gebhart/patrepeval huggingface dataset:
Interactions of aluminum nanoparticles with human epidermal keratinocytes (2009)

Aluminum nanoparticles (Al NP) have been used in applications as diverse as drug delivery, material surface coatings and an ingredient for solid rocket fuel in military explosives and artillery. Although Al NP are used in many civilian and military applications, the health and safety implications of these nanosize particles are not known. To understand the interactions and biological activity of Al NP in human cells, cultured human neonatal epidermal keratinocytes (HEK) were exposed for 24 h to 50 and 80 nm Al NP in concentrations from 4.0 to 0.0004 mg ml(-1) to assess the cytotoxicity and inflammatory potential. UV-Vis measurements and nanoparticle controls revealed that the Al NP interact with the assay dyes. Viability did not decrease in HEK exposed to both the 50 and the 80 nm Al NP at all treatment concentrations with MTT, CellTiter 96 AQueous One (96 AQ) and alamar Blue (aB) viability assays. The 96 AQ and aB assays interact with the Al NP less than MTT, and proved to be the best assays to use with these Al NP. TEM depicted Al NP localized within the cytoplasmic vacuoles of the cells. Cytokine data was variable, indicating possible nanoparticle interactions with the cytokine assays. These studies illustrate the difficulties involved in assessing the biological safety of nanomaterials such as Al NP due to media- and temperature-dependent particle agglomeration and nanoparticle interactions with biomarkers of cytotoxicity.
Smart sensor for electrical machine monitoring through statistical analysis (2012)

These days monitoring systems for electrical machines require high-performance instrumentation, low-cost primary sensors, and characteristics of online signal processing. Smart sensors are an approach to increase performance and overcome costs in monitoring systems. This work presents preliminary results on the implementation of a smart sensor for electrical machine monitoring integrated as a low-cost SoC. The proposed smart sensor is based on a reconfigurable hardware architecture implemented into a field programmable gate array. It extracts statistics like mean, variance, information entropy, and the distribution histogram from the acquired signal. It can work as a standalone system, showing obtained results on a VGA screen or LCD, or streaming out obtained results for further processing. Two study cases demonstrate its effectiveness during electrical machine monitoring: Detection of time-dependent harmonic effects on the voltage signal provided by a VSD. Identification of broken bars and unbalance in induction motors.
Creation of a Chloroplast Microsatellite Reporter for Detection of Replication Slippage in Chlamydomonas reinhardtii (2008)

Microsatellites are composed of short tandem direct repeats; deletions or duplications of those repeats through the process of replication slippage result in microsatellite instability relative to other genomic loci. Variation in repeat number occurs so frequently that microsatellites can be used for genotyping and forensic analysis. However, an accurate assessment of the rates of change can be difficult because the presence of many repeats makes it difficult to determine whether changes have occurred through single or multiple events. The current study was undertaken to experimentally assess the rates of replication slippage that occur in vivo in the chloroplast DNA of Chlamydomonas reinhardtii. A reporter construct was created in which a stretch of AAAG repeats was inserted into a functional gene to allow changes to be observed when they occurred at the synthetic microsatellite. Restoration of the reading frame occurred through replication slippage in 15 of every million viable cells. Since only one-third of the potential insertion/deletion events would restore the reading frame, the frequency of change could be deduced to be 4.5 x 10(-5). Analysis of the slippage events showed that template slippage was the primary event, resulting in deletions rather than duplications. These findings contrasted with events observed in Escherichia coli during maintenance of the plasmid, where duplications were the rule.
Study of the Yellowstone crustal magmatic system with multiphysics data (2020)

Yellowstone volcanic field is characterized by hotspots, extensive earthquakes, ground deformation, and contains the world’s largest concentration of hydrothermal features. Most of the previous geophysical studies in the Yellowstone area were based on separate inversions of different geophysical data, which suffered from inadequate data coverage, limited sensitivity, measurement errors, and nonuniqueness of the inverse problems. Joint inversion of multiphysics data is a practical approach to reduce the nonuniqueness and uncertainties in the inverse model parameters. This paper presents the results of joint inversion of the gravity and P-wave traveltimes data produced by local earthquakes in the Yellowstone area. We apply a novel joint inversion method based on Gramian constraints and multiscale resampling to image the crustal magmatic system of the Yellowstone. Our results have revealed a consistent L-shaped low-density and low-velocity anomaly just beneath the Yellowstone caldera. Presentation Date: Tuesday, October 13, 2020 Session Start Time: 8:30 AM Presentation Time: 10:10 AM Location: 360C Presentation Type: Oral
Surface modification of Fe3O4@SiO2 microsphere by silane coupling agent (2013)

In the present study, Fe3O4@SiO2 core–shell microspheres were prepared via two steps. First, Fe3O4 nanoparticles were synthesized by co-precipitation of Fe+3 and Fe+2 as reaction substrates and NaOH as precipitant. Second, the surface of Fe3O4 was coated with silica by hydrolysis of tetraethylorthosilicate as the silica source. Subsequently, in order to reduce the amount of interaction and the agglomeration of Fe3O4@SiO2 microspheres, the silica shell of these particles was modified by vinyltriethoxysilane as the silane coupling agent. The structural properties of the samples were characterized by X-ray diffraction, scanning electron microscopy, transmission electron microscopy, and Fourier transform infrared spectroscopy analyses. The results indicated that the average sizes of Fe3O4 and Fe3O4@SiO2 particles were about 50 and 500 nm, respectively. Also, the surface characterization of Fe3O4@SiO2 microspheres showed that the silane coupling agent was covalently coupled with the silica surface.
Data from A Novel Anti-HER2 Antibody–Drug Conjugate XMT-1522 for HER2-Positive Breast and Gastric Cancers Resistant to Trastuzumab Emtansine (2023)

&lt;div&gt;Abstract&lt;p&gt;Most patients with HER2-positive breast or gastric cancer exhibit primary or acquired resistance to trastuzumab emtansine (T-DM1), and such patients may have limited therapeutic options. XMT-1522 is a novel anti-HER2 antibody–drug conjugate. We compared XMT-1522 to T-DM1 in preclinical models. The effects of XMT-1522 and T-DM1 on cell survival and apoptosis were compared in six HER2-positive breast cancer or gastric cancer cell lines, of which three lines were T-DM1–sensitive (N-87, OE-19, JIMT-1) and three T-DM1–resistant (RN-87, ROE-19, SNU-216). We compared these agents also in the HER2-negative breast cancer cell line MCF-7, and in mouse RN-87 and JIMT-1 xenograft models. Cell survival was assessed using the AlamarBlue method and apoptosis with the Caspase-Glo 3/7 method. XMT-1522 inhibited the growth of all six HER2-positive cell lines. The proportions of cells that survived XMT-1522 treatment were smaller as compared with T-DM1, particularly in the T-DM1–resistant cell lines. XMT-1522 induced more cell apoptosis compared with T-DM1. While RN-87 and JIMT-1 xenograft tumors progressed on T-DM1 treatment, all tumors responded to XMT-1522, and all but one tumor disappeared during the XMT-1522 treatment. XMT-1522 had a strong antitumor effect on RN-87 and JIMT-1 xenografts that progressed on T-DM1. We conclude that XMT-1522 was effective in HER2-positive breast cancer and gastric cancer cell lines resistant to T-DM1, and in xenograft models resistant to T-DM1. The results support the testing of XMT-1522 in clinical trials in patients with HER2-positive cancer.&lt;/p&gt;&lt;/div&gt;
Reply (2011)

Vertraue Experimenten : DFT‐Rechnungen besagen, dass Wasserstoffbrücken von Wassermolekülen in einem siebenfach koordinierten Ruthenium‐Oxo‐Komplex den Singulettgrundzustand stabilisieren. Übereinstimmend belegen Experimente für einen neuartigen siebenfach koordinierten, pentaganol‐bipyramidalen Ruthenium‐Oxo‐Komplex einen Singulettgrundzustand. Trotzdem zeigt er die gleiche Reaktivität wie ein analoger Triplettkomplex.
The Antituberculosis Antibiotic Capreomycin Inhibits Protein Synthesis by Disrupting Interaction between Ribosomal Proteins L12 and L10 (2014)

Capreomycin is a second-line drug for multiple-drug-resistant tuberculosis (TB). However, with increased use in clinics, the therapeutic efficiency of capreomycin is decreasing. To better understand TB resistance to capreomycin, we have done research to identify the molecular target of capreomycin. Mycobacterium tuberculosis ribosomal proteins L12 and L10 interact with each other and constitute the stalk of the 50S ribosomal subunit, which recruits initiation and elongation factors during translation. Hence, the L12-L10 interaction is considered to be essential for ribosomal function and protein synthesis. Here we provide evidence showing that capreomycin inhibits the L12-L10 interaction by using an established L12-L10 interaction assay. Overexpression of L12 and/or L10 in M. smegmatis, a species close to M. tuberculosis, increases the MIC of capreomycin. Moreover, both elongation factor G-dependent GTPase activity and ribosome-mediated protein synthesis are inhibited by capreomycin. When protein synthesis was blocked with thiostrepton, however, the bactericidal activity of capreomycin was restrained. All of these results suggest that capreomycin seems to inhibit TB by interrupting the L12-L10 interaction. This finding might provide novel clues for anti-TB drug discovery.
An Expert-guided Hierarchical Graph Attention Network for Post-traumatic Stress Disorder Highly-associative Genetic Biomarkers Identification (2023)

Abstract Post-traumatic Stress Disorder (PTSD) is a common debilitating mental disorder, that occurs in some individuals following extremely traumatic events. Traditional identification of Genetic Markers (GM) for PTSD is mainly based on a statistical clinical approach by comparing PTSD patients with normal controls. However, these statistical studies present limitations, often generating inconsistent results. Few studies have yet examined thoroughly the role of somatic mutations, PTSD disease pathways and their relationships. Capitalizing on deep learning techniques, we have developed a novel hierarchical graph attention network to identify highly correlational GM (HGMs) of PTSD. The network presents the following novelties: First, both a hierarchical graph structure and a graph attention mechanism have been integrated into a model to develop a graph attention network (GAtN) model. Second, domain-specific knowledge, including somatic mutations, genes, PTSD pathways and their correlations have been incorporated into the graph structures. Third, 12 somatic mutations having high or moderate impacts on proteins or genes have been identified as the potential HGMs for PTSD. Fourth, our study is carefully guided by prominent PTSD literature or clinical experts of the field; any high saliency HGMs generated from our model are further verified by existing PTSD-related authoritative medical journals. Our study illustrates the utility and significance of a hybrid approach, integrating both AI and expert-guided/domain-specific knowledge for thorough identification of biomarkers of PTSD, while building on the nature of convergence and divergence of PTSD pathways. Our expert-guided AI-driven methodology can be extended to other pathological-based HGM identification studies; it will transform the methodology of biomarker identification for different life-threatening diseases to speed up the complex lengthy procedures of new biomarkers identification.
Time crystals: the search for a new phase of matter (2022)

Pedram Roushan, from Google’s Quantum AI team in California, describes this elusive form of matter – and how it could be simulated on the company’s Sycamore quantum processor.
Skeletal photoinduced rearrangement of diarylethenes: ethene bridge effects (2023)

A skeletal photorearrangement involving UV-induced 6π-electrocyclization of diarylethenes with various ethene bridges has been studied. It has been found that deprotonation is the predominant step among the three possible alternative reaction pathways (radical abstraction, deprotonation, or sigmatropic shift) following 6π-electrocyclization, and incorporation of an electronegative carbonyl group into the geminal position to the phenyl residue results in a reduction in the reaction time and an increase in the yield of the desired product. The significant increase in the reaction time in less polar solvents (toluene, TCM) also indicates a large contribution of the deprotonation step to the skeletal photorearrangement of diarylethenes. Performing the reaction in toluene in the presence of tertiary amines leads to a reduction in the reaction time and an increase in the yield of the desired product. The best results were achieved when the reaction was carried out in toluene in the presence of DIPEA. The experimental results are in good agreement with the DFT calculations.
A Novel Chromosome Abnormality in Human Neuroblastoma and Antifolate-Resistant ChineseHamster Cell Lines in Culture 1 2 (1976)

Four cell lines, SK-N-SH, SK-N-MC, SK-N-BE(2), and IMR-32, established in vitro from tumor tissue of patients with neuroblastoma were analyzed by trypsin-Giemsa banding methods. In two of the lines a large, abnormally staining chromosome region was observed. This "homogeneously staining region" (HSR) was considerably longer than any of the bands present in normal human cells and, as revealed by both G- and Q-banding, stained with an intermediate intensity. It was located on chromosomes No 6, 10, 17, or 19 of the SK-N-BE(2) cell line and on chromosome No 1 of the IMR-32 line. In concurrent studies, long HSR's were also observed in Chinese hamster sublines that had been exposed to and had developed high levels of resistance to methotrexate or methasquin and high levels of activity of target enzyme dihydrofolate reductase. For several sublines with the highest levels of enzyme activity, approximately 2% of the total cell protein was dihydrofolate reductase. Of 13 independently derived sublines with acquired resistance to antifolate, only those 7 with greater than 100-fold increases in enzyme activity consistently exhibited HSR's. These regions comprised 2-5% of the total length of the chromosome complement and were specifically localized, as demonstrated by G-banding. Analysis of chromosome replication patterns of the HSR in human neuroblastoma and in drug-resistant Chinese hamster cells by tritiated thymidine radioautography indicated that the long, abnormally staining region replicated relatively rapidly and synchronously and terminated replication before the midpoint of the S phase. The HSR thus appeared to represent a novel chromosome abnormality that may be present in cells with specialized functions. Drug-resistant Chinese hamster cells were characterized by overproduction of target enzyme, whereas human neuroblastoma cells had phenotypes of normal neuronal cells. Whether the HSR is transcriptionally active was not elucidated.
Efficient continuous removal of nitrates from water with cationic cellulose nanopaper membranes (2017)

Nitrates constitute a severe problem for the quality of potable water. The removal of nitrates from water can be performed utilizing continuously operating cellulose nanopaper ion-exchangers, which so far are unfortunately of only moderate efficiency. Here we demonstrate cationic cellulose nanopapers comprising cellulose nanofibrils carrying a high amount of ammonium groups (1.6 g mmol−1, i.e. 0.62 mmol g−1), which are anticipated to enable efficient removal of nitrate ions from aqueous solutions. Thin nanopapers were shown to have high adsorption capacities. Therefore we prepared low grammage nanopapers using a papermaking process from cellulose nanofibrils prepared from paper mill sludge. The performance of these cationic nanopapers was characterized by their permeance, with these new cationic nanopapers having a permeance of more than 100 L m−2 h−1 MPa−1, which is far greater than the permeance of conventional nanopapers. Furthermore, nitrate ions were successfully removed from water by capturing them through adsorption onto the cationic nanopaper by primarily an ion-exchange mechanism. These cationic nanopapers possessed adsorption capacities of almost 300 mg g−1, which is superior to commonly used nanopaper ion-exchangers and batch-wise applied adsorbents. Utilization of an industrial side-stream in combination with very good membrane performance demonstrates the use of resource efficient technologies in an important sector.
Stereocontrol in Horner-Wadsworth-Emmons condensations of .alpha.-phosphono lactones with aldehydes: a synthesis of integerrinecic acid and senecic acid lactones (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereocontrol in Horner-Wadsworth-Emmons condensations of .alpha.-phosphono lactones with aldehydes: a synthesis of integerrinecic acid and senecic acid lactonesKoo Lee, John A. Jackson, and David F. WiemerCite this: J. Org. Chem. 1993, 58, 22, 5967–5971Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/jo00074a023https://doi.org/10.1021/jo00074a023research-articleACS PublicationsRequest reuse permissionsArticle Views709Altmetric-Citations36LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Knowledge Graph Induction enabling Recommending and Trend Analysis: A Corporate Research Community Use Case (2022)

A research division plays an important role of driving innovation in an organization. Drawing insights, following trends, keeping abreast of new research, and formulating strategies are increasingly becoming more challenging for both researchers and executives as the amount of information grows in both velocity and volume. In this paper we present a use case of how a corporate research community, IBM Research, utilizes Semantic Web technologies to induce a unified Knowledge Graph from both structured and textual data obtained by integrating various applications used by the community related to research projects, academic papers, datasets, achievements and recognition. In order to make the Knowledge Graph more accessible to application developers, we identified a set of common patterns for exploiting the induced knowledge and exposed them as APIs. Those patterns were born out of user research which identified the most valuable use cases or user pain points to be alleviated. We outline two distinct scenarios: recommendation and analytics for business use. We will discuss these scenarios in detail and provide an empirical evaluation on entity recommendation specifically. The methodology used and the lessons learned from this work can be applied to other organizations facing similar challenges.
Static and transient modeling of fast moving ball actuator as a display device (2016)

FMBA(Fast Moving Ball Actuator), developed as novel electronic-paper display, has already proven its operability and functionality. However, optimization issues related with low operating voltage, high refresh rate, fine pixel and higher display resolution, etc. are still remaining to be improved for a successful commercialization. In order to optimize such issues effectively, static and transient model were developed and verified by comparing the calculated results to the measured. The static model is based on the force balancing equation between the driving and the holding forces while the transient model is developed from Newton’s 2nd law by adding the inertia as well as the resistive damping forces caused by the surroundings. With the simplified static model, driving voltage of 30.71 V was obtained, which is reasonably matched to the measured voltage of 40 V. Based on the transient model, also, the transient response of the device can be estimated within reasonable margin. Considering the absence of reliable key parameters of surface roughness, static and dynamic frictional coefficient, and refractive indices, the developed static and transient models account well the experimental results and thus they are expected to contribute further improvements in FMBA.
Leveraging Downlink for Regulation of Distributed Uplink CDMA. (2006)

Abstract — In this paper, we formulate an optimal rate alloca-tion scheme for uplink and downlink in a single-cell CDMA system. Using concepts from game theory, we show that it is possible to construct a game in which the socially optimal rate allocation arises as a subgame perfect Nash equilibrium. We further show that this equilibrium can be achieved via a distributed algorithm at the uplink using practical signaling mechanisms. I.
Élaboration d'un modèle d'écoulements turbulents en faible profondeur : application au ressaut hydraulique et aux trains de rouleaux (2015)

Colloque avec actes et comité de lecture. Internationale.
The Mammalian Gene of Acetylcholinesterase-associated Collagen (1997)

The collagen-tailed or asymmetric forms (A) represent a major component of acetylcholinesterase (AChE) in the neuromuscular junction of higher vertebrates. They are hetero-oligomeric molecules, in which tetramers of catalytic subunits of type T (AChET) are attached to the subunits of a triple-stranded collagen "tail." We report the cloning of a rat AChE-associated collagen subunit, Q. We show that collagen tails are encoded by a single gene, COLQ. The ColQ subunits form homotrimers and readily form collagen-tailed AChE, when coexpressed with rat AChET. We found that the same ColQ subunits are incorporated, in vivo, in asymmetric forms of both AChE and butyrylcholinesterase. A splice variant from the COLQ gene encodes a proline- rich AChE attachment domain without the collagen domain but does not represent the membrane anchor of the brain tetramer. The COLQ gene is expressed in cholinergic tissues, brain, muscle, and heart, and also in noncholinergic tissues such as lung and testis.