Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of sister species identifies factors underpinning plastid compatibility in green sea slugs

The only animal cells known that can maintain functional plastids (kleptoplasts) in their cytosol occur in the digestive gland epithelia of sacoglossan slugs. Only a few species of the many hundred known can profit from kleptoplasty during starvation long-term, but why is not understood. The two sister taxa Elysia cornigera and Elysia timida sequester plastids from the same algal species, but with a very different outcome: while E. cornigera usually dies within the first two weeks when deprived of food, E. timida can survive for many months to come. Here we compare the responses of the two slugs to starvation, blocked photosynthesis and light stress. The two species respond differently, but in both starvation is the main denominator that alters global gene expression profiles. The kleptoplasts' ability to fix CO2 decreases at a similar rate in both slugs during starvation, but only E. cornigera individuals die in the presence of functional kleptoplasts, concomitant with the accumulation of reactive oxygen species (ROS) in the digestive tract. We show that profiting from the acquisition of robust plastids, and key to E. timida's longer survival, is determined by an increased starvation tolerance that keeps ROS levels at bay.
Enzyme-linked immunosorbent assay for immunoglobulin G subclass antibodies specific for enterobacterial Re core glycolipid in healthy individuals and in patients infected by gram-negative bacteria

An enzyme-linked immunosorbent assay was developed to study the subclass distribution of immunoglobulin G (IgG) specific to the core glycolipid (CGL) of the Re mutant of Salmonella minnesota R595 in serum samples from individuals with an IgG response toward these antigens. In a group of healthy blood donors, we detected predominantly the IgG2 and IgG1 subclasses. In a group of patients in an intensive care unit who developed infectious complications due to gram-negative bacteria, the anti-CGL IgG activity was due mainly to the IgG2 and IgG3 subclasses. In all serum samples found to be IgG positive, the assay for anti-CGL IgG2 was positive. This subclass was revealed to play a predominant role in patients displaying a seroconversion or a significant rise in their antibody response toward CGL. IgG4 was found or appeared only in patients with confirmed bacteremia. In addition, we observed a drop in anti-CGL IgG2 before the death of patients undergoing a septic shock or an irreversible organ failure, suggesting that the anti-CGL IgG2 activity could be used as a marker of the evolution of the illness in this group of patients.
Biochemical Analysis of Matrix Metalloproteinase Activation of Chemokines CCL15 and CCL23 and Increased Glycosaminoglycan Binding of CCL16*

Background: Proteases responsible for a CCL15-(25–92) product have not been elucidated. Results: All 14 CC monocyte chemoattractants, including CCL15, are processed by multiple MMPs. Conclusion: MMP-processing of CCL15, CCL23, and CCL16 functional activity is altered by MMP processing. Significance: This is the first study showing MMPs can activate CC chemokines and hence monoycte chemoattraction with potential to propagate inflammation. Leukocyte migration and activation is orchestrated by chemokines, the cleavage of which modulates their activity and glycosaminoglycan binding and thus their roles in inflammation and immunity. Early research identified proteolysis as a means of both activating or inactivating CXC chemokines and inactivating CC chemokines. Recent evidence has shown activating cleavages of the monocyte chemoattractants CCL15 and CCL23 by incubation with synovial fluid, although the responsible proteases could not be identified. Herein we show that CCL15 is processed in human synovial fluid by matrix metalloproteinases (MMPs) and serine proteases. Furthermore, a family-wide investigation of MMP processing of all 14 monocyte-directed CC chemokines revealed that each is precisely cleaved by one or more MMPs. By MALDI-TOF-MS, 149 cleavage sites were sequenced including the first reported instance of CCL1, CCL16, and CCL17 proteolysis. Full-length CCL15-(1–92) and CCL23-(1–99) were cleaved within their unique 31 and 32-amino acid residue extended amino termini, respectively. Unlike other CCL chemokines that lose activity and become receptor antagonists upon MMP cleavage, the prominent MMP-processed products CCL15-(25–92, 28–92) and CCL23-(26–99) are stronger agonists in calcium flux and Transwell CC receptor transfectant and monocytic THP-1 migration assays. MMP processing of CCL16-(1–97) in its extended carboxyl terminus yields two products, CCL16-(8–77) and CCL16-(8–85), with both showing unexpected enhanced glycosaminoglycan binding. Hence, our study reveals for the first time that MMPs activate the long amino-terminal chemokines CCL15 and CCL23 to potent forms that have potential to increase monocyte recruitment during inflammation.
A Novel Approach towards Segmentation of Breast Tumors from Screening Mammograms for Efficient Decision Support System

This paper presents a novel approach to finding a priori interesting regions in mammograms. In order to delineate those regions of interest (ROI’s) in mammograms, which appear to be prominent, a topographic representation called the iso-level contour map consisting of iso-level contours at multiple intensity levels and region segmentation based-thresholding have been proposed. The simulation results indicate that the computed boundary gives the detection rate of 99.5% accuracy. Keywords—Breast Cancer, Mammogram, and Segmentation.
An Analytical Solution of Effect of Water Content on Solute Transport in Saturated and Unsaturated Porous Media

Most of the researchers use the coordinate transformation (x ut) in order to evaluate the equation for advection-dispersion of a moving fluid in porous media. Further, the boundary conditions C = 0 at x =  and C = C0 at x = –  for t  0 are used, which results in a symmetrical concentration distribution. The objective of this paper is to find the solution of differential equation in longitudinal direction that avoids this transformation, thus giving rise to an asymmetrical concentration distribution. It is then shown that the solution approaches that given by symmetrical boundary conditions, provided the dispersion coefficient D is small and the region near the source will not be considered. The solution has been obtained for the dispersion model of longitudinal mixing with variable coefficients in a finite length initially solute free domain. In the beginning, homogeneous domain is studied for dependent advection-dispersion along with uniform flow. The solution has been obtained for the uniform velocity by considering spatially dependent due to the heterogeneity of the domain and the dispersion proportional to the square of the velocity. The velocity is linearly interpolated and small increment along the finite domain. The input condition has been considered continuous of uniform and of increasing nature both. The solutions are obtained for both the domains by using Duhamel’s theorem and integral solution technique. The new independent space and time variables processes has been introduced. The effects of the dependency of dispersion with time and the heterogeneity of the domain on the solute transport are studied separately with the help of graphs.
MR spectroscopy in HIV and stimulant dependence

HIV infection and abuse of central nervous system (CNS) stimulants are both associated with brain damage and dysfunction. CNS stimulant overdose can lead to microinfarction, hemorrhagic lesions, and vasculitis (Bostwick, 1981; Cahill et al., 1981), and may impact frontostriatal systems. Investigations of HIV-infected (HIV+) individuals have demonstrated deficits in attention, speed of information processing, motor functioning, executive functioning, and learning efficiency. These deficits are consistent with frontostriatal involvement (Heaton et al., 1995; Martin, 1994). Given the rise in AIDS cases attributable to drug use at a time when the number of AIDS cases due to sexual transmission is stable or declining, it is critical to determine if drug use, especially CNS stimulants, potentiates HIV-related neuronal injury.
CD24 on the Resident Cells of the Central Nervous System Enhances Experimental Autoimmune Encephalomyelitis1

CD24 is a cell surface glycoprotein that is expressed on both immune cells and cells of the CNS. We have previously shown that CD24 is required for the induction of experimental autoimmune encephalomyelitis (EAE), an experimental model for the human disease multiple sclerosis (MS). The development of EAE requires CD24 expression on both T cells and non-T host cells in the CNS. To understand the role of CD24 on the resident cells in the CNS during EAE development, we created CD24 bone marrow chimeras and transgenic mice in which CD24 expression was under the control of a glial fibrillary acidic protein promotor (AstroCD24TG mice). We showed that mice lacking CD24 expression on the CNS resident cells developed a mild form of EAE; in contrast, mice with overexpression of CD24 in the CNS developed severe EAE. Compared with nontransgenic mice, the CNS of AstroCD24TG mice had higher expression of cytokine genes such as IL-17 and demyelination-associated marker P8; the CNS of AstroCD24TG mice accumulated higher numbers of Th17 and total CD4+ T cells, whereas CD4+ T cells underwent more proliferation during EAE development. Expression of CD24 in CD24-deficient astrocytes also enhanced their costimulatory activity to myelin oligodendrocyte glycoprotein-specific, TCR-transgenic 2D2 T cells. Thus, CD24 on the resident cells in the CNS enhances EAE development via costimulation of encephalitogenic T cells. Because CD24 is increased drastically on resident cells in the CNS during EAE, our data have important implications for CD24-targeted therapy of MS.
Transparently interposing user code at the system interface

The author reports on the development of an object-oriented toolkit which substantially increases the ease of interposing user code between clients and instances of the system interface by allowing such code to be written in terms of the high-level objects provided by this interface, rather than in terms of the intercepted system calls themselves. This toolkit helps enable new interposition agents to be written which otherwise would not have been attempted. It is used to construct several agents including protected environments for running untrusted binaries, modified file system namespaces, logical devices implemented entirely in user space, transparent network data compression and/or encryption agents, and system call tracing tools. Examples of other agents which could be built include transactional software environments and emulators for other operating system environments. <<ETX>>
A generalized eigensolver based on smoothed aggregation (GES‐SA) for initializing smoothed aggregation (SA) multigrid

Consider the linear system Ax=b, where A is a large, sparse, real, symmetric, and positive‐definite matrix and b is a known vector. Solving this system for unknown vector x using a smoothed aggregation (SA) multigrid algorithm requires a characterization of the algebraically smooth error, meaning error that is poorly attenuated by the algorithm's relaxation process. For many common relaxation processes, algebraically smooth error corresponds to the near‐nullspace of A. Therefore, having a good approximation to a minimal eigenvector is useful to characterize the algebraically smooth error when forming a linear SA solver. We discuss the details of a generalized eigensolver based on smoothed aggregation (GES‐SA) that is designed to produce an approximation to a minimal eigenvector of A. GES‐SA may be applied as a stand‐alone eigensolver for applications that desire an approximate minimal eigenvector, but the primary purpose here is to apply an eigensolver to the specific application of forming robust, adaptive linear solvers. This paper reports the first stage in our study of incorporating eigensolvers into the existing adaptive SA framework. Copyright © 2008 John Wiley & Sons, Ltd.
A New Riemannian Setting for Surface Registration

We present a new approach for matching regular surfaces in a Riemannian setting. We use a Sobolev type metric on deformation vector fields which form the tangent bundle to the space of surfaces. In this article we compare our approach with the diffeomorphic matching framework. In the latter approach a deformation is prescribed on the ambient space, which then drags along an embedded surface. In contrast our metric is defined directly on the deformation vector field and can therefore be called an inner metric. We also show how to discretize the corresponding geodesic equation and compute the gradient of the cost functional using finite elements.
Evidence for the role of PPAR‐β/δ in the development of spinal cord injury

Evidence suggests a biological role for peroxisome proliferator activated receptor (PPAR)‐β/δ in the pathogenesis of a number of diseases. The aim of the present study was to evaluate the contribution of PPAR‐β/δ in the secondary damage following experimental spinal cord injury (SCI) in mice. Spinal cord trauma was induced by the application of vascular clips to the dura via a four‐level T5–T8 laminectomy. SCI resulted in severe trauma characterized by oedema, neutrophil infiltration, production of inflammatory mediators, tissue damage, and apoptosis. The high affinity PPAR‐β/δ agonist GW0742 (0.3 mg/kg, i.p.) 1 and 6 h after the SCI significantly reduced: (1) the degree of spinal cord inflammation and tissue injury, (2) neutrophil infiltration, (3) nitrotyrosine formation, (4) pro‐inflammmaory cytokines, (5) NF‐κB activation, (6) iNOS expression and (6) apoptosis (TUNEL staining, FasL, Bax and Bcl‐2 expression). Moreover, GW0742 significantly ameliorated the recovery of locomotory function (evaluated by motor score). In order to elucidate whether the protective effects of GW0742 are related to activation of the PPAR‐β/δ, we investigated the function of PPAR‐β/δ antagonist, GSK0660, on the protective effects of GW0742. GSK0660 (1 mg/kg i.p. 30 min prior to GW0742)significantly blunted the protective effect of the PPAR‐β/δ agonist. Our results demonstrate that GW0742 treatment reduces the development of inflammation and tissue injury associated with spinal cord trauma.
Research of the Relationship of E-service Quality , Customer Satisfaction and Customer Loyalty in C 2 C Online Shopping

There are five major findings by using confirmatory factor analysis and structural equation modeling technique through survey data: (1) The service quality of C2C online shop is affected by four dimensions which are Web design, ease of use, reliability, and customer service; (2) The individual dimensions of service quality influences the customer satisfaction significantly positively; (3) The dimensions of ease of use and reliability influence the customer loyalty significantly positively; (4) The dimensions of web design and customer service influence customer loyalty indirectly by customer satisfaction; (5) The customer satisfaction significantly affects the customer loyalty. The results of this study have important meanings for managers of online shops to improve the customer loyalty. Online stores can devote valuable resources to the important e-service quality attributes identified by this study. At last, the directions of further research are suggested.
Sequential Principal Curves Analysis

This work includes all the technical details of the Sequential Principal Curves Analysis (SPCA) in a single document. SPCA is an unsupervised nonlinear and invertible feature extraction technique. The identified curvilinear features can be interpreted as a set of nonlinear sensors: the response of each sensor is the projection onto the corresponding feature. Moreover, it can be easily tuned for different optimization criteria; e.g. infomax, error minimization, decorrelation; by choosing the right way to measure distances along each curvilinear feature. Even though proposed in [Laparra et al. Neural Comp. 12] and shown to work in multiple modalities in [Laparra and Malo Frontiers Hum. Neuro. 15], the SPCA framework has its original roots in the nonlinear ICA algorithm in [Malo and Gutierrez Network 06]. Later on, the SPCA philosophy for nonlinear generalization of PCA originated substantially faster alternatives at the cost of introducing different constraints in the model. Namely, the Principal Polynomial Analysis (PPA) [Laparra et al. IJNS 14], and the Dimensionality Reduction via Regression (DRR) [Laparra et al. IEEE TGRS 15]. This report illustrates the reasons why we developed such family and is the appropriate technical companion for the missing details in [Laparra et al., NeCo 12, Laparra and Malo, Front.Hum. Neuro. 15]. See also the data, code and examples in the dedicated sites this http URL and this http URL effects.html
Collaborative Semantic Authoring

In the context of the semantic Web, notions of collaboration, interoperability, and reuse are intrinsically interrelated: interoperability implies reuse, which in turn is a form of collaboration. If we adopt this viewpoint, the semantic Web becomes essentially a medium for knowledge exchange, in which the knowledge produced by one agent is consumed by another agent, possibly to create new knowledge. A collaboration-centric perspective on the semantic Web introduces both challenges and interesting research directions. Clearly, it's no longer desirable that the process of authoring semantic content necessarily take place in a room full of experts and ontologists. Indeed, as we move from classic Web 2.0 technologies to scenarios in which semantic content is created, our technologies need to change so that it becomes possible to create and exchange knowledge transparently, in accordance with the medium's openness and the knowledge producers' various goals and skill levels. In this article, we examine three modalities for collaborative semantic authoring based on selecting and reusing external, open semantic resources. These three ways of creating semantic content correspond to three levels of interaction between the user and the created resources. We illustrate each level by describing a tool we designed in the context of our research on semantic Web applications at the Knowledge Media Institute.
Robust loop closing over time for pose graph SLAM

Long-term autonomous mobile robot operation requires considering place recognition decisions with great caution. A single incorrect decision that is not detected and reconsidered can corrupt the environment model that the robot is trying to build and maintain. This work describes a consensus-based approach to robust place recognition over time, that takes into account all the available information to detect and remove past incorrect loop closures. The main novelties of our work are: (1) the ability of realizing that, in light of new evidence, an incorrect past loop closing decision has been made; the incorrect information can be removed thus recovering the correct estimation with a novel algorithm; (2) extending our proposal to incremental operation; and (3) handling multi-session, spatially related or unrelated scenarios in a unified manner. We demonstrate our proposal, the RRR algorithm, on different odometry systems, e.g. visual or laser, using different front-end loop-closing techniques. For our experiments we use the efficient graph optimization framework g2o as back-end. We back our claims up with several experiments carried out on real data, in single and multi-session experiments showing better results than those obtained by state-of-the-art methods, comparisons against whom are also presented.
Field Evaluation of a Rapid Immunochromatographic Assay for Detection of Trypanosoma cruzi Infection by Use of Whole Blood

ABSTRACT Laboratory and clinical diagnostic classification of seropositive individuals, followed by treatment and supportive therapy, is an established component of Chagas' disease control in areas where this disease is endemic. However, most Chagas' disease patients live in remote areas where neither equipped laboratories nor skilled human resources are widely available. Employing a rapid diagnostic test (RDT), when using whole blood samples, is the best option for Chagas' disease control. A high sensitivity and specificity for the Chagas Stat-Pak RDT (Chembio Diagnostic Systems, Inc., Medford, NY) has been reported for assays using serum and plasma, but its validity for the detection of antibodies to Trypanosoma cruzi infection in whole blood is unknown. This cross-sectional study measured the sensitivity and specificity of the Chagas Stat-Pak with whole blood, using conventional serological assays for comparison. The interobserver reliability in the interpretation of the Chagas Stat-Pak results and “ease-of-use” criterion needed to perform the Chagas Stat-Pak and conventional assays were also measured. The Chagas Stat-Pak yielded a high specificity (99.0%, 95% confidence interval [CI] = 98.4 to 99.4%) but a relatively low sensitivity (93.4%, 95% CI = 87.4 to 97.1%). The interobserver reliability was excellent (kappa [n = 1,913] = 0.999, P < 0.0001), and the quantified ease-of-use criterion suggested that the RDT is simple to perform. Despite the attributes of the Chagas Stat-Pak, it is not an ideal diagnostic test for the population investigated in the present study due to its relatively low sensitivity and high cost. The RDT manufacturer is called upon to improve the test if the international community hopes to make progress in controlling Chagas infections in areas where this disease is endemic.
Paraphrasing Treebanks for Stochastic Realization Ranking

This paper1 describes a novel approach to the task of realization ranking, i.e. the choice among competing paraphrases for a given input semantics, as produced by a generation system. We also introduce a notion of symmetric treebanks, which we define as the combination of (a) a set of pairings of surface forms and associated semantics plus (b) the sets of alternative analyses for the surface form and sets of alternate realizations of the semantics. For inclusion of alternate analyses and realizations in the symmetric treebank, we propose to make the underlying linguistic theory explicit and operational, viz. in the form of a broad-coverage computational grammar. Extending earlier work on grammar-based treebanks in the Redwoods (Oepen et al. [13]) paradigm, we present a fully automated procedure to produce a symmetric treebank from existing resources. To evaluate the utility of an initial (albeit smallish) such ‘expanded’ treebank, we report on experimental results for training stochastic discriminative models for the realization ranking task. Our work is set within the context of a Norwegian–English machine translation project (LOGON; Oepen et al. [11]). The LOGON system builds on a relatively conventional semantic transfer architecture—based on Minimal Recursion Semantics (MRS; Copestake et al. [5])—and quite generally aims to combine a ‘deep’ linguistic backbone with stochastic processes for ambiguity management and improved robustness. In this paper we focus on the isolated subtask of ranking the output of the target language generator. For target language realization, LOGON uses the LinGO English Resource Grammar (ERG; Flickinger [6]) and LKB generator, a lexically-driven chart generator that accepts MRS-style input semantics (Carroll et al. [2]). Over a representative LOGON data set, the generator already produces an average of 45 English realizations per input MRS; see Figure 1 for an example. As we expect to move to