantitative imaging of element composition and mass fraction using dual‐energy CT: Three‐material decomposition (2009)

In principle, dual-energy CT can only accurately decompose a mixture into two materials. To decompose a mixture into three constitute materials using dual-energy CT measurements, a third criteria must be provided to solve for three unknowns with only two spectral measurements. One solution is to assume that the sum of the volumes of three constituent materials is equivalent to the volume of the mixture (i.e., volume conservation), but this is not always true. A more generalized solution is to use the principle of mass conservation, which assumes that the sum of the masses of the three constituent materials is equivalent to the mass of the mixture. In this article, a mass-conservation based, three-material decomposition dual-energy CT algorithm is described and experimental validation of the accuracy of the technique presented. The results demonstrate that the proposed method can accurately measure elemental concentrations under low noise imaging conditions. Clinically, this may be applied to measure the mass fraction of any chemical element in a three-material mixture of solutions without the requirement of volume conservation.
Erythropoietin induces the tyrosine phosphorylation of its own receptor in human erythropoietin-responsive cells. (1992)

Using the human erythropoietin-responsive hematopoietic cell line UT-7, we showed that erythropoietin (Epo) rapidly and specifically induced the tyrosine phosphorylation of its own receptor (M(r) 75,000) and increased the tyrosine phosphorylation of other proteins of M(r) 140,000, 120,000, 95,000, 60,000, 57,000, and 42,000. Neither granulocyte-macrophage colony-stimulating factor, interleukin 3, interleukin 6, nor the kit ligand induced the phosphorylation of the M(r) 75,000 receptor protein, although these growth factors induced the phosphorylation of other proteins. Cross-linking experiments using 125I-Epo indicated that the UT-7 cells expressed three Epo receptor subunits, of M(r) 100,000, 85,000, and 75,000, among which only the M(r) 75,000 subunit was tyrosine-phosphorylated following activation with Epo.