gebhart/patrepeval huggingface dataset:
Lipopolysaccharide Primes the NALP3 Inflammasome by Inhibiting Its Ubiquitination and Degradation Mediated (2015)

Weidentifiedanovelpathwayofinflammasomeprimingthatmayserveasaspringboardforfuturetranslationalstudies.The inflammasome is a multiprotein complex that augmentstheproinflammatoryresponsebyincreasingthegenerationandcellularreleaseofkeycytokines.Specifically,theNALP3inflam-masomerequirestwo-stepsignaling,primingandactivation,tobe functional to release the proinflammatory cytokines IL-1and IL-18. The priming process, through unknown mecha-nisms, increases the protein levels of NALP3 and pro-IL-1 incells. Here we show that LPS increases the NALP3 protein life-span without significantly altering steady-state mRNA inhumancells.LPSexposurereducestheubiquitin-mediatedpro-teasomalprocessingofNALP3byinducinglevelsofanE3ligasecomponent, FBXO3, which targets FBXL2. The latter is anendogenous mediator of NALP3 degradation. FBXL2 recog-nizes Trp-73 within NALP3 for interaction and targets Lys-689withinNALP3forubiquitinligationanddegradation.Auniquesmall molecule inhibitor of FBXO3 restores FBXL2 levels,resulting in decreased NALP3 protein levels in cells and,thereby, reducing the release of IL-1 and IL-18 in humaninflammatory cells after NALP3 activation. Our findingsuncover NALP3 as a molecular target for FBXL2 and suggestthat therapeutic targeting of the inflammasome may serve as aplatform for preclinical intervention.
Characterization of Interfacial Bond Strength by Dynamic Analysis (1992)

Short beam shear, double cantilever beam, and torsional dynamic mechanical (DMA) tests were performed on composite materials systems to characterize the interfacial bond strength. The composite materials were unidirectional flat laminate with different fiber surface treatments and sizings. The results indicated that the DMA test was superior to the short beam shear and double cantilever beam test for measuring fiber/ matrix bonding. The DMA tests detected the effect of surface treatment with much greater accuracy than the standard mechanical tests. Also, DMA tests readily detected the differ ence in fiber/matrix bonding of PAN-based and pitch-based fibers. The DMA test had the additional feature of being able to isolate fiber/matrix interface effects from matrix and fiber effects.
Roles for inositol-phosphoryl ceramide synthase 1 (IPC1) in pathogenesis ofC. neoformans (2001)

Cryptococcus neoformans is a leading cause of life-threatening fungal infection in immunocompromised patients. Inositol-phosphoryl ceramide synthase 1 (Ipc1) is a fungus-specific enzyme, encoded by the essential IPC1 gene, that catalyzes the formation of complex sphingolipids and may also regulate the levels of phytoceramide and diacylglycerol. Here, we investigated the functions of this essential gene by modulating its expression in C. neoformans using a galactose-inducible promoter. Down-regulation of IPC1 significantly lowers the expression of certain virulence traits such as melanin pigmentation and, remarkably, impairs pathogenicity of C. neoformans in an established rabbit model. Interestingly, we found that IPC1 down-regulation significantly decreases the intracellular growth of C. neoformans in the J774.16 murine macrophage-like cells. Finally, we studied the effect of IPC1 expression under different stress conditions and found that down-regulation of IPC1 confers a defect on in vitro growth at low pH. Because this environment is similar to that in the phagolysosome of J774.16 macrophage-like cells, our findings indicate that down-regulation of IPC1 confers a growth defect in vivo through a pH-dependent mechanism. In conclusion, our study is the first to define a novel and crucial function of Ipc1 in fungal pathogenesis.
EXOGENOUS HORMONES AND OTHER DRUG EXPOSURES OF CHILDREN WITH CONGENITAL HEART DISEASE1 (1979)

A history of oral contraceptive use, hormonal pregnancy tests, prescribed hormones and other drugs was obtained from 390 mothers of infants with congenital heart disease and 1254 mothers of normal infants in Massachusetts. The data show a small positive association between estrogen/progesterone exposure and cardiac malformation, the prevalence ratio estimate of exposed to non-exposed being 1.5 (90 per cent confidence limits are 1.0, 2.1). No association was evident, however, between hormones and trunco-conal or any other class of defect among the cases, an observation which casts doubt on a causal relationship betweem hormones and cardiovascular malformations. Several other drugs were reported more frequently by cases' mothers. These include: ampicillin; aspirin; a combined anti-nausea agent (doxylamine succinate, dicyclomine hydrochloride and pyridoxine hydrochloride); chlordiazopoxide, codeine, diazepam, diphenylhydantoin; insulin; phenobarbital; phenothiazine; phenylephrine; and tetracycline.
Assumed Multivariate Beta-PDF Modeling for Turbulent Nonpremixed Flames (2007)

Numerical simulation based on a moment method is conducted to investigate the feasibility of an assumed probability density function (PDF) approach in the configuration of a turbulent jet nonpremixed flame. In this study, a multivariate β-PDF is employed to account for turbulence-chemistry interaction. The multivariate β-PDF approach has an advantage that only one additional transport equation of sum of composition variances is solved to determine the shape of species PDF to transport equations of mean compositions. The numerical simulation is carried out for H3 flame. Reaction mechanism is a single-step irreversible reaction including H2, O2 and H2O species. The results are compared with those from measurements and a combined PDF/moment method that detailed reaction mechanism is applied. Velocity distributions obtained by the multivariate β-PDF approach show good agreement with measurements and combined PDF/moment results, which indicates that the present approach can predict the flow pattern of nonpremixed flames. The present approach also provides good predictions in terms of mean temperature and mass fraction. PDFs of mass fraction obtained by the present approach are similar to those by the combined PDF/moment method. On the other hand, the variance of temperature is underpredicted, which is attributed to an approximation of temperature variance. In order to achieve a good prediction of the reaction rate, a PDF approximation of enthalpy is proposed for the evaluation of mean reaction rate.
Genetic Evaluation of Candidate Genes for the Mom1 Modifier of Intestinal Neoplasia in Mice (1996)

As genetic mapping of quantitative trait loci (QTL) becomes routine, the challenge is to identify the underlying genes. This paper develops rigorous genetic tests for evaluation of candidate genes for a QTL, involving determination of allelic status in inbred strains and fine-structure genetic mapping. For the Mom1 modifier of intestinal adenomas caused by ApcMin, these tests are used to evaluate two candidate genes: Pla2g2a, a secretory phospholipase, and Rap1GAP, a GTPase activating protein. Rap1GAP passes the first test but is excluded by a single fine-structure recombinant. Pla2g2a passes both tests and is a strong candidate for Mom1. Significantly, we also find that ApcMin-induced adenomas remain heterozygous for the Mom1 region, consistent with Mom1 acting outside the tumor lineage and encoding a secreted product.
Supplementary Data from Telomerase Peptide Vaccination Combined with Temozolomide: A Clinical Trial in Stage IV Melanoma Patients (2023)

&lt;p&gt;Supplementary Figures S1-S4; Supplementary Materials and Methods; Supplementary Tables S1-S2.&lt;/p&gt;
Application of Multi-ported CAM for Parallel Coding (2006)

This paper presents a parallel coding architecture using a flexible multi-ported content addressable memory (CAM). A previously reported flexible multi-port content addressable memory (FMCAM) technology (Kumaki et al., 2004) is improved by additional schemes for a single search mode and counting value setting and enables the fast parallel coding operation. Evaluation results for Huffman encoding within the JPEG application show that the proposed architecture can reduce the required clock-cycle number by 93% is comparison to a conventional DSP. Furthermore, the performance per unit area, measured in MOPS/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , can be improved by a factor 3.8 in comparison to a conventional DSP
Real-Time Polymerase Chain Reaction and Melting Curve Analysis (2006)

Monitoring polymerase chain reaction (PCR) once each cycle is a powerful method to detect and quantify the presence of nucleic acid sequences and has become known as "real-time" PCR. Absolute quantification of initial template copy number can be obtained, although quantification relative to a control sample or second sequence is often adequate. Melting analysis following PCR monitors duplex hybridization as the temperature is changed and is a simple method for sequence verification and genotyping. Melting analysis is often conveniently performed immediately after PCR in the same reaction tube. The fluorescence of either DNA dyes that are specific to double-strands or fluorescently labeled oligonucleotide probes can be monitored for both real-time quantification and melting analysis. When used together with rapid temperature control, these methods allow amplification and genotyping in less than a half hour.
Independent expression and cellular processing of Mr 72,000 type IV collagenase and interstitial collagenase in human tumorigenic cell lines. (1990)

The regulation of Mr 72,000 type IV collagenase and interstitial collagenase expression was studied in vitro. Three tumorigenic human cell lines were used, together with human fetal lung fibroblasts as a nontumorigenic control. Mr 72,000 type IV collagenase was expressed constitutively by all four cell lines, whereas only A2058 melanoma cells exhibited constitutive expression of interstitial collagenase. Treatment of cells with transforming growth factor beta 1 (TGF-beta 1) and 12-O-tetradecanoylphorbol-13-acetate (TPA) revealed an opposite pattern of regulation of these two metalloproteinases. Specifically, TPA increased interstitial collagenase mRNA levels in each cell line and decreased type IV collagenase mRNA levels in control fibroblasts and the tumorigenic cell lines, HT-1080 and A2058. TGF-beta 1 treatment increased type IV collagenase mRNA levels in each cell line and decreased interstitial collagenase mRNA levels in A2058 melanoma cells. Interstitial collagenase mRNA induction was accompanied in all cell lines by elevated interstitial procollagenase in the conditioned medium, as detected by zymography. Changes in Mr 72,000 type IV collagenase expression revealed a more complex pattern of regulation. TPA and TGF-beta 1 treatment of HT-1080 cells resulted in the appearance of two bands of gelatinolytic activity with a molecular weight of approximately 62,000 and 59,000. The Mr 62,000 species was also induced by TGF-beta 1 treatment of A2058 cells. Addition of affinity-purified radiolabeled Mr 72,000 type IV procollagenase to TPA-treated HT-1080 cells demonstrated that both species were products of the Mr 72,000 proenzyme and that exogenous proenzyme could be processed by these cells. Western blot analysis with specific antipeptide antibodies revealed that both the Mr 62,000 and 59,000 species were derived from the Mr 72,000 proenzyme by amino-terminal cleavage. There was no evidence for cellular processing of either interstitial procollagenase or the Mr 92,000 type IV procollagenase. These results demonstrate that the Mr 72,000 type IV collagenase is under the control of different regulatory elements from interstitial collagenase, at the level of both mRNA expression and cellular processing, and that this processing appears to be the result of a phorbol ester and TGF-beta 1-inducible cellular activation mechanism. The ratio of active enzyme species to latent Mr 72,000 proenzyme may provide a better correlation with invasive potential than overall levels of this widely expressed metalloproteinase.
Momentum considerations inside near-zero index materials (2021)

Near-zero-index (NZI) materials, i.e. materials having a phase refractive index close to zero, are known to enhance or inhibit light-matter interactions. Most theoretical derivations of fundamental radiative processes rely on energetic considerations and detailed balance equations, but not on momentum considerations. Because momentum exchange should also be incorporated into theoretical models, we investigate momentum inside the three categories of NZI materials, i.e. inside epsilon-and-mu near-zero (EMNZ), epsilon-near-zero (ENZ) and mu-near-zero (MNZ) materials. In the context of Abraham-Minkowski debate in dispersive materials, we show that Minkowski-canonical momentum of light is zero inside all categories of NZI materials while Abraham-kinetic momentum of light is zero in ENZ and MNZ materials but nonzero inside EMNZ materials. We theoretically demonstrate that momentum recoil, transfer momentum from the field to the atom and Doppler shift are inhibited in NZI materials. Fundamental radiative processes inhibition is also explained due to those momentum considerations inside three-dimensional NZI materials. Lastly, absence of diffraction pattern in slits experiments is seen as a consequence of zero Minkowski momentum. Those findings are appealing for a better understanding of fundamental light-matter interactions at the nanoscale as well as for lasing applications.
Ultrasound Attenuation Measurements of the Liver in Vivo Using a Commercial Sector Scanner (1984)

Attenuation measurements of various tissue mimicking phantoms and three different groups of patients were obtained using a modified commercial sector scanner. Estimates of attenuation were made using the spectral shift method with mean frequencies at different depths of a region of interest being obtained by both zero crossing and fast Fourier transform techniques. The accuracy and precision of both techniques was compared in phantoms and it was found that the FFT technique yielded less day-to-day variation (SD=3 percent) than the zero crossing technique (5 percent). For larger regions of interest, the range of variation in both techniques was more similar. Day-to-day variation in livers of normal patients was much larger than that seen in phantoms (10 to 15 percent) suggesting that in vivo measurements may be less precise due to actual daily changes in patients' livers. Attenuation estimates of phantoms were high by approximately 0.16 dB/MHz/cm compared to values obtained by transmission techniques. The attenuation values of livers in a group of 31 normal patients ranged from 0.214 dB/cm/MHz to 0.849 dB/cm/MHz with a mean of 0.627 +/- 0.126 dB/cm/MHz for the zero crossing technique while the mean value using the FFT technique was 0.86 +/- 0.168 dB/cm/MHz. A group of 26 Gauchers disease patients also showed wide variation with a mean attenuation value of 0.768 +/- 0.21 dB/cm/MHz using the FFT technique. This was significantly different than that of the normal group (p less than .05). Also, a group of 22 chronic B hepatitis patients was examined, having a mean attenuation value of 0.823 +/- 0.21 dB/cm/MHz, not significantly different from those of normal patients. Highly significant differences were found between the three groups when the power spectrum bandwidths of signals received were compared. These differences may be due to differences in the dependence of attenuation as a function of frequency between the groups and may represent a useful tissue characterization parameter.
Avis en réponse à la saisine 150519 - dossier C-NL-13-01. Paris, le 7 septembre 2015 (2015)

Le Haut Conseil des biotechnologies (HCB) a été saisi le 20 mai 2015 par les autorités compétentes françaises (le ministère de l’Agriculture, de l’Agroalimentaire et de la Forêt) d’une demande d’avis relative au dossier C/NL/13/01 de demande de mise sur le marché de la lignée d’oeillets génétiquement modifiés FLO-40685-1 à des fins d’importation et de commercialisation de fleurs coupées. Ce dossier a été déposé par la société Suntory Holdings Limited auprès des autorités compétentes néerlandaises dans le cadre de la directive 2001/18/CE. Conformément à cette directive, la Commission européenne a adressé le rapport d’évaluation des Pays-Bas ainsi que le dossier du pétitionnaire à l’ensemble des Etats membres. Par cette saisine, les autorités compétentes françaises consultent le HCB au stade ultime de la préparation au vote des Etats membres à la Commission européenne. Le Comité scientifique (CS)2 du HCB a examiné le dossier en séance du 25 juin 2015 sous la présidence de Jean-Christophe Pagès. Le présent avis a été adopté par voie électronique le 7 septembre 2015 et publié le 10 septembre 2015.
When Your Gain Is My Pain and Your Pain Is My Gain: Neural Correlates of Envy and Schadenfreude (2009)

We often evaluate the self and others from social comparisons. We feel envy when the target person has superior and self-relevant characteristics. Schadenfreude occurs when envied persons fall from grace. To elucidate the neurocognitive mechanisms of envy and schadenfreude, we conducted two functional magnetic resonance imaging studies. In study one, the participants read information concerning target persons characterized by levels of possession and self-relevance of comparison domains. When the target person's possession was superior and self-relevant, stronger envy and stronger anterior cingulate cortex (ACC) activation were induced. In study two, stronger schadenfreude and stronger striatum activation were induced when misfortunes happened to envied persons. ACC activation in study one predicted ventral striatum activation in study two. Our findings document mechanisms of painful emotion, envy, and a rewarding reaction, schadenfreude.
The presence and release of alpha 2-antiplasmin from human platelets (1981)

An antigen immunochemically indistinguishable from plasma alpha 2-antiplasmin, the primary plasmin inhibitor, was detected in human platelets. By radioimmunoassay, 33-114 ng alpha 2-antiplasmin antigen was quantitated in the detergent-soluble extract of 10(9) washed human platelets from 10 normal donors with a mean level of 62 +/- 24 ng/10(9) platelets. Plasma alpha 2-antiplasmin, either in the platelet suspending medium or on the surface of the platelets, could account for less than 8% of the antigen present in the platelet extracts. When stimulated with thrombin, the platelets released alpha 2-antiplasmin antigen without cell lysis, and greater than 85% of the alpha 2-antiplasmin antigen was released at a high thrombin dose. At a lower dose of thrombin, alpha 2-antiplasmin and platelet factor 4 were partially released without concomitant secretion of serotonin. No alpha 2-antiplasmin antigen was detected in extracts or red blood cells, polymorphonuclear leukocytes, and adherent and nonadherent mononuclear cells. Thus, the platelet is the only peripheral blood cell containing significant amounts of alpha 2-antiplasmin.
Data from Randomized Phase II Trial of Carboplatin–Paclitaxel Compared with Carboplatin–Paclitaxel–Trastuzumab in Advanced (Stage III–IV) or Recurrent Uterine Serous Carcinomas that Overexpress Her2/Neu (NCT01367002): Updated Overall Survival Analysis (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Uterine-serous-carcinoma (USC) is an aggressive variant of endometrial cancer. On the basis of preliminary results of a multicenter, randomized phase II trial, trastuzumab (T), a humanized-mAb targeting Her2/Neu, in combination with carboplatin/paclitaxel (C/P), is recognized as an alternative in treating advanced/recurrent HER2/Neu-positive USC. We report the updated survival analysis of NCT01367002.&lt;/p&gt;Patients and Methods:&lt;p&gt;Eligible patients had stage III to IV or recurrent disease. Participants were randomized 1:1 to receive C/P for six cycles ± T followed by maintenance T until progression or toxicity. Progression-free survival (PFS) was the primary endpoint; overall survival (OS) and toxicity were secondary endpoints.&lt;/p&gt;Results:&lt;p&gt;Sixty-one patients were randomized. After a median-follow-up of 25.9 months, 43 progressions and 38 deaths occurred among 58 evaluable patients. Updated median-PFS continued to favor the T-arm, with medians of 8.0 months versus 12.9 months in the control and T-arms (HR = 0.46; 90% CI, 0.28–0.76; &lt;i&gt;P&lt;/i&gt; = 0.005). Median-PFS was 9.3 months versus 17.7 months among 41 patients with stage III to IV disease undergoing primary treatment (HR = 0.44; 90% CI, 0.23–0.83; &lt;i&gt;P&lt;/i&gt; = 0.015), and 7.0 months versus 9.2 months among 17 patients with recurrent disease (HR = 0.12; 90% CI, 0.03–0.48; &lt;i&gt;P&lt;/i&gt; = 0.004). OS was higher in the T compared with the control arm, with medians of 29.6 months versus 24.4 months (HR = 0.58; 90% CI, 0.34–0.99; &lt;i&gt;P&lt;/i&gt; = 0.046). The benefit was most notable in those with stage III to IV disease, with survival median not reached in the T-arm versus 24.4 months in the control arm (HR = 0.49; 90% CI, 0.25–0.97; &lt;i&gt;P&lt;/i&gt; = 0.041). Toxicity was not different between arms.&lt;/p&gt;Conclusions:&lt;p&gt;Addition of T to C/P increased PFS and OS in women with advanced/recurrent HER2/Neu-positive USC, with the greatest benefit seen for the treatment of stage III to IV disease.&lt;/p&gt;&lt;/div&gt;
Gravel-pack damage removal in horizontal and vertical wells (1999)

Abstract Gravel-packs can be damaged by a variety of mechanisms which include scale formation, fines migration, paraffin and asphaltene deposition resulting in a damage skin of 10-300. Frequently damage removal treatments do not remove this damage completely from all the producing zones, resulting in a short treatment life and/or inadequate production. This can be attributed to poor diversion and/or improper damage characterization. This paper focuses on several aspects of improved damage removal in gravel-packed wells. A methodology to assist in the proper identification of the damage mechanism and the design process for more effective treatments is presented. An integrated approach using an overall systems analysis coupled with log, water analysis and numerical simulations of the gravel-pack/matrix damage removal is recommended. A numerical model to simulate acid treatments of gravelpacked well is presented and used to evaluate several treatments performed on wells from the Gullfaks field in the North Sea. Results indicated greater than 75% of the damage is in the gravel pack. The model incorporates a detailed wellbore model integrated with a reservoir mode for simulation of acidizing treatments in horizontal and vertical gravel-packed wells. An algorithm for quantifying the damage in the gravelpack is discussed in detail. Various diversion techniques and fluid formulations are evaluated using the simulator and compared to field results with emphasis on pre and posttreatment production logs. The results of this study helped us establish guidelines for identifying the damage mechanism and in designing optimal treatments for matrix stimulation of gravel-packed wells.