gebhart/patrepeval huggingface dataset:
Organogenesis and pattern formation in the mouse: RNA distribution patterns suggest a role for <i>Bone Morphogenetic Protein-2A (BMP-2A)</i> (1990)

Bone morphogenetic protein-2A (BMP-2A) is a member of the transforming growth factor beta (TGF beta) gene family that has been implicated in cartilage and bone formation. Here we use in situ hybridization to show that BMP-2A RNA is expressed in a variety of embryonic epithelial and mesenchymal tissues outside of the developing skeletal system, including cell populations known to play important roles in morphogenesis. Thus, high levels of transcripts are found in developing limb buds (ventral ectoderm and apical ectodermal ridge), heart (myocardium of the atrioventricular canal), whisker follicles (ectodermal placodes, hair matrix and precortex cells), tooth buds (epithelial buds, dental papilla and odontoblasts), and craniofacial mesenchyme, as well as a number of other sites. The expression patterns of BMP-2A are different from those of TGF beta-1, -2 and -3, and this is illustrated in detail in the developing whisker follicles. These results suggest that BMP-2A plays multiple roles in morphogenesis and pattern formation in the vertebrate embryo.
Einführung in die Kristallographie (1958)

"Einführung in die Kristallographie." Geologiska Föreningen i Stockholm Förhandlingar, 80(4), pp. 504–505
ChemInform Abstract: TELOMERIZATION OF POLYHYDRIC ALCOHOLS WITH BUTADIENE CATALYZED BY LOW‐VALENCE PALLADIUM COMPLEXES (1980)

Abstract Durch niedervalente Palladiumkomplexe katalysierte Telomerisierungen mehratomiger Alkohole mit Butadien.
Modeling and implementation of elastic object manipulation in virtual space (1998)

A new technology that has been used to construct virtual environments in the computer, where objects behave as if they were real ones, has been drawing attention. This paper studies virtual manipulation of elastic objects as a fundamental example of nonrigid materials. An elastic object modeled by a combination of material points and springs can be deformed with a rigid cylindrical manipulator controlled by a mouse in imitation of actual actions such as hitting or thrusting. The dynamic response of the elastic object in a collision with the manipulator is generated by a numerical method of solution based on physics and is displayed in real time. An improved spring model is presented in which the amplitude is restricted by elastic energy when the elastic object receives extensive external force. The results of implementation show the effectiveness of the spring model and interactivity of the system. © 1998 Scripta Technica. Electron Comm Jpn Pt 3, 81(4): 42–50, 1998
Infection of orthopedic implants and the use of antibiotic-loaded bone cements: A review (2001)

Infections by bacteria are a serious complication following orthopedic implant surgery, that can usually only be cured by removing the implant, since the biofilm mode of growth of infecting bacteria on an implant surface protects the organisms from the host immune system and antibiotic therapy. Over the past few decades, attempts have been made to prevent and cure orthopedic implant infections by incorporating antibiotics in polymethylmethacrylate bone cements, in primary and revision surgery. However, the clinical efficacy of antibiotic-releasing bone cements is not accepted by all and the long-term exposure to low doses from antibiotic-releasing bone cements in patients is strongly related to the emerging threat of antibiotic resistance in medicine today. In this article, we start by reviewing the mechanisms governing the formation of an infectious biofilm on orthopedic implant materials, the release mechanisms and properties of clinically-used, antibiotic-loaded bone cements. The clinical efficacy of antibiotic-loaded bone cements is evaluated analyzing separatedly the prophylactic and therapeutic uses of these products.
88. AAV Clades: Their Ability To Recombine and Cross Species-Barriers (2004)

A study was performed to evaluate the molecular presence of AAV in both human and nonhuman primates. PCR methodology was used to clone and characterize the variability in the cap sequence. The biological properties of these capsid structures were assessed using pseudotyped rAAV in gene transfer, neutralizing antibody and in vitro recepterology studies. This variety of novel genotypes led to the identifications of several capsids that showed a remarkable serology, tropism and/or gene transfer efficiency. In order to better understand this variation on a molecular level, a full phylogenetic study was performed.
Pain reduction with oral methotrexate in knee osteoarthritis, a pragmatic phase iii trial of treatment effectiveness (PROMOTE): study protocol for a randomized controlled trial (2015)

Current Controlled Trials identifier: ISRCTN77854383 (registered: 25 October 2013).
Potters, Oculists and Eye-Troubles (1983)

Malain Vernhet has published in Gallia a summary of one of the most important discoveries made at La Graufesenque for many years; a mass of waste associated with a large kiln contained the work of about forty potters, some familiar in the last stages of the export-trade to Britain. Among the decorated bowls were some with the potter's stamp L.COSI, conventionally dated to the late Flavian period. Several of them bore reliefs which prove that the style continued down towards 120: thus, on one bowl, which is illustrated, we see figures of a seated warrior turning his sword on himself, labelled DECIBALV, and of a prisoner condemned ad bestias, identified as PARTV. AS M. Vernhet remarks, reference is to the suicide of the Dacian king, Decebalus, in 106 and to the Parthian triumph, which Trajan did not live to experience, in 117. The design thus epitomizes the great conquests of the reign, and in all its provincial crudity speaks to us directly of facts, away from which the noble commemorative monuments in Rome and at Benevento all too readily, perhaps, beguile us.
Hokua – A Wavelet Method for Audio Fingerprinting (2009)

In recent years, multimedia identification has become important as the volume of digital media has dramatically increased. With music files, one method of identification is audio fingerprinting. The underlying method for most algorithms is the Fourier transform. However, due to a lack of temporal resolution, these algorithms rely on the short-time Fourier transform. We propose an audio fingerprinting algorithm that uses a wavelet transform, which has good temporal resolution. In this thesis, we examine the basics of certain topics that are needed in understanding audio fingerprinting techniques. We also look at a brief history of work done in this field. We introduce a new algorithm, called the Hokua algorithm. We developed Hokua to take advantage of certain properties of the wavelet transform. The algorithm uses coefficient peaks of wavelet transforms to identify a sample query. The various algorithms are compared.
A role for haptics in mobile interaction (2006)

Mobile interaction can potentially be enhanced with well-designed haptic control and display. However, advances have been limited by a vicious cycle whereby inadequate haptic technology obstructs inception of vitalizing applications. We present the first stages of a systematic design effort to break that cycle, beginning with specific usage scenarios and a new handheld display platform based on lateral skin stretch. Results of a perceptual device characterization inform mappings between device capabilities and specific roles in mobile interaction, and the next step of hardware re-engineering.
REVERSAL OF <scp>d</scp> -CYCLOSERINE INHIBITION OF BACTERIAL GROWTH BY ALANINE (1962)

Zygmunt, Walter A. (Mead Johnson & Co., Evansville, Ind.). Reversal of d-cycloserine inhibition of bacterial growth by alanine. J. Bacteriol. 84:154-156. 1962.-Reversal of the antibacterial activity of d-4-amino-3-isoxazolidone by alanine in bacterial cultures actively growing on chemically defined media was compared in cultures requiring exogenous alanine and those capable of its synthesis. dl-Alanine was the most effective reversal agent in Pediococcus cerevisiae, an alanine-requiring organism, and d-alanine was effective in Escherichia coli and Staphylococcus aureus, organisms synthesizing alanine. With all three cultures, l-alanine was the least effective reversal agent.
YKL-40 IDENTIFIED BY PROTEOMIC ANALYSIS AS A BIOMARKER OF SEPSIS (2009)

To investigate changes in protein expression by proteomic analysis in the sera of patients with sepsis and to identify new biomarkers of sepsis. A total of 45 consecutive patients with severe sepsis or septic shock (sepsis group), 22 healthy volunteers, and 23 patients undergoing off-pump coronary artery bypass grafting (control group). Serum samples from eight patients of each group underwent proteomic analysis involving removal of 12 major proteins and subsequent reversed-phase high-performance liquid chromatography fractionation and one-dimensional electrophoresis. The intensity of 41 bands (with 12 proteins identified) increased and that of 42 bands (with 22 proteins identified) decreased in the sepsis group. Results of proteomic analysis successfully validated by Western blotting and/or enzyme-linked immunosorbent assay for three proteins (YKL-40, lipocalin 2, and S100A9) increased in the sepsis group as well as two proteins (retinol-binding protein, vitamin D-binding protein) decreased. Serum YKL-40 levels (sYKL-40) on intensive care unit (ICU) admission were assessed by enzyme-linked immunosorbent assay between the two groups; resulting YKL-40 was significantly higher in the sepsis group (P < 0.001). Furthermore, sYKL-40 on ICU admission was significantly higher in patients with positive blood culture (P < 0.005), patients with septic shock (P < 0.05), and patients requiring continuous hemodiafiltration (P < 0.05) or hydrocortisone replacement therapy (P < 0.005) during subsequent treatment. A positive correlation between sYKL-40 and blood IL-6 level on ICU admission was noted in the sepsis group (r = 0.465, P < 0.01). YKL-40 identified by proteomic analysis is considered as a biomarker of sepsis. However, further investigation is needed to clarify its roles and clinical usefulness as a biomarker.
Optimal Self-Tuning PID Controller Based on Low Power Consumption for a Server Fan Cooling System (2015)

Recently, saving the cooling power in servers by controlling the fan speed has attracted considerable attention because of the increasing demand for high-density servers. This paper presents an optimal self-tuning proportional-integral-derivative (PID) controller, combining a PID neural network (PIDNN) with fan-power-based optimization in the transient-state temperature response in the time domain, for a server fan cooling system. Because the thermal model of the cooling system is nonlinear and complex, a server mockup system simulating a 1U rack server was constructed and a fan power model was created using a third-order nonlinear curve fit to determine the cooling power consumption by the fan speed control. PIDNN with a time domain criterion is used to tune all online and optimized PID gains. The proposed controller was validated through experiments of step response when the server operated from the low to high power state. The results show that up to 14% of a server's fan cooling power can be saved if the fan control permits a slight temperature response overshoot in the electronic components, which may provide a time-saving strategy for tuning the PID controller to control the server fan speed during low fan power consumption.
Subsite specificity of the active site of glucosyltransferases from Streptococcus sobrinus. (1994)

Oral bacterial glucosyltransferases use sucrose as a substrate in synthesis of either alpha-1,3 water-insoluble glucans (GTF-I) or alpha-1,6 water-soluble glucans (GTF-S). The binding specificity of the glucosyl and fructosyl subsites of the sucrose-binding site was examined to identify ligands that bind exclusively to each subsite. Such compounds can be used as reporter ligands to localize the subsite binding of any reversible or irreversible active site inhibitor. In examining potential subsite-specific ligands, binding affinity to GTF-I was consistently stronger than binding to GTF-S. Fructose was found to be a moderate GTF inhibitor, but free glucose, alpha-methylglucoside and glucose epimers were very weak inhibitors. In contrast, glucose transition-state analogues, D-glucano-1,5-lactone, 1-deoxynojirimycin (dNJ), and most N-alkyl derivatives of dNJ were moderate to strong inhibitors; in particular N-methyl-dNJ was found to be the strongest GTF inhibitor identified to date. Multiple inhibitor kinetic analysis established nonexclusive binding of fructose and dNJ at the respective subsites. Binding of fructose and N-alkyl-dNJ derivatives was, to a small degree, partially exclusive. Fructose and dNJ were used as reporter ligands to localize the subsite specificity of two test inhibitors: a reversible inhibitor, Zn2+, and an irreversible inhibitor, diethyl pyrocarbonate (DEP). Zn2+ paired with dNJ in multiple inhibitor kinetic analysis showed no competition between the inhibitors, while Zn2+ paired with fructose decreased ligand affinity 7-fold, establishing Zn2+ binding exclusively at the fructose subsite. Analogous experiments adapted to the irreversible inhibitor DEP indicated that it reacts at both subsites or induces a protein conformational change at one subsite that alters ligand binding at the adjacent subsite.
Using hierarchical histogram representation for the EM clustering algorithm enhancement (2017)

This paper is devoted to EM clustering improvement using hierarchical multivariate histogram for probability density representation. We propose to store and operate with the image histogram by means of a special tree data structure. This allows to speed up computations in the case of multivariate input. We also answer the questions of the algorithm initialization and offer an initialization rule, which exploits the proposed histogram-tree structure. We have tested our algorithm modification and initialization rule using remote sensing images. Obtained results have confirmed that the modified algorithm is faster and the initialization rule provides better clustering in comparison with the traditional EM algorithm implementation.
Simulation-based decision support for bringing a project back on track: the case of RUP-based software construction (2012)

RUP-based development has proven successful in various contexts. The iterative and phased development approach provides a framework for how to develop software efficiently and effectively. Yet, there are plenty of occasions that the projects go off-track in terms of the key parameters of the project such as quality, functionality, cost, and schedule. The challenge for the software project manager is to bring the project back on track. Simulation, in general, and system dynamics based simulation in particular, is established as a method to pro-actively evaluate possible scenarios and decisions. The main contribution of this paper is a method called SIM-DASH; it combines three established techniques for providing decision support to the software project manager in the context of RUP-based development. SIM-DASH consists of (i) a system dynamics modeling and simulation component for RUP-based construction, (ii) dashboard functionality providing aggregated and visualized information for comparing actual versus targeted performance, and (iii) knowledge and experience base describing possible actions that have proven successful in the past for how to bring a project back on track. As part of (iii), decision trees and experience-based guidelines are used. The interplay between these three components provides pre-evaluated actions for bringing the current project iteration back on track. As proof-of-concept, a case study is provided to illustrate the key steps of the method and to highlight its principal advantages. For this purpose, SIM-DASH was substantiated retrospectively for a real-world SAP web system development project within the banking field. While the method is applicable for different issues and scenarios, we study its impact for the specific issue of adding personnel to testing and/or development in order to ensure improved project performance to achieve established quality levels of feature development.
<i>Staphylococcus aureus</i>Accessory Gene Regulator<i>(agr)</i>Group II: Is There a Relationship to the Development of Intermediate‐Level Glycopeptide Resistance? (2003)

We previously determined that all 6 Staphylococcus aureus strains with confirmed intermediate-level resistance to glycopeptides (glycopeptide intermediate S. aureus [GISA]) from the United States that we tested belonged to accessory gene regulator (agr) group II. In the present study, we found that 56% of surveyed bloodstream methicillin-resistant S. aureus isolates (n = 148) at our hospital were agr group II, whereas only 24% of methicillin-susceptible S. aureus isolates (n = 33) were agr group II (P = .001). Population analysis of genetically engineered agr-null and parent wild-type strains of groups I, II, and IV revealed that, when agr function is lost, the agr group II knockout S. aureus was most likely to develop glycopeptide heteroresistance after growth in 1 microg/mL but not 16 microg/mL vancomycin. This strain was unique in showing decreased autolysis after growth in these conditions. This study suggests that some S. aureus strains have an intrinsic survival advantage under a glycopeptide selective pressure, which is possibly related to reduced autolysis after exposure to subinhibitory concentrations of glycopeptide.
Chameleon (2012)

The rise of multi-core processors has shifted performance efforts towards parallel programs. However, single-threaded code, whether from legacy programs or ones difficult to parallelize, remains important. Proposed asymmetric multicore processors statically dedicate hardware to improve sequential performance, but at the cost of reduced parallel performance. However, several proposed mechanisms provide the best-of-both-worlds by combining multiple cores into a single, more powerful processor for sequential code. For example, Core Fusion merges multiple cores to pool caches and functional units, and Intel's Turbo Boost raises the clock speed of a core if the other cores on a chip are powered down. These reconfiguration mechanisms have two important properties. First the set of available cores and their capabilities can vary over short time scales. Current operating systems are not designed for rapidly changing hardware: the existing hotplug mechanisms for reconfiguring processors require global operations and hundreds of milliseconds to complete. Second, configurations may be mutually exclusive: using power to speed one core means it cannot be used to speed another. Current schedulers cannot manage this requirement. We present Chameleon, an extension to Linux to support dynamic processors that can reconfigure their cores at runtime. Chameleon provides processor proxies to enable rapid reconfiguration, execution objects to abstract the processing capabilities of physical CPUs, and a cluster scheduler to balance the needs of sequential and parallel programs. In experiments that emulate a dynamic processor, we find that Chameleon can reconfigure processors 100,000 times faster than Linux and allows applications full access to hardware capabilities: sequential code runs at full speed on a powerful execution context, while parallel code runs on as many cores as possible.
Retinoic acid modulates extracellular urokinase-type plasminogen activator activity in DU-145 human prostatic carcinoma cells. (1995)

Effects of all-trans retinoic acid (RA) on the net enzymatic activity of secreted, extracellular urokinase-type plasminogen activator (u-PA) in DU-145 human prostatic carcinoma cells were examined to assess the potential use of retinoids in human prostate cancer prevention and treatment. u-PA is associated with tumor progression involving invasion and metastasis. Based on a chromogenic substrate assay, results show that DU-145 cells secrete five times more u-PA than normal human prostatic epithelium. DU-145 cells were treated with 0.1 to 10 micrometer RA for 48 h. This short treatment of cells with RA did not inhibit growth. After a 48-h treatment of cultures with RA, serum-free conditioned medium was analyzed for u-PA activity by SDS-PAGE zymography. Two major bands of u-PA with Mr of approximately 54,000 (high molecular weight u-PA) and approximately 33,000 (low molecular weight u-PA) were detected. Plasminogen-dependent catalytic activity of these bands could be specifically inhibited with antibody to u-PA, confirming that these bands represent u-PA. A 48-h treatment with 1.0 micrometer RA reduced u-PA activity in conditioned medium to 51.6% of control. A 50% reduction in free u-PA antigen level, as compared to control, was further demonstrated at 1.0 micrometer RA by Western blot analysis and densitometry. These results show that RA can decrease the net extracellular urokinase activity produced by prostatic carcinoma cells. It is proposed that these effects of RA may have important implications not only in the chemoprevention of prostate cancer, by inhibition of promotion of prostatic intraepithelial neoplasia to invasive carcinoma, but also in tumor progression during invasion and metastasis, by decreasing extracellular matrix degradation, as shown in our accompanying article (M. M. Webber and A. Waghray, Clin. Cancer Res., 1: 755-761, 1995).
Electronic Post-compensation for Nonlinear Phase Fluctuations in a 1000-km 20-Gbit/s Optical Quadrature Phase-shift Keying Transmission System Using the Digital Coherent Receiver (2008)

We demonstrate electronic post-compensation for nonlinear phase fluctuation in a 1000-km 20-Gbit/s optical quadrature phase-shift keying (QPSK) transmission system, where group-velocity dispersion is well managed. The inter-symbol interference (ISI) at the transmitter induces the nonlinear phase fluctuation through self-phase modulation (SPM) of the signal transmitted through a fiber. However, when the optimized phase shift proportional to the intensity fluctuation is given to the complex amplitude of the signal electric field by using a digital coherent receiver, the nonlinear phase fluctuation can be reduced effectively.
Definition of a pool of epitopes that recapitulates the T cell reactivity against major house dust mite allergens (2015)

A detailed map of Der p and Der f antigens defined a pool of epitopes that can be used to detect ex vivo HDM responses.
Induction of the high-affinity IgE receptor (FcɛRI) on human mast cells by IL-4 (1996)

The high-affinity IgE receptor (Fc epsilon RI) is necessary for the induction of IgE-mediated allergic reactions. Cross-linking of Fc epsilon RI expressed on mast cells causes the release of various inflammatory mediators, which trigger allergic reactions. Recently, mast cells lacking Fc epsilon RI have been observed in vivo and in vitro, suggesting the presence of regulational mechanisms in the induction of Fc epsilon RI. In this report, we demonstrate that IL-4 up-regulates Fc epsilon RI in cultured human mast cells, which are grown from cord blood mononuclear cells in the presence of stem cell factor and IL-6, and usually lack Fc epsilon RI expression. At the protein level, the induction of Fc epsilon RI was observed by flow cytometric analysis and the induced Fc epsilon RI expression was stable for at least 23 days in the presence of IL-4. Consistently, Northern blot analysis demonstrated the increase of alpha chain mRNA of Fc epsilon RI and revealed that the up-regulation of Fc epsilon RI occurred at the transcriptional level. Fc epsilon RI induced by IL-4 was functional and caused histamine and beta-hexosaminidase release from mast cells upon cross-linking. Taken together, these results indicate a new role of IL-4 in allergic reactions, besides the stimulation of IgE production.