gebhart/patrepeval huggingface dataset:
Photon-counting and analog operation of a 24-pixel photon number resolving detector based on superconducting nanowires (2016)

We investigate the transition from the photon-counting to the linear operation mode in a large-dynamic range photon-number-resolving-detector (PNRD). A 24-pixel photon-number-resolving-detector, based on superconducting nanowires in a series configuration, has been fabricated and characterized. The voltage pulses, generated by the pixels, are summed up into a single readout pulse whose height is proportional to the detected photon number. The device can resolve up to twenty-five distinct output levels corresponding to the detection of n = 0-24 photons. Due to its large dynamic range, high sensitivity, high speed and wide wavelength range, this device has potential for linear detection in the few tens of photons range. We show its application in the detection of analog optical signals at frequencies up to few hundred MHz and investigate the limits related to the finite number of pixels and to the pixel's dead time.
Health Program Planning/Evaluation 2012-2013 Grant Application (2014)

Tyler Begley proposes a plan to get junior high and high school students to eat more fruits and vegetables in this essay written for HED 4430: Health Program Planning and Evaluation, taught by Dr. Mary Chace at Wright State University.
Lifestyle and risk factor management and use of drug therapies in coronary patients from 15 countries. Principal results from EUROASPIRE II Euro Heart Survey Programme (2001)

This European survey of coronary patients shows a high prevalence of unhealthy lifestyles, modifiable risk factors and inadequate use of drug therapies to achieve blood pressure and lipid goals. There is considerable potential throughout Europe to raise the standard of preventive cardiology through more effective lifestyle intervention, control of other risk factors and optimal use of prophylactic drug therapies in order to reduce coronary morbidity and mortality.
Evaluation of negative results of BacT/Alert 3D automated blood culture system. (2005)

Although automated continuous-monitoring blood culture systems are both rapid and sensitive, false-positive and false-negative results still occur. The objective of this study, then, was to evaluate negative results occurring with BacT/Alert 3D blood culture systems. A total of 1032 samples were cultured with the BacT/Alert 3D automated blood culture system, using both aerobic (FA) and anaerobic (FN) [corrected] media, and 128 of these samples yielded positive results. A total of 904 negative blood samples were then subcultured in 5% sheep blood agar, eosin methylene blue, chocolate agar, and sabouraud-dextrose agar. Organisms growing on these subcultures were subsequently identified using both Vitek32 (bioMerieux, Durham, NC) and conventional methods. Twenty four (2.6%) of the 904 subcultures grew on the subculture media. The majority (83.3%) of these were determined to be gram-positive microorganisms. Fourteen (58.3%) were coagulase-negative staphylococci, two (8.3%) were Bacillus spp., one (4.2%) was Staphylococcus aureus, and one (4.2%) was identified as Enterococcus faecium. Streptococcus pneumoniae and Neisseria spp. were isolated together in two (8.3%) vials. Gram-negative microorganisms comprised 12.5% of the subcultures, of which two (8.3%) were found to be Pseudomonas aeruginosa, and one (4.2%) was Pseudomonas fluorescens. The other isolate (4.2%) was identified as Candida albicans. We conclude that the subculture of negative results is valuable in the BacT/Alert 3D system, especially in situations in which only one set of blood cultures is taken.
Flow Cytometric Analysis of Normal B Lymphoid Development (1988)

Identification of the antigens expressed on marrow B lineage cells can be used to develop a model for the sequential acquisition of cell surface antigens during B lymphocyte development. The data suggest that the surface antigen expression is highly controlled during the development of B cells with the coordinated acquisition of multiple cell surface antigens during the maturational process. The developmental scheme in figure 6 is inferred from the expression of cell surface antigens on single samples. Confirmation of the progression from one stage to the next requires the isolation of a particular stage with subsequent induction to the next stage in-vitro. These data suggest that the development of B lymphoid cells may be discrete rather than continuous. The most immature cells identifiable in the bone marrow express CD34+ as well as HLA-DR. The earliest recognizable B lineage cells (CD19+, bright CD10+) also express CD34+. These cells are smaller by forward light scattering when compared to the cells which express only CD34+ (precursor of myeloid cells). Cells within stage I also express TdT in the nucleus and are proliferating. As the cells progress from stage I to stage II, the B lineage cells lose cell surface CD34 and nuclear TdT. At this time the density of HLA-DR and CD45 increases while the amount of CD10 decreases. These changes occur with no detectable change in cell size as assessed by forward light scattering. HLA-DP is first detected on the cells at this time. The progression of cells from stage II to stage III is marked by the acquisition of CD20, HLA-DQ, and sIgM. The amount of CD45 increases further in the transition between stage II and stage III. The acquisition CD21 and CD22 as well as the loss of CD10 distinguishes stage IV from stage III. Once the cellular composition of normal marrow has been defined, perturbations from homeostasis can be identified. Since marrow is the tissue most sensitive to injury by most antineoplastic chemotherapy and radiotherapy regimens, a means of quantifying the changes from the normal state can provide an assessment of the cytotoxic injury produced in individual patients. By monitoring the return to normal, it may be possible to more precisely individualize therapy for each patient. With a clear understanding of normal hematopoiesis, it should also be possible to identify maturational blocks which occur in hypoplastic marrow states. This may provide a means of identifying the regulatory points for each lineage and provide strategies for overcoming the inhibition of development.(ABSTRACT TRUNCATED AT 400 WORDS)
Initiator‐fragment incorporation radical polymerization of diallyl phthalate: Kinetics, formation of hyperbranched polymer, and iridescent porous film thereof (2006)

Abstract Diallyl phthalate (DAP) was polymerized in toluene using dimethyl 2,2′‐azobisisobutyrate (MAIB) of high concentrations (0.1–0.9 mol/L) as initiator. The polymerization of DAP of 1.50 mol/L with MAIB of 0.50 mol/L proceeded homogeneously at 80°C without gelation to give soluble polymers in a high yield of 93%. Kinetic results of the homogeneous polymerization at 80°C suggest significant contributions of the degradative chain transfer and the primary radical termination as shown by the rate equation, R p = k [MAIB] 0.8 [DAP] 1.0 ( R p = polymerization rate). The polymer formed in the polymerization of DAP (1.30 mol/L) with MAIB (0.50 mol/L) at 80°C for 8 h consisted of the DAP units with (17 mol %) and without (47 mol %) double bond and the methoxycarbonylpropyl group (36 mol %) as MAIB‐fragment. The large fraction of the incorporated initiator‐fragment as terminal group indicates that the polymer has a hyperbranched structure. The film cast from a solution of the hyperbranched poly(DAP) in tetrahydrofuran showed an iridescent color. The confocal scanning laser microscope image of the film revealed that the iridescent film contained the pores of about 1 μm arranged in an ordered array. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 102: 408–415, 2006
PRMT5, a Novel TRAIL Receptor-Binding Protein, Inhibits TRAIL-Induced Apoptosis via Nuclear Factor-κB Activation (2009)

Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) is a member of the TNF superfamily and has selective antitumor activity. Although TNF-alpha-induced intracellular signaling pathways have been well studied, TRAIL signaling is not fully understood. Here, we identified a novel TRAIL receptor-binding protein, protein arginine methyltransferase 5 (PRMT5), as a result of proteomic screening. PRMT5 selectively interacted with death receptor 4 and death receptor 5 but not with TNF receptor 1 or Fas. PRMT5 gene silencing sensitized various cancer cells to TRAIL without affecting TRAIL resistance in nontransformed cells. PRMT5 contributed to TRAIL-induced activation of inhibitor of kappaB kinase (IKK) and nuclear factor-kappaB (NF-kappaB), leading to induction of several NF-kappaB target genes. Although IKK inhibition increased sensitivity to both TRAIL and TNF-alpha, PRMT5 knockdown potentiated TRAIL-mediated cytotoxicity alone. PRMT5 had no effect on TNF-alpha-mediated NF-kappaB signaling. These results show the selectivity of PRMT5 for TRAIL signaling. The PRMT5 small interfering RNA-mediated susceptibility to TRAIL was rescued by ectopic expression of active IKKbeta, confirming the involvement of PRMT5 in TRAIL resistance by activating the NF-kappaB pathway. Collectively, our findings suggest the therapeutic potential of PRMT5 in TRAIL-based cancer treatments
Enhancing 9 nm node dense patterned defect optical inspection using polarization, angle, and focus (2013)

To measure the new SEMATECH 9 nm node Intentional Defect Array (IDA) and subsequent small, complex defects, a methodology has been used to exploit the rich information content generated when simulating or acquiring several images of sub-wavelength-sized defects through best focus. These images, which are <i>xy</i> planes, collected using polarized illumination are stacked according to focus position, <i>z</i>, and through interpolation, volumetric pixels (“voxels”) are formed sized approximately 40 nm per side. From the image data, an intensity can be assigned to each (<i>x,y,z</i>) position. These four-dimensional matrices are extensively filtered for defect detection using multi-dimensional intensity thresholding, nearest-neighbor criteria, continuity requirements, and other techniques standard to optical defect inspection. A simulation example with oblique angles of illumination is presented. Experimental results are shown from the NIST <i>λ</i>=193 nm Microscope using full-field illumination. Volumetric data analysis is compared against the processing of single 2-D images. Defect metrics for comparing planar and volumetric data are developed with the potential shown for a five-fold increase in defect sensitivity using volumetric data versus conventional imaging.
Recent Development of Polymer Electrolyte Membranes for Direct Methanol Fuel Cell Application - A Review (2010)

Direct methanol fuel cell (DMFC) system has tremendous potential to be developed as energy converters due to the simplicity and low temperature of its operation. However, the weaknesses of commercial polymer electrolyte membrane of the cell, perfluorinated ionomer (PFI) membrane, such as methanol crossover, limited operating temperature, susceptibility to osmotic swelling and high costs are among the factors hindering the commercialization of DMFC. This paper reviews a number of studies that have been recently performed in order to overcome the weaknesses. This review has classified the membrane development into three different branches, namely the modification of PFI membranes, the development of other fluoropolymer membranes, and the development of non-fluorinated polymers membranes.
A new operation for the prevention and treatment of amputation neuromas (1989)

A stump neuroma is caused by the disorganised growth of axon cylinders into proliferating granulation tissue, but this is stopped by an undamaged epineural sleeve. We report experiments in the rat in which the epineural sleeve of the stump of the sciatic nerve was freed from nerve fascicles for about 5 mm and then sealed with a synthetic tissue adhesive. Neuroma formation was largely prevented in comparison with the results of other methods. This new technique has been used to treat 68 painful neuromas in 36 patients. All but three of the patients were cured or improved and none were made worse.
Intestinal alkaline phosphatase prevents metabolic syndrome in mice (2013)

Metabolic syndrome comprises a cluster of related disorders that includes obesity, glucose intolerance, insulin resistance, dyslipidemia, and fatty liver. Recently, gut-derived chronic endotoxemia has been identified as a primary mediator for triggering the low-grade inflammation responsible for the development of metabolic syndrome. In the present study we examined the role of the small intestinal brush-border enzyme, intestinal alkaline phosphatase (IAP), in preventing a high-fat-diet-induced metabolic syndrome in mice. We found that both endogenous and orally supplemented IAP inhibits absorption of endotoxin (lipopolysaccharides) that occurs with dietary fat, and oral IAP supplementation prevents as well as reverses metabolic syndrome. Furthermore, IAP supplementation improves the lipid profile in mice fed a standard, low-fat chow diet. These results point to a potentially unique therapy against metabolic syndrome in at-risk humans.
Replication and encapsidation of recombinant Turnip yellow mosaic virus RNA (2008)

Turnip yellow mosaic virus (TYMV) is a positive strand RNA virus that infects mainly Cruciferae plants. In this study, the TYMV genome was modified by inserting an extra subgenomic RNA promoter and a multiple cloning site. This modified TYMV was introduced into Nicotiana benthamiana using a Agrobacterium-mediated T-DNA transfer system (agroinfiltration). When a gene encoding beta-glucuronidase or green fluorescent protein was expressed using this modified TYMV as a vector, replication of the recombinant viruses, especially the virus containing beta-glucuronidase gene, was severely inhibited. The suppression of replication was reduced by co-expression of viral silencing suppressor genes, such as tombusviral p19, closteroviral p21 or potyviral HC-Pro. As expected, two subgenomic RNAs were produced from the recombinant TYMV, where the larger one contained the foreign gene. An RNase protection assay revealed that the recombinant subgenomic RNA was encapsidated as efficiently as the genuine subgenomic RNA.
Living Neural Networks: Dynamic Network Analysis of Developing Neural Progenitor Cells (2016)

ABSTRACT The architecture of the mammalian brain has been characterized through decades of innovation in the field of network neuroscience. However, the assembly of the brain from progenitor cells is an immensely complex process, and a quantitative understanding of how neural progenitor cells (NPCs) form neural networks has proven elusive. Here, we introduce a method that integrates graph-theory with long-term imaging of differentiating human NPCs to characterize the evolution of spatial and functional network features in NPCs during the formation of neural networks in vitro. We find that the rise and fall in spatial network efficiency is a characteristic feature of the transition from immature NPC networks to mature neural networks. Furthermore, networks at intermediate stages of differentiation that display high spatial network efficiency also show high levels of network-wide spontaneous electrical activity. These results support the view that network-wide signaling in immature progenitor cells gives way to a hierarchical form of communication in mature neural networks. We also leverage graph theory to study the spatial features of individual cell types in developing cultures, uncovering spatial features of polarized neuroepithelium. Finally, we employ our method to uncover aberrant network features in a neurodevelopmental disorder using induced pluripotent stem cell (iPSC) models. The “Living Neural Networks” method bridges the gap between developmental neurobiology and network neuroscience, and offers insight into the relationship between developing and mature neural networks.
Transcriptional regulation of the <i>Pseudomonas aeruginosa</i> type III secretion system (2006)

Type III secretion systems (T3SS) function by translocating effector proteins into eukaryotic host cells and are important for the virulence of many Gram-negative bacterial pathogens. Although the secretion and translocation machineries are highly conserved between different species, each pathogen translocates a unique set of effectors that subvert normal host cell physiology to promote pathogenesis. The uniqueness of each pathogen is further reflected in the diversity of mechanisms used to regulate T3SS gene expression. Pseudomonas aeruginosa utilizes a complex set of signalling pathways to modulate T3SS expression in response to extracellular and intracellular cues. Whereas some pathways are dedicated solely to regulating the T3SS, others co-ordinately regulate expression of the T3SS with multiple virulence functions on a global scale. Emerging regulatory themes include coupling of T3SS transcription with type III secretory activity, global regulatory control through modulation of cAMP biosynthesis, repression by a variety of stresses, involvement of multiple two component regulatory systems, and an inverse relationship between T3SS expression and multicellular behaviour. Factors controlling activation of T3SS expression likely contribute to the environmental survival of the organism and to the pathogenesis of acute P. aeruginosa infections. Conversely, active repression of the T3SS might contribute to the persistence of chronic infections.
Molecular Recognition of Human Liver Cancer Cells Using DNA Aptamers Generated via Cell-SELEX (2015)

Most clinical cases of liver cancer cannot be diagnosed until they have evolved to an advanced stage, thus resulting in high mortality. It is well recognized that the implementation of early detection methods and the development of targeted therapies for liver cancer are essential to reducing the high mortality rates associated with this disease. To achieve these goals, molecular probes capable of recognizing liver cancer cell-specific targets are needed. Here we describe a panel of aptamers able to distinguish hepatocarcinoma from normal liver cells. The aptamers, which were selected by cell-based SELEX (Systematic Evolution of Ligands by Exponential Enrichment), have Kd values in the range of 64-349 nM toward the target human hepatoma cell HepG2, and also recognize ovarian cancer cells and lung adenocarcinoma. The proteinase treatment experiment indicated that all aptamers could recognize target HepG2 cells through surface proteins. This outcome suggested that these aptamers could be used as potential probes for further research in cancer studies, such as developing early detection assays, targeted therapies, and imaging agents, as well as for the investigation of common membrane proteins in these distinguishable cancers.
Uncharged AZT and D4T Derivatives of Phosphonoformic and Phosphonoacetic Acids as Anti-HIV Pronucleosides (2004)

Two series of new lipophilic phosphonoformate and phosphonoacetate derivatives of AZT and d4T were synthesized and evaluated as anti-HIV agents. The efficacy of some of the synthesized compounds in cell cultures infected with HIV-1 was higher than that of the parent nucleosides and only slightly correlated to their stability in the phosphate buffer and human blood serum. The synthesized phosphonates are most probably prodrug forms of the corresponding nucleosides.
Novel uncooled detector based on gallium nitride micromechanical resonators (2012)

This work presents measured results demonstrating an uncooled infrared (IR) detector based on gallium nitride (GaN) micromechanical resonators. GaN-based photonic detectors are typically designed to operate in the ultraviolet (UV) regime as the absorption spectrum of wide-band gap GaN peaks at a wavelength of ~360 nm. In contrast, the transduction mechanism of the device presented in this work is the pyroelectric perturbation of a GaN micromechanical resonator, allowing the detection of radiation in the IR regime. IR radiation within the absorption spectrum of the resonating stack material (mainly the IR absorber) is converted into heat causing pyroelectric charge release, which in turn shifts the resonant frequency via changes in the acoustic velocity of GaN. A thin-film IR absorber based on carbon-nanotube nanocomposite is proposed, which offers IR absorptivity of more than 95%. As a proof of concept, we demonstrate a GaN resonant detector operated at 119 MHz, which exhibits an IR sensitivity of ~4 Hz/10nW.
Lymphatic Vessels, Inflammation, and Immunity in Skin Cancer (2015)

The tumor microenvironment and tumor-associated inflammation are now appreciated not only for their role in cancer progression but also for their response to therapy. The lymphatic vasculature is a less-appreciated component of this microenvironment that coordinates local inflammation and immunity and thereby critically shapes local responses. A mechanistic understanding of the complexities of lymphatic vessel function in the unique context of skin provides a model to understand how regional immune dysfunction drives cutaneous malignancies, and as such lymphatic vessels represent a biomarker of cutaneous immunity that may provide insight into cancer prognosis and effective therapy.
Synthesis of some benzimidazole‐ and benzothiazole‐derived ligand systems and their precursory diacids (1983)

Abstract Procedures are described for the preparation of various bidentate and linear tetradentate benzimidazoles and benzothiazoles incorporating units such as pyridyl and thioether, and for the preparation of certain thioether dicarboxylic acids precursory to them. Condensations of ortho ‐functinal anilines with carboxylic acids were carried out in polyphosphoric acid or refluxing HCl solution. Syntheses are reported for: [HO 2 C(CH 2 )2S(CH 2 ) 2 ] 2 X (X = O, S), 1,9‐bis(benzimidazol‐2‐yl)‐2,5,8‐trithianonane, 1,11‐bis( N ‐methylbenzimidazol‐2‐yl)‐3,6,9‐trithiaundecane, 1,11‐bis(2‐benzimidazol‐2‐yl)‐6‐oxo‐3,9‐dithiaundecane, 2‐(2‐pyridyl)benzothiazole, 2,6‐bis(benzothiazol‐2‐yl)pyridine, 2‐(2‐pyridyl)‐ N ‐methylbenzimidazole, 2‐(2‐pyridylmethyl)benzimidazole and 2‐( N ‐methyl‐2‐piperidyl)benzimidazole. The compounds were characterized, where appropriate, by their mass, uv and 1 H‐nmr spectra.
Prooxidant activity of melatonin promotes fas‐induced cell death in human leukemic Jurkat cells (2001)

The antioxidant activity of melatonin (MEL) has been considered to constitute part of its physiological as well as pharmacological effects. However, as described herein we found a profound prooxidant activity of micro- to millimolar concentrations of MEL in the human leukemic Jurkat cell line. This prooxidant effect was increased in glutathione-depleted cells and counteracted by antioxidants. As a consequence MEL promoted fas-induced cell death. These data therefore indicate that MEL may be a modulator of the cellular redox status, but does not necessarily act as an intracellular antioxidant.
Design and Synthesis of Pyridone-Containing 3,4-Dihydroisoquinoline-1(2 <i>H</i> )-ones as a Novel Class of Enhancer of Zeste Homolog 2 (EZH2) Inhibitors (2016)

A new enhancer of zeste homolog 2 (EZH2) inhibitor series comprising a substituted phenyl ring joined to a dimethylpyridone moiety via an amide linkage has been designed. A preferential amide torsion that improved the binding properties of the compounds was identified for this series via computational analysis. Cyclization of the amide linker resulted in a six-membered lactam analogue, compound 18. This transformation significantly improved the ligand efficiency/potency of the cyclized compound relative to its acyclic analogue. Additional optimization of the lactam-containing EZH2 inhibitors focused on lipophilic efficiency (LipE) improvement, which provided compound 31. Compound 31 displayed improved LipE and on-target potency in both biochemical and cellular readouts relative to compound 18. Inhibitor 31 also displayed robust in vivo antitumor growth activity and dose-dependent de-repression of EZH2 target genes.