gebhart/patrepeval huggingface dataset:
Liposome-Encapsulated MTP-PE: A Novel Biologic Agent for Cancer Therapy (1993)

Liposome-encapsulated muramyl tripeptide phosphatidylethanolamine (L-MTP-PE), a new biologic response modifier, was designed to target the immunomodulator to monocytes and macrophages. Human monocytes/macrophages phagocytize L-MTP-PE, with subsequent upregulation of interleukin (IL)-1 alpha, IL-1 beta, IL-6, IL-8, tumor necrosis factor (TNF)-alpha, and monocyte chemotactic and activating factor genes and with the production and secretion of these cytokines in vitro. L-MTP-PE-activated macrophages kill tumor but not normal cells in vitro. Following i.v. infusion of L-MTP-PE into cancer patients, its uptake was demonstrated in liver, spleen, lung, and in and around metastases to lung. We also investigated whether L-MTP-PE therapy administered in a neoadjuvant setting could improve the disease-free interval in relapsed osteosarcoma patients with lung metastasis. Patients received either a 12- or 24-week course of L-MTP-PE after surgical removal of all metastases. Following L-MTP-PE infusion, induction of circulating TNF-alpha, IL-6, neopterin, and C-reactive protein was demonstrated. Disease-free intervals were calculated from the day of surgery to the day of relapse in each group and were compared with the disease-free interval for a historical control group. Those patients receiving 24 weeks of L-MTP-PE showed a significant (p < 0.03) prolongation in time to relapse. These data indicate that L-MTP-PE is an active agent against osteosarcoma and warrants further investigation in an adjuvant setting.
Viscoelastic Properties of Poly(vinyl alcohol) Hydrogels Having Permanent and Transient Cross-Links Studied by Microrheology, Classical Rheometry, and Dynamic Light Scattering (2013)

Dynamics of poly(vinyl alcohol) (PVA) hydrogels having chemical and physical transient cross-links simultaneously (dual cross-link PVA gels) were studied by microrheology based on diffusing-wave spectroscopy (DWS), classical rheology and single dynamic light scattering (DLS), and compared with those of corresponding chemical and physical PVA gels. Three different relaxation modes (fast, intermediate and slow modes) are observed for physical gels, while one mode (fast mode) is found for chemical gels, and two (fast and intermediate) for dual cross-link gels. The three modes are attributed respectively to Brownian diffusion of PVA polymer or collective diffusion of the network or gel mode (fast mode), macroscopic stress relaxation (intermediate mode whose characteristic time shows q0 dependence) and Brownian diffusion of aggregates (slow mode). Microrheological measurements are in good agreement with macrorheological showing segmental Rouse mode dynamics in the high frequency range. For physical gels, we found Maxwell type viscoelasticity characterized by a crossover frequency (maximum of G″) and G′ ∼ ω2 and G″ ∼ ω1 in the lower frequency range. The chemical gels displayed an elastic plateau with low G″ at low frequency. For the dual cross-link gel a maximum of G″ was observed, and its characteristic time agrees with that of the intermediate mode measured by DLS. We show that this relaxation mode corresponds to the associative Rouse mode characterized by G′ = G″ ∼ ω0.5, depending on the dissociation rate of the reversible transient cross-links. We propose a stress relaxation mechanism of the PVA chains in the presence of elastically inactive but associative transient cross-links which induces incomplete stress relaxation.
Compiler-Assisted GPU Thread Throttling for Reduced Cache Contention (2019)

Modern GPUs concurrently deploy thousands of threads to maximize thread level parallelism (TLP) for performance. For some applications, however, maximized TLP leads to significant performance degradation, as many concurrent threads compete for the limited amount of the data cache. In this paper, we propose a compiler-assisted thread throttling scheme, which limits the number of active thread groups to reduce cache contention and consequently improve the performance. A few dynamic thread throttling schemes have been proposed to alleviate cache contention by monitoring the cache behavior, but they often fail to provide timely responses to the dynamic changes in the cache behavior, as they adjust the parallelism afterwards in response to the monitored behavior. Our thread throttling scheme relies on compile-time adjustment of active thread groups to fit their memory footprints to the L1D capacity. We evaluated the proposed scheme with GPU programs that suffer from cache contention. Our approach improved the performance of original programs by 42.96% on average, and this is 8.97% performance boost in comparison to the static thread throttling schemes.
A reliable method for the detection of BRCA1 and BRCA2 mutations in fixed tumour tissue utilising multiplex PCR-based targeted next generation sequencing (2015)

Detection of BRCA1/2 variants in fixed tissue is feasible, and could be performed prospectively to facilitate optimum treatment decisions for ovarian or breast cancer patients.
Fhit-deficient normal and cancer cells are mitomycin C and UVC resistant (2004)

To identify functions of the fragile tumour suppressor gene, FHIT, matched pairs of Fhit-negative and -positive human cancer cell clones, and normal cell lines established from Fhit -/- and +/+ mice, were stressed and examined for differences in cell cycle kinetics and survival. A larger fraction of Fhit-negative human cancer cells and murine kidney cells survived treatment with mitomycin C or UVC light compared to matched Fhit-positive cells; approximately 10-fold more colonies of Fhit-deficient cells survived high UVC doses in clonigenic assays. The human cancer cells were synchronised in G1, released into S and treated with UVC or mitomycin C. At 18 h post mitomycin C treatment approximately 6-fold more Fhit-positive than -negative cells had died, and 18 h post UVC treatment 3.5-fold more Fhit-positive cells were dead. Similar results were obtained for the murine -/- cells. After low UVC doses, the rate of DNA synthesis in -/- cells decreased more rapidly and steeply than in +/+ cells, although the Atr-Chk1 pathway appeared intact in both cell types. UVC surviving Fhit -/- cells appear transformed and exhibit >5-fold increased mutation frequency. This increased mutation burden could explain the susceptibility of Fhit-deficient cells in vivo to malignant transformation.
<i>Lactobacillus plantarum</i>‐derived extracellular vesicles induce anti‐inflammatory M2 macrophage polarization <i>in vitro</i> (2020)

Probiotics offer various health benefits. <i>Lactobacillus plantarum</i> has been used for decades to enhance human intestinal mucosal immunity and improve skin barrier integrity. Extracellular vesicles (EVs) derived from eukaryotic or prokaryotic cells have been recognized as efficient carriers for delivery of biomolecules to recipient cells, and to efficiently regulate human pathophysiology. However, the mechanism underlying the beneficial effects of probiotic bacteria-derived EVs on human skin is unclear. Herein, we investigated how <i>L. plantarum</i>-derived EVs (LEVs) exert beneficial effects on human skin by examining the effect of LEVs on cutaneous immunity, particularly on macrophage polarization. LEVs promoted differentiation of human monocytic THP1 cells towards an anti-inflammatory M2 phenotype, especially M2b, by inducing biased expression of cell-surface markers and cytokines associated with M2 macrophages. Pre- or post-treatment with LEVs under inflammatory M1 macrophage-favouring conditions, induced by LPS and interferon-γ, inhibited M1-associated surface marker, <i>HLA-DRα</i> expression. Moreover, LEV treatment significantly induced expression of macrophage-characteristic cytokines, IL-1β, GM-CSF and the representative anti-inflammatory cytokine, IL-10, in human skin organ cultures. Hence, LEVs can trigger M2 macrophage polarization <i>in vitro</i>, and induce an anti-inflammatory phenomenon in the human skin, and may be a potent anti-inflammatory strategy to alleviate hyperinflammatory skin conditions.
Ungual and Transungual drug delivery (2011)

Topical therapy is desirable in treatment of nail diseases like onychomycosis (fungal infection of nail) and psoriasis. The topical treatment avoids the adverse effects associated with systemic therapy, thereby enhancing the patient compliance and reducing the treatment cost. However the effectiveness of the topical therapies has been limited due to the poor permeability of the nail plate to topically applied therapeutic agents. Research over the past one decade has been focused on improving the transungual permeability by means of chemical treatment, penetration enhancers, mechanical and physical methods. The present review is an attempt to discuss the different physical and chemical methods employed to increase the permeability of the nail plate. Minimally invasive electrically mediated techniques such as iontophoresis have gained success in facilitating the transungual delivery of actives. In addition drug transport across the nail plate has been improved by filing the dorsal surface of the nail plate prior to application of topical formulation. But attempts to improve the trans-nail permeation using transdermal chemical enhancers have failed so far. Attempts are on to search suitable physical enhancement techniques and chemical transungual enhancers in view to maximize the drug delivery across the nail plate.
Estimation of Causal Effects with Multiple Treatments: A Review and New Ideas (2017)

The propensity score is a common tool for estimating the causal effect of a binary treatment in observational data. In this setting, matching, subclassification, imputation or inverse probability weighting on the propensity score can reduce the initial covariate bias between the treatment and control groups. With more than two treatment options, however, estimation of causal effects requires additional assumptions and techniques, the implementations of which have varied across disciplines. This paper reviews current methods, and it identifies and contrasts the treatment effects that each one estimates. Additionally, we propose possible matching techniques for use with multiple, nominal categorical treatments, and use simulations to show how such algorithms can yield improved covariate similarity between those in the matched sets, relative the pre-matched cohort. To sum, this manuscript provides a synopsis of how to notate and use causal methods for categorical treatments.
Screening and identification of resistant sources against <i>Sclerotinia sclerotiorum</i> causing white mold disease in common bean (2020)

Abstract White mold caused by Sclerotinia sclerotiorum (Lib.) de Bary is a devastating constraint in common bean ( Phaseolus vulgaris L.) production, affecting plants at both seedling and adult stages. Being a crop of small‐area, resource‐poor, farmers and given the high cost of fungicides, farmers prefer the use of region‐specific landraces or resistant accessions. In this study, we compared various methods of bean plant inoculation with S. sclerotiorum and found modified straw test method of inoculation as most accurate and effective. Using this method, we screened a panel of 516 common bean germplasm procured from 22 countries through the National Bureau of Plant Genetic Resources (NBPGR; New Delhi, India) against white mold pathogen. Only 12 accessions were found resistant, whereas 121 were moderately resistant to white mold. Among exotic resistant accessions, EC271515, EC271475, EC271523, and EC271528 were from the Colombian region, while the remaining four, EC530910, EC530913, EC530916, and EC531044, belonged to Columbia. Of the four resistant landraces from India, IC280353 was a collection from Jammu and Kashmir State, whereas landraces IC278744, IC278709, and IC278734 were from Himachal Pradesh. Considering the area under disease progress curve (AUDPC), incubation period, infection rate, and lesion length, EC‐271475 followed by EC‐530916 were concluded to be the best accessions against white mold. Further, the statistical analysis also confirms the highly resistant nature of phenotypically screened common bean accessions. One exotic accession, EC271475, possessing resistance to S. sclerotiorum was also resistant to bean common mosaic virus (BCMV) strain NL‐7n and could be used in common bean breeding programs.
Improving a<i>Synechocystis</i>-based photoautotrophic chassis through systematic genome mapping and validation of neutral sites (2015)

The use of microorganisms as cell factories frequently requires extensive molecular manipulation. Therefore, the identification of genomic neutral sites for the stable integration of ectopic DNA is required to ensure a successful outcome. Here we describe the genome mapping and validation of five neutral sites in the chromosome of Synechocystis sp. PCC 6803, foreseeing the use of this cyanobacterium as a photoautotrophic chassis. To evaluate the neutrality of these loci, insertion/deletion mutants were produced, and to assess their functionality, a synthetic green fluorescent reporter module was introduced. The constructed integrative vectors include a BioBrick-compatible multiple cloning site insulated by transcription terminators, constituting robust cloning interfaces for synthetic biology approaches. Moreover, Synechocystis mutants (chassis) ready to receive purpose-built synthetic modules/circuits are also available. This work presents a systematic approach to map and validate chromosomal neutral sites in cyanobacteria, and that can be extended to other organisms.
Providing accountability and liability protection for UAV operations beyond visual line of sight (2018)

Current off-the-shelf Unmanned Aerial Vehicle (UAV) Flight Data Recorders do not address liability and accountability in the event of an accident. This limitation makes it difficult for necessary stakeholders to determine parties at fault, especially when future operations are expected to be conducted Beyond Visual Line-of-Sight (BVLoS). While both on-board and off-board recorders currently exist, the data collected is unsuitable for insurance claims and other legal matters since non-repudiation and tamper-proof mechanisms are not implemented. At the same time, with ongoing developments and improvements to Internet of Things (IoT) telecommunications infrastructure such as LTE-M, 5G, SigFox and NB-IoT protocols, usage of TCP/IP channels and cloud services for UAV Command and Control systems is increasing. This research proposes a real-time, off-board flight logging service using a secure graph database scheme for storage and analysis of flight data recordings. By representing series of logs as an encrypted block chain in graph nodes of a database, it is possible to construct accurate time-lines and enable non-repudiation of operator-UAV and UAV-UAV interactions that provide irrefutable evidence. For proof of concept, this design integrates into the UAV as a Service architecture for BVLOS operations we have proposed in previous publications. The details of the recording protocol, integration into the UAV as a Service platform, data generation simulation and performance results are discussed.
YBa2Cu3O7 nanobridges fabricated by direct-write electron beam lithography (1992)

A direct method for nondamaging, nanometer-scale patterning of high Tc superconductor thin films is presented. We have fabricated superconducting nanobridges in high-quality, epitaxial thin-film YBa2Cu3O7 (YBCO) by combining direct-write electron beam lithography and an improved aqueous etchant. Weak links with both length and width dimensions less than 20 nm have exhibited critical currents at 77 K of 4–20 μA and IcRn products of 10–100 μV which compare favorably with results for other YBCO junction technologies. We have used this technique in the fabrication of a shock-wave pulse former as an initial demonstration of its applicability to monolithic superconductive electronics.
Identification of HLA-A0201 restricted epitope of novel cancer/testis antigens VCX/Y and generation of antigen-specific T-cell receptor engineered T cells for treatment of solid tumor malignancies. (2018)

160 Background: To identify HLA-A0201 restricted epitope of novel cancer/testis antigen VCX/Y, generate antigen specific T cells and T-cell receptor (TCR) engineered T cells for adoptive cell therapy (ACT) of solid cancer patients. Methods: Reverse-immunology method was used to identify HLA-A0201 restricted epitope of VCX/Y. The high binding score peptide or whole length of VCX3A mRNA were pulsed or transfected to mature dendritic cells (mDC) from HLA-A0201+ donor and then stimulated autologous naïve T cells. Tetramer guided sorting were performed to purify the epitope specific T cells and CTL clones were generated with limiting dilution. TCR were cloned out from high activity CTL clone and the recombinant of retrovirus vector were constructed to introduce the TCR to allogeneic PBMC to generate the TCR engineered T cells. Results: One peptide which its sequence was shared with all VCX/Y members was identified. Interesting, only CTL clone generated from simulation of VCX3A mRNA transfected DC can recognize naturally processed VCX/Y presented by HLA-A0201+ tumor cells. Cold target inhibition detection confirmed that this VCX/Y peptide was naturally processed and recognized by HLA-A0201+ CTL clone. After infection of retrovirus containing the TCR from high activity of CTL clone, the TCR engineered T cells can recognize HLA-A2+ tumor cells but not normal lung cells. Moreover, these TCR engineered T cells specifically secreted IFN-γ in response to T2 cells pulsed with peptide, as well as HLA-A0201+ and VCX/Y overexpressed tumor cells. Conclusions: VCX/Y peptide we identified is a novel candidate peptide antigen for vaccine or for endogenous adoptive T cell therapy. The correlated high activity TCR gene can generate TCR engineered T cells from patients with anti-tumor activity and offer an alternative adoptive T cell treatment for patients with VCX/Y expressing solid tumor malignancies.
Power-to-liquid<i>via</i>synthesis of methanol, DME or Fischer–Tropsch-fuels: a review (2020)

A review of power-to-liquid for methanol, DME and FT-fuels focusing on commercial synthesis technologies and current power-to-liquid concepts.
Results guide to CEPXS/ONELD: A one-dimensional coupled electron-photon discrete ordinates code package (1990)

CEPXS/ONELD is a discrete ordinates code package for one-dimensional coupled electron-photon transport over the energy range of 100 MeV to 1.0 keV. In this Results Guide, CEPXS/ONELD predictions are compared to the predictions of Monte Carlo codes and to experiment. These comparisons are made for a variety of quantities, including energy deposition, charge deposition and electron current spatial profiles as well as electron and photon spectra. Sensitivity studies are presented that show how the numerical approximations of CEPXS/ONELD can affect the accuracy of predictions. Guidelines for the efficient and accurate use of the code package are given. All examples involve one-dimensional planar geometry and non-adjoint transport. 35 refs.
Treatment of Experimental Viral Myocarditis With Interleukin-10 (1999)

These findings provide new insights into the in vivo effects of IL-10 on viral infection and suggest a therapeutic effect of IL-10 on viral myocarditis.
Energy broadening of an electron optical line source (1989)

The energy broadening due to electron–electron interactions of an electron optical line source and a line shaped beam have been theoretically analyzed and compared to its axially symmetric counterpart. An analytical approach was developed to evaluate the energy spread in an electron source. Monte Carlo methods were used to evaluate the energy broadening induced in a thin electron optical lens of 10× magnification. The results predict that the focusing of line shaped beams have an induced energy spread up to 27% lower than round beams.
Dendritic cells fused with mastocytoma cells elicit therapeutic antitumor immunity (1998)

Characterization of the spontaneous immune response that frequently occurs in tumor-bearing animals, as well as immunization using dendritic cells pulsed with tumor antigens, suggests that a limiting factor of the tumor-specific immune response may be a defect in the co-stimulatory signal that is required for optimal activation of T cells. In this work, we describe a new approach to improve the antigen-presenting capacity of tumor cells, which does not require a source of purified tumor-associated antigen. We fused P815 mastocytoma cells with bone marrow-derived dendritic cells. We obtained one hybrid that displayed the phenotypic and functional properties of dendritic cells and expressed mRNA coding for the tumor-associated antigen P815 A/B. Injections of irradiated hybrid cells prevented the growth of pre-implanted mastocytoma and induced long-lasting tumor resistance. Int. J. Cancer76:250–258, 1998.© 1998 Wiley-Liss, Inc.
<title>Coastal mine detection using the COBRA multispectral sensor</title> (1996)

The Coastal Systems Station (CSS) at Panama City, FL is developing an airborne multispectral sensor system which flies on an unmanned aerial vehicle for detecting mines in a coastal environment. This system is called the Coastal Battlefield Reconnaissance and Analysis (COBRA) system and has successfully completed preliminary developmental testing (DT-0). For this program, the Environmental Research Institute of Michigan (ERIM) developed a fieldable ground station including integrated aircraft tracking, real-time sensor data analysis, and a post processor testbed for developing and evaluating mine and minefield detection algorithms. A fully adaptive multispectral Constant False Alarm Rate mine detection algorithm was implemented in the post-processor by ERIM, along with patterned and scatterable minefield detection algorithms developed by CSS. The algorithms do not require prior knowledge of mine spectral signatures and thus are ideal for detecting a wide variety of mines with unknown or changing spectral signatures. COBRA DT-0 testing has been performed on actual minefields deployed at coastal and inland test sites. Preliminary results show that the COBRA system, coupled with these algorithms, meets the required minefield detection performance goals. This paper reviews the algorithm theory and implementation, overviews the ground station design, and presents minefield detection results from actual minefield imagery collected over realistic scenes during DT-0 testing.© (1996) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.