gebhart/patrepeval huggingface dataset:
Numerical Analysis of Lateral Wave Propagation in Drill-String for Stability Monitoring (2014)

In this paper, the propagation of lateral waves in a drill-string are studied by using a new numerical method and a stability monitoring scheme is proposed. The drill-string is modeled as a linear beam structure under gravitational field effects. An iterative wavelet-based spectral finite element method (WS-FEM) model is developed to obtain a high fidelity response. Numerical simulations of the lateral impact wave propagation at the bottom-hole-assembly (BHA) are conducted and a time-frequency analysis technique is applied to the response in order to identify the relationship between the position of the transition point between positive and negative strain and the dispersive properties of the lateral wave. Based on the results, a new monitoring scheme is proposed to monitor the stability of the drill-string based on a combination of lateral impact wave analysis at the BHA and the axial acoustic telemetry technique.
Using the Spiral Model and MBASE to Generate New Acquisition Process Models: SAIV, CAIV, and SCQAIV (2002)

In this article, we show how you can use the MBASE process framework to generate a family of acquisition process models for delivering usersatisfactory systems under schedule, cost, and quality constraints. We present the six major steps of the Schedule/Cost/Schedule-Cost-Quality as Independent Variable (SAIV/CAIV/SCQAIV) process using SAIV and a representative Department of Defense (DoD) Command, Control, and Communications Interoperability application as context. We then summarize our experience in using SAIV on 26 University of Southern California electronic services projects, followed by discussions of SAIV/CAIV/SCQAIV application in the commercial and defense sectors, of model application within the DoD acquisition framework, and of the resulting conclusions.
REAL-TIME AND ON-SITE RESERVOIR FLUID CHARACTERISATION USING SPECTRAL ANALYSIS AND PVT EXPRESS (2004)

Obtaining an adequate fluid characterisation early in the life of a reservoir is becoming a key requirement for successful hydrocarbon development. This work presents and discusses a number of new fluid sampling and fluid characterisation technologies that can be deployed either down hole or at surface in the early stages of the exploration and development cycle to achieve this objective. Techniques discussed include methods to monitor and quantify oil-based mud contamination, gas-liquid-ratio (GLR) and basic fluid composition in real time during open-hole formation testing operations. In addition, we demonstrate the applicability of new surface analysis techniques that allow for rapid, accurate, and reliable measurements of key fluid properties, such as saturation pressure, gas-oil ratio, extended carbon number composition, viscosity, and density, on-site within a few hours of retrieving reservoir fluid samples at surface. Finally, prediction tools used to extend these limited measurements to a traditional PVT fluid characterisation are presented along with example measurements from all the techniques described. In conclusion, it is shown that the implementation of these techniques in a complementary program can reduce the risk associated with making key development decisions that are based on an understanding of reservoir fluid properties.
FUN-LDA: A LATENT DIRICHLET ALLOCATION MODEL FOR PREDICTING TISSUE-SPECIFIC FUNCTIONAL EFFECTS OF NONCODING VARIATION (2016)

A BSTRACT We describe here a new method based on a latent Dirichlet allocation model for predicting functional effects of noncoding genetic variants in a cell type and tissue specific way (FUN-LDA) by integrating diverse epigenetic annotations for specific cell types and tissues from large scale epige-nomics projects such as ENCODE and Roadmap Epigenomics. Using this unsupervised approach we predict tissue-specific functional effects for every position in the human genome. We demonstrate the usefulness of our predictions using several validation experiments. Using eQTL data from several sources, including the Genotype-Tissue Expression project, the Geuvadis project and Twin-sUK cohort, we show that eQTLs in specific tissues tend to be most enriched among the predicted functional variants in relevant tissues in Roadmap. We further show how these integrated functional scores can be used to derive the most likely cell/tissue type causally implicated for a complex trait using summary statistics from genome-wide association studies, and estimate a tissue-based correlation matrix of various complex traits. We find large enrichment of heritability in functional components of relevant tissues for various complex traits, with FUN-LDA yielding the highest enrichment estimates relative to existing methods. Finally, using experimentally validated functional variants from the literature and variants possibly implicated in disease by previous studies, we rigorously compare FUN-LDA to state-of-the-art functional annotation methods such as GenoSky-line, ChromHMM, Segway, and IDEAS, and show that FUN-LDA has better prediction accuracy and higher resolution compared to these methods. In summary, we describe a new approach and perform rigorous comparisons with the most commonly used functional annotation methods, providing a valuable resource for the community interested in the functional annotation of noncoding variants. Scores for each position in the human genome and for each ENCODE/Roadmap tissue are available from http://www.columbia.edu/~ii2135/funlda.html .
First-in-human phase I clinical trial of the NY-ESO-1 protein cancer vaccine with NOD2 and TLR9 stimulants in patients with NY-ESO-1-expressing refractory solid tumors (2020)

Cholesteryl pullulan (CHP) is a novel antigen delivery system. CHP and New York esophageal squamous cell carcinoma 1 (NY-ESO-1) antigen complexes (CHP-NY-ESO-1) present multiple epitope peptides to the MHC class I and II pathways. Adjuvants are essential for cancer vaccines. MIS416 is a non-toxic microparticle that activates immunity via the nucleotide-binding oligomerization domain 2 (NOD2) and TLR9 pathways. However, no reports have explored MIS416 as a cancer vaccine adjuvant. We conducted a first-in-human clinical trial of CHP-NY-ESO-1 with MIS416 in patients with NY-ESO-1-expressing refractory solid tumors. CHP-NY-ESO-1/MIS416 (μg/μg) was administered at 100/200, 200/200, 200/400 or 200/600 (cohorts 1, 2, 3 and 4, respectively) every 2 weeks for a total of 6 doses (treatment phase) followed by one vaccination every 4 weeks until disease progression or unacceptable toxicity (maintenance phase). The primary endpoints were safety and tolerability, and the secondary endpoint was the immune response. In total, 26 patients were enrolled. Seven patients (38%) continued vaccination in the maintenance phase. Grade 3 drug-related adverse events (AEs) were observed in six patients (23%): anorexia and hypertension were observed in one and five patients, respectively. No grade 4-5 drug-related AEs were observed. Eight patients (31%) had stable disease (SD). Neither augmentation of the NY-ESO-1-specific IFN-γ-secreting CD8<sup>+</sup> T cell response nor an increase in the level of anti-NY-ESO-1 IgG1 was observed as the dose of MIS416 was increased. In a preclinical study, adding anti-PD-1 monoclonal antibody to CHP-NY-ESO-1 and MIS416 induced significant tumor suppression. This combination therapy is a promising next step.
Sparse Wide-Area Control of Power Systems using Data-driven Reinforcement Learning (2019)

In this paper we present an online wide-area oscillation damping control (WAC) design for uncertain models of power systems using ideas from reinforcement learning. We assume that the exact small-signal model of the power system at the onset of a contingency is not known to the operator and use the nominal model and online measurements of the generator states and control inputs to rapidly converge to a state-feedback controller that minimizes a given quadratic energy cost. However, unlike conventional linear quadratic regulators (LQR), we intend our controller to be sparse, so its implementation reduces the communication costs. We, therefore, employ the gradient support pursuit (GraSP) optimization algorithm to impose sparsity constraints on the control gain matrix during learning. The sparse controller is then implemented using distributed communication. The proposed method is validated using the IEEE 39-bus power system model with 1149 unknown parameters.
Noncontact torsional wave transduction in a rotating shaft using oblique magnetostrictive strips (2006)

A noncontact method to generate and measure torsional waves in rotating shafts by a set of magnetostrictive patches and a solenoid is proposed. The main issues in the present wave experiment are how to generate torsional waves having sufficient power and how not to interfere with shaft rotational motion. Magnetostrictive patches are bonded obliquely to the shaft axis for pure torsional wave generation and an arrayed patch configuration is employed for sufficient power generation and frequency localization. For uninterrupted shaft rotation, a solenoid encircling a rotating shaft wirelessly supplies or detects the ac magnetic field in the patches. The validity and performance of the proposed wave transduction method were checked by several experiments. An application of this method to the detection of a circumferential crack in a rotating shaft is also presented.
Light‐Driven Transport of a Liquid Marble with and against Surface Flows (2016)

Abstract Liquid marbles, that is, liquid drops coated by a hydrophobic powder, do not wet any solid or liquid substrate, making their transport and manipulation both highly desirable and challenging. Herein, we describe the light‐driven transport of floating liquid marbles and emphasize a surprising motion behavior. Liquid marbles are deposited on a water solution containing photosensitive surfactants. Irradiation of the solution generates photoreversible Marangoni flows that transport the liquid marbles toward UV light and away from blue light when the thickness of the liquid substrate is large enough (Marangoni regime). Below a critical thickness, the liquid marbles move in the opposite direction to that of the surface flow at a speed increasing with decreasing liquid thickness (anti‐Marangoni). We demonstrate that the anti‐Marangoni motion is driven by the free surface deformation, which propels the non‐wetting marble against the surface flow. We call this behavior “slide effect”.
ChemInform Abstract: Structure‐Reactivity Correlations for Reactions of Substituted Phenolate Anions with Acetate and Formate Esters (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Transmural Nerve Stimulation of Blood Vessels <i>in vitro</i>: a Critical Examination (1980)

Use of the method of transmural nerve stimulation depends on the assumption that stimulation parameters can be chosen to selectively and maximally activate nerves without stimulating vascular smooth muscle directly. When commercial stimulators are used with low impedance electrodes, it may not be possible to validate this assumption, due to the limited current output in this situation. To circumvent this limitation a coupling device which provides a very low source impedance to the electrodes is described. Using this device in experiments on preparations of rabbit ear artery, we have demonstrated that it is possible to selectively activate nerves, without stimulating smooth muscle directly. Adrenergic nerve activation was blocked with guanethidine, phentolamine or tetrodotoxin, while responses to direct smooth muscle activation persist in the presence of these drugs. Appropriate parameters for supramaximal nerve stimulation vary with the type of preparation and electrode arrangement. The possibility of variation with tissue and species is also discussed.
Unique Lead Adsorption Behavior of Activated Hydroxyl Group in Two-Dimensional Titanium Carbide (2014)

The functional groups and site interactions on the surfaces of two-dimensional (2D) layered titanium carbide can be tailored to attain some extraordinary physical properties. Herein a 2D alk-MXene (Ti3C2(OH/ONa)(x)F(2-x)) material, prepared by chemical exfoliation followed by alkalization intercalation, exhibits preferential Pb(II) sorption behavior when competing cations (Ca(II)/Mg(II)) coexisted at high levels. Kinetic tests show that the sorption equilibrium is achieved in as short a time as 120 s. Attractively, the alk-MXene presents efficient Pb(II) uptake performance with the applied sorption capacities of 4500 kg water per alk-MXene, and the effluent Pb(II) contents are below the drinking water standard recommended by the World Health Organization (10 μg/L). Experimental and computational studies suggest that the sorption behavior is related to the hydroxyl groups in activated Ti sites, where Pb(II) ion exchange is facilitated by the formation of a hexagonal potential trap.
Measuring urban rainfall using microwave links from commercial cellular communication networks (2011)

The estimation of rainfall using commercial microwave links is a new and promising measurement technique. Commercial link networks cover large parts of the land surface of the earth and have a high density, particularly in urban areas. Rainfall attenuates the electromagnetic signals transmitted between antennas within this network. This attenuation can be calculated from the difference between the received powers with and without rain and is a measure of the path‐averaged rainfall intensity. This study uses a 17‐day data set of, on average, 57 single‐frequency links from 2009 to estimate rainfall in the Rotterdam region, a densely populated delta city in Netherlands (≈1250 km 2 , &gt;1 million inhabitants). A methodology is proposed where nearby links are used to remove signal fluctuations that are not related to rainfall in order to be able to reliably identify wet and dry weather spells. Subsequently, received signal powers are converted to path‐averaged rainfall intensities, taking into account the temporal sampling protocol and attenuation due to wet antennas. Link‐based rainfall depths are compared with those based on gauge‐adjusted radar data. In addition, the rainfall retrieval algorithm is applied to an independent data set of 21 rainy days in 2010 with on average 16 single‐frequency links in the same region. Rainfall retrievals are compared against gauge‐adjusted radar rainfall estimates over the link path. Moreover, the retrieval algorithm is also tested using high‐resolution research link data to investigate the algorithm's sensitivity to temporal rainfall variations. All presented comparisons confirm the quality of commercial microwave link data for quantitative precipitation estimation over urban areas.
PlyPH, a Bacteriolytic Enzyme with a Broad pH Range of Activity and Lytic Action against Bacillus anthracis (2006)

We have cloned a lytic enzyme, PlyPH, with a specific lytic effect on Bacillus anthracis strains. PlyPH remains active between pH 4 and 10.5, and a single dose rescued a significant percentage of mice infected intraperitoneally with an attenuated B. anthracis strain. We propose PlyPH as a novel therapeutic agent.
Phase-specific signatures of wound fibroblasts and matrix patterns define cancer-associated fibroblast subtypes (2022)

ABSTRACT Healing wounds and cancers present remarkable cellular and molecular parallels, but the specific roles of the healing phases are largely unknown. We developed a bioinformatics pipeline to identify genes and pathways that define distinct phases across the time course of healing. Their comparison to cancer transcriptomes revealed that a resolution-phase wound signature is associated with increased severity in skin cancer and enriches for extracellular matrix-related pathways. Comparisons of transcriptomes of early- and late-phase wound fibroblasts vs skin cancer-associated fibroblasts (CAFs) identified an “early-wound” CAF subtype, which localizes to the inner tumor stroma and expresses collagen-related genes that are controlled by the RUNX2 transcription factor. A “late-wound” CAF subtype localizes to the outer tumor stroma and expresses elastin-related genes. Matrix imaging of primary melanoma tissue microarrays validated these matrix signatures and identified collagen- vs elastin-rich niches within the tumor microenvironment, whose spatial organization predicts survival and recurrence. These results identify wound-regulated genes and matrix patterns with prognostic potential in skin cancer.
Prolactin receptor in human endometriotic tissues (2002)

The PRLR is expressed in normal endometrium, while cells of the endometriotic tissues did not express the PRLR, at least during the mid-late proliferative phase of the menstrual cycle. The absence of the PRLR in the endometriotic tissues could not be correlated with the serum prolactin levels. These results suggest the existence of differential regulation of PRLR expression between normal and endometriotic tissue.
Quantum-Computational Hybrid Cryptography based on the Boolean Hidden Matching Problem (2019)

International audience
Synthese und zytostatische Wirkung einiger 2‐Phenyl‐3‐alkyl(aryl)‐2, 3‐dihydro‐1, 3, 2(λ5)‐benzoxazaphosphorin‐4‐on‐Derivate (1992)

Preparation of 2,3-dihydro-1,3,2-benzoxazaphosphorin-4-one derivatives and their 2-oxo derivatives is described. Compounds 1 and 12 have anticancer activity.
Electron cryo-microscopy structure of the canonical TRPC4 ion channel (2018)

ABSTRACT Canonical transient receptor channels (TRPC) are non-selective cation channels. They are involved in receptor-operated Ca 2+ signaling and have been proposed to act as store-operated channels (SOC). Their malfunction is related to cardiomyopathies and their modulation by small molecules has been shown to be effective against renal cancer cells. The molecular mechanism underlying the complex activation and regulation is poorly understood. Here, we report the electron cryo-microscopy structure of zebrafish TRPC4 in its unliganded (apo), closed state at an overall resolution of 3.6 Å. The structure reveals the molecular architecture of the cation conducting pore, including the selectivity filter and lower gate. The cytoplasmic domain contains two key hubs that have been shown to interact with modulating proteins. Structural comparisons with other TRP channels give novel insights into the general architecture and domain organization of this superfamily of channels and help to understand their function and pharmacology.
The contribution of peroxynitrite generation in HIV replication in human primary macrophages (2007)

Results support the role of superoxide anions in HIV-1 replication in M/M and suggest that MnTBAP may counteract HIV-1 replication in combination with other antiretroviral treatments.
In ovo inoculation of chicken embryos with probiotic bacteria and its effect on posthatch Salmonella susceptibility (2014)

The feasibility of establishing probiotic bacteria in the intestine of broiler chickens by in ovo inoculation was investigated, followed by verifying possible subsequent protection against Salmonella Enteriditis infection. In a first study, 7 commercially available probiotics were screened for compatibility with in ovo inoculation. Two of these probiotics, one being a Enterococcus faecium and the other a Bacillus subtilis, were selected for colonizing the chick gut without compromising hatchability. In a second study, these 2 products were administered in ovo and in the feed to chicks reared until 18 d in comparison with noninoculated chicks and with chicks fed an antibiotic. All chicks were orally challenged with Salmonella Enteritidis at 4 d of age. Results showed reduced performance of Salmonella Enteritidis challenged chicks fed no additives compared with challenged chicks fed antibiotic, but no significant differences in mortality was observed. Probiotics offered in ovo or through the diet could only partially recover performance compared with antibiotic-fed chicks. A significant reduction in the number of Salmonella Enteritidis positive chicks was observed when chicks were in ovo inoculated with E. faecium and continued receiving it in the diet. This work establishes standards for future in ovo colonization research and emphasizes its value as a promising method to deliver individual precise dose of probiotics to poultry in mass scale at the earliest possible age based on the competitive exclusion concept. In ovo colonization with probiotic can therefore become an important ally in combination with other approaches to combat Salmonella and other intestinal bacterial infections in poultry.
Stability and electronic structure of the low-Σgrain boundaries in CdTe: a density functional study (2015)

Using first-principles density functional calculations, we investigate the relative stability and electronic structure of the grain boundaries (GBs) in zinc-blende CdTe. Among the low-Σ-value symmetric tilt Σ3 (111), Σ3 (112), Σ5 (120), and Σ5 (130) GBs, we show that the Σ3 (111)GB is always the most stable due to the absence of dangling bonds and wrong bonds. The Σ5 (120) GBs, however, are shown to be more stable than the Σ3 (112) GBs, even though the former has a higher Σ value, and the latter is often used as a model system to study GB effects in zinc-blende semiconductors. Furthermore, we find that although containing wrong bonds, the Σ5 (120) GBs are electrically benign due to the short wrong bond lengths, and thus are not as harmful as the Σ3 (112) GBs also having wrong bonds but with longer bond lengths.
Consenso FT-CUP em redes desconhecidas: um estudo experimental (2016)

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Neutron yield study of direct-drive, low-adiabat cryogenic D2 implosions on OMEGA laser system (2009)

Neutron yields of direct-drive, low-adiabat (α≈2 to 3) cryogenic D2 target implosions on the OMEGA laser system [T. R. Boehly et al., Opt. Commun. 133, 495 (1997)] have been systematically investigated using the two-dimensional (2D) radiation hydrodynamics code DRACO [P. B. Radha et al., Phys. Plasmas 12, 056307 (2005)]. Low-mode (ℓ≤12) perturbations, including initial target offset, ice-layer roughness, and laser-beam power imbalance, were found to be the primary source of yield reduction for thin-shell (5 μm), low-α, cryogenic targets. The 2D simulations of thin-shell implosions track experimental measurements for different target conditions and peak laser intensities ranging from 2.5×1014–6×1014 W/cm2. Simulations indicate that the fusion yield is sensitive to the relative phases between the target offset and the ice-layer perturbations. The results provide a reasonable good guide to understanding the yield degradation in direct-drive, low-adiabat, cryogenic, thin-shell-target implosions. Thick-shell (10 μm) implosions generally give lower yield over clean than low-ℓ-mode DRACO simulation predictions. Simulations including the effect of laser-beam nonuniformities indicate that high-ℓ-mode perturbations caused by laser imprinting further degrade the neutron yield of thick-shell implosions. To study ICF compression physics, these results suggest a target specification with a ≤30 μm offset and ice-roughness of σrms<3 μm are required.