gebhart/patrepeval huggingface dataset:
Strands hybridize in postreplicative adenovirus overlap recombination. (1991)

We describe a postreplicative mechanism for adenovirus overlap recombination. An adenovirus minichromosome system was used to study overlap recombination driven by adenovirus DNA replication. Crossing-over appeared to occur equally at, but not within, the borders of the overlap between partner molecules. We propose that recombination in the minichromosome system proceeds through an intermediate formed by direct hybridization of complementary sequences on displaced strands generated by adenovirus-specific DNA replication. Some, but not all, heterologous regions in the intermediate are susceptible to mismatch correction. This pathway is intrinsically nonreciprocal and differs significantly from other adenovirus recombinational mechanisms that have been described previously.
Mechanism of crosslinking of proteins by glutaraldehyde III. Reaction with collagen in tissues (1985)

Bovine pericardium, a dense collagenous connective tissue, was crosslinked with glutaraldehyde using different modalities of fixation. The degree of crosslinking was evaluated as a function of the ability of CNBr and pronase to solubilize collagen. Our results suggest that glutaraldehyde fixes primarily the surface of the fibers and creates a polymeric network which hinders the further crosslinking of the interstitium of the fiber. When a low concentration of glutaraldehyde was used, a slow time-dependent crosslinking process was observed. This slow process is maintained over a long period of time, greatly beyond that required for the actual penetration of glutaraldehyde to occur.
Novel synthetic luteolin analogue-caused sensitization of tumor necrosis factor-α-induced apoptosis in human tumor cells (2008)

Studies on the sensitization, by novel alkynyl luteolin analogues, of TNF-alpha-induced apoptosis in HeLa and HepG2 cells revealed that LA-12 showed better sensitizing effects on TNF-alpha-induced cell death than luteolin, suggesting great potential for alkynyl luteolin analogues in cancer therapy.
Selection of Nitrate-nonutilizing Mutants of Hypoxylon atropunctatum, a Fungal Pathogen on Oak Species (2000)

Latent infections of healthy-appearing oaks of Hypoxylon atropunctatum complicates field studies by interfering with inoculation experiments to follow pathogenesis, fungal development and reproduction of this canker rot fungus. Mutants with unique and easily scorable phenotypes would be useful for inoculation studies. There is a broad range in the capacity of wild-type isolates to utilize nitrate as a sole nitrogen sources. Several types of nitrate-nonutilization mutants (nit1, Nit3, NitM) were selected from nitrate-utilizing wild-type isolates. Also, a few mutants of Hypoxylon atropunctatum were selected that could only grow poorly on basal medium supplemented with various nitrogen sources and even on yeast extract agar. These unknown mutants need to be characterized further. Nit mutants of Hypoxylon atropunctatum were readily selected, grew well and were recovered after inoculation into oak stems. These results suggest that nit mutants could be useful for inoculation studies in trees that contain latent infections.
Coupling efficiency of light to surface plasmon polariton for single subwavelength holes in a gold film (2008)

The excitation of surface plasmon polaritons (SPP) by focusing a laser beam on single subwavelength holes opened in a thin gold film is studied both experimentally and theoretically. By means of leakage radiation microscopy, quantitative measurements of the light-SPP coupling efficiency are performed for holes with different sizes and shapes. The system is studied theoretically by using a modal expansion method to calculate the fraction of the incident energy which is scattered by the hole into a surface plasmon. We demonstrate that a single subwavelength hole can be used to generate SPP with an efficiency up to 28%.
Clinical Cancer Proteomics:  Promises and Pitfalls (2005)

Proteome analysis promises to be valuable for the identification of tissue and serum biomarkers associated with human malignancies. In addition, proteome technologies offer the opportunity to analyze protein expression profiles and to analyze the activity of signaling pathways. Many published proteomic studies of human tumor tissue are associated with weaknesses in tumor representativity, sample contamination by nontumor cells and serum proteins. Studies often include a moderate number of tumors which may not be representative of clinical materials. It is therefore very important that biomarkers identified by proteomics are validated in representative tumor materials by other techniques, such as immunohistochemistry. Proteome technologies can be used to identify disease markers in human serum. Tumor derived proteins are present at nanomolar to picomolar concentrations in cancer patient sera, 10(6)-10(9)-fold lower than albumin, and will give rise to correspondingly smaller spots/peaks in protein separations. This leads to the need to prefractionate serum samples before analysis. Despite various pitfalls, proteomic analysis is a promising approach to the identification of biomarkers, and for generation of protein expression profiles that can be analyzed by artificial learning methods for improved diagnosis of human malignancy. Recent advances in the field of proteomic analysis of human tumors are summarized in the present review.
Time - of - arrival and Direction - of - arrival Estimation Techniques for IR - UWB Signals (2016)

This paper deals with how a ultra wideband signal (UWB) can be used to estimate time of arrival (TOA) and direction of arrival (DOA). The paper has also elucidated a comparative study of the performance of the four algorithms used for TOA estimation, namely multiple signal classification (MUSIC), deconvolution, maximum likelihood (ML) estimation and two stage estimation under the multipath non-line-of-sight (NLOS) channel conditions given in IEEE 802.15.3a model. MUSIC has given the best result in terms of accuracy. Coherent signal subspace method (CSM) of DOA estimation works well for a wideband signal by condensing the wide subspace into a narrow subspace using focusing matrices. The frequency to which the wide subspace is focused is called the focusing frequency and is calculated by minimizing a certain subspace fitting error. The above algorithm has been chosen because it involves MUSIC, which has this innate ability to separate multipath components, thereby making it the best choice for multipath channels.
Self-Assembled Thermoreversible Gels of Nonpolar Liquids by Racemic Propargylic Alcohols with Fluorinated and Nonfluorinated Aromatic Rings (2008)

The synthesis and colloidal study of a new class of low molecular weight organogelators is reported. Racemic propargylic alcohols with perfluoroaryl and nonfluorinated aryl rings are capable of forming gels in alkane liquids and/or silicone oil. A full colloidal characterization of alkane gels prepared from (R/S)-1-pentafluorophenyl-3-phenylprop-2-yn-1-ol [(R/S)- 1] was conducted, including both structural [optical microscopy, scanning electron microscopy (SEM), powder X-ray diffraction (XRD), attenuated total reflectance infrared spectroscopy (ATR-IR)] and thermal stability [differential scanning calorimetry (DSC)] studies. A model of the organization of gelator molecules within gel fibers has been proposed primarily based on the correlation of diffraction data for the powder XRD pattern of a gel and a simulated powder pattern from a sublimed crystal of the gelator. Furthermore, structural requirements for propargylic alcohol gelators were investigated by subjecting derivatives with modified structures to gelation tests. An enantiomerically enriched sample [(R)- 1, 83% ee] fails to entrap the solvent under conditions where the racemate successfully forms a gel. The remaining racemic derivatives (with p-alkoxy or p-alkyl substituents on the nonfluorinated arene) form gels or partial gels in silicone oil and in some alkane preparations.
Spectral Boundary Adaptation on Heart Rate Variability for Sleep and Wake Classification (2014)

A method of adapting the boundaries when extracting the spectral features from heart rate variability (HRV) for sleep and wake classification is described. HRV series can be derived from electrocardiogram (ECG) signals obtained from single-night polysomnography (PSG) recordings. Conventionally, the HRV spectral features are extracted from the spectrum of an HRV series with fixed boundaries specifying bands of very low frequency (VLF), low frequency (LF), and high frequency (HF). However, because they are fixed, they may fail to accurately reflect certain aspects of autonomic nervous activity which in turn may limit their discriminative power, e.g. in sleep and wake classification. This is in part related to the fact that the sympathetic tone (partially reflected in the LF band) and the respiratory activity (modulated in the HF band) vary over time. In order to minimize the impact of these variations, we adapt the HRV spectral boundaries using time-frequency analysis. Experiments were conducted on a data set acquired from two groups with 15 healthy and 15 insomnia subjects each. Results show that adapting the HRV spectral features significantly increased their discriminative power when classifying sleep and wake. Additionally, this method also provided a significant improvement of the overall classification performance when used in combination with other HRV non-spectral features. Furthermore, compared with the use of actigraphy, the classification performed better when combining it with the HRV features.
Network Fusion Information and Intelligence Sharing for a Networked World (2012)

This article appeared in Homeland Security Affairs (October 2012), v.8, article 17
Active broadband polymer stabilized liquid crystals (2001)

We consider the realization and the electro-optical behaviour of a polymer network stabilized liquid crystal whose reflection band has been broadened. We particularly emphasize the reflective properties (mean value of the selective reflection and bandwidth, and the parameters of broadening) and their evolution with voltage. Broadband active films can be obtained under special conditions of polymerization. A mechanism concerning the broadening of the reflection band is put forward based on inhomogeneous consumption of a chiral monomer within the samples.
Access Control based on Attribute Certificates for Medical Intranet Applications (2001)

Access control in clinical intranet applications can be successfully and securely managed through the use of digital certificates and the DIMEDAC security policy.
Synthesis of a novel poly(<i>para</i>‐phenylene ethynylene) for highly selective and sensitive sensing mercury (II) ions (2008)

Abstract A new poly( p ‐phenylene ethynylene) derivative with pendant 2,2′‐bipyridyl groups and glycol units (PPE‐bipy) has been prepared, and its metal ion sensing properties were investigated. The polymer of PPE‐bipy exhibited high selectivity for Hg 2+ as compared with Li + , Na + , K + , Ba 2+ , Ca 2+ , Mg 2+ , Al 3+ , Mn 2+ , Ag + , Zn 2+ , Pb 2+ , Ni 2+ , Cd 2+ , Cu 2+ , Co, 2+ and Fe 3+ in THF/EtOH (1:1, v/v) solution. The fluorescence of PPE‐bipy was efficiently quenched by Hg 2+ ions, and the detection limit was found to be 8.0 nM in a THF/EtOH (1:1, v/v) solvent system. PPE‐bipy also showed a selective chromogenic behavior toward Hg 2+ ions by changing the color of the solution from slight yellow to colorless, which can be detected with the naked eye. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1998–2007, 2008
Origin of cells and network information (2015)

All cells are derived from one cell, and the origin of different cell types is a subject of curiosity. Cells construct life through appropriately timed networks at each stage of development. Communication among cells and intracellular signaling are essential for cell differentiation and for life processes. Cellular molecular networks establish cell diversity and life. The investigation of the regulation of each gene in the genome within the cellular network is therefore of interest. Stem cells produce various cells that are suitable for specific purposes. The dynamics of the information in the cellular network changes as the status of cells is altered. The components of each cell are subject to investigation.
Disparity search range estimation based on dense stereo matching (2013)

This paper presents a scheme for estimating disparity search range based on hierarchical stereo matching. It is important to specify a proper range of search space, since it prevents the solution from being trapped in local minima, and saves a lot of time for estimating disparity maps. Conventionally, it has been estimated by finding a sparse set of the correspondences via feature matching techniques. Instead, we address this problem by considering how the dense correspondences, the ultimate goal of estimating search range, can be estimated without search range. First, we estimate the dense correspondences by adapting a simple local stereo matching technique with an arbitrary search range. The hierarchical scheme is leveraged for reducing computational costs and memory usages. Then, reliable checking techniques are performed for eliminating unreliable correspondences. Finally, the range of search space is estimated by observing the distribution of the reliable correspondences. For the quantitative evaluation, a new error metric, biased root mean squared error (B-RMSE), is proposed, which differentiates the estimated search range whether it is narrower or wider than true disparity range. The experimental results show that the proposed method gives more accurate search range compared to the conventional method.
Advances in treatment of COVID-19 (2020)

The novel coronavirus pneumonia is an acute infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The global pandemic of this novel coronavirus pneumonia has greatly threatened human health and brought enormous economy losses. By the end of May 20, 2020, the pandemic of this disease had caused more than 2.70 million infections and more than 320 thousand deaths. This paper reviewed the recent advances in the treatment of the novel coronavirus pneumonia to provide basic references for disease control.
Engineering a Human Bone Marrow Model: A Case Study on ex Vivo Erythropoiesis (1998)

Bone marrow, with its intricate, three-dimensional tissue structure facilitating cell-cell interactions, provides a microenvironment supporting the production of hundreds of billions of multilineal blood cells everyday. We have developed a three-dimensional bone marrow culture system in which marrow cells are cultured in a reactor packed with porous microspheres. The culture supports a three-dimensional growth configuration and multilineal hemopoiesis mimicking the bone marrow in vivo. We studied ex vivo human erythropoiesis using the three-dimensional culture system. The system sustained extensive erythropoiesis at low erythropoietin concentrations (0.2 U/mL), plus stem cell factor, interleukin-3, granulocyte-macrophage colony-stimulating factor, and insulin-like growth factor-I. Erythroid cell production lasted for more than 5 weeks, and the percentage of erythroid cells in the nonadherent cell population was approximately 60%. Flow cytometric analysis using cell surface markers specific for erythroid cells (CD71 and glycophorin-A) indicated that the culture produced early, intermediate, and late erythroid cells. As the culture progressed, the erythroid cell population shifted gradually toward mature cell types. When compared to the three-dimensional culture, the traditional flask cultures failed to support extensive erythropoiesis under the same conditions. This indicates that the three-dimensional bone marrow culture system provides a microenvironment conducive to erythropoiesis under more physiological conditions and is a better bone marrow model.
The lectin-like interaction between recombinant tumor necrosis factor and uromodulin. (1988)

The polypeptide of uromodulin, an immunosuppressive glycoprotein isolated from human urine, has been shown to be identical to that of Tamm-Horsfall glycoprotein and is synthesized exclusively in the kidney (Hession, C., Decker, J. M., Sherblom, A. P., Kumar, S. (1987) Science 237, 1479-1484). Uromodulin binds recombinant murine interleukin 1 alpha with high affinity, and this binding can be inhibited by addition of specific saccharides (Muchmore, A. V., and Decker, J. M. (1987) J. Immunol. 138, 2541-2546). We now report that uromodulin binds recombinant human tumor necrosis factor (rTNF) with high affinity. Both diacetylchitobiose and Man(alpha 1-6)(Man(alpha 1-3]-Man-O-ethyl are effective inhibitors of the binding, whereas a wide variety of other saccharides are not inhibitory. Although Tamm-Horsfall glycoprotein contains predominantly tetraantennary N-linked chains, the binding to rTNF is unaffected by removal of terminal sialic acid, galactose, and N-acetylhexosamine residues. Fractionation of a Pronase digest of uromodulin by gel filtration yields material that inhibits the binding of uromodulin to rTNF but is of lower molecular weight than the major oligosaccharide. Uromodulin does not inhibit the cytotoxic activity of rTNF as monitored by lysis of tumor cell targets but effectively protects mice from lethal challenge with lipopolysaccharide, an event that may involve lymphokine toxicity. We have previously shown that rTNF binds to sections of human kidney and is localized in the same region as uromodulin. Thus, rTNF interacts with uromodulin via carbohydrate chains that are less processed than the major tetraantennary chain, and this interaction may be critical in promoting clearance and/or reducing toxicity of TNF and other lymphokines.
Effects of biotic and abiotic stress on the growth of three genotypes of <i>Lolium perenne</i> with and without infection by the fungal endophyte <i>Neotyphodium lolii</i> (2004)

Summary The combinations of three genotypes of Lolium perenne with and without (i) infection by the fungal endophyte Neotyphodium lolii , (ii) infection by ryegrass mosaic virus and (iii) one of five different forms of abiotic stress were studied in pot experiments in a glasshouse. The five abiotic stress treatments were (i) low pH (compared with ‘optimal’ pH), (ii) cutting plants to a height of 1 cm (compared with 5 cm), (iii) shading (compared with no shading), (iv) cutting plants at 2‐weekly intervals (compared with 6 wk) and (v) low nitrogen applied (compared with ‘high’ nitrogen applied). On average, over the five experiments, the accumulated herbage dry weight was 10% more for N. lolii ‐infected plants than uninfected, 22% more for virus‐free plants than infected, and 265% more for ‘unstressed’ plants than for plants with abiotic stress. The effects of N. lolii infection on plant growth when the plants were under abiotic or biotic stress were not consistent.
Influenza Virus−Liposome Lipid Mixing Is Leaky and Largely Insensitive to the Material Properties of the Target Membrane (1996)

Monolayer intrinsic curvature, void stabilization, and membrane rupture tension have been suggested as important factors determining the rate of membrane fusion. Here, we have studied the kinetics of fusion between influenza virus and target liposomes as a function of various target membrane material properties. In order to examine the fusion process directly, a simple prebinding step is used and proven to be adequate to achieve fusion-rate-limiting kinetics. To test the hypothesis about membrane curvature and void stabilization, we studied the lipid mixing kinetics with dioleoylphosphatidylcholine (DOPC)/ganglioside GD1a (GD1a) liposomes containing lysooleoylphosphatidylcholine (LPC, positive curvature), dioleoyglycerol (DOG, negative curvature), arachidonic acid (AA, negative curvature), and hexadecane (HD, void stabilization). DOG, AA, and HD (at 4 mol%) showed no significant effect on the fusion kinetics, while LPC reversibly inhibited influenza HA mediated fusion only at very high concentrations. Using target liposomes with different membrane rupture tension values, no obvious correlation between membrane rupture tension and the rate of lipid mixing was observed. Moreover, a reported potential antiviral compound, tert-butylhydroquinone (t-b-HQ) (Bodian et al., 1993), showed no significant effect on the kinetics of influenza fusion. Finally leakage of liposome contents was detected during lipid mixing. For encapsulated molecules smaller than 450 MW, the kinetics of leakage is very similar to the kinetics of lipid mixing. In fact, leakage was also detected for encapsulated molecules up to 10 000 MW, suggesting that HA mediated lipid mixing is a very leaky process. Since "nonleaky fusion" has been the foundation of influenza fusion models, our work suggests the need for a major revision in the modeling of this process.
A high frequency of <i>Mamu‐A *01</i> in the rhesus macaque detected by polymerase chain reaction with sequence‐specific primers and direct sequencing (1997)

SIV infection of rhesus macaques is an excellent model for HIV infection of humans. Unfortunately, it is has been difficult to identify macaques expressing particular MHC class I alleles. Here we describe the use of PCR-SSP for Mamu-A*01 typing of rhesus macaques. The Mamu-A*01 allele was amplified from genomic DNA using Mamu-A*01-specific primers and positive PCR products were directly sequenced. Our technique identified 15 Mamu-A*01-positive animals of 68 tested. We validated our molecular analysis by showing that lymphocytes from 8 Mamu-A*01-positive animals expressed Mamu-A*01 as determined by immunoprecipitation and 1-D IEF. The technical simplicity and accuracy of this typing method should facilitate selection of Mamu-A*01-positive rhesus macaques for AIDS virus pathogenesis and vaccine studies.
[Treatment of malignant pleural effusion using vindesine and cisplatine intrapleurally injection (observation of 60 cases)]. (2001)

The treatment to use Vindesine and cisplatine through thoracic tube is regarded as effective, slight side-effect and well tolerated method for malignant pleural effusion.
Robust estimation of a multi-layered motion representation (2002)

In order to recover an accurate representation of a scene containing multiple moving objects, one must use estimation methods that can recover both model parameters and segmentation at the same time. Traditional approaches to this problem rely on an edge-based discontinuity model, and have problems with transparent phenomena. The authors introduce a layered model of scene segmentation based on explicitly representing the support of a homogeneous region. The model employs parallel robust estimation techniques, and uses a minimal-covering optimization to estimate the number of objects in the scene. Using a simple direct motion model of translating objects, they successfully segment real image sequences containing multiple motions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>