gebhart/patrepeval huggingface dataset:
Genetic and Physiological Architecture of Early Vigor in Aegilops tauschii, the D-Genome Donor of Hexaploid Wheat. A Quantitative Trait Loci Analysis (2005)

Plant growth can be studied at different organizational levels, varying from cell, leaf, and shoot to the whole plant. The early growth of seedlings is important for the plant's establishment and its eventual success. Wheat (Triticum aestivum, genome AABBDD) seedlings exhibit a low early growth rate or early vigor. The germplasm of wheat is limited. Wild relatives constitute a source of genetic variation. We explored the physiological and genetic relationships among a range of early vigor traits in Aegilops tauschii, the D-genome donor. A genetic map was constructed with amplified fragment-length polymorphism and simple sequence repeat markers, and quantitative trait loci (QTL) analysis was performed on the F(4) population of recombinant inbred lines derived from a cross between contrasting accessions. The genetic map consisted of 10 linkage groups, which were assigned to the seven chromosomes and covered 68% of the D genome. QTL analysis revealed 87 mapped QTLs (log of the odds >2.65) in clusters, 3.1 QTLs per trait, explaining 32% of the phenotypic variance. Chromosomes 1D, 4D, and 7D harbored QTLs for relative growth rate, biomass allocation, specific leaf area, leaf area ratio, and unit leaf rate. Chromosome 2D covered QTLs for rate and duration of leaf elongation, cell production rate, and cell length. Chromosome 5D harbored QTLs for the total leaf mass and area and growth rate of the number of leaves and tillers. The results show that several physiological correlations between growth traits have a genetic basis. Genetic links between traits are not absolute, opening perspectives for identification of favorable alleles in A. tauschii to improve early vigor in wheat.
Enzyme replacement in a canine model of Hurler syndrome. (1994)

The Hurler syndrome (alpha-L-iduronidase deficiency disease) is a severe lysosomal storage disorder that is potentially amenable to enzyme-replacement therapy. Availability of a canine model of the disease and a sufficient supply of corrective enzyme have permitted a therapeutic trial lasting 3 mo. Recombinant human alpha-L-iduronidase, purified to apparent homogeneity from secretions of a stably transfected Chinese hamster ovary cell line, was administered i.v. to homozygous affected animals in doses of approximately 1 mg. The enzyme rapidly disappeared from the circulation in a biphasic manner, with t1/2 of 0.9 and 19 min, respectively, and was taken up primarily by the liver. Biopsy of the liver before and after a very short trial (seven doses administered over 12 days) showed remarkable resolution of lysosomal storage in both hepatocytes and Kupffer cells. After weekly administration of enzyme to three affected animals over a period of 3 mo, the level of enzyme was about normal in liver and spleen, lower but significant in kidney and lung, and barely detectable (0-5% of normal) in brain, heart valves, myocardium, cartilage, and cornea. Light and electron microscopic examination of numerous tissues showed normalization of lysosomal storage in liver, spleen, and kidney glomeruli, but there was no improvement in brain, heart valves, or cornea. Even though the treated dogs developed complement-activating antibodies against alpha-L-iduronidase, clinical symptoms could be prevented by slow infusion of enzyme and premedication.
1-Substituted 4-Aryl-5-pyridinylimidazoles:  A New Class of Cytokine Suppressive Drugs with Low 5-Lipoxygenase and Cyclooxygenase Inhibitory Potency (1996)

A series of 1-alkyl- or -aryl-4-aryl-5-pyridinylimidazoles (A) were prepared and tested for their ability to bind to a recently discovered protein kinase termed CSBP and to inhibit lipopolysaccharide (LPS)-stimulated TNF production in mice. The kinase, CSBP, appears to be involved in a signaling cascade initiated by a number of inflammatory stimuli and leading to the biosynthesis of the inflammatory cytokines IL-1 and TNF. Two related imidazole classes (B and C) had previously been reported to bind to CSBP and to inhibit LPS-stimulated human monocyte IL-1 and TNF production. The members of the earlier series exhibited varying degrees of potency as inhibitors of the enzymes of arachidonic acid metabolism, PGHS-1 and 5-LO. Several of the more potent CSBP ligands and TNF biosynthesis inhibitors among the present series of N-1-alkylated imidazoles (A) were tested as inhibitors of PGHS-1 and 5-LO and were found to be weak to inactive as inhibitors of these enzymes. One of the compounds, 9 (SB 210313) which lacked measureable activity as an inhibitor of the enzymes of arachidonate metabolism, and had good potency in the binding and in vivo TNF inhibition assays, was tested for antiarthritic activity in the AA rat model of arthritis. Compound 9 significantly reduced edema and increased bone mineral density in this model.
Opsonic requirements for staphylococcal phagocytosis. Heterogeneity among strains. (1977)

Efficient phagocytosis of staphylococci by human neutrophilis is dependent on bacterial opsonization by serum factors. These factors include specific antibodies as well as components of the classical and alternative complement systems. In this study the opsonic requirements of three strains of S. aureus and three strains of S. epidermidis were investigated by incubating [3H]thymidine-labelled bacteria in sera with different opsonic activities and measuring rates of phagocytosis by human neutrophils. Opsonization of S. aureus Cowan I and 502 A depended primarily on activation of the classical complement pathway. Effective opsonization occurred in the absence of immunoglobulin but not in the absence of complement. A protein A deficient mutant of S. aureus Cowan I was poorly opsonized in the absence of IgG, however. S. aureus Wood 46 and two strains of S. epidermidis were opsonized primarily through the alternative complement pathway and depended on the presence of serum IgG. A third S. epidermidis strain was efficiently opsonized in heat-inactivated serum without complement activity. Thus, a heterogeneity of opsonic requirements was found among staphylococcal strains. It is proposed that cell wall protein A may be an important determinant of this heterogeneity.
Osteoprotegerin Gene Polymorphisms in Men with Coronary Artery Disease (2004)

Osteoprotegerin (OPG) antagonizes receptor activator of nuclear factor-kappaB ligand (RANKL), the principal regulator of osteoclasts. Of note, OPG-deficient mice display osteoporosis and arterial calcification. Recently, OPG gene polymorphisms have been associated with osteoporosis and early predictors of cardiovascular disease. In this study, we examined OPG gene polymorphisms in 468 men who had absence of coronary artery disease (CAD) or single-, double-, or triple-vessel disease on coronary angiography. Denaturing gradient gel electrophoresis followed by DNA sequencing revealed nucleotide substitutions 149 T-->C, 163 A-->G, 209 G-->A, 245 T-->G, 950 T-->C (all promoter), 1181 G-->C (exon 1), and 6890 A-->C (intron 4), respectively. Although single polymorphisms were not associated with CAD, linkage of polymorphisms 950 and 1181 revealed that haplotypes were overrepresented in men with CAD (chi(2) = 17.05; P = 0.03) with an increased risk of CAD in carriers of genotypes 950 TC/1181 GC and 950 CC/1181 CC (odds ratio, 1.67; 95% confidence interval, 1.02-2.72; P = 0.04). Furthermore, serum OPG levels were correlated with the presence of a C allele at position 950 (P = 0.02). In summary, linkage of genetic variations of the OPG gene at positions 950 and 1181 may confer an increased risk of CAD in Caucasian men.
New advances in the treatment of <em>Clostridium difficile</em> infection (CDI) (2008)

Clostridium difficile infections (CDI) have increased in frequency throughout the world. In addition to an increase in frequency, recent CDI epidemics have been linked to a hypervirulent C. difficile strain resulting in greater severity of disease. Although most mild to moderate cases of CDI continue to respond to metronidazole or vancomycin, refractory and recurrent cases of CDI may require alternative therapies. This review provides a brief overview of CDI and summarizes studies involving alternative antibiotics, toxin binders, probiotics, and immunological therapies that can be considered for treatment of acute and recurrent CDI in severe and refractory situations.
Cloning and analysis of strong promoters is made possible by the downstream placement of a RNA termination signal. (1981)

Downstream placement of a strong transcriptional termination signal has made possible the cloning of bacteriophage T5 promoters known to exhibit high signal strength. The cloning system constructed contains two easily assayable indicator functions whose expression is controlled by the integration of promoters and terminators, respectively. By assessing transcription within the indicator regions, the efficiency of promoters as well as termination signals can be determined in vitro and in vivo.
Nonlinear thermal stress/strain analyses of copper filled TSV (through silicon via) and their flip-chip microbumps (2008)

Most of TSVs are filled with the copper, even siliconpoly and tungsten are the alternatives. The coefficient of thermal expansion (CTE) of copper (∼17.5×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−6</sup> /°C) is a few times higher than that of silicon (∼2.5×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−6</sup> /°C). Thus, when the copper filled TSV is subjected to temperature loadings, there is a very large local thermal expansion mismatch between the copper and the silicon/dielectric (e.g., SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> ), which will create very large stresses and strains at the interfaces between the copper and the silicon and between the copper and the dielectric. These stresses/strains can be high enough to introduce delamination between the interfaces. In this study, the nonlinear thermal stresses and strains at the interfaces between the copper, silicon, and dielectric have been determined for a wide-range of aspect ratios (of the silicon thickness and the TSV diameter). One of the major applications of TSV is as an interposer. Because of Moore’s (scaling/integration) law, the silicon chip is getting bigger, the pin-out is getting higher, and the pitch is getting finer. Thus, the conventional substrates, e.g., BT (bismaleimide triazine) cannot support these kinds of silicon chips anymore and a silicon interposer (substrate) is needed to redistribute the very fine-pitch and high pin-count pads on the chip to much larger pitch and less pin-count through the silicon vias on the silicon substrate. Depending on the via-size and pitch of the copper filled TSV, the effective CTE of the copper filled TSV interposer could be as high as 10x10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">−6</sup> /°C. Consequently, the global thermal expansion mismatch between the silicon chip and the copper filled TSV substrate can be very large and the bumps (usually very small, e.g., microbumps) between them may not be able to survive under thermal conditions. In this study, the nonlinear stresses and strains in the microbumps between the silicon chip and copper filled TSV interposer (with and without underfills) have been determined for a wide-range of via sizes and pitches, and various temperature conditions. These results should be useful for (1) making a decision if underfills are necessary for the reliability of microbumps, and (2) selecting underfill materials to minimize the stresses and strains in the microbumps.
Genetic and molecular analysis of the gypsy chromatin insulator of Drosophila. (1996)

Boundary or insulator elements set up independent territories of gene activity by establishing higher order domains of chromatin structure. The gypsy retrotransposon of Drosophila contains an insulator element that represses enhancer-promoter interactions and is responsible for the mutant phenotypes caused by insertion of this element. The gypsy insulator inhibits the interaction of promoter-distal enhancers with the transcription complex without affecting the functionality of promoter-proximal enhancers; in addition, these sequences can buffer a transgene from chromosomal position effects. Two proteins have been identified that bind gypsy insulator sequences and are responsible for their effects on transcription. The suppressor of Hairy-wing [su(Hw)] protein affects enhancer function both upstream and downstream of its binding site by causing a silencing effect similar to that of heterochromatin. The modifier of mdg4 [mod(mdg4)] protein interacts with su(Hw) to transform this bi-directional repression into the polar effect characteristic of insulators. These effects seem to be modulated by changes in chromatin structure.
Efficiently mining long patterns from databases (1998)

We present a pattern-mining algorithm that scales roughly linearly in the number of maximal patterns embedded in a database irrespective of the length of the longest pattern. In comparison, previous algorithms based on Apriori scale exponentially with longest pattern length. Experiments on real data show that when the patterns are long, our algorithm is more efficient by an order of magnitude or more.
Structures of Human Cytosolic NADP-dependent Isocitrate Dehydrogenase Reveal a Novel Self-regulatory Mechanism of Activity (2004)

Isocitrate dehydrogenases (IDHs) catalyze the oxidative decarboxylation of isocitrate to alpha-ketoglutarate, and regulation of the enzymatic activity of IDHs is crucial for their biological functions. Bacterial IDHs are reversibly regulated by phosphorylation of a strictly conserved serine residue at the active site. Eukaryotic NADP-dependent IDHs (NADP-IDHs) have been shown to have diverse important biological functions; however, their regulatory mechanism remains unclear. Structural studies of human cytosolic NADP-IDH (HcIDH) in complex with NADP and in complex with NADP, isocitrate, and Ca2+ reveal three biologically relevant conformational states of the enzyme that differ substantially in the structure of the active site and in the overall structure. A structural segment at the active site that forms a conserved alpha-helix in all known NADP-IDH structures assumes a loop conformation in the open, inactive form of HcIDH; a partially unraveled alpha-helix in the semi-open, intermediate form; and an alpha-helix in the closed, active form. The side chain of Asp279 of this segment occupies the isocitrate-binding site and forms hydrogen bonds with Ser94 (the equivalent of the phosphorylation site in bacterial IDHs) in the inactive form and chelates the metal ion in the active form. The structural data led us to propose a novel self-regulatory mechanism for HcIDH that mimics the phosphorylation mechanism used by the bacterial homologs, consistent with biochemical and biological data. This mechanism might be applicable to other eukaryotic NADP-IDHs. The results also provide insights into the recognition and specificity of substrate and cofactor by eukaryotic NADP-IDHs.
Structural Investigation of Molecular Organization in Self-Assembled Monolayers of a Semifluorinated Amidethiol (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructural Investigation of Molecular Organization in Self-Assembled Monolayers of a Semifluorinated AmidethiolT. J. Lenk, V. M. Hallmark, C. L. Hoffmann, J. F. Rabolt, D. G. Castner, C. Erdelen, and H. RingsdorfCite this: Langmuir 1994, 10, 12, 4610–4617Publication Date (Print):December 1, 1994Publication History Published online1 May 2002Published inissue 1 December 1994https://pubs.acs.org/doi/10.1021/la00024a037https://doi.org/10.1021/la00024a037research-articleACS PublicationsRequest reuse permissionsArticle Views642Altmetric-Citations170LEARN 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-Alertsclose Get e-Alerts
Requirement of the integrin beta 3 subunit for carcinoma cell spreading or migration on vitronectin and fibrinogen (1992)

FG human pancreatic carcinoma cells use integrin alpha v beta 5 as their primary vitronectin receptor since they fail to express integrin alpha v beta 3. These cells are unable to form focal contacts, spread, or migrate on vitronectin but readily do so on collagen in a beta 1 integrin-dependent manner. Transfection of FG cells with a cDNA encoding the integrin beta 3 subunit results in the surface expression of a functional integrin alpha v beta 3 heterodimer providing these cells with novel adhesive and biological properties. Specifically, FG cells expressing beta 3 acquire the capacity to attach and spread on vitronectin as well as fibrinogen with beta 3 localization to focal contacts. Moreover, these cells gain the capacity to migrate through a porous membrane in response to either vitronectin or fibrinogen. These results demonstrate that the beta 3 and beta 5 integrin subunits when associated with alpha v, promote distinct cellular responses to a vitronectin extracellular environment.
Galectin-3 Mediates IL-4-Induced Survival and Differentiation of B Cells: Functional Cross-Talk and Implications during Trypanosoma cruzi Infection (2004)

The role of transcription factors in B cell survival and differentiation has been delineated during the last years. However, little is known about the intermediate signals and the intracellular pathways that control these events. In this study, we provide evidence both in vitro and in vivo, showing that galectin-3 (Gal-3), a beta-galactoside-binding protein, is a critical mediator of B cell differentiation and survival. Although Gal-3 is not expressed in resting B cells from normal mice, its expression is markedly induced after activation with stimuli such as IL-4 and CD40 cross-linking. These signals promote survival and block the final differentiation of these cells, thus allowing the rising of a memory B cell phenotype. In addition, Gal-3 is expressed in B cells from Trypanosoma cruzi-infected mice, which received signals for activation and differentiation in vivo. By using an antisense strategy, we determined that Gal-3 is a critical signal mediating the effects of IL-4 on B cell fate. Blockade of intracellular Gal-3 in vitro abrogated IL-4-induced survival of activated B cells, favoring the differentiation toward a plasma cell pathway. Moreover, B cells with restrained endogenous Gal-3 expression failed to down-regulate the Blimp-1 transcription factor after IL-4 stimulation. Finally, inhibition of Gal-3 in vivo skewed the balance toward plasma cell differentiation, which resulted in increased Ig production and parasite clearance during T. cruzi infection. Thus, the present study provides evidence of a novel role for Gal-3 as an intracellular mediator of B cell survival and a checkpoint in IL-4-induced B cell commitment toward a memory phenotype.
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology (2009)

Despite its wide usage in biological databases and applications, the role of the gene ontology (GO) in network analysis is usually limited to functional annotation of genes or gene sets with auxiliary information on correlations ignored. Here, we report on new capabilities of VisANT--an integrative software platform for the visualization, mining, analysis and modeling of the biological networks--which extend the application of GO in network visualization, analysis and inference. The new VisANT functions can be classified into three categories. (i) Visualization: a new tree-based browser allows visualization of GO hierarchies. GO terms can be easily dropped into the network to group genes annotated under the term, thereby integrating the hierarchical ontology with the network. This facilitates multi-scale visualization and analysis. (ii) Flexible annotation schema: in addition to conventional methods for annotating network nodes with the most specific functional descriptions available, VisANT also provides functions to annotate genes at any customized level of abstraction. (iii) Finding over-represented GO terms and expression-enriched GO modules: two new algorithms have been implemented as VisANT plugins. One detects over-represented GO annotations in any given sub-network and the other finds the GO categories that are enriched in a specified phenotype or perturbed dataset. Both algorithms take account of network topology (i.e. correlations between genes based on various sources of evidence). VisANT is freely available at http://visant.bu.edu.
Aircraft design using collaborative optimization (1996)

Collaborative optimization is a recently developed method for solving multidisciplinary design problems. It preserves a degree of disciplinary autonomy and allows parallel optimization. In this paper collaborative optimization is applied to two aircraft design problems to illustrate its implementation and performance characteristics. The first example, a relatively simple wing design problem, is solved using both collaborative and sequential optimization. The results are compared with those obtained using a direct, single-level optimization strategy. Collaborative optimization is shown to converge to the correct solution, while sequential disciplinary suboptimization converges to a nonoptimal result. The second example, an aircraft sizing problem, involves static aeroelastic feedback between disciplines and more complex analysis codes within the subproblems. The complete problem, in forty-five design variables and twenty-six constraints, was solved using both collaborative and single-level optimization. Both methods converge to the correct solution. The performance of the optimization strategy and the effect of increasing problem dimensionality is discussed.
Redetermination ofpara-aminopyridine (fampridine, EL-970) at 150 K (2005)

The structure of fampridine (EL-970) or 4-aminopyridine, C₅H₆N₂, has been redetermined at 150 K. The room-temperature structure has been reported previously [Chao &amp; Schempp (1977). Acta Cryst. B33, 1557-1564]. Pyramidalization at the amine N atom occurs in fampridine, with the N atom 0.133 (11) Å from the plane of the three C/H/H atoms to which it is bonded; the interplanar angle between the pyridyl ring and NH2 group is 21 (2)°. Aggregation in the solid state occurs by N-H...N and N-H...[pi](pyridine) interactions with N...N and N...[pi](centroid) distances of 2.9829 (18) and 3.3954 (15) Å, respectively; a C-H...[pi](pyridine) contact completes the intermolecular interactions [C...[pi](centroid) = 3.6360 (16) Å].