gebhart/patrepeval huggingface dataset:
A Facile Method for the Construction of Oligonucleotide Microarrays (2008)

In recent years, the oligonucleotide-based microarray technique has emerged as a powerful and promising tool for various molecular biological studies. Here, a facile protocol for the construction of an oligonucleotide microarray is demonstrated that involves immobilization of oligonucleotide-trimethoxysilyl conjugates onto virgin glass microslides. The projected immobilization strategy reflects high immobilization efficiency ( approximately 36-40%) and signal-to-noise ratio ( approximately 98), and hybridization efficiency ( approximately 32-35%). Using the proposed protocol, aminoalkyl, mercaptoalkyl, and phosphorylated oligonucleotides were immobilized onto virgin glass microslides. Briefly, modified oligonucleotides were reacted first with 3-glycidyloxypropyltriethoxysilane (GOPTS), and subsequently, the resultant conjugates were directly immobilized onto the virgin glass surface by making use of silanization chemistry. The constructed microarrays were then used for discrimination of base mismatches. On subjecting to different pH and thermal conditions, the microarray showed sufficient stability. Application of this chemistry to manufacture oligonucleotide probe-based microarrays for detection of bacterial meningitis is demonstrated. Single-step reaction for the formation of conjugates with the commercially available reagent (GOPTS), omission of capping step and surface modification, and efficient immobilization of oligonucleotides onto the virgin glass surface are the key features of the proposed strategy.
GRAIL: a gene related to anergy in lymphocytes (2003)

Apoptosis is a principal mechanism in metazoans by which superfluous or potentially harmful cells are eliminated. Deregulation of this process leads to a variety of diseases such as cancer and autoimmune diseases. Stimuli that can induce apoptosis are relatively diverse, and include the death factors (Fas ligand, tumor necrosis factor and TRAIL), DNA damage, and oxidative stress. Regardless of the origin of the apoptotic stimulus, commitment to apoptosis leads to activation of caspases, a family of cysteine proteases. Cleavage of a select group of cellular substrates by caspases is responsible for the morphological and biochemical changes that characterize apoptotic cell death. The degradation of nuclear DNA into nucleosomal units is one of the features of apoptotic cell death, and is mediated by a caspase-activated DNase (CAD). Cells deficient in CAD undergo cell death without the DNA fragmentation, but CAD-null mice did not show any adverse phenotypes. A close examination of the apoptotic cells in these mice indicated that apoptotic cells are always in macrophages. It seems that at an early stage of apoptosis, the dying cells present an 'eat me signal' on their surface. This signal is recognized by macrophages for engulfment, and DNase II in the lysosomes of macrophages degrades DNA of apoptotic cells. Mice deficient in both CAD and DNase II genes were established, and the development of various organs was found to be severely impaired in these mutant mice. The mice accumulated a large amount of undigested DNA in macrophages in various tissues during development. This accumulation of DNA in macrophages activated the innate immunity to induce the expression of the interferon gene. The interferon thus produced seems to be responsible for the impaired tissue development. These results indicate that the degradation of DNA during apoptotic cell death is an essential step of apoptosis to maintain mammalian homeostasis.
High harmonic generation from ions in a capillary discharge (2006)

We demonstrate a significant extension of the high harmonic cutoff by generation in a pre-ionized plasma created with a capillary discharge. In xenon, the cutoff extends from ~ 95 to 140 eV.
Birefringence correction for single-mode fiber couplers (1982)

We apply a two-port, lumped-element birefringence model to single-mode fiber couplers. By application of twist and compression to output leads, the effects of circular and linear birefringence can be essentially eliminated. Resulting output polarization states are linear and unrotated for any linear inputs in both splitters and combiners. Compensation stability is investigated.
Application of a Reassortant Cucumber mosaic virus Vector for Gene Silencing in Tomato and Chili Pepper Plants (2012)

We developed a reassortant RNA virus vector derived from <TEX>$Cucumber$</TEX> <TEX>$mosaic$</TEX> <TEX>$virus$</TEX> (CMV), which has advantages of very wide host range and can efficiently induce gene silencing in a few model plants. Certain CMV isolates, however, show limited host ranges presumably because they naturally co-evolved with their own hosts. We used a reassortant comprised of two strains of CMV, Y-CMV and Gn-CMV, to broaden the host range and to develop a virus vector for virus-induced gene silencing (VIGS). Gn-CMV could infect chili pepper and tomato more efficiently than Y-CMV. Gn-CMV RNA1, 3 and Y-CMV RNA2-A1 vector were newly reconstructed, and the transcript mixture of RNA1 and 3 genomes of Gn-CMV and RNA2 genome of Y-CMV RNA2 containing portions of the endogenous phytoene desaturase (PDS) gene (CMV2A1::PDSs) was inoculated onto chili pepper (cv. Chung-yang), tomato (cvs. Bloody butcher, Tigerella, Silvery fir tree, and Czech bush) and <TEX>$Nicotiana$</TEX> <TEX>$benthamiana$</TEX>. All the tested plants infected by the reassortant CMV vector showed typical photo-bleaching phenotypes and reduced expression levels of <TEX>$PDS$</TEX> mRNA. These results suggest that the reassortant CMV vector would be a useful tool for the rapid induction of the RNA silencing of endogenous genes in chili pepper and tomato plants.
Bioabsorbable Material–Containing Phosphorylcholine Group-Rich Surfaces for Temporary Scaffolding of the Vessel Wall (2008)

Novel blends of poly(L-lactic acid) (PLLA) and a water-soluble amphiphilic poly(2-methacryloyloxyethyl phosphorylcholine-co-n-butyl methacrylate) (PMB30W) were prepared as materials for temporary scaffolding to provide mechanical support to the vessel wall until adequate vascular healing is achieved, after which the scaffold disappears. The PLLA/PMB30W cast films demonstrated higher breaking strengths than PLLA cast films, and their Young's modulus was similar to that of PLLA under dry conditions. A high density of phosphorylcholine head groups on the inner surface of PLLA/PMB30W tubing was developed by repeated coatings with the PLLA/PMB30W blend polymer solutions. The PLLA/PMB30W tubing showed stable degradation behaviors similar to those of the PLLA tubing. This is the first report that demonstrates cell membrane-like materials that can be used in temporary scaffolding of the vessel wall; these materials are characterized by strong mechanical properties and stable degradation behaviors that are superior or similar to those of high-molecular-weight PLLA.
Block-Diagonal MIMO Equalization for Polarization-Multiplexed OFDM Transmission With Direct Detection (2011)

We propose a novel digital signal processing (DSP)-based multiple-input-multiple-output (MIMO) equalization algorithm set for polarization-multiplexed orthogonal frequency-division multiplexing transmission with direct detection (POLMUX-OFDM-DD), based on block-diagonal matrix processing. The new methodology significantly reduces legacy zero forcing (ZF)-based equalization complexity, and enables performance gains via efficient minimum mean square error (MMSE) and maximum likelihood (ML) detection. The new block-diagonal MMSE and ML algorithms are experimentally shown to extend transmission distance from 870 to 900 km and beyond 960 km, respectively, in 20-Gb/s standard single-mode fiber (SSMF) POLMUX OFDM quadrature-phase-shift-keying (QPSK)-DD transmission. The new algorithms are highly attractive for future cost-efficient, DSP-based optical metro/access systems.
5.3: Discharge Observation of Plasma Tubes (2003)

Abstract The plasma tube array display presents the wall size display with very high luminous efficacy. Discharging in plasma tube was observed to estimate the structure for high luminous efficacy. From the results of the observation, it is estimated that not only the discharge gap but also the discharge cavity effects to the luminous efficacy. With this result new structure was tries and 3.7 lm/W was achieved as the luminous efficacy.
Correction of Gradient Nonlinearity Bias in Quantitative Diffusion Parameters of Renal Tissue with Intravoxel Incoherent Motion (2015)

Spatially non-uniform diffusion weighting bias due to gradient nonlinearity (GNL) causes substantial errors in apparent diffusion coefficient (ADC) maps for anatomical regions imaged distant from magnet isocenter. Our previously-described approach allowed effective removal of spatial ADC bias from three orthogonal DWI measurements for mono-exponential media of arbitrary anisotropy. The present work evaluates correction feasibility and performance for quantitative diffusion parameters of the two-component IVIM model for well-perfused and nearly isotropic renal tissue. Sagittal kidney DWI scans of a volunteer were performed on a clinical 3T MRI scanner near isocenter and offset superiorly. Spatially non-uniform diffusion weighting due to GNL resulted both in shift and broadening of perfusion-suppressed ADC histograms for off-center DWI relative to unbiased measurements close to isocenter. Direction-average DW-bias correctors were computed based on the known gradient design provided by vendor. The computed bias maps were empirically confirmed by coronal DWI measurements for an isotropic gel-flood phantom. Both phantom and renal tissue ADC bias for off-center measurements was effectively removed by applying pre-computed 3D correction maps. Comparable ADC accuracy was achieved for corrections of both <i>b</i>-maps and DWI intensities in presence of IVIM perfusion. No significant bias impact was observed for IVIM perfusion fraction.
A 2D nearest-neighbor quantum architecture for factoring in polylogarithmic depth (2013)

We present a 2D nearest-neighbor quantum architecture for Shor's algorithm to factor an $n$-bit number in $O(\log^3n)$ depth. Our implementation uses parallel phase estimation, constant-depth fanout and teleportation, and constant-depth carry-save modular addition. We derive upper bounds on the circuit resources of our architecture under a new 2D model which allows a classical controller and parallel, communicating modules. We provide a comparison to all previous nearest-neighbor factoring implementations. Our circuit results in an exponential improvement in nearest-neighbor circuit depth at the cost of a polynomial increase in circuit size and width.
Lignosulfonate-mediated cellulase adsorption: enhanced enzymatic saccharification of lignocellulose through weakening nonproductive binding to lignin (2013)

The results reported in this study also suggest significant advantages of SPORL pretreatment in terms of water consumption and process integration, that is, it should abolish the steps of solid substrate washing and pretreatment hydrolysate detoxification for direct simultaneous saccharification and combined fermentation (SSCombF) of enzymatic and pretreatment hydrolysate, thereby facilitating bioprocess consolidation. Furthermore, this study not only has practical significance to biorefinery and bioenergy, but it also provides scientific importance to the molecular design of composite enzyme-polyelectrolyte systems, such as immobilized enzymes and enzyme activators, as well as to the design of enzyme separation processes using water-soluble polyelectrolytes.
The Presence of Two Cyclase Thioesterases Expands the Conformational Freedom of the Cyclic Peptide Occidiofungin (2013)

Occidiofungin is a cyclic nonribosomally synthesized antifungal peptide with submicromolar activity produced by the Gram-negative bacterium Burkholderia contaminans. The biosynthetic gene cluster was confirmed to contain two cyclase thioesterases. NMR analysis revealed that the presence of both thioesterases is used to increase the conformational repertoire of the cyclic peptide. The loss of the OcfN cyclic thioesterase by mutagenesis results in a reduction of conformational variants and an appreciable decrease in bioactivity against Candida species. Presumably, the presence of both asparagine and β-hydroxyasparagine variants coordinates the enzymatic function of both of the cyclase thioesterases. OcfN has presumably evolved to be part of the biosynthetic gene cluster due to its ability to produce structural variants that enhance antifungal activity against some fungi. The enhancement of the antifungal activity from the incorporation of an additional cyclase thioesterase into the biosynthetic gene cluster of occidiofungin supports the need to explore new conformational variants of other therapeutic or potentially therapeutic cyclic peptides.
A Practical, Protecting-Group-Free Synthesis of a PI3K/mTOR Inhibitor (2015)

We report a practical and protecting-group-free synthesis amenable to produce multikilogram amounts of PI3K/mTOR inhibitor GDC-0980. The route employed metalation/formylation and reductive amination followed by a metal catalyzed Suzuki–Miyaura cross-coupling. The metalation was performed via triarylmagnesiate intermediates allowing formylation under noncryogenic conditions. 2-Picoline·BH3 was employed to replace Na(OAc)3BH in the reductive amination and to eliminate the use of molecular sieves. A concise one-step synthesis was developed for the selective monoamidation of piperazine with (S)-lactate to produce the piperazine lactamide starting material. The boronic acid was produced from 2-amino-5-bromopyrimidine in a one-step and protecting-group-free approach. The final crystallization in 1-propanol and water afforded the API in 59% overall yield in four steps and >99% purity by HPLC.
An All-In-One Convolutional Neural Network for Face Analysis (2017)

We present a multi-purpose algorithm for simultaneous face detection, face alignment, pose estimation, gender recognition, smile detection, age estimation and face recognition using a single deep convolutional neural network (CNN). Theproposed method employs a multi-task learning framework that regularizes the shared parameters of CNN and builds a synergy among different domains and tasks. Extensive experiments show that the network has a better understanding of face and achieves state-of-the-art result for most of these tasks.
Method for determining the molten pool configuration in melting of metals (1990)

The invention provides a method of quantitatively determining the molten pool configuration in melting of metals. The method includes the steps of introducing hafnium metal seeds into a molten metal pool at intervals to form ingots, neutron activating the ingots and determining the hafnium location by radiometric means. Another object is to provide a method that yields information on the fundamental processes occurring during melting of metals, such as titanium and zirconium which has bearing on attempts to eliminate nitride inclusions, which weaken high-technology rotating parts, such as turbine blades and disks. A further object of the invention is the provision of a method that generates useful quantitative data on mass transfer within a molten pool of metal.
Reconfigurable neuromorphic crossbars based on titanium oxide memristors (2016)

Memristor crossbars are capable of implementing learning algorithms in a much more energy‐ and area‐efficient manner compared with traditional systems. However, the programmable nature of memristor crossbars must first be explored on a smaller scale to see if physical devices are suitable for applications of reconfigurable computing. The reconfigurability of these devices through small scale memristor crossbar implementations is demonstrated. It is shown that a crossbar containing eight memristors is capable of learning several different two‐input Boolean logic functions. A strong foundation is provided to build on demonstrating that physical memristor crossbars can be programmed as linear classifiers.
Methylation microarray analysis of late-stage ovarian carcinomas distinguishes progression-free survival in patients and identifies candidate epigenetic markers. (2002)

The data suggest that a higher degree of CpG island methylation is associated with early disease recurrence after chemotherapy. The differential methylation hybridization assay also identified a select group of CpG island loci that are potentially useful as epigenetic markers for predicting treatment outcome in ovarian cancer patients.
An effective scheduling method to single-arm cluster tools for processing multiple wafer types (2022)

Recently, in semiconductor manufacturing, cluster tools have to process multiple wafer types concurrently due to product customization. Different wafer types may have different processing routes, which causes deadlocks and complicates the scheduling problem of cluster tools. This work aims to develop a general method to resolve the scheduling problem of single-arm cluster tools with a general mix of wafer types. To this end, a generic Petri net model controlled by self-loops is developed to optimally avoid deadlocks. Based on the Petri net model, an earliest starting strategy is adopted to operate single-arm cluster tools once wafers enter the tools. In order to maximize the productivity, a particle swarm optimization algorithm is constructed to determine the releasing sequence of raw wafers. Numerical examples are provided to validate the effectiveness and efficiency of the proposed method.
Multi–Detector Row CT Systems and Image-Reconstruction Techniques (2005)

The introduction in 1998 of multi-detector row computed tomography (CT) by the major CT vendors was a milestone with regard to increased scan speed, improved z-axis spatial resolution, and better utilization of the available x-ray power. In this review, the general technical principles of multi-detector row CT are reviewed as they apply to the established four- and eight-section systems, the most recent 16-section scanners, and future generations of multi-detector row CT systems. Clinical examples are used to demonstrate both the potential and the limitations of the different scanner types. When necessary, standard single-section CT is referred to as a common basis and starting point for further developments. Another focus is the increasingly important topic of patient radiation exposure, successful dose management, and strategies for dose reduction. Finally, the evolutionary steps from traditional single-section spiral image-reconstruction algorithms to the most recent approaches toward multisection spiral reconstruction are traced.
Image-space automatic motion correction for MRI images (2004)

Automatic retrospective motion correction algorithms based on iterative optimization of an image quality measure have been demonstrated in a variety of MRI acquisitions. These algorithms are computationally intensive and may require several minutes per image or more. One computational bottleneck is the need for an inverse FFT at each iteration to reconstruct and evaluate the image. We describe a method for performing the iterative search primarily in image space, greatly reducing the number of FFTs required. This can significantly increase the computational speed, particularly when the evaluation is performed only on a sub-region of the image.
Abstract 1055: Genome-wide DNA methylation analysis in precancerous conditions associated with hepatitis B virus and hepatitis C virus infection (2015)

Abstract The aim of this study is to reveal the significance of DNA methylation alterations in precancerous conditions associated with hepatitis virus infection. Genome-wide DNA methylation analysis using Infinium HumanMethylation450 BeadChip (Illumina) has been performed in 36 specimens of normal liver tissue obtained from patients without hepatocellular carcinomas (HCCs), 12 and 24 specimens of noncancerous liver tissues obtained from hepatitis B virus (HBV) infection-positive and hepatitis C virus (HCV) infection-positive patients with HCCs, respectively, and 24 samples of HCC themselves. On 21,106 CpG sites, alterations of DNA methylation levels were already evident in tissue specimens showing chronic hepatitis and liver cirrhosis, which are considered to be precancerous conditions, compared to normal liver tissues, and were inherited by HCC themselves. Unsupervised hierarchical clustering analysis based on DNA methylation levels at the 21,106CpG sites appropriately classified tissue specimens into normal, precancerous and cancerous clusters, indicating that DNA methylation alterations may participate continuously in hepatocarcinogenesis from the precancerous stage until cancers have become established. The incidence of DNA methylation alterations was higher at the precancerous stage of HCV-positive patients than that of HBV-positive patients. The incidence of DNA methylation alterations that actually occurred at the chronic hepatitis and liver cirrhosis stages but were restored in HCC themselves, which may be associated with inflammation or fibrosis, but may not participate in carcinogenesis itself, was at the almost equal levels regardless of probe annotations or hepatitis viruses. Many Infinium probes showing DNA methylation alterations participating continuously in multistage hepatocarcinogenesis were shared between HBV-positive and HCV-positive patients: only a small number of probes showed HBV-positive patient-specific DNA methylation alterations. On the other hand, DNA hypermethylation on regions around the transcription start sites was especially frequent during carcinogenesis in HCV-positive patients. We now intend to make the carcinogenetic risk estimation based on DNA methylation profiles at the precancerous stage clinically practical using liver biopsy specimens obtained prior to interferon therapy from patients who are followed up because of chronic liver diseases. Citation Format: Eri Arai, Ying Tian, Masahiro Gotoh, Yoriko Takahashi, Hidenori Ojima, Tomoo Kosuge, Yae Kanai. Genome-wide DNA methylation analysis in precancerous conditions associated with hepatitis B virus and hepatitis C virus infection. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1055. doi:10.1158/1538-7445.AM2015-1055
Carbonate melt-based flue gas desulphurisation: material balance and economic advantage (2018)

We have recently proposed a two-stage process for scrubbing sulphur from flue gas of coal-fired power plants: 1) the gas is brought into contact with a (Na, K, Li)-carbonate eutectic melt, producing sulphates; 2) the eutectic is regenerated by purging with CO from coal combustion, and recycled. Only the coal requires continual replenishing. In the current work, a combined scrubbing/regeneration flow diagram is presented and the material balance calculated. The economic advantages of the dual process are evaluated, taking into consideration high value end-products and the effect of sulphur content on the quantity of additional coal required for CO production. [Received: March 24, 2017; Accepted: July 17, 2017]