gebhart/patrepeval huggingface dataset:
Requirement of Cysteine Residues in Exons 16 of the Extracellular Domain of the Luteinizing Hormone Receptor for Gonadotropin Binding (1996)

The functional importance of cysteine residues in the extracellular domain and the extracellular loops (EL1 and EL2) to hormone binding of the rat luteinizing hormone receptor (LHR) was investigated. For this purpose, cysteines in the seven-transmembrane holoreceptor (Form A) and its hormone-binding splice variant (Form B) were replaced by serine residues, and mutant receptors were expressed in COS1 and/or insect cells. Within the extracellular domain, individual replacement of all four cysteines from Exon 1 abolished hormone binding activity, and replacement of Cys-109 and Cys-134 from exons 5 and 6 caused a 75% decrease in both cell surface and total cellular solubilized LHR hormone binding activity. Mutations of Cys-257 and -258 (Exon 9), Cys-321 and -331, and Cys-417 and -492 of EL1 and EL2, respectively (Exon 11), showed no surface hormone binding activity on intact cells, but exhibited wild type levels of total hormone binding activity when recovered from detergent-solubilized cellular extracts. This finding indicated that expression of high affinity LHR binding activity at the cell surface is independent of the acquisition of the high affinity binding conformation. Other cysteine residues, including Cys-282 (exon 10), and Cys-314 (exon 11) were not essential for hormone binding activity or plasma membrane insertion. This study demonstrates that the functional hormone binding domain utilizes all cysteines N-terminal to exon 7 and localizes the binding site to this N-terminal region of the extracellular domain.
A time-multiplexed switched-capacitor circuit for neural network applications (2003)

A time-multiplexed switched-capacitor computational block with some neural network characteristics is under development. The goal of this work is not to model biological neuron qualities exactly but rather to emulate their primary characteristics to the extent necessary to solve some types of problems not suited to digital processing. The circuit operation and limitations on its performance are described. The circuit is intended to serve as a coprocessor to a digital microprocessor. Circuit functionality has been demonstrated with breadboarded circuit, and the circuit is currently being integrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Asexual Stage and Fruit Formation of Cordyceps staphylinidaecola (2003)

Beauveria속균은 2000년 9월 1일부터 2002년 8월 31일까지 총 151개 표본이 채집되었고 분리된 균주는 25개다. 분리된 균주는 대부분 Beauveria bassiana에 속하는 것으로 나타내었다. 춘천시 삼악산에서 채집한 유충노랑곰보 동충하초의 특성은 기주를 균사에 의하여 쌓여있으며 자좌는 기주로부터 하나 내지 4개가 나오며 분생포자도 같이 형성되었다. 밝은 노란색의 자좌는 45 mm 이고 머리는 <TEX>$17mm{\times}4mm$</TEX> 이고 자루 28mm 이지만 경계는 뚜렷하지 않았다. 자낭각은 머리에 조밀하게 분포되어 있고 묻힌형이고 크기는 <TEX>$530{\sim}550{\times}290{\sim}300{\mu}m$</TEX>이었고 자낭은 <TEX>$400{\sim}450{\times}4{\sim}5{\mu}m$</TEX>이었다. 자낭포자는 실 모양이고 2차 포자로 분열한 후 바로 둥근 2차 포자를 형성하였다. Cordyceps staphyl- indaecola의 불완전 세대는 형태적인 특징인 분생자경은 rachis로 분생포자세포는 정단으로 생장하였으며 작은 목에서부터 원형의 분생포자를 형성하였다. 크기는 <TEX>$2.6{\sim}3.4{\times}1.2{\sim}1.9{\mu}m$</TEX>로 Beauveria bassiana로 동정하였다. 균사생육에 가장 적합한 배지는 HM이었고 기본 액체배지로는 HM, MCM 배지에서 우수한 건조 균체량을 나타내었다. 11일간 배양하여 <TEX>$25^{\circ}C$</TEX>에서 가장 우수한 생장과 밀도를 나타냈으며 <TEX>$pH6.5{\sim}pH8.5$</TEX>까지 배지에서 균사생장이 양호하였다. 현미와 번데기 배지에서 균사가 배지의 표면을 채우는 데 일주일이 걸리며 15일이나 18일이 되면 밝은 균사집합체에서 분생자병속이 형성되기 시작하였고 40일 후에는 분생자병속에 분생포자가 형성되기도 하나 간혹 자낭각이 형성되는 자좌도 있었다. 배양에서 형성된 자실체와 자연에서 채집한 자실체는 형태적으로 비슷하나 인공적으로 머리부분에서 자낭각이 형성하게 하는 것은 매우 어려운 것으로 나타났다. One hundred fifty one specimens of Beauveria spp. from 19 different locations were collected from September 1 to August 31, 2002. Most of the isolates were identified as Beauveria. bassiana. Cordyceps staphylinidaecola collected from Mt. Obong in Chunchon City covered the host with mycelia which were produced 1 to 4 stromata along with asexual spores. The size of bright yellow ununiform stromata were about 45 mm and the head about <TEX>$17mm{\times}4mm$</TEX>. Perithecia completely immersed were <TEX>$530{\sim}550{\times}290{\sim}300{\mu}m$</TEX> in size and mainly scattered on the head. Ascospore produced in asci in the size of <TEX>$400{\sim}450{\times}4{\sim}5{\mu}m$</TEX> developed thread-like secondary spores, which were directly separated into secondary conidial spores. Conidia produced at apical portion of synnemata were <TEX>$2.6{\sim}3.4{\times}1.2{\sim}1.9{\mu}m$</TEX> in size. High density of mycelium was observed at <TEX>$25^{\circ}C$</TEX> ranged from pH 6.5 to 8.5 after 11 days of inoculation. It took 15 to 18 days after inoculation to fully grow on the medium mixed brown rice with pupa. Mycelium developed stromata on the medium 30 days after completion of mycelial growth, where perithecia were produced in 40 days.
Locked nucleic acid containing antisense oligonucleotides enhance inhibition of HIV‐1 genome dimerization and inhibit virus replication (2004)

We have evaluated antisense design and efficacy of locked nucleic acid (LNA) and DNA oligonucleotide (ON) mix-mers targeting the conserved HIV-1 dimerization initiation site (DIS). LNA is a high affinity nucleotide analog, nuclease resistant and elicits minimal toxicity. We show that inclusion of LNA bases in antisense ONs augments the interference of HIV-1 genome dimerization. We also demonstrate the concomitant RNase H activation by six consecutive DNA bases in an LNA/DNA mix-mer. We show ON uptake via receptor-mediated transfection of a human T-cell line in which the mix-mers subsequently inhibit replication of a clinical HIV-1 isolate. Thus, the technique of LNA/DNA mix-mer antisense ONs targeting the conserved HIV-1 DIS region may provide a strategy to prevent HIV-1 assembly in the clinic.
Fasudil attenuates lipopolysaccharide-induced acute lung injury in mice through the Rho/Rho kinase pathway. (2010)

The Rho/Rho kinase pathway may play an important role in the pathogenesis of LPS-induced ALI and fasudil, as a ROCK inhibitor, could decrease neutrophil transendothelial migration by attenuating cytoskeletal rearrangement of endothelial cells, leading to the inhibition of ALI development.
Introduction (2002)

The opening ceremonies of the 2002 Winter Olympics in Salt Lake City featured, among the nods to Utah Native Americans and culturally diverse musicians, a U.S. flag disinterred from the carnage of the World Trade Center. The cause of some initial discomfort to officials of the International Olympic Committee, the wounded flag did make it to the February 8 event, carried into the stadium before a hushed crowd of 55,000. Too fragile to fly, this new symbol of global unity bore the hurt of all civilized nations. Yielded from the ground of ontological innocence, a space of victims and heroes, the flag arose phoenixlike from the ashes. Such are the conditions under which the catastrophe -encoded most simply as 911has continued to circulate. The Olympic episode would stand as a banner for international cooperation, even as one nation exercised a supreme unilateralism that was reconciled with calls for infinite retribution. From Ground Zero, a new era dawned as the flag moved from the fallen global pinnacle to the world's level playing field. Henceforth, it was presumed, everything would be different. Whatever was building before that dayespecially doubt at the fairness at the world's field -would have to be forgotten. For those of a critical disposition, the urgency would seem to be to remind the public of those other times, of those prior issues that remain.
Effect of ketoconazole and amphotericin B on encapsulated and non-encapsulated strains of Cryptococcus neoformans (1983)

Growth inhibition studies were done on an encapsulated and non-encapsulated strain of Cryptococcus neoformans at the minimal inhibitory concentration and one-half the minimal inhibitory concentration of ketoconazole and amphotericin B alone and in combination. Growth of both strains was significantly inhibited by ketoconazole, amphotericin B, and the combined drugs at the minimal inhibitory concentration of each drug over a 5-day period. Calculation of the expected inhibition of growth for both strains with both drugs showed antagonism at 24 h followed by an additive effect and synergy for the remaining 4 days of the assay. Although similar results were obtained for both strains with one-half the minimal inhibitory concentration, an additive effect was observed with the drug combination at 24 h for the encapsulated strain, and an antagonistic effect was observed with the non-encapsulated strain.
Technical Note—Cost Formulas for Continuous Review Inventory Models with Fixed Delivery Lags (1983)

In continuous review models with a fixed delivery lag T, the state of the system is conveniently described by the net inventory position = (inventory on hand) plus (outstanding orders), in spite of most cost components depending on the actual inventory on hand. To relate these two inventory concepts one observes that the distribution of the inventory on hand at time t + T is determined by the inventory position at time t. This explains the standard convention of charging the expected costs incurred in [S n + T, S n+1 + T) to the decision made at time S n , where S n denotes the nth decision epoch. This paper derives simple expressions for the expected costs in [S n + T, S n+1 + T) as a function of the inventory position just after decision epoch S n .
Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes (2017)

Assembly of 30S ribosomes involves the hierarchical addition of ribosomal proteins that progressively stabilize the folded 16S rRNA. Here, we use three-color single molecule FRET to show how combinations of ribosomal proteins uS4, uS17 and bS20 in the 16S 5' domain enable the recruitment of protein bS16, the next protein to join the complex. Analysis of real-time bS16 binding events shows that bS16 binds both native and non-native forms of the rRNA. The native rRNA conformation is increasingly favored after bS16 binds, explaining how bS16 drives later steps of 30S assembly. Chemical footprinting and molecular dynamics simulations show that each ribosomal protein switches the 16S conformation and dampens fluctuations at the interface between rRNA subdomains where bS16 binds. The results suggest that specific protein-induced changes in the rRNA dynamics underlie the hierarchy of 30S assembly and simplify the search for the native ribosome structure.Ribosomes assemble through the hierarchical addition of proteins to a ribosomal RNA scaffold. Here the authors use three-color single-molecule FRET to show how the dynamics of the rRNA dictate the order in which multiple proteins assemble on the 5' domain of the E. coli 16S rRNA.
Microemulsion 에 의한 초미립 SiO2 의 제조 (1994)

The ultrafine particles of relatively pure SiO₂ were prepared by means of a water/isooctane/ AOT microemulsion system. The reactant added to the microemulsion system was tetraethoxysilane and the aqueous solution of ammonia was also added to adjust the PH of the micoremulsion system. The SiO₂ particles precipitated in a microemulsion reactor was dried and then calcined properly in order to obtain ultrafine SiO₂ powders. The condition of drying and calcination process was found to influece the purity of final product. The SiO₂ powders prepared in this way(especially water-in-oil microemulsion) had substantially increased number of micropores in them compared to the powders prepared by other methods. The combination of materials forming the microemulsion system was also found to influence the size and porosity of SiO₂ powders as well as the stability of microemulsion systems.
Is glycine a surrogate for a <scp>d</scp>‐amino acid in the collagen triple helix? (2006)

Collagen is the most abundant protein in animals. Every third residue in a collagen strand is a glycine with phi, psi = -70 degrees, 175 degrees. A recent computational study suggested that replacing these glycine residues with D-alanine or D-serine would stabilize the collagen triple helix. This hypothesis is of substantial importance, as the glycine residues in collagen constitute nearly 10% of the amino acid residues in humans. To test this hypothesis, we synthesized a series of collagen mimic peptides that contain one or more D-alanine or D-serine residues replacing the canonical glycine residues. Circular dichroism spectroscopy and thermal denaturation experiments indicated clearly that the substitution of glycine with D-alanine or D-serine greatly disfavors the formation of a triple helix. Host-guest studies also revealed that replacing a single glycine residue with D-alanine is more destabilizing than is its replacement with L-alanine, a substitution that results from a common mutation in patients with collagen-related diseases. These data indicate that the glycine residues in collagen are not a surrogate for a D-amino acid and support the notion that the main-chain torsion angles of a glycine residue in the native structure (especially, phi > 0 degrees ) are critical determinants for its beneficial substitution with a D-amino acid in a protein.
Identification of Small Aliphatic Aldehydes in Pretreated Lignocellulosic Feedstocks and Evaluation of Their Inhibitory Effects on Yeast (2015)

Six lignocellulosic hydrolysates produced through acid pretreatment were analyzed for the occurrence of formaldehyde, acetaldehyde, and glycolaldehyde. Acetaldehyde was found in all six (0.3-1.6 mM) and formaldehyde in four (≤ 4.4 mM), whereas glycolaldehyde was not detected. To assess the relevance of these findings, fermentations with yeast and formaldehyde or acetaldehyde were performed in the concentration interval 0.5-10 mM. Formaldehyde already inhibited at 1.0 mM, whereas 5.0 mM acetaldehyde was needed to obtain a clear inhibitory effect. After 24 h of fermentation, 1.5 mM formaldehyde reduced the glucose consumption by 85%, the balanced ethanol yield by 92%, and the volumetric productivity by 91%. The results show that formaldehyde and acetaldehyde are prevalent in pretreated lignocellulose and that formaldehyde in some cases could explain a large part of the inhibitory effects on yeast by lignocellulosic hydrolysates, as three of six hydrolysates contained ≥ 1.9 mM formaldehyde, which was shown to be strongly inhibitory.
A Comparison of Image Segmentation Algorithms (2018)

Unsupervised image segmentation algorithms have matured to the point where they generate reasonable segmentations, and thus can begin to be incorporated into larger systems. A system designer now has an array of available algorithm choices, however, few objective numerical evaluations exist of these segmentation algorithms. As a first step towards filling this gap, this paper presents an evaluation of two popular segmentation algorithms, the mean shift-based segmentation algorithm and a graph-based segmentation scheme. We also consider a hybrid method which combines the other two methods. This quantitative evaluation is made possible by the recently proposed measure of segmentation correctness, the Normalized Probabilistic Rand (NPR) index, which allows a principled comparison between segmentations created by different algorithms, as well as segmentations on different images. For each algorithm, we consider its correctness as measured by the NPR index, as well as its stability with respect to changes in parameter settings and with respect to different images. An algorithm which produces correct segmentation results with a wide array of parameters on any one image, as well as correct segmentation results on multiple images with the same parameters, will be a useful, predictable and easily adjustable preprocessing step in a larger system. Our results are presented on the Berkeley image segmentation database, which contains 300 natural images along with several ground truth hand segmentations for each image. As opposed to previous results presented on this database, the algorithms we compare all use the same image features (position and colour) for segmentation, thereby making their outputs directly comparable.
Kinase-targeted cancer therapies: progress, challenges and future directions (2018)

The human genome encodes 538 protein kinases that transfer a γ-phosphate group from ATP to serine, threonine, or tyrosine residues. Many of these kinases are associated with human cancer initiation and progression. The recent development of small-molecule kinase inhibitors for the treatment of diverse types of cancer has proven successful in clinical therapy. Significantly, protein kinases are the second most targeted group of drug targets, after the G-protein-coupled receptors. Since the development of the first protein kinase inhibitor, in the early 1980s, 37 kinase inhibitors have received FDA approval for treatment of malignancies such as breast and lung cancer. Furthermore, about 150 kinase-targeted drugs are in clinical phase trials, and many kinase-specific inhibitors are in the preclinical stage of drug development. Nevertheless, many factors confound the clinical efficacy of these molecules. Specific tumor genetics, tumor microenvironment, drug resistance, and pharmacogenomics determine how useful a compound will be in the treatment of a given cancer. This review provides an overview of kinase-targeted drug discovery and development in relation to oncology and highlights the challenges and future potential for kinase-targeted cancer therapies.
Large field optical tomography system (2013)

Optical measurement technologies become more and more import in many fields of nondestructive testing. One of these technologies is the optical coherence tomography (OCT). By now mostly used in medical applications, such as ophthalmology and dermatology, relevance of OCT for testing of non-biological samples in manufacturing and research is increasing. For this reason new OCT measurement systems for fast volume inspection are needed. In this paper we present an automated high speed swept source based OCT system with a scan rate of 100.000 A-scans per second. The advantage of high scan rates of such systems until know lead into high costs for appropriate light sources. Furthermore the big size of available sources makes system integration and miniaturization difficult. With a new kind of MEMS-based light sources components with smaller dimensions and a cost reduction of more than 50% are possible. We combine the MEMS-based swept source OCT system with a table top robot for large-area inspections. The field of view of commercial systems is limited to few centimeters. Our new system is capable of measuring up to 400mm in square. With inherent software the acquisition of A-Scans at any position in the working area and of any quantity is possible. Once calibrated for a sample, the system can perform an automated measurement. Therefore our OCT system can be used as a tool for testing scenarios in research, for failure analyses and for semi-automated production processes.
Relaxation of gaseous spin-polarized<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mmultiscripts><mml:mrow><mml:mi mathvariant="normal">He</mml:mi></mml:mrow><mml:mprescripts/><mml:mrow/><mml:mrow><mml:mn>3</mml:mn></mml:mrow><mml:mrow/><mml:mrow/></mml:mmultiscripts></mml:mrow></mml:math>targets due to ionizing radiation (1988)

The theory of spin-polarized $^{3}\mathrm{He}$ relaxation due to hyperfine coupling in $^{3}\mathrm{He}^{+}$ and due to spin-rotation coupling in $^{3}\mathrm{He}_{2}^{+}$ is presented. Comparison is made between the theory and recent experiments which utilized spin-polarized $^{3}\mathrm{He}$ as a charged-particle beam target. The theory predicts that at low He pressures applying a magnetic field significantly reduces the $^{3}\mathrm{He}$ depolarization rate due to formation of $^{3}\mathrm{He}_{2}^{+}$. At high He pressures the relaxation rate decreases with pressure. In addition, charge-transfer processes with foreign gases suppress $^{3}\mathrm{He}$ depolarization by reducing the $^{3}\mathrm{He}^{+}$ and $^{3}\mathrm{He}_{2}^{+}$ concentrations.
Numerical correction of reference phases in phase-shifting interferometry by iterative least-squares fitting (1994)

We present a new computational algorithm of phase-shifting interferometry that can effectively eliminate the uncertainty errors of reference phases encountered when we obtain multiple interferograms. The algorithm treats the reference phases as additional unknowns and we determine their exact values by analyzing interferograms using the numerical least-squares technique. A series of simulations prove that this algorithm can improve measuring accuracy because it is unaffected by the nonlinear and random errors of phase shifters.
Impact of the filament morphology on the retention characteristics of Cu/Al<inf>2</inf>O<inf>3</inf>-based CBRAM devices (2016)

In this paper, we demonstrate that the morphology of the conductive filament is the key parameter to control the data retention characteristics of CBRAM devices. In particular, we prove that the evolution of the LRS and HRS distributions is qualitatively related to the filament shape, whereas it is influenced quantitatively by the materials constituting the CBRAM stack, and we propose the peculiar hourglass filament shape as a solution for enabling optimal retention performances. Further analysis of the effect of cycling on retention confirms the key role of the filament morphology in the CBRAM data retention trend.
CRISPR/Cas9-mediated targeted chromosome elimination (2017)

CRISPR/Cas9-mediated targeted chromosome elimination offers a new approach to develop animal models with chromosome deletions, and a potential therapeutic strategy for human aneuploidy diseases involving additional chromosomes.
A Scalable Tridiagonal Solver for GPUs (2011)

We present the design and evaluation of a scalable tridiagonal solver targeted for GPU architectures. We observed that two distinct steps are required to solve a large tridiagonal system in parallel: 1) breaking down a problem into multiple sub problems each of which is independent of other, and 2) solving the sub problems using an efficient algorithm. We propose a hybrid method of tiled parallel cyclic reduction(tiled PCR) and thread-level parallel Thomas algorithm(p-Thomas). Algorithm transition from tiled PCR to p-Thomas is determined by input system size and hardware capability in order to achieve optimal performance. The proposed method is scalable as it can cope with various input system sizes by properly adjusting algorithm trasition point. Our method on a NVidia GTX480 shows up to 8.3x and 49x speedups over multithreaded and sequential MKL implementations on a 3.33GHz Intel i7 975 in double precision, respectively.
WebSphere Dynamic Cache: Improving J2EE application performance (2004)

The Dynamic Cache is part of the IBM solution for improving performance of Java 2 Platform, Enterprise Edition (J2EE™) applications running within WebSphere Application Server. It supports caching of Java™ servlets, JavaServer Pages™ (JSP™), WebSphere® command objects, Web services objects, and Java objects. This paper describes the techniques used by the Dynamic Cache for caching these objects and demonstrates the performance improvement gained by applying these techniques to a typical enterprise Web application.