gebhart/patrepeval huggingface dataset:
Aldosterone mediates metastatic spread of renal cancer via the G protein‐coupled estrogen receptor (GPER) (2016)

Although aldosterone is a known regulator of renal and cardiovascular function, its role as a regulator of cancer growth and spread has not been widely considered. This study tested the hypothesis that aldosterone regulates cancer cell growth/spread via G protein-coupled estrogen receptor (GPER) activation. In vitro in murine renal cortical adenocarcinoma (RENCA) cells, a widely used murine in vitro model for the study of renal cell adenocarcinoma, aldosterone increased RENCA cell proliferation to a maximum of 125 ± 3% of control at a concentration of 10 nM, an effect blocked by the GPER antagonist G15 or by GPER knockdown using short interfering (sh) RNA techniques. Further, aldosterone increased RENCA cell migration to a maximum of 170 ± 20% of control at a concentration of 100 nM, an effect also blocked by G15 or by GPER down-regulation. In vivo, after orthotopic RENCA cell renal transplantation, pulmonary tumor spread was inhibited by pharmacologic blockade of aldosterone effects with spironolactone (percentage of lung occupied by metastasis: control = 68 ± 13, spironolactone = 26 ± 8, P < 0.05) or inhibition of aldosterone synthesis with a high dietary salt diet (percentage of lung: control = 44 ± 6, high salt = 12 ± 3, P < 0.05), without reducing primary tumor size. Additionally, adrenalectomy significantly reduced the extent of pulmonary tumor spread, whereas aldosterone infusion recovered pulmonary metastatic spread toward baseline levels. Finally, inhibition of GPER either with the GPER antagonist G15 or by GPER knockdown comparably inhibited RENCA cell pulmonary metastatic cancer spread. Taken together, these findings provide strong evidence for aldosterone serving a causal role in renal cell cancer regulation via its GPER receptor; thus, antagonism of GPER represents a potential new target for treatment to reduce metastatic spread.-Feldman, R. D., Ding, Q., Hussain, Y., Limbird, L. E., Pickering, J. G., Gros, R. Aldosterone mediates metastatic spread of renal cancer via the G protein-coupled estrogen receptor (GPER).
A novel sialylation site on Neisseria gonorrhoeae lipooligosaccharide links heptose II lactose expression with pathogenicity (2018)

Abstract Sialylation of lacto-W-neotetraose (LNnT) extending from heptose I (HepI) of gonococcal lipooligosaccharide (LOS) contributes to pathogenesis. Previously, gonococcal LOS sialyltransterase (Lst) was shown to sialylate LOS in Triton X-100 extracts of strain 15253, which expresses lactose from both HepI and HepII, the minimal structure required for mAb 2C7 binding. Ongoing work has shown that growth of 15253 in cytidine monophospho-W-acetylneuraminic acid (CMP-Neu5Ac)-containing media enables binding to CD33/Siglec-3, a cell surface receptor that binds sialic acid, suggesting that lactose termini on LOS of intact gonococci can be sialylated. Neu5Ac was detected on LOSs of strains 15253 and a MS11 mutant with only lactose from HepI and HepII by mass spectrometry; deleting HepII lactose rendered Neu5Ac undetectable. Resistance of HepII lactose Neu5Ac to desialylation by α2-3-specific neuraminidase suggested an α2-6-linkage. Although not associated with increased factor H binding, HepII lactose sialylation inhibited complement C3 deposition on gonococci. 15253 mutants that lacked Lst or HepII lactose were significantly attenuated in mice, confirming the importance of HepII Neu5Ac in virulence. All 75 minimally passaged clinical isolates from Nanjing, China, expressed HepII lactose, evidenced by reactivity with mAb 2C7; mAb 2C7 was bactericidal against the first 62 (of 75) isolates that had been collected sequentially and were sialylated before testing. mAb 2C7 effectively attenuated 15253 vaginal colonization in mice. In conclusion, this novel sialylation site could explain the ubiquity of gonococcal HepII lactose in vivo . Our findings reiterate the candidacy of the 2C7 epitope as a vaccine antigen and mAb 2C7 as an immunotherapeutic antibody.
Mechanism of gallic acid biosynthesis in bacteria (Escherichia coli) and walnut (Juglans regia) (2011)

Gallic acid (GA), a key intermediate in the synthesis of plant hydrolysable tannins, is also a primary anti-inflammatory, cardio-protective agent found in wine, tea, and cocoa. In this publication, we reveal the identity of a gene and encoded protein essential for GA synthesis. Although it has long been recognized that plants, bacteria, and fungi synthesize and accumulate GA, the pathway leading to its synthesis was largely unknown. Here we provide evidence that shikimate dehydrogenase (SDH), a shikimate pathway enzyme essential for aromatic amino acid synthesis, is also required for GA production. Escherichia coli (E. coli) aroE mutants lacking a functional SDH can be complemented with the plant enzyme such that they grew on media lacking aromatic amino acids and produced GA in vitro. Transgenic Nicotiana tabacum lines expressing a Juglans regia SDH exhibited a 500% increase in GA accumulation. The J. regia and E. coli SDH was purified via overexpression in E. coli and used to measure substrate and cofactor kinetics, following reduction of NADP+ to NADPH. Reversed-phase liquid chromatography coupled to electrospray mass spectrometry (RP-LC/ESI–MS) was used to quantify and validate GA production through dehydrogenation of 3-dehydroshikimate (3-DHS) by purified E. coli and J. regia SDH when shikimic acid (SA) or 3-DHS were used as substrates and NADP+ as cofactor. Finally, we show that purified E. coli and J. regia SDH produced GA in vitro.
Patent Reviews: 4,488,775; 4,497,540; 4,498,009; 4,500,163; 4,500,175; 4,501,470; 4,501,961; 4,502,756; 4,504,110; 4,504,111; 4,504,121; 4,504,124; 4,504,122; 4,509,857; 4,504,125; 4,504,123; 4,504,128; 4,505,535; 4,505,536; 4,505,550; 4,505,553; 4,507,776 (1985)

The patent number, date of issuance by the U.S. Patent Office, and classification are shown on the first line. The filing date is that of the first application (although some patents may derive from earlier applications with earlier claim dates). Any opinions expressed are those of the reviewers and do not reflect the opinions of the organizations with which they are associated, the Optical Society of America, or this journal. Printed copies of these patents may be ordered from the Commissioner of Patents, Washington, DC 20231: telephone (703) 557-3158, URL http://patents.uspto.gov. Inquiries about patents should be addressed to the Patents Office, not to this journal or to OSA.
Experimental Data Report for Semiscale Mod-3 Blowdown Heat Transfer Test S-07-3 (Baseline Series) (1978)

Recorded test data are presented for Test S-07-3 of the Semiscale Mod-3 baseline test series. This test is one of several Semiscale Mod-3 experiments conducted to investigate the thermal and hydraulic phenomena accompanying a hypothesized loss-of-coolant accident in a pressurized water reactor (PWR) system. Test S-07-3 was conducted from initial conditions of 15.90 MPa and 558 K to investigate the response of the Semiscale Mod-3 system to a blowdown transient following a simulated double-ended offset shear of the broken loop cold leg piping. The specific objectives of this test were (a) to evaluate the effects of containment pressure on end-of-blowdown conditions and (b) to assess the effect of locating the pressurizer in the broken loop rather than the intact loop. During the test, cooling water was injected into the cold leg of the intact loop to simulate emergency core coolant injection in a PWR.
Entanglement generation via phase-matched processes: different Bell states within the linewidth (2007)

It is shown, theoretically and experimentally, that at any type-II spontaneous parametric down-conversion (SPDC) phase matching, the decoherence-free singlet Bell state is always present within the natural bandwidth and can be filtered out by a proper spectral selection. Instead of the frequency selection, one can perform time selection of the two-photon time amplitude at the output of a dispersive fibre. Applications to quantum communication are outlined.
Quantifying Corneal Toricity From Videokeratography With Fourier Analysis (1996)

The Fourier method yields highly repeatable toricity values and thus provides a sensitive means of detecting longitudinal toricity change in normal corneas.
Comprehensive Nitrogen Budgets for Controlled Tile Drainage Fields in Eastern Ontario, Canada (2014)

Excessive N loading from subsurface tile drainage has been linked to water quality degradation. Controlled tile drainage (CTD) has the potential to reduce N losses via tile drainage and boost crop yields. While CTD can reduce N loss from tile drainage, it may increase losses through other pathways. A multiple-year field-scale accounting of major N inputs and outputs during the cropping season was conducted on freely drained and controlled tile drained agricultural fields under corn ( L.)-soybean [ (L.) Merr.] production systems in eastern Ontario, Canada. Greater predicted gaseous N emissions for corn and soybean and greater observed lateral seepage N losses were observed for corn and soybean fields under CTD relative to free-draining fields. However, observed N losses from tile were significantly lower for CTD fields, in relation to freely drained fields. Changes in residual soil N were essentially equivalent between drainage treatments, while mass balance residual terms were systematically negative (slightly more so for CTD). Increases in plant N uptake associated with CTD were observed, probably resulting in higher grain yields for corn and soybean. This study illustrates the benefits of CTD in decreasing subsurface tile drainage N losses and boosting crop yields, while demonstrating the potential for CTD to increase N losses via other pathways related to gaseous emissions and groundwater seepage.
Higher Order Naïve Bayes: A Novel Non-IID Approach to Text Classification (2010)

The underlying assumption in traditional machine learning algorithms is that instances are Independent and Identically Distributed (IID). These critical independence assumptions made in traditional machine learning algorithms prevent them from going beyond instance boundaries to exploit latent relations between features. In this paper, we develop a general approach to supervised learning by leveraging higher order dependencies between features. We introduce a novel Bayesian framework for classification termed Higher Order Naïve Bayes (HONB). Unlike approaches that assume data instances are independent, HONB leverages higher order relations between features across different instances. The approach is validated in the classification domain on widely used benchmark data sets. Results obtained on several benchmark text corpora demonstrate that higher order approaches achieve significant improvements in classification accuracy over the baseline methods, especially when training data is scarce. A complexity analysis also reveals that the space and time complexity of HONB compare favorably with existing approaches.
3D model retrieval from mechanical drawings analysis (2011)

Indexed by SCOPUS\nAbstract — Computer Aided Engineering (CAE) techniques provide effective solutions for automating the whole product development chain process. Designers, engineers, manufacturing professionals and researchers can now leverage solid modeling data\nand multi-physics analysis in ways that were inconceivable just few years ago. Among CAE techniques, Computer Aided Design (CAD) has been the most effective in providing methodologies capable of compressing product design and manufacturing cycles, assuring faster turnaround time between design and simulation and improving product quality. Designers and manufacture companies reap the rewards of 3D CAD modelling; as a consequence, research is unceasingly stimulated to look forward. On one hand, research aims to improve capabilities of existing CAD methods and tools; on the other hand novel approaches are extensively investigated with the ambition of carrying out innovative CAD techniques capable of lighting sparking design innovation and creativity. This is particularly true for mechanical design: fast and robust 3D retrieval from 2D drawings that was considered future trend few years ago, is now a key target for commercial software houses like Dassault Systems® and Autodesk® as well as a vigorous focus from an academic outlook. Unfortunately, even if a number of works have been carried out during the last decades, these are mainly described by a conceptual point of view. To derive an orderly procedure covering the necessary steps for retrieving 3D models from mechanical drawings could provide a dramatic boost to researchers and practitioners that introduce this issue on their research.\nTherefore, the main aim of the present work is to carry out a systematic clear and concise step-by-step procedure for 3D retrieval starting from wireframe models. Since the intent is to afford an as clear as possible, guided, procedure for 3D reconstruction, mathematical description is limited to the simplest case of polyhedral objects. The proposed procedures, inspired by state of the art works, can be effectively contribute to speed-up the possible implementation of methodologies confronting the 3D reconstruction problem.
Thin film notch filters as platforms for biological image processing (2023)

Many image processing operations involve the modification of the spatial frequency content of images. Here we demonstrate object-plane spatial frequency filtering utilizing the angular sensitivity of a commercial spectral bandstop filter. This approach to all-optical image processing is shown to generate real-time pseudo-3D images of transparent biological and other samples, such as human cervical cancer cells. This work demonstrates the potential of non-local, non-interferometric approaches to image processing for uses in label-free biological cell imaging and dynamical monitoring.
Estrogen and estrogen receptor antagonists stimulate transcription from the human retinoic acid receptor-alpha 1 promoter via a novel sequence. (1996)

We and others previously reported that up-regulation of retinoic acid receptor-alpha (RAR alpha) RNA and protein levels is elicited by estrogen in human breast cancer cells. We set out to determine the mechanism by which estrogen up-regulates RAR alpha. Cloning of 500 bp of the human (h) RAR alpha 1 promoter has been reported previously; we obtained this 500-bp DNA sequence by PCR techniques from human genomic DNA and tested its activity in the context of a luciferase-containing reporter vector in Hep G2 cell contransactivation assays. Estradiol elicited a 6- to 8-fold increase in luciferase activity from the reporter vector driven by hRAR alpha promoter sequence between -491 and +36 bp that was dependent on the presence of contransfected estrogen receptor (ER). Analysis of various truncated versions of this promoter sequence indicated that two regions of the sequence are sensitive to estrogen stimulation. The first resides in the region -49 to -79 bp upstream from the transcription start site and conferred approximately 2-fold activation by estrogen. This region does not contain a consensus estrogen response element, and ER binding to this DNA sequence was not observed. The second responsive sequence lies at -455 to -491 bp and conferred in additional 4- to 6-fold activation by estrogen. This upstream sequence contains two A/TGGTCA half-sites; however, direct binding of ER to this sequence was not observed. Additionally, ER DNA-binding domain mutants that are not capable of binding to DNA were just as effective as wild type ER in their ability to confer estrogen responsiveness to the RAR alpha promoter, implying that ER DNA-binding ability is not required for the estrogen-induced increase in transcriptional activity. Mutation of either half-site or of an additional immediate downstream sequence in the context of the -491 to +36 bp construct reduced the luciferase activity induction by estrogen from 6-fold to 1.5- to 2-fold. Placement of the region between -455 to -491 bp upstream of an SV40 promoter-driven luciferase vector conferred approximately 20- to 30-fold stimulation of luciferase activity by estrogen in an ER-dependent manner. The ER antagonists, 4-hydroxy-tamoxifen, keoxifene, and ICI 164384, each acted as weak agonist via the hRAR alpha promoter in contransactivation assays, exhibiting 20-30% of the efficacy that was demonstrated by estradiol. Interestingly, upon treatment of MCF7 cells with estradiol or the ER antagonists, increased levels of RAR alpha RNA and protein were observed with the antagonists as well as with estrogen.
Prévision de la tenue de structures composites tissés 3D en présence de singularités = Strength analysis of 3D woven composite structures with high stress gradient (2009)

National audience
Computational Estimates of Fluoride Affinity of Boron-Based Anion Receptors (2009)

Ab initio calculations were carried out to study the structure–property relationship of anion receptors to establish a guidance for developing advanced electrolyte for lithium-ion batteries. A group of 25 well-selected anion receptors was investigated to illustrate the impact of structural rigidity and the substitution of electron-withdrawing groups, such as F and , as well as the substitution of alkoxyl groups. The calculation results showed that the fluoride affinity of an anion receptor can be reduced by the introduction of alkoxyl groups to the boron center and that the fluoride affinity increases with the substitution of electron-withdrawing groups.
Integrated circuit layout design screening (2013)

Integrated Circuits (IC) have evolved over the last few decades from modest circuit complexities to highly complex circuit realizations in meeting the market needs. Considering the heavy investments of time, manpower and financial resources in the development of the advanced chips, the original developers of the chip, per force, take steps to protect the various Intellectual Properties (IP) through appropriate IP regimes operating in their countries. In the competitive world of numerous product ranges and less time to market the products, the probabilities of infringements i.e copying of earlier works into the circuits is increasing and hence, there is severe need of capturing the circuit elements with infringements. The IP registering authorities would assess and in some cases evaluate the IC Layout Design filings made for the chip submitted for IP registration including absence of infringements. A well informed developer will also be vigilant to monitor the market to trace any illegal circuit infringement business through copying of their chip works. From these perspectives, it can be seen that screening of the IC Layout Designs (ICLDs) in detail including comparing them with suspicious candidates becomes vital.
A Full Adaptive Observer for DC Servo Motors (2003)

An adaptive observer estimating all parameters and load torque is proposed for DC servo motors. The observer uses no direct feedback but the adaptation schemes use current and speed measurements. Both the observer and adaptations are simple to implement for real-time applications. Simulation results are satisfactory for the full adaptive observer. If the observer works in parallel with only load torque and armature resistance adaptations, the results are very good even if very low-quality sensors are used. In this simulation, only a single hall sensor is used as a rotational transducer, which produces a single pulse per revolution, and very high level noise and disturbance are added in order to provide a more realistic simulation.
Late-gestation betamethasone enhances coronary artery responsiveness to angiotensin II in fetal sheep (2004)

Antenatal glucocorticoids are used to promote the maturation of fetuses at risk for preterm delivery. While perinatal glucocorticoid exposure has clear immediate benefits to cardiorespiratory function, there is emerging evidence of adverse long-term effects. To determine if antenatal betamethasone alters vascular reactivity, we examined isometric contraction of endothelium-intact coronary and mesenteric arteries isolated from twin fetal sheep at 121-124 days gestation (term being 145 days). One twin received betamethasone (10 microg/h iv) while the second twin received vehicle (0.9% NaCl) for 48 h immediately before the final physiological measurements and tissue harvesting. Fetuses that received betamethasone had higher mean arterial blood pressures than the saline-treated twin controls (53 +/- 1 vs. 48 +/- 1 mmHg, P < 0.05). Coronary vessels from betamethasone-treated fetuses exhibited enhanced peak responses to ANG II (72 +/- 17 vs. 23 +/- 6% of the maximal response to 120 mM KCl, P < 0.05). There was no significant difference in response of the coronary arteries to other vasoactive compounds [KCl, U-46619, sodium nitroprusside, 8-bromo-cGMP (8-BrcGMP), isoproterenol, and forskolin]. Contractile responses to ANG II were similar in betamethasone and control mesenteric arteries (48 +/- 17 vs. 36 +/- 12% of the maximal response to 10-6 M U-46619). Western blot analysis revealed AT1 receptor protein expression was increased by betamethasone in coronary but not in mesenteric arteries. These findings demonstrate that antenatal betamethasone exposure enhances coronary but not mesenteric artery vasoconstriction to ANG II by selectively upregulating coronary artery AT1 receptor protein expression.
Contribution of the Phosphodiester Backbone and Glycosyl Linkage Intrinsic Torsional Energetics to DNA Structure and Dynamics (1999)

The intrinsic conformational energetics of macromolecules are an important contribution to their structure and dynamics. This information, however, is lacking for most dihedrals about rotatable bonds in nucleic acids. To bridge this gap, high-level ab initio quantum mechanical calculations have been performed on a number of furanose-based model compounds designed to model the intrinsic torsional energetics of the dihedrals ε, γ, β, and χ in deoxyribonucleic acid (DNA). Energy profiles have been obtained with furanose in both the C3‘ endo and C2‘ endo conformations, to model the torsions in the context of the two conformational ranges populated by the sugar in DNA. The resulting energy profiles are compared to the corresponding crystallographically determined population distributions, with which they can be reconciled to a large extent. This suggests that the models used to derive these energy surfaces are relevant to DNA. Torsion ε is found to be intrinsically very flexible with the low-energy regions encompassing the BI and BII substates. The BI internal energy is found to be on the order of 1.5 kcal/mol more stable than the BII conformation. The torsional energy barrier between BI and BII is relatively low, on the order of 2.1 kcal/mol. Estimates of other torsional energy barriers suggest that the paths of lowest energy between γ = g+ and γ = g- and between the χ anti and syn orientations are through γ = 0° and χ = 120°, respectively. The χ energy surfaces offer insights into the contribution of base−furanose interactions to the corresponding distributions in DNA and its components, in terms of purines versus pyrimidines, and point to the unique properties of cytosine. These surfaces also indicate that a syn base interacts more favorably with a north furanose than with a south furanose, in contrast with a widely accepted view.