gebhart/patrepeval huggingface dataset:
Epigenetic regulation of the alternatively activated macrophage phenotype (2009)

Alternatively activated (M2) macrophages play critical roles in diverse chronic diseases, including parasite infections, cancer, and allergic responses. However, little is known about the acquisition and maintenance of their phenotype. We report that M2-macrophage marker genes are epigenetically regulated by reciprocal changes in histone H3 lysine-4 (H3K4) and histone H3 lysine-27 (H3K27) methylation; and the latter methylation marks are removed by the H3K27 demethylase Jumonji domain containing 3 (Jmjd3). We found that continuous interleukin-4 (IL-4) treatment leads to decreased H3K27 methylation, at the promoter of M2 marker genes, and a concomitant increase in Jmjd3 expression. Furthermore, we demonstrate that IL-4-dependent Jmjd3 expression is mediated by STAT6, a major transcription factor of IL-4-mediated signaling. After IL-4 stimulation, activated STAT6 is increased and binds to consensus sites at the Jmjd3 promoter. Increased Jmjd3 contributes to the decrease of H3K27 dimethylation and trimethylation (H3K27me2/3) marks as well as the transcriptional activation of specific M2 marker genes. The decrease in H3K27me2/3 and increase in Jmjd3 recruitment were confirmed by in vivo studies using a Schistosoma mansoni egg-challenged mouse model, a well-studied system known to support an M2 phenotype. Collectively, these data indicate that chromatin remodeling is mechanistically important in the acquisition of the M2-macrophage phenotype.
Modeling and analysis of an off-line battery charger for single cell lithium batteries (2004)

Several papers have addressed the issues of modeling and analysis of switching mode converters, but few have targeted systems with a battery load. In this paper, by using the PWM switch model, an analytical model is given for the control loops of an off-line flyback charger. System performance under different charging currents and voltages are analyzed and compared with the resistive load. A real application system is analyzed using the model, and the model prediction is compared with lab measurement.
Methodology to build medical ontology from textual resources. (2006)

In the medical field, it is now established that the maintenance of unambiguous thesauri goes through ontologies. Our research task is to help pneumologists code acts and diagnoses with a software that represents medical knowledge through a domain ontology. In this paper, we describe our general methodology aimed at knowledge engineers in order to build various types of medical ontologies based on terminology extraction from texts. The hypothesis is to apply natural language processing tools to textual patient discharge summaries to develop the resources needed to build an ontology in pneumology. Results indicate that the joint use of distributional analysis and lexico-syntactic patterns performed satisfactorily for building such ontologies.
Serum Gonadotropin Levels in Patients with Germ-Cell Tumors of the Testis: Interrelations, Possible Cross-Reactions and Interpretation of Beta-Hcg Level (1997)

The concentration of FSH, LH, LTH, testosterone and beta-hCG was estimated in 177 serum samples from 86 patients with malignant germ-cell tumors of the testis. The objectives of the investigation were the following: the detection of interrelations of hypophyseal gonadotropins at different beta-hCG levels; the determination of the significance of borderline values of beta-hCG; the analysis of the effect of elevated concentrations of beta-hCG on pituitary gonadotropins: the detection of possible cross-reactions during gonadotropin determinations. The RIA method was used to estimate levels of three gonadotropins. The results revealed that there was no cross-reaction between FSH and beta-hCG at RIA assays. When the serum level of beta-hCG of tumor origin exceeded 100 U/l a subtotal inhibition of FSH secretion was observed. Pathologically increased values of beta-hCG were found not only in serum with subnormal-FSH levels, but also when FSH levels were excessively elevated (exceeding 50 U/l). In the latter case the elevated beta-hCG levels could possibly be the consequence of the secretion of beta subunits by the hypophysis or a cross-reaction with LH, and not of a tumor. With values of beta-hCG over 100 U/l cross-reaction with LH occurs, so the true LH levels cannot be assessed. For an adequate interpretation of elevated values of beta-hCG in the serum (i.e. whether they are tumor-derived or not), it is necessary to have values of FSH from the same serum sample.
High purity, self-sustained, pressurized hydrogen production from ammonia in a catalytic membrane reactor (2021)

The combination of catalytic decomposition of ammonia and in situ separation of hydrogen holds great promise for the use of ammonia as a clean energy carrier. However, finding the optimal catalyst – membrane pair and operation conditions have proved challenging. Here, we demonstrate that cobalt-based catalysts for ammonia decomposition can be efficiently used together with a Pd-Au based membrane to produce high purity hydrogen at elevated pressure. Compared to a conventional packed bed reactor, the membrane reactor offers several operational advantages that result in energetic and economic benefits. The robustness and durability of the combined system has been demonstrated for>1000 h on stream, yielding a very pure hydrogen stream (>99.97 % H2) and recovery (>90 %). When considering the required hydrogen compression for storage/utilization and environmental issues, the combined system offers the additional advantage of production of hydrogen at moderate pressures along with full ammonia conversion. Altogether, our results demonstrate the possibility of deploying high pressure (350 bar) hydrogen generators from ammonia with H2 efficiencies of circa 75% without any external energy input and/or derived CO2 emissions.
Targeting <i>Mycobacterium tuberculosis</i> Biotin Protein Ligase (MtBPL) with Nucleoside-Based Bisubstrate Adenylation Inhibitors (2015)

Mycobacterium tuberculosis (Mtb), responsible for both latent and symptomatic tuberculosis (TB), remains the second leading cause of mortality among infectious diseases worldwide. Mycobacterial biotin protein ligase (MtBPL) is an essential enzyme in Mtb and regulates lipid metabolism through the post-translational biotinylation of acyl coenzyme A carboxylases. We report the synthesis and evaluation of a systematic series of potent nucleoside-based inhibitors of MtBPL that contain modifications to the ribofuranosyl ring of the nucleoside. All compounds were characterized by isothermal titration calorimetry (ITC) and shown to bind potently with K(D)s ≤ 2 nM. Additionally, we obtained high-resolution cocrystal structures for a majority of the compounds. Despite fairly uniform biochemical potency, the whole-cell Mtb activity varied greatly with minimum inhibitory concentrations (MIC) ranging from 0.78 to >100 μM. Cellular accumulation studies showed a nearly 10-fold enhancement in accumulation of a C-2'-α analogue over the corresponding C-2'-β analogue, consistent with their differential whole-cell activity.
Usage-Based Online Testing for Proactive Adaptation of Service-Based Applications (2011)

Increasingly, service-based applications (SBAs) are composed of third-party services available over the Internet. Even if third-party services have shown to work during design-time, they might fail during the operation of the SBA due to changes in their implementation, provisioning, or the communication infrastructure. As a consequence, SBAs need to dynamically adapt to such failures during run-time to ensure that they maintain their expected functionality and quality. Ideally the need for an adaptation is proactively identified, i.e., failures are predicted before they can lead to consequences such as costly compensation and roll-back activities. Currently, approaches to predict failures are based on monitoring. Due to its passive nature, however, monitoring might not cover all relevant service executions, which can diminish the ability to correctly predict failures. In this paper we demonstrate how online testing, as an active approach, can improve failure prediction by considering a broader range of service executions. Specifically, we introduce a framework and prototypical implementation that exploits synergies between monitoring, online testing and quality prediction. For online test selection and assessment we adapt usage-based testing strategies. We experimentally evaluate the strengths of our approach in predicting the need for an adaptation of an SBA.
A two phase hybrid RSS/AoA algorithm for indoor device localization using visible light (2012)

A two phase hybrid algorithm for estimating the location of a mobile node, which has the capability of measuring signal strength, azimuth, and elevation, in a smart space environment over the visible light channel is proposed. In contrast to conventional triangulation approaches which are performed in a simplified plane, the smart room architecture requires a non-planar solution due to the illumination requirement. Furthermore, conventional triangulation approaches can at times produce numerically ill-defined solutions, thereby prohibiting a notion of target location. Instead of solely relying on triangulation, the mobile node estimate their locations through a two phase approach in which they firstly exploit the signal strength observables with unique IDs to establish a coarse estimate, and secondly use the azimuth and elevation observables to establish a fine estimate. In many cases, the fine estimate will improve upon the coarse estimate; however when triangulation fails, the algorithm yield the coarse estimate rather than a localization failure. Since the environment model relies on the primary requirement of adequate illumination, the number of LED anchors and transmit power for communication functions are determined. Simulation results confirm the effectiveness of the hybrid two phase localization approach in a smart space indoor environment by having a median coarse phase accuracy of 34.88 cm and a fine phase median accuracy of 13.95 cm.
Optoelectronic Components for Higher Order Modulation Formats (2013)

Discussion on Modulators ✓ LN-based modulators still are in advance in terms of performance and useful for high-end LH systems. Silica-LN hybrid modulators provides highly advanced modulation formats. ✓ InP-based modulators are applicable for advanced modulation formats and have advantages of small chip size and low driving voltage. They are promising candidates for cost-effective small form-factor transceivers for middle range applications. ✓ Remarkable performance enhancements in Si-based modulators have been made in recent years. Further reduction of Vp at high baud rate is preferred for the next step. ✓ Higher-level integration – LDs, Modulators, Drivers, PR&PBC, monitor PDs – Monolithic or Hybrid
Polymerization and copolymerization of 2‐phthalimidomethyl 1,3‐butadiene. I. Preliminary studies of free radical polymerization and polymerizations initiated by various transition metal allyl complexes (1980)

Abstract 2‐Phthalimidomethyl 1,3‐butadiene was homopolymerized and copolymerized with butadiene by free radical initiators; r 1 and r 2 were close to 1. All the attempts to polymerize 2PMB anionically have been unsuccessful. Preliminary studies of various η 3 ‐allylic catalysts showed that η 3 ‐allyl M 0 (CO) 3 OOCCF 3 initiates the polymerization of butadiene and is not sensitive to N ‐methyl phthalimide (NMP); neither does it initiate the copolymerization of butadiene and 2PMB. On the other hand, a catalyst that results from the reaction of allyl trifluoroacetate with nickel tetracarbonyl is efficient for the copolymerization of butadiene and 2PMB. η 3 ‐Allyl nickel trifluoroacetate was prepared in heptane or benzene and used in benzene or methylene chloride. In all cases it initiated the copolymerization of butadiene with 2PMB
Periodontal infection, impaired fasting glucose and impaired glucose tolerance: results from the Continuous National Health and Nutrition Examination Survey 2009–2010 (2014)

Periodontal infection was positively associated with prevalent impaired glucose tolerance in a cross-sectional study among a nationally representative sample.
Image content based improvements to locally adaptive video enhancement (2002)

Three classes of adaptations to systems for video processing are presented. These three techniques are special purpose modifications to commonly used algorithms. The first technique limits excursions of peak white and black with minimum compromise of edge enhancement. The second is a method of preserving perceived chroma when processing luminance. The third is an adaptive contrast term to control the enhancement level in black regions of an image such that noise often associated with dark scene material is not enhanced. All three techniques have been installed on various real-time image processors made by DigiVision for specialty tasks such as night vision and medical endoscopy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Biofunctional TiO2 nanoparticle-mediated photokilling of cancer cells using UV irradiation (2010)

Cancer cell-specific photokilling was successfully demonstrated using antibody-immobilized TiO2 nanoparticles with only 1 J cm−2 UV irradiation.
Solid-phase PCR in a picowell array for immobilizing and arraying 100 000 PCR products to a microscope slide (2012)

We present a method for performing highly parallel PCR reactions in a picowell array (PWA) simultaneously immobilizing generated PCR products in a covalent and spatially-resolved manner onto a microscope slide via solid-phase PCR (SP-PCR). This so called PWA-SP-PCR was performed in picowell arrays featuring 100,000 wells cm(-2) of 19 pL reaction volumes with a surface-to-volume ratio of 0.2 μm(-1). Positive signals were obtained in 97.2% of the 110,000 wells in an area of 110 mm(2). Immobilized DNA was either indirectly detected using streptavidin-Cy5 or directly by molecular hybridisation of Cy3- and/or Cy5-labelled probes. Amplification and immobilization was demonstrated for template DNA ranging from 100 bp up to 1513 bp lengths. Even single DNA molecules were successfully amplified and immobilized demonstrating digital solid-phase PCR. Compared to widely established emulsion based PCR (emPCR) approaches, leading to PCR products immobilized onto bead surfaces in a highly parallel manner, the novel technique results in direct spatial registration of immobilized PCR products in a microarray format. This enables the subsequent use for massively parallel analysis similar to standard microarrays.
Lowering the error-rate floors of moderate-length high-rate irregular ldpc codes (2003)

This paper presents a specialized class of irregular low-density parity-check (LDPC) codes of moderate length (lo3 5 n 5 lo4) and high rate (R 2 3/4). Codes in this class admit low-complexity encoding and have lower error rate floors than other irregular LDPC code design approaches. It is also shown that this class of LDPC codes is equivalent to a class of systematic serial turbo codes. Code designs of moderate-length, high rate codes which yield bit error rate floors below lo-' are presented.
Room-Temperature Transesterification of Edible and Nonedible Oils Using a Heterogeneous Strong Basic Mg/La Catalyst (2008)

Magnesium−lanthanum-mixed oxide catalysts with different Mg/La ratios are prepared by coprecipitation at a constant pH method. The prepared catalysts were characterized by various techniques, such as X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), temperature-programmed desorption of CO2 (CO2-TPD), and Brunauer−Emmett−Teller (BET) surface area. These catalysts are evaluated for transesterification of both edible and nonedible oils to their corresponding fatty acid methyl esters. The catalyst with a Mg/La weight ratio of 3:1 is showing optimum performance toward transesterification of oils, and it exhibited excellent activity even at room temperature. The disclosed catalyst is also tolerable for the transesterification of oils containing both water and free fatty acids. The catalyst can be easily recovered and reused with consistent activity. The exceptional activity of the Mg/La (3:1) catalyst during transesterification is endorsed because of the presence of the highest number of strong basic sites as evidenced by CO2-TPD compared to other Mg/La analogues. The higher basic strength of Mg/La (3:1) is also evidenced by XPS measurements, because the catalyst showed a negative shift in O1s binding energy, which indicates the presence of strong basic sites.
Shared epitopes between Mycoplasma pneumoniae major adhesin protein P1 and a 140-kilodalton protein of Mycoplasma genitalium (1987)

Previous serological data have demonstrated cross-reactive antigens between two pathogenic species of mycoplasmas, M. pneumoniae and M. genitalium. Preliminary analysis of sera and monoclonal antibodies (MAbs) to protein antigens of these species showed an immunodominance of adhesin P1 (165 kilodaltons [kDa]) of M. pneumoniae in mice and hamsters and a 140-kDa protein of M. genitalium in mice and experimentally infected chimpanzees. To further characterize these two proteins, we assayed multiple anti-P1 and anti-140-kDa protein MAbs by enzyme-linked immunosorbent assay, immunoblot, and radioimmunoprecipitation techniques. The 140-kDa M. genitalium protein was shown to be surface accessible and insensitive to levels of trypsin which readily degrade protein P1. Peptide mapping was used to identify a unique class of MAbs which bound a cross-reactive molecule common to both the major adhesin protein P1 of M. pneumoniae and the 140-kDa protein of M. genitalium. MAbs generated against both M. pneumoniae and M. genitalium which were reactive with this determinant blocked M. pneumoniae attachment to chicken erythrocytes.
Effect of Doxorubicin/Pluronic SP1049C on Tumorigenicity, Aggressiveness, DNA Methylation and Stem Cell Markers in Murine Leukemia (2013)

SP1049C therapy effectively suppresses the tumorigenicity and aggressiveness of P388 cells in a mouse model. This may be due to enhanced activity of SP1049C against CSC and/or altered epigenetic regulation restricting appearance of malignant cancer cell phenotype.
Prevalence of c-KIT Mutations in Gonadoblastoma and Dysgerminomas of Patients with Disorders of Sex Development (DSD) and Ovarian Dysgerminomas (2012)

Activating c-KIT mutations (exons 11 and 17) are found in 10-40% of testicular seminomas, the majority being missense point mutations (codon 816). Malignant ovarian dysgerminomas represent ~3% of all ovarian cancers in Western countries, resembling testicular seminomas, regarding chromosomal aberrations and c-KIT mutations. DSD patients with specific Y-sequences have an increased risk for Type II Germ Cell Tumor/Cancer, with gonadoblastoma as precursor progressing to dysgerminoma. Here we present analysis of c-KIT exon 8, 9, 11, 13 and 17, and PDGFRA exon 12, 14 and 18 by conventional sequencing together with mutational analysis of c-KIT codon 816 by a sensitive and specific LightCycler melting curve analysis, confirmed by sequencing. The results are combined with data on TSPY and OCT3/4 expression in a series of 16 DSD patients presenting with gonadoblastoma and dysgerminoma and 15 patients presenting pure ovarian dysgerminomas without DSD. c-KIT codon 816 mutations were detected in five out of the total of 31 cases (all found in pure ovarian dysgerminomas). A synonymous SNP (rs 5578615) was detected in two patients, one DSD patient (with bilateral disease) and one patient with dysgerminoma. Next to these, three codon N822K mutations were detected in the group of 15 pure ovarian dysgerminomas. In total activating c-KIT mutations were found in 53% of ovarian dysgerminomas without DSD. In the group of 16 DSD cases a N505I and D820E mutation was found in a single tumor of a patient with gonadoblastoma and dysgerminoma. No PDGFRA mutations were found. Positive OCT3/4 staining was present in all gonadoblastomas and dysgerminomas investigated, TSPY expression was only seen in the gonadoblastoma/dysgerminoma lesions of the 16 DSD patients. This data supports the existence of two distinct but parallel pathways in the development of dysgerminoma, in which mutational status of c-KIT might parallel the presence of TSPY.
TRENDS IN THE DISTRIBUTION OF THE PRECIOUS METALS IN THE LAC-DES-ILES COMPLEX, NORTHWESTERN ONTARIO (1984)

The Archean Lac-des-Iles complex, located in northwestern Ontario, is a sulfide-bearing layered mafic_ u]tramaJil !qdf. The magmatic sulfide and platinum-group element @GE) mineralization is commonly associated with mafic cumulates. Later geological processes involving a fluid phase, however, have altered primary silicaies, redistributed the Cu-Ni sutfides and produced pGE-bearing tellurides, arsenides, bismuthotellurides and sulfides. In several PGE-bearing samples, secondary violarite-siegenite, sphalerite, galena and clausthalite have been identified. Whole-rock chemical compositions demonstrate that a strong relative enrichment of @t + pd), in most cases, oc_ curs at low Cu, Ni and Au concentrations. The ratios Cu,z(Cu + Ni) and Pt,/(pt + pd) are highly variable even if mineral alteration and lithological groupings are considered. The geochemical data indicate that hydrothermal processes are active in the mobilization and concentration of the precious metals, inasmuch as: (l) most pGE minerals are associated with secondary sulfides and silicates, even where_the pyroxene and plagioclase are not totally aliered, and (2) the highest PGE values are associated with once plroxene-rich rocks, now predominantly composed of
Actinomyces naeslundii in initial dental biofilm formation (2009)

The combined use of confocal laser scanning microscopy (CLSM) and fluorescent in situ hybridization (FISH) offers new opportunities for analysis of the spatial relationships and temporal changes of specific members of the microbiota of intact dental biofilms. The purpose of this study was to analyse the patterns of colonization and population dynamics of Actinomyces naeslundii compared to streptococci and other bacteria during the initial 48 h of biofilm formation in the oral cavity. Biofilms developed on standardized glass slabs mounted in intra-oral appliances worn by ten individuals for 6, 12, 24 and 48 h. The biofilms were subsequently labelled with probes against A. naeslundii (ACT476), streptococci (STR405) or all bacteria (EUB338), and were analysed by CLSM. Labelled bacteria were quantified by stereological tools. The results showed a notable increase in the number of streptococci and A. naeslundii over time, with a tendency towards a slower growth rate for A. naeslundii compared with streptococci. A. naeslundii was located mainly in the inner part of the multilayered biofilm, indicating that it is one of the species that attaches directly to the acquired pellicle. The participation of A. naeslundii in the initial stages of dental biofilm formation may have important ecological consequences.
Cold Promoted Activation of Factor VII (1972)

Summary Several known activators of the plasma kallikrein system were tested for the ability to induce cold promoted activation of factor VII. All the prekallikrein activators tested (EACA, trypsin, acetone, urokinase, kaolin, Liquoid, ellagic acid) revealed generation of factor VII activator activity (CPA). Simultaneously the plasma kallikrein system was activated. A good correlation was demonstrated between the factor VII activation and the kallikrein activity. Glandular kallikrein, bradykinin, or kallidin revealed no effect on the coagulation system. Thus, the correlation between the factor VII activation and the kallikrein system seemed to be restricted to plasma kallikrein.