gebhart/patrepeval huggingface dataset:
[P‐209]: Beta‐secretases for production of beta‐amyloid in the major regulated secretory pathway are identified as cathepsins B and L: Implications for cysteine proteases as drug targets for AD (2005)

The extracellular accumulation of neurotoxic beta-amyloid (Abeta) peptides in brain plays an important role in the development of Alzheimer's disease. The production of Abeta peptides occurs by proteolytic processing of APP at beta- and gamma-secretase sites at the N- and C-termini of Abeta peptides, respectively. Inhibition of secretase proteases is a logical approach for drug inhibition of Abeta production for AD. In this study, the primary subcellular site of Abeta production was demonstrated to occur in the regulated secretory pathway of model neuronal chromaffin cells, compared to a minor portion produced by the constitutive secretory pathway. Chromaffin cells are an excellent neuronal model for brain neuroproteases of the regulated secretory pathway for peptide neurotransmitter production, and thus, provide an excellent model for discovery of brain proteases. Because it is known from studies of peptide neurotransmitter biosynthesis that different proteases are present in each of these two secretory pathways, we sought to identify the major Abeta-secretase in regulated secretory vesicles. Beta-secretase activity in such isolated secretory vesicles was subjected to extensive purification and identified by peptide sequencing. Results demonstrated two distinct proteolytic pathways consisting of (a) cathepsin B cleavage of the Abeta-secretase site, and (b) cathepsin L cleavage adjacent to the Abeta-secretase site at Lys-Met, followed by methionine aminopeptidase. Colocalization of cathepsins B and L with Abeta peptides in regulated secretory vesicles was illustrated by electron microscopy. Efficient cleavage of the wild-type Abeta-secretase site by cathepsins B and L was illustrated by kcat/Km kinetic constants of 31,700 and 8,620 M-1s-1, respectively, with little cleavage of the Swedish mutant Abeta-secretase site. Since the majority of Alzheimer's patients express wild-type APP, proteases with specificity for the normal Abeta-secretase site are relevant to the disease. In contrast, BACE 1 shows poor catalytic efficiency for the wild-type Abeta-secretase site. Significantly, the selective cathepsin B inhibitor CA074 blocked Abeta production in regulated secretory vesicles isolated from neuronal chromaffin cells. These findings implicate the cysteine proteases cathepsin B and cathepsin L in the regulated secretory pathway as important new therapeutic targets for protease inhibitor drugs to Abeta of Alzheimer's disease.
Comment on “Test of constancy of speed of light with rotating cryogenic optical resonators” (2005)

A recent experiment by Antonini et al. [Phys. Rev. A 71, 050101 (2005)] set new limits on Lorentz violating parameters in the framework of the photon sector of the standard model extension, ${\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{\ensuremath{\kappa}}}_{e\ensuremath{-}}^{ZZ}$, and the Robertson--Mansouri--Sexl framework, $\ensuremath{\beta}\ensuremath{-}\ensuremath{\delta}\ensuremath{-}1∕2$. The experiment had significant systematic effects caused by the rotation of the apparatus which was only partly analyzed and taken into account. We show that this is insufficient to put a bound on ${\stackrel{\ifmmode \tilde{}\else \~{}\fi{}}{\ensuremath{\kappa}}}_{e\ensuremath{-}}^{ZZ}$, and that the bound on $\ensuremath{\beta}\ensuremath{-}\ensuremath{\delta}\ensuremath{-}1∕2$ represents a fivefold, not tenfold, improvement as claimed.
Generating idempotent filters (1991)

Median based idempotent filter structures are introduced. Two approaches to generate these filters are studied: weighted median filters and median filter cascades. Two subclasses of n-dimensional idempotent weighted median filters, called Class 1 and Class 2 filters, are introduced. It is shown that both Class 1 and Class 2 filters suppress impulsive noise from n-dimensional input signals and yet have almost no effect on the noncorrupted parts of the signal. These filters are therefore well suited for preprocessing purposes. Likely applications of these filters are in speech processing, image processing, and image sequence processing, where the filter mask is typically three-dimensional. Sufficient conditions for a filter cascade to be idempotent are given. Two idempotent median filter cascades and their advantages are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Religion and family planning (2016)

Religion is embedded in the culture of all societies. It influences matters of morality, ideology and decision making, which concern every human being at some point in their life. Although the different religions often lack a united view on matters such contraception and abortion, there is sometimes some dogmatic overlap when general religious principles are subject to the influence of local customs. Immigration and population flow add further complexities to societal views on reproductive issues. For example, present day Europe has recently faced a dramatic increase in refugee influx, which raises questions about the health care of immigrants and the effects of cultural and religious differences on reproductive health. Religious beliefs on family planning in, for example, Christianity, Judaism, Islam and Hinduism have grown from different backgrounds and perspectives. Understanding these differences may result in more culturally competent delivery of care by health care providers. This paper presents the teachings of the most widespread religions in Europe with regard to contraception and reproduction.
Silica Nanoparticles with Continuously Tunable Sizes: Synthesis and Size Effects on Cellular Contrast Imaging (2008)

Controlling the size of silica nanoparticles (NPs) on a continuously variable scale was achieved by systematically varying the organic solvent(s) used in water-in-oil microemulsion synthesis. A number of individual as well as binary solvent mixtures were investigated for tuning silica NP size. The results demonstrated that the size of a silica NP was continuously tunable over as range of 20−100 nm by varying the alkane chain length of the organic solvent(s) being used. A simple physical model was proposed to describe the size effect and identify the principle factors needed for precisely controlling the size of a silica NP. In the model, the alkane chain length(s) of the organic solvent(s) primarily determined the average size of a silica NP when other synthetic conditions were fixed, whereas variance in size was affected by water droplet percolation with the precursor microemulsion. The significance and utility of these tunable silica NPs was evaluated for bioimaging applications. Specifically, dye-doped silica NPs of variable but precise size were used for in vitro contrast imaging of cells. The results demonstrated that precise control of silica NPs size can be used to reduce cytotoxicity, optimize luminescence signal intensity, and selectively discriminate between structures both inside and outside of cellular membranes.
Supplementary Figure 7 from Evidence for the Ubiquitin Protease UBP43 as an Antineoplastic Target (2023)

&lt;p&gt;PDF file, 88K, Model of UBP43 action in tumors and how inhibition of UBP43 activity represents a new therapeutic target.&lt;/p&gt;
Broad-range polymerase chain reaction for detection and identification of bacteria. (1994)

Detection and identification of fastidious pathogenic bacteria have traditionally presented an obstacle to the clinical and laboratory microbiologist. The diagnosis of disease caused by these bacteria is often empiric relying on clinical observations or indirect laboratory tests. Recently, a technique called broad-range polymerase chain reaction (PCR) has been integrated into studies designed to detect and identify previously uncharacterized bacterial pathogens. By using regions of the bacterial 16S ribosomal RNA (rRNA) gene that are highly conserved to prime synthesis of the remainder of this gene, PCR amplification can be performed directly from clinical samples which may contain small numbers of bacteria. The resulting PCR-amplified DNA can be sequenced to identify variable regions of the 16S rRNA gene that are bacteria-specific. This technique has proven valuable in identifying new fastidious bacterial pathogens that have resisted detection and identification by traditional microbiological methods.
ChemInform Abstract: C‐C BOND FORMATION BY RADICAL ADDITION TO ALKENES (1984)

Abstract Die aus Alkylquecksilberchloriden (I) und Natriumborhydrid generierten Radikale addieren an Alkylidenmalodinitrile (II) zu gesättigten Derivaten (III), die mit Schwefelsäure zu Alkansäuren (IV) verseift werden.
Sulbactam Combined With the Novel β-lactamase Inhibitor ETX2514 for the Treatment of Multidrug-Resistant Acinetobacter baumannii Infections (2016)

Background. Multidrug-resistant (MDR) Acinetobacter baumannii infections are of great concern due to high mortality rates and limited number of treatment options. -lactamase (BL) expression, especially class D, is an important resistance mechanism in this organism. The novel BL inhibitor ETX2514 has potent activity against class A, C, and D serine BLs. The MIC 90 of sulbactam (SUL) in the presence of ETX2514 is 4 mg/L against a large, globally diverse set of MDR A. baumannii clinical isolates from 2014. In this study, we investigate the mechanism of synergy of this combination alone or in the presence of imipenem (IPM) or meropenem (MEM), whose spectra of target inhibition vary across bacterial species Methods. MICs were performed according to CLSI guidelines. The frequency of resistance (FOR) to SUL/ETX2514 was determined in several clinical isolates of A. baumannii. Resistant mutants were analyzed by whole-genome sequencing. Morphological changes were examined by microscopy. PBP acylation rates were determined by competition with BOCILLIN FL in fluorescence polarization assays.
A new method of scenario analysis for strategic planning (1988)

Abstract We first present scenario analysis as a qualitative forecasting technique useful for strategic planning. Then we develop an overview of the two classes of methods for scenario analysis described in the literature. Based on both classes, a new method is developed which especially fits the needs of strategic planning. The method can be divided into three stages: 1. Determination of compatible scenarios, 2. Determination of scenario probabilities, and 3. Determination of main scenarios. An example is given to illustrate the method.
Autolysis of Calcium-Activated Neutral Protease of Chicken Skeletal Muscle1 (1981)

The conditions and process of autolysis of calcium-activated neutral protease (CANP) were examined. Optimal conditions for autolysis were the same as those required for expression of activity of CANP. The autolysis proceeded rapidly by a strictly limited proteolysis. During autolysis the molecular weight of CANP changed from 82 K (native CANP or mCANP) to 79 K and then 60 K. The 79 K and 60 K molecular species were both active at microM order of Ca2+ (muCANP), whereas the native CANP is active at mM order of Ca2+ (mCANP). Various proteases examined did not produce muCANP from mcanp under the conditions tested. Furthermore, muCANP did not yield muCANP from mCANP at lower Ca2+ concentrations where only muCANP was active. Therefore, muCANP is produced from mCANP only by the specific autolysis of mCANP.
Composite Gene Module Discovery using Non-negative Independent Component Analysis (2006)

Gene module discovery can provide comprehensive molecular portrait of biological regulation and functional genomics. We present a new analytic strategy - nonnegative independent component analysis to reveal some gene module composite. The results show that by grouping genes in the latent space, we can find statistically more significant enrichment of gene annotations within clusters. Further, this approach has been applied to a muscular dystrophy data set for gene module discovery
Inhibition of Energy Transfer between Conjugated Polymer Chains in Host/Guest Nanocomposites Generates White Photo- and Electroluminescence (2006)

The generation of white light requires the combination of two or more chromophores that emit simultaneously. The observed color of a mixture of light-emitting molecules, however, originates generally only from the lowest band-gap species because of efficient energy transfer between the chromophores which is difficult to avoid. Here we report on a nanocomposite material designed to yield pure and stable white photo- and electroluminescence. In this material, red, green, and blue emitting conjugated polymers are confined within the galleries of a layered semiconducting host matrix. The host hinders polymer pi-pi interactions which are responsible for the energy transfer between polymer chains, consequently, emission from the three chromophores is observed simultaneously resulting in white photoluminescence. The efficacy of the nanocomposites is demonstrated in simple single-layer white-emitting polymer diodes. The mechanism suggested here for white light generation, supported by extensive luminescence measurements, is in contrast to that previously reported in white-emitting polymer diodes where efficient energy transfer between polymer chains was essential for obtaining white light.
Nanostructured Organic Solar Cells: Toward High Efficiency, Large Scale and Versatility. (2012)

This dissertation is devoted to searching for solutions to realize low-cost, high efficiency and scalable organic solar cells (OSC), and their versatile application. For this purpose, my research has been focused on various nanostructures, which can be usable to maximize the performances of OSCs, and the effective fabrication processes to achieve those nanostructures. Furthermore novel device concepts based on those nanostructures have been introduced. First part of dissertation is about controlling the nanostructures in photoactive layers to develop more efficient OSC devices. A new process, named as ESSENCIAL, inducing superior bulk heterojunction (BHJ) morphology was developed. Compared with conventional annealing based-methods, the optimized BHJ morphology showing well-organized charge transporting pathways with high crystallinity was achieved. Moreover, by controlling the interface of the photoactive layer, further improvement of power conversion efficiency (PCE) was possible using BHJ structure. A new type of heterojunction nanostructure based on bilayer concept was also introduced. By maximizing interdiffusion of electron-donor and -acceptor, the optimized heterojunction morphology having internal quantum efficiency approaching about 100% was demonstrated. As another effort to realize the ideal interdigitated donor-acceptor structures, sub-20 nm scale nanopillars were prepared. Nanopillar and nanohole type nanoimprint lithography (NIL) molds were fabricated from a self-assembled block copolymer nanotemplate, and NIL-based nanopatterns are made in organic semiconductor. All these nanostructures could be realized by advanced processing that can be extended to high-speed manufacturing toward low-cost and high efficiency OSCs. Secondly, various nanostructures such as plasmonic nanostructures and light trapping structures were developed to enhance the absorption of light in OSC devices. NIL-based plasmonic nanostructures exhibit strong and tunable light extinction, and the enhanced electromagnetic field induces the increased photocurrent, leading to improved PCE. Moreover, by introducing periodic nanostructure at the metal electrode working as reflector in OSC, I could enhance the optical path length across a broad wavelength range of incident light. Lastly, the dual-function devices working as color filters and solar cells were demonstrated by applying photonic nanostructures to OSCs. This new conceptual device can recycle the wasted energy in color filter to generate the electricity for the revolutionary energy-saving e-media.
Contributions of distal and proximal promoter elements to glucocorticoid regulation of osteocalcin gene transcription. (1995)

Previous studies identified several glucocorticoid response elements (GREs) in the 5'-promoter region of the rat osteocalcin (OC) gene by purified receptor binding. The present study addresses functionality of the GRE sequences in the proximal promoter at nucleotide (nt) -16 to -1 downstream of the TATA element together with the GRE half-element in the OC box at nt -86 to -81. This was done by assaying glucocorticoid responsiveness [at 10(-6) M dexamethasone (DEX)], and in combination with 10(-8) M 1,25-dihydroxyvitamin D3, of a series of deleted and mutated OC promoter reporter constructs (OCCAT) in osteoblast-like cells, the ROS 17/2.8 rat osteosarcoma line. Promoter deletion analysis revealed an additional GRE in the distal promoter at nt -697 to -683 that functions to suppress OC transcription. In the absence of this upstream negative GRE (nGRE), the -531 OCCAT construct exhibited enhanced promoter activity in response to DEX (1.8-fold DEX/Control), but further deletion (-348 and -108 OCCAT constructs) restored DEX suppression to OC promoter activity (0.6- and 0.8-fold DEX/Control, respectively). Mutations introduced in both the proximal GRE (nt -16 to -1) and the half-GRE in the OC box, or in the proximal GRE alone, nearly abrogated DEX responsiveness of OC promoter activity. Both distal and proximal GREs specifically bound glucocorticoid receptor present in ROS 17/2.8 nuclear extracts as shown by competition with wild type and mutated oligonucleotides and antibody inhibition of binding. Furthermore, both GREs, independently, conferred DEX-responsive transcriptional repression to the heterologous thymidine kinase basal promoter. We also report that glucocorticoid suppression of 1,25-dihydroxyvitamin D3-stimulated transcription occurs independently of distal or proximal GREs. Taken together, these results demonstrate that in vivo responsiveness of OC to DEX involves the integrative activities of several functional promoter elements.
Electrochemical Studies on Reduction of Solid Nb[sub 2]O[sub 5] in Molten CaCl[sub 2]-NaCl Eutectic (2004)

Electrodeoxidation of solid to niobium was achieved by constant voltage electrolysis in molten eutectic at a controlled potential of 3.1 V. A number of important parameters affecting the extent and rate of electrodeoxidation have been investigated experimentally to better understand the electrodeoxidation process. The present results revealed that the structural features, which had been optimized by varying the pellet fabrication conditions, were closely interrelated and changed during the course of electrolysis under the experimental conditions used. It was found that the porous cathode with a large surface area would facilitate the cathodic oxygen ionization at the cathode/electrolyte interface and that the porosity must be large enough to enable the dissolved in the melt to diffuse readily out of the porous cathode. The optimal electrolysis duration and temperature were also determined experimentally. Furthermore, a conceptual model was proposed for explaining the electrodeoxidation mechanism. The model was based on two distinct processes occurring during the entire course of electrodeoxidation, (i) reduction of the oxide materials to Nb-O solid solutions and removal of the oxygen from the Nb-O solid solutions, which both relied on the oxygen ionization at the cathode. The proposed model was confirmed by the experimental results. © 2004 The Electrochemical Society. All rights reserved.
Tailoring Optical Properties of Luminescent Semiconducting Nanocrystals through Hydrostatic, Anisotropic Static, and Dynamic Pressures (2020)

Luminescent semiconductor nanocrystals are a fascinating class of materials because of their size-dependent emissions. Numerous past studies have demonstrated that semiconductor nanoparticles with radii smaller than their Bohr radius experience quantum confinement and thus size-dependent emissions. Exerting pressure on these nanoparticles represents an additional, more dynamic, strategy to alter their size and shift their emission. The application of pressure results in the lattices becoming strained and the electronic structure altered. In this Minireview, colloidal semiconductor nanocrystals are first introduced. The effects of uniform hydrostatic pressure on the optical properties of metal halide perovskite (ABX<sub>3</sub> ), II-VI, III-V, and IV-VI semiconductor nanocrystals are then examined. The optical properties of semiconductor nanocrystals under static and dynamic anisotropic pressure are then summarized. Finally, future research directions and applications utilizing the pressure-dependent optical properties of semiconductor nanocrystals are discussed.
Front Matter: Volume 10414 (2017)

This PDF file contains the front matter associated with SPIE Proceedings Volume 10414 including the Title Page, Copyright information, Table of Contents, Introduction, and Conference Committee listing.
High photoluminescence of shortwave infrared-emitting anisotropic surface charged gold nanoclusters (2019)

Incorporating anisotropic surface charges on atomically precise gold nanoclusters (Au NCs) led to a strong absorption in the near-infrared region and could enable the formation of self-assembled Au NCs exhibiting an intense absorption band at ∼1000 nm. This surface modification showed a striking enhancement of the photoluminescence in the Shortwave Infrared (SWIR) region with a quantum yield as high as 6.1% in water.
Variant calling for cpn60 barcode sequence-based microbiome profiling (2019)

Abstract Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution. Sequence data from the 5’ region of the cpn60 barcode amplified from the human vaginal microbiome (n=45), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database in terms of number of OTU formed, and overall community composition. Variant calling resulted in microbiome profiles that were consistent in apparent composition to those generated with the other methods but with significant logistical advantages. Variant calling is rapid, achieves high resolution of taxa, and does not require reference sequence data. Our results further demonstrate that 150 bp from the 5’ end of the cpn60 barcode sequence is sufficient to provide species-level resolution of microbiota.
Odor Quality: Semantically Generated Multidimensional Profiles Are Stable (1982)

Odors of ten compounds were characterized by approximately 150 subjects who used a list of 146 descriptors. Duplicate profiles correlated highly (P less than .001) and consistently higher than profiles of different odors. Profiles also agreed with those obtained previously. Thus, profiles based on combined responses of many subjects are stable constructs.