gebhart/patrepeval huggingface dataset:
Vernalization and Gibberellin Physiology of Winter Canola (Endogenous Gibberellin (GA) Content and Metabolism of [3H]GA1 and [3H]GA20 (1995)

Winter canola (Brassica napus cv Crystal) is an oilseed crop that requires vernalization (chilling treatment) for the induction of stem elongation and flowering. To investigate the role of gibberellins (GAs) in vernalization-induced events, endogenous GA content and the metabolism of [3H]GAs were examined in 10-week vernalized and nonvernalized plants. Shoot tips were harvested 0, 8, and 18 d postvernalization (DPV), and GAs were purified and quantified using 2H2-internal standards and gas chromatography-selected ion monitoring. Concentrations of GA1, GA3, GA8, GA19, and GA20 were 3.1-, 2.3-, 7.8-, 12.0-, and 24.5-fold higher, respectively, in the vernalized plants at the end of the vernalization treatment (0 DPV) relative to the nonvernalized plants. Thermoregulation apparently occurs prior to GA19 biosynthesis, since vernalization elevated the concentration of all of the monitored GAs. [3H]GA20 or [3H]GA1 was applied to the shoot tips of vernalized and nonvernalized plants, and after 24 h, plants were harvested at 6, 12, and 15 DPV. Following high-performance liquid chromatography analyses, vernalized plants showed increased conversion of [3H]GA20 to a [3H]GA1-like metabolite and reduced conversion of [3H]GA1 or [3H]GA20 to polar 3H-metabolites, putative glucosyl conjugates. These results demonstrate that vernalization influences GA content and GA metabolism, with GAs serving as probable regulatory intermediaries between chilling treatment and subsequent stem growth.
Developmental and functional adaptation of contractile proteins in cardiac and skeletal muscles (1986)

The goal of this review is to summarize our knowledge of the plasticity of striated muscles in terms of contractile proteins. During development or when the working conditions are changed, the intrinsic physiological properties of both cardiac and skeletal muscles are modified. These modifications generally adapt the muscle to the new environmental requirements. One of the best examples is compensatory overload obtained in fast skeletal muscle by synergistic tenotomy and in a fast ventricle, such as in rats, by aortic banding. In both cases, after a few weeks the initial speed of shortening for the unloaded muscle drops, whereas the maximum tension developed remains unchanged. Heat measurements show that efficiency (i.e., g work/mol ATP) is improved at the fiber level. The fast skeletal muscle becomes slow, fatigue resistant, and then more adapted to endurance. For the ventricle as a whole to become slow is beneficial only if one contraction is considered; however, it is detrimental in terms of cardiac output and leads finally to failure. This adaptational process is partly explained by quantitative and qualitative changes in contractile proteins. Protein synthesis is rapidly enhanced and muscles hypertrophy, which in turn multiplies the contractile units and for the cardiac cylinder normalizes the wall stress. In the meantime the structure and, for myosin, the biological activity of several contractile proteins are modified. These modifications are very unlikely to be posttranscriptional and are in fact explained by several isoform shifts. In both tissues, for example, the expression of the gene coding for a fast myosin (MHCf in skeletal muscle, alpha-MHC in ventricles) is repressed and that of the gene coding for a slow myosin (beta-MHC in both tissues) is stimulated. This is accompanied by a coordinated increase in synthesis of other contractile proteins and, in skeletal muscle only, by isoform shifts of myosin light chains and of the TM-TN regulatory system. Other changes are less well understood. During development it has recently been discovered that three different MHCs (MHCemb, MHCneo, and MHCf) appear sequentially in fast skeletal muscle, which explains, for example, several contradictions of immunological cross-reactions. Currently, however, the functional significance of this finding is unknown, and the well-known decrease of shortening velocity observed in cardiac and skeletal muscles during fetal life is unexplained in terms of contractile proteins.(ABSTRACT TRUNCATED AT 400 WORDS)
Red blood cell pH, the Bohr effect, and other oxygenation‐linked phenomena in blood O2 and CO2 transport (2004)

The discovery of the S-shaped O2 equilibrium curve and the Bohr effect in 1904 stimulated a fertile and continued research into respiratory functions of blood and allosteric mechanisms in haemoglobin (Hb). The Bohr effect (influence of pH/CO2 on Hb O2 affinity) and the reciprocal Haldane effect (influence of HbO2 saturation on H+/CO2 binding) originate in the Hb oxy-deoxy conformational change and allosteric interactions between O2 and H+/CO2 binding sites. In steady state, H+ is passively distributed across the vertebrate red blood cell (RBC) membrane, and intracellular pH (pHi) changes are related to changes in extracellular pH, Hb-O2 saturation and RBC organic phosphate content. As the Hb molecule shifts between the oxy and deoxy conformation in arterial-venous gas transport, it delivers O2 and takes up CO2 and H+ in tissue capillaries (elegantly aided by the Bohr effect). Concomitantly, the RBC may sense local O2 demand via the degree of Hb deoxygenation and release vasodilatory agents to match local blood flow with requirements. Three recent hypotheses suggest (1) release of NO from S-nitroso-Hb upon deoxygenation, (2) reduction of nitrite to vasoactive NO by deoxy haems, and (3) release of ATP. Inside RBCs, carbonic anhydrase (CA) provides fast hydration of metabolic CO2 and ensures that the Bohr shift occurs during capillary transit. The formed H+ is bound to Hb (Haldane effect) while HCO3- is shifted to plasma via the anion exchanger (AE1). The magnitude of the oxylabile H+ binding shows characteristic differences among vertebrates. Alternative strategies for CO2 transport include direct HCO3- binding to deoxyHb in crocodilians, and high intracellular free [HCO3-] (due to high pHi) in lampreys. At the RBC membrane, CA, AE1 and other proteins may associate into what appears to be an integrated gas exchange metabolon. Oxygenation-linked binding of Hb to the membrane may regulate glycolysis in mammals and perhaps also oxygen-sensitive ion transport involved in RBC volume and pHi regulation. Blood O2 transport shows several adaptive changes during exposure to environmental hypoxia. The Bohr effect is involved via the respiratory alkalosis induced by hyperventilation, and also via the pHi change that results from modulation of RBC organic phosphate content. In teleost fish, beta-adrenergic activation of Na+/H+ exchange rapidly elevates pHi and O2 affinity, particularly under low O2 conditions.
Highly stable and reusable imprinted artificial antibody used for in situ detection and disinfection of pathogens (2015)

Sandwich ELISA methods have been widely used for biomarker and pathogen detection because of their high specificity and sensitivity. However, the main drawbacks of this assay are the cost, the time-consuming procedure for the isolation of antibodies and their poor stability. To overcome these restrictions, we herein fabricated artificial antibodies based on imprinting technology and developed a sandwich ELISA for pathogen detection. Both the capture and detection antibodies were obtained <i>via</i> an <i>in situ</i> method, with simplicity, rapidity and low cost. The peroxidase mimics, the CeO<sub>2</sub> nanoparticles, as signal generators were integrated with the detection antibody. The fabricated artificial antibodies exhibited not only natural antibody-like binding affinities and selectivities, but also superior stability and reusability. The detection limit was about 500 CFU mL<sup>-1</sup>, which is much lower than that of traditional ELISA methods (10<sup>4</sup> to 10<sup>5</sup> CFU mL<sup>-1</sup>). Furthermore, the capture antibody can disinfect pathogens <i>in situ</i>.
Bis(2-diphenylphosphinoxynaphthalen-1-yl)methane: transition metal chemistry, Suzuki cross-coupling reactions and homogeneous hydrogenation of olefins (2005)

Transition metal complexes of bis(2-diphenylphosphinoxynaphthalen-1-yl)methane (1) are described. Bis(phosphinite) 1 reacts with Group 6 metal carbonyls, [Rh(CO)2Cl]2, anhydrous NiCl2, [Pd(C3H5)Cl]2/AgBF4 and Pt(COD)I2 to give the corresponding 10-membered chelate complexes 2, 3 and 5-8. Reaction of 1 with [Rh(COD)Cl]2 in the presence of AgBF4 affords a cationic complex, [Rh(COD){Ph2P(-OC10H6)(mu-CH2)(C10H6O-)PPh2-kappaP,kappaP}]BF4 (4). Treatment of 1 with AuCl(SMe2) gives mononuclear chelate complex, [(AuCl){Ph2P(-OC10H6)(mu-CH2)(C10H6O-)PPh2-kappaP,kappaP}] (9) as well as a binuclear complex, [Au(Cl){mu-Ph2P(-OC10H6)(mu-CH2)(C10H6O-)PPh2-kappaP,kappaP}AuCl] (10) with ligand 1 exhibiting both chelating and bridged bidentate modes of coordination respectively. The molecular structures of 2, 6, 7, 9 and 10 are determined by X-ray studies. The mixture of Pd(OAc)2 and effectively catalyzes Suzuki cross-coupling reactions of a range of aryl halides with aryl boronic acid in MeOH at room temperature or at 60 degrees C, giving generally high yields even under low catalytic loads. The cationic rhodium(I) complex, [Rh(COD){Ph2P(-OC10H6)(mu-CH2)(C10H6O-)PPh2-kappaP,kappaP}]BF4 (4) catalyzes the hydrogenation of styrenes to afford the corresponding alkyl benzenes in THF at room temperature or at 70 degrees C with excellent turnover frequencies.
Location based ATM locator system using OpenStreetMap (2014)

Money transaction through ATM machine wherever we go has become phenomenon in our day-to-days activities as it is safe to keep a ATM card rather than keeping cash. When we need cash in any unknown area or during any emergency situation, we need to know about nearest ATM booth from where we can avail this opportunity. In addition, a tourist or new comer may face difficulty in having ATM help without this information. Hence, we have proposed a location based ATM locator system (LBALS) using OpenStreetMap, a growing open source digital map where ATM booths and fast tracks are mapped. Database contains detail information about all available ATM booths and fast tracks of different banks. It requires GPS supported android device with application installed on it for the user. Textual information are provided of nearest ATM booths or fast tracks from user's current position when he requires the information. Some Markers indicate ATM booths or fast tracks on the map. Dijkstra's algorithm has been applied to show the possible shortest path between user and an ATM booth. Haversine formula is also used to calculate perpendicular distance. Implemented LBALS is tested for some random locations in a specific region of our country.
Unit Magnification Optical System without Seidel Aberrations (1959)

A unit magnification system is described which is free from Seidel aberrations and which can be used at very high aperture. The leading higher order aberrations are derived.A method using this system for reproducing photographically small groups of lines with a spacing of 6000 lines/in. is described.Several other possible applications of the system are outlined.
Characterization ofATM mutations in 41 Nordic families with Ataxia Telangiectasia (2000)

The Ataxia Telangiectasia Mutation (ATM) gene is mutated in the rare recessive syndrome Ataxia Telangiectasia (AT), which is characterized by cerebellar degeneration, immunodeficiency, and cancer predisposition. In this study, 41 AT families from Denmark, Finland, Norway, and Sweden were screened for ATM mutations. The protein truncation test (PTT), fragment length and heteroduplex analyses of large (0.8-1.2 kb) cDNA fragments were used. In total, 67 of 82 (82%) of the disease-causing alleles were characterized. Thirty-seven unique mutations were detected of which 25 have not previously been reported. The mutations had five different consequences for the ATM transcript: mutations affecting splicing (43%); frameshift mutations (32%); nonsense mutations (16%); small in-frame deletions (5%); and one double substitution (3%). In 28 of the probands mutations were found in both alleles, in 11 of the probands only one mutated allele was detected, and no mutations were detected in two Finnish probands. One-third of the probands (13) were homozygous, whereas the majority of the probands (26) were compound heterozygote with at least one identified allele. Ten alleles were found more than once; one Norwegian founder mutation constituted 57% of the Norwegian alleles. Several sequence variants were identified, none of them likely to be disease-causing. Some of them even involved partial skipping of exons, leading to subsequent truncation of the ATM protein.
Are Silicone Hydrogel Contact Lenses More Comfortable Than Hydrogel Contact Lenses? (2012)

The current literature review was intended to investigate whether the use of silicone hydrogel contact lenses has resulted in improved comfort compared with that of hydrogel contact lenses when both are used for daily wear. The conclusion reached is that silicone hydrogel contact lenses, which were initially developed to eliminate hypoxia during overnight wear, have not significantly improved comfort compared with the comfort achieved with hydrogel contact lenses when worn on a daily wear basis, even though a body of the published literature would suggest to the contrary. A careful review and consideration of the literature demonstrates that the relative comfort achieved with the two types of contact lenses is in fact highly dependent on the study methodology: Although refitting studies have concluded enhanced comfort with silicone hydrogels, the more robust study designs involving concurrent controls and masking were not able to show a difference, and some even concluded an inferior performance. Evidence-based review has however clearly demonstrated that comfort cannot be considered in isolation but is contact lens specific and depends on the material surface and bulk properties, lens design characteristics, and modality of use of the contact lens, and may also be significantly influenced by the replacement frequency and interaction with any lens care system that may be used.
Regulation of Gi and Go by mastoparan, related amphiphilic peptides, and hydrophobic amines. Mechanism and structural determinants of activity. (1990)

Mastoparan (MP), a cationic, amphiphilic tetradecapeptide, stimulates guanine nucleotide exchange by GTP-binding regulatory proteins (G proteins) in a manner similar to that of G protein-coupled receptors. 1) MP stimulated exchange by isolated G protein alpha subunits and alpha beta gamma trimers. Relative stimulation was greater with alpha beta gamma trimers and beta gamma subunits could increase net MP-stimulated activity. 2) MP action was enhanced by reconstitution of trimeric G protein into phospholipid vesicles. Hill coefficients for activation were 2-4. The membrane-bound alpha-helical conformation of MP appeared to be the activating species. 3) MP blocked the ability of Go to increase the affinity of muscarinic receptors for agonist ligands, suggesting that MP and the receptor may compete for a common binding site on Go. 4) MP stimulated steady state GTPase activity at less than 1 microM Mg2+ and stimulated the dissociation of both GDP and guanosine 5'-O-(3-thiotriphosphate) at less than 1 nM Mg2+. Millimolar Mg2+ blocked the stimulatory effect of MP. Both high and low affinity Mg2+ binding sites are on the alpha subunit. 5) Increasing the amphiphilicity or hydrophobicity of MP enhanced its regulatory activity more than 2-fold and lowered the EC50 more than 10-fold. Several natural amphiphilic peptides also displayed modest stimulatory activity. 6) Benzalkonium chloride competitively antagonized the stimulation of Gi by MP but potently stimulated nucleotide exchange on Go. Because cationic, amphiphilic sequences on the cytoplasmic faces of receptors are required for G protein regulation, these findings suggest that nucleotide exchange on G proteins is regulated by the presentation of multiple cationic structures on the inner face of the plasma membrane.
Regulation of motility and invasion of cancer cells by human monocytic cells. (1995)

Tumour tissues are frequently seen with monocyte/macrophage infiltration. This study was to establish the role of monocytes on the motile and invasive behaviour of human cancer cells. By using a co-culture technique, we have shown that both human peripheral blood monocytes and a monocytic cell line, U937, stimulated colon and breast cancer cell colony scattering, motility, and invasion into a basement membrane (Matrigel). This effect was enhanced when monocytic cells were stimulated by a particulate stimulus. IL-4 and IL-10 reduced these effects of monocytes. We conclude that monocytic cells enhance the motility and invasion of tumour cells. These effects can be regulated by inhibitory cytokines of monocytes.
Human Neoplastic and Normal Cells in Tissue Culture. I. Cell Lines Derived From Malignant Melanomas and Normal Melanocytes2 (1976)

Forty-six cell lines derived from 31 human melanomas obtained from 28 patients were cultured. Fourteen of 16 lines have produced malignant tumors when injected into nude (thymus-deficient) mice. Tumors in 5 of the nude mice metastasized to distant lymph nodes and/or to the lungs of the mouse host. Extreme variability from line to line was observed for doubling time (34 to 106 hr), plating efficiency (0-86%), and melanin production. All tested lines had type B glucose-6-phosphate dehydrogenase, thereby excluding HeLa cell contamination. HeLa cells have been grown for some time in our laboratory. Our results clearly demonstrated that HeLa cell contamination does not occur invariably in heteroploid lines growing in a laboratory simultaneously with Hela cells, provided that proper care is taken to avoid such occurrence. Multiple cell lines derived from the same tumor had identical phosphoglucomutase enzyme phenotype, which suggested a lack of significant cross-contamination between the lines. Four long-term cultures of normal human uveal embryo melanocytes have also been established and characterized. Although all produced melanin after reaching saturation density, they differed from the melanoma cells morphologically; they were flat, not refringent, and lacked piling up and plating ability. When melanoma cells were exposed to bromodeoxyuridine (BUDR) for long periods, a phenotypic change toward non-neoplastic characteristics was observed. Cells became flat and not refringent and, when injected into nude mice, tumors appeared after a long latent period. These changes were completely reversible in vitro and in vivo. The BUDR-treated cultures were undistinguishable from the untreated mother cultures after 2 to 3 passages. Lines derived from tumors in nude mice (obtained by injection of BUDR-treated cells) were again indistinguishable from the untreated mother line. Normal melanocytes were mostly euploid; all the melanoma cells were aneuploid. All 29 cell lines derived from 14 patients had an average chromosome number higher than 46. Detailed group-by-group chromosome analysis always showed an excess of C chromosomes, which suggested that hyperreduplication of one or more C chromosomes is a specific characteristic of human melanomas.
Mice and Rats (Laboratory and Feral) are not a Reservoir for PRRS Virus (1994)

Porcine reproductive and respiratory syndrome (PRRS) is caused by an unclassified arterivirus. The syndrome was first reported in the USA in 1987 as epizootics of reproductive failure in sows and respiratory disease in nursery, growing, and fattening pigs. An enzootic form of the disease has now emerged, characterized by interstitial pneumonia and an increased incidence of secondary infections. Because the disease has now become enzootic on many farms, rodents were investigated as a possible reservoir for the infection. Wild rodents from an endemically infected farm were trapped, and virus isolation for PRRS virus (PRRSV) was attempted using porcine primary alveolar macrophage cultures. PRRSV was not isolated from serum and selected pooled tissues (thymus, lung, and spleen) of 14 feral mice and 2 feral rats. Also, transmission experiments were carried out on 3-week-old Balb/c mice and 12-week-old Fischer-344 rats to determine if these species were susceptible to infection. The rodents were inoculated intranasally, orally, and intraperitoneally with a virus proven to transmit PRRS to pigs. Virus isolations from selected pooled tissues (lung, spleen, thymus, and kidney) and from serum were negative, and there were neither gross nor microscopic lesions. Weight gains and white blood cell counts were not significantly different between treated and control groups. These results indicate that rodents are not susceptible to infection with PRRSV and therefore are probably not a reservoir for the disease.
Heritability of alternative splicing in the human genome (2007)

Alternative pre-mRNA splicing increases proteomic diversity and provides a potential mechanism underlying both phenotypic diversity and susceptibility to genetic disorders in human populations. To investigate the variation in splicing among humans on a genome-wide scale, we use a comprehensive exon-targeted microarray to examine alternative splicing in lymphoblastoid cell lines (LCLs) derived from the CEPH HapMap population. We show the identification of transcripts containing sequence verified exon skipping, intron retention, and cryptic splice site usage that are specific between individuals. A number of novel alternative splicing events with no previous annotations in either the RefSeq and EST databases were identified, indicating that we are able to discover de novo splicing events. Using family-based linkage analysis, we demonstrate Mendelian inheritance and segregation of specific splice isoforms with regulatory haplotypes for three genes: OAS1, CAST, and CRTAP. Allelic association was further used to identify individual SNPs or regulatory haplotype blocks linked to the alternative splicing event, taking advantage of the high-resolution genotype information from the CEPH HapMap population. In one candidate, we identified a regulatory polymorphism that disrupts a 5' splice site of an exon in the CAST gene, resulting in its exclusion in the mutant allele. This report illustrates that our approach can detect both annotated and novel alternatively spliced variants, and that such variation among individuals is heritable and genetically controlled.
System Evolution Tracking through Execution Trace Analysis (2005)

Execution traces produced from instrumented code reflect a system's actual implementation. This information can be used to recover interaction patterns between different entities such as methods, files, or modules. Some solutions for the detection of patterns and their visualization exist, but are limited to small amounts of data and are incapable of comparing data from different versions of a large software system. In this paper, we propose a methodology to analyze and compare the execution traces of different versions of a software system to provide insights into its evolution. We recover high-level module views that facilitate the comprehension of each module's evolution. Our methodology allows us to track the evolution of particular modules and present the findings in three different kinds of visualizations. Based on these graphical representations, the evolution of the concerned modules can be tracked and comprehended much more effectively. Our EvoTrace approach uses standard database technology and instrumentation facilities of development tools, so exchanging data with other analysis tools is facilitated. Further, we show the applicability of our approach using the Mozilla open source system consisting of about 2 million lines of C/C++ code.