gebhart/patrepeval huggingface dataset:
Identification of a protein in several Borrelia species which is related to OspC of the Lyme disease spirochetes (1993)

Using oligonucleotide probes which have previously been shown to be specific for the ospC gene found in the Lyme disease spirochete species Borrelia burgdorferi, B. garinii, and group VS461, we detected an ospC homolog in other Borrelia species including B. coriaceae, B. hermsii, B. anserina, B. turicatae, and B. parkeri. In contrast to the Lyme disease spirochetes, which carry the ospC gene on a 26-kb circular plasmid, we mapped the gene in other Borrelia species to linear plasmids which varied in size among the isolates tested. Some isolates carry multiple copies of the gene residing on linear plasmids of different sizes. The analyses conducted here also demonstrate that these Borrelia species contain a linear chromosome. Northern (RNA) blot analyses demonstrated that the gene is transcriptionally expressed in all species examined. High levels of transcriptional expression were observed in some B. hermsii isolates. Transcriptional start site analyses revealed that the length of the untranslated leader sequence was identical to that observed in the Lyme disease spirochete species. By Western blotting (immunoblotting) with antiserum (polyclonal) raised against the OspC protein of B. burgdorferi, we detected an immunoreactive protein of the same molecular weight as the OspC found in Lyme disease spirochete species. The results presented here demonstrate the presence of a protein that is genetically and antigenically related to OspC which is expressed in all species of the genus Borrelia tested.
Hyperspectral image classification and dimensionality reduction: an orthogonal subspace projection approach (1994)

Most applications of hyperspectral imagery require processing techniques which achieve two fundamental goals: 1) detect and classify the constituent materials for each pixel in the scene; 2) reduce the data volume/dimensionality, without loss of critical information, so that it can be processed efficiently and assimilated by a human analyst. The authors describe a technique which simultaneously reduces the data dimensionality, suppresses undesired or interfering spectral signatures, and detects the presence of a spectral signature of interest. The basic concept is to project each pixel vector onto a subspace which is orthogonal to the undesired signatures. This operation is an optimal interference suppression process in the least squares sense. Once the interfering signatures have been nulled, projecting the residual onto the signature of interest maximizes the signal-to-noise ratio and results in a single component image that represents a classification for the signature of interest. The orthogonal subspace projection (OSP) operator can be extended to k-signatures of interest, thus reducing the dimensionality of k and classifying the hyperspectral image simultaneously. The approach is applicable to both spectrally pure as well as mixed pixels.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Direct detection of single-base extension reaction using genetic field effect transistor (2005)

We have proposed a novel field effect transistor (FET) in combination with single-base extension for a direct, simple and non-labeled DNA sequencing, which is based on detection of molecular recognition at the gate insulator by the field effect. The intrinsic negative charges generated by DNA polymerase-assisted incorporation of deoxynucleotides can be transduced directly into electrical signal. Mere, we demonstrate that single-base extension at the gate surface can be detected directly as a shift of the threshold voltage of the FET. Moreover, it was possible to determine the base sequence of the target DNA by the iterative cycles of single-base extension with each deoxynucleotides and measurement of the threshold voltage.
The Emperor’s Clothes (2003)

The spectrum of plaque vulnerability, instability, and hence, risk, is dynamic and is further modulated by the blood environment.
Lcl of Legionella pneumophila Is an Immunogenic GAG Binding Adhesin That Promotes Interactions with Lung Epithelial Cells and Plays a Crucial Role in Biofilm Formation (2011)

Legionellosis is mostly caused by Legionella pneumophila and is defined by a severe respiratory illness with a case fatality rate ranging from 5 to 80%. In vitro and in vivo, interactions of L. pneumophila with lung epithelial cells are mediated by the sulfated glycosaminoglycans (GAGs) of the host extracellular matrix. In this study, we have identified several Legionella heparin binding proteins. We have shown that one of these proteins, designated Lcl, is a polymorphic adhesin of L. pneumophila that is produced during legionellosis. Homologues of Lcl are ubiquitous in L. pneumophila serogroups but are undetected in other Legionella species. Recombinant Lcl binds to GAGs, and a Δlpg2644 mutant demonstrated reduced binding to GAGs and human lung epithelial cells. Importantly, we showed that the Δlpg2644 strain is dramatically impaired in biofilm formation. These data delineate the role of Lcl in the GAG binding properties of L. pneumophila and provide molecular evidence regarding its role in L. pneumophila adherence and biofilm formation.
The UUAG-specific RNA binding protein, heterogeneous nuclear ribonucleoprotein D0. Common modular structure and binding properties of the 2xRBD-Gly family. (1995)

Human cDNA clones encoding the UUAG-binding heterogeneous nuclear ribonucleoprotein (hnRNP) D0 protein have been isolated and expressed. The protein has two RNA-binding domains (RBDs) in the middle part of the protein and an RGG box, a region rich in glycine and arginine residues, in the C-terminal part ("2xRBD-Gly" structure). The hnRNP A1, A2/B1, and D0 proteins, all possess common features of the 2xRBD-Gly structure and binding specificity toward RNA. Together, they form a subfamily of RBD class RNA binding proteins (the 2xRBD-Gly family). One of the structural characteristics shared by these proteins is the presence of several isoforms presumably resulting from alternative splicing. Filter binding assays, using the recombinant hnRNP D0 proteins that have one of the two RBDs, indicated that one RBD specifically binds to the UUAG sequence. However, two isoforms with or without a 19-amino acid insertion at the N-terminal RBD showed different preference toward mutant RNA substrates. The 19-amino acid insertion is located in the N-terminal end of the first RBD. This result establishes the participation of the N terminus of RBD in determining the sequence specificity of binding. A similar insertion was also reported with the hnRNP A2/B1 proteins. Thus, it might be possible that this type of insertion with the 2xRBD-Gly type RNA binding proteins plays a role in "fine tuning" the specificity of RNA binding. RBD is supposed to bind with RNA in general and sequence-specific manners. These two discernible binding modes are proposed to be performed by different regions of the RBD. A structural model of these two binding sites is presented.
Improvement in runoff parameterization for global climate modelling (2001)

grantor: University of Toronto
APOE genotype influences acquisition and recall following traumatic brain injury (2002)

APOE has been demonstrated to influence traumatic brain injury (TBI) outcome. The relationship between APOE genotype and memory following TBI was examined in 110 participants in the Defense and Veterans' Head Injury Program. Memory performance was worse in those who had an APOE epsilon 4 allele (n = 30) than those who did not (n = 80), whereas genotype groups did not differ on demographic or injury variables or on measures of executive functioning. These data support a specific role for the APOE protein in memory outcome following TBI, and suggest an APOE isoform-specific effect on neuronal repair processes.
Depilation induced anagen as a model to study hedgehog pathway antagonist IPI-926: Implications for biomarker development (2008)

2827 The Hedgehog cell signaling pathway is normally active during embryonic development and plays a critical role in controlling the growth and differentiation of pluripotent progenitor cells in many tissues, including the skin. The Sonic Hedgehog ligand (SHH) is a key regulator of hair follicle growth and cycling and serves as a switch between the resting (telogen) and the growth (anagen) stage of the hair cycle. The hair cycle in the C57BL/6 mouse has been extensively characterized and post depilation provides a highly standardized model in which to explore Hedgehog pathway biology. Using 7 week old C57BL/6 mice which are in the telogen phase of the hair cycle, anagen and subsequently hair re-growth were initiated via chemical depilation with Nair. As a result of anagen initiation, the hair follicle cycle is synchronized allowing for reproducible measurement of Hedgehog target gene expression over time in the skin. Shaved skin, containing hair follicles which remain in telogen, serves as a control. From days 6 through 14 post depilation, corresponding to mid to late anagen, Hedgehog target gene expression was measured by RT-PCR. The Hedgehog signaling pathway is active during anagen as SHH, Gli-1, Gli-2, HHIP and PTCH-1 were all up-regulated in the depilated but not the shaved skin samples. The highest level of Hedgehog target gene expression was noted on day 10 post depilation. Smoothened (SMO) levels remained constant throughout the study and did not differ between telogen and anagen. Having established the up-regulation of Hedgehog target genes during depilation induced anagen, our novel SMO antagonist IPI-926 was evaluated in this model. IPI-926 is an orally bioavailable cyclopamine derivative with favorable PK properties and is a potent inhibitor of the Hedgehog pathway. To test compound activity, a single oral dose of either vehicle or IPI-926 was administered on day 10 post depilation. At various time points post dose, both shaved and depilated skin samples were collected to evaluate gene expression. In a dose-proportional manner, IPI-926 completely inhibited GLI-1 up-regulation in the depilated skin as early as 8 hours post dose and maintains complete inhibition out to 48 hours. IPI-926 also inhibits GLI-1 expression induced as a result of natural anagen, which occurs at approximately 12 weeks of age. Of note, after hair follicle synchronization, onset of melanogenesis occurs on Day 9 post depilation and hair re-growth by day 14. Daily administration of IPI-926 or BID administration of the SHH blocking antibody, 5E1, both inhibited hair re-growth post depilation. Collectively this data suggests that Hedgehog target gene expression and regulation in the hair follicle offers an attractive and obtainable biomarker for Hedgehog pathway antagonists under evaluation in the clinic as anti-cancer agents.
Clinical utility of hyaluronic acid values in serum and bronchoalveolar lavage fluid as tumor marker for bronchogenic carcinoma. (1996)

Various authors have proposed the use of hyaluronic acid (HA) as a tumor marker. In order to analyze its usefulness as a marker in bronchogenic carcinoma, the most common carcinoma in men, we determined the HA values in serum and bronchoalveolar lavage fluid (BAL). We performed prospective studies on two groups of patients: 81 diagnosed as having bronchial carcinoma and 34 with benign respiratory diseases. HA values were higher in patients with cancer than in those with benign diseases (serum: 79.8 ng/ml vs 63.7 ng/ml; BAL: 927 ng/mg vs 522 ng/mg). Also, the percentage of patients with levels exceeding the established cutoff was greater in the group with cancer than in the group with benign disease (serum: 24.6 vs 17.6; BAL: 25.3 vs 3). Statistically significant differences in these percentages were found in BAL (p<0.01). Patients with extended small cell carcinoma had higher HA values (p =0.04) than those with limited disease, and the percentage of patients with abnormal HA values was larger in the group with extended disease than in the group with limited disease (p = 0.004). The serial determinations of HA values in serum reflected the clinical evolution after treatment in 73% of the small cell carcinomas. Most of the patients with benign diseases whose HA values exceeded the cutoff level suffered from acute infectious dis-eases. Once these cases were excluded, the specificity of HA value determination in the diagnosis of carcinoma was very high (serum 96%, BAL 100%). The determination of HA levels in serum or BAL did not have any prognostic value in this study. We conclude that the HA levels in serum and BAL could be of interest as a tumor marker, especially in patients with small cell carcinoma.
A genome-wide association study identifies an association of a common variant in TERT with susceptibility to idiopathic pulmonary fibrosis (2008)

In order to identify a gene(s) susceptible to idiopathic pulmonary fibrosis (IPF), we conducted a genome-wide association (GWA) study by genotyping 159 patients with IPF and 934 controls for 214 508 tag single-nucleotide polymorphisms (SNPs). We further evaluated selected SNPs in a replication sample set (83 cases and 535 controls) and found a significant association of an SNP in intron 2 of the TERT gene (rs2736100), which encodes a reverse transcriptase that is a component of a telomerase, with IPF; a combination of two data sets revealed a p value of 2.9 x 10(-8) (GWA, 2.8 x 10(-6); replication, 3.6 x 10(-3)). Considering previous reports indicating that rare mutations of TERT are found in patients with familial IPF, we suggest that the common genetic variation within TERT may contribute to the risk of sporadic IFP in the Japanese population.
Different regulation of haloperoxidation during agar oligosaccharide-activated defence mechanisms in two related red algae, Gracilaria sp. and Gracilaria chilensis (2007)

The related red seaweeds Gracilaria sp. from the eastern Mediterranean and Gracilaria chilensis from Chile were similar in their enzymatic inventory for halogenation. In both species, halogenation was dependent upon H(2)O(2) and thus driven by haloperoxidases. These could be inhibited with phosphate and reversibly inhibited with azide and were therefore apparently dependent upon vanadate. Both species generated in the first line bromoform and other brominated halocarbons. Gel electrophoresis under non-denaturating conditions demonstrated that both species expressed halogenating peroxidases. Elicitation of Gracilaria sp. with agar oligosaccharides resulted in marked increases in bromination, iodination, and chlorination. Production rates of volatile halocarbons and phenol red bromination both increased by a factor of eight, presumably due to increased availability for haloperoxidases of H(2)O(2) during the oxidative burst response. Elicitation of Gracilaria sp. also triggered a release of bromide ions through DIDS-sensitive anion channels, which allowed for some bromination in bromide-free medium. However, this effect was relatively limited. By contrast, agar oligosaccharide oxidation in G. chilensis did not increase halogenation. Obviously, agar oligosaccharide oxidation does not provide sufficient amounts of hypohalous acids for such increases, because it does not deliver H(2)O(2) at the active site of vanadium-dependent haloperoxidases. These results correlate with earlier findings that the agar oligosaccharide-elicited oxidative burst controls microorganisms while agar oligosaccharide oxidation does not.
Acyclic Analogues of Adenosine Bisphosphates as P2Y Receptor Antagonists:  Phosphate Substitution Leads to Multiple Pathways of Inhibition of Platelet Aggregation (2002)

Activation by ADP of both P2Y(1) and P2Y(12) receptors in platelets contributes to platelet aggregation, and antagonists at these receptor subtypes have antithrombotic properties. In an earlier publication, we have characterized the SAR as P2Y(1) receptor antagonists of acyclic analogues of adenine nucleotides, containing two phosphate groups on a symmetrically branched aliphatic chain, attached at the 9-position of adenine. In this study, we have focused on antiaggregatory effects of P2Y antagonists related to a 2-chloro-N(6)-methyladenine-9-(2-methylpropyl) scaffold, containing uncharged substitutions of the phosphate groups. For the known nucleotide (cyclic and acyclic) bisphosphate antagonists of P2Y(1) receptors, there was a significant correlation between inhibition of aggregation induced by 3.3 microM ADP in rat platelets and inhibition of P2Y(1) receptor-induced phospholipase C (PLC) activity previously determined in turkey erythrocytes. Substitution of the phosphate groups with nonhydrolyzable phosphonate groups preserved platelet antiaggregatory activity. Substitution of one of the phosphate groups with O-acyl greatly reduced the inhibitory potency, which tended to increase upon replacement of both phosphate moieties of the acyclic derivatives with uncharged (e.g., ester) groups. In the series of nonsymmetrically substituted monophosphates, the optimal antagonist potency occurred with the phenylcarbamate group. Among symmetrical diester derivatives, the optimal antagonist potency occurred with the di(phenylacetyl) group. A dipivaloyl derivative, a representative uncharged diester, inhibited ADP-induced aggregation in both rat (K(I) 3.6 microM) and human platelets. It antagonized the ADP-induced inhibition of the cyclic AMP pathway in rat platelets (IC(50) 7 microM) but did not affect hP2Y(1) receptor-induced PLC activity measured in transfected astrocytoma cells. We propose that the uncharged derivatives are acting as antagonists of a parallel pro-aggregatory receptor present on platelets, that is, the P2Y(12) receptor. Thus, different substitution of the same nucleoside scaffold can target either of two P2Y receptors in platelets.
Myocardial hibernation: a delicate balance (2004)

The pathophysiology of myocardial hibernation is characterized as a situation of reduced regional contractile function distal to a coronary artery stenosis that recovers after removal of the coronary stenosis. A subacute "downregulation" of contractile function in response to reduced regional myocardial blood flow exists, which normalizes regional energy and substrate metabolism but does not persist for more than 12-24 h. Chronic hibernation develops in response to one or more episodes of myocardial ischemia-reperfusion, possibly progressing from repetitive stunning with normal blood flow to hibernation with reduced blood flow. An upregulation of a protective gene program is seen in hibernating myocardium, putting it into the context of preconditioning. The morphology of hibernating myocardium is characterized by both adaptive and degenerative features.
Improvement of diagnostic criteria in growth hormone insensitivity syndrome: solutions and pitfalls (1994)

A survey to identify children and adolescents with primary growth hormone insensitivity syndrome (GHIS) yielded 38 patients who were positively identified using a scoring system that included five criteria: height, basal growth hormone (GH), GH binding protein, basal insulin-like growth factor I (IGF-I) and the increase of IGF-I after 4 days of GH administration (IGF generation test). Because of an overlap of the accepted and excluded groups with respect to points scored, an attempt was made to improve the scoring system. The new criteria were: height below -3 SDS, basal GH 4 mU/l or above, GH binding below 10%, basal IGF-I and basal IGF binding protein-3 (IGFBP-3) below the 0.1 centile for age, an increase of IGF-I in the IGF generation test less than 15 micrograms/l, and the increase of IGFBP-3 less than 0.4 mg/l. With this scoring system, a clear separation between the accepted and the excluded groups was obtained. IGFBP-3 was included to give the GH-dependent parameters of the IGF system more weight and because the accuracy of IGFBP-3 in the IGF generation tests was greater than the accuracy of IGF-I, when the group of patients with GHIS was compared with a group of patients with GH deficiency. Unexpectedly, the IGF generation test was unable to segregate both cohorts completely. In the GHIS-positive group, a significant correlation was found between basal IGF-I or IGFBP-3 levels corrected for age (SDS) and height SDS (r = 0.49, p < 0.002 and r = 0.61, p < 0.0001, respectively). There was also a significant correlation between the changes of IGF-I or IGFBP-3 in the IGF generation test and height SDS. That is, the patients with a slight response to GH were those with the least growth retardation, suggesting the existence of partial GH insensitivity.
Evidence for Independent Genetic Control of the Multiple Forms of Maize Endosperm Branching Enzymes and Starch Synthases (1981)

Soluble starch synthase and starch-branching enzymes in extracts from kernels of four maize genotypes were compared. Extracts from normal (nonmutant) maize were found to contain two starch synthases and three branching enzyme fractions. The different fractions could be distinguished by chromatographic properties and kinetic properties under various assay conditions. Kernels homozygous for the recessive amylose-extender (ae) allele were missing branching enzyme IIb. In addition, the citrate-stimulated activity of starch synthase I was reduced. This activity could be regenerated by the addition of branching enzyme to this fraction. No other starch synthase fractions were different from normal enzymes. Extracts from kernels homozygous for the recessive dull (du) allele were found to contain lower branching enzyme IIa and starch synthase II activities. Other fractions were not different from the normal enzymes. Analysis of extracts from kernels of the double mutant ae du indicated that the two mutants act independently. Branching enzyme IIb was absent and the citrate-stimulated reaction of starch synthase I was reduced but could be regenerated by the addition of branching enzyme (ae properties) and both branching enzyme IIa and starch synthase II were greatly reduced (du properties). Starch from ae and du endosperms contains higher amylose (66 and 42%, respectively) than normal endosperm (26%). In addition, the amylopectin fraction of ae starch is less highly branched than amylopectin from normal or du starch. The above observations suggest that the alterations of the starch may be accounted for by changes in the soluble synthase and branching enzyme fractions.
Friction Features of Geosynthetics Through the Pullout Test (2003)

Recently, construction of the reinforced earth structures, which adopts reinforcing materials of geosynthetic, is rapidly increasing due to its good economic advantages, beautiful appearance, and convenient construction. Nonetheless, the most important factor of interpretation and design of the reinforced earth structures, which is assessment ways of friction features between earth and geosynthetic, has not been standardized yet. It has great difference of interpretation and design methods which suggested to the design engineer. This study is to present the way how to assess more reasonably friction features between geogrid and weathered granite soil through the pullout test. Based on a large-scale pullout test of geogrid, the maximum shear stress, interface fricton angle, and friction efficiency are presented with consideration of various test condition.