gebhart/patrepeval huggingface dataset:
Abstract 663: YK-4-279 inhibits ERG and ETV1 mediated prostate cancer cell invasion (2011)

Abstract Chromosomal translocations involving the ETS family of transcription factors are found in a majority of prostate cancers, including the most clinically aggressive forms. These translocations produce a chimeric gene, which fuses the promoter region of an androgen responsive gene, such as TMPRSS2, to the coding region of ETS factors, most frequently ETV1 or ERG. Over-expression of ETS factors in prostate cancer cells results in a more invasive phenotype. The high prevalence of these rearrangements, and their biological significance represents a novel therapeutic target for the treatment of prostate cancer. We recently reported the development of YK-4-279, a small molecule inhibitor of EWS-FLI1 oncoprotein in Ewing's Sarcoma. ERG and ETV1 belong to the same class of ETS factors as FLI1. Due to the close homology of FLI1 with ERG and ETV1, we tested the ability of YK-4-279 to inhibit ETS biological activity in prostate cell-lines such as VCaP and LNCaP that demonstrate androgen dependent ERG and ETV1 expression, respectively. YK-4-279 inhibited ERG and ETV1 mediated transcription of target genes such as PLAU, PLAT, ADAM19 and MMP-13, which are involved in breakdown of the extracellular matrix and metastasis. YK-4-279 reduced the motility and invasive phenotype of ETV1-fusion positive LNCaP cells and ERG fusion-positive VCaP cells in in vitro invasion assays. However, ETS fusion-negative PC-3 cells were unresponsive to YK-4-279. ERG knockdown in VCaP cells resulted in a loss of drug responsiveness. Transient ERG expression in PC-3 cells resulted in an increased invasive phenotype, which was reduced by YK-4-279. Our results demonstrate that YK-4-279 inhibits ERG and ETV1 biological activity in fusion-positive prostate cancer cells leading to decreased motility and invasion. Therefore, YK-4-279 may have an impact on metastasis in prostate cancer, which is a leading cause of death, and it may be further evaluated for its clinical applications in prostate cancer, in addition to Ewing's sarcoma. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 663. doi:10.1158/1538-7445.AM2011-663
The effect of surface roughness on the adhesion of elastic solids (1975)

Abstract This paper describes a study of the adhesion between elastic solids and the effect of roughness in reducing the adhesion. The experiments were carried out between optically smooth rubber spheres and a hard smooth flat surface of Perspex which could be roughened to various degrees. The radius of the rubber spheres was varied by a factor of 8, their elastic modulus by a factor of 10, while the centre line average (c.l.a.)of the roughened Perspex surface was varied from 0.12 to 1.5 μm. The results show that c.l.a. roughnesses which are small compared with the overall deformation occurring at the region of the rubber-Perspex contact can produce an extremely large reduction in adhesion. The effect is more marked for rubbers of higher modulus. On the other hand the curvature of the sphere (over the range examined) has little influence. For this reason and because the analytical problem of a sphere on a rough flat is extremely complicated a theoretical analysis has been developed for the simpler case of a smooth flat in contact with a rough flat surface. As in Greenwood & Williamson (1966) the rough surface is modelled by asperities all of the same radius of curvature and with heights following a Gaussian distribution of standard deviation σ. The overall contact force is obtained by applying the contact theory of Johnson, Kendall & Roberts (1971) to each individual asperity. The theory predicts that the adhesion expressed as a fraction of the maximum value depends upon a single parameter, 1/Δe,which is the ratio between a and the elastic displacement δC that the tip of an asperity can sustain before it pulls off from the other surface. The analysis shows that the adhesion parameter may also be regarded as representing the statistical average of a competition between the compressive forces exerted by the higher asperities trying to prize the surfaces apart and the adhesive forces between the lower asperities trying to hold the surfaces together. Although the theory is derived for two nominally plane surfaces it is found to fit the experimental results for a sphere on a flat reasonably well.
Cellular Senescence and the Biology of Aging, Disease, and Frailty (2015)

Population aging simultaneously highlights the remarkable advances in science, medicine, and public policy, and the formidable challenges facing society. Indeed, aging is the primary risk factor for many of the most common chronic diseases and frailty, which result in profound social and economic costs. Population aging also reveals an opportunity, i.e. interventions to disrupt the fundamental biology of aging could significantly delay the onset of age-related conditions as a group, and, as a result, extend the healthy life span, or health span. There is now considerable evidence that cellular senescence is an underlying mechanism of aging and age-related conditions. Cellular senescence is a process in which cells lose the ability to divide and damage neighboring cells by the factors they secrete, collectively referred to as the senescence-associated secretory phenotype (SASP). Herein, we discuss the concept of cellular senescence, review the evidence that implicates cellular senescence and SASP in age-related deterioration, hyperproliferation, and inflammation, and propose that this underlying mechanism of aging may play a fundamental role in the biology of frailty.
Armored BCMA CAR T Cells Eliminate Multiple Myeloma and Are Resistant to the Suppressive Effects of TGF-β (2022)

CAR T-cell therapies targeting the B-cell maturation antigen eliminate tumors in relapsed/refractory multiple myeloma patients, however durable remissions remain difficult to attain. Transforming growth factor beta (TGF-β) is a multifunctional cytokine abundantly expressed in the multiple myeloma bone marrow niche, where it promotes an immunosuppressive tumor microenvironment. We hypothesized that BCMA CAR T-cells armored to resist the suppressive effects of TGF-β will provide an advantage in treating multiple myeloma. The armored B2ARM CAR T cells, co-expressing BCMA targeting CAR with TGF-β dominant-negative receptor II, were generated by lentiviral transduction of primary human CD4+ and CD8+ T cells. The B2ARM CAR T cells eliminated MM.1S multiple myeloma targets in long-term cytotoxicity assays, even under TGF-β-high conditions, whereas cytotoxic function of the non-armored B2 CAR -T cells was inhibited by TGF-β. Concordantly, after long-term exposure to targets in the presence of TGF-β, the B2ARM CAR T cells were enriched for Granzyme B, CD107a, Ki67 and polyfunctional cells T-cells (double or triple-positive for IFN-γ, IL-2 and/or TNF-α), as determined by flow cytometry. In addition, the B2ARM CAR T-cells, but not the conventional B2 CAR T-cells, resisted the TGF-β-mediated suppression of activation (CD25), exhaustion (PD-1, LAG3), and differentiation to T effectors (CD45RA+ CD45RO-CD62L-). In NSG mice bearing RPMI-8226 tumors overexpressing TGF-β, the B2ARM CAR mediated 100% tumor rejection and survival, superior infiltration of tumors on day 7 post CAR T treatment (%CD3+CAR+), and greater expression of IFN-γ, TNF-α, Ki67, Granzyme B, and PD-1, as compared to tumor-infiltrating non-armored B2 CAR T-cells. In NSG RPMI-8226 xenograft model in which tumors were additionally supplemented with TGF-β injections on days -1 through 11 of CAR T treatment, the B2ARM CAR T cells rejected tumors faster than the non-armored B2 CARs, and showed greater numbers of CD3+ and CD3+CAR+, central memory (CD45RO+CD62L+) and effector memory (CD45RO+CD62L-) T cells in the peripheral blood 18 days after treatment. In summary, the armored B2ARM CAR T cells mediate superior persistence, proliferation, multi-functionality, effector differentiation and anti-tumor function in pre-clinical models of multiple myeloma, while abrogating TGF-β-mediated suppression.
A model for manipulation of objects with virtual hand in 3D virtual space (1999)

This paper describes a system for virtual object manipulation with a virtual hand. It is necessary that we be able to grasp, move, and release virtual objects with the hand similarly to real ones in order to have experiences in various virtual worlds. Therefore, we developed a new model for object manipulation with a virtual hand. Basic hand actions such as grasping, moving, and releasing are implemented and gravity and inertia are introduced in a simplified way in the proposed model. The objects are naturally moved with interactive rate in a picture generated by the graphics workstation. © 1999 Scripta Technica, Syst Comp Jpn, 30(11): 22–32, 1999
Iontophoretic drug delivery: History and applications (2011)

The goal of delivery system is to get optimal therapeutic management. But, it still remains a challenge in the field of pharmaceuticals for delivery of ionic species and some non ionic. Several transdermal approaches have been used and recently there has been a great attention in using iontophoretic technique for the transdermal drug delivery of medications, both ionic and non ionic. This technique of facilitated movement of ions across a membrane under the influence of an externally applied electric potential difference is one of the most promising physical skin penetrations enhancing method. The payback of using iontophoretic technique includes improved systemic bioavailability ensuing from bypassing the first metabolism. Variables due to oral administration, such as pH, the presence of food or enzymes and transit times can all be eliminated. This article is an overview of the history of iontophoresis, mechanism, principles and factors influencing iontophoresis and its application for various dermatological conditions.
DNA Marker Analysis of Loci underlying Resistance to Soybean Cyst Nematode (<i>Heterodera glycines</i> Ichinohe) (1994)

Inheritance of resistance to soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is oligogenic and complex. DNA markers, such as restriction fragment length polymorphisms (RFLPs), can be used to identify loci associated with complex genetic characters, including SCN resistance. To uncover these associations, 56 F 2 lines from a crass between a susceptible (M83‐15) and a resistant (M85‐1430) soybean [ Glycine max (L.) Merr.] inbred line were mapped for DNA marker polymorphisms. F 3 lines derived from these F 2 individuals were assayed for SCN disease response in the greenhouse to a field isolate of SCN from Minnesota that tested as Race 3. The F 2 genotypic classes for each of 43 DNAm arkers were then contrasted with SCN disease response to identify marker loci associated with SCN resistance. Two unlinked RFLP markers, pA85 and pB32, were found to be significantly associated with SCN disease response, together accounting for 51.7% of total phenotypic variation. Based on RFLP analysis, individual F 2:3 lines that retained either one or both resistance loci were identified. Lines that possess both resistance loci could be valuable in developing resistant soybean lines free of linkage drag, while lines that have just one of the resistance loci may be useful as single‐gene differentials for SCN race determination.
Soot reference materials for instrument calibration and intercomparisons: a workshop summary with recommendations (2012)

Abstract. Soot, which is produced from biomass burning and the incomplete combustion of fossil and biomass fuels, has been linked to regional and global climate change and to negative health problems. Scientists measure the properties of soot using a variety of methods in order to quantify source emissions and understand its atmospheric chemistry, reactivity under emission conditions, interaction with solar radiation, influence on clouds, and health impacts. A major obstacle currently limiting progress is the absence of established standards or reference materials for calibrating the many instruments used to measure the various properties of soot. The current state of availability and practicability of soot standard reference materials (SRMs) was reviewed by a group of 50 international experts during a workshop in June of 2011. The workshop was convened to summarize the current knowledge on soot measurement techniques, identify the measurement uncertainties and limitations related to the lack of soot SRMs, and identify attributes of SRMs that, if developed, would reduce measurement uncertainties. The workshop established that suitable SRMs are available for calibrating some, but not all, measurement methods. The community of users of the single-particle soot-photometer (SP2), an instrument using laser-induced incandescence, identified a suitable SRM, fullerene soot, but users of instruments that measure light absorption by soot collected on filters did not. Similarly, those who use thermal optical analysis (TOA) to analyze the organic and elemental carbon components of soot were not satisfied with current SRMs. The workshop, and subsequent, interactive discussions, produced a number of recommendations for the development of new SRMs, and their implementation, that would be suitable for the different soot measurement methods.
Immune and inflammatory mechanisms in the development of atherosclerosis (1993)

Investigations over the past 10 years have shown that the immune system is involved in the development of atherosclerosis. There is evidence for an inflammatory process in the vessel wall and also for an involvement of specific immunological mechanisms in atherogenesis.
Meningitic Escherichia coli K1 Penetration and Neutrophil Transmigration Across the Blood–Brain Barrier are Modulated by Alpha7 Nicotinic Receptor (2011)

Alpha7 nicotinic acetylcholine receptor (nAChR), an essential regulator of inflammation, is abundantly expressed in hippocampal neurons, which are vulnerable to bacterial meningitis. However, it is unknown whether α7 nAChR contributes to the regulation of these events. In this report, an aggravating role of α7 nAChR in host defense against meningitic E. coli infection was demonstrated by using α7-deficient (α7(-/-)) mouse brain microvascular endothelial cells (BMEC) and animal model systems. As shown in our in vitro and in vivo studies, E. coli K1 invasion and polymorphonuclear neutrophil (PMN) transmigration across the blood-brain barrier (BBB) were significantly reduced in α7(-/-) BMEC and α7(-/-) mice. Stimulation by nicotine was abolished in the α7(-/-) cells and animals. The same blocking effect was achieved by methyllycaconitine (α7 antagonist). The tight junction molecules occludin and ZO-1 were significantly reduced in the brain cortex of wildtype mice infected with E. coli and treated with nicotine, compared to α7(-/-) cells and animals. Decreased neuronal injury in the hippocampal dentate gyrus was observed in α7(-/-) mice with meningitis. Proinflammatory cytokines (IL-1β, IL-6, TNFα, MCP-1, MIP-1alpha, and RANTES) and adhesion molecules (CD44 and ICAM-1) were significantly reduced in the cerebrospinal fluids of the α7(-/-) mice with E. coli meningitis. Furthermore, α7 nAChR is the major calcium channel for nicotine- and E. coli K1-increased intracellular calcium concentrations of mouse BMEC. Taken together, our data suggest that α7 nAChR plays a detrimental role in the host defense against meningitic infection by modulation of pathogen invasion, PMN recruitment, calcium signaling and neuronal inflammation.
The use of a reference tissue arterial input function with low-temporal-resolution DCE-MRI data (2010)

Pharmacokinetic modeling is a promising quantitative analysis technique for cancer diagnosis. However, diagnostic dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) of the breast is commonly performed with low temporal resolution. This limits its clinical utility. We investigated for a range of temporal resolutions whether pharmacokinetic parameter estimation is impacted by the use of data-derived arterial input functions (AIFs), obtained via analysis of dynamic data from a reference tissue, as opposed to the use of a standard AIF, often obtained from the literature. We hypothesized that the first method allows the use of data at lower temporal resolutions than the second method. Test data were obtained by downsampling high-temporal-resolution rodent data via a k-space-based strategy. To fit the basic Tofts model, either the data-derived or the standard AIF was used. The resulting estimates of K(trans) and v(e) were compared with the standard estimates obtained by using the original data. The deviations in K(trans) and v(e), introduced when lowering temporal resolution, were more modest using data-derived AIFs compared with using a standard AIF. Specifically, lowering the resolution from 5 to 60 s, the respective changes in K(trans) were 2% (non-significant) and 18% (significant). Extracting the AIF from a reference tissue enables accurate pharmacokinetic parameter estimation for low-temporal-resolution data.
Speckle reduction mechanism in laser rear projection displays using a small moving diffuser (2010)

Recently, a practical method of speckle reduction in laser rear projection displays that uses an optical system with a small moving diffuser has attracted much attention. In this paper, a model of the speckle generation and reduction mechanism in the system is presented. We investigated the speckle, focusing on the physical aspects of its generation, rather than treating it statistically. We found that the granularity of the speckle patterns generated by the small diffuser corresponded to the size of the coherent regions on the projection screen. This determined the efficiency of the speckle reduction when the small diffuser was rotated.
Minisatellite Variant Repeat Unit Mapping Using PCR (MVR-PCR) (2003)

Since the discovery of DNA fingerprinting ten years ago (1), the direct analysis of DNA variation has been successfully used in a wide range of applications and has become an important tool in forensic science (2,3). Most DNA typing systems assay DNA fragment length at repeated loci showing tandem repeats, for example, minisatellites and microsatellites, which exhibit allelic variation in tandem-repeat copy number (4-10). However, despite the great discriminatory power and sensitivity of this approach, it has inherent limitations that have prevented its full potential from being realized. The most informative loci, hypervariable minisatellites, have quasicontinous allele-length distributions, with many more alleles than can be resolved by agarosegel electrophoresis, making unequivocal identification of individual alleles impossible (3,6,11-16). This has led to protracted arguments over the definition of match criteria and the extent to which allele-size estimates are prone to error (17-19). This problem can, in principle, be overcome by using microsatellites, which have fewer and smaller alleles that can be precisely sized on sequencing gels (9,10). Although microsatellites have now been widely adopted in the construction of investigative forensic databases, these loci also have attendant drawbacks, the most important being restricted allelic variability, as compared to hypervariable minisatellites.
<title>Electro-optic switch for antenna beam steering</title> (1990)

A fiber-optic delay network consisting of eight different and selectable fiber delays has been demonstrated over a 1 to 11 GHz frequency range. The delay networks can be used as a three-bit resolution beam steerer for an electronically steered antenna. Discrete delay increments were selected by switching the bias current of high speed 1.3-micron laser diodes pigtailed to the delay lines.
Degradation analysis and health monitoring of lithium ion batteries (2011)

Title of Document: DEGRADATION ANALYSIS AND HEALTH MONITERING OF LITHIUM ION BATTERIES Nicholas Dane Williard, Master of Science, 2011 Directed By: Prof Michael Pecht, Dr. Michael Osterman, Department of Mechanical Engineering Degradation and health monitoring of lithium-ion batteries is explored through life-cycle testing and failure analysis. Test samples comprised of four different battery types from two different manufactures underwent aging and charge/discharge cycling using a variety of load profiles including constant current discharge, pulsed discharge, and varying depths of discharge. Data from in situ monitoring of several parameters including current, voltage, temperature and internal resistance, was analyzed in order to find the best features that could be used to track and characterize battery performance degradation. Degraded samples were disassembled according to a newly developed disassembly methodology that considered the effects of the environment on post-disassembly failure analysis results. Several different failure analysis methods were used in order to gain an understanding of how degradation mechanisms propagate from a materials stand point. Battery electrodes were investigated to observe changes in their chemical and mechanical structures. DEGRADATION ANALYSIS AND HEALTH MONITERING OF LITHIUM ION BATTERIES
A Recommendation System Based on Extreme Gradient Boosting Classifier (2018)

Shopping online has become the mainstream way of shopping of the society in recent years. Consumer behavior records on shopping website contain a lot of important information that can be used as basis for commodity recommendations. But traditional collaborative filtering-based recommendation systems are sometimes difficult to handle noise in behavior records. In this paper, we proposed a complex model based on eXtreme Gradient Boosting(xgboost) algorithm with a series of methods of features extraction to build a recommender system based on behavior records of consumers got from Alibaba mobile client. The system had a good performance on the data set with f1-score of 7.97% and has high time efficiency.
Determination of Hepatitis C Virus Genotype by Direct Sequence Analysis of Products Generated with the Amplicor HCV Test (1999)

Consistent with other members of the family Flaviviridae, hepatitis C virus (HCV) demonstrates a high degree of sequence variation throughout the coding regions of its genome. However, there is a high degree of sequence conservation found within the 5' untranslated region (UTR) of the genome, making this region a target of choice for most nucleic acid amplification-based detection assays. In this study, the Amplicor HCV test, a commercially available assay which detects the 5'UTR, was used for the detection of HCV RNA in 669 serum samples obtained from a cohort of liver transplantation patients. Amplification products obtained from the HCV-positive cases were subjected to direct sequencing and genotyping based upon seven phylogenetically informative regions within the 5'UTR. Of the 669 specimens, 416 (62.2%) tested positive for the presence of HCV RNA. Of these, 372 (89.4%) specimens were successfully classified into 11 HCV genotypes and subtypes after computer-assisted analysis of the sequence data. Forty-four (10.6%) of the HCV RNA-positive specimens were not classifiable, the majority corresponding to low-titer specimens as determined by the Chiron Quantiplex HCV RNA 2. 0 assay. Additional comparative studies targeting the NS-5 region of the viral genome generally confirmed the accuracy and sensitivity of the 5'UTR-based classifications, with the exception of the misclassification of a small number of type 1a cases as type 1b. We conclude that although the high sequence conservation within the 5'UTR results in the misclassification of a small number of HCV subtypes, the overall gains of efficiency, the shorter turnaround time, the inclusion of contamination control measures, and the low rate of test failure compared to that of methods based on the NS-5 gene together constitute significant advantages over other techniques.