gebhart/patrepeval huggingface dataset:
Mutational analysis of a ribonuclease III processing signal (1993)

A mutational approach was employed to identify sequence and structural elements in a ribonuclease III processing signal that are important for in vitro enzymatic cleavage reactivity and selectivity. The substrate analyzed was the bacteriophage T7 R1.1 processing signal, a 60 nucleotide irregular RNA hairpin exhibiting an upper and lower dsRNA stem, separated by an asymmetric internal loop which contains the scissile phosphodiester bond. Altering the length of either the upper or lower dsRNA segment in R1.1 RNA dose not change the site of RNase III cleavage. However, decreasing the size of either the upper or lower dsRNA segment causes a progressive inhibition of processing reactivity. Omitting monovalent salt from the reaction buffer promotes cleavage of otherwise unreactive R1.1 deletion mutants. Accurate processing is maintained with R1.1 variants containing specific point mutations, designed to disrupt Watson-Crick (WC) base-pairing in a conserved sequence element within the upper dsRNA stem. The internal loop is not required for processing reactivity, as RNase III can accurately and efficiently cleave R1.1 variants in which this structure is WC base-paired. Moreover, an additional cleavage site is utilized in these variants, which occurs opposite the canonical site, and is offset by two nucleotides. The fully base-paired R1.1 variants form a stable complex with RNase III in Mg(2+)-free buffer, which can be detected by a gel electrophoretic mobility shift assay. In contrast, the complex of wild-type R1.1 RNA with RNase III is unstable during nondenaturing gel electrophoresis. Thus, a functional role of the T7 R1.1 internal loop is to enforce single enzymatic cleavage, which occurs at the expense of RNase III binding affinity.
Randomized multicenter phase II study of flavopiridol (alvocidib), cytarabine, and mitoxantrone (FLAM) versus cytarabine/daunorubicin (7+3) in newly diagnosed acute myeloid leukemia (2015)

Serial studies have demonstrated that induction therapy with FLAM [flavopiridol (alvocidib) 50 mg/m(2) days 1-3, cytarabine 667 mg/m(2)/day continuous infusion days 6-8, and mitoxantrone (FLAM) 40 mg/m(2) day 9] yields complete remission rates of nearly 70% in newly diagnosed poor-risk acute myeloid leukemia. Between May 2011-July 2013, 165 newly diagnosed acute myeloid leukemia patients (age 18-70 years) with intermediate/adverse-risk cytogenetics were randomized 2:1 to receive FLAM or 7+3 (cytarabine 100 mg/m(2)/day continuous infusion days 1-7 and daunorubicin 90 mg/m(2) days 1-3), across 10 institutions. Some patients on 7+3 with residual leukemia on day 14 received 5+2 (cytarabine 100 mg/m(2)/day continuous infusion days 1-5 and daunorubicin 45 mg/m(2) days 1-2), whereas patients on FLAM were not re-treated based on day 14 bone marrow findings. The primary objective was to compare complete remission rates between one cycle of FLAM and one cycle of 7+3. Secondary end points included safety, overall survival and event-free survival. FLAM led to higher complete remission rates than 7+3 alone (70% vs. 46%; P=0.003) without an increase in toxicity, and this improvement persisted after 7+3+/-5+2 (70% vs. 57%; P=0.08). There were no significant differences in overall survival and event-free survival in both arms but post-induction strategies were not standardized. These results substantiate the efficacy of FLAM induction in newly diagnosed AML. A phase III study is currently in development. This study is registered with clinicaltrials.gov identifier: 01349972.
Nucleotide sequence of pilA, the gene encoding the structural component of type 1 pili in Escherichia coli (1985)

The pilA gene of Escherichia coli J96 encoding pilin, the structural component of type 1 pili, was sequenced and found to specify a polypeptide 159 amino acids long preceded by a 23-amino-acid signal peptide. As determined from the DNA sequence, the mature peptide lacked tryptophane and methionine, two amino acids previously shown to be lacking in type 1 pili from E. coli. Also, the amino-terminal sequence of amino acids inferred from the DNA sequence corresponded to earlier 20-amino-acid amino-terminal sequences determined by protein sequencing. In addition, piliation was abolished after a mutation was introduced into the pilA coding region in vitro. A possible site for initiation of transcription and a possible site encoding translation initiation were suggested 85 and 7 base pairs, respectively, from the pilA start codon. There appeared to be scant DNA sequence homology and scant amino acid sequence homology between type 1 pilin and other pilin species isolated from uropathogenic and enteropathogenic E. coli.
Proteolytic Activation of Recombinant Pro-memapsin 2 (Pro-β-secretase) Studied with New Fluorogenic Substrates (2000)

Memapsin 2 (beta-secretase), a membrane-anchored aspartic protease, is involved in the cleavage of beta-amyloid precursor protein to form beta-amyloid peptide. The primary structure of memapsin 2 suggests that it is synthesized in vivo as pro-memapsin 2 and converted to memapsin 2 by an activating protease [Lin et al. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 1456-1460]. To simulate this activation mechanism and to produce stable mature memapsin 2 for kinetic/specificity studies, we have investigated the activation of recombinant pro-memapsin 2 by several proteases with trypsin-like specificity. Clostripain, kallikrein, and trypsin increased the activity of pro-memapsin 2. Clostripain activation was accompanied by the cleavage of the pro region to form mainly two activation products, Leu(30p)- and Gly(45p)-memapsin 2. Another activation product, Leu(28p)-memapsin 2, was also purified. Kinetics of the activated memapsin 2 were compared with pro-memapsin 2 using two new fluorogenic substrates, Arg-Glu(5-[(2-aminoethyl)amino]naphthalene-1-sulfonic acid (EDANS))-Glu-Val-Asn-Leu-Asp-Ala-Glu-Phe-Lys(4-(4-dimethylaminophe nyl azo)benzoic acid (DABCYL))-Arg and (7-methoxycoumarin-4-yl)acetyl (MCA))-Ser-Glu-Val-Asn-Leu-Asp-Ala-Glu-Phe-Lys(2,4-dinitrophenyl (DNP)). These results establish that the activity of pro-memapsin 2 stems from a part-time and reversible uncovering of its active site by its pro region. Proteolytic removal of part of the pro-peptide at Leu(28p) or Gly(45p), which diminishes the affinity of the shortened pro-peptide to the active site, results in activated memapsin 2. These results also suggest that Glu(33p)-memapsin 2 observed in the cells expressing this enzyme [Vassar et al. (1999) Science 286, 735-741; Yan et al. (1999) Nature 402, 533-537] is an active intermediate of in vivo activation, or that the peptide Glu(33p)-Arg(44p) may serve a regulatory role.
Identifying robust plans through plan diagram reduction (2008)

Estimates of predicate selectivities by database query optimizers often differ significantly from those actually encountered during query execution, leading to poor plan choices and inflated response times. In this paper, we investigate mitigating this problem by replacing selectivity error-sensitive plan choices with alternative plans that provide robust performance. Our approach is based on the recent observation that even the complex and dense "plan diagrams" associated with industrial-strength optimizers can be efficiently reduced to "anorexic" equivalents featuring only a few plans, without materially impacting query processing quality. Extensive experimentation with a rich set of TPC-H and TPC-DS-based query templates in a variety of database environments indicate that plan diagram reduction typically retains plans that are substantially resistant to selectivity errors on the base relations. However, it can sometimes also be severely counter-productive, with the replacements performing much worse. We address this problem through a generalized mathematical characterization of plan cost behavior over the parameter space, which lends itself to efficient criteria of when it is safe to reduce. Our strategies are fully non-invasive and have been implemented in the Picasso optimizer visualization tool.
The Seven Amino Acids of Human RAMP2 (86) and RAMP3 (59) Are Critical for Agonist Binding to Human Adrenomedullin Receptors (2001)

When co-expressed with a receptor activity-modifying protein (RAMP) accessory protein, calcitonin receptor-like receptor (CRLR) can function as a calcitonin gene-related peptide receptor (CRLR-RAMP1) or an adrenomedullin (AM) receptor (CRLR-RAMP2/3). Here we report on the structural domain(s) involved in selective AM binding that were examined using various RAMP chimeras and deletion mutants. Co-expression of chimeric RAMPs and CRLR in HEK293 cells revealed that residues 77-101, situated in the extracellular N-terminal domain of human RAMP2 (hRAMP2), were crucial for selective AM-evoked cAMP production. More detailed analysis showed that deletion of hRAMP2 residues 86-92 significantly attenuated high-affinity (125)I-AM binding and AM-evoked cAMP production despite full cell surface expression of the receptor heterodimer and that deletion of hRAMP3 residues 59-65 had a similar effect. There is little sequence identity between hRAMP3 residues 59-65 and hRAMP2 residues 86-92; moreover, substituting alanine for Trp(86) (Ala(87)), Met(88), Ile(89), Ser(90), Arg(91), or Pro(92) of hRAMP2 had no effect on AM-evoked cAMP production. It thus seems unlikely that any one amino acid residue is responsible for determining selective AM binding or that AM binds directly to these peptide segments. Instead these findings suggest that the respective seven-amino acid sequences confer selectivity either by directly contributing to the structure of ligand binding pocket or by allosteric modulation of the conformation of CRLR.
A method for evaluating the selectivity of electrodes implanted for nerve simulation (1991)

The scale of stimulating electrodes possible for use in functional electrical stimulation to restore motor and sensory function is rapidly approaching that of individual neurons. Although the electrodes may approach the dimensions of single nerve cells, it is unclear if the region of excitation elicited by each electrode will be correspondingly small. Previous techniques for evaluating this have either been tedious or have lacked the resolution necessary. This paper describes a method that uses the refractory interaction of the compound action potentials elicited by a stimulus pulse pair, along with high-resolution recording of those potentials, to achieve measurements of the selectivity of stimulation down to the scale of a few axon diameters. The feasibility of this technique is demonstrated in sciatic nerves of frogs (Rana Catesbiana) acutely implanted with a sapphire electrode array.
Organic solar cell based on multistep charge separation system (1992)

The p-n heterojunction organic solar cell composed of n-type multilayer of two different perylene pigments and p-type metal-free phthalocyanine pigment was investigated. A downward potential step of the conduction band in the n-type multilayer enhanced the photocurrent quantum efficiency by a factor of about 3, owing to the suppression of the charge recombination of photogenerated carriers in the vicinity of the p-n junction. The multistep charge separation system consisting of energetically well-arranged organic thin layers was shown to offer an effective system to obtain highly efficient organic solar cells.
Vascular endothelial growth factor and glioma angiogenesis: Coordinate induction of VEGF receptors, distribution of VEGF protein and possible In vivo regulatory mechanisms (1994)

We have previously suggested that tumor angiogenesis in human gliomas is regulated by a paracrine mechanism involving vascular endothelial growth factor (VEGF) and flt-1 (VEGF-receptor 1). VEGF, an endothelial-cell-specific mitogen, is abundantly expressed in glioma cells which reside along necrotic areas, whereas flt-1, a tyrosine-kinase receptor for VEGF, is expressed in tumor endothelial cells, but not in endothelial cells in normal adult brain. Recently, a second tyrosine-kinase receptor which binds VEGF with high affinity, designated KDR or flk-1, has been described. We performed in situ hybridization for VEGF mRNA, flt-1 mRNA and KDR mRNA on serial sections of normal brain, low-grade and high-grade glioma specimens. We show that KDR mRNA is co-expressed with flt-1 in vascular cells in glioblastoma but not in low-grade glioma. Since flt-1 and KDR are not expressed in endothelial cells in the normal adult brain, the coordinate up-regulation of 2 receptors for VEGF appears to be a critical event which controls tumor angiogenesis. Immunocytochemistry with a monoclonal anti-VEGF antibody revealed significant amounts of VEGF protein in the same glioma cells that expressed VEGF mRNA. The largest amount of VEGF immunoreactivity, however, was detected on the vasculature of glioblastomas, the site where VEGF exerts its biological functions. These findings suggest that VEGF is produced and secreted by glioma cells and acts on tumor endothelial cells which express VEGF receptors. To further characterize VEGF-producer cells in vivo, we investigated cellular proliferation, immunoreactivity to the p53 tumor-suppressor gene product and epidermal-growth-factor-receptor (EGFR) expression on serial sections by immunocytochemistry. VEGF-producer cells did not show increased cellular proliferation, p53 immunoreactivity or EGFR immunoreactivity as compared with glioma cells which did not express VEGF. Our studies therefore do not demonstrate evidence for a growth advantage of VEGF-producer cells in vivo or VEGF induction by p53 mutation or EGFR over-expression.
Discovery of Novel P1 Groups for Coagulation Factor VIIa Inhibition Using Fragment-Based Screening (2015)

A multidisciplinary, fragment-based screening approach involving protein ensemble docking and biochemical and NMR assays is described. This approach led to the discovery of several structurally diverse, neutral surrogates for cationic factor VIIa P1 groups, which are generally associated with poor pharmacokinetic (PK) properties. Among the novel factor VIIa inhibitory fragments identified were aryl halides, lactams, and heterocycles. Crystallographic structures for several bound fragments were obtained, leading to the successful design of a potent factor VIIa inhibitor with a neutral lactam P1 and improved permeability.
Synthesis and Modification of Functional Poly(lactide) Copolymers: Toward Biofunctional Materials (2008)

A polylactide copolymer with pendant benzyloxy groups has been synthesized by the copolymerization of a benzyl-ether substituted monomer with lactide. Debenzylation of the polymer to provide pendant hydroxyl groups followed by modification with succinic anhydride affords the corresponding carboxylic acid functionalized copolymer that is amenable to standard carbodiimide coupling conditions to attach amine-containing biological molecules. An amino-substituted biotin derivative was coupled to the carboxyl functional groups of copolymer films as proof-of-concept. In a demonstration of the function of these new materials, an RGD-containing peptide sequence was tethered to copolymer films at various densities and was shown to enhance the adhesion of epithelial cells. This strategy provides the opportunity for the attachment of a variety of ligands, allowing for the fabrication of a versatile class of biodegradable, biocompatible materials.
An overview of amines as nutritional supplements to counteract cancer cachexia (2014)

Cancer cachexia is a complex multifactorial syndrome characterized by loss of skeletal muscle mass (with or without loss of fat mass) that cannot be fully reversed by conventional nutritional support and leads to progressive functional impairment. Recently, some amino acids and other amine dietary supplements have been highlighted in medical field due to positive effects upon diseases evolving skeletal muscle atrophy. Therefore, the aim of this brief review is to discuss the putative application of amines as dietary supplements to counteract skeletal muscle wasting on cancer cachexia. Specifically, we focus in two nutritional supplements: (1) branched-chain amino acids (BCAAs) and (2) creatine. Both BCAAs and creatine may attenuate proteolysis and enhance proteins synthesis in skeletal muscle. Although more experimental studies and clinical trials are still necessary to elucidate this therapeutic application, several evidences have demonstrated that amines supplementation is a promising coadjuvant treatment to cancer cachexia.
Microfluidics-Assisted Diffusion Self-Assembly: Toward the Control of the Shape and Size of Pectin Hydrogel Microparticles (2014)

We demonstrated the generation of pectin hydrogel microparticles having complex shapes either by combining the phenomenon of gelation and water diffusion-induced self-assembly in microfluidic channels (on-chip) or by the deformation of the pregelled droplets outside the channels (off-chip) at a fluid-fluid interface. We proved that by tuning the mode of pectin cross-linking (CaCl2 vs CaCO3) and the degree of shrinking (water content in the dimethyl carbonate (DMC) organic continuous phase) we can control the shape of the final particle. Sphere, doughnut, oblate ellipsoid, or mushroom-type morphologies were thus produced, demonstrating the ability to control the formation of anisotropic biopolymer-based hydrogel microparticles using microfluidics. Shape changes were explained by the redistribution of calcium ions in combination with the local Peclet number experienced by the microdroplets during the on-chip process. Moreover, during the off-chip process, the interplay between elastic and viscous forces for microdroplets entering the CaCl2-DMC interface caused deformation of the pregelled droplets to occur and therefore resulted in the formation of microparticles with a mushroom-like morphology.
Charcot–Marie–Tooth disease-associated mutant tRNA synthetases linked to altered dimer interface and neurite distribution defect (2007)

Charcot-Marie-Tooth (CMT) diseases are the most common heritable peripheral neuropathy. At least 10 different mutant alleles of GARS (the gene for glycyl-tRNA synthetase) have been reported to cause a dominant axonal form of CMT (type 2D). A unifying connection between these mutations and CMT has been unclear. Here, mapping mutations onto the recently determined crystal structure of human GlyRS showed them within a band encompassing both sides of the dimer interface, with two CMT-causing mutations being at sites that are complementary partners of a "kissing" contact across the dimer interface. The CMT phenotype is shown here to not correlate with aminoacylation activity. However, most mutations affect dimer formation (to enhance or weaken). Seven CMT-causing variants and the wild-type protein were expressed in transfected neuroblastoma cells that sprout primitive neurites. Wild-type GlyRS distributed into the nascent neurites and was associated with normal neurite sprouting. In contrast, all mutant proteins were distribution-defective. Thus, CMT-causing mutations of GlyRS share a common defect in localization. This defect may be connected in some way to a change in the surfaces at the dimer interface.
DRYING METHODS PRESERVING THE TEXTURAL PROPERTIES OF GELS (1989)

To preserve more or less the gels textural properties during their drying step three main methods can be applied which differ roughly by the temperature and pressure range in which they are conducted. In increasing temperatures and pressures ranking one may distinguish : i) the freeze drying process giving "cryogels" (low pressures and temperatures), ii) the ordinary drying method leading to xerogels (ordinary or low pressures and temperatures) and finally, iii) the supercritical drying method producing aerogels (high pressures and temperatures).
Signal Processing for Air-Coupled Impact-Echo using Microphone Arrays (2012)

Impact-echo is an acoustic method for non-destructive testing of concrete structures. It is based on the use of elastic waves created by the impact of a small steel sphere on the concrete surface and analysis of multiple reflections in the frequency domain. In combination with imaging techniques cross-sectional views of the structure can be obtained. Conventional sensors need to be pressed against the surface at each measurement position and lifted up to be moved, which makes field testing quite time-consuming. Furthermore, rough concrete surfaces make it hard to achieve good coupling. Therefore, the use of air-coupled microphones instead of contact sensors is often seen as an attractive and promising alternative. However, in practical applications noise from the environment and especially impact noise from the steel sphere itself often make the use of microphones very difficult. In previous studies mechanical barriers have been used to shield the microphone against acoustic interference. This paper presents a technique based on signal processing algorithms in combination with arrays of two or more microphones, thus minimizing the interfering signal components. This makes the system resistant against acoustic noise caused by motors or wheels when using systems in motion, thus providing the basis for a significant increase in measurement speed compared to systems using conventional contact transducers. As no coupling is necessary, measurements are much less dependent on the roughness of the measurement surface.
Effects of Temperature on Lipid Unsaturation (1987)

(1987). Effects of Temperature on Lipid Unsaturation. Biotechnology and Genetic Engineering Reviews: Vol. 5, No. 1, pp. 245-268.
Raster-to-Vector: Revisiting Floorplan Transformation (2017)

This paper addresses the problem of converting a rasterized floorplan image into a vector-graphics representation. Unlike existing approaches that rely on a sequence of lowlevel image processing heuristics, we adopt a learning-based approach. A neural architecture first transforms a rasterized image to a set of junctions that represent low-level geometric and semantic information (e.g., wall corners or door end-points). Integer programming is then formulated to aggregate junctions into a set of simple primitives (e.g., wall lines, door lines, or icon boxes) to produce a vectorized floorplan, while ensuring a topologically and geometrically consistent result. Our algorithm significantly outperforms existing methods and achieves around 90% precision and recall, getting to the range of production-ready performance. The vector representation allows 3D model popup for better indoor scene visualization, direct model manipulation for architectural remodeling, and further computational applications such as data analysis. Our system is efficient: we have converted hundred thousand production-level floorplan images into the vector representation and generated 3D popup models.