gebhart/patrepeval huggingface dataset:
Mixture Suppression of Perceived Intensities in an Odor Mixture (2008)

Four components (geranylacetone, 2-pentylfiiran, 2-ethyl-1-hexanol and n-valeraldehyde) were selected as representative model chemicals for evaluation of perceived odor intensities. Initially, odor intensity adjustment of these four components was performed at the 'moderate' level on a labeled magnitude scale. The contribution of individual components around the moderate concentration was evaluated as follows: (I) measurement of the odor intensity change of single components, (II) measurement of the odor intensity change in a mixture when one component in the 4 chemical mixture was increased in concentration, (III) comparison between the intensity change of single component (I) and the intensity change in the mixed solution (II). In the case of 2-ethyl-1-hexanol and 2-pentylfiiran, both intensities were strongly suppressed in the mixture. Conversely, the intensity change of n-valeraldehyde in the mixture was almost the same as that of the single component. Four compounds had different contributions to the odor intensities in the mixture. Therefore, mixture suppression has to be re-evaluated on the basis of individual chemical characters.
Massive Diversity in Whole-Genome Sequences of Streptococcus suis Strains from Infected Pigs in Switzerland (2019)

Here we report the whole-genome sequences of 15 clinical Streptococcus suis strains isolated from pigs in Switzerland. Although they originated from the same host and geographic origin, the strains showed a large amount of diversity.
Enhanced Performance Test Mix for High-Throughput LC/MS Analysis of Pharmaceutical Compounds (2006)

LC/MS is being used for the routine analysis of small molecules in both the discovery and development stages within the pharmaceutical industry. In drug discovery, LC/MS is relied upon to confirm the identity and assess the purity of chemical entities. To ensure the quality of LC/MS analysis, it is important that the LC/MS system is operating within defined performance criteria. Performance monitoring of the system with a standard compound mix offers many advantages over other alternatives, since it monitors the LC/MS system as an integrated unit under the same working conditions as those used for the analysis of samples. It is also a convenient approach, because the test mix can be injected as part of the automated sequence. Use of a test mix for similar purposes has been described previously (Tang, L.; Fitch, W. L.; Alexander, M. S.; Dolan, J. W. Anal. Chem. 2000, 72, 5211-5218). To monitor the performance of ArQule's LC/MS operation (with UV and ELS detection) in greater detail, a set of eight compounds was selected from a collection of 137 commercially available "druglike" compounds. The compounds are generally stable and compliant with the rule-of-five criteria. This enhanced mix has a balanced selection of pKa values and covers the typical range of hydrophobicity and molecular masses of pharmaceutical compounds. Moreover, the selected compounds can generally be ionized using ESI and APCI modes with positive and negative polarity. The test mix can be used under formic acid or ammonium hydroxide conditions and with methanol or acetonitrile as an organic modifier. Performance monitoring with the enhanced mix is demonstrated with respect to ionization and mass measurement, as well as changes in gradient profile, flow rate, buffer pH, and ionic strength.
In vivo toxicity and pharmacokinetic features of B43 (anti-CD19)-genistein immunoconjugate in nonhuman primates. (1998)

B43 (anti-CD19)-genistein immunoconjugate targets genistein, a naturally occurring protein tyrosine kinase-inhibitory isoflavone to the membrane-associated antiapoptotic CD19-LYN complexes and triggers apoptotic cell death. In this preclinical study, the toxicity profiles of B43-genistein as well as unconjugated genistein were evaluated in cynomolgus monkeys. B43-genistein and genistein were administered either as single bolus injections or daily injections for 5-10 consecutive days via the i.v. route to monkeys. Neither genistein nor B43-genistein was toxic to cynomolgus monkeys, and no test article-related histopathological lesions were found in any of the two genistein-treated or five B43-genistein-treated cynomolgus monkeys. B43-genistein showed a favorable pharmacokinetics in monkeys, with a plasma half-life of 10-23 h. Plasma samples from B43-genistein-treated monkeys elicited potent and CD19 antigenspecific antileukemic activity against human CD19+ leukemia cells in vitro. To our knowledge, this is the first preclinical toxicity and pharmacokinetic study of a tyrosine kinase inhibitor-containing immunoconjugate in nonhuman primates.
An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm (2015)

We present the first accelerated implementation of BWA-MEM, a popular genome sequence alignment algorithm widely used in next generation sequencing genomics pipelines. The Smith-Waterman-like sequence alignment kernel requires a significant portion of overall execution time. We propose and evaluate a number of FPGA-based systolic array architectures, presenting optimizations generally applicable to variable length Smith-Waterman execution. Our kernel implementation is up to 3× faster, compared to software-only execution. This translates into an overall application speedup of up to 45%, which is 96% of the theoretically maximum achievable speedup when accelerating only this kernel.
Research on the Fault Location Method of Double-terminal MMC-HVDC Transmission Line without the Influence of Wave Velocity (2020)

Abstract Due to its own advantages, MMC-HVDC transmission system has been widely used in power transmission and grid connection. According to the existing double-terminal traveling wave fault location method of MMC-HVDC transmission lines, a double-terminal traveling wave location method is proposed, which is not affected by wave velocity. The wavelet transform is performed on the voltage traveling wave signals at both ends to determine the time when the traveling wave reaches both ends of the line, and the distance of the fault point is calculated. It effectively reduces the influence of the uncertainty of traveling wave velocity on the positioning results and improves the positioning accuracy. The simulation of PSCAD and Matlab software proves the effectiveness and correctness of the method.
Mathematical determination of the tibial insertion of the patellar tendon using computed tomography images (1995)

Misalignment of the extensor apparatus is an essential factor in impairment of the patellar-femoral joint. This may be partly or entirely responsible for patellar dislocation or lateral patellar-femoral arthrosis. One surgical method to correct the pathology is medial transposition of the patellar ligament on the tibial tuberosity (anteriorly or posteriorly, distally or ventrally). These interventions correct misalignment of the extensor apparatus relative to statistical norms. We propose a mathematical method based on the use of computed tomography (CT) images to determine the ideal tibial insertion for the patellar tendon. This method is based on biomechanical modeling and the use of equipressure criteria. It is the first step in allowing the use of mathematics to model correctly tibial insertion of the patellar ligament, an entirely new development. This is important because it will allow surgeons greater accuracy in distal correction of extensor apparatus misalignments. J Imag Guid Surg 1:226–236 (1995). © 1996 Wiley-Liss, Inc.
Modulation of cardiomyocyte activity using pulsed laser irradiated gold nanoparticles (2016)

Can photothermal gold nanoparticle mediated laser manipulation be applied to induce cardiac contraction? Based on our previous work, we present a novel concept of cell stimulation. A 532 nm picosecond laser was employed to heat gold nanoparticles on cardiomyocytes. This leads to calcium oscillations in the HL-1 cardiomyocyte cell line. As calcium is connected to the contractility, we aimed to alter the contraction rate of native and stem cell derived cardiomyocytes. A contraction rate increase was particularly observed in calcium containing buffer with neonatal rat cardiomyocytes. Consequently, the study provides conceptual ideas for a light based, nanoparticle mediated stimulation system.
Gastrin-releasing peptide receptor (GRPr) promotes EMT, growth, and invasion in canine prostate cancer (2016)

These data demonstrated that the GRPr is important in prostate cancer growth and progression and targeting GRPr may be a promising strategy for treatment of prostate cancer. Prostate 76:796-809, 2016. © 2016 Wiley Periodicals, Inc.
Theory of unsymmetric polymer–polymer interfaces (1975)

Solutions have been obtained to equations which described the interface between two immiscible polymers and are more general than the equations first introduced by Helfand and Tagami. Gaussian random−walk statistics are assumed for the macromolecules. As a consequence of the present work, limitations of the earlier theory are removed, particularly the assumption that the properties of the two polymers when pure are identical. Calculations are performed for a variety of polymers and comparison with experiment is made.
Recovering traceability links between a simple natural language sentence and source code using domain ontologies (2009)

This paper proposes an ontology-based technique for recovering traceability links between a natural language sentence specifying features of a software product and the source code of the product. Some software products have been released without detailed documentation. To automatically detect code fragments associated with the functional descriptions written in the form of simple sentences, the relationships between source code structures and problem domains are important. In our approach, we model the knowledge of the problem domains as domain ontologies. By using semantic relationships of the ontologies in addition to method invocation relationships and the similarity between an identifier on the code and words in the sentences, we can detect code fragments corresponding to the sentences. A case study within a domain of painting software shows that we obtained results of higher quality than without ontologies.
Peroxone chemistry : formation of H_2O_3 and ring-(HO_2) (HO_3) from O_3/H_2O_2 (2002)

The recent observation [Wentworth, P., Jones, L. H., Wentworth, A. D., Zhu, X. Y., Larsen, N. A., Wilson, I. A., Xu, X., Goddard, W. A., Janda, K. D., Eschenmoser, A. & Lerner, R. A. (2001) Science 293, 1806–1811] that antibodies form H_2O_2 from ^1O_2 plus H_2O was explained in terms of the formation of the H_2O_3 species that in the antibody reacts with a second H_2O_3 to form H_2O_2. There have been few reports of the chemistry for forming H_2O_3, but recently Engdahl and Nelander [Engdahl, A. & Nelander, B. (2002) Science 295, 482–483] reported that photolysis of the ozone–hydrogen peroxide complex in argon matrices leads to significant concentrations of H_2O_3. We report here the chemical mechanism for this process, determined by using first-principles quantum mechanics. We show that in an argon matrix it is favorable (3.5 kcal/mol barrier) for H_2O_2 and O_3 to form a [(HO_2)(HO_3)] hydrogen-bonded complex [head-to-tail seven-membered ring (7r)]. In this complex, the barrier for forming H_2O_3 plus ^3O_2 is only 4.8 kcal/mol, which should be observable by means of thermal processes (not yet reported). Irradiation of the [(HO_2)(HO_3)-7r] complex should break the HO–OO bond of the HO_3 moiety, eliminating ^3O_2 and leading to [(HO_2)(HO)]. This [(HO_2)(HO)] confined in the matrix cage is expected to rearrange to also form H_2O_3 (observed experimentally). We show that these two processes can be distinguished isotopically. These results (including the predicted vibrational frequencies) suggest strategies for synthesizing H_2O_3 and characterizing its chemistry. We suggest that the [(HO_2)(HO_3)-7r] complex and H_2O_3 are involved in biological, atmospheric, and environmental oxidative processes.
Graph Signal Processing: Overview, Challenges and Applications (2017)

Research in Graph Signal Processing (GSP) aims to develop tools for processing data defined on irregular graph domains. In this paper we first provide an overview of core ideas in GSP and their connection to conventional digital signal processing. We then summarize recent developments in developing basic GSP tools, including methods for sampling, filtering or graph learning. Next, we review progress in several application areas using GSP, including processing and analysis of sensor network data, biological data, and applications to image processing and machine learning. We finish by providing a brief historical perspective to highlight how concepts recently developed in GSP build on top of prior research in other areas.
Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data (2020)

Supplementary data are available at Bioinformatics online.
Quantification of Active Sites for the Determination of Methanol Oxidation Turn-over Frequencies Using Methanol Chemisorption and in Situ Infrared Techniques. 2. Bulk Metal Oxide Catalysts (2001)

Bulk metal oxide catalysts, especially bulk mixed-metal molybdates such as Fe2(MoO4)3, often exhibit high methanol oxidation activity and selectivity. However, the difficulties involved in determining active surface site densities on these catalysts have, in the past, generally prevented side-by-side comparisons of their intrinsic activities, or turn-over frequencies (TOFs). In the present study, high temperature (110 °C) methanol chemisorption and in-situ infrared spectroscopy have been employed to directly and quantitatively determine the number of active metal oxide surface sites available for methanol oxidation. The IR spectra indicate that methanol chemisorption on these catalysts produces both associatively adsorbed, intact Lewis-bound surface methanol species (CH3OHads, species I) on acidic sites, as well as dissociatively adsorbed surface methoxy species (−OCH3, species II) on less acidic or basic sites. In fact, the Lewis acidity of bulk mixed-metal molybdates relative to the methanol probe molecule was found to decrease as follows: Fe2(MoO4)3, NiMoO4 (species I predominates) > MnMoO4, CoMoO4, ZnMoO4, Al2(MoO4)3 > Ce(MoO4)2 > Bi2Mo3O12 > Zr(MoO4)2 (species II predominates). It also appears that Mo cations are the primary methanol chemisorption sites in many of the bulk mixed-metal molybdates, including commercially important Fe2(MoO4)3. By quantifying the surface concentrations of the adsorbed methoxylated reaction intermediates from the IR spectra, it was then possible to normalize the catalytic methanol oxidation activities for the calculation of TOFs. The methanol oxidation TOFs of bulk molybdates were shown to be relatively similar to those of model supported catalysts with the same co-cation (e.g., MoO3/NiO vs NiMoO4)possibly due to the formation of a “monolayer” of surface molybdenum oxide species on the surfaces of the bulk metal molybdates. In addition, the bulk mixed-metal molybdates were found to exhibit the same ligand effect as that discovered previously in supported metal oxide catalysts, in which the TOF generally decreases with increasing ligand cation electronegativity due to electronic variations in localized M−O−Ligand bonds.
Antibody response of infected mice to outer membrane proteins of Pseudomonas aeruginosa (1984)

The antibody response to outer membrane proteins of Pseudomonas aeruginosa was studied in mice experimentally infected with P. aeruginosa 220. The infection consisted of an abscess established by subcutaneous injection of bacteria. Sera from these mice were analyzed by indirect radioimmunoprecipitation and immunoblot methods for the presence of antibodies to proteins of the isolated outer membrane. Sera from mice 14 days postinfection were shown to contain antibodies directed against proteins that comigrated with the major outer membrane proteins F (porin), H2, and I (lipoprotein). A 16,000-dalton protein that did not appear to be a major outer membrane protein also elicited a significant antibody response in some instances. It is concluded that mice, in response to infection, elicit an immunological response to outer membrane proteins of P. aeruginosa.
The Buchwald–Hartwig Amination After 25 Years (2019)

Abstract The Pd‐catalyzed coupling of aryl (pseudo)halides and amines is one of the most powerful approaches for the formation of C(sp 2 )−N bonds. The pioneering reports from Migita and subsequently Buchwald and Hartwig on the coupling of aminostannanes and aryl bromides rapidly evolved into general and practical tin‐free protocols with broad substrate scope, which led to the establishment of what is now known as the Buchwald–Hartwig amination. This Minireview summarizes the evolution of this cross‐coupling reaction over the course of the past 25 years and illustrates some of the most recent applications of this well‐established methodology.
Approximation of the second fundamental form of a hypersurface of a Riemannian manifold (2003)

We give a general Riemannian framework to the study of approximation of curvature measures, using the theory of the normal cycle. Moreover, we introduce a differential form which allows to define a new type of curvature measure encoding the second fundamental form of a hypersurface, and to extend this notion to geometric compact subsets of a Riemannian manifold . Finally, if a geometric compact subset is close to a smooth hypersurface of a Riemannian manifold, we compare their second fundamental form (in the previous sense), and give a bound of their difference in terms of geometric invariants and the mass of the involved normal cycles.
Design, Synthesis, and Fungicidal Evaluation of Novel Pyrazole-furan and Pyrazole-pyrrole Carboxamide as Succinate Dehydrogenase Inhibitors (2017)

The identification of novel succinate dehydrogenase (SDH) inhibitors represents one of the most attractive directions in the field of fungicide research and development. During our continuous efforts to pursue inhibitors belonging to this class, some structurally novel pyrazole-furan carboxamide and pyrazole-pyrrole carboxamide derivatives have been discovered via the introduction of scaffold hopping and bioisosterism to compound 1, a remarkably potent lead obtained by pharmacophore-based virtual screening. As a result of the evaluation against three destructive fungi, including Sclerotinia sclerotiorum, Rhizoctonia solani, and Pyricularia grisea, a majority of them displayed potent fungicidal activities. In particular, compounds 12I-i, 12III-f, and 12III-o exhibited excellent fungicidal activity against S. sclerotiorum and R. solani comparable to that of commercial SDHI thifluzamide and 1.
Supplementary Tables 1 - 2 from Multisite Validation Study to Determine Performance Characteristics of a 92-Gene Molecular Cancer Classifier (2023)

&lt;p&gt;PDF file, 85KB, Supplemental Table 1: Performance characteristics of the 92-gene assay for tumor subclassification. Supplemental Table 2: Pre-analytical variables and effects on 92-gene assay performance&lt;/p&gt;
Plant diversity to support humans in a CELSS ground-based demonstrator (1981)

A controlled ecological life support system (CELSS) for human habitation in preparation for future long duration space flights is considered. The success of such a system depends upon the feasibility of revitalization of food resources and the human nutritional needs which are to be met by these food resources. Edible higher plants are prime candidates for the photoautotrophic components of this system if nutritionally adequate diets can be derived from these plant sources to support humans. Human nutritional requirements information based on current knowledge are developed for inhabitants envisioned in the CELSS ground based demonstrator. Groups of plant products that can provide the nutrients are identified.
150 Consecutive Cases of Delayed Post Mastectomy Reconstruction with TRAM Flap and Results. (2011)

Purpose: This is the report on the results of 150 consecutive cases of delayed postmastectomy reconstruction with TRAM flap performed by single surgeon. The purpose of this study is to review the merits, demerits and other considerations of this method by analyzing the results. Methods: 150 patients were reviewed retrospectively who had breast reconstruction by a single surgeon from July 2001 to July 2008. Reviewed factors include demographic factors, mastectomy method, adjuvant therapies (such as radiation, chemotherapy) complication rate, simultaneous contralateral breast procedure rate, secondary touch-up procedure rate, and patients' satisfaction. Results: Ovarall TRAM flap complication rate was 22.6%. Among them, donor site complication rate was 36%, simultaneous contralateral breast procedure rate was 44.6%, secondary touch-up procedure rate was 40%. All rates were higher compared to immediate reconstruction with TRAM flap. But the patients' satisfaction was about the same as immediate reconstruction. Conclusion: Delayed postmastectomy reconstruction with TRAM flap can yield satisfactory results despite of relatively high complication rate and concomitant procedure rate when it is performed by a experienced surgeon.
Curcumin Attenuates Beta-Amyloid-Induced Neuroinflammation via Activation of Peroxisome Proliferator-Activated Receptor-Gamma Function in a Rat Model of Alzheimer's Disease (2016)

Neuroinflammation is known to have a pivotal role in the pathogenesis of Alzheimer's disease (AD), and curcumin has been reported to have therapeutical effects on AD because of its anti-inflammatory effects. Curcumin is not only a potent PPARγ agonist, but also has neuroprotective effects on cerebral ischemic injury. However, whether PPARγ activated by curcumin is responsible for the anti-neuroinflammation and neuroprotection on AD remains unclear, and needs to be further investigated. Here, using both APP/PS1 transgenic mice and beta-amyloid-induced neuroinflammation in mixed neuronal/glial cultures, we showed that curcumin significantly alleviated spatial memory deficits in APP/PS1 mice and promoted cholinergic neuronal function in vivo and in vitro. Curcumin also reduced the activation of microglia and astrocytes, as well as cytokine production and inhibited nuclear factor kappa B (NF-κB) signaling pathway, suggesting the beneficial effects of curcumin on AD are attributable to the suppression of neuroinflammation. Attenuation of these beneficial effects occurred when co-administrated with PPARγ antagonist GW9662 or silence of PPARγ gene expression, indicating that PPARγ might be involved in anti-inflammatory effects. Circular dichroism and co-immunoprecipitation analysis showed that curcumin directly bound to PPARγ and increased the transcriptional activity and protein levels of PPARγ. Taking together, these data suggested that PPARγ might be a potential target of curcumin, acting to alleviate neuroinflammation and improve neuronal function in AD.