gebhart/patrepeval huggingface dataset:
Identification of Human Toll-like Receptor 2-Agonistic Activity in Dihydropyridine–Quinolone Carboxamides (2018)

Using a multiplexed, reporter gene-based, high-throughput screen, we identified 9-fluoro-7-hydroxy-3-methyl-5-oxo-<i>N</i>-(pyridin-3-ylmethyl)-2,3-dihydro-1<i>H</i>,5<i>H</i>-pyrido[3,2,1-ij]quinoline-6-carboxamide as a TLR2 agonist. Preliminary structure-activity relationship studies on the carboxamide moiety led to the identification of analogues that induce chemokines and cytokines in a TLR2-dependent manner. These results represent new leads for the development of vaccine adjuvants.
Complex Plasmas in Strong Magnetic Field Environments (2005)

To complete our picture of general complex plasmas, experiments under the influence of high magnetic fields have been carried out in a radio frequency (rf) discharge with and without embedded micro‐particles. The influence of the strong magnetic field on the plasma with respect to its homogeneity as well as on the isotropy of the particle interaction was studied. We observed a filamentation of the plasma at low pressures and low powers even in the absence of particles. The plasma filaments moved around — traced by embedded particles — and suddenly changed to a crystalline like arrangement.
CD4 T cell epitope abundance in ferritin core potentiates responses to hemagglutinin nanoparticle vaccines (2022)

Nanoparticle vaccines based on H. pylori ferritin are increasingly used as a vaccine platform for many pathogens, including RSV, influenza, and SARS-CoV-2. They have been found to elicit enhanced, long-lived B cell responses. The basis for improved efficacy of ferritin nanoparticle vaccines remains unresolved, including whether recruitment of CD4 T cells specific for the ferritin component of these vaccines contributes to cognate help in the B cell response. Using influenza HA-ferritin nanoparticles as a prototype, we have performed an unbiased assessment of the CD4 T cell epitope composition of the ferritin particles relative to that contributed by influenza HA using mouse models that express distinct constellations of MHC class II molecules. The role that these CD4 T cells play in the B cell responses was assessed by quantifying follicular helper cells (T<sub>FH</sub>), germinal center (GC) B cells, and antibody secreting cells. When mice were immunized with equimolar quantities of soluble HA-trimers and HA-Fe nanoparticles, HA-nanoparticle immunized mice had an increased overall abundance of T<sub>FH</sub> that were found to be largely ferritin-specific. HA-nanoparticle immunized mice had an increased abundance of HA-specific isotype-switched GC B cells and HA-specific antibody secreting cells (ASCs) relative to mice immunized with soluble HA-trimers. Further, there was a strong, positive correlation between CD4 T<sub>FH</sub> abundance and GC B cell abundance. Thus, availability of helper CD4 T cell epitopes may be a key additional mechanism that underlies the enhanced immunogenicity of ferritin-based HA-Fe-nanoparticle vaccines.
Research on Ontology Matching Approach in Semantic Web (2008)

The major purpose of applying ontology is to share and reuse knowledge. However, a large amount of heterogeneous ontologies are constructed in semantic Web, because there is not a common criterion for building ontology. Under the background, an ontology matching approach is put forward. It converts the ontology matching to the problem of building RDF (resource description framework) graph matching tree. Moreover, the approach presents a structural similarity measure based on the entities of nodes from the matching tree, compensating the inadequacies of the linguistic similarity measure. Our implementation and experimental results are given to demonstrate the effectiveness of the matching approach.
ChemInform Abstract: A NOVEL BIOGENETIC‐TYPE SYNTHESIS OF AN ORSELLINIC ACID DERIVATIVE (1975)

Abstract Das aus dem Lactonäther (I) mit Fluorsulfonsäuremethylester (II) hergestellte neue Pyryliumsalz (III) reagiert mit dem Wittig‐Reagens (IV) in Tetrahydrofuran über die nicht isolierbare′ Zwischenstufe (V) zu dem Orsellinsäurederivat (VI), ohne daß gleichzeitig Isomere als Nebenprodukte gebildet werden.
The REVIEW system: from formal specifications to natural language (2002)

Formal descriptions, while difficult for most human readers to understand, are convenient for specifying large software systems, where completeness and consistency are important issues. Informal specifications can offer advantages in conciseness and readability, but ambiguities and contradictions are an unavoidable side-effect. Since a specification often acts as a formal contract between the software developer and the customer, it is essential that both sides be able to fully understand the specification document. Systems have been proposed which help the software client better understand the specification by automatically paraphrasing it in natural language. The authors describe the architecture of the REVIEW system, which forms a part of the Metaview metasystem for capturing requirements information. Some example natural language outputs are shown for a sample requirements database.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effects of thermal history on impact‐modified, high‐flow polycarbonate (1995)

Abstract Miles Inc. recently developed an impact‐modified, high‐flow polycarbonate to help meet the material requirements for thin wall applications. Melt temperature and heat aging were found to affect its impact strength, yield stress, and dynamic mechanical relaxations. The results are explained in terms of the presence of polycarbonate's high‐energy intramolecular conformations formed as a result of intermolecular packing effects during molding, their rearrangement to trans‐tans conformations, and the increased interlocking between neighboring chains during heat aging.
Scale-invariant probabilistic latent component analysis (2011)

In this paper, we present a new method for decomposing musical spectrograms. This method is similar to shift-invariant Probabilistic Latent Component Analysis, but, when the latter works with constant Q spectrograms (i.e. with a logarithmic frequency resolution), our technique is designed to decompose standard short time Fourier transform spectrograms (i.e. with a linear frequency resolution). This makes it possible to easily reconstruct the latent signals (which can be useful for source separation).
Ethanol‐type fermentation from carbohydrate in high rate acidogenic reactor (1997)

It has been found, in this study, that a new ethanol-type fermentation can be obtained in a continuous flow, high-rate acidogenic reactor receiving molasses as the feed. The operating pH must be maintained at about 4.5 to avoid onset of propionic fermentation. The acidogenic reactor had a VSS level of 20 g/L and its organic loading was as high as 80 to 90 kg COD/m3 d. The operating ORP was around -250 mV. The ethanol-type fermentation was characterized by a simultaneous production of acetic acid and ethanol, while the yield of propionic was minimal even at a high organic loading rate of 80 to 90 kg COD/m3 d, and also, the hydrogen partial pressure was as high as 50 kPa. Thus, this study has shown that the production of propionic acid is not always related to high hydrogen partial pressure. When the operating pH was increased to 5.5, the yield of propionic acid became significant. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 54: 428–433, 1997.
An electromechanical model of the heart for image analysis and simulation (2006)

This paper presents a new three-dimensional electromechanical model of the two cardiac ventricles designed both for the simulation of their electrical and mechanical activity, and for the segmentation of time series of medical images. First, we present the volumetric biomechanical models built. Then the transmembrane potential propagation is simulated, based on FitzHugh-Nagumo reaction-diffusion equations. The myocardium contraction is modeled through a constitutive law including an electromechanical coupling. Simulation of a cardiac cycle, with boundary conditions representing blood pressure and volume constraints, leads to the correct estimation of global and local parameters of the cardiac function. This model enables the introduction of pathologies and the simulation of electrophysiology interventions. Moreover, it can be used for cardiac image analysis. A new proactive deformable model of the heart is introduced to segment the two ventricles in time series of cardiac images. Preliminary results indicate that this proactive model, which integrates a priori knowledge on the cardiac anatomy and on its dynamical behavior, can improve the accuracy and robustness of the extraction of functional parameters from cardiac images even in the presence of noisy or sparse data. Such a model also allows the simulation of cardiovascular pathologies in order to test therapy strategies and to plan interventions.
A dual-polarized planar array antenna for Ku-band satellite communications (2002)

The authors propose a low sidelobe dual-polarized planar array antenna for Ku-band satellite communications. In conventional dual-polarized planar array antennas using strip lines and microstrip patch antennas, it is difficult to obtain low sidelobe characteristics because the aperture distribution is deformed from the desired one by electrical coupling between feed lines and element antennas. In the proposed antenna, rectangular coaxial lines have been adopted as feed lines in order to reduce coupling between feed lines. We have developed a dual-polarized element antenna shielded by a cavity, in order to reduce coupling between element antennas and feed lines. Also, we have developed an element antenna arrangement forming the desired aperture distribution by adjusting the number of antenna elements in each row. These developed techniques can achieve sidelobe levels of less than -23 dB which would be lower than those of the conventional dual-polarized planar array antennas.
Importance of Candida Species Other than C. albicans as Pathogens in Oncology Patients (1995)

A number of surveys have documented increased rates of candida infection over the past several decades. In this assessment of the frequency and distribution of non-albicans Candida species among patients with cancer, 37 reports that were published between 1952 and 1992 and that described 1,591 cases of systemic candida infection were reviewed. Species other than Candida albicans accounted for 46% of all systemic candida infections in patients with cancer; specifically, Candida tropicalis accounted for 25%, Candida glabrata for 8%, Candida parapsilosis for 7%, and Candida krusei for 4%. Other species were uncommon. C. tropicalis was the predominant pathogenic Candida species in five reports, C. glabrata in two, C. krusei in two, and Candida stellatoidea in one. The perception that, over time, a greater proportion of candida infections have been caused by non-albicans species was not borne out. The wide variability in reported findings was striking and was due in part to differences in the underlying disease affecting the patients described. For example, patients with leukemia were more likely to be infected by C. albicans or C. tropicalis but less likely to be infected by C. glabrata than patients with other types of cancer. The recent increase in the rate of bone marrow transplantation may also have contributed to discrepancies among reports. Bone marrow transplant recipients were more likely to be infected by C. krusei or C. lusitaniae. The other factors partially responsible for the variability among reports included common-source contamination and the pressures imposed by antimicrobial measures.
A semiselective medium for the isolation of Acidovorax valerianellae from soil and plant debris (2006)

Bacterial black spot of corn‐salad ( Valerianella locusta ) caused by Acidovorax valerianellae appeared in France in the beginning of the 1990s. The disease is now widespread in the main area of corn‐salad production and is responsible for high depreciation and significant economic losses every year. A semiselective medium is described for the detection of the bacterium in various environments and to identify primary sources of inoculum. The medium TSAV (tryptic soy broth, 3 g L −1 , agar 15 g L −1 , 5‐fluorouracyl 5 mg L −1 , novobiocin 5 mg L −1 , propiconazole 5 mg L −1 ) increased chances of obtaining cultures of A. valerianellae from naturally infested soil and from root‐debris. Using TSAV, the pathogen was detected in root‐debris up to 39 days after the harvest of a diseased crop. As only a few days usually separates harvest from the next sowing date, soil is likely to be an important source of inoculum for the next crop.
Electron mediated/enhanced ferromagnetism in a hydrogen-annealed Mn:Ge magnetic semiconductor (2011)

We report on the carrier type changes of the p-type for as-grown Mn:Ge films to n-type for post-annealed samples in a hydrogen ambient. The hydrogen-annealed samples exhibit the increased Curie temperature, from 165 to 198 K, and the enhanced magnetic moment, from 0.78 to 1.10 μB/Mn. The first principles calculation using the all-electron full-potential linearized augmented plane wave method indicates that the addition of an electron carrier strengthens the ferromagnetic coupling between the Mn atoms, while the hole carrier caused it to weaken.
Scalable Speculative Parallelization on Commodity Clusters (2010)

While clusters of commodity servers and switches are the most popular form of large-scale parallel computers, many programs are not easily parallelized for execution upon them. In particular, high inter-node communication cost and lack of globally shared memory appear to make clusters suitable only for server applications with abundant task-level parallelism and scientific applications with regular and independent units of work. Clever use of pipeline parallelism (DSWP), thread-level speculation (TLS), and speculative pipeline parallelism (Spec-DSWP) can mitigate the costs of inter-thread communication on shared memory multicore machines. This paper presents Distributed Software Multi-threaded Transactional memory (DSMTX), a runtime system which makes these techniques applicable to non-shared memory clusters, allowing them to efficiently address inter-node communication costs. Initial results suggest that DSMTX enables efficient cluster execution of a wider set of application types. For 11 sequential C programs parallelized for a 4-core 32-node (128 total core) cluster without shared memory, DSMTX achieves a geomean speedup of 49×. This compares favorably to the 15x speedup achieved by our implementation of TLS-only support for clusters.
Gα Subunit Coordinates with Ephrin-B to Balance Self-Renewal and Differentiation in Neural Progenitor Cells (2010)

Proper development of the mammalian brain requires that neural progenitor cells balance self-renewal and differentiation under precise temporal and spatial regulation, but the underlying mechanisms are not well understood. In this study, we identify Gα subunit as a positive regulator of mammalian neurogenesis, working with the regulator of G protein signaling (RGS)-mediated ephrin-B signaling pathway as two opposing forces to maintain a balance between self-renewal and differentiation in the developing mouse cerebral cortex. Multiple Gα(i) subunits are expressed by cortical neural progenitor cells during the course of cortical neurogenesis. Activation of Gα(i) signaling, through in utero electroporation-mediated expression of wild-type and constitutively active Gα(i) subunits, counteracts the function of ephrin-B in cortical neural progenitors to induce differentiation. Genetic knock-in of an RGS-insensitive G184SGα(i2) causes early cell cycle exit and a reduction of cortical neural progenitor cells and leads to a defect in the production of late born cortical neurons, similar to what is observed in mutant mice with deficiency in ephrin-B reverse signaling pathway. This study reveals a role of Gα subunit in mammalian neurogenesis and uncovers a developmental mechanism, coordinated by the Gα and ephrin-B signaling pathways, for control of the balance between self-renewal and differentiation in neural progenitor cells.
W-band power divider based on H-plane slot waveguide bridge (2012)

In this paper, a novel W-band waveguide power divider based on H-plane slot bridge is presented. The divider, relying on the H-plane waveguide multi-step couplers, consists of a coupling gap in the narrow common wall between two WR10 waveguides and two arc debosses in H-plane of the two waveguides. The power dividing is realized by adjusting the length of the coupling gap and radius of the arc deboss. The designed divider has a good performance over 80-90GHz. The amplitude balance of two output ports is within ±0.3dB; the reflection coefficient is less than -22dB and the isolation is greater than 22dB. The proposed structure allows the mechanical tolerance within 0.2mm.
A phase I study of SDX-102 for the treatment of patients with MTAP-deficient recurrent malignant gliomas (2007)

2063 Background: De novo purine biosynthesis entails two metabolic pathways of which one pathway is frequently impaired in cancer due to gene deletion of the rate limiting enzyme, methythioadenosine phosphorylase (MTAP). In MTAP-deficient cancers, SDX-102 inhibits purine biosynthesis by blocking the remaining synthetic pathway. This study was to determine the maximum tolerated dose (MTD), toxicity and pharmacokinetic activity of SDX-102 in the treatment of recurrent MTAP-deficient malignant gliomas. Methods: Eligible patients had recurrent supratentorial MTAP-deficient malignant gliomas treated previously with surgery, radiation and = 2 regimens of chemotherapy. Dose escalation was conducted separately for patients taking enzyme inducing anti-seizure drugs (EIASD+) and for those not (EIASD-). The starting dose in both groups was 80 mg/m 2 /day continuous infusion for 5 days every 3 weeks, cycle length was 3 weeks. Dose escalation was in a stepwise fashion in cohorts of three patients, up to a maximum dose of 125 mg/m 2 /day. Results: 118 patients were screened of which 39 (33%) had MTAP-deficient tumors. 21 patients (14 males/7 females) were enrolled between 9/17/04 and 3/17/06. Median age was 50 years (23–76); median KPS was 90 (60–100); 16 patients (76%) had GBM. Two dose levels of SDX-102 were tested in the EIASD+ group: 80 mg/m 2 /day (n=4) and 100 mg/m 2 /day (n=3), 3/3 dose limiting toxicity (DLT) were noted with grade 3 mucositis at 100 mg/m 2 /day , so in the EIASD+ group the MTD was 80 mg/m 2 /day. Three dose levels were tested in the EIASD- group: 80 mg/m 2 /day (n=4), 100 mg/m 2 /day (n=7), 1/3 patients had DLT (Grade 4 mucositis) at 100 mg/m 2 /day and the cohort was expanded for additional 3 patients without DLT noted; and 125 mg/m 2 /day (n=3) amongst whom no DLT was observed. No MTD was determined in the EIASD- group because the MTAP assay became unavailable through the sponsor. There were a range of 1–14 cycles administered in this patient population. Conclusions: SDX-102 infusion is safe and feasible in patients with recurrent MTAP-deficient malignant gliomas. The MTD in EIASD+ patients is 80 mg/m 2 /day. The EIASD-group MTD has not been determined however the highest dose tested is 125 mg/m 2 /day. No significant financial relationships to disclose.
Identification and characterization of human HES2, HES3, and HES5 genes in silico (2004)

MMTV induces the mouse mammary tumor through the dysregulation of Notch, Wnt, or Fgf signaling pathway. Activation of Notch signaling pathway leads to transcriptional activation of Hes family genes through the interaction between Notch intracellular domain and RBPSUH (CSL). Hes family proteins are mammalian homologs of Drosophila Hairy and Enhancer of split. Hes family of transcriptional repressors with basic Helix-loop-helix (bHLH) and Orange domains are implicated in the cell fate determination of stem cells (or precursor cells) by suppressing the expression of tissue-specific transcriptional activators. Human HES1, HES4, HES6, and HES7 genes have been reported by other groups. Here, we identified and characterized human HES2, HES3 and HES5 genes by using bioinformatics. FLJ33803 (AK091122.1) was the representative human HES2 cDNA. HES2 gene, encoding a 173-aa protein, was located within human genome sequence AL031848.11. HES3 gene, encoding a 186-aa protein, was identified within human genome sequence AL031847.17. HES5 gene, encoding a 166-aa protein, was identified within human genome sequence AL139246.20. HES2 and HES3 genes were mapped to human chromosome 1p36.31, while HES5 gene to 1p36.32. HES2 mRNA was expressed in placenta, pancreatic cancer, colon cancer with RER, cervical cancer, and in head and neck tumors. HES5 mRNA was expressed in fetal heart, and brain tumors. Human HES family proteins were found consisting of bHLH, Orange, Proline-rich domains, and WRPW motif. Phylogenetic analyses revealed that HES family proteins were distantly related except a paralog pair of HES1 and HES4. HES family genes are pharmacogenomic targets in the field of regenerative medicine and oncology.
Natural Spread and Molecular Analysis of Grapevine Leafroll-Associated Virus 3 in Australia (1995)

Natural spread of grapevine leafroll disease was observed in a Pinot Noir clonal evaluation trial in South Australia. The trial consisted of 13 clones with the spread apparently initiated from 3 leafroll-infected clones : Antav 543, Geisenheim 20, and Bourgogne H199A. The occurrence of grapevine leafroll-associated virus 3 (GLRaV-3) was suspected. All 104 vines in the trial were tested by enzyme-linked immunosorbent assay using antibody to GLRaV-3 and by slot blot hybridization analysis using double-stranded RNA as target and labeled GLRaV-3-specific cDNA as probe. Both tests linked GLRaV-3 with the disease spread and detected the infection prior to the onset of symptoms. A cDNA clone from an Italian isolate of GLRaV-3 hybridized in Northern blots with three major dsRNAs of 19.5, 1.9, and 0.9 kbp extracted from leafroll-infected vines. The cloned cDNA insert of approximately 1 kbp was sequenced, and a set of primers designed based on the sequence was used to obtain a corresponding polymerase chain reaction product from the Antav 543 isolate grown in Australia. The nucleotide sequence of the cDNA clones from the two isolates of GLRaV-3 showed 99.5% identity and contained an open reading frame (ORF) encoding a putative protein with a molecular mass of 20.4 kDa with no significant homology to known protein sequences. This ORF was mapped near the 3'-end of the plus strand viral genome and had a 3'-untranslated AU-rich region of approximately 347 nucleotide residues.