gebhart/patrepeval huggingface dataset:
Lax leaf maize: cell wall composition and nutritional value (2000)

Forage nutritive value, which comprises traits such as digestibility, fibre, lignin and protein content, is an important criterion for maize (Zea mays L) harvested as silage. Lines with a characteristic phenotype (‘lax leaf’) could be useful sources of genes for improved nutritive value in maize. A study was conducted to characterise the cell wall composition of the lax leaf line. Lax leaf inbreds and inbreds representing ‘normal’ maize were evaluated for cell wall neutral sugars, uronic acids, Klason lignin and phenolic acids in five tissues from the ear node and the internode above it. Acid detergent fibre (ADF) and neutral detergent fibre (NDF) and 48 h in vitro true digestibility (IVTD) were predicted using near-infrared reflectance spectrophotometry (NIRS) calibrated with a subset of the scanned samples. Lax leaf inbred tissues had lower levels of ADF, NDF, lignin and xylose and were more digestible than tissues from the inbreds representing ‘normal’ maize. It was not known whether the lax leaf phenotype resulted from alterations in nutritive value traits or whether laxness and nutritive value traits are independent from one another. A second study was conducted to determine the nature of genetic control of the lax leaf character and to determine the genotypic relation between the lax leaf character and nutritive value. A recombinant inbred mapping population was developed from a cross between the lax leaf line and an inbred line with stiff upright leaves. Whole-plant samples from each recombinant inbred line were evaluated for ADF, NDF, acid detergent lignin (ADL) and IVTD of dry matter using NIRS. Laxness, measured by number of broken leaves, was associated with lower nutritive value in this population (genetic correlations 0.16–0.34), which was contrary to expectation. Amplified restriction fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers were used to identify linkage groups associated with the lax leaf character, digestibility and fibre content. Several linkage groups were associated with both the lax leaf character and nutritive value. Where these characters were associated with the same linkage group, the lax leaf parent allele was associated with greater laxness but reduced nutritive value. The lax leaf parent allele was associated with increased nutritive value in linkage groups unassociated with the lax leaf character. While the lax leaf line may be a good source for alleles for improved nutritive value, selection for laxness will not likely be accompanied by improvement in forage quality. © 2000 Society of Chemical Industry
Site-Specific Oligonucleotide Binding Represses Transcription of the Human c- myc Gene in Vitro (1988)

A 27-base-long DNA oligonucleotide was designed that binds to duplex DNA at a single site within the 5' end of the human c-myc gene, 115 base pairs upstream from the transcription origin P1. On the basis of the physical properties of its bound complex, it was concluded that the oligonucleotide forms a colinear triplex with the duplex binding site. By means of an in vitro assay system, it was possible to show a correlation between triplex formation at -115 base pairs and repression of c-myc transcription. The possibility is discussed that triplex formation (site-specific RNA binding to a DNA duplex) could serve as the basis for an alternative program of gene control in vivo.
Format and geometries matter: Structure-based design defines the functionality of bispecific antibodies (2020)

Multispecific antibodies can be generated in different formats. More than two decades of R&D in the field of bispecific antibody engineering revealed that the design and choice of format can have a profound impact on the antibody functionality. This holds in particular true for entities that elicit (inter-)cellular processes such as receptor activation, receptor internalization, receptor clustering or the formation of immunological synapses between two cells. This review covers design parameters that influence the functionality of multispecific formats, with particular focus on T cell-recruiting bispecific antibodies. We describe formats that display the same size and domain sequences but a varying geometry. The structural composition of (artificial) immune synapses is reviewed and allows conclusions why some formats that share size and domain composition are more effective than others. To support the statement that the geometry matters, we present a recently designed antibody format that is characterized by its compact shape. The TriFab-Contorsbody consists of two tumor cell-targeting entities and one moiety for T cell recruitment. The unique barrel-like shape provides a 35-fold increase in potency compared to an IgG-like molecule with identical domain sequences.
Accurate iris segmentation based on novel reflection and eyelash detection model (2002)

The authors propose a novel noise detection model for accurate segmentation of an iris. Eyelash, eyelid and reflection are three main noises. Eyelid has already been solved by a traditional eye model; however, eyelash and reflection have not been tackled. To determinate a pixel in an eyelash, the model presented follows the three criteria: 1) separable eyelash condition; 2) non-informative condition; and 3) connective criterion. The first and second conditions handle separable and multiple eyelashes respectively. The last criterion avoids misclassification of strong iris texture as a single and separable eyelash. For reflection, strong reflection points are detected by a threshold and the weak reflection points around the strong points are determined by connective criterion and statistical test. A number of images are selected to evaluate the accuracy and necessity of our noise detection model and the results are encouraging.
Safety and pharmacodynamic effects of a pharmacological chaperone on α-galactosidase A activity and globotriaosylceramide clearance in Fabry disease: report from two phase 2 clinical studies (2012)

Migalastat HCl is a candidate pharmacological chaperone that provides a novel genotype-specific treatment for FD. It enhanced α-Gal A activity and resulted in GL-3 substrate decrease in patients with responsive GLA mutations. Phase 3 studies are ongoing.
Nanomechanical properties and mineral concentration in articular calcified cartilage and subchondral bone (2003)

We studied articular calcified cartilage (ACC) and the immediately subchondral bone (SCB) in normal and osteoarthritic human femoral heads. Thick slices of human normal reference post mortem (PM) and osteoarthritic (OA) femoral heads (age 55-89 years) were embedded in PMMA, micromilled, carbon coated and studied using quantitative backscattered electron (qBSE) imaging to determine variations in degree of mineralization. With exact microanatomical location, nanoindentation was performed on the same block faces in representative superior (more highly loaded) and medial regions of the joint surface. Using a partial unloading method, elastic modulus as a function of indenter penetration depth was determined using a spherical tipped diamond indenter. A pointed indenter was used to determine the tissue hardness in selected locations. The relationship between mineralization and indentation modulus was more distinct in ACC than in SCB, the latter having a higher matrix concentration with variable collagen orientation. In OA, the bulk of the measurements were coincident with those in the PM samples, although there was a greater range in the levels of mineralization and modulus in ACC. In OA, extremely hypermineralized ACC was found in ACC proper, especially in superior regions, and translocated into SCB and hyaline cartilage. The very highly mineralized cartilage fragments may function as a hard grinding abrasive, accelerating wear rates whether attached to or fragmented from the eburnated surfaces of OA ACC. Highly mineralized regions would also alter loading patterns and thereby contribute to further destruction of the joint tissues.
Striatal Restricted Adenosine A2 Receptor (RDC8) Is Expressed by Enkephalin but Not by Substance P Neurons: An In Situ Hybridization Histochemistry Study (1991)

RDC8 has been recently cloned and characterized as an adenosine A2 receptor. This receptor is expressed exclusively by medium-sized neurons of the striatum as demonstrated by in situ hybridization. We have now studied the relationship of this receptor with three major components of the rat caudate-putamen: enkephalin, substance P, and choline acetyltransferase. Our results demonstrate that the adenosine A2 receptor is expressed exclusively by the enkephalinergic striatal subpopulation but not by the substance P-containing or cholinergic neurons.
The CD94/NKG2-A inhibitory receptor complex is involved in natural killer cell-mediated recognition of cells expressing HLA-G1 (1997)

Human NK cells bear surface receptors that inhibit their cytolytic activity upon specific recognition of MHC class Ia Ags; little is known about the capacity of class Ib molecules to regulate NK cell function. We have studied the roles of different NK inhibitory receptors in recognition of the class Ib HLA-G. To this end, we analyzed the ability of an HLA-defective tumor cell line (721.221) transfected with the membrane form of HLA-G1, which contains the three external domains, to inhibit the cytolytic activity mediated by a panel of NK clones from several donors. A substantial proportion of peripheral blood NK clones appeared to be significantly inhibited by the HLA-G1-transfected cell line (referred to as .221-G1); nevertheless, no relation was observed between the expression and the function of serologically identifiable Ig-SF receptors (p58/p70) and specific recognition of .221-G1 cells. Moreover, p58 killer cell inhibitory receptor-IgG soluble fusion proteins specifically bound to 721.221 transfectants bearing their corresponding HLA-C ligands, but only a weak reactivity with .221-G1 cells was detectable. By contrast, most NK clones blocked by HLA-G1 expressed the CD94/NKG2-A inhibitory receptor, and moreover, CD94-specific mAbs reconstituted their cytolytic activity comparably to anti-HLA class I mAbs. These data support the idea that the CD94/NKG2 receptor complex is involved in the recognition of cells expressing HLA-G1.
Chemical synthesis and expression of a calmodulin gene designed for site-specific mutagenesis (1985)

A gene coding for a calmodulin was synthesized and expressed in Escherichia coli. The gene was produced by the enzymatic ligation of 61 chemically synthesized DNA fragments. The gene possesses 27 unique, regularly spaced, restriction endonuclease cleavage sites to facilitate gene mutagenesis by the replacement of specific gene segments with synthetic double-stranded DNA. An expression vector containing the calmodulin gene was used to transform E. coli. Purification and characterization of calmodulin (VU-1 calmodulin) expressed by these transformants showed that it lacks two posttranslational modifications: an amino-terminal blocking group and N epsilon, N epsilon, N epsilon-trimethyllysine at position 115. The cyclic nucleotide phosphodiesterase activator properties of VU-1, higher plant, and vertebrate calmodulins were not statistically different. However, VU-1 calmodulin was found to activate nicotinamide adenine dinucleotide (NAD) kinase to a maximal level that was at least 3-fold higher than that found with higher plant and vertebrate calmodulins. This higher level of activation is also characteristic of calmodulins from Dictyostelium discoideum and Chlamydomonas reinhardtii [Roberts, D. M., Burgess, W. H., & Watterson, D. M. (1984) Plant Physiol. 75, 796-798; Marshak, D. R., Clarke, M., Roberts, D. M., & Watterson, D. M. (1984) Biochemistry 23, 2891-2899]. The only common feature among Dictyostelium, Chlamydomonas, and VU-1 calmodulins not found in higher plant and vertebrate calmodulins is an unmethylated lysine at position 115. The results indicate that the lack of methylation of lysine-115 may contribute to the maximal level of NAD kinase activation.(ABSTRACT TRUNCATED AT 250 WORDS)
Toward an Efficient DNAzyme (1997)

A 33-nucleotide, guanine-rich DNA oligomer, PS5.ST1, has been reported to catalyze the metallation of mesoporphyrin IX (MPIX) by copper and zinc ions. In this paper we report a thorough investigation of the properties of this DNAzyme. We have established that a 24-nucleotide sequence (PS5.M), from within PS5.ST1, is both the minimal and most optimal catalytic unit. We have found that three related porphyrins are acceptable as substrates by this DNAzyme, of which protoporphyrin IX is preferred as a substrate over the expected substrate, MPIX. We have determined that it is unlikely that a strong, catalytically relevant binding site for copper ions exists in the DNAzyme and that high concentrations of copper destroy the active DNAzyme. This enzyme, whose folded structure likely contains guanine quartets, requires potassium ions for activity; we have shown that as little as 1 mM potassium is sufficient for its catalytic robustness, whereas as much as 0.5 M sodium still will not support catalysis. In determining the pH, temperature, and salt optima for the catalyzed reaction, we have found an unexpected stabilizing role for Tris buffer in both the catalyzed and background metallation reactions. As a consequence of various steps of optimization, we now have a vastly improved DNAzyme, one whose enzymatic parameters compare well both with those of natural ferrochelatases, as well as with those of artificially derived chelatases, composed of protein (a catalytic antibody) and RNA. The existence of this array of biocatalysts for porphyrin metallations allows one-to-one comparisons of the ways in which different biopolymers solve a given catalytic problem.
Investigation of Pulse Transit Times utilizing multisite reflectance photoplethysmography under conditions of artificially induced peripheral vasoconstriction (2014)

Pulse Transit Time (PTT) is the time it takes for an arterial pulsation to travel from the heart to a peripheral site. In recent times, PTT has been advocated as a marker for assessing increased vascular resistance. However, the reliability of PTT as a marker for cardiovascular risks and its inverse relation to beat-to-beat blood pressure is still being investigated. In order to validate the technique as a reliable marker of vascular resistance, PTT measurements were made using photoplethysmographic (PPG) signals obtained from multiple measurement sites in 12 healthy volunteers undergoing right hand immersion in ice water for 30 secs. PTT measurements were made from the ear canal (EC), the left (LIF) and right index fingers (RIF) using custom made photoplethysmographic probes. Activation of the sympathetic nervous system during the ice water immersion caused an increase in vascular resistance, which is associated with an increase in mean arterial pressure and a decrease in PTT in all measurement sites. However, the change in PTT was much larger in the RIF when compared to the LIF and the EC. This demonstrates the cerebral flow autoregulation and the profound peripheral vasoconstriction seen in the right hand. After the ice immersion period, the mean PTT measured from the EC returned to baseline, whereas the LIF PTT exceeded baseline values. This is due to the local vasodilation resulted from the activation of a thermoregulation mechanism.
Database‐Assisted Object Retrieval for Real‐Time 3D Reconstruction (2015)

Abstract In recent years, real‐time 3D scanning technology has developed significantly and is now able to capture large environments with considerable accuracy. Unfortunately, the reconstructed geometry still suffers from incompleteness, due to occlusions and lack of view coverage, resulting in unsatisfactory reconstructions. In order to overcome these fundamental physical limitations, we present a novel reconstruction approach based on retrieving objects from a 3D shape database while scanning an environment in real‐time. With this approach, we are able to replace scanned RGB‐D data with complete, hand‐modeled objects from shape databases. We align and scale retrieved models to the input data to obtain a high‐quality virtual representation of the real‐world environment that is quite faithful to the original geometry. In contrast to previous methods, we are able to retrieve objects in cluttered and noisy scenes even when the database contains only similar models, but no exact matches. In addition, we put a strong focus on object retrieval in an interactive scanning context — our algorithm runs directly on 3D scanning data structures, and is able to query databases of thousands of models in an online fashion during scanning.
Organoiron-mediated alkylation of phosphite esters: synthesis of (dicarbonyl)(.eta.5-cyclopentadienyl)iron-derived nucleoside phosphonate esters (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrganoiron-mediated alkylation of phosphite esters: synthesis of (dicarbonyl)(.eta.5-cyclopentadienyl)iron-derived nucleoside phosphonate estersDon Bergstrom and Theresa SchmaltzCite this: J. Org. Chem. 1992, 57, 3, 873–876Publication Date (Print):January 1, 1992Publication History Published online1 May 2002Published inissue 1 January 1992https://pubs.acs.org/doi/10.1021/jo00029a017https://doi.org/10.1021/jo00029a017research-articleACS PublicationsRequest reuse permissionsArticle Views96Altmetric-Citations6LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Fast environmental lighting for local-PCA encoded BTFs (2004)

Rendering geometric models with complex surface materials in arbitrary lighting environments is a challenging problem. In order to relight and render geometries covered with complex, measured BTFs two problems have to be addressed: the memory problem resulting from the large size of the measured BTF data and the light integration problem resulting from summing up the contributions from all measured light-sources. In this paper we describe how highly efficient BTF compression methods like local-PCA and suitable representations of environmental light based on spherical harmonics can be combined leading to fast environmental lighting for efficiently encoded BTFs. As a side effect the method supports precomputed radiance transfer
Cloning, Overexpression, and Mutagenesis of the Sporobolomyces salmonicolor AKU4429 Gene Encoding a New Aldehyde Reductase, Which Catalyzes the Stereoselective Reduction of Ethyl 4-Chloro-3-Oxobutanoate to Ethyl ( S )-4-Chloro-3-Hydroxybutanoate (1999)

We cloned and sequenced the gene encoding an NADPH-dependent aldehyde reductase (ARII) in Sporobolomyces salmonicolor AKU4429, which reduces ethyl 4-chloro-3-oxobutanoate (4-COBE) to ethyl (S)-4-chloro-3-hydroxybutanoate. The ARII gene is 1,032 bp long, is interrupted by four introns, and encodes a 37,315-Da polypeptide. The deduced amino acid sequence exhibited significant levels of similarity to the amino acid sequences of members of the mammalian 3beta-hydroxysteroid dehydrogenase-plant dihydroflavonol 4-reductase superfamily but not to the amino acid sequences of members of the aldo-keto reductase superfamily or to the amino acid sequence of an aldehyde reductase previously isolated from the same organism (K. Kita, K. Matsuzaki, T. Hashimoto, H. Yanase, N. Kato, M. C.-M. Chung, M. Kataoka, and S. Shimizu, Appl. Environ. Microbiol. 62:2303-2310, 1996). The ARII protein was overproduced in Escherichia coli about 2, 000-fold compared to the production in the original yeast cells. The enzyme expressed in E. coli was purified to homogeneity and had the same catalytic properties as ARII purified from S. salmonicolor. To examine the contribution of the dinucleotide-binding motif G(19)-X-X-G(22)-X-X-A(25), which is located in the N-terminal region, during ARII catalysis, we replaced three amino acid residues in the motif and purified the resulting mutant enzymes. Substrate inhibition of the G(19)-->A and G(22)-->A mutant enzymes by 4-COBE did not occur. The A(25)-->G mutant enzyme could reduce 4-COBE when NADPH was replaced by an equimolar concentration of NADH.
TRPV1 antagonists attenuate antigen-provoked cough in ovalbumin sensitized guinea pigs. (2006)

We examined the molecular pharmacology and in vivo effects of a TRPV1 receptor antagonist, N-(4-Tertiarybutylphenyl)-4(3-cholorphyridin-2-yl)-tetrahydro-pyrazine1(2H) - carboxamide (BCTC) on the guinea pig TRPV1 cation channel. BCTC antagonized capsaicin-induced activation and PMA-mediated activation of guinea pig TRPV1 with IC50 values of 12.2 +/- 5.2 nM, and 0.85 +/- 0.10 nM, respectively. In addition, BCTC (100 nM) completely blocked the ability of heterologously expressed gpTRPV1 to respond to decreases in pH. Thus, BCTC is able to block polymodal activation of gpTRPV1. Furthermore, in nodose ganglia cells, capsaicin induced Ca2+ influx through TRPV1 channel was inhibited via BCTC in a concentration dependent manner. In in vivo studies capsaicin (10 - 300 muM) delivered by aerosol to the pulmonary system of non-sensitized guinea pigs produced an increase in cough frequency. In these studies, the tussigenic effects of capsaicin (300 muM) were blocked in a dose dependent fashion when BCTC (0.01-3.0 mg/kg, i.p.) was administered 30 minutes before challenge. The high dose of BCTC (3.0 mg/kg, i.p) produced a maximum inhibition of capsaicin-induced cough of 65%. We also studied the effects of BCTC (0.03 and 3.0) when administered 60 minutes before capsaicin. Under these conditions, BCTC (3.0 mg/kg, i.p) produced a maximum decrease in capsaicin-induced cough of 31%. In ovalbumin passively sensitized guinea pigs, we found that BCTC (1 and 3 mg/kg, i.p.) attenuated antigen ovalbumin (0.3%) cough responses by 27% and 60%, respectively. We conclude that TRPV1 channel activation may play role in cough mediated by antigen in sensitized guinea pigs. Our results supports increasing evidence that TRPV1 may play a role in the generation of the cough response.