gebhart/patrepeval huggingface dataset:
Automation in the High-throughput Selection of Random Combinatorial Libraries—Different Approaches for Select Applications (2010)

Automation in combination with high throughput screening methods has revolutionised molecular biology in the last two decades. Today, many combinatorial libraries as well as several systems for automation are available. Depending on scope, budget and time, a different combination of library and experimental handling might be most effective. In this review we will discuss several concepts of combinatorial libraries and provide information as what to expect from these depending on the given context.
Drum Transcription in the presence of pitched instruments using Prior Subspace Analysis (2003)

This paper demonstrates the use of Prior Subspace Analysis (PSA) as a method for transcribing drums in the presence of pitched instruments. PSA uses prior subspaces that represent the sources to be transcribed to overcome some of the problems associated with other subspace methods such as Independent Subspace Analysis (ISA) or sub-band ISA. The use of prior knowledge results in improved robustness for transcription purposes and enables the method to work more readily in the presence of pitched instruments than other subspace methods. The system presented in this paper attempts to extend the use of PSA to transcribe drum sounds in the presence of interfering pitched instruments.
Sensitivity Test for 5-Fluorouracil and Its Analogues, 1-(2-Tetrahydrofuryl)-5-Fluorouracil, Uracil/1-(2-Tetrahydrofuryl)-5-Fluorouracil (4:1) and 1-Hexylcarbamoyl-5-Fluorouracil, Using the Subrenal Capsule Assay (1988)

The chemosensitivity of 20 human neoplastic tissues including 13 gastric and 7 colorectal cancers was tested using 5-fluorouracil (5-FU) and its analogues: 1-(2-tetrahydrofuryl)-5-FU (FT), uracil/FT (UFT) and 1-hexylcarbamoyl-5-FU (HCFU), and the in vivo subrenal capsule (SRC) assay. The relative variation of tumor size (delta TS/TSo) was calculated as follows: delta TS/TS0 = (TS6-TS0/TS0) x 100%, where TS6 was the tumor size on day 6 and TS0 on day 0, and the chemosensitivity was considered to be sensitive when delta TS/TS0 in the treated group was decreased to below -10%. The mean tumor size was -10.9 +/- (SD) 10.9% for 5-FU, -12.3 +/- 17.1% for FT, -18.4 +/- 15.8% for UFT and -17.9 +/- 15.4% for HCFU. The decrease of tumor size was marked when exposed to UFT (p less than 0.01) or HCFU (p less than 0.02), compared with that to 5-FU. Positive correlations were noted between the tumor sizes of 5-FU and its analogues (5-FU vs. FT, r = 0.851; 5-FU vs. UFT, r = 0.746; 5-FU vs. HCFU, r = 0.685). In 9 tissues resistant to 5-FU, 2 (22%) were sensitive to FT, 4 (44%) to UFT, 5 (56%) to HCFU and 7 tissues (78%) to at least one of these analogues. These results suggest that the SRC assay is useful for predicting the effective drug among 5-FU and 5-FU analogues, for individual patients with cancer.
Sequence-independent inhibition of in vitro vascular smooth muscle cell proliferation, migration, and in vivo neointimal formation by phosphorothioate oligodeoxynucleotides. (1996)

Phosphorothioate oligodeoxynucleotides (PS oligos) are antisense (sequence-specific) inhibitors of vascular smooth muscle cell (SMC) proliferation when targeted against different genes. Recently an aptameric G-quartet inhibitory effect of PS oligos has been demonstrated. To determine whether PS oligos manifest non-G-quartet, non-sequence-specific effects on human aortic SMC, we examined the effects of S-dC28, a 28-mer phosphorothioate cytidine homopolymer, on SMC proliferation induced by several SMC mitogens. S-dC28 significantly inhibited SMC proliferation induced by 10% FBS as well as the mitogens PDGF, bFGF, and EGF without cytotoxicity. Moreover, S-dC28 abrogated PDGF-induced in vitro migration in a modified micro-Boyden chamber. Furthermore, S-dC28 manifested in vivo antiproliferative effects in the rat carotid balloon injury model. S-dC28 suppressed neointimal cross-sectional area by 73% and the intima/media area ratio by 59%. Therefore, PS oligos exert potent non-G-quartet, non-sequence-specific effects on in vitro SMC proliferation and migration as well as in vivo neointimal formation.
Variation at the NFATC2 Locus Increases the Risk of Thiazolidinedione-Induced Edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) Study (2010)

Genetic variation at the NFATC2 locus contributes to edema among individuals who receive rosiglitazone.
Mycophenolate Mofetil or Intravenous Cyclophosphamide for Lupus Nephritis (2005)

In this 24-week trial, mycophenolate mofetil was more effective than intravenous cyclophosphamide in inducing remission of lupus nephritis and had a more favorable safety profile.
VideoNOC (2018)

Video streaming traffic is rapidly growing in mobile networks. Mobile Network Operators (MNOs) are expected to keep up with this growing demand, while maintaining a high video Quality of Experience (QoE). This makes it critical for MNOs to have a solid understanding of users' video QoE with a goal to help with network planning, provisioning and traffic management. However, designing a system to measure video QoE has several challenges: i) large scale of video traffic data and diversity of video streaming services, ii) cross-layer constraints due to complex cellular network architecture, and iii) extracting QoE metrics from network traffic. In this paper, we present VideoNOC, a prototype of a flexible and scalable platform to infer objective video QoE metrics (e.g., bitrate, rebuffering) for MNOs. We describe the design and architecture of VideoNOC, and outline the methodology to generate a novel data source for fine-grained video QoE monitoring. We then demonstrate some of the use cases of such a monitoring system. VideoNOC reveals video demand across the entire network, provides valuable insights on a number of design choices by content providers (e.g., OS-dependent performance, video player parameters like buffer size, range of encoding bitrates, etc.) and helps analyze the impact of network conditions on video QoE (e.g., mobility and high demand).
Denatured state of ovalbumin in high concentrations of urea as evaluated by disulfide rearrangement analysis. (1994)

To investigate the highly denatured state of ovalbumin (molecular mass of 42.7 kDa, four cysteine sulfhydryls and one cystine disulfide) using the disulfide rearrangement approach, we established the peptide-mapping procedure using a cysteine-labeling technique with a fluorescent dye that allows the quantitative analyses for the disulfide-involved half-cystines. Ovalbumin denatured at a low protein concentration in 8-10 M urea, in which the protein showed complete unfolding as evaluated by far-UV CD spectra, was analyzed for the disulfide-involved half-cystines using the peptide-mapping procedure. Data clearly showed that the number of free sulfhydryls and intrachain disulfides were four and one, respectively, but that all six half-cystines are labeled with the dye. These results strongly suggested that 15 disulfide isomers that are theoretically possible for a molecule having one disulfide and four sulfhydryls are all generated during the denaturation. The quantitative data for the ratios of the observed labeling values for the six half-cystines, relative to the overall labeling values, were consistent with the view that the distribution of the 15 possible disulfide isomers at equilibrium depends on the number of amino acid residues separating the two half-cystines to the power of -1.9 to -2.0. Essentially, the same non-gaussian chain nature was also observed with kinetic data for sulfhydryl-disulfide exchanges after denaturation of native ovalbumin.
Playing it real again (2013)

We repeated a study on the usage of a magic lens and a static peephole interface for playing a find-and-select game in a public space. While we reproduced the study setup and procedure the task was conducted in a public transportation stop with different characteristics. The results on usage duration and user preference were significantly different from those reported for previous conditions. We investigate possible causes, specifically the differences in the spatial characteristics and the social contexts in which the study took place.
Expression and Purification of Recombinant Human Annexin V in Escherichia Coli (2000)

Human annexin V cDNA was cloned into plasmid pET19b and fused to a ten consecutive histidine tag at N-terminal. When expressed in E. coli BL21(DE3) LysS, the recombinant His10-annexin V accumulated in soluble form in the cytoplasm. By two-step chromatography, i.e., metal chelate affinity chromatography and anion exchange chromatography, recombinant His10-annexin V was purified to homogeneity on silver-stained SDS-PAGE gel. Recombinant annexin V, 7.4 mg, was obtained from a 1 litre flask culture.
Altered Expression Pattern of Topoisomerase IIα, in Ovarian Tumor Epithelial and Stromal Cells after Platinum-Based Chemotherapy (2006)

TOP2A mRNA and protein expression in ovarian cancer exhibits specific patterns in tumor epithelial and adjacent stromal cells, which are differentially modulated after platinum-based chemotherapy. These data support the recently discovered importance of the stromal compartment in tumor progression and suggest that tumor stromal cells might be relevant to the development of chemotherapy resistance in ovarian cancer.
Energetics of Si x O y C z Polymer‐Derived Ceramics Prepared Under Varying Conditions (2008)

Incorporation of carbon at the molecular level can create unusual amorphous and nanostructures of Si–C–O polymer‐derived ceramics by controlled pyrolysis of crosslinked polysiloxanes. These ceramics can resist crystallization to ultrahigh temperatures. In this work, we support earlier studies that the resistance to crystallization of these nanodomain networks is due to thermodynamic as well as kinetic factors. Calorimetric measurements of heats of dissolution in a molten oxide solvent show that these ceramics posses a negative enthalpy relative to their crystalline constituents (silicon carbide, cristobalite, and graphite). Si–C–O ceramics pyrolyzed at 1000° and 1450°C appear somewhat more energetically stable than those prepared at 1200°C.
The Roles of γ1 Heavy Chain Membrane Expression and Cytoplasmic Tail in IgG1 Responses (1997)

In antibody responses, B cells switch from the expression of immunoglobulin (Ig) mu and delta heavy (H) chains to that of other Ig classes (alpha, gamma, or epsilon), each with a distinct effector function. Membrane-bound forms of alpha, gamma, and epsilon, but not mu and delta, have highly conserved cytoplasmic tails. Mutant mice unable to express membrane gamma1 H chains or producing tailless gamma1 H chains failed to generate efficient IgG1 responses and IgG1 memory. H chain membrane expression after class switching is thus required for these functions, and class switching equips the B cell antigen receptor with a regulatory cytoplasmic tail that naïve B cells lack.
Clumping Factor A Interaction with Complement Factor I Increases C3b Cleavage on the Bacterial Surface ofStaphylococcus aureusand Decreases Complement-Mediated Phagocytosis (2010)

The human complement system is important in the immunological control of Staphylococcus aureus infection. We showed previously that S. aureus surface protein clumping factor A (ClfA), when expressed in recombinant form, bound complement control protein factor I and increased factor I cleavage of C3b to iC3b. In the present study, we show that, compared to the results for the wild type, when isogenic ClfA-deficient S. aureus mutants were incubated in serum, they bound less factor I, generated less iC3b on the bacterial surface, and bound fewer C3 fragments. It has been shown previously that two amino acids in ClfA (P(336) and Y(338)) are essential for fibrinogen binding. However, S. aureus expressing ClfA(P336A Y338S) was less virulent than ClfA-deficient strains in animal models. This suggested that ClfA contributed to S. aureus virulence by a mechanism different than fibrinogen binding. In the present study, we showed that S. aureus expressing ClfA(P336A Y338S) was more susceptible to complement-mediated phagocytosis than a ClfA-null mutant or the wild type. Unlike ClfA, ClfA(P336A Y338S) did not enhance factor I cleavage of C3b to iC3b and inhibited the cofactor function of factor H. Fibrinogen enhanced factor I binding to ClfA and the S. aureus surface. Twenty clinical S. aureus strains all expressed ClfA and bound factor I. High levels of factor I binding by clinical strains correlated with poor phagocytosis. In summary, our results suggest that the interaction of ClfA with factor I contributes to S. aureus virulence by a complement-mediated mechanism.
Cell–matrix adhesion (2007)

The complex interactions of cells with extracellular matrix (ECM) play crucial roles in mediating and regulating many processes, including cell adhesion, migration, and signaling during morphogenesis, tissue homeostasis, wound healing, and tumorigenesis. Many of these interactions involve transmembrane integrin receptors. Integrins cluster in specific cell-matrix adhesions to provide dynamic links between extracellular and intracellular environments by bi-directional signaling and by organizing the ECM and intracellular cytoskeletal and signaling molecules. This mini review discusses these interconnections, including the roles of matrix properties such as composition, three-dimensionality, and porosity, the bi-directional functions of cellular contractility and matrix rigidity, and cell signaling. The review concludes by speculating on the application of this knowledge of cell-matrix interactions in the formation of cell adhesions, assembly of matrix, migration, and tumorigenesis to potential future therapeutic approaches.
Virus-transformed pre-B cells show ordered activation but not inactivation of immunoglobulin gene rearrangement and transcription. (1991)

Virus-transformed pre-B cells undergo ordered immunoglobulin (Ig) gene rearrangements during culture. We devised a series of highly sensitive polymerase chain reaction assays for Ig gene rearrangement and unrearranged Ig gene segment transcription to study both the possible relationship between these processes in cultured pre-B cells and the role played by heavy (H) chain (mu) protein in regulating gene rearrangement. Our analysis of pre-B cell cultures representing various stages of maturity revealed that transcription of each germline Ig locus precedes or is coincident with its rearrangement. Cell lines containing one functional rearranged H chain allele, however, continue to transcribe and to rearrange the allelic, unrearranged H chain locus. These cell lines appear to initiate but not terminate rearrangement events and therefore provide information about the requirements for activating rearrangement but not about allelic exclusion mechanisms.
Role of group-specific component (vitamin D binding protein) in clearance of actin from the circulation in the rabbit. (1988)

The possible role of group specific component (Gc) (vitamin D-binding protein) in the clearance of cellular actin entering the circulation was examined with 125I-labeled Gc and actin injected into a rabbit model. Although filamentous F-actin is depolymerized primarily by plasma gelsolin, greater than or equal to 90% 125I-actin injected in either monomeric G- or F-form became complexed eventually with Gc (1:1 molar ratio). Clearance of Gc complexes was much faster (greater than 90% within 5 h) than that of native Gc (t1/2 = 17.2 h). Nephrectomy did not significantly alter the clearance of either Gc or actin. Since Gc complexes are dramatically increased in situations of tissue necrosis such as in fulminant hepatic failure, the current results suggest a crucial role for Gc in sequestration and clearance of released cellular actin.
Theory of Transverse Cavity Mode Selection in Homojunction and Heterojunction Semiconductor Diode Lasers (1971)

A discussion of the transverse electromagnetic modes in single and double heterojunction lasers is presented. Three basic structures are analyzed: a laser with single heterojunction and optical cavity defined by the (p+-p) heterojunction and p-n junction; a double heterojunction laser with the second heterojunction at the p-n junction; and another double heterojunction unit which can have a large range of optical cavities because the second heterojunction is in the n region spaced a controlled distance from the p-n junction. Since the dielectric discontinuity at a heterojunction is an order of magnitude larger than at a p-n junction, these double heterojunction lasers can have high-order transverse modes. To model the observed radiation fields and, in particular, the preference for high-order modes, the optical properties of the junction region are treated as a five-layer dielectric slab. The two outer regions are bulk p+ and n+ (AlGa)As in the double heterojunction structures and p+(AlGa)As and n+ GaAs in the single heterojunction structures. The section between the p+ heterojunction and the p-n junction, which is customarily treated as the active section of the laser, has here been partitioned into two regions: a gain region adjacent to the p-n junction where recombination occurs and a lower gain region adjacent to the p-p+ heterojunction. In fact the latter region may be absorbing. The width of the first gain region is associated with the electron diffusion length in heavily doped p-type GaAs. For a suitable partition the modal gain of the high-order modes becomes larger than for the low-order modes, resulting in the highest mode reaching threshold first. In contrast, were the region between the n-p junction and the p-p+ heterojunction uniformly inverted, the laser would operate in the fundamental mode, contrary to experimental observation. Machine calculations indicate that structures radiating high-order modes have a gain region narrower than 1 μm.
Role of the antithrombin-binding pentasaccharide in heparin acceleration of antithrombin-proteinase reactions. Resolution of the antithrombin conformational change contribution to heparin rate enhancement. (1992)

The synthetic antithrombin-binding heparin pentasaccharide and a full-length heparin of approximately 26 saccharides containing this specific sequence have been compared with respect to their interactions with antithrombin and their ability to promote inhibition and substrate reactions of antithrombin with thrombin and factor Xa. The aim of these studies was to elucidate the pentasaccharide contribution to heparin's accelerating effect on antithrombin-proteinase reactions. Pentasaccharide and full-length heparins bound antithrombin with comparable high affinities (KD values of 36 +/- 11 and 10 +/- 3 nM, respectively, at I 0.15) and induced highly similar protein fluorescence, ultraviolet and circular dichroism changes in the inhibitor. Stopped-flow fluorescence kinetic studies of the heparin binding interactions at I 0.15 were consistent with a two-step binding process for both heparins, involving an initial weak encounter complex interaction formed with similar affinities (KD 20-30 microM), followed by an inhibitor conformational change with indistinguishable forward rate constants of 520-700 s-1 but dissimilar reverse rate constants of approximately 1 s-1 for the pentasaccharide and approximately 0.2 s-1 for the full-length heparin. Second order rate constants for antithrombin reactions with thrombin and factor Xa were maximally enhanced by the pentasaccharide only 1.7-fold for thrombin, but a substantial 270-fold for factor Xa, in an ionic strength-independent manner at saturating oligosaccharide. In contrast, the full-length heparin produced large ionic strength-dependent enhancements in second order rate constants for both antithrombin reactions of 4,300-fold for thrombin and 580-fold for factor Xa at I 0.15. These enhancements were resolvable into a nonionic component ascribable to the pentasaccharide and an ionic component responsible for the additional rate increase of the larger heparin. Stoichiometric titrations of thrombin and factor Xa inactivation by antithrombin, as well as sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the products of these reactions, indicated that pentasaccharide and full-length heparins similarly promoted the formation of proteolytically modified inhibitor during the inactivation of factor Xa by antithrombin, whereas only the full-length heparin was effective in promoting this substrate reaction of antithrombin during the reaction with thrombin.(ABSTRACT TRUNCATED AT 400 WORDS)
Comparison of self- and conventional-ligating brackets in the alignment stage (2011)

This prospective study investigated the difference in clinical efficiency between Damon™ 3 self-ligating brackets (SLB) compared with Mini Diamond conventional ligating brackets (CLBs) during tooth alignment in straightwire fixed appliance therapy. Twenty-nine patients (10 males and 19 females), aged between 14 and 30 years, were randomly divided into two groups: 14 patients received the SLB and 15 received the CLB. Upper arch impressions were taken for pre-treatment records (T(0)). A transpalatal arch was soldered to both maxillary first molar bands prior to extraction of the maxillary first premolars, followed by straightwire fixed appliances (0.022 × 0.028 inch). A 0.014 inch nickel titanium (NiTi) wire was used as the levelling and aligning archwire. Four monthly reviews were undertaken and impressions of the upper arch were taken at each appointment (T(1), T(2), T(3), and T(4)). Displacements of the teeth were determined using Little's irregularity index (LII). Data were analysed using the Mann-Whitney U-test. In the aligning stage, the CLB group showed significantly faster alignment of the teeth compared with the SLB group at the T(1)-T(2) interval (P < 0.05). However, there were no differences at T(2)-T(3), and T(3)-T(4) for either group (P > 0.05). The CLB group showed 98 per cent crowding alleviation compared with 67 per cent for the SLB after 4 months of alignment and levelling. Mini Diamond brackets aligned the teeth faster than Damon™ 3 but only during the first month. There was no difference in efficacy between the two groups in the later 3 weeks. Alleviation of crowding was faster with CLB than with SLB.
Microstructural Characterization of Bombyx mori Silk Fibers (1998)

The microstructure of Bombyx mori silk fibers before and after degumming was examined by transmission electron microscopy (TEM), selected area electron diffraction (SAED), wide-angle X-ray scattering (WAXS), and low-voltage high-resolution scanning electron microscopy (LVHRSEM). LVHRSEM micrographs of the neat cocoon revealed a network of pairs of twisting filaments. After degumming, there were only individual filaments showing a surface texture consistent with an oriented fibrillar structure in the fiber interior. WAXS patterns confirmed the oriented β-sheet crystal structure common to silkworm and spider (dragline) silks. Low-dose SAED results were consistent with the WAXS data and revealed that the crystallographic texture did not vary significantly across the fiber diameter. TEM observations of individual microtomed fibers indicated a nominally triangular cross section and a 0.5−2 μm sericin coating. After degumming to remove the sericin, a banded feature was revealed with a characteristic spacing of nominally 600 nm along the fiber axis. These bands were oriented in a roughly parabolic or V-shape pointing along one axis within a given fiber. We hypothesize that this orientation was induced by the extrusion and drawing during the spinning process. Equatorial dark field (DF) images revealed that axial and lateral sizes of the β-sheet crystallites in silk fibroin ranged from 20 to 170 nm and from 1 to 24 nm, respectively. Crazes developed in the degummed silk fiber parallel to the fiber direction. The formation of these crazes suggests that there are significant lateral interactions between microfibrils in silk fibers.