Miracle-dz/UniFAR-FTUs huggingface dataset:
Vibrio cholerae hemagglutinin/lectin/protease hydrolyzes fibronectin and ovomucin: F.M. Burnet revisited.

Cholera vibrios produce a single polymeric protein that (i) causes hemagglutination; (ii) appears to participate in their attachment to gut epithelium; (iii) may mediate their detachment from gut epithelium; and (iv) is a protease that hydrolyzes fibronectin and mucin, cleaves lactoferrin, and nicks the A subunit of the choleragen-related heat-labile enterotoxin of Escherichia coli.
Public and Private Forms of Opportunism Within the Organization: A Joint Examination of Budget and Effort Behavior

ABSTRACT: We assert that some forms of opportunistic behavior within the organization are relatively transparent and, therefore, public in nature. Further, while organizations can tightly control such public opportunism, it may not be optimal for them to do so in the presence of private opportunism. To study how public and private forms of opportunism differ and interact, we jointly examine budget and effort behavior in a participative budgeting experiment. We group participants into producer/manager pairs and set the parameters such that the producer extracts the largest share of surplus from the manager by publicly setting the budget at zero and privately providing low effort. When the producer unilaterally sets the budget, the public opportunism of budgetary slack is higher and more affected by learning than the private opportunism of low effort. Giving the manager the power to reject the budget not only reduces budgetary slack by about 50 percent, but also generates reciprocity expectations and behavi.
Can electronic medical images replace hard‐copy film? Defining and testing the equivalence of diagnostic tests

Electronic medical images are an efficient and convenient format in which to display, store and transmit radiographic information. Before electronic images can be used routinely to screen and diagnose patients, however, it must be shown that readers have the same diagnostic performance with this new format as traditional hard‐copy film. Currently, there exist no suitable definitions of diagnostic equivalence. In this paper we propose two criteria for diagnostic equivalence. The first criterion (‘population equivalence’) considers the variability between and within readers, as well as the mean reader performance. This criterion is useful for most applications. The second criterion (‘individual equivalence’) involves a comparison of the test results for individual patients and is necessary when patients are followed radiographically over time. We present methods for testing both individual and population equivalence. The properties of the proposed methods are assessed in a Monte Carlo simulation study. Data from a mammography screening study is used to illustrate the proposed methods and compare them with results from more conventional methods of assessing equivalence and inter‐procedure agreement. Copyright © 2001 John Wiley & Sons, Ltd.
Collision between deformable objects using fast-marching on tetrahedral models

This paper presents an approach to handling collision between deformable objects using tetrahedral decomposition. The tetrahedral volumetric model is often used to simulate deformable objects that handle cuts and splits. Interaction between such objects in a complex environment is still an open problem in interactive simulation. This paper is mainly focused on obtaining a fast computation of a reliable penalty response. The method consists in using an approximated distance map to compute a penalty based response. We propose to compute the distances to the boundary using a modified "Closest Point" algorithm derived from Fast Marching. The presented algorithm, inspired by the [FL01], has the advantage of computing rapidly the "Closest Point" in the volumetric tetrahedral mesh without any use of an additional computation grid. From the resulting distance map a response is computed using a new "segment-in-object" response that offers more reliable results than the "point-in-object" generally used in previous works. Using this collision model, simulation at interactive rate can be considered in an environment composed of objects that can be deformed and cut.
In Vitro Biotransformation of Two Human CYP3A Probe Substrates and Their Inhibition during Early Zebrafish Development

At present, the zebrafish embryo is increasingly used as an alternative animal model to screen for developmental toxicity after exposure to xenobiotics. Since zebrafish embryos depend on their own drug-metabolizing capacity, knowledge of their intrinsic biotransformation is pivotal in order to correctly interpret the outcome of teratogenicity assays. Therefore, the aim of this in vitro study was to assess the activity of cytochrome P450 (CYP)—a group of drug-metabolizing enzymes—in microsomes from whole zebrafish embryos (ZEM) of 5, 24, 48, 72, 96 and 120 h post-fertilization (hpf) by means of a mammalian CYP substrate, i.e., benzyloxy-methyl-resorufin (BOMR). The same CYP activity assays were performed in adult zebrafish liver microsomes (ZLM) to serve as a reference for the embryos. In addition, activity assays with the human CYP3A4-specific Luciferin isopropyl acetal (Luciferin-IPA) as well as inhibition studies with ketoconazole and CYP3cide were carried out to identify CYP activity in ZLM. In the present study, biotransformation of BOMR was detected at 72 and 96 hpf; however, metabolite formation was low compared with ZLM. Furthermore, Luciferin-IPA was not metabolized by the zebrafish. In conclusion, the capacity of intrinsic biotransformation in zebrafish embryos appears to be lacking during a major part of organogenesis.
Design of a random distribution frequency selective surface

In this paper, a novel frequency selective surface (FSS) using random distribution method is investigated. This FSS can diffuse the reflected wave analogy to array antenna. The reflectivity of three-layer stacked cross patches are studied at first. Then an array of 20×20 FSS is constructed and simulated. Finally a 300mmx300mm three-layer random surface is fabricated and measured. More than 5dB RCS reduction in 7-20GHz is obtained from measurement. Both the simulation and measurement results demonstrate the validity of this design.
Detection of video sequences using compact signatures

Digital representations are widely used for audiovisual content, enabling the creation of large online repositories of video, allowing access such as video on demand. However, the ease of copying and distribution of digital video makes piracy a growing concern for content owners. We investigate methods for identifying coderivative video content---that is, video clips that are derived from the same original source. By using dynamic programming to identify regions of similarity in video signatures, it is possible to efficiently and accurately identify coderivatives, even when these regions constitute only a small section of the clip being searched. We propose four new methods for producing compact video signatures, based on the way in which the video changes over time. The intuition is that such properties are likely to be preserved even when the video is badly degraded. We demonstrate that these signatures are insensitive to dramatic changes in video bitrate and resolution, two parameters that are often altered when reencoding. In the presence of mild degradations, our methods can accurately identify copies of clips that are as short as 5 s within a dataset 140 min long. These methods are much faster than previously proposed techniques; using a more compact signature, this query can be completed in a few milliseconds.
Antibody Phage Display Libraries: Contributions to Oncology

Since the advent of phage display technology, dating back to 1985, antibody libraries displayed on filamentous phage surfaces have been used to identify specific binders for many different purposes, including the recognition of tumors. Phage display represents a high-throughput technique for screening billions of random fusion antibodies against virtually any target on the surface or inside cancer cells, or even soluble markers found in patient serum. Many phage display derived binders targeting important tumor markers have been identified. Selection directed to tumoral cells’ surfaces lead to the identification of unknown tumoral markers. Also the improvement of methods that require smaller amounts of cells has opened the possibility to use this approach on patient samples. Robust techniques combining an antibody library displayed on the phage surface and protein microarray allowed the identification of auto antibodies recognized by patient sera. Many Ab molecules directly or indirectly targeting angiogenesis have been identified, and one of them, ramucirumab, has been tested in 27 phase I–III clinical trials in a broad array of cancers. Examples of such antibodies will be discussed here with emphasis on those used as probes for molecular imaging and other clinical trials.
Equilibrium species counts and migration model tradeoffs for biogeography-based optimization

Motivated by the migration mechanisms of ecosystems, various extensions to biogeography-based optimization (BBO) are proposed. BBO is an original optimization method based on the mathematical model of organism distribution in biological systems. BBO is an evolutionary process that achieves information sharing by species migration. This paper generalizes the equilibrium species count in biogeography theory, discusses various migration models in BBO, and investigates performance through benchmark functions. The performance study shows the most effect migration scheme for BBO and shows that it is a promising candidate for optimization.
Random Sampling from Pseudo-Ranked B+ Trees

In the past, two basic approaches for sampling f5-om B+ trees have been suggested: sampling from the ranked trees and acceptance/rejection sampling i? om non-ranked trees. The first approach requires the entire root-to-leaf path to be updated with each insertion and deletion. The second has no update overhead, but incurs a high rejection rate for the compressed-key B+ trees commonly used in practice. In this paper we introduce a new sampling method based on pseudo-ranked B+ trees, which are B+ trees supplemented with information loosely describing the estimated rank limits. This new method exhibits a very small rejection rate while paying only a marginal cost of the tree update overhead. We also present comparative efficiency measurements of different methods that were run on production databases and on several prototype workload simulations.
A graphical model to determine the subcellular protein location in artificial tissues

Location proteomics is concerned with the systematic analysis of the subcellular location of proteins. In order to perform comprehensive analysis of all protein location patterns, automated methods are needed. With the goal of extending automated subcellular location pattern analysis methods to high resolution images of tissues, 3D confocal microscope images of polarized CaCo2 cells immunostained for various proteins were collected. A three-color staining protocol was developed that permits parallel imaging of proteins of interest as well as DNA and the actin cytoskeleton. The collection is composed of 11 to 21 images for each of the 9 proteins that depict major subcellular patterns. A classifier was trained to recognize the subcellular location pattern of segmented cells with an accuracy of 89.2%. Using the Prior Updating method allowed improvement of this accuracy to 99.6%. This study demonstrates the benefit of using a graphical model approach for improving the pattern classification in tissue images.
Remote Sensing Based Monitoring of Winter Wheat Powdery Mildew at a Regional Scale Using Random Forest Model

Wheat powdery mildew is one of the main diseases of wheat. The emergence and spread have seriously affected the yield and quality of wheat. It is of great significance to accurately monitor the occurrence of such a plant disease at a regional scale. Satellite remote sensing imagery has been extensively utilized in monitoring and assessing various plant diseases, due to its own particular advantages of real-time performance, wide coverage, high tempo-spatial resolution, etc. It is therefore suitable as a data source for monitoring the occurrence of wheat powdery mildew. Gaocheng District, Zhao County and Jinzhou City of Hebei Province, China were used as the study area. A total of eleven features were extracted from Landsat 8 OLI (Operational Land Imager) remote sensing data. Due to the existence of inter-band correlation, the Relief-F algorithm was used to carry out the feature selection. According to the weight value of each feature, three features were determined as the input into the created monitoring model. Consequently, the monitoring model was respectively established using the random forest (RF) and support vector machine (SVM). The analysis results show that the overall accuracy (OA) of RF model reaches 84% with the Kappa coefficient of 0.67, which are better than the SVM model of 73% and 0.47.
Superparamagnetic beads as self-assembling matter for microfluidic applications

Superparamagnetic beads have become a helpful tool for biomedical analysis in lab-on-a-chip systems. The polymer shell of the beads can be functionalized with a large variety of chemical groups and biomolecules, allowing, e.g., the targeted capture of specific analytes such as DNA, antigens or antibodies. As the beads are composed of superparamagnetic nanoparticles embedded in a polymer matrix, external magnetic fields can be used to agglomerate or transport beads and bound analytes. With the help of magnetoresistive sensors, the stray field of the beads can be detected, making it possible to use them as markers. However, in all these applications, the bead concentration is usually kept low to prevent particle dipole interactions. Lately, the use of higher concentrations, where dipole interactions take place, has attracted interest. Here, external magnetic fields can be used to form superstructures of interacting beads. These structures can be either 1-, 2- or 3-dimensional, depending on the properties of the magnetic field. Thus, superparamagnetic beads can be used as reconfigurable matter in microfluidic systems, allowing for the assembly and disassembly of simple structures within seconds. These self-assembling structures can then perform specific functions inside the microfluidic channels of the chip, e.g. particle flow control or the formation of reconfigurable sensor surfaces. In this thesis, the kinetics of this agglomeration into supraparticle structures has been evaluated kinetically. Additionally, four different applications in microfluidic systems have been developed.
Maximization of Good Chips Per Wafer by Optimization of Memory Redundancy

In the optimization of the number of good chips per wafer, yield is obviously one key factor. It plays the major role in the manufacturing phase, as at this time circuit design and chip area cannot be modified. In the design phase, however, chip area as the second factor defining good chips per wafer can still be influenced. If there are no strong relationships between yield and chip area, both can be optimized independently. In some cases, however, there are such strong relationships, and an optimum of yield gain versus area growth has to be found. Maybe the most important example where strong relationships between area and yield have to be considered is the estimation of optimum memory redundancy. In this paper, we will review and discuss relationships between yield and area and present methods for optimization of good chips per wafer, with special focus on the optimization of memory redundancy
Importance of the Broad Regional Interaction for Spectral Tuning in Natronobacterium pharaonis Phoborhodopsin (Sensory Rhodopsin II)*

Natronobacterium pharaonis phoborhodopsin (ppR; also called N. pharaonis sensory rhodopsin II, NpsRII) is a photophobic sensor in N. pharaonis, and has a shorter absorption maximum (λmax, 500 nm) than those of other archaeal retinal proteins (λmax, 560–590 nm) such as bacteriorhodopsin (bR). We constructed chimeric proteins between bR and ppR to investigate the long range interactions effecting the color regulation among archaeal retinal proteins. The λmax of B-DEFG/P-ABC was 545 nm, similar to that of bR expressed in Escherichia coli (λmax, 550 nm). B-DEFG/P-ABC means a chimera composed of helices D, E, F, and G of bR and helices A, B, and C of ppR. This indicates that the major factor(s) determining the difference in λmax between bR and ppR exist in helices DEFG. To specify the more minute regions for the color determination between bR and ppR, we constructed 15 chimeric proteins containing helices D, E, F, and G of bR. According to the absorption spectra of the various chimeric proteins, the interaction between helices D and E as well as the effect of the hydroxyl group around protonated Schiff base on helix G (Thr-204 for ppR and Ala-215 for bR) are the main factors for spectral tuning between bR and ppR.
Highly linear broadband GaN-based low-noise amplifier

A highly linear broadband low-noise amplifier is presented in this paper. The circuit is based on a GaN power transistor, directly bonded into a hybrid microstrip circuit. In order to achieve the highest linearity possible, a large device is used and biased in class A. Broadband low-noise operation in the range of 1.7 – 2.3 GHz is achieved, with a gain of about 15 dB and a noise figure below 2 dB, although matching of the large transistor cell is tedious. A record output IP3 of 49 dBm is measured for this device. This proves that the GaN technology is capable of combining extremely high linearity with low noise performance.
GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update

Summary: GenAlEx: Genetic Analysis in Excel is a cross-platform package for population genetic analyses that runs within Microsoft Excel. GenAlEx offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences. Both frequency-based (F-statistics, heterozygosity, HWE, population assignment, relatedness) and distance-based (AMOVA, PCoA, Mantel tests, multivariate spatial autocorrelation) analyses are provided. New features include calculation of new estimators of population structure: G′ST, G′′ST, Jost’s Dest and F′ST through AMOVA, Shannon Information analysis, linkage disequilibrium analysis for biallelic data and novel heterogeneity tests for spatial autocorrelation analysis. Export to more than 30 other data formats is provided. Teaching tutorials and expanded step-by-step output options are included. The comprehensive guide has been fully revised. Availability and implementation: GenAlEx is written in VBA and provided as a Microsoft Excel Add-in (compatible with Excel 2003, 2007, 2010 on PC; Excel 2004, 2011 on Macintosh). GenAlEx, and supporting documentation and tutorials are freely available at: http://biology.anu.edu.au/GenAlEx. Contact: rod.peakall@anu.edu.au
Analysis and results for H-MIMO - a hybrid of spatial multiplexing and adaptive beamforming

The use of multiple antennas at both ends of a wireless link can provide substantial increases in capacity. In MIMO systems, the multiple antennas could be utilized in different ways to maximize performance in a particular environment. In F.R. Farrokhi et al. 2002, a spatial multiplexing system was compared with a system that uses multiple antennas to perform adaptive beamforming. In this paper, we evaluate the performance of a hybrid MIMO (H-MIMO) system where the antennas are used in a combination of these two modes. Through simulations, we show that, over a wide range of target outages and Ricean K factors, the hybrid systems can achieve higher efficiencies for users who are farther from the base station or, alternatively, can provide higher capacities to a larger percentage of users in a cell
MuNeG — The framework for multilayer network generator

It is a common problem that cost of extracting data for network analysis could be very high. Also sometimes in the Internet is it hard to find graph with desired features such as node degree or clustering level. Because of that graph generators can than be very helpful. In the past bunch of models of such generators was developed: random graphs, small worlds and scale free networks. All of these generators were developed to quickly and efficiently create networks with desired parameters. However all of this models produce single layer graphs. Domain of multiplexes or multilayer graphs has not already been so deeply analysed, also because it is hard to collect multilayer data among real datasets or there is hard to define what kind of information layers exactly should represent. Proposed MuNeG - Multilayer Network Generator can produce, based on set of input parameters, multiplex networks - networks where each node has its counterpart in each layer. The carried out experiments proved that MuNeG graphs have different network and social parameters depends on input values. This feature gives user a very handful tool to generate multiplex networks on purpose of social network or complex network analysis. Generator features, input parameters and their influence on so called graph theory measures such as: node degree, average shortest path, diameter or clustering are described in the following article.
Cold Ischaemic Injury in Kidney Transplantation

Kidney transplantation is considered the best treatment for end stage renal failure (ESRF) with longer life expectancy and superior quality of life compared to dialysis therapy [1-3]. However, a major constraint to transplantation is the lack of suitable organ donors. To increase the number of available organs there has been an incentive to use ‘marginal’ donors such as donation after cardiac death (DCD) and expanded criteria donors (ECD), in addition to kidneys from the traditional living and deceased donors [4,5]. Although an important source of organs for transplantation, once transplanted a significant proportion of these kidneys have early graft dysfunction.
Role of the calcium modulated cyclases in the development of the retinal projections

Transmembrane isoforms of adenylate cyclases (AC) integrate a wide variety of extracellular signals from neurotransmitters to morphogens and can also regulate cAMP production in response to calcium entry. Based on observations in the barrelless mouse strain, the Adcy1 gene (AC1) was involved in the segregation of binocular retinal inputs. To determine the potential role of other AC isoforms we localized the Adcy genes in the visual centres during development, using in situ hybridization. Six different AC subtypes were found in the developing retinal ganglion cell layer (RGC; AC1, AC2, AC3, AC5, AC8, and AC9), and three AC subtypes were expressed in the central brain targets, the dorsal lateral geniculate nucleus (AC1 and AC8), the ventral lateral geniculate nucleus (AC2 and AC8) and the superior colliculus (AC1, AC2, AC8). Using a genetic approach we tested the role of the calcium modulated cyclases AC1, AC5 and AC8 for the segregation retinal fibres. Ipsilateral retinal axons remained exuberant in the AC1–/– mice, with overlapping retinal projections from both eyes in the superior colliculus and the visual thalamus. These abnormalities were similar to those of barrelless mouse mutants. No abnormalities were detectable in the AC5–/– or the AC8–/– mice. Similar abnormalities were noted in the single AC1–/– and the AC1/AC8 double‐knockout mice (DKO). Thus, only AC1 is required for the maturation of the retinal axon terminals whereas AC5 and AC8 are not needed. The specificity of AC1′s action is linked to its cellular localization in the RGCs and to its distinctive functional profile, compared with the other cyclases expressed in the same cells.