Miracle-dz/UniFAR-FTUs huggingface dataset:
Chapter 4 Cyclosporin A-induced reduction of bile salt synthesis associated with increased plasma lipids in children after liver transplantation

Background: Hyperlipidemia is a common side effect of Cyclosporin A (CsA) after solid organ transplantation. CsA also markedly reduces the synthesis rate of bile salts in rats and can inhibit biliary bile salt secretion. It is not known, however, whether CsA inhibits the synthesis of bile salts in humans, and whether the hyperlipidemic effects of CsA are related to bile salt metabolism. Objectives: To assess the effects of CsA on the synthesis rate of bile salts and on plasma triglycerides and cholesterol levels in pediatric liver transplant patients. Methods: Before and after discontinuation of CsA treatment after liver transplantation, synthesis rate and pool size of the primary bile salts cholate and chenodeoxycholate were determined using a stable isotope dilution technique and related to plasma lipids. Results: In 6 children (age: 3-16 years) CsA treatment was discontinued at 2 years (median 2.3 years) after liver transplantation. Discontinuation of CsA increased synthesis rate of chenodeoxycholate (+38%, p < 0.001) and cholate (+21%, p < 0.05) and the pool size of chenodeoxycholate (+ 54%, p < 0.001). Discontinuation of CsA decreased plasma levels of cholesterol (-18%, p < 0.05) and triglycerides (-23%, p < 0.05). Bile salt synthesis rate appeared inversely correlated with plasma cholesterol (r s = -0.82, p < 0.01) and plasma triglyceride levels (r s = -0.62, p < 0.05). Conclusions: CsA inhibits bile salt synthesis and increases plasma concentration of cholesterol and triglycerides in pediatric liver transplant patients. Suppression of bile salt synthesis by long-term CsA treatment may contribute to hyperlipidemia and thus to increased risk for cardiovascular disease.
Molecular determinants of selective dopaminergic vulnerability in Parkinson’s disease: an update

Numerous disorders of the central nervous system (CNS) are attributed to the selective death of distinct neuronal cell populations. Interestingly, in many of these conditions, a specific subset of neurons is extremely prone to degeneration while other, very similar neurons are less affected or even spared for many years. In Parkinson’s disease (PD), the motor manifestations are primarily linked to the selective, progressive loss of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNpc). In contrast, the very similar DA neurons in the ventral tegmental area (VTA) demonstrate a much lower degree of degeneration. Elucidating the molecular mechanisms underlying the phenomenon of differential DA vulnerability in PD has proven extremely challenging. Moreover, an increasing number of studies demonstrate that considerable molecular and electrophysiologic heterogeneity exists among the DA neurons within the SNpc as well as those within the VTA, adding yet another layer of complexity to the selective DA vulnerability observed in PD. The discovery of key pathways that regulate this differential susceptibility of DA neurons to degeneration holds great potential for the discovery of novel drug targets and the development of promising neuroprotective treatment strategies. This review provides an update on the molecular basis of the differential vulnerability of midbrain DA neurons in PD and highlights the most recent developments in this field.
SWEEPER: An Efficient Disaster Recovery Point Identification Mechanism

Data corruption is one of the key problems that is on top of the radar screen of most CIOs. Continuous Data Protection (CDP) technologies help enterprises deal with data corruption by maintaining multiple versions of data and facilitating recovery by allowing an administrator restore to an earlier clean version of data. The aim of the recovery process after data corruption is to quickly traverse through the backup copies (old versions), and retrieve a clean copy of data. Currently, data recovery is an ad-hoc, time consuming and frustrating process with sequential brute force approaches, where recovery time is proportional to the number of backup copies examined and the time to check a backup copy for data corruption. In this paper, we present the design and implementation of SWEEPER architecture and backup copy selection algorithms that specifically tackle the problem of quickly and systematically identifying a good recovery point. We monitor various system events and generate checkpoint records that help in quickly identifying a clean backup copy. The SWEEPER methodology dynamically determines the selection algorithm based on user specified recovery time and recovery point objectives, and thus, allows system administrators to perform trade-offs between recovery time and data currentness. We have implemented our solution as part of a popular Storage Resource Manager product and evaluated SWEEPER under many diverse settings. Our study clearly establishes the effectiveness of SWEEPER as a robust strategy to significantly reduce recovery time.
Efficient Techniques for Multimedia Information Hiding using Color Visual Cryptography

In this paper, a novel approach is presented for multimedia information hiding using visual cryptography. The approach combines both the steganographic and cryptographic effect to improve the quality of security and to increase the payload. Both are important parameters in information hiding. The proposed techniques provide three levels of security without reducing the payload and the image quality. The experiments done on various images and the results obtained showed the robustness of the technique. The proposed techniques are vulnerable to various transformation and geometric attacks and can be considered fragile except for the salt and pepper. The results shown in terms of quality and performance are promising for future work.
Intrusion detection in virtual machine environments

A virtual machine is a software replica of an underlying real machine. Multiple virtual machines can operate on the same host machine concurrently, without interfere each other. Such concept is becoming valuable in production computing systems, due to its benefits in terms of costs and portability. As they provide a strong isolation between the virtual environment and the underlying real system, virtual machines can also be used to improve the security of a computer system in face of attacks to its network services. This work presents a new approach to achieve this goal, by applying intrusion detection techniques to virtual machine based systems, thus keeping the intrusion detection system out of reach from intruders. The results obtained from a prototype implementation confirm the usefulness of this approach.
Discretization effects in the fundamental matrix computation

A polyhedron represents the solution set of an approximate system modeling the epipolar constraints. We introduce a new robust approach for the computation of the fundamental matrix taking into account the intrinsic errors involved in the discretization process. The problem is modeled as an approximate equation system and reduced to a linear programming form. This approach is able to compute the solution set instead of trying to compute only a single vertex of the solution polyhedron as in previous approaches. Outliers are considered as sample point matches whose errors are much bigger that the expected uncertainty ε. We suggest ways to deal with outliers and present an analysis with experiments in synthetic images.
Selection of Learning Algorithms for Trading Systems Based onBiased

In our previous trading system for the S&P 500 index, promising results were obtained by partitioning the historic data into disjoint subsets used to design two biased local estimators whose partial estimates were combined into a trading recommendation 3, 4]. The objective of this study is to explore whether using cascade-correlation learning instead or in addition to the previously used back-propagation to train either one or both of the local estimators improves the trading system's performance. Several learning algorithm combinations were explored and tested using real nancial data. The system yielding the best results used a mixture of learning algorithms (both back-propagation and cascade-correlation) and achieved an annual rate of return of 20.49% without a commission and 14.37% with a 0.05% commission over a ve year trading period. This is signiicantly better than the annual rate of return achieved by both the buy and hold strategy (13.36%) and a system connguration that did not use the cascade-correlation algorithm (11.54% with no commission, 5.35% with a 0.05% commission).
Periodic Control Update Overheads in OpenFlow-Based Enterprise Networks

Software-defined networks (SDNs) detach the forwarding plane from the control plane and communicate instruction sets between the separated planes via the OpenFlow protocol. This arrangement solves some current challenges. However, it introduces challenges of its own that cut across security, scalability and lack of well-defined standards for northbound Application Programming Interfaces (API). This paper studies selected periodic control overheads exhibited by an operational OpenFlow network, and makes comparisons with selected distributed protocols running on legacy network architectures. Results from our simulations show OpenFlow generates significantly higher periodic control traffic (byte and packet count) when determining network state.
Feline Papillomas and Papillomaviruses

Papillomaviruses (PVs) are highly species- and site-specific pathogens of stratified squamous epithelium. Although PV infections in the various Felidae are rarely reported, we identified productive infections in six cat species. PV-induced proliferative skin or mucous membrane lesions were confirmed by immunohistochemical screening for papillomavirus-specific capsid antigens. Seven monoclonal antibodies, each of which reacts with an immunodominant antigenic determinant of the bovine papillomavirus L1 gene product, revealed that feline PV capsid epitopes were conserved to various degrees. This battery of monoclonal antibodies established differential expression patterns among cutaneous and oral PVs of snow leopards and domestic cats, suggesting that they represent distinct viruses. Clinically, the lesions in all species and anatomic sites were locally extensive and frequently multiple. Histologically, the areas of epidermal hyperplasia were flat with a similarity to benign tumors induced by cutaneotropic, carcinogenic PVs in immunosuppressed human patients. Limited restriction endonuclease analyses of viral genomic DNA confirmed the variability among three viral genomes recovered from available frozen tissue. Because most previous PV isolates have been species specific, these studies suggest that at least eight different cat papillomaviruses infect the oral cavity (tentative designations: Asian lion, Panthera leo, P1PV; snow leopard, Panthera uncia, PuPV-1; bobcat, Felis rufus, FrPV; Florida panther, Felis concolor, FcPV; clouded leopard, Neofelis nebulosa, NnPV; and domestic cat, Felis domesticus, FdPV-2) or skin (domestic cat, F. domesticus, FdPV-1; and snow leopard, P. uncia, PuPV-2).
A Multilevel Index Model to Expedite Web Service Discovery and Composition in Large-Scale Service Repositories

The number of web services has grown drastically. Then how to manage them efficiently in a service repository is an important issue to address. Given a special field, there often exists an efficient data structure for a class of objects, e.g., the Google' Bigtable is very suitable for webpages' storage and management. Based on the theory of the equivalence relations and quotient sets, this work proposes a multilevel index model for large-scale service repositories, which can be used to reduce the execution time of service discovery and composition. Its novel use of keys as inspired by the key in relational database can effectively remove the redundancy of the commonly-used inverted index. Its four function-based operations are for the first time proposed to manage and maintain services in a repository. The experiments validate that the proposed model is more efficient than the existing structures, i.e., sequential and inverted index ones.
Colonization of plants by human pathogenic bacteria in the course of organic vegetable production

In recent years, increasing numbers of outbreaks caused by the consumption of vegetables contaminated with human pathogenic bacteria were reported. The application of organic fertilizers during vegetable production is one of the possible reasons for contamination with those pathogens. In this study laboratory experiments in axenic and soil systems following common practices in organic farming were conducted to identify the minimal dose needed for bacterial colonization of plants and to identify possible factors like bacterial species or serovariation, plant species or organic fertilizer types used, influencing the success of plant colonization by human pathogenic bacteria. Spinach and corn salad were chosen as model plants and were inoculated with different concentrations of Salmonella enterica sv. Weltevreden, Listeria monocytogenes sv. 4b and EGD-E sv. 1/2a either directly (axenic system) or via agricultural soil amended with spiked organic fertilizers (soil system). In addition to PCR- and culture-based detection methods, fluorescence in situ hybridization (FISH) was applied in order to localize bacteria on or in plant tissues. Our results demonstrate that shoots were colonized by the pathogenic bacteria at inoculation doses as low as 4 × 10 CFU/ml in the axenic system or 4 × 105 CFU/g in the soil system. In addition, plant species dependent effects were observed. Spinach was colonized more often and at lower inoculation doses compared to corn salad. Differential colonization sites on roots, depending on the plant species could be detected using FISH-CLSM analysis. Furthermore, the transfer of pathogenic bacteria to plants via organic fertilizers was observed more often and at lower initial inoculation doses when fertilization was performed with inoculated slurry compared to inoculated manure. Finally, it could be shown that by introducing a simple washing step, the bacterial contamination was reduced in most cases or even was removed completely in some cases.
Genome sequence and description of Nesterenkonia massiliensis sp. nov. strain NP1T

Nesterenkonia massiliensis sp. nov., strain NP1T, is the type strain of Nesterenkonia massiliensis sp. nov., a new species within the genus Nesterenkonia. This strain, whose genome is described here, was isolated from the feces of a 32-year-old French woman suffering from AIDS and living in Marseille. Nesterenkonia massiliensis is a Gram-positive aerobic coccus. Here, we describe the features of this bacterium, together with the complete genome sequencing and annotation. The 2,726,371 bp long genome (one chromosome but no plasmid) contains 2,663 protein-coding and 51 RNA genes, including 1 rRNA operon.
Identification of a new intestinal spirochete with pathogenicity for chickens

Two intestinal spirochete isolates obtained from chickens with diarrhea were examined by electron microscopy, biochemical tests, rRNA gene restriction pattern analysis, and multilocus enzyme electrophoresis. One isolate (strain 91-1207/C1) was pathogenicity tested in vivo in chickens. The chicken spirochetes were morphologically indistinguishable from Serpulina innocens and Serpulina hyodysenteriae and phenotypically similar to S. innocens. However, the chicken spirochetes could be distinguished from S. innocens, S. hyodysenteriae, and other swine intestinal spirochetes by rRNA gene restriction pattern analysis and multilocus enzyme electrophoresis. In pathogenicity tests in 1-day-old chicks and 14-month-old hens, chicken spirochete 91-1207/C1 produced pale-yellow, watery cecal contents and mild lymphocytic typhlitis. These findings support the conclusion that avian intestinal spirochetes can be pathogenic to commercial poultry and that the microorganisms are different from intestinal spirochetes that infect pigs.
Information-Geometric Optimization Algorithms: A Unifying Picture via Invariance Principles

We present a canonical way to turn any smooth parametric family of probability distributions on an arbitrary search space X into a continuous-time black-box optimization method on X, the information-geometric optimization (IGO) method. Invariance as a major design principle keeps the number of arbitrary choices to a minimum. The resulting IGO flow is the flow of an ordinary differential equation conducting the natural gradient ascent of an adaptive, time-dependent transformation of the objective function. It makes no particular assumptions on the objective function to be optimized. The IGO method produces explicit IGO algorithms through time discretization. It naturally recovers versions of known algorithms and offers a systematic way to derive new ones. In continuous search spaces, IGO algorithms take a form related to natural evolution strategies (NES). The cross-entropy method is recovered in a particular case with a large time step, and can be extended into a smoothed, parametrization-independent maximum likelihood update (IGO-ML). When applied to the family of Gaussian distributions on Rd, the IGO framework recovers a version of the well-known CMA-ES algorithm and of xNES. For the family of Bernoulli distributions on {0, 1}d, we recover the seminal PBIL algorithm and cGA. For the distributions of restricted Boltzmann machines, we naturally obtain a novel algorithm for discrete optimization on {0, 1}d. All these algorithms are natural instances of, and unified under, the single information-geometric optimization framework. The IGO method achieves, thanks to its intrinsic formulation, maximal invariance properties: invariance under reparametrization of the search space X, under a change of parameters of the probability distribution, and under increasing transformation of the function to be optimized. The latter is achieved through an adaptive, quantile-based formulation of the objective. Theoretical considerations strongly suggest that IGO algorithms are essentially characterized by a minimal change of the distribution over time. Therefore they have minimal loss in diversity through the course of optimization, provided the initial diversity is high. First experiments using restricted Boltzmann machines confirm this insight. As a simple consequence, IGO seems to provide, from information theory, an elegant way to simultaneously explore several valleys of a fitness landscape in a single run.
3D binary signatures

In this paper, we propose a novel binary descriptor for 3D point clouds. The proposed descriptor termed as 3D Binary Signature (3DBS) is motivated from the matching efficiency of the binary descriptors for 2D images. 3DBS describes keypoints from point clouds with a binary vector resulting in extremely fast matching. The method uses keypoints from standard keypoint detectors. The descriptor is built by constructing a Local Reference Frame and aligning a local surface patch accordingly. The local surface patch constitutes of identifying nearest neighbours based upon an angular constraint among them. The points are ordered with respect to the distance from the keypoints. The normals of the ordered pairs of these keypoints are projected on the axes and the relative magnitude is used to assign a binary digit. The vector thus constituted is used as a signature for representing the keypoints. The matching is done by using hamming distance. We show that 3DBS outperforms state of the art descriptors on various evaluation metrics.
Representation of Cardiac Electrical Activity by a Moving Dipole for Normal and Ectopic Beats in the Intact Dog

We evaluated the ability of a computer procedure to locate cardiac electrical activity from body surface potentials during normal and ectopic beats in six intact dogs. The location of the dipole that best reconstructed the signals recorded from 26 thoracic electrodes was computed by using a torso model. This model was designed from geometrical measurements made on the first dog. Chronically implanted subepicardial electrodes produced ectopic foci at three known locations: apex, and right and left ventricles. For the normal QRS complex, the dipole started in the middle of the septum, moved upward, then to the left, downward, and back to the right; it remained stationary at the level of the base during repolarization. After ectopic stimulation the dipole started its course at a distance of 1.9 ± 0.8 (SD) cm from the stimulus site and then traversed the heart, moving away from the ectopic site; during the T wave, it roughly followed the QRS path, but at a slower speed. The speed of the dipole ranged between 0 and 6 m/sec, and its orientation often did not coincide with the direction of its path. The location of the dipole appeared to be close to the corresponding wavefronts when these were unique and dipolar, especially during the early and terminal portions of the QRS. The results show that the initial location of the dipole can give the approximate position of an ectopic focus in vivo, and that the trajectory of the dipole during QRS can portray the passage of an ectopic beat across the heart. Circ Res 46: 415-425, 1980
A revision of Cyanonectria and Geejayessia gen. nov., and related species with Fusarium-like anamorphs

A revision of Fusarium-like species associated with the plant genus Buxus led to a reconsideration of generic concepts in the Fusarium clade of the Nectriaceae. Phylogenetic analyses of the partial second largest subunit of the RNA polymerase II (rpb2) and the larger subunit of the ATP citrate lyase (acl1) gene exons confirm the existence of a clade, here called the terminal Fusarium clade, that includes genera such as Fusarium sensu stricto (including its Gibberella teleomorphs), Albonectria, Cyanonectria, “Haematonectria”, the newly described genus Geejayessia, and “Nectria” albida. Geejayessia accommodates five species. Four were previously classified in Nectria sensu lato, namely the black perithecial, KOH–species G. atrofusca and the orange or reddish, KOH+ G. cicatricum, G. desmazieri and G. zealandica. Geejayessia celtidicola is newly described. Following our phylogenetic analyses showing its close relationship with Cyanonectria cyanostoma, the former Gibbera buxi is recombined as the second species of Cyanonectria. A three gene phylogenetic analysis of multiple strains of each morphological species using translation elongation factor 1 α (tef-1), rpb2 and acl1 gene exons and introns confirms their status as distinct phylogenetic species. Internal transcribed spacer of the ribosomal RNA gene cluster and nuclear large ribosomal subunit sequences were generated as additional DNA barcodes for selected strains. The connection of Fusarium buxicola, often erroneously reported as the anamorph of G. desmazieri, with the bluish black and KOH+ perithecial species C. buxi is reinstated. Most Cyanonectria and Geejayessia species exhibit restricted host ranges on branches or twigs of Buxus species, Celtis occidentalis, or Staphylea trifolia. Their perithecia form caespitose clusters on well-developed, mostly erumpent stromata on the bark or outer cortex of the host and are relatively thin-walled, mostly smooth, and therefore reminiscent of the more or less astromatous, singly occurring perithecia of Cosmospora, Dialonectria, and Microcera. The cell walls in outer- and inner layers of the perithecial walls of Cyanonectria and Geejayessia have inconspicuous pore-like structures, as do representative species of Albonectria, Fusarium sensu stricto, “Haematonectria”, and “Nectria” albida. The taxonomic significance of these structures, which we call Samuels' pores, is discussed.