gebhart/patrepeval huggingface dataset:
ATRP in Waterborne Miniemulsion via a Simultaneous Reverse and Normal Initiation Process (2004)

Atom transfer radical polymerization with simultaneous reverse and normal initiation process was conducted in a miniemulsion system with the use of highly active transition-metal complexes formed by hydrophobic ligands at concentrations 5−8 times lower than in a typical reverse ATRP process. The molecular weights were essentially determined by the concentration of alkyl halide (used in ∼5-fold excess to a standard radical initiator) and much less affected by the concentration of a standard radical initiator (e.g., AIBN) and/or CuII complex. Controlled polymerizations of methacrylate, acrylate, and styrene were demonstrated by a linear correlation between molecular weights and monomer conversions and relatively low polydispersities (Mw/Mn < 1.3). The resulting latexes showed good colloidal stability with an average particle sized around 250−300 nm. Oil-soluble initiator (e.g., AIBN) provided better control over polymerization than water-soluble initiator (e.g., VA-044). Well-defined waterborne 3-arm star polystyrene and poly(n-butyl acrylate) were synthesized by adding a trifunctional alkyl halide to a reverse ATRP initiating system.
Factor VIII A3 Domain Residues 1954−1961 Represent an A1 Domain-Interactive Site (2005)

Factor VIIIa consists of subunits designated A1, A2, and A3C1C2. Reassociation of the A1 and A3C1C2 subunits monitored by the factor Xa generation assay and fluorescence resonance energy transfer yielded intersubunit affinity values (K(d)) of 58.0 +/- 12.5 and 58.8 +/- 16.8 nM, respectively. These affinity values were equivalent to that previously determined for factor VIII heavy and light chains [Wakabayashi, H., et al. (2001) Biochemistry 40, 10293-10300], suggesting that the A2 domain makes a minimal contribution to the interchain affinity in factor VIII. Ca(2+) showed no effect on A1/A3C1C2 intersubunit affinity (K(d) = 51.6 +/- 16.6 nM), while Cu(2+) enhanced the A1/A3C1C2 intersubunit affinity approximately 5-fold (K(d) = 12.5 +/- 2.3 nM). A synthetic peptide to A3 domain residues 1954-1961 inhibited association of the A1 and A3C1C2 subunits (K(i) = 65.8 +/- 11.9 microM). Three factor VIII point mutants, His1957Ala, Gly1960Val, and His1961Asp, were stably expressed in BHK cells and purified. All mutants exhibited reduced specific activity (39, 42, and 4%, respectively) compared with that of wild-type factor VIII, and their activity was less stable following heat denaturation analysis (t(1/2) values of 13.3 +/- 0.7, 8.7 +/- 0.3, and 8.1 +/- 0.1 min, respectively) compared with that of the wild type (18.8 +/- 0.8 min). This reduced stability appeared to result from an approximately 2-fold increased dissociation rate for the Gly1960Val and His1961Asp dimers as judged by solid-phase binding assays. We propose that residues 1954-1961 of the A3 domain contribute to interactions with the A1 domain, facilitating their association in factor VIII.
2-Diazoacetoacetic acid, an efficient and convenient reagent for the synthesis of α-diazo-β-ketoesters (2006)

The formation of various alpha-diazo acetoacetic esters can be obtained in a single transformation with good to excellent yields using readily available 2-diazoacetoacetic acid.
Bayesian SegNet: Model Uncertainty in Deep Convolutional Encoder-Decoder Architectures for Scene Understanding (2015)

We present a deep learning framework for probabilistic pixel-wise semantic segmentation, which we term Bayesian SegNet. Semantic segmentation is an important tool for visual scene understanding and a meaningful measure of uncertainty is essential for decision making. Our contribution is a practical system which is able to predict pixel-wise class labels with a measure of model uncertainty. We achieve this by Monte Carlo sampling with dropout at test time to generate a posterior distribution of pixel class labels. In addition, we show that modelling uncertainty improves segmentation performance by 2-3% across a number of state of the art architectures such as SegNet, FCN and Dilation Network, with no additional parametrisation. We also observe a significant improvement in performance for smaller datasets where modelling uncertainty is more effective. We benchmark Bayesian SegNet on the indoor SUN Scene Understanding and outdoor CamVid driving scenes datasets.
Critical current density enhancement in YBa2Cu3O6.8 films on buffered metallic substrates (1991)

A transition buffer, consisting of subbuffers grown at different temperatures, was used to enhance the crystallinity and the transport properties of YBa2Cu3O6.8 (YBCO) films on metallic substrates. Films were fabricated using in situ laser deposition and were strongly c-axis oriented. Critical temperature of 87 K and critical current density of 3×104 A/cm2 at 77 K were obtained for a 0.5-μm-thick YBCO film with a 0.2 μm transition yttrium- stabilized ZrO2 buffer layer. Also, the magnetic field dependence of Jc could be enhanced by using Pt-coated metallic substrates.
Highly efficient gene delivery by mRNA electroporation in human hematopoietic cells: superiority to lipofection and passive pulsing of mRNA and to electroporation of plasmid cDNA for tumor antigen loading of dendritic cells (2001)

Designing effective strategies to load human dendritic cells (DCs) with tumor antigens is a challenging approach for DC-based tumor vaccines. Here, a cytoplasmic expression system based on mRNA electroporation to efficiently introduce tumor antigens into DCs is described. Preliminary experiments in K562 cells using an enhanced green fluorescent protein (EGFP) reporter gene revealed that mRNA electroporation as compared with plasmid DNA electroporation showed a markedly improved transfection efficiency (89% versus 40% EGFP(+) cells, respectively) and induced a strikingly lower cell toxicity (15% death rate with mRNA versus 51% with plasmid DNA). Next, mRNA electroporation was applied for nonviral transfection of different types of human DCs, including monocyte-derived DCs (Mo-DCs), CD34(+) progenitor-derived DCs (34-DCs) and Langerhans cells (34-LCs). High-level transgene expression by mRNA electroporation was obtained in more than 50% of all DC types. mRNA-electroporated DCs retained their phenotype and maturational potential. Importantly, DCs electroporated with mRNA-encoding Melan-A strongly activated a Melan-A-specific cytotoxic T lymphocyte (CTL) clone in an HLA-restricted manner and were superior to mRNA-lipofected or -pulsed DCs. Optimal stimulation of the CTL occurred when Mo-DCs underwent maturation following mRNA transfection. Strikingly, a nonspecific stimulation of CTL was observed when DCs were transfected with plasmid DNA. The data clearly demonstrate that Mo-DCs electroporated with mRNA efficiently present functional antigenic peptides to cytotoxic T cells. Therefore, electroporation of mRNA-encoding tumor antigens is a powerful technique to charge human dendritic cells with tumor antigens and could serve applications in future DC-based tumor vaccines.
The amino acid substitution in albumin Roma: 321 Glu → Lys (1988)

Albumin Roma is an electrophoretically slow moving genetic variant of human serum albumin found in 22 unrelated families. The protein was isolated from the serum of a healthy, heterozygous subject. Analysis of CNBr fragments by isoelectric focusing allowed us to localize the mutation to fragment CNBr IV (residues 299-329). This fragment was isolated on a preparative scale by RP-HPLC and subjected to tryptic digestion. Sequential analysis of two abnormal tryptic peptides, purified by RP-HPLC, revealed that the variant arises from the substitution of glutamic acid 321 by lysine. This amino acid replacement, probably resulting from a point mutation in the structural gene, causes a change in the net charge of +2 units which is in keeping with the decreased electrophoretic mobility of the native protein.
Efficient approximate search on string collections (2009)

This tutorial provides a comprehensive overview of recent research progress on the important problem of approximate search in string collections. We identify existing indexes, search algorithms, filtering strategies, selectivity-estimation techniques and other work, and comment on their respective merits and limitations.
Painting-to-3D model alignment via discriminative visual elements (2014)

This article describes a technique that can reliably align arbitrary 2D depictions of an architectural site, including drawings, paintings, and historical photographs, with a 3D model of the site. This is a tremendously difficult task, as the appearance and scene structure in the 2D depictions can be very different from the appearance and geometry of the 3D model, for example, due to the specific rendering style, drawing error, age, lighting, or change of seasons. In addition, we face a hard search problem: the number of possible alignments of the painting to a large 3D model, such as a partial reconstruction of a city, is huge. To address these issues, we develop a new compact representation of complex 3D scenes. The 3D model of the scene is represented by a small set of discriminative visual elements that are automatically learned from rendered views. Similar to object detection, the set of visual elements, as well as the weights of individual features for each element, are learned in a discriminative fashion. We show that the learned visual elements are reliably matched in 2D depictions of the scene despite large variations in rendering style (e.g., watercolor, sketch, historical photograph) and structural changes (e.g., missing scene parts, large occluders) of the scene. We demonstrate an application of the proposed approach to automatic rephotography to find an approximate viewpoint of historical paintings and photographs with respect to a 3D model of the site. The proposed alignment procedure is validated via a human user study on a new database of paintings and sketches spanning several sites. The results demonstrate that our algorithm produces significantly better alignments than several baseline methods.
Oculus: faster sequence alignment by streaming read compression (2012)

Oculus efficiently condenses redundant input reads and wraps existing aligners to provide nearly identical SAM output in a fraction of the aligner runtime. It includes a number of useful features, such as tunable performance and fidelity options, compatibility with FASTA or FASTQ files, and adherence to the SAM format. The platform-independent C++ source code is freely available online, at http://code.google.com/p/oculus-bio.
A mutation in human immunodeficiency virus type 1 protease at position 88, located outside the active site, confers resistance to the hydroxyethylurea inhibitor SC-55389A (1997)

The hydroxyethylurea human immunodeficiency virus type 1 (HIV-1) protease inhibitors SC-55389A and SC-52151 were used to select drug-resistant variants in vitro. One clinical HIV-1 strain (89-959) and one laboratory HIV-1 strain (LAI) were passaged in peripheral blood mononuclear cells or CEMT4 cells in the presence of SC-55389A. Resistant isolates from both strains consistently had a mutation to serine for asparagine at amino acid 88 (N88S) in the protease gene either alone or in combination with a change to phenylalanine at position 10. The N88S mutation, recreated by oligonucleotide-mediated site-directed mutagenesis in HXB2, was sufficient to confer resistance to SC-55389A. In contrast, SC-52151-resistant variants selected from the monocytotropic strain SF162 had multiple substitutions in the protease gene (I11V, M461, F53L, A71V, and N88D), and the N88D mutation, re-created by oligonucleotide-mediated site-directed mutagenesis in HXB2, did not confer resistance to SC-52151. The potencies of L735,524 and Ro31-8959 were not reduced when these compounds were assayed against variants with either the N88S or N88D substitution. Position 88 is in a helix that lies behind the substrate binding pocket and may indirectly influence inhibitor binding through interactions with the amino acid at position 31. The selected mutations were persistent in the viral populations after more than 20 passages in the absence of drugs. Passaging of virus first in SC-55389A alone and then in combination with SC-52151 resulted in the accumulation of more mutations in the protease gene (L10F, D35E, D37M, I47V, 154L, A71V, V82I, and S88D) and in the selection of a variant that was cross-resistant to multiple protease inhibitors. These results indicate that a mutation in the HIV-1 protease at a position that is located outside of the substrate binding pocket confers resistance to a protease inhibitor and that mutations in the protease gene accumulate with increasing selection pressure and can persist in the absence of selection pressure.
Three Classes of Nuclear Import Signals Bind to Plant Nuclei (1995)

Three nuclear localization signals (NLS), including an unusual Mat alpha 2-like NLS from maize (Zea mays) R, were found to compete for binding to plant nuclei. In addition, the authentic yeast Mat alpha 2 NLS, which does not function in mammals, was shown to function in plants in vivo. Our results indicate that plants possess a site at the nuclear pore complex that recognizes the three known classes of NLSs.
Phosphorylated Galectin-3 Mediates Tumor Necrosis Factor-related Apoptosis-inducing Ligand Signaling by Regulating Phosphatase and Tensin Homologue Deleted on Chromosome 10 in Human Breast Carcinoma Cells (2007)

Galectin-3 (GAL3), a beta-galactoside-binding lectin, confers chemoresistance to a wide variety of cancer cell types. It may exhibit anti- or pro-apoptotic activity depending on the nature of the stimulus. We report here that introducing phosphorylated galectin-3 (P-GAL3) into GAL3-null, tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-resistant human breast carcinoma cells promotes TRAIL-induced apoptotic cell death by stimulating the phosphorylation/inactivation of the pro-apoptotic molecule Bad resulting in the inhibition of mitochondrial depolarization and the release of cytochrome c. Exposure of the transfectant cells to TRAIL leads to the recruitment of the initiator capase-8 followed by activation of the effector caspase-9, independent of cytochrome c, and subsequently the processing of the executioner caspase-3. P-GAL3 and phosphatase and tensin homologue deleted on chromosome 10 (PTEN) were coordinately expressed, with concomitant dephosphorylation of Akt in TRAIL-sensitive cells. In contrast, overexpression of phospho-mutant GAL3 (incapable of phosphorylation) failed to elicit similar responses. Depletion of PTEN using small interference RNAs reinstated Akt phosphorylation and conferred TRAIL resistance. In addition phosphatidylinositol 3-kinase inhibitors rendered the phospho-mutant GAL3-resistant cells sensitive to TRAIL. These findings suggest a pivotal role for P-GAL3 in promoting TRAIL sensitivity through activation of a nonclassic apoptotic pathway and identify P-GAL3 as a novel regulator of PTEN.
Blade atrial septostomy: Experience with the first 50 procedures (1991)

We have performed 50 blade and balloon atrial septostomies in 46 patients with diagnoses of transposition of the great arteries--32 patients; mitral atresia or stenosis--10 patients; total anomalous pulmonary venous drainage--2 patients; tricuspid atresia--1 patient; and pulmonary valve atresia with hypoplastic right ventricle--1 patient. The patients' age ranged from 1 day to 72 months (median = 8 months) and weights ranged from 2.7 to 14.5 kg. In patients with transposition the systemic saturation increased from an average of 62% to 74.6% (p less than 0.001) and the inter-atrial mean pressure gradient was reduced from 7.74 +/- 5.3 to 1.4 +/- 2.04 mm Hg. Patients with mitral atresia had no significant increase in systemic arterial saturation but a significant decrease in the mean inter-atrial gradient from 19.6 +/- 12.4 to 3.8 +/- 5.3 mm Hg. In three patients the blade septostomy was unsuccessful for technical reasons and the condition of the patient. Complications included one death due to atrial laceration, blood loss requiring transfusion in 5 patients, transient CVA in one patient, and failure of the blade to close in one patient. We have found the palliative use of the blade catheter in conjunction with balloon atrial septostomy to be an effective and safe procedure.
The Wnt/β-catenin pathway in human fibrotic-like diseases and its eligibility as a therapeutic target (2015)

The canonical Wnt signaling pathway is involved in a variety of biological processes like cell proliferation, cell polarity, and cell fate determination. This pathway has been extensively investigated as its deregulation is linked to different diseases, including various types of cancer, skeletal defects, birth defect disorders (including neural tube defects), metabolic diseases, neurodegenerative disorders and several fibrotic diseases like desmoid tumors. In the "on state", beta-catenin, the key effector of Wnt signaling, enters the nucleus where it binds to the members of the TCF-LEF family of transcription factors and exerts its effect on gene transcription. Disease development can be caused by direct or indirect alterations of the Wnt/β-catenin signaling. In the first case germline or somatic mutations of the Wnt components are associated to several diseases such as the familial adenomatous polyposis (FAP) - caused by germline mutations of the tumor suppressor adenomatous polyposis coli gene (APC) - and the desmoid-like fibromatosis, a sporadic tumor associated with somatic mutations of the β-catenin gene (CTNNB1). In the second case, epigenetic modifications and microenvironmental factors have been demonstrated to play a key role in Wnt pathway activation. The natural autocrine Wnt signaling acts through agonists and antagonists competing for the Wnt receptors. Anomalies in this regulation, whichever is their etiology, are an important part in the pathogenesis of Wnt pathway linked diseases. An example is promoter hypermethylation of Wnt antagonists, such as SFRPs, that causes gene silencing preventing their function and consequently leading to the activation of the Wnt pathway. Microenvironmental factors, such as the extracellular matrix, growth factors and inflammatory mediators, represent another type of indirect mechanism that influence Wnt pathway activation. A favorable microenvironment can lead to aberrant fibroblasts activation and accumulation of ECM proteins with subsequent tissue fibrosis that can evolve in fibrotic disease or tumor. Since the development and progression of several diseases is the outcome of the Wnt pathway cross-talk with other signaling pathways and inflammatory factors, it is important to consider not only direct inhibitors of the Wnt signaling pathway but also inhibitors of microenvironmental factors as promising therapeutic approaches for several tumors of fibrotic origin.
Automated Extraction of DNA and RNA from a Single Formalin-Fixed Paraffin-Embedded Tissue Section for Analysis of Both Single-Nucleotide Polymorphisms and mRNA Expression (2010)

This fully automated process allowed an efficient simultaneous extraction of both RNA and DNA from a single FFPE section and subsequent dual analysis of selected genes. High gene expression and genotyping detection rates demonstrate the feasibility of molecular profiling from limited archival patient samples.
Analysis of Lsm1p and Lsm8p domains in the cellular localization of Lsm complexes in budding yeast (2009)

In eukaryotes, two heteroheptameric Sm-like (Lsm) complexes that differ by a single subunit localize to different cellular compartments and have distinct functions in RNA metabolism. The cytoplasmic Lsm1-7p complex promotes mRNA decapping and localizes to processing bodies, whereas the Lsm2-8p complex takes part in a variety of nuclear RNA processing events. The structural features that determine their different functions and localizations are not known. Here, we analyse a range of mutant and hybrid Lsm1 and Lsm8 proteins, shedding light on the relative importance of their various domains in determining their localization and ability to support growth. Although no single domain is either essential or sufficient for cellular localization, the Lsm1p N-terminus may act as part of a nuclear exclusion signal for Lsm1-7p, and the shorter Lsm8p N-terminus contributes to nuclear accumulation of Lsm2-8p. The C-terminal regions seem to play a secondary role in determining localization, with little or no contribution coming from the central Sm domains. The essential Lsm8 protein is remarkably resistant to mutation in terms of supporting viability, whereas Lsm1p appears more sensitive. These findings contribute to our understanding of how two very similar protein complexes can have different properties.
Structure of conformationally constrained peptides: From model compounds to bioactive peptides (1989)

The use of backbone conformational constraints has acquired increasing importance in the design and synthesis of structurally restricted agonists and antagonists of bioactive peptides. Here I discuss the preferred conformations of four among the most popular types of such peptide surrogates: (a) Peptides from C alpha, alpha-dialkylated residues, (b) tetrazolyl peptides, (c) (gamma- and delta-) lactam-containing peptides, and (d) thiated peptides. Emphasis is given to conformational energy computations and x-ray diffraction analyses of selected model compounds and analogues of small bioactive peptides such as the formylmethionyl tripeptide chemoattractant and MIF.
Intravenous Pamidronate Prevents Femoral Bone Loss and Renal Stone Formation During 90-Day Bed Rest (2004)

Resistive exercise increased bone formation but could not reduce bone resorption and the risk of renal stones. In contrast, inhibition of bone resorption by pamidronate could preserve bone mineral and reduce the risk of renal stone formation during prolonged bed rest.
Quantification of silver‐stained proteins resolved by two‐dimensional electrophoresis: Genetic variability as related to abundance and solubility in two maize lines (1994)

Relative abundance and solubility of proteins from etiolated coleoptiles of maize were investigated using two-dimensional electrophoresis (2-D PAGE). Automatic quantification of silver-stained polypeptides on replicate 2-D gels made it possible to test the linearity of the relationship between spot integrated optical density and protein amount in the range from 15 micrograms to 135 micrograms per gel, in two inbred lines. A linear response was found for more than 60% of the spots in each genotype. When a linear response was found in both lines for a given spot, the slope values were similar in 94% of the cases, indicating the reliability of silver staining for polypeptide quantification. The parameters of the curves allowed the definition of protein classes of different abundances that could be compared for genetic variability between the two lines. From a comparison between standard 2-D patterns (trichloroacetic acid-acetone extracted proteins) and patterns obtained from Tris buffer extracted proteins, it appeared that 92% of the proteins visualized in the standard gels were soluble. No difference in genetic variability, either qualitative or quantitative, was evidenced between the various classes of abundance, or between soluble and insoluble proteins.