gebhart/patrepeval huggingface dataset:
Strategems in vitro for gene therapies directed to dominant mutations (1997)

A major difficulty associated with the design of gene therapies for autosomal dominant diseases is the immense intragenic heterogeneity often encountered in such conditions. In order to overcome such difficulties we have designed, and evaluated in vitro, three strategies which avoid a requirement to target individual mutations for genetic suppression. In the first, normal and mutant alleles are suppressed by targeting sequences in transcribed but untranslated regions of transcript (UTRs), enabling introduction of a replacement gene with the correct coding sequencing but altered UTRs to prevent suppression. A second approach involves suppression in coding sequence and concurrent introduction of a replacement gene by exploiting the degeneracy of the genetic code. A third strategy utilises intragenic polymorphism to suppress the disease allele specifically, the advantage being that a proportion of patients with different disease mutations have the same polymorphism. These approaches provide a wider choice of target sequence than those directed to single disease mutations and are appropriate for many mutations within a given gene. General methods for suppression may be directed towards the primary defect or a secondary effect associated with the disease process, such as apoptosis. Three general methods targeting the primary defect which circumvent problems of allelic genetic heterogeneity are explored in vitro using hammerhead ribozymes designed to target transcripts from the rhodopsin, peripherin and collagen 1A1 and 1A2 genes, extensive genetic heterogeneity being a feature of associated disease pathologies.
Biosynthetic Gene Cluster for the Polyenoyltetramic Acid α-Lipomycin (2006)

The gram-positive bacterium Streptomyces aureofaciens Tü117 produces the acyclic polyene antibiotic alpha-lipomycin. The entire biosynthetic gene cluster (lip gene cluster) was cloned and characterized. DNA sequence analysis of a 74-kb region revealed the presence of 28 complete open reading frames (ORFs), 22 of them belonging to the biosynthetic gene cluster. Central to the cluster is a polyketide synthase locus that encodes an eight-module system comprised of four multifunctional proteins. In addition, one ORF shows homology to those for nonribosomal peptide synthetases, indicating that alpha-lipomycin belongs to the classification of hybrid peptide-polyketide natural products. Furthermore, the lip cluster includes genes responsible for the formation and attachment of d-digitoxose as well as ORFs that resemble those for putative regulatory and export functions. We generated biosynthetic mutants by insertional gene inactivation. By analysis of culture extracts of these mutants, we could prove that, indeed, the genes involved in the biosynthesis of lipomycin had been cloned, and additionally we gained insight into an unusual biosynthesis pathway.
Surfactant Protein-D Inhibits Lung Inflammation Caused by Ventilation in Premature Newborn Lambs (2010)

Treatment with rhSP-D-containing surfactant inhibited lung inflammation and enhanced the resistance of surfactant to inhibition, supporting its potential usefulness for prevention of lung injury in the preterm newborn.
Efficient Sparse Pose Adjustment for 2D mapping (2010)

Pose graphs have become a popular representation for solving the simultaneous localization and mapping (SLAM) problem. A pose graph is a set of robot poses connected by nonlinear constraints obtained from observations of features common to nearby poses. Optimizing large pose graphs has been a bottleneck for mobile robots, since the computation time of direct nonlinear optimization can grow cubically with the size of the graph. In this paper, we propose an efficient method for constructing and solving the linear subproblem, which is the bottleneck of these direct methods. We compare our method, called Sparse Pose Adjustment (SPA), with competing indirect methods, and show that it outperforms them in terms of convergence speed and accuracy. We demonstrate its effectiveness on a large set of indoor real-world maps, and a very large simulated dataset. Open-source implementations in C++, and the datasets, are publicly available.
Essential role for both CD80 and CD86 costimulation, but not CD40 interactions, in allergen-induced Th2 cytokine production from asthmatic bronchial tissue: role for alphabeta, but not gammadelta, T cells. (1999)

CD80 and CD86 interact with CD28 and deliver costimulatory signals required for T cell activation. We demonstrate that ex vivo allergen stimulation of bronchial biopsy tissue from mild atopic asthmatic, but not atopic nonasthmatic, subjects induced production of IL-5, IL-4, and IL-13. Explants from both study groups did not produce IFN-gamma, but secreted the chemokine RANTES without any overt stimulation. In addition to allergen, stimulation of asthmatic explants with mAbs to CD3 and TCR-alphabeta but not TCR-gammadelta induced IL-5 secretion. Allergen-induced IL-5 and IL-13 production by the asthmatic tissue was inhibited by anti-CD80 and, to a lesser extent, by anti-CD86 mAbs. In contrast, the production of these cytokines by PBMCs was not affected by mAbs to CD80, was inhibited by anti-CD86, and was strongly attenuated in the presence of both Abs. FACS analysis revealed that stimulated asthmatic bronchial tissue was comprised of CD4+ T cells that expressed surface CD28 (75. 3%) but little CTLA-4 (4.0%). Neutralizing mAbs to CD40 ligand had no effect on the cytokine levels produced by asthmatic tissue or PBMCs. Collectively, these findings suggest that allergen-specific alphabeta T cells are resident in asthmatic bronchial tissue and demonstrate that costimulation by both CD80 and CD86 is essential for allergen-induced cytokine production. In contrast, CD86 appears to be the principal costimulatory molecule required in PBMC responses. Attenuation of type 2 alphabeta T cell responses in the bronchial mucosa by blocking these costimulatory molecules may be of therapeutic potential in asthma.
Peripheral neuromodulation via posterior tibial nerve stimulation - a potential treatment for faecal incontinence? (2010)

PTNS is a potentially efficacious, technically simple and minimally invasive alternative treatment modality for faecal incontinence. These early results are encouraging, but we await medium- and long-term follow-up, and a larger randomised trial comparing PTNS with alternative treatments and placebo.
Mitochondrial electron transport as a source for nitric oxide in the unicellular green alga Chlorella sorokiniana (2004)

Wild type (WT), and nitrate reductase (NR)- and nitrite-reductase (NiR)-deficient cells of Chlorella sorokiniana were used to characterize nitric oxide (NO) emission. The NO emission from nitrate-grown WT cells was very low in air, increased slightly after addition of nitrite (200 microM), but strongly under anoxia. Importantly, even completely NR-free mutants, as well as cells grown on tungstate, emitted NO when fed with nitrite under anoxia. Therefore, this NO production from nitrite was independent of NR and other molybdenum cofactor enzymes. Cyanide and inhibitors of mitochondrial complex III, myxothiazol or antimycin A, but not salicylhydroxamic acid (inhibitor of alternative oxidase) inhibited NO production by NR-free cells. In contrast, NiR-deficient cells growing on nitrate accumulated nitrite and emitted NO at very high equal rates in air and anoxia. This NO emission was 50% inhibited by salicylhydroxamic acid, indicating that in these cells the alternative oxidase pathway had been induced and reduced nitrite to NO.
Does stimulation of the GPi control dyskinesia by activating inhibitory axons? (2001)

A 69-year-old woman with Parkinson's disease and levodopa-induced dyskinesias had a deep brain stimulation (DBS) electrode inserted into the right globus pallidus internus (GPi). During the operation, the GPi was mapped with dual microelectrode recordings. Stimulation through one microelectrode in GPi inhibited the firing of GPi neurons recorded with another microelectrode 600--1,000 microm distant. The inhibition could be obtained with pulse widths of 150 micros and intensities as low as 10 microA. Single stimuli inhibited GPi neurons for approximately 50 ms. Trains of 300 Hz stimuli inhibited GPi neuron firing almost completely. Postoperatively, stimulation through macroelectrode contacts located in the posterior ventral pallidum controlled the patient's dyskinesias. The effect could be obtained with pulse widths of 50 micros and frequencies as low as 70--80 Hz. We postulate stimulation of the ventral pallidum controls dyskinesias by activating large axons which inhibit GPi neurons.
Characterization of TAP‐Independent and Brefeldin A‐Resistant Presentation of Sendai Virus Antigen to CD8+ Cytotoxic T Lymphocytes (1995)

H-2Kb-transfected T2 cells, which lack both TAP1/2 and LMP2/7 genes, are able to efficiently process and present Sendai virus Antigen to Kb-restricted Sendai virus-specific CTL. This presentation is not inhibited by Brefeldin A (BFA). Here we extend our analysis of this novel antigen presentation pathway. We show that presentation of Sendai virus antigen was not due to sensitization of T2Kb cells by peptides in the virus preparation or peptides released from virus infected cells. Also, the ability to present Sendai virus in a BFA resistant fashion was specific for cells of the T2 lineage. Re-expression of TAP1/2 genes in T2Kb cells did not alter the capability to present antigen in a BFA resistant fashion, i.e. the presence of a functional TAP transporter complex did not relocate (all) peptides to the classical pathway for antigen processing and presentation. We found that co-infection of T2Kb cells with either Sendai virus plus influenza virus or Sendai virus plus VSV did not relocate presentation of influenza or VSV antigen to the TAP independent BFA resistant antigen presentation pathway. Peptide elution experiments and studies with peptide-specific CTL firmly demonstrated that the antigen presented by T2Kb cells after infection with Sendai virus was the natural Sendai virus epitope NP324-332. The same epitope, when expressed as a minigene in vaccinia virus, could be presented also by T2Kb cells but this presentation could be blocked by BFA. Thus, the TAP independent BFA resistant presentation of antigen seem cell (T2 lineage) and virus (Sendai virus) specific, but not epitope specific. The ability of T2Kb cells to present Sendai virus antigen in a TAP independent BFA resistant fashion was only partially blocked by lysosomal inhibitors such as methylamine, ammonium chloride and chloroquine. These findings demonstrate that TAP1/2-independent and BFA-resistant class I processing is only expressed in certain cell types, in parallel with classical MHC class I processing, and that Sendai virus selectively can enter this pathway. Hypothetical models for the TAP-independent class I processing are discussed.
Brassinosteroids Regulate Dissociation of BKI1, a Negative Regulator of BRI1 Signaling, from the Plasma Membrane (2006)

Brassinosteroids, the steroid hormones of plants, are perceived at the plasma membrane by a leucine-rich repeat receptor serine/threonine kinase called BRI1. We report a BRI1-interacting protein, BKI1, which is a negative regulator of brassinosteroid signaling. Brassinosteroids cause the rapid dissociation of BKI1-yellow fluorescent protein from the plasma membrane in a process that is dependent on BRI1-kinase. BKI1 is a substrate of BRI1 kinase and limits the interaction of BRI1 with its proposed coreceptor, BAK1, suggesting that BKI1 prevents the activation of BRI1.
Enzymatic multiplex DNA sequencing (1991)

The problem of reading DNA sequence films has been reformulated using an easily implemented, multiplex version of enzymatic DNA sequencing. By utilizing a uniquely tagged primer for each base-specific sequencing reaction, the four reactions can be pooled and electrophoresed in a single lane. This approach has been previously proposed for use with fluorescently labelled probes (1), and is analogous to the principle used in four-dye fluorescence sequencing except that the signals are resolved following electrophoresis (2). After transfer to a nylon membrane, images are obtained separately for each of the four reactions by hybridization using oligonucleotide probes. The images can then be superimposed to reconstitute a complete sequence pattern. In this way the correction of gel distortion effects and accurate band registration are considerably simplified, as each of the four base-specific ladders require very similar corrections. The methods therefore provide the basis for a second generation of more accurate and reliable film reading programs, as well as being useful for conventional multiplex sequencing. Unlike the original multiplex protocol (3), the approach described is suitable for small projects, as multiple cloning vectors are not used. Although more than one vector can be utilized, only a library of fragments cloned into any single phage, phagemid or plasmid vector is actually required, together with a set of tagged oligonucleotide primers.
Oversecretion of interleukin-15 from skeletal muscle reduces adiposity (2008)

Obesity is a risk factor for development of insulin resistance, type 2 diabetes, cardiovascular disease, osteoarthritis, and some forms of cancer. Many of the adverse health consequences of excess fat deposition are caused by increased secretion of proinflammatory adipokines by adipose tissue. Reciprocal muscle-to-fat signaling factors, or myokines, are starting to be identified. Interleukin-15 (IL-15) is a cytokine that is highly expressed in muscle tissue and that, on the basis of cell culture experiments, has been proposed to act as a circulating myokine that inhibits adipose tissue deposition. To test this hypothesis in vivo, two lines of transgenic mice that overexpressed IL-15 mRNA and protein in skeletal muscle tissue were constructed. By substitution of the inefficient native IL-15 signal peptide with a more efficient signal peptide, one of the transgenic mouse lines also exhibited elevated secretion of IL-15 in the circulation. Overexpression of IL-15 in muscle tissue without secretion in the bloodstream resulted in no differences in body composition. Elevated circulating levels of IL-15 resulted in significant reductions in body fat and increased bone mineral content, without appreciably affecting lean body mass or levels of other cytokines. Elevated circulating levels of IL-15 also inhibited adiposity induced by consumption of a high-fat/high-energy diet in male, but not female, transgenic mice. Female mice with elevated serum IL-15 exhibited increased deposition of lean body mass on a low-fat/low-energy diet and a high-fat/high-energy diet. These findings indicate that muscle-derived circulating IL-15 can modulate adipose tissue deposition and support addition of IL-15 to the growing list of potential myokines that are increasingly being implicated in regulation of body composition.
Activation of immobilized plasminogen by tissue activator. Multimolecular complex formation. (1985)

Ternary complex formation of tissue plasminogen activator (TPA) and plasminogen (Plg) with thrombospondin (TSP) or histidine-rich glycoprotein (HRGP) has been demonstrated using an enzyme-linked immunosorbent assay, an affinity bead assay, and a rocket immunoelectrophoresis assay. The formation of these complexes was specific, concentration dependent, saturable, lysine binding site-dependent, and inhibitable by fluid phase plasminogen. Apparent Kd values were approximately 12-36 nM for the interaction of TPA with TSP-Plg complexes and 15-31 nM with HRGP-Plg complexes. At saturation the relative molar stoichiometry of Plg:TPA was 3:1 within the TSP-containing complexes and 1:1 within HRGP-containing complexes. The activation of Plg to plasmin by TPA on TSP- and HRGP-coated surfaces was studied using a synthetic fluorometric plasmin substrate (D-Val-Leu-Lys-7-amino-4-trifluoromethyl coumarin). Kinetic analysis demonstrated a marked increase in the affinity of TPA for plasminogen in the presence of surface-associated TSP or HRGP. Compared to fluid phase activation or activation on fibronectin- or Factor VIII-related antigen-coated surfaces there was a 35-fold increase in efficiency of plasmin generation. A substantial amount (up to 71%) of the plasmin formed remained surface-associated and was found to be protected from inhibition by alpha 2-plasmin inhibitor. Greater than 200-fold increase in inhibitor concentration was required to effect 50% inhibition. Complex formation of locally released tissue plasminogen activator with Plg immobilized on TSP or HRGP surfaces may thus play an important role in effecting proteolytic events in nonfibrin-containing microenvironments.
A Faster Parallel Algorithm and Efficient Multithreaded Implementations for Evaluating Betweenness Centrality on Massive Datasets (2009)

We present a new lock-free parallel algorithm for computing betweenness centralityof massive small-world networks. With minor changes to the data structures, ouralgorithm also achieves better spatial cache locality compared to previous approaches. Betweenness centrality is a key algorithm kernel in HPCS SSCA#2, a benchmark extensively used to evaluate the performance of emerging high-performance computing architectures for graph-theoretic computations. We design optimized implementations of betweenness centrality and the SSCA#2 benchmark for two hardware multithreaded systems: a Cray XMT system with the Threadstorm processor, and a single-socket Sun multicore server with the UltraSPARC T2 processor. For a small-world network of 134 million vertices and 1.073 billion edges, the 16-processor XMT system and the 8-core Sun Fire T5120 server achieve TEPS scores (an algorithmic performance count for the SSCA#2 benchmark) of 160 million and 90 million respectively, which corresponds to more than a 2X performance improvement over the previous parallel implementations. To better characterize the performance of these multithreaded systems, we correlate the SSCA#2 performance results with data from the memory-intensive STREAM and RandomAccess benchmarks. Finally, we demonstrate the applicability of our implementation to analyze massive real-world datasets by computing approximate betweenness centrality for a large-scale IMDb movie-actor network.
Astrocytes modulate retinal vasculogenesis: effects on fibronectin expression (1994)

Vasculogenesis is the formation of blood-vessels by differentiation of vascular precursor cells. Experiments using retinal models were designed to test the hypothesis that astrocytes influence this process by effects on the composition of the extracellular matrix. Retinal vasculogenesis was studied in relation to the migration of astrocytes and expression of the extracellular matrix proteins laminin and fibronectin by in vivo experiments in neonatal rats. The results show that astrocytes spread into the retina just ahead of the newly formed vessels, where they probably initiate vasculogenesis. They also establish that fibronectin, but not laminin, is expressed in the zone of vasculogenesis immediately prior to vessel formation. Increased amounts of fibronectin mRNA indicate that fibronectin is synthesized by cells within this same region during this same time period. Later, as the new vessels form, differentiation of endothelial cells is correlated with the appearance of pericytes in the vessel wall and laminin in the vascular basement membrane. In vitro experiments using conditioned medium approaches showed that astrocytes stimulate endothelial cell fibronectin expression. Taken together with the in vivo observations these in vitro results suggest that fibronectin expression is an essential component in the initiation of retinal vasculogenesis. This study is the first indication that astrocytes influence the fibronectin component of the extracellular matrix during retinal vasculogenesis and that expression of fibronectin precedes that of laminin in this process.
Synthesis and Electroluminescent Properties of Copolymers Based on Fluorene and 2,5-Di(2-hexyloxyphenyl)thiazolothiazole (2005)

A novel series of soluble conjugated random copolymers were synthesized via the Suzuki coupling reaction of 9,9-dihexylfluorene (DHF) and 2,5-di(2-hexyloxyphenyl)thiazolothiazole (TZ), with the TZ composition varying from 5 to 50 mol % in the copolymers. All of the copolymers exhibited good thermal stability and excellent solubility in common organic solvents, such as chloroform, toluene, and tetrahydrofuran. The electrochemical and photophysical properties were characterized in detail. Under UV excitation, these copolymers emitted bright blue fluorescence at around 416−420 nm in CHCl3 solution and 446−451 nm in thin film form. Light-emitting diodes fabricated with the copolymers emitted bright blue light with external quantum efficiencies of 0.06−0.44%. The electroluminescence (EL) efficiency of the copolymer with a TZ content of 50% was more than 3 times that of the fluorene homopolymer. Preliminary EL studies showed that these copolymers had good electron transport properties arising from the introduction of TZ units. These copolymers are thus efficient blue emissive materials for polymer light-emitting diodes (PLEDs).
Engineering Issues in Synthesis-Gas Fermentations (1997)

Biomass-derived synthesis gas can be readily converted into fuels and chemicals by anaerobic microorganisms. However, synthesis-gas fermentations typically exhibit low volumetric productivities due, in part, to low cell densities, production of unwanted by-products, and slow transfer of the synthesis gas into the liquid phase. Engineering approaches to improve bioreactor productivities are discussed, and recent advances in this area are summarized. Particular emphasis is placed on the use of bioreactor design to increase biocatalyst concentrations, development of metabolic models to study pathway regulation and the use of microbubble dispersions to enhance synthesis-gas mass transfer.
Operationalizing a Frailty Index from a Standardized Comprehensive Geriatric Assessment (2004)

The FI-CGA is a valid, reliable, and sensible clinical measure of frailty that permits risk stratification of future adverse outcomes.
A New Derivation of Average Molecular Weights of Nonlinear Polymers (1976)

A new method for calculating average molecular weights is presented for nonlinear polymers. In contrast to the previous methods of Flory and Stockmayer which first calculate the distribution of all species and then use the distributions to calculate average properties, the new method calculates these properties directly. In contrast to the method of Gordon, probability generating functions are not required. Starting with elementary probability and utilizing the recursive nature of network polymers property relations can be developed more simply. We illustrate the method for calculations of Mw Mz, and the gel point for a wide variety of polyfunctional polymerizations.