gebhart/patrepeval huggingface dataset:
Light scattering into silicon-on-insulator waveguide modes by random and periodic gold nanodot arrays (2009)

Experimental characterization and finite-element numerical simulations of the electromagnetic interaction between random or periodic Au nanodot arrays patterned atop a silicon-on-insulator (SOI) photodetector and incident electromagnetic plane waves have been performed at wavelengths of 400–1100nm. The presence of the Au nanodots is found to lead to increased electromagnetic field amplitude within the semiconductor and, consequently, increased photocurrent response for both cases. Random arrays tend to exhibit broad increases in photocurrent over wavelength, whereas periodic arrays demonstrate sharp resonance peaks in the photocurrent absorption spectrum. Such features are due to the coupling of normally incident light into waveguide modes that satisfy the Bragg diffraction condition. Analysis of the dispersion relation of the waveguide modes allows for accurate prediction of the resonance peaks in the photocurrent absorption spectrum of the SOI photodetectors patterned with periodic nanodot arrays.
Immunomodulation Effects of Mesenchymal Stromal Cells on Acute Graft-versus-Host Disease after Hematopoietic Stem Cell Transplantation (2014)

Refractory acute graft-versus-host disease (aGVHD) is a major cause of death after allogeneic hematopoietic stem cell transplantation. This study evaluated the immunomodulation effects of mesenchymal stromal cells (MSCs) from bone marrow of a third-party donor for refractory aGVHD. Forty-seven patients with refractory aGVHD were enrolled: 28 patients receiving MSC and 19 patients without MSC treatment. MSCs were given at a median dose of 1 × 10(6) cells/kg weekly until patients got complete response or received 8 doses of MSCs. After 125 doses of MSCs were administered, with a median of 4 doses (range, 2 to 8) per patient, overall response rate was 75% in the MSC group compared with 42.1% in the non-MSC group (P = .023). The incidence of cytomegalovirus, Epstein-Barr virus infections, and tumor relapse was not different between the 2 groups during aGVHD treatment and follow-up. The incidence and severity of chronic GVHD in the MSC group were lower than those in the non-MSC group (P = .045 and P = .005). The ratio of CD3(+)CD4(+)/CD3(+)CD8(+) T cells, the frequencies of CD4(+)CD25(+)Foxp3(+) regulatory T cells (Tregs), and the levels of signal joint T cell-receptor excision DNA circles (sjTRECs) after MSCs treatment were higher than those pretreatment. MSC-treated patients exhibited higher Tregs frequencies and sjTRECs levels than those in the non-MSC group at 8 and 12 weeks after treatment. MSCs derived from bone marrow of a third-party donor are effective to refractory aGVHD. It might reduce the incidence and severity of chronic GVHD in aGVHD patients by improving thymic function and induction of Tregs but not increase the risks of infections and tumor relapse.
Clinical status of agents being developed for leishmaniasis (2005)

Leishmaniasis, which exists in both visceral and cutaneous forms, is currently treated with intramuscular antimony or intravenous amphotericin B. The primary unmet need is for oral therapy. Of the several drugs in clinical development, miltefosine is unique in being an oral agent with efficacy against both forms of the disease. Sitamaquine is an oral agent with substantial but not sufficient efficacy against visceral disease. Oral fluconazole has been shown to be more effective than placebo in one instance: for Leishmania major cutaneous disease from Saudi Arabia. Paromomycin is in widespread trial. Topical paromomycin formulations are being tested for cutaneous disease, and intramuscular paromomycin is in Phase III trial for Indian visceral disease. The most likely replacements for present therapy are oral miltefosine for many of the visceral and cutaneous syndromes, intramuscular paromomycin for visceral disease and topical paromomycin for some forms of cutaneous disease.
Characterization of MHC class II-presented peptides generated from an antigen targeted to different endocytic compartments (2000)

We evaluated the capacity of the secretory pathway or of different endocytic compartments in B cell lines to generate MHC class II-presented peptides from the antigen ovalbumin (OVA). Sorting signals from the transferrin receptor (TFR), targeted a chimeric OVA fusion protein to early endosomes and led to the generation of 8 of 12 presented peptides. Sorting signals from the lysosome-associated membrane protein 1 (LAMP-1), targeted an OVA fusion protein to lysosomes, and led to the generation of 9 of 12 peptides. In contrast, OVA with only a signal sequence led to the generation of only 2 presented peptides. There were both qualitative and quantitative differences in the generation of peptides from the different fusion proteins, suggesting that multiple distinct compartments are involved in generating different epitopes. One peptide was presented better from the TFR fusion protein, while all others were presented better from the LAMP-1 construct. Twelve peptides were generated from exogenously supplied OVA, including 3 peptides that were not generated from any of the fusion proteins. Since most endogenously synthesized foreign antigens are rarely presented on class II molecules, these studies further suggest a strategy whereby antigens in DNA-based vaccines could be targeted to endocytic compartments to enhance immunogenicity.
Exercise Training and Peripheral Arterial Disease (2012)

Peripheral arterial disease (PAD) is a common vascular disease that reduces blood flow capacity to the legs of patients. PAD leads to exercise intolerance that can progress in severity to greatly limit mobility, and in advanced cases leads to frank ischemia with pain at rest. It is estimated that 12 to 15 million people in the United States are diagnosed with PAD, with a much larger population that is undiagnosed. The presence of PAD predicts a 50% to 1500% increase in morbidity and mortality, depending on severity. Treatment of patients with PAD is limited to modification of cardiovascular disease risk factors, pharmacological intervention, surgery, and exercise therapy. Extended exercise programs that involve walking approximately five times per week, at a significant intensity that requires frequent rest periods, are most significant. Preclinical studies and virtually all clinical trials demonstrate the benefits of exercise therapy, including improved walking tolerance, modified inflammatory/hemostatic markers, enhanced vasoresponsiveness, adaptations within the limb (angiogenesis, arteriogenesis, and mitochondrial synthesis) that enhance oxygen delivery and metabolic responses, potentially delayed progression of the disease, enhanced quality of life indices, and extended longevity. A synthesis is provided as to how these adaptations can develop in the context of our current state of knowledge and events known to be orchestrated by exercise. The benefits are so compelling that exercise prescription should be an essential option presented to patients with PAD in the absence of contraindications. Obviously, selecting for a lifestyle pattern that includes enhanced physical activity prior to the advance of PAD limitations is the most desirable and beneficial.
Unexpected Functions of FcεRI on Antigen-Presenting Cells (2001)

In contrast to mast cells and basophils, the high affinity IgE receptor (FcepsilonRI) on antigen-presenting cells (APC) shows structural and functional differences. It consists only of a minimal structure of one alpha- and two gamma-chains and enables APC to efficiently take up and present antigen in IgE-mediated delayed-type hypersensitivity reactions that are thought to play a pivotal role in atopic diseases. However, recent studies of FcepsilonRI signal transduction and function on APC suggest additional mechanisms by which FcepsilonRI engagement on APC could affect inflammatory reactions. FcepsilonRI ligation is able to induce major signaling events like protein tyrosine kinase activation including p72(syk) leading to PLC-gamma1 phosphorylation and consecutive calcium influx. Late signaling events like the activation of transcription factors such as NF-kappaB provide a link to the release of proinflammatory cytokines and chemokines, Th-polarizing factors such as IL-12 and the induction of antiapoptotic factors. FcepsilonRI-mediated IL-10 production in monocytes could also influence their differentiation. Since there are hints that in vivo a functional FcepsilonRI signaling pathway only exists in individuals from an atopic background, we suggest that these unexpected mechanisms may have an effect on inflammatory reactions in atopic diseases.
Molecular definition of human β<sub>2</sub>-glycoprotein (α<sub>2</sub>-GPI) by cDNA cloning and inter-species differences of β<sub>2</sub>-GPI in alternation of anticardiolipin binding (1991)

Human beta 2-glycoprotein I (beta 2-GPI) is involved in cardiolipin (CL) binding of anticardiolipin antibodies (aCL) in systemic lupus erythematosus (SLE). We examined the inter-species differences of beta 2-GPI in alternation of CL binding of aCL. beta 2-GPI preparations were obtained from human, bovine, and rat sera by sequential CL--polyacrylamide affinity, DEAE--cellulose, and anti-human IgG-conjugated Sepharose CL-4B column chromatography, and they had apparent molecular weights of 50, 53, and 55 kDa respectively. Human beta 2-GPI not only enhanced CL binding by aCL in SLE but also depressed it by those in syphilis. Either bovine and rat beta 2-GPI exerted no or quite small inhibition of the binding of syphilitic aCL compared with human beta 2-GPI whereas all three species of beta 2-GPI generated binding of aCL in SLE to a similar degree. Further, a complete cDNA clone, p beta 2-GPI, was isolated from a human hepatoma cell line, HepG2, and its nucleotide sequence was analyzed. The sequences of bovine and rat counterpart molecules (beta 2-GPI) are highly homologous to that of the deduced sequence, and their corresponding regions are 84.0 and 82.5% identical to the complete domain and to the amino acid sequence 53-326 of human beta 2-GPI respectively. One of major differences appears at position 154 in human beta 2-GPI, and might be associated with the inhibitory effect on the binding of syphilitic aCL. The sequencing analysis of these beta 2-GPI proteins might provide leads to functional sites of domains which would be associated with such serological phenomena.
Beet necrotic yellow vein virus 42 kDa triple gene block protein binds nucleic acid in vitro (1996)

The triple gene block (TGB) of beet necrotic yellow vein virus RNA 2 is required for cell-to-cell movement of the virus RNA. The protein P42 encoded by the 5'-proximal gene of the TGB has consensus sequence motifs characteristic of an ATP/GTP-dependent helicase. P42 was over-expressed in Escherichia coli and shown to bind both single- and double-stranded RNA and DNA by Northwestern blotting. Site-directed mutagenesis located the nucleic acid-binding domain to the N-terminal 24 amino acids of the protein and a point mutation or deletions in the region of P42 containing the helicase consensus sequences did not affect nucleic acid-binding activity of the immobilized protein. Electrophoretic mobility-shift assays revealed that P42 also binds nucleic acids in solution and that deletion of the N-terminal region inhibits this binding. Mutations in both the N-terminal nucleic acid-binding domain and the helicase domain blocked infection of leaves, indicating that both regions of P42 are important for its activity in vivo.
SUGGESTED METHOD FOR THE PREPARATION AND TESTING OF ASPHALT EMULSION TREATED MIXTURES USING MARSHALL EQUIPMENT (1977)

The study described deals with the establishment of a method for preparing and testing asphalt emulsion treated mixtures (AETM) using the Marshall equipment. One aggregate type (sand and gravel), and one asphalt emulsion type and grade were used in the study. The AETM were evaluated with emphasis on the coating, workability of the mix, ease of handling of the mix, curing rate and amount of moisture retained in the mixture before and after compaction. Based on these factors, a method for preparing the standard Marshall specimen was developed. Using the pre-determined method of preparing and testing the standard Marshall specimens, a laboratory investigation concerning the effect of asphalt emulsion content and initial added moisture content on the design parameters and properties of asphalt emulsion treated mixtures using Marshall equipment is presented.
A review of multisite pacing to achieve cardiac resynchronization therapy (2014)

Non-response to cardiac resynchronization therapy remains a significant problem in up to 30% of patients. Multisite stimulation has emerged as a way of potentially overcoming non-response. This may be achieved by the use of multiple leads placed within the coronary sinus and its tributaries (dual-vein pacing) or more recently by the use of multipolar (quadripolar) left ventricular pacing leads which can deliver pacing stimuli at multiple sites within the same vein. This review covers the role of multisite pacing including the interaction with the underlying pathophysiology, the current and planned studies, and the potential pitfalls of this technology.
An effective collaboration model between industry and university based on the theory of self organization (2015)

Purpose – This study aims to investigate the relationship between university and industry as two major infrastructures of national innovation system in all leading scientific and industrial settings. Design/methodology/approach – Large complex organizations with high technology that follow non-linear dynamic rules need to define concepts and adopt new approaches to achieve organizational efficiency and effectiveness. Among various models, a dynamic model of innovation was developed based on a joint investment between industry and university. Hence, the concepts of systems thinking and system dynamics were used. Findings – The results reveal three levels of industry and university communication from the lower levels to the higher levels. Originality/value – The value of this paper lies in adding two axes of “type of relationship” and “form of relationship” to the axis of “strength of relationship”, and a static three-dimensional space as a spatial capacity of the relationship between the industry and the university has been organized. Further, this is the first study that investigates the dynamic relationship between industry and university based on the self-organization theory and system thinking.
Systemic gene delivery to the central nervous system using Adeno-associated virus (2014)

Adeno-associated virus (AAV)-mediated gene delivery has emerged as an effective and safe tool for both preclinical and clinical studies of neurological disorders. The recent discovery that several serotypes are able to cross the blood-brain-barrier when administered systemically has been a real breakthrough in the field of neurodegenerative diseases. Widespread transgene expression after systemic injection could spark interest as a therapeutic approach. Such strategy will avoid invasive brain surgery and allow non-focal gene therapy promising for CNS diseases affecting large portion of the brain. Here, we will review the recent results achieved through different systemic routes of injection generated in the last decade using systemic AAV-mediated delivery and propose a brief assessment of their values. In particular, we emphasize how the methods used for virus engineering could improve brain transduction after peripheral delivery.
Deletion of Amino Acid Residues 18-75 Inactivates the Plasma Membrane Ca2+ Pump (1996)

A mutant of the plasma membrane Ca2+ pump hPMCA4b(d18-75)(ct120) containing a deletion of the N-terminal amino acid residues 18-75 and lacking the C-terminal 120 amino acid residues was expressed in COS-1 cells. The deletion in the N-terminal region did not significantly affect the level of expression of the Ca2+ pump. Tryptic digestion of the hPMCA4b(d18-75)(ct120) mutant resulted in the appearance of the same fragments obtained by proteolysis of the hPMCA4b(ct120) enzyme, suggesting that deletion of residues 18-75 neither impeded the insertion in the membrane nor extensively affected the folding of the mutant protein. The functional competence of the hPMCA4b(d18-75)(ct120) enzyme was examined by measuring the Ca2+ transport and the Ca2+ ATPase activity of COS-1 cell microsomes expressing the mutant protein. Both tests proved the mutant to be inactive. Under conditions in which hPMCA4b(ct120) becomes phosphorylated, hPMCA4b(d18-75)(ct120) was incapable of reacting with ATP and Ca2+ to form the phosphoenzyme. Taken together these results suggest that the segment of amino acids 18-75 is essential for the activity of the plasma membrane Ca2+ pump.
Recent Progress in Quantum-Dot Semiconductor Optical Amplifiers for Optical Signal Processing (2005)

This paper reviews recent developments in optical signal processing based on quantum-dot semiconductor optical amplifiers. With an ultrafast gain response unique to quantum dots, an optical regenerator having receiver-sensitivity improving capability of 4 dB at a BER of 10−9 and operating speed of > 40 Gb/s has been successfully realized with an SOA chip. This performance achieved together with simplicity of structure suggests a potential for low-cost realization of regenerative transmission systems.
Effects of alignment of graphene flakes on water permeability of graphene-epoxy composite film (2014)

In this study, the electric field-assisted alignment of graphene flakes in B-stage graphene-epoxy composite film was demonstrated. Compared with conventional electric field-induced alignment method which involves curing liquid phase polymer matrix, the electric field application on B-stage composite film with controlled viscosity can achieve graphene flake alignment without any curing reactions, thereby enabling further processes such as film application, assembly and curing. B-stage graphene-epoxy composite was prepared by solution-mixing method, and electric field was applied parallel to the film with various temperature and electric field strengths. Cross-sectional SEM images revealed that graphene flakes were horizontally aligned better as film viscosity decreased and electric field strength increased. However, curing reaction at high temperature should be considered because high temperature was needed to achieve low viscosity. The aligned graphene-epoxy composite film showed lower water vapor transmission rate (WVTR).
Substrate noise analysis and experimental verification for the efficient noise prediction of a digital PLL (2006)

Substrate noise is a major impediment to mixed-signal integration. This paper describes a CAD tool that can be used at any stage of the design cycle to estimate the substrate noise generated by large digital circuits. The results have been verified with substrate noise measurements on a 480 MHz digital PLL implemented in a 90 nm CMOS process on a high resistivity substrate.
The Evolutionary Ecology of Ethanol Production and Alcoholism (2004)

Understanding the evolutionary ecology of ethanol production may yield insights into why humans are prone to excessive consumption of ethanol. In particular, Dudley (2000) suggested that human ancestors developed a genetically based attraction to ethanol because they could use its odor plume to locate fruiting trees and because of health benefits from its consumption. If so, ethanol should be common in wild fruits and frugivores should prefer fruits with higher ethanol content. A literature review reveals that ethanol is indeed common in wild fruits but that it typically occurs in very low concentrations. Furthermore, frugivores strongly prefer ripe over rotting fruits, even though the latter may contain more ethanol. (Data on ethanol content of ripe and rotting wild fruit are lacking.) These results cast doubt on Dudley's hypothesis and raise the question of how humans became exposed to sufficiently high concentrations of ethanol to allow its excessive consumption. Because fermentation is an ancient and widespread practice, I suggest that humans "discovered" ethanol while using fermentation as a food preservation technique. They may have been predisposed to consume ethanol from previous and beneficial exposure to much lower doses or they may have become addicted to it at high concentrations because of fortuitous physiological responses.
Targeting cell surface β<sub>2</sub>‐microglobulin by pentameric IgM antibodies (2011)

Monoclonal antibodies (mAbs) specific for human β(2) -microglobulin (β(2) M) have been shown to induce tumour cell apoptosis in haematological and solid tumours via recruiting major histocompatibility complex (MHC) class I molecules into and excluding cytokine receptors from the lipid rafts. Based on these findings, we hypothesized that IgM anti-β(2) M mAbs might have stronger apoptotic effects because of their pentameric structure. Our results showed that, compared with IgG mAbs, IgM anti-β(2) M mAbs exhibited stronger tumouricidal activity in vitro against different tumour cells, including myeloma, mantle cell lymphoma, and prostate cancer, and in vivo in a human-like xenografted myeloma mouse model without damaging normal tissues. IgM mAb-induced apoptosis is dependent on the pentameric structure of the mAbs. Disrupting pentameric IgM into monomeric IgM significantly reduced their ability to induce cell apoptosis. Monomeric IgM mAbs were less efficient at recruiting MHC class I molecules into and exclusion of cytokine receptors from lipid rafts, and at activating the intrinsic apoptosis cascade. Thus, we developed and validated the efficacy of anti-β(2) M IgM mAbs that may be utilized in the clinical setting and showed that IgM anti-β(2) M mAbs may be more potent than IgG mAbs at inducing tumour apoptosis.
Investigation of phonon coherence and backscattering using silicon nanomeshes (2017)

Phonons can display both wave-like and particle-like behaviour during thermal transport. While thermal transport in silicon nanomeshes has been previously interpreted by phonon wave effects due to interference with periodic structures, as well as phonon particle effects including backscattering, the dominant mechanism responsible for thermal conductivity reductions below classical predictions still remains unclear. Here we isolate the wave-related coherence effects by comparing periodic and aperiodic nanomeshes, and quantify the backscattering effect by comparing variable-pitch nanomeshes. We measure identical (within 6% uncertainty) thermal conductivities for periodic and aperiodic nanomeshes of the same average pitch, and reduced thermal conductivities for nanomeshes with smaller pitches. Ray tracing simulations support the measurement results. We conclude phonon coherence is unimportant for thermal transport in silicon nanomeshes with periodicities of 100 nm and higher and temperatures above 14 K, and phonon backscattering, as manifested in the classical size effect, is responsible for the thermal conductivity reduction.
Oxygenation of hydrocarbons by cytochrome P-450 model compounds: modification of reactivity by axial ligands. (1983)

The rate of olefin oxygenation catalyzed by synthetic metalloporphyrins is examined, employing sodium hypochlorite as the oxygen atom source. The rate of epoxidation and the stability of the catalyst are shown to be dependent on the nature of the axial ligand employed. A rationale for this effect is presented and analogy is made to the role of the thiolate ligand in cytochrome P-450.