gebhart/patrepeval huggingface dataset:
Differential regulation of endogenous and transduced beta-globin genes during infection of erythroid cells with a herpes simplex virus type 1 recombinant (1990)

We infected murine erythroleukemia cells with a nondefective herpes simplex virus (HSV) type 1 recombinant bearing the rabbit beta-globin gene under the control of its own promoter, in order to compare the regulation of a cellular gene residing in the viral genome to that of its active endogenous counterpart. We found that the viral globin gene was activated by HSV immediate-early polypeptides, whereas expression of the endogenous beta-globin gene was strongly suppressed: transcription was greatly inhibited, and beta-globin mRNA was rapidly degraded. Degradation of globin mRNA was induced by a component of the infecting virion and required a functional UL41 gene product. These results demonstrate that HSV products can have opposing effects on the expression of homologous genes located in the cellular and viral genomes and suggest that the preferential expression of HSV genes that occurs during infection is not achieved solely through sequence-specific differentiation between viral and cellular promoters or mRNAs.
Ultrahigh-Q photonic crystal nanocavities fabricated by CMOS process technologies (2017)

We fabricated photonic crystal high-quality factor (Q) nanocavities on a 300-mm-wide silicon-on-insulator wafer by using argon fluoride immersion photolithography. The heterostructure nanocavities showed an average experimental Q value of 1.5 million for 12 measured samples. The highest Q value was 2.3 million, which represents a record for a nanocavity fabricated by complementary metal-oxide-semiconductor (CMOS)-compatible machinery. We also demonstrated an eight-channel drop filter with 4 nm spacing consisting of arrayed nanocavities with three missing air holes. The standard deviation in the drop wavelength was less than 1 nm. These results will accelerate ultrahigh-Q nanocavity research in various areas.
Plasmacytoid dendritic cells in the duodenum of individuals diagnosed with myalgic encephalomyelitis are uniquely immunoreactive to antibodies to human endogenous retroviral proteins. (2013)

Myalgic encephalomyelitis (ME) is a debilitating illness of unknown etiology characterized by neurocognitive dysfunction, inflammation, immune abnormalities and gastrointestinal distress. An increasing body of evidence suggests that disruptions in the gut may contribute to the induction of neuroinflammation. Therefore, reports of human endogenous retroviral (HERV) expression in association with neuroinflammatory diseases prompted us to investigate the gut of individuals with ME for the presence of HERV proteins. In eight out of 12 individuals with ME, immunoreactivity to HERV proteins was observed in duodenal biopsies. In contrast, no immunoreactivity was detected in any of the eight controls. Immunoreactivity to HERV Gag and Env proteins was uniquely co-localized in hematopoietic cells expressing the C-type lectin receptor CLEC4C (CD303/BDCA2), the co-stimulatory marker CD86 and the class II major histocompatibility complex HLA-DR, consistent with plasmacytoid dendritic cells (pDCs). Although the significance of HERVs present in the pDCs of individuals with ME has yet to be determined, these data raise the possibility of an involvment of pDCs and HERVs in ME pathology. To our knowledge, this report describes the first direct association between pDCs and HERVs in human disease.
The Galvanotactic Migration of Keratinocytes is Enhanced by Hypoxic Preconditioning (2015)

The endogenous electric field (EF)-directed migration of keratinocytes (galvanotaxis) into wounds is an essential step in wound re-epithelialization. Hypoxia, which occurs immediately after injury, acts as an early stimulus to initiate the healing process; however, the mechanisms for this effect, remain elusive. We show here that the galvanotactic migration of keratinocytes was enhanced by hypoxia preconditioning as a result of the increased directionality rather than the increased motility of keratinocytes. This enhancement was both oxygen tension- and preconditioning time-dependent, with the maximum effects achieved using 2% O2 preconditioning for 6 hours. Hypoxic preconditioning (2% O2, 6 hours) decreased the threshold voltage of galvanotaxis to < 25 mV/mm, whereas this value was between 25 and 50 mV/mm in the normal culture control. In a scratch-wound monolayer assay in which the applied EF was in the default healing direction, hypoxic preconditioning accelerated healing by 1.38-fold compared with the control conditions. Scavenging of the induced ROS by N-acetylcysteine (NAC) abolished the enhanced galvanotaxis and the accelerated healing by hypoxic preconditioning. Our data demonstrate a novel and unsuspected role of hypoxia in supporting keratinocyte galvanotaxis. Enhancing the galvanotactic response of cells might therefore be a clinically attractive approach to induce improved wound healing.
Principles of<scp>MEA</scp>preparation (2010)

Abstract A brief history of the evolution of the fuel cell electrode, emphasizing the technological developments that have lead to the contemporary polymer electrolyte membrane electrode assembly (MEA). This is followed by a discussion of the requirements, functions and properties of individual components and processes by which they are fabricated into MEAs. Lastly, basic in situ electrochemical techniques that may be applied as diagnostic tools to understand and advance the performance of MEA technology are reviewed.
A model for boron short time annealing after ion implantation (1993)

A simulation model is proposed for boron diffusion in silicon. It is especially useful for analyzing the short time annealing process subsequent to ion implantation. This model takes into account nonequilibrium diffusion and reactions of point defects and defect-dopant pairs, considering their charge states, and the dopant inactivation by the introduction of a boron clustering reaction. It is assumed that the boron-interstitial-silicon pair (BI) is a dominant diffusion species that contributes to the total boron diffusion. A primary model parameter, the binding energy of BI, is determined and used to reproduce the equilibrium gaseous source diffusion data. Using a single set of reasonable parameter values, the model covers not only the equilibrium diffusion conditions, from intrinsic, but also the nonequilibrium postimplantation diffusion. Experimental boro distribution profiles can be accurately reproduced. It is shown that the time constant for the BI dissociation reaction rules the transient behavior of boron diffusion enhancement during postimplantation annealing.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Comparing MR image intensity standardization against tissue characterizability of magnetization transfer ratio imaging (2006)

These results suggest that standardized T2, PD, and T1 images and their tissue-specific intensity signatures may be useful for characterizing disease.
Real-time hardware design for improving laser detection and ranging accuracy (2012)

Digital signal processing algorithms for estimating target range and backscatter intensity from laser detection and ranging systems are limited by the sampling rate of data collected and computation time requirements. An interpolating matched filter algorithm, deployed on a field programmable gate array, improves range accuracy while maintaining a low sampling rate and unity throughput. Research and simulation results comparing the effectiveness of different reference waveform models and interpolation factors are presented. A matched filter with zero padding interpolation using a Gaussian shape reference waveform and an interpolation factor of thirty-two showed an eighty-seven percent improvement in range accuracy over the peak detector design currently used in real-time LADAR systems.
Recursive systematic convolutional codes and application to parallel concatenation (2002)

This paper deals with a new class of convolutional codes called recursive systematic convolutional (RSC) codes. These codes are very attractive when compared with the best known convolutional codes at low signal to noise ratio (SNR) and high code rate. A comparison with the best known convolutional codes is performed in terms of weight spectrum and bit error rate (BER) on a memoryless Gaussian channel. A new design of parallel concatenation is proposed, well matched to RSC codes and much more attractive than serial concatenation for it needs only one clock timing recovery for the decoding.
Investigation of depth-resolved nanoscale structural changes in regulated cell proliferation and chromatin decondensation (2013)

We correct minor errors in two equations reported in our paper [Biomed. Opt. Express 4, 596-613 (2013)]; an additional factor of two was mistakenly incorporated in Eqs. (3) and (4). We give the correct equations below. All the simulations and experiments in the previous paper were performed using the correct equations, and therefore, remain the same.[This corrects the article on p. 596 in vol. 4, PMID: 23577294.].
Effizientes Testen heterogener Leitsystemkonfigurationen (2012)

Die Simulation als Mittel zum Testen der Leitsystem-Konfiguration hat sich uber die letzten Jahre etabliert. Aufgrund des hohen manuellen Aufwands fokussieren simulationsbasierte Testmethoden meist auf den funktionalen Bereich, wobei ausschlieslich die Steuerungslogik, nicht aber die Konfiguration der Subsysteme getestet wird. Der Beitrag stellt eine Methode vor, mit der die Vorteile simulationsbasierter Tests um die Moglichkeiten aktueller Hardware-Emulatoren erweitert werden. Hierzu wird ein Framework prasentiert, welches die fur einen Subsystemtest notwendigen Emulatoren integriert und automatisch konfiguriert.
Perfringolysin O: The Underrated Clostridium perfringens Toxin? (2015)

The anaerobic bacterium Clostridium perfringens expresses multiple toxins that promote disease development in both humans and animals. One such toxin is perfringolysin O (PFO, classically referred to as θ toxin), a pore-forming cholesterol-dependent cytolysin (CDC). PFO is secreted as a water-soluble monomer that recognizes and binds membranes via cholesterol. Membrane-bound monomers undergo structural changes that culminate in the formation of an oligomerized prepore complex on the membrane surface. The prepore then undergoes conversion into the bilayer-spanning pore measuring approximately 250–300 Å in diameter. PFO is expressed in nearly all identified C. perfringens strains and harbors interesting traits that suggest a potential undefined role for PFO in disease development. Research has demonstrated a role for PFO in gas gangrene progression and bovine necrohemorrhagic enteritis, but there is limited data available to determine if PFO also functions in additional disease presentations caused by C. perfringens. This review summarizes the known structural and functional characteristics of PFO, while highlighting recent insights into the potential contributions of PFO to disease pathogenesis.
A genetic programming approach to logic function synthesis by means of multiplexers (2003)

This paper presents an approach based on the use of genetic programming to synthesize logic functions. The proposed approach uses the 1-control line multiplexer as the only design unit, defining any logic function (defined by a truth table) through the replication of this single unit. Our fitness function first explores the search space trying to find a feasible design and then concentrates on the minimization of such (fully feasible) circuit. The proposed approach is illustrated using several sample Boolean functions.
A paradigm shift in patterning foundation from frequency multiplication to edge-placement accuracy: a novel processing solution by selective etching and alternating-material self-aligned multiple patterning (2016)

Overlay errors, cut/block and line/space critical-dimension (CD) variations are the major sources of the edge-placement errors (EPE) in the cut/block patterning processes of complementary lithography when IC technology is scaled down to sub-10nm half pitch (HP). In this paper, we propose and discuss a modular technology to reduce the EPE effect by combining selective etching and alternating-material (dual-material) self-aligned multiple patterning (altSAMP) processes. Preliminary results of altSAMP process development and material screening experiment are reported and possible material candidates are suggested. A geometrical cut-process yield model considering the joint effect of overlay errors, cut-hole and line CD variations is developed to analyze its patterning performance. In addition to the contributions from the above three process variations, the impacts of key control parameters (such as cut-hole overhang and etching selectivity) on the patterning yield are examined. It is shown that the optimized altSAMP patterning process significantly improves the patterning yield compared with conventional SAMP processes, especially when the half pitch of device patterns is driven down to 7 nm and below.
Activated carbon from sugar cane bagasse by carbonization in the presence of inorganic acids (1994)

Abstract Dried ground bagasse, impregnated with 50% inorganic acids and carbonized at 500°C, showed the sequence H 3 PO 4 > H 2 SO 4 > HCl > HNO 3 , with respect to the efficiency of activation. Treatment with phosphoric acid of various concentrations (30–50 wt%) was followed by carbonization at 300–500°C for 3 h. Pore structure parameters were determined from the low‐temperature adsorption of nitrogen, by applying the BET and α s methods. Activated carbons obtained at low temperatures are essentially microporous with a low degree of mesoporosity. At higher temperatures products of higher surface area and total pore volume with developed mesoporosity and low microporosity are formed. An increase in the period of carbonization leads to a small decrease in both surface area and pore volume. Activated carbons with surface areas > 1000 m 2 g −1 and mean pore dimensions around 2·0 nm, suitable for various purposes, are thus obtained.
Real-Time Digital Signal Processing: Implementations, Applications, and Experiments with the Tms320c55x (2001)

From the Publisher:
Real-time functionality is the latest challenge facing high performance digital signal processors and DSP applications. Its successful deployment requires a thorough understanding of DSP theory as well as mastery of skills in real-time DSP design and implementation techniques. With this in mind Real-time Digital Signal Processing offers readers a hands-on tutorial approach, using the latest Texas Instruments TM320C55x processor in illustrative experiments and field applications. 
Features include: 
* A wealth of lab-exercises and experiments using MATLAB, C and the TMS320C55x assembly language, covering everything from basic concepts to telecommunications applications. 

* A review of the fundamentals of real-time DSP theories in practice, plus programming examples using the Code Composer Studio development environment. 

* Guidance on the selection of DSP chips to suit a variety of applications along with a consideration of real-time constraints, hardware options and fixed and floating point devices. 

* Accompanying website providing software for use with the end-of-chapter experiments detailed throughout the book. This practical guide will prove a valuable tool for students of digital signal processing and a self-contained reference for practising engineers and systems programmers developing new DSP applications.
β‐secretase as a target for the treatment of Alzheimer's disease (2002)

Finding inhibitors of the first step of the amyloid cascade, A beta (42) generation, is a major goal of Alzheimer's disease drug development. Two target protease activities, beta-and gamma-secretase, were detected more than 10 years ago but progress in this area has been slow because the enzymes were not identified. Using an expression cloning strategy we have identified a novel membrane bound aspartic protease, BACE1, as beta-secretase. The enzyme has been characterized in detail. The X-ray crystal structure, which is critical for rational inhibitor design, has been solved and shown to be similar to that of other pepsin family members. Our recent knockout studies show that BACE1 is critical for A beta generation, but the knockout mice show an otherwise normal phenotype, raising the possibility that therapeutic BACE1 inhibition could be accomplished without major mechanism based toxicity. Target-mediated toxicity of beta-secretase inhibition cannot be ruled out, however, as long as the major substrates of this enzyme are unknown. Although various peptidic beta-secretase inhibitors have been published, the key challenge now is the generation of more drug-like compounds that could be developed for therapeutic purposes. The focus of this review is progress in the beta-secretase field from the identification of the enzyme in 1999 to the most recent publications.
The human volatilome: volatile organic compounds (VOCs) in exhaled breath, skin emanations, urine, feces and saliva (2014)

Breath analysis is a young field of research with its roots in antiquity. Antoine Lavoisier discovered carbon dioxide in exhaled breath during the period 1777-1783, Wilhelm (Vilém) Petters discovered acetone in breath in 1857 and Johannes Müller reported the first quantitative measurements of acetone in 1898. A recent review reported 1765 volatile compounds appearing in exhaled breath, skin emanations, urine, saliva, human breast milk, blood and feces. For a large number of compounds, real-time analysis of exhaled breath or skin emanations has been performed, e.g., during exertion of effort on a stationary bicycle or during sleep. Volatile compounds in exhaled breath, which record historical exposure, are called the 'exposome'. Changes in biogenic volatile organic compound concentrations can be used to mirror metabolic or (patho)physiological processes in the whole body or blood concentrations of drugs (e.g. propofol) in clinical settings-even during artificial ventilation or during surgery. Also compounds released by bacterial strains like Pseudomonas aeruginosa or Streptococcus pneumonia could be very interesting. Methyl methacrylate (CAS 80-62-6), for example, was observed in the headspace of Streptococcus pneumonia in concentrations up to 1420 ppb. Fecal volatiles have been implicated in differentiating certain infectious bowel diseases such as Clostridium difficile, Campylobacter, Salmonella and Cholera. They have also been used to differentiate other non-infectious conditions such as irritable bowel syndrome and inflammatory bowel disease. In addition, alterations in urine volatiles have been used to detect urinary tract infections, bladder, prostate and other cancers. Peroxidation of lipids and other biomolecules by reactive oxygen species produce volatile compounds like ethane and 1-pentane. Noninvasive detection and therapeutic monitoring of oxidative stress would be highly desirable in autoimmunological, neurological, inflammatory diseases and cancer, but also during surgery and in intensive care units. The investigation of cell cultures opens up new possibilities for elucidation of the biochemical background of volatile compounds. In future studies, combined investigations of a particular compound with regard to human matrices such as breath, urine, saliva and cell culture investigations will lead to novel scientific progress in the field.
Amination and Subsequent Derivatization of Epoxy-Activated (1980)

We have found a simple procedure to convert epoxy-activated agarose into amino derivatives using ammonia solution. The amino derivatives of agarose were succinylated with succinic anhydride and then activated with N-hydroxysuccinimide according to the method of Cuatrecasas and Parikh. Formula: (See Text). Coupling of the ligand to the activated agarose (shown above) was performed under mild conditions. The adsorbent thus obtained has no charged group in the linkage region between the ligand and agarose, thus reducing the nonspecific adsorption, and the bonds formed (ether and amide bonds) are stable even in an alkaline medium. Lens culinaris hemagglutinin-Sepharose 4B prepared by this method was successfully used for the affinity chromatography of solubilized human red blood cell membrane in detergent solution and was stable when elution was performed with borate buffer, pH 9.8.
Constitutive expression of hypoxia-inducible factor-1alpha renders pancreatic cancer cells resistant to apoptosis induced by hypoxia and nutrient deprivation. (2001)

Hypovasculature is an outstanding characteristic of pancreatic cancers in imaging diagnosis, suggesting that blood supply is poor in pancreatic cancer tissues. Despite poor blood supply, pancreatic cancer cells survive and proliferate in severe hypoxia and nutrient deprivation. To demonstrate how pancreatic cancer cells adapt themselves to hypoxia and nutrient deprivation, we investigated the expression of hypoxia-inducible factor 1alpha (HIF-1alpha) protein and HIF-1-inducible genes in human pancreatic cancer cell lines in comparison with other cancer cell lines. We found that HIF-1alpha protein was constitutively expressed in 15 of 20 pancreatic cancer cell lines (75%) but in none of other cancer cell lines tested in this study. The cells with constitutive expression of HIF-1alpha were more resistant to apoptosis induced by hypoxia and glucose deprivation than those without constitutive expression of HIF-1alpha. Transfection with HIF-1alpha transformed the latter cells resistant to apoptosis and increased in vivo tumorigenicity. Furthermore, anaerobic metabolism-associated genes, Glut1 and aldolase A, were more highly expressed in the cells with constitutive expression of HIF-1alpha than in the cells without it. These results suggest that constitutive expression of HIF-1alpha contributes to the survival and proliferation of pancreatic cancer cells in hypoxia and glucose deprivation through the activation of anaerobic metabolism.
Altered touch (2017)

In this paper, (1) we developed a fingertip haptic display with integrated force, tactile and thermal feedback in a miniature form-factor such that it can be worn easily and used with augmented reality applications without affecting the existing tracking technologies. (2) we propose the concept of "Altered Touch", where the integrated fingertip haptic display stated in (1) was used to alter the haptic properties of real objects by rendering projected visual and haptic feedback. The system consists of our own force display Gravity Grabber mechanism[Minamizawa et al. 2007] to render vertical, shearing forces, high frequency tactile vibrations, and a peltier module for thermal display. The integrated haptic display module weighs less than 50g, can be easily interfaced to a PC with just one micro USB cable, and works standalone from any other additional hardware. In this paper we use this wearable haptic actuator in several augmented reality applications to alter the softness/hardness and hot/cold sensation and several use cases have been discussed. Furthermore, the haptic display could be expanded to design a haptic glove that can interact with both virtual and augmented worlds.