gebhart/patrepeval huggingface dataset:
Pigment Epithelium-Derived Factor Supports Normal Development of Photoreceptor Neurons and Opsin Expression after Retinal Pigment Epithelium Removal (2000)

Dysfunction of the retinal pigment epithelium (RPE), its loss, or separation from the underlying neural retina results in severe photoreceptor degeneration. Pigment epithelium-derived factor (PEDF) is a glycoprotein with reported neuroprotective and differentiation properties that is secreted in abundance by RPE cells. The "pooling" of PEDF within the interphotoreceptor matrix places this molecule in a prime physical location to affect the underlying neural retina. The purpose of this study was to analyze the morphogenetic activity of PEDF in a model of photoreceptor dysmorphogenesis induced by removal of the RPE. Eyes were dissected from embryonic Xenopus laevis, and the RPE was removed before culturing in medium containing PEDF, PEDF plus anti-PEDF antibodies, or medium alone. Control retinas were maintained with an adherent RPE. Light and electron microscopic analysis was used to examine retinal ultrastructure. Opsin was localized immunocytochemically and quantified as an index of outer segment membranous material and photoreceptor protein expression. Removal of the RPE resulted in an aberrant assembly of photoreceptor outer segments, loss of fine subcellular ultrastructure in photoreceptors, and a reduction in opsin protein levels when compared with control retinas. The addition of PEDF prevented the dysmorphic photoreceptor changes induced by RPE removal. In particular, photoreceptor ultrastructure, outer segment membrane assembly, and steady-state levels of opsin were equivalent to control conditions. Anti-PEDF antibodies completely blocked the morphogenetic activity of PEDF. These results indicate that PEDF is able to mimic the supportive role of the RPE on photoreceptors during the final stages of retinal morphogenesis.
Advanced modulation strategy for a three-phase AC-DC dual active bridge for V2G (2011)

The introduction of Plug-in Hybrid Electric Vehicles (PHEV) and Electric Vehicles (EV) into the consumer market provides opportunities and challenges to implement Vehicle-2-Grid (V2G). V2G is a vehicle that can connect to the grid and consume power to charge its battery pack or supply power to the grid. This paper presents research on a novel converter that implements bidirectional power flow between the grid and a vehicles battery pack. The main advantages of this converter are the following: i) soft switching for all switches of the input converter independent of the load, Zero Current Switching (ZCS) ii) The switching of the input converter is simplified i.e four-step commutation is not required for the four quadrant switches of the input side converter iii) The average power flow through the converter is a linear function of the control variable so the control is simple iv) open loop input power factor correction, v) high power density, vi) isolation. The entire topology has been simulated with the proposed modulation method and simulation results confirm the analytical predictions.
Introduction to Metrology Applications in IC Manufacturing (2015)

Metrology has grown significantly, especially in semiconductor manufacturing, and such growth necessitates increased expertise. Until now, this field has never had book written from the perspective of an engineer in a modern IC manufacturing and development environment. The topics in this Tutorial Text range from metrology at its most basic level to future predictions and challenges, including measurement methods, industrial applications, fundamentals of traditional measurement system characterization and calibration, measurement system characterization and calibration, semiconductor-specific applications, optical metrology measurement techniques, charged particle measurement techniques, x-ray and in situ metrology, hybrid metrology, and mask making. Includes example spreadsheets of measurement uncertainty analysis--specifically, precision, matching, and relative accuracy
Novel Si structures for photonic applications (1998)

Although silicon is the paramount material for the microelectronic industry, bulk Si is of little use for photonic devices owing to its indirect band-gap, which prevents the all-important direct optical transitions. However, a new type of luminescent Si has opened up its future for photonic applications. This new material is light-emitting SiO<SUB>2</SUB>/Si superlattices, fabricated in our laboratory. Our theoretical calculations showed that the energy band within the silicon layer has direct bandgap character, a result of strong quantum-confinement caused by the large band-offset at the SiO<SUB>2</SUB>/Si interface, so that the direct optical transition is not only possible but also vigorous. For a quantum-confined amorphous silicon, the breakdown of angular momentum will naturally make all optical transition possible. Our experiments have shown that SiO<SUB>2</SUB>/Si superlattices can indeed emit bright light. Moreover, the band-gap or the wavelength can be tuned over the visible range by changing the Si layer thickness, in good agreement with quantum confinement theory. The luminescence intensity as a function of Si layer thickness is found to increase, reach a maximum, and then decrease. Theoretical studies show that this phenomena is caused by competition between an increased overlap of electron-hole wave functions in the normal direction to the quantum well and an increased exciton radius in the plane of the quantum well.
Impflücken und Impfnebenwirkungen – eine aktuelle Übersicht (2019)

The success of vaccination programs is jeopardized by gaps in vaccine coverage of the target population. These are frequently due to a lack of awareness, but also result from misconceptions of adverse effects of vaccines. Subject of this article are the current vaccination rates of children, adolescents and adults as well as of medical personnel in Germany, the reporting and surveillance system for adverse effects of vaccines, the magnitude of registered permanent vaccine-induced damages and the possible immunological mechanisms underlying vaccine-triggered autoimmune diseases.
Reinventing High Performance Computing: Challenges and Opportunities (2022)

The world of computing is in rapid transition, now dominated by a world of smartphones and cloud services, with profound implications for the future of advanced scientific computing. Simply put, high-performance computing (HPC) is at an important inflection point. For the last 60 years, the world's fastest supercomputers were almost exclusively produced in the United States on behalf of scientific research in the national laboratories. Change is now in the wind. While costs now stretch the limits of U.S. government funding for advanced computing, Japan and China are now leaders in the bespoke HPC systems funded by government mandates. Meanwhile, the global semiconductor shortage and political battles surrounding fabrication facilities affect everyone. However, another, perhaps even deeper, fundamental change has occurred. The major cloud vendors have invested in global networks of massive scale systems that dwarf today's HPC systems. Driven by the computing demands of AI, these cloud systems are increasingly built using custom semiconductors, reducing the financial leverage of traditional computing vendors. These cloud systems are now breaking barriers in game playing and computer vision, reshaping how we think about the nature of scientific computation. Building the next generation of leading edge HPC systems will require rethinking many fundamentals and historical approaches by embracing end-to-end co-design; custom hardware configurations and packaging; large-scale prototyping, as was common thirty years ago; and collaborative partnerships with the dominant computing ecosystem companies, smartphone, and cloud computing vendors.
Ion-implanted WN 0.25 μm gate MESFET fabricated using i-line photolithography for application to MMIC and digital IC (2002)

Straightforward WN 0.25 /spl mu/m gate MESFET process based on direct ion-implantation and i-line photolithography with double exposure process has produced high performance MESFETs. The maximum transconductance of 600 mS/mm and the k-factor of 450 ms/Vmm were obtained. As high as 65 GHz of cut-off frequency has been realized without any deembedding of parasitic effects. The MESFET shows the minimum noise figure of 0.87 dB and the associated gain of 9.97 dB at 12 GHz.
Flywheel peak power buffer for electric/hybrid vehicles (2003)

Kinetic energy storage systems have considerable potential for use as peak power buffers in drive-trains for electric and hybrid vehicles, as a means of enhancing their performance and improving efficiency. The paper describes a flywheel system based around a cylindrical fibre composite rim, which is supported on magnetic bearings and incorporates an integral motor/generator. Particular consideration is given to minimising power losses, by appropriate choice of magnetic circuit design and magnetic materials, so as to obtain a high 'round-trip' efficiency and limit the temperature rise of the rim.
Overlapping Community Detection Algorithm Based on Coarsening and Local Overlapping Modularity (2019)

Community detection is an important research direction in the field of complex network analysis. It aims to discover community structures in complex networks. Algorithms based on dynamic distance mechanism can find stable communities with various shapes. However, they still cannot discover overlapping or outlier communities. This paper proposes an overlapping community discovery algorithm based on coarsening and local overlapping modularity. First, to reduce the running time, a new equation for computing the local overlapping modularity increment is derived. This equation finds the overlapping communities, accurately and quickly. Second, a new similarity measuring strategy is designed to reduce the number of outlier communities. The experiments on artificial and real datasets show that the proposed algorithm can discover the overlapping communities, accurately and efficiently.
Hydrogen Peroxide-Mediated Killing of Caenorhabditis elegans : a Common Feature of Different Streptococcal Species (2004)

Recently, we reported that Streptococcus pyogenes kills Caenorhabditis elegans by the use of hydrogen peroxide (H2O2). Here we show that diverse streptococcal species cause death of C. elegans larvae in proportion to the level of H2O2 produced. H2O2 may mask the effects of other pathogenicity factors of catalase-negative bacteria in the C. elegans infection model.
Global Regulatory DNA Potentiation by SMARCA4 Propagates to Selective Gene Expression Programs via Domain-Level Remodeling (2020)

The human genome encodes millions of regulatory elements, of which only a small fraction are active within a given cell type. Little is known about the global impact of chromatin remodelers on regulatory DNA landscapes and how this translates to gene expression. We use precision genome engineering to reawaken homozygously inactivated SMARCA4, a central ATPase of the human SWI/SNF chromatin remodeling complex, in lung adenocarcinoma cells. Here, we combine DNase I hypersensitivity, histone modification, and transcriptional profiling to show that SMARCA4 dramatically increases both the number and magnitude of accessible chromatin sites genome-wide, chiefly by unmasking sites of low regulatory factor occupancy. By contrast, transcriptional changes are concentrated within well-demarcated remodeling domains wherein expression of specific genes is gated by both distal element activation and promoter chromatin configuration. Our results provide a perspective on how global chromatin remodeling activity is translated to gene expression via regulatory DNA.
Successful Growth of Conductive Highly Crystalline Sn-Doped α-Ga2O3 Thin Films by Fine-Channel Mist Chemical Vapor Deposition (2012)

Highly crystalline α-phase gallium oxide (Ga 2 O 3 ) thin films were grown by fine-channel mist chemical vapor deposition on c -sapphire substrates at 400 °C at a deposition rate of more than 20 nm/min. The thin films were doped with Sn(IV) atoms, which were obtained from Sn(II) chloride by the reaction SnCl 2 + H 2 O 2 + 2HCl→SnCl 4 + 2H 2 O. Conductive α-phase Ga 2 O 3 thin films were successfully grown from source solutions containing less than 10 at. % Sn(IV). The source solution containing 4 at. % Sn(IV) resulted in obtaining a thin film with an n-type conductivity as high as 0.28 S cm -1 , a mobility of 0.23 cm 2 V -1 s -1 , a carrier concentration of 7×10 18 cm -3 , and a full width at half maximum (FWHM) of the (0006) reflection X-ray rocking curve as low as 64 arcsec.
Bacterial Production of Tetrodotoxin and Anhydrotetrodotoxin (1986)

Journal Article Bacterial Production of Tetrodotoxin and Anhydrotetrodotoxin Get access Takeshi Yasumoto, Takeshi Yasumoto Department of Food Chemistry, Tohoku University, Tsutsumidori Sendai 980, Japan Search for other works by this author on: Oxford Academic Google Scholar Daisuke Yasumura, Daisuke Yasumura Department of Food Chemistry, Tohoku University, Tsutsumidori Sendai 980, Japan Search for other works by this author on: Oxford Academic Google Scholar Mari Yotsu, Mari Yotsu Department of Food Chemistry, Tohoku University, Tsutsumidori Sendai 980, Japan Search for other works by this author on: Oxford Academic Google Scholar Tooru Michishita, Tooru Michishita Department of Food Chemistry, Tohoku University, Tsutsumidori Sendai 980, Japan Search for other works by this author on: Oxford Academic Google Scholar Amane Endo, Amane Endo Department of Food Chemistry, Tohoku University, Tsutsumidori Sendai 980, Japan Search for other works by this author on: Oxford Academic Google Scholar Yuichi Kotaki Yuichi Kotaki Shokei Junior Women's College, Hachiman, Sendai 980, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 50, Issue 3, 1 March 1986, Pages 793–795, https://doi.org/10.1080/00021369.1986.10867470 Published: 01 March 1986 Article history Received: 09 August 1985 Published: 01 March 1986
Role of 14-3-3-Mediated p38 Mitogen-Activated Protein Kinase Inhibition in Cardiac Myocyte Survival (2003)

14-3-3 family members are dimeric phosphoserine-binding proteins that regulate signal transduction, apoptotic, and checkpoint control pathways. Targeted expression of dominant-negative 14-3-3eta (DN-14-3-3) to murine postnatal cardiac tissue potentiates Ask1, c-jun N-terminal kinase (JNK), and p38 mitogen-activated protein kinase (MAPK) activation. DN-14-3-3 mice are unable to compensate for pressure overload, which results in increased mortality, dilated cardiomyopathy, and cardiac myocyte apoptosis. To evaluate the relative role of p38 MAPK activity in the DN-14-3-3 phenotype, we inhibited cardiac p38 MAPK activity by pharmacological and genetic methods. Intraperitoneal injection of SB202190, an inhibitor of p38alpha and p38beta MAPK activity, markedly increased the ability of DN-14-3-3 mice to compensate for pressure overload, with decreased mortality. DN-14-3-3 mice were bred with transgenic mice in which dominant-negative p38alpha (DN-p38alpha) or dominant-negative p38beta (DN-p38beta) MAPK expression was targeted to the heart. Compound transgenic DN-14-3-3/DN-p38beta mice, and to a lesser extent compound transgenic DN-14-3-3/DN-p38alpha mice, exhibited reduced mortality and cardiac myocyte apoptosis in response to pressure overload, demonstrating that DN-14-3-3 promotes cardiac apoptosis due to stimulation of p38 MAPK activity.
Orientation of the cytoplasmically made subunits of beef heart cytochrome c oxidase determined by protease digestion and antibody binding experiments (1988)

The topology of several of the cytoplasmically made subunits of beef heart cytochrome c oxidase has been determined by protease digestion of oriented membrane preparations, using subunit-specific antibodies to identify cleavage products. Reconstituted vesicles of cytochrome c oxidase and asolectin were used as a vesicle preparation with the C domain of the enzyme available for protease digestion. Submitochondrial particles were used as vesicles with the M domain outermost. Trypsin and/or proteinase K cleaved polypeptides CIV, ASA, AED, STA, and IHQ. Cleavage of CIV, STA, and IHQ was from the M domains only and involved the removal of a fragment from the N-terminus in each case. Polypeptide AED was cleaved from the C side in the N-terminal part, while ASA was cleaved from both the C and M domains. Polypeptide fragments were electroblotted from polyacrylamide gels onto derivatized glass paper and sites of proteolytic cleavage determined by N-terminal sequence analysis.
Acetylcholinesterase Clustering at the Neuromuscular Junction Involves Perlecan and Dystroglycan (2020)

Formation of the synaptic basal lamina at vertebrate neuromuscular junction involves the accumulation of numerous specialized extracellular matrix molecules including a specific form of acetylcholinesterase (AChE), the collagenic-tailed form. The mechanisms responsible for its localization at sites of nerve– muscle contact are not well understood. To understand synaptic AChE localization, we synthesized a fluorescent conjugate of fasciculin 2, a snake α-neurotoxin that tightly binds to the catalytic subunit. Prelabeling AChE on the surface of Xenopus muscle cells revealed that preexisting AChE molecules could be recruited to form clusters that colocalize with acetylcholine receptors at sites of nerve–muscle contact. Likewise, purified avian AChE with collagen-like tail, when transplanted to Xenopus muscle cells before the addition of nerves, also accumulated at sites of nerve–muscle contact. Using exogenous avian AChE as a marker, we show that the collagenic-tailed form of the enzyme binds to the heparan-sulfate proteoglycan perlecan, which in turn binds to the dystroglycan complex through α-dystroglycan. Therefore, the dystroglycan–perlecan complex serves as a cell surface acceptor for AChE, enabling it to be clustered at the synapse by lateral migration within the plane of the membrane. A similar mechanism may underlie the initial formation of all specialized basal lamina interposed between other cell types.
Small RNAs: Regulators and guardians of the genome (2007)

Small non-coding RNAs comprise several classes and sizes, but all share a unifying function in cellular physiology: epigenetic regulation of gene expression. Here, we review the salient aspects of recent studies on the biogenesis and function of three classes of small RNAs: miRNAs, siRNAs, and piRNAs. Although the mechanisms are becoming clear by which siRNA-triggered mRNA cleavage silences genes, more studies are needed on several issues regarding miRNA-mediated translation repression. Piwi proteins have been suggested to co-operate in amplifying piRNA biogenesis to maintain transposon silencing in the germ line genome, but details of this process are still unknown as well as the functional consequences of piRNA expression at discrete genomic loci.
Partial characterization and comparison of cell wall proteinases from 5 strains of Streptococcus lactis (1987)

Cell wall proteinases from 5 strains of Streptococcus lactis including one S. lactis subsp. diacetylactis were compared and partially characterized. They shared sorne common enzymatic features: only one activity optimum at 30-40C, at pH 5.5-6 on casein and 4-4.5 on haemoglobin. Crude cell wall extracts from the S. lactis strains were fully inhibited by DFP, but this inhibition was only partial for the S. lactis subsp. diacetylactis strain. Electrophoregrams of as!, {3 and K-casein hydrolysates obtained with the cell-wall extracts of these strains were quite similar for each protein substrate. {3-caseinwas preferentially broken down; as! and K-caseins were hydrolysed to a lesser extent.
A Multi-Scale Model of the Whole Human Body based on Dynamic Parsimonious Flux Balance Analysis (2016)

The multi-scale modelling approach is a powerful mathematical technique for simulating and analyzing complex biological systems such as the human body. This tool can help study the interactions of the various networks in a living organism, from the cellular level up to the population scale, in one framework. In this paper, a generic mathematical model is developed that describes human metabolism with 237 serum metabolites integrated with a chosen set of human metabolic networks. A new computational approach is presented for solving the resulting dynamic problem using parsimonious flux balance analysis (pFBA). To illustrate the performance of the proposed approach, the human hepatocyte genome scale model is selected for the metabolic network to be included. The simulation results show that the proposed approach has promise with respect to both computational efficiency and convergence. To demonstrate the potential application of the developed model, prediction of amino acid biomarkers for a set of inborn errors of metabolism (IEM) is considered as an example. All the simulations are performed using MATLAB and the COBRA toolbox. This framework has the potential to simulate various human metabolic disorders to help with the diagnosis of associated human diseases and to suggest novel treatment strategies. In addition, it opens the door to new opportunities for personalized medicine.
Identifying Disruptive Innovation: Innovation Theory and the Defense Industry (2009)

Clayton Christensen developed a powerful framework for evaluating innovations and choosing business strategies to respond to technological change. 1 He divides innovations into two categories, "disruptive" and "sustaining," based mainly on whether or not the new product's performance is measured by new metrics.Sustaining innovations improve performance along an established trajectory that is familiar to traditional customers.Disruptive innovations, on the other hand, offer a different kind of performance that does not help traditional customers with their normal business practices.Christensen argues that incumbent firms will sensibly cater to their established customers, because they understand the established market well and work hard to preserve good customer relationships.As a result, incumbents will tend to focus on sustaining innovations and will neglect disruptive ones.However, this tendency will leave them vulnerable to new entrants that lack established customer ties and are therefore willing to pursue disruptive innovations, initially by selling to fringe customers.Christensen describes cases in a wide range of industries in which competition from new firms selling disruptive innovations led to the collapse of well-known, well-managed incumbent firms.In this article, we improve on Christensen's theory in a way that makes it more analytically useful-making the theory more predictive than descriptive.Christensen actually defines disruptive innovations as those in which incumbent firms lose out in the post-innovation competition, conflating cause and effect.That choice helps make his case histories engaging and easy to read.But it also makes his theory hard to test and hard to apply ex ante rather than ex post, because it requires analysts to know the outcome of the post-innovation competition before they can assign the value of the independent variable-that is, before they can decide whether the innovation in question is disruptive or sustaining.Christensen also introduces auxiliary assumptions about the nature of competition in the product market that complicate the story.In this article, we remedy those problems, classifying innovations explicitly in terms of a single dimension