gebhart/patrepeval huggingface dataset:
Diversity of Antibody Binding to V3 Peptides Representing Consensus Sequences of HIV Type 1 Genotypes A to E: An Approach for HIV Type 1 Serological Subtyping (1996)

We investigated whether V3-binding assays might be useful to analyze human immunodeficiency virus type 1 (HIV-1) variants in different geographic regions. We showed that strong cross-reactivity between subtype-specific V3 peptides is almost inevitable in standard indirect enzyme-linked immunosorbent assays (EIA), impairing precise serological subtyping. We therefore developed a subtype-specific EIA (HIV-1 SSEIA) that uses the principle of blocking by an excess of peptide in the liquid phase. Using 231 serum samples collected from HIV-1-infected individuals in 10 different geographical areas from 4 continents, we showed that this approach detected the dominant subtype reactivity in more than 97% of the cases. Internal controls (0 and 100% blocking) were used for every sample such that comparative analysis was possible, independent of both the individual humoral response and the time of collection during the course of infection. This was validated by the excellent concordance of the serological profiles of couples and the temporal stability of the serological profile in individuals. The geographical distribution of the various subtypes in the SSEIA was in agreement with the present knowledge of the distribution of the various genotypes. Although the goal of this study was not an extensive seroepidemiological survey, our results showed that the various profiles in most of the regions were relatively homogeneous, but in central Africa there was a large diversity of serological profiles. Cluster analysis identified a limited number of V3 serogroups of serotypes within the HIV-1 group M. Five serogroups, some of them divided into subgroups, were identified and characterized by a mean serological profile. Our data confirmed that subtypes A and C, although being dissimilar genetic subtypes, present conserved antigenic properties in the V3 region, and that the D subtype is probably the most divergent within the group M (B Korber et al., J Virol 1994;68:6730). Cluster analysis showed a clear correlation between position within the dendrogram and geographical origin of the samples. This is further support for the reliability and thereof the usefulness of the SSEIA. This simple methodology may help facilitate the analysis of the distribution of various HIV-1 subtypes circulating in different populations and regions.
Light propagation in a cylindrical waveguide with a complex, metallic, dielectric function (1994)

Motivated by problems in scanning near-field optical microscopy, we discuss light propagation in circular dielectric waveguides with finite aluminum cladding. In order to understand the origin of the different solutions, optical modes are first investigated for the dielectric waveguide with infinite aluminum cladding and for the aluminum cylinder. For aluminum a plasma dispersion law is assumed, leading to complex dielectric constants with negative real parts and to generally complex propagation constants. The dependence of the dispersion on the geometry and on the frequency is discussed for the various kinds of modes. We find that the existence of most of the modes is limited to certain frequencies and geometries, i.e., the solutions have a cutoff in the complex propagation constant plane. Contrary to dielectric waveguide theory, where cutoff describes the abrupt transition from propagating to evanescent modes, no other solution is generated when cutoff of a mode is reached. Surface modes and other kinds of modes, such as guided or bulk modes, can either couple between each other or transform into each other.
The rise of the gadgets (2003)

The emergence of networkable gadgets, ranging from printers and DSL routers to gaming consoles, cameras, and personal data assistants (PDA), can pose serious risks to an otherwise secure infrastructure. In this installment of Attack Trends, the author examines sample vulnerabilities and research that might point to novel attack vectors that administrators should consider when planning a well thought-out information security strategy.
Performance of list-mode data acquisition with ECAT EXACT HR positron emission scanner (2004)

Recently list mode (event-by-event) data acquisition with positron emission tomography (PET) has been widely noticed because the list mode acquisition is superior to the conventional frame mode data acquisition in terms of (1) higher efficiency of data storage, (2) higher temporal resolution and (3) higher flexibility of data manipulation. The aim of this study is to investigate the performance of list mode data acquisition with ECAT HR and HR + PET scanners(CTI PET Systems). The cylindrical phantom (16 cm diameter and 16 cm long) filled with /sup 11/C solution for HR and /sup 15/O solution for HR+ was scanned several times varying the radioactivity with list mode and frame mode acquisitions. The scans with the septa (2D mode) and without the septa (3D mode) were also carried out in order to evaluate the effect of interplane septa on quality of the list mode data. The acquired list mode data were sorted to sinogram and reconstructed using filtered back-projection algorithm. The count rate performance of the list mode data was comparable to the frame mode data. However list mode acquisition could not be performed if radioactivity in the field-of-view was high (more than 3 mCi for 3D mode) due to lack of transfer speed for sending data from memory to hard disk. 10 replicated data set from one list mode data were generated to estimate the noise in the reconstructed image. The reconstructed images with 3D mode has more than 60% better signal-to-noise ratio compared to the image with 2D mode. Generated file size of list mode was also evaluated. In the case of HR+ with 3D list mode, list mode data with 2.31 MBytes/s for 1mCi injection were generated. Out results suggest that careful attention must be paid for protocol of the list mode data acquisition in order to obtain the highest performance of the PET scanner.
A Novel Approach for Affinity-Based Screening of Target Specific Ligands:  Application of Photoreactive <scp>d</scp>-Glyceraldehyde-3-phosphate Dehydrogenase (2003)

A novel application of the photoaffinity technique has been developed for the efficient discovery of small ligand and macromolecule interaction. The approach, photoaffinity capture, uses a photoreactive protein together with immobilized ligand for the rapid screening of competitive inhibitors. The set of photoreactive glyceraldehyde-3-phosphate dehydrogenase (photo-GAPDH) and immobilized dye ligand was prepared and examined as a model system. The photo-GAPDH was shown to efficiently capture the immobilized ligand. When nonimmobilized competitive ligands were included in the system, the capture was prevented in accordance with the affinity of the ligands. The present approach would provide an efficient tool for affinity-based screening of ligand libraries.
Techniques for Evaluation of LAMP Amplicons and their Applications in Molecular Biology (2015)

Loop-mediated isothermal amplification (LAMP) developed by Notomi et al. (2000) has made it possible to amplify DNA with high specificity, efficiency and rapidity under isothermal conditions. The ultimate products of LAMP are stem-loop structures with several inverted repeats of the target sequence and cauliflower-like patterns with multiple loops shaped by annealing between every other inverted repeats of the amplified target in the similar strand. Because the amplification process in LAMP is achieved by using four to six distinct primers, it is expected to amplify the target region with high selectivity. However, evaluation of reaction accuracy or quantitative inspection make it necessary to append other procedures to scrutinize the amplified products. Hitherto, various techniques such as turbidity assessment in the reaction vessel, post-reaction agarose gel electrophoresis, use of intercalating fluorescent dyes, real-time turbidimetry, addition of cationic polymers to the reaction mixture, polyacrylamide gel-based microchambers, lateral flow dipsticks, fluorescence resonance energy transfer (FRET), enzyme-linked immunosorbent assays and nanoparticle-based colorimetric tests have been utilized for this purpose. In this paper, we reviewed the best-known techniques for evaluation of LAMP amplicons and their applications in molecular biology beside their advantages and deficiencies. Regarding the properties of each technique, the development of innovative prompt, cost-effective and precise molecular detection methods for application in the broad field of cancer research may be feasible.
Release factors differing in specificity for terminator codons. (1968)

In a previous paper, initiator and terminator trinucleotides were shown to stimulate sequentially the binding of f-Met-tRNA to ribosomes and the release of free f-methionine from the ribosomal intermediate.1The formation of f-methio- nine was dependent upon a terminator codon, such as UGA, UAA, or UAG, and the release factor R discovered by Capecchi.2The separation of R into two components is described in this report.R1 cor- responds to the codons UAA and UAG; R2, to UAA and UGA.Methods.-R assay: The termination assay is described elsewhere.1Each reaction contained the following components in a final volume of 50 Al: 0.05 M Tris-acetate, pH 7.2; 0.03 M magnesium acetate; 0.05 M potassium acetate; 4-6 AMmoles of the (f ['H]- Met-tRNAf ..AUG.-.Ribosome) complex (4.0-6.7 A/Amoles of TCA-precipitable f ['H]- Met-tRNAf, 0.02 A2W0 unit was present/reaction); 0.96 A260 unit-of E. coli B ribosomes (washed with 0.5 M ammonium chloride); 0.17 mumole of AUG; and, where indicated, 7-7.7 mInmoles of terminator trinucleotide, and an R preparation.Reactions were incu- bated for 16 min at 30°unless otherwise stated; hence, the rate of f [3H]-methionine formation was determined in all experiments.The preparation of tRNAfMet (E. coli B), fractionated by benzoylated-DEAE-cellulose column chromatography,' was the gift of Dr. Michael Wilcox.The tRNAfmet was acylated with ['H]-methyl-methionine (3.1 c/mmole, Schwarz BioResearch Corp.) and then converted to f['H]-Met-tRNAfMet.lRibosomes were obtained from E. coli B as described by Lucas-Lenard and Lipmann,4 except that seven, rather than five, 0.5 M ammonium chloride washes were employed.R fractionation: Escherichia coli B supernatant and ribosome fractions, treated with DNase but not "preincubated," were prepared as described previously,5 except that cells were lysed with a French pressure cell at 18,000 psi, 0.005 M DTT replaced ,B-mercaptoethanol, and extracts were centrifuged for 5 hr at 137,000 X g.Release factors (prep.A, Table 1) were obtained as follows: R was precipitated by the addition of 116 gm of ammonium sulfate to 359 ml of the S-137 fraction; the pH was maintained at 7.8 by the addition of 0.5 N ammonium hydroxide.All steps were per- formed at 4°.The precipitate was collected by centrifugation at 30,000 X g for 15 min, dissolved in 139 ml of buffer A (0.05 M Tris-chloride, pH 8.0; 0.15 M potassium chloride; 0.001 M EDTA, adjusted to pH 7 with NaOH; and 0.003 M DTT) and dialyzed against
Encoder-Decoder Residual Network for Real Super-Resolution (2019)

Real single image super-resolution is a challenging task to restore lost information and attenuate noise from images mixed unknown degradations complicatedly. Classic single image super-resolution, aims to enhance the resolution of bicubically degraded images, has recently obtained great success via deep learning. However, these existing methods do not perform well for real single image super-resolution. In this paper, we propose an Encoder-Decoder Residual Network (EDRN) for real single image super-resolution. We adopt an encoder-decoder structure to encode highly effective features and embed the coarse-to-fine method. The coarse-to-fine structure can gradually restore lost information and reduce noise effects. We empirically rethink and discuss the usage of batch normalization. Compared with state-of-the-art methods in classic single image super-resolution, our EDRN can efficiently restore the corresponding high-resolution image from a degraded input image. Our EDRN achieved the 9th place for PSNR and top 5 for SSIM in the final result of NTIRE 2019 Real Super-resolution Challenge. The source code and the trained model are available at https://github.com/yyknight/NTIRE2019_EDRN.
Ethylene production in relation to nitrogen metabolism in<i>Saccharomyces cerevisiae</i> (2014)

We have previously shown that ethylene production in Saccharomyces cerevisiae expressing the ethylene-forming enzyme (EFE) from Pseudomonas syringae is strongly influenced by variations in the mode of cultivation as well as the choice of nitrogen source. Here, we have studied the influence of nitrogen metabolism on the production of ethylene further. Using ammonium, glutamate, glutamate/arginine, and arginine as nitrogen sources, it was found that glutamate (with or without arginine) correlates with a high ethylene production, most likely linked to an observed increase in 2-oxoglutarate levels. Arginine as a sole nitrogen source caused a reduced ethylene production. A reduction of arginine levels, accomplished using an arginine auxotrophic ARG4-deletion strain in the presence of limiting amounts of arginine or through CAR1 overexpression, did however not correlate with an increased ethylene production. As expected, arginine was necessary for ethylene production as ethylene production in the ARG4-deletion strain ceased at the time when arginine was depleted. In conclusion, our data suggest that high levels of 2-oxoglutarate and a limited amount of arginine are required for successful ethylene production in yeast.
Effects of nitrogen-fixing and non-nitrogen-fixing tree species on soil properties and nitrogen transformation during forest restoration in southern China (2010)

Abstract The role of different plantation tree species in soil nutrient cycling is of great importance for the restoration of degraded lands. The objective of the present study was to evaluate the potential of N-fixing and non-N-fixing tree species to recuperate degraded land in southern China. The soil properties and N transformations in six forest types (two N-fixing plantations, three non-N-fixing plantations and a secondary shrubland) established in 1984 were compared. The N-fixing forests had 40–50% higher soil organic matter and 20–50% higher total nitrogen concentration in the 0–5 cm soils than the non-N-fixing forests. Soil inorganic N was highest under the secondary shrubland. The N-fixing Acacia auriculiformis plantation had the highest soil available P. There were no significant differences in soil N mineralization and nitrification among the forest types, but seasonal variation in these N processes was highly significant. In the rainy season, the rates of N mineralization (7.41–11.3 kg N ha−1 month−1) were similar to values found in regional climax forests, indicating that soil N availability has been well recovered in these forest types. These results suggest that N-fixing species, particularly Acacia mangium, are more efficient in re-establishing the C and N cycling processes in degraded land in southern China. Moreover, the N-fixing species A. auriculiformis performed better than other species in improving soil P availability.
Differentiation of adult-type Leydig cells occurs in gonadotrophin-deficient mice (2003)

During mammalian testis development distinct generations of fetal and adult Leydig cells arise. Luteinising hormone (LH) is required for normal adult Leydig cell function and for the establishment of normal adult Leydig cell number but its role in the process of adult Leydig cell differentiation has remained uncertain. In this study we have examined adult Leydig cell differentiation in gonadotrophin-releasing hormone (GnRH)-null mice which are deficient in circulating gonadotrophins. Adult Leydig cell differentiation was assessed by measuring expression of mRNA species encoding four specific markers of adult Leydig cell differentiation in the mouse. Each of these markers (3beta-hydroxysteroid dehydrogenase type VI (3betaHSD VI), 17beta-hydroxysteroid dehydrogenase type III (17betaHSD III), prostaglandin D (PGD)-synthetase and oestrogen sulphotransferase (EST)) is expressed only in the adult Leydig cell lineage in the normal adult animal. Real-time PCR studies showed that all four markers are expressed in adult GnRH-null mice. Localisation of 3betaHSD VI and PGD-synthetase expression by in situ hybridisation confirmed that these genes are expressed in the interstitial tissue of the GnRH-null mouse. Treatment of animals with human chorionic gonadotrophin increased expression of 3betaHSD VI and 17betaHSD III within 12 hours further indicating that differentiated, but unstimulated cells already exist in the GnRH-null mouse. Thus, while previous studies have shown that LH is required for adult Leydig cell proliferation and activity, results from the present study show that adult Leydig cell differentiation will take place in animals deficient in LH.
Successful Use of Locally Applied Polyhexamethylene Biguanide as an Adjunct to the Treatment Of Fungal Osteomyelitis (2013)

Fungal osteomyelitis is rare in immunocompetent patients and is often difficult to cure, even with optimal medical and surgical management. The authors present two cases of fungal osteomyelitis in which the common swimming pool cleaner, polyhexamethylene biguanide, was used successfully as an adjunct to standard surgical and medical treatment. Also presented is a literature review on the use of polyhexamethylene biguanide for this indication. The authors recommend that this safe and well-tolerated compound be considered as part of the treatment for fungal osteomyelitis.
Highly Undersampled Magnetic Resonance Image Reconstruction Using Two-Level Bregman Method With Dictionary Updating (2013)

In recent years Bregman iterative method (or related augmented Lagrangian method) has shown to be an efficient optimization technique for various inverse problems. In this paper, we propose a two-level Bregman Method with dictionary updating for highly undersampled magnetic resonance (MR) image reconstruction. The outer-level Bregman iterative procedure enforces the sampled k-space data constraints, while the inner-level Bregman method devotes to updating dictionary and sparse representation of small overlapping image patches, emphasizing local structure adaptively. Modified sparse coding stage and simple dictionary updating stage applied in the inner minimization make the whole algorithm converge in a relatively small number of iterations, and enable accurate MR image reconstruction from highly undersampled k-space data. Experimental results on both simulated MR images and real MR data consistently demonstrate that the proposed algorithm can efficiently reconstruct MR images and present advantages over the current state-of-the-art reconstruction approach.
Atrial Fibrillation Electroanatomical 3D Mapping Optimisation Thanks to a Novel High-density Mapping Catheter – The Inquiry™ AFocus™ II (2010)

The OneMap™ tool, a new software feature of the EnSite Velocity™ System, and the new Inquiry™ AFocus™ II double loop duodecapolar diagnostic catheter (DDC) were created to provide faster data collection to efficiently deal with complex arrhythmias such as persistent atrial fibrillation ablation (AF). Our study was performed to compare acquisition criteria, time needed to create the maps, number of collected points, relevance of complex fractionated atrial electrogram (CFE) mapping and correlation between CFE maps with the new DDC and a 4mm irrigated ablation catheter (ABL), Therapy™ Cool Path™ Duo, using the OneMap tool. Ten patients undergoing persistent AF ablation were enrolled. With the DDC, more points were collected (485±173 versus 183±37) and the time needed to create CFE maps was shorter (12±4 versus 24±2 minutes). There were 39 zones detected with the DDC against 35 with the ABL. The correlation between the maps was 80%; however, four additional regions were detected with the DDC (an 11% increase). In conclusion, the Inquiry AFocus II DDC is a feasible, fast and accurate tool for automatic CFE mapping using OneMap.
Role and regulation of acylethanolamides in energy balance: focus on adipocytes and <i>β</i>‐cells (2007)

The endocannabinoid, arachidonoylethanolamide (AEA), and the peroxisome proliferator-activated receptor (PPAR)-alpha ligand, oleylethanolamide (OEA) produce opposite effects on lipogenesis. The regulation of OEA and its anti-inflammatory congener, palmitoylethanolamide (PEA), in adipocytes and pancreatic beta-cells has not been investigated. We report here the results of studies on acylethanolamide regulation in these cells during obesity and hyperglycaemia, and provide an overview of acylethanolamide role in metabolic control. We analysed by liquid chromatography-mass spectrometry OEA and PEA levels in: 1) mouse 3T3F442A adipocytes during insulin-induced differentiation, 2) rat insulinoma RIN m5F beta-cells kept in 'low' or 'high' glucose, 3) adipose tissue and pancreas of mice with high fat diet-induced obesity (DIO), and 4) in visceral fat or blood of obese or type 2 diabetes (T2D) patients. In adipocytes, OEA levels remain unchanged during differentiation, whereas those of PEA decrease significantly, and are under the negative control of both leptin and PPAR-gamma. PEA is significantly downregulated in subcutaneous adipose tissue of DIO mice. In RIN m5F insulinoma beta-cells, OEA and PEA levels are inhibited by 'very high' glucose, this effect being enhanced by insulin, whereas in cells kept for 24 h in 'high' glucose, they are stimulated by both glucose and insulin. Elevated OEA and PEA levels are found in the blood of T2D patients. Reduced PEA levels in hypertrophic adipocytes might play a role in obesity-related pro-inflammatory states. In beta-cells and human blood, OEA and PEA are down- or up-regulated under conditions of transient or chronic hyperglycaemia, respectively.
Adaptive Correlation Tracking of Targets With Changing Scale (1996)

Algorithms for tracking targets imaged through a zoom lens must accommodate changes in the magnification of the target. This requirement poses particular problems for correlation techniques, which usually are not invariant to scale changes. An adaptive correlation method has been developed that selectively updates the correlation template in response to scale changes in an image sequence. The algorithm estimates a subset of the parameters of the affine transformation between the template and the matched image patch and updates the template only when the scaling exceeds given bounds. The selective template update enables the correlation to track targets at varying scale while decreasing the risk of template drift.
Neonatal Stroke in Mice Causes Long-Term Changes in Neuronal Notch-2 Expression That May Contribute to Prolonged Injury (2010)

These results suggest that Notch-2 up-regulation after neonatal ischemia is detrimental to neuronal survival.