gebhart/patrepeval huggingface dataset:
Differentiable Causal Discovery Under Unmeasured Confounding (2020)

The data drawn from biological, economic, and social systems are often confounded due to the presence of unmeasured variables. Prior work in causal discovery has focused on discrete search procedures for selecting acyclic directed mixed graphs (ADMGs), specifically ancestral ADMGs, that encode ordinary conditional independence constraints among the observed variables of the system. However, confounded systems also exhibit more general equality restrictions that cannot be represented via these graphs, placing a limit on the kinds of structures that can be learned using ancestral ADMGs. In this work, we derive differentiable algebraic constraints that fully characterize the space of ancestral ADMGs, as well as more general classes of ADMGs, arid ADMGs and bow-free ADMGs, that capture all equality restrictions on the observed variables. We use these constraints to cast causal discovery as a continuous optimization problem and design differentiable procedures to find the best fitting ADMG when the data comes from a confounded linear system of equations with correlated errors. We demonstrate the efficacy of our method through simulations and application to a protein expression dataset. Code implementing our methods is open-source and publicly available at https://gitlab.com/rbhatta8/dcd and will be incorporated into the Ananke package.
MiR-33 Contributes to the Regulation of Cholesterol Homeostasis (2010)

Cholesterol metabolism is tightly regulated at the cellular level. Here we show that miR-33, an intronic microRNA (miRNA) located within the gene encoding sterol-regulatory element-binding factor-2 (SREBF-2), a transcriptional regulator of cholesterol synthesis, modulates the expression of genes involved in cellular cholesterol transport. In mouse and human cells, miR-33 inhibits the expression of the adenosine triphosphate-binding cassette (ABC) transporter, ABCA1, thereby attenuating cholesterol efflux to apolipoprotein A1. In mouse macrophages, miR-33 also targets ABCG1, reducing cholesterol efflux to nascent high-density lipoprotein (HDL). Lentiviral delivery of miR-33 to mice represses ABCA1 expression in the liver, reducing circulating HDL levels. Conversely, silencing of miR-33 in vivo increases hepatic expression of ABCA1 and plasma HDL levels. Thus, miR-33 appears to regulate both HDL biogenesis in the liver and cellular cholesterol efflux.
Opening of Epoxides to Olefins or Halohydrins with Vanadium (II)-Tetrahydrofuran or Vanadium(III)-Tetrahydrofuran Complexes (1992)

A variety of epoxides were deoxygenated to give the corresponding alkenes through the use of a [V2Cl3(THF)6]2[Zn2Cl6] complex prepared from VCl3(THF)3 and zinc. The reaction proceeds with a partial inversion of the configuration of the acyclic cis epoxide. Treatment of the epoxides with the vanadium(III) reagent, VCl3(THF)3, afforded the corresponding chlorohydrins in good yields.
SIDE FAULT MAPPING ENABLED BY 2D TRANSVERSE INVERSION ON NEW DEEP DIRECTIONAL RESISTIVITY MEASUREMENTS (2021)

Faulting is one type of structural trap for hydrocarbon reservoirs. With more and more fields moving toward the brownfield or mature operations stage of life, the opportunity to target bypassed or attic oil in the vicinity of bounding fault(s) is becoming more and more attractive to operators. However, without an effective logging-while-drilling (LWD) tool to locate and map a fault parallel to the well trajectory, it has been challenging and potentially high risk to optimally place a well to drain oil reserves near the fault. Operators often plan these horizontal wells at a significant distance away from the mapped fault position to avoid impacts to the well construction and production of the well. Often, the interpreted fault position, based on seismic data, can have significant lateral uncertainty, and uncertainties attached to standard well survey measurements make it challenging to place the well near the fault. This often results in the wells being placed much farther from the fault than expected, which is not optimal for maximizing recovery. In other cases, due to uncertainty in the location of the fault, the wells would accidentally penetrate the side faults and cause drilling and other issues. Conventional remote boundary detection LWD tools do not assist with locating the fault position, as they only detect formation boundaries above or below the trajectory and not to the side. In this paper, the authors propose a novel approach for mapping features like a fault parallel to the well trajectory, which was previously impossible to map accurately. This new approach utilizes a new class of deep directional resistivity measurements acquired by a reservoir mapping-while-drilling tool. The deep directional resistivity measurements are input to a newly devised inversion algorithm, resulting in high-resolution reservoir mapping on the transverse plane, which is perpendicular to the well path. These new measurements have a strong sensitivity to resistivity in contrast to the sides of the wellbore, making them suitable for side fault detection. The new inversion in the transverse plane is not limited to detecting a side fault; it can also map any feature on the transverse plane to the well path, which further broadens the application of this technology. Using the deep directional resistivity data acquired from a horizontal ultra-ERD well recently drilled in the Wandoo Field offshore Western Australia, the authors tested this approach against the well results and existing control wells. Excellent mapping of the main side fault up to 30 m to the side of the well was achieved with the new approach. Furthermore, the inversion reveals other interesting features like lateral formation thickness variations and the casing of a nearby well. In addition, the methodology of utilizing this new approach for guiding geosteering parallel to side fault in real time is elaborated, and the future applications are discussed.
Laboratory Experiments on Ultrasonic Logging Through Casing for Barrier Integrity Validation (2017)

Verification of annular barriers is essential for well integrity, with ultrasonic methods being central in well integrity testing for many decades. By doing ultrasonic pitch-catch measurements on a bench top laboratory setup developed to replicate an oil well casing, we were able to show that the beam width, −6dB, of the leaky Lamb wave propagating in the pipe widens only from 14 to 20.4 mm after 140mm of propagation in the pipe. This indicates that the excited Lamb wave has beam-like features, with litle spreading perpendicular to the propagation direction, hence, can be used to evaluate a limited area of the pipe. When introducing two pipes in the experimental setup, as an extension of a previously conducted simulation study by Viggen et al. [1], we could observe multiple Lamb wave packets being excited in the pipes. By adjusting the setup to replicate casing eccentricity, the effects of this could be observed in the measurements.
Mixed color/level lines and their stereo-matching with a modified Hausdorff distance (2011)

Level sets appear a suitable basis to decomposing an image into a meaningful organization of basic entities. Handling images by a basis of associated sets proves more effective than considering images as the collection of acquired intensity values, even in several frequency bands, due to the variou s noise sources. Then, level lines and sets are more stable features to support recognition than edges likely resulting from high pass filtering. Color being assumed more informative than intensity is preferred to exhibit the set basis. In the paper, color lines are defined after level lines and they are extracted and characterized consecutively. Greater information is conveyed by color lines resulting into more efficient grouping towards objects. A novel Hausdorff-inspired disparity finder is introduced fed in by color lines with respect to epipolar constraints. The efficient disparity map obtained by pixel wise line-matching between left and right images justifies our technical choices.
Ultracapacitor Applications and Evaluation for Hybrid Electric Vehicles (Presentation) (2009)

Describes the use of ultracapacitors in advanced hybrid and electric vehicles and discusses thermal and electrical testing of lithium ion capacitors for HEV applications.
TERNA PARA DIRIGIR EL CENTRO DE INVESTIGACIÓN SOBRE FIJACIÓN DE NITRÓGENO (1997)

EL CONSEJO TECNICO DE LA INVESTIGACION CIENTIFICA APROBO EN SU SESION ORDINARIA DEL 13 DE MARZO LA TERNA PARA LA DIRECCION DEL CENTRO DE INVESTIGACION SOBRE FIJACION DE NITROGENO PARA EL PERIODO 1997-2001. LOS CANDIDATOS QUE LA INTEGRAN SON: GEORGINA HERNANDEZ DELGADO, ESPERANZA MARTINEZ ROMERO Y DAVID RENE ROMERO CAMARENA. SE ANOTAN DATOS CURRICULARES DE LA TERNA.
Role of Fig2p in Agglutination in Saccharomyces cerevisiae (2002)

In W303-derived strains, disruption of FIG2 increased agglutinability of alpha cells, but not a cells, and did not alter expression of alpha-agglutinin, binding of 125I-labeled alpha-agglutinin, or mating efficiency. Fig2p overexpression led to alpha-cell-specfic suppression of agglutinability. These results imply that Fig2p is an indirect masker of the active sites in alpha-agglutinin.
Hepatitis B virus pX activates NF-kappa B-dependent transcription through a Raf-independent pathway (1996)

In this study, we characterized the molecular events involved in the activation of the ubiquitous transcription factor NF-kappa B by the viral transactivator pX. pX expression in HeLa cells determines a manyfold increase in NF-kappa B-dependent transcription, which is associated with an increase in p50/p65 heterodimer DNA-binding activity. Since the I kappa B-alpha inhibitory subunit proteolytic degradation, which follows its phosphorylation/modification, is a key event in NF-kappa B activation by different stimuli (such as growth factors, phorbol esters, tumor necrosis factor, UV irradiation, and oxygen radicals), we investigated pX effects on I kappa B-alpha, as well as the possible involvement of known signalling pathways in pX-induced NF-kappa B-dependent transcription. We observed that although pX had no direct effect on p50 or p65, it was able to restore the I kappa B-alpha-suppressed p50/p65 activity. More directly, the stable expression of pX in HeLa cells resulted in reduced levels of I kappa B-alpha in the cytoplasm. Pretreatment of the cells with H7, calphostin C, tyrphostin 25, or N-acetylcysteine did not impair the effects of pX on NF-kappa B, thus ruling out the involvement of protein kinase C, tyrosine kinases, and oxygen radicals. Finally, while most of the known NF-kappa B-activating agents converge on Raf-1 protein kinase, when Raf-1 activity is blocked by overexpression of a dominant negative mutant, the effects of pX on NF-kappa B are not impaired. Thus, we suggest that although pX is able to activate the Ras/Raf-1-signalling pathway, it triggers NF-kappa B activation by an as yet unidentified Raf-1-independent pathway.
Effects of diet on the fecal excretion and bacterial modification of acidic and neutral steroids, and implications for colon carcinogenesis. (1981)

Diet-induced changes in the excretion and fecal concentration of bile acids have been associated with enhancement or reduction of chemically initiated colon carcinogenesis in experimental animals. Dietary lipid increases the excretion and fecal concentration of bile acids. Certain types of dietary fiber such as pectin and lignin also increase fecal sterol output. However, the predominant effect of food-derived fiber (e.g., wheat brain) is to increase stool bulk and, hence, reduce the concentration of fecal sterols. Although it has been suggested that the tumor-promoting activity of bile acids is enhanced following bacterial dehydroxylation, dietary factors appear to have limited effect on bacterial flora or acidic sterol degradation in the colon.
Room temperature CW operation of orange light (625 nm) emitting InGaAlP laser (1992)

An InGaAIP laser, operating under continuous wave excitation, having a record short wavelength of 625 nm at room temperature, has been constructed. This was accomplished employing a tensile strained (δa/a = −1%) multiquantum well active region and a six pair multiquantum barrier sturcture.
The angiogenic effect of ONO-1301, a novel long-acting prostacyclin agonist loaded in PLGA microspheres prepared using different molecular weights of PLGA, in a murine sponge model (2013)

The purpose of this study was to evaluate the angiogenic effect of topical application of three types of ONO-1301-loaded poly (lactide-co-glycolide) microspheres (ONO-1301 PLGA MS). ONO-1301 PLGA MS were prepared with PLGA 5010, 5020 and 5050 (with molecular weights of 10 K, 20 K and 50 K, respectively), using the solvent evaporation method. The lactide:glycolide ratio was fixed at 50:50; only the molecular weight was varied. The microspheres had an average diameter of almost 25 µm, and a loading efficiency of at least 70%. The sustained-release effect and its dependence on the molecular weight of the polymer used was confirmed in an in vitro drug-release test and by measuring subcutaneous plasma levels after administration of the three types of ONO-1301 PLGA MS to rats for 28 days. In the murine sponge model, the three types of ONO-1301 PLGA MS were administered to mice in a subcutaneously placed sponge and hemoglobin and hepatocyte growth factor (HGF) levels in the sponge were measured at predefined intervals up to 28 days. The hemoglobin and HGF levels obtained were significantly higher than those obtained after daily administration of ONO-1301 powder. Additional in vivo fluorescence imaging showed that PLGA MS remained in the sponge for 28 days. In conclusion, the three types of ONO-1301 PLGA MS prepared with PLGA three different molecular weight suppress the burst release, stimulate angiogenesis on topical application in a murine sponge model. This formulation may therefore be capable of improving the clinical picture in some types of vascular disease.
Barrelene, a New Convenient Synthesis (1997)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTBarrelene, a New Convenient SynthesisSergio Cossu, Simone Battaggia, and Ottorino De LucchiView Author Information Dipartimento di Chimica, Università Ca' Foscari di Venezia, Dorsoduro 2137, I-30123 Venezia, Italy Cite this: J. Org. Chem. 1997, 62, 12, 4162–4163Publication Date (Web):June 13, 1997Publication History Received4 December 1996Published online13 June 1997Published inissue 13 June 1997https://pubs.acs.org/doi/10.1021/jo962267fhttps://doi.org/10.1021/jo962267fbrief-reportACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views1098Altmetric-Citations22LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Addition reactions,Adducts,Aromatic compounds,Hydrocarbons,Organic reactions Get e-Alerts
Errata: New noninvasive index for evaluation of the vascular age of healthy and sick people (2012)

The <i>Journal of Biomedical Optics</i> (JBO) is an open access journal that publishes peer-reviewed papers on the use of novel optical systems and techniques for improved health care and biomedical research.
Single-Winged Autorotating Brake for Sensor Deployment on Mars (1995)

The following pages describe the development of a nonlinear simulation, results for the Martian entry problem, and a sizing study to determine whether the approach is feasible. The nonlinear simulation is described here and results are presented for several cases using Martian and Terrestrial atmosphere models. The results show that a 2.5 kg payload could be successfully delivered to the Martian surface using this approach and the report suggests an earth-based test of the system. Prior to the specific analysis presented here, a theoretical study of the mechanics of autorotation was completed, and a summary of this work is also included as part of this final report.
A Fuzzy-Logic Autonomous Agent Applied as a Supervisory Controller in a Simulated Environment (2004)

An unsupervised learning system, implemented as an autonomous agent is presented. A simulation of a challenging path planning problem is used to illustrate the agent design and demonstrate its problem solving ability. The agent, dubbed the ORG, employs fuzzy logic and clustering techniques to efficiently represent and retrieve knowledge and uses innovative sensor modeling and attention focus to process a large number of stimuli. Simple initial fuzzy rules (instincts) are used to influence behavior and communicate intent to the agent. Self-reflection is utilized so the agent can learn from its environmental constraints and modify its own state. Speculation is utilized in the simulated environment, to produce new rules and fine-tune performance and internal parameters. The ORG is released in a simulated shallow water environment where its mission is to dynamically and continuously plan a path to effectively cover a specified region in minimal time while simultaneously learning from its environment. Several paths of the agent design are shown, and desirable emergent behavior properties of the agent design are discussed.
Codewords Detection in Microblogs Focusing on Differences in Word Use Between Two Corpora (2020)

In recent years, drug trafficking using microblogs has risen and become a social problem. A common method of cyber patrols for cracking down on crimes, such as drug trafficking, involves searching for crime-related keywords. However, criminals who post crime-inducing messages make maximum use of "codewords" rather than keywords, such as enjo kosai, marijuana, and methamphetamine, to camouflage their criminal intentions. Research suggests that these codewords change once they become popular; therefore, searching for a specific word requires significant effort to keep track of the latest codewords. In this study, we focused on the appearance of codewords and those likely to be included in incriminating posts with aim to detect codewords with the high likelihood of inclusion in incriminating posts. We proposed new methods for detecting codewords based on differences in word usage and conducted experiments on concealed-word detection in order to evaluate method effectiveness. The results showed that the proposed method was capable of detecting concealed words other than those in the initial list and to better degree relative to baseline methods. These findings demonstrated the ability of the proposed method to rapidly and automatically detect codewords that change over time and blog posts that induce crimes, thereby potentially reducing the burden of continuous monitoring of codewords.
Wireless sensor networks for spectrum sensing to support opportunistic spectrum access networks: Protocol design and fundamental trade-offs (2011)

Supporting secondary users through a collateral network dedicated to spectrum sensing has been recently proposed as a mean to overcome spectrum sensing limitations of secondary devices. Building on this idea, we propose a protocol for a Wireless Sensor Network (WSN) to support secondary devices of an Opportunistic Spectrum Access (OSA) network. We examine the fundamental tradeoff between the statistics of the primary network traffic for which the WSN is able to support the OSA network and the interference range or, equivalently, the transmit power of secondary transmitters. We optimize the parameters of the proposed protocol to achieve the minimum delay for delivering channel availability information to secondary users, thus maximizing the portion of time they can effectively use idle primary channels to send their data. We further provide simulation results to demonstrate the feasibility and effectiveness of our design, and point at possible research directions to improve the proposed system capabilities.
Medicinal chemistry applied to a synthetic protein: Development of highly potent HIV entry inhibitors (2004)

We have used total chemical synthesis to perform high-resolution dissection of the pharmacophore of a potent anti-HIV protein, the aminooxypentane oxime of [glyoxylyl1]RANTES(2-68), known as AOP-RANTES, of which we designed and made 37 analogs. All involved incorporation of one or more rationally chosen nonnatural noncoded structures, for which we found a clear comparative advantage over coded ones. We investigated structure-activity relationships in the pharmacophore by screening the analogs for their ability to block the HIV entry process and produced a derivative, PSC-RANTES [N-nonanoyl, des-Ser1[L-thioproline2, L-cyclohexylglycine3]-RANTES(2-68)], which is 50 times more potent than AOP-RANTES. This promising group of compounds might be optimized yet further as potential prophylactic and therapeutic anti-HIV agents. The remarkable potency of our RANTES analogs probably involves the unusual mechanism of intracellular sequestration of CC-chemokine receptor 5 (CCR5), and it has been suggested that this arises from enhanced affinity for the receptor. We found that inhibitory potency and capacity to induce CCR5 down-modulation do appear to be correlated, but that unexpectedly, inhibitory potency and affinity for CCR5 do not. We believe this study represents the proof of principle for the use of a medicinal chemistry approach, above all one showing the advantage of noncoded structures, to the optimization of the pharmacological properties of a protein. Medicinal chemistry of small molecules is the foundation of modern pharmaceutical practice, and we believe we have shown that techniques have now reached the point at which the approach could also be applied to the many macromolecular drugs now in common use.