Miracle-dz/UniFAR-FTUs huggingface dataset:
Reduced life span of anergic self-reactive B cells in a double- transgenic model

The life span of anergic self-reactive B cells was determined by 5- bromo-2'-deoxyuridine (BrdU) loading of tolerant double-transgenic (Dbl- Tg) mice produced by mating hen egg lysozyme (HEL)-transgenic mice with the corresponding immunoglobulin-transgenic (Ig-Tg) mice, the B cells of which express anti-HEL IgM and IgD. B cells from Dbl-Tg mice, despite being exposed to soluble antigen throughout their development, are not deleted, but persist in an anergic state. As a prelude to studying the life span of these anergic B cells, BrdU was administered to nontransgenic mice; B cells from the bone marrow, spleen, and lymph nodes displayed distinct kinetic profiles based on reciprocal expression of the B220 isoform of CD45 and heat-stable antigen (HSA). Thus, immature B220lo/HSAhi B cells incorporated BrdU rapidly suggesting recent generation from dividing precursors, whereas uptake by B cells expressing the mature B220hi/HSAlo phenotype was significantly slower, consistent with a longer life span. Such gating allowed analysis to be directed at the stable mature B cell population in transgenic mice. Comparison of BrdU uptake in Ig- and Dbl-Tg mice indicated that B cells from Dbl-Tg mice were renewed at a much higher rate (50% renewal times of 0.64 vs. 3.4 wk for total B cells, and 1.2 vs. 5.0 wk for mature B200hi/HSAlo cells from Dbl- and Ig-transgenic mice, respectively). This difference was even more marked when analysis in Dbl-Tg mice was restricted to HEL-binding cells, which had a 50% renewal time of 3-4 d compared with 4-5 wk for non-HEL-binding B cells. While the proportion of B cells in cell cycle, and the rate of entry of newly generated B cells into the spleen of Ig- and Dbl-Tg mice, were similar, B cell numbers were reduced in Dbl-Tg mice. It was therefore concluded that anergic B cells have a markedly decreased life span in the periphery. According to studies in radiation chimeras produced by reconstituting HEL-transgenic recipients expressing different serum levels of antigen with Ig-Tg bone marrow, the reduced life span of anergic B cells was associated with the anergic state per se, the serum concentration of HEL being important only in attaining the critical threshold necessary for tolerance induction. B cells rendered tolerant by exposure to soluble self-antigen therefore survive for a relatively short period in an anergic state once they have reached peripheral lymphoid tissue and fail to enter the long-lived compartment. (ABSTRACT TRUNCATED AT 400 WORDS)
Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

Accurate genome-wide identification of orthologs is a central problem in comparative genomics, a fact reflected by the numerous orthology identification projects developed in recent years. However, only a few reports have compared their accuracy, and indeed, several recent efforts have not yet been systematically evaluated. Furthermore, orthology is typically only assessed in terms of function conservation, despite the phylogeny-based original definition of Fitch. We collected and mapped the results of nine leading orthology projects and methods (COG, KOG, Inparanoid, OrthoMCL, Ensembl Compara, Homologene, RoundUp, EggNOG, and OMA) and two standard methods (bidirectional best-hit and reciprocal smallest distance). We systematically compared their predictions with respect to both phylogeny and function, using six different tests. This required the mapping of millions of sequences, the handling of hundreds of millions of predicted pairs of orthologs, and the computation of tens of thousands of trees. In phylogenetic analysis or in functional analysis where high specificity is required, we find that OMA and Homologene perform best. At lower functional specificity but higher coverage level, OrthoMCL outperforms Ensembl Compara, and to a lesser extent Inparanoid. Lastly, the large coverage of the recent EggNOG can be of interest to build broad functional grouping, but the method is not specific enough for phylogenetic or detailed function analyses. In terms of general methodology, we observe that the more sophisticated tree reconstruction/reconciliation approach of Ensembl Compara was at times outperformed by pairwise comparison approaches, even in phylogenetic tests. Furthermore, we show that standard bidirectional best-hit often outperforms projects with more complex algorithms. First, the present study provides guidance for the broad community of orthology data users as to which database best suits their needs. Second, it introduces new methodology to verify orthology. And third, it sets performance standards for current and future approaches.
A mapping schema and interface for XML stores

Most XML storage efforts have focused on mapping documents to relational databases. Mapping choices range from storing documents verbatim to shredding documents into relations in various ways. These choices are usually hard-coded into each storage system which makes sharing loading and querying utilities and exchanging information between different XML storage systems hard. To address these issues, we designed MXM and IMXM, a mapping schema and an interface API to define and query XML-to-relational mappings.A mapping is expressed as an instance of MXM. MXM is declarative, concise and captures most existing XML-to-relational mappings. Mappings can be expressed for documents for which no schema information is provided or documents that conform to either a DTD or an XML Schema. IMXM is an interface that allows querying of information contained in a MXM mapping. IMXM is designed as a library of functions which makes it easy to use inside any utility or application that needs to gain access to the XML-to-relational mapping. MXM is extensible and can incorporate new XML-to-relational mappings. We implemented a prototype to define mappings as instances of MXM and generate a repository of meta information on the XML and the relational data and the mapping choices. We implemented IMXM on top of this repository and used it for generating a relational schema and loading XML documents.
A Multi-Source Information System via the Internet for End-Stage Renal Disease: Scalability and Data Quality

A Multi-Source Information System (MSIS), has been designed for the Renal Epidemiology and Information Network (REIN) dedicated to End-Stage Renal Disease (ESRD). MSIS aims at providing reliable follow-up data for ESRD patients. It is based on an n-tier architecture, made out of a universal client, a dynamic Web server connected to a production database and to a data warehouse. MSIS is operational since 2002 and progressively deployed in 9 regions in France. It includes 11,500 patients. MSIS facilitates documenting medical events which occur during the course of ESRD patient' health care and provides means to control the quality of each patient's record and reconstruct the patient trajectory of care. Consolidated data are made available to a data warehouse and to a geographic information system for analysis and data representation in support of public-health decision making.
A Label-Free Electrochemical Aptasensor for the Analysis of The Potassium Ion

Herein, a simple and novel electrochemical method for the detection of potassium ions (K+) was developed. In the presence of potassium ions, the potassium ions aptamer will form a G-quadruplex complex. Thus, further addition of hemin in the presence of potassium ions will lead to the formation of a recombined G-quadruplex. Then the electroactive label, hemin, will give an electrochemical response. The linear range of the method covered a large variation of K+ concentration from 0.1 nM to 0.1 μM and the detection limit of 0.1 nM was obtained. Moreover, this assay was able to detect K+ with high selectivity and had great potential applications.
Spiral galaxies with a central plateau in the gas velocity curve along the major axis

We present the minor-axis kinematics of ionized gas and stars for a sample of 5 spiral galaxies, which are characterized by either a zero or a shallow gas velocity gradient along their major axis. The asymmetric velocity profiles observed along the minor axis of NGC 4064 and NGC 4189 can be explained as due to the presence of a bar. This is also the case of NGC 4178, where the innermost portion of the gaseous disk is nearly face on. In NGC 4424 and NGC 4941, we measured non-zero gas velocities only in the central regions along the minor axis, and gas velocities drop to zero at larger radii. This kinematic feature is suggestive of the presence of an orthogonally-rotating gaseous component, which is confined in the innermost regions (i.e. an inner polar disk) and needs to be confirmed with integral-field spectroscopy.
Anti-Melanogenic Potentials of Nanoparticles from Calli of Resveratrol-Enriched Rice against UVB-Induced Hyperpigmentation in Guinea Pig Skin

We already reported that genetically engineered resveratrol-enriched rice (RR) showed to down-regulate skin melanogenesis. To be developed to increase the bioactivity of RR using calli from plants, RR was adopted for mass production using plant tissue culture technologies. In addition, high-pressure homogenization (HPH) was used to increase the biocompatibility and penetration of the calli from RR into the skin. We aimed to develop anti-melanogenic agents incorporating calli of RR (cRR) and nanoparticles by high-pressure homogenization, examining the synergistic effects on the inhibition of UVB-induced hyperpigmentation. Depigmentation was observed following topical application of micro-cRR, nano-calli of normal rice (cNR), and nano-cRR to ultraviolet B (UVB)-stimulated hyperpigmented guinea pig dorsal skin. Colorimetric analysis, tyrosinase immunostaining, and Fontana-Masson staining for UVB-promoted melanin were performed. Nano-cRR inhibited changes in the melanin color index caused by UVB-promoted hyperpigmentation, and demonstrated stronger anti-melanogenic potential than micro-cRR. In epidermal skin, nano-cRR repressed UVB-promoted melanin granules, thereby suppressing hyperpigmentation. The UVB-enhanced, highly expressed tyrosinase in the basal layer of the epidermis was inhibited by nano-cRR more prominently than by micro-cRR and nano-cNR. The anti-melanogenic potency of nano-cRR also depended on pH and particle size. Nano-cRR shows promising potential to regulate skin pigmentation following UVB exposure.
Significant junctures on the way towards becoming a user of assistive technology in Alzheimer's disease

Abstract Objective: The aim of this study was to describe how persons in the early stages of Alzheimer's disease (AD) became users of assistive technology (AT), and what the use of AT came to mean to these users and, when relevant, their significant others. Methods: Persons with AD were provided with individually chosen AT during a six-month period. Semi-structured interviews were conducted during the intervention period. The data were analysed with a constant comparative approach. Results: On the way towards becoming a user of AT, four junctures were identified, at which significant decisions were made by the participants. These decisions influenced whether to become a user or not and related to how the initial decision was made, how the routines to incorporate the AT were adjusted, whether the participant trusted the AT, and whether the participants felt an increased sense of capacity when using the AT. As users, the participants perceived how time and effort was saved, how worries and stress decreased, and how their sense of safety increased, which enabled them to perform valued activities, e.g. health-promoting and social activities, to a greater extent and in a more relaxed way than before. Conclusions: The findings support the view that AT can positively affect the activity performance of people with AD when the potential user can identify difficulties and needs and is motivated and able to make changes to overcome them, given that appropriate human support is available.
Automatic Identification of Expressions of Locations in Tweet Messages using Conditional Random Fields

In this paper, we propose an automatic identification model, capable of extracting expressions of locations (EoLs) within Twitter messages. Moreover, we participated in the competition of ALTA Shared Task 2014 and our best-performing system is ranked among the top 3 systems (2nd in the public leaderboard). In our model, we explored the validity of the use of a wide variety of lexical, structural and geospatial features as well as a machine learning model Conditional Random Fields (CRF). Further, we investigated the effectiveness of stacking and self-training.
Computer-aided translation backed by machine translation

A number of tools to support translators (computer-aided translation, CAT) exist, as there are many systems of machine translation (MT). So far, the integration of the two system types was little or none. The aim of this paper is to examine a tighter coupling of MT and CAT. We introduce our web-based CAT tool implemented using the modern AJAX technology that communicates with Moses MT system on the server side to provide the translator with suggested translations of individual phrases of the source sentence as well as several options of the complete continuation of the output sentence. The suggested continuation is based on what has been already translated and what the user has already written as the output. Hopefully, the proposed user interface and the MT system at the back end will accelerate and simplify the process of translation.
Mosquito RUNX4 in the immune regulation of PPO gene expression and its effect on avian malaria parasite infection

Prophenoloxidases (PPOs) are key enzymes of the melanization reaction, which is a prominent defense mechanism of arthropods. The mosquito Aedes aegypti has ten PPO genes in the genome, four of which (PPO1, PPO3, PPO5, and PPO8) were expressed in response to microbial infection. Cactus depletion resulted in transcriptional activation of these four genes, suggesting this up-regulation to be under the control of the Toll pathway. The silencing of Cactus also led to developmental arrest and death of the avian malaria parasite, Plasmodium gallinaceum. We discovered that RUNT-related transcription factor 4 (RUNX4), the orthologue of Drosophila Lozenge, bound to the RUNT binding motif in the promoter of mosquito PPO genes and stimulated the expression of Drosophila PPO-A1 and PPO3 in S2 cell line. The immune effects caused by Cactus depletion were eliminated by double knockdown of Cactus/RUNX4. These findings suggest that RUNX4 regulates PPO gene expression under the control of the Toll pathway and plays a critical role in restricting parasite development.
Crystalline silica exposure and lung cancer mortality in diatomaceous earth industry workers: a quantitative risk assessment

OBJECTIVE To use various exposure-response models to estimate the risk of mortality from lung cancer due to occupational exposure to respirable crystalline silica dust. METHODS Data from a cohort mortality study of 2342 white male California diatomaceous earth mining and processing workers exposed to crystalline silica dust (mainly cristobalite) were reanalyzed with Poisson regression and Cox's proportional hazards models. Internal and external adjustments were used to control for potential confounding from the effects of time since first observation, calendar time, age, and Hispanic ethnicity. Cubic smoothing spline models were used to assess the fit of the models. Exposures were lagged by 10 years. Evaluations of the fit of the models were performed by comparing their deviances. Lifetime risks of lung cancer were estimated up to age 85 with an actuarial approach that accounted for competing causes of death. RESULTS Exposure to respirable crystalline silica dust was a significant predictor (p<0.05) in nearly all of the models evaluated and the linear relative rate model with a 10 year exposure lag seemed to give the best fit in the Poisson regression analysis. For those who died of lung cancer the linear relative rate model predicted rate ratios for mortality from lung cancer of about 1.6 for the mean cumulative exposure to respirable silica compared with no exposure. The excess lifetime risk (to age 85) of mortality from lung cancer for white men exposed for 45 years and with a 10 year lag period at the current Occupational Safety and Health Administration (OSHA) standard of about 0.05 mg/m3 for respirable cristobalite dust is 19/1000 (95% confidence interval (95% CI) 5/1000 to 46/1000). CONCLUSIONS There was a significant risk of mortality from lung cancer that increased with cumulative exposure to respirable crystalline silica dust. The predicted number of deaths from lung cancer suggests that current occupational health standards may not be adequately protecting workers from the risk of lung cancer.
Ananthropologicalnursing Science: nursing accompaniment theory

The development of the theory "An anthropological nursing science: Nursing accompaniment theory" was strongly influenced by the existential-phenomenological and personological world and life view of Western-European philosophers of the nineteenth and twentieth century, as well as by developments in the fields of philosophical anthropology and fundamental agogics in South Africa during the seventies. Opsomming Die ontwikkeling van die teorie "'n Antropologiese verpleegkundige: Verpleegbegeleidingsteorie" word sterk be'invloed deur die eksistensie-fenomenologiese en personologiese wereld- en lewensbeskouing van Wes-Europese wysgere van die negentiende en twintigste eeu, asook ontwikkelinge in Suid-Afrika gedurende die sewentigs op terreine van die wysgerige antropologie en fundamentele agogie. *Please note: This is a reduced version of the abstract. Please refer to PDF for full text.
Changes in EEG Rhythms during Television Viewing: Preliminary Comparisons with Reading and other Tasks

The purpose of this study was to provide preliminary data for comparing EEG activity during television viewing with EEG during reading and other tasks commonly used in psychophysiological research. EEG was recorded from left and right occipital locations in 18 subjects and a 2 × 2 × 6 × 5 (sex × site × task × trial) mixed factorial design was used in the analysis of alpha and beta EEG. Significant task effects were obtained for both alpha and beta scores and internal analyses indicated that the highest levels of beta and the lowest amounts of alpha were associated with the two tasks (reading and TV) which presented participants with specific patterns of sensory stimulation whereas tasks calling for mental relaxation (eyes open and eyes closed) and tasks requiring only mental operations (imagine and counting) were associated with lower beta levels and higher alpha. Although not statistically significant, more beta activity was observed during reading than during TV and more alpha was observed during TV than during reading. No main effects or interaction terms involving sex differences or hemispheric effects were significant.
A Graph Matching Algorithm Using Data-Driven Markov Chain Monte Carlo Sampling

We propose a novel stochastic graph matching algorithm based on data-driven Markov Chain Monte Carlo (DDMCMC) sampling technique. The algorithm explores the solution space efficiently and avoid local minima by taking advantage of spectral properties of the given graphs in data-driven proposals. Thus, it enables the graph matching to be robust to deformation and outliers arising from the practical correspondence problems. Our comparative experiments using synthetic and real data demonstrate that the algorithm outperforms the state-of-the-art graph matching algorithms.
Analysis of in planta Expressed Orphan Genes in the Rice Blast Fungus Magnaporthe oryzae

Genomes contain a large number of unique genes which have not been found in other species. Although the origin of such “orphan” genes remains unclear, they are thought to be involved in species-specific adaptive processes. Here, we analyzed seven orphan genes (MoSPC1 to MoSPC7) prioritized based on in planta expressed sequence tag data in the rice blast fungus, Magnaporthe oryzae. Expression analysis using qRT-PCR confirmed the expression of four genes (MoSPC1, MoSPC2, MoSPC3 and MoSPC7) during plant infection. However, individual deletion mutants of these four genes did not differ from the wild-type strain for all phenotypes examined, including pathogenicity. The length, GC contents, codon adaptation index and expression during mycelial growth of the four genes suggest that these genes formed during the evolutionary history of M. oryzae. Synteny analyses using closely related fungal species corroborated the notion that these genes evolved de novo in the M. oryzae genome. In this report, we discuss our inability to detect phenotypic changes in the four deletion mutants. Based on these results, the four orphan genes may be products of de novo gene birth processes, and their adaptive potential is in the course of being tested for retention or extinction through natural selection.
Modeling Cross-Device Systems with Use Case Diagrams

In: S. España, M. Ivanović, M. Savić (eds.): Proceedings of the CAiSE’16 Forum at the 28th International Conference on Advanced Information Systems Engineering, Ljubljana, Slovenia, 13-17.6. 2016, published at http://ceur-ws.org Abstract. Information systems often support a variety of different device types like desktop computers, smartphones or tablets. Some can even be used in a cross-device manner, i.e., using multiple devices in parallel or being able to switch from one device to another while interacting with the system. Even though there is increasing support to implement such cross-device systems, existing modeling languages only provide limited means to specify them. In this paper, we present an extended form of UML use case diagrams, which allows to properly take the cross-device features of a system into account and serves as a first step towards a model-based development process for cross-device systems.
How to improve your PubMed/MEDLINE searches: 3. advanced searching, MeSH and My NCBI

Summary Although the basic PubMed search is often helpful, the results may sometimes be non-specific. For more control over the search process you can use the Advanced Search Builder interface. This allows a targeted search in specific fields, with the convenience of being able to select the intended search field from a list. It also provides a history of your previous searches. The search history is useful to develop a complex search query by combining several previous searches using Boolean operators. For indexing the articles in MEDLINE, the NLM uses a controlled vocabulary system called MeSH. This standardised vocabulary solves the problem of authors, researchers and librarians who may use different terms for the same concept. To be efficient in a PubMed search, you should start by identifying the most appropriate MeSH terms and use them in your search where possible. My NCBI is a personal workspace facility available through PubMed and makes it possible to customise the PubMed interface. It provides various capabilities that can enhance your search performance.
Personal(ized) Health Monitoring, Personalization, and Personality

Use of technology in individual health monitoring is predicted to be widespread in near future healthcare systems and in smart home environments. The term Personalized Health Monitoring (PHM) is proposed for these applications. A framework describing aspects of personalization and personality that are relevant to personalized health monitoring is presented. The framework addresses personal data, adaptability, feedback, and personality. Influence of personality on approach, interaction, and adherence to PHM technology are discussed. Personality is both a variable influencing monitored data, as well as a variable that can be monitored itself. An agenda for future research in the field of Personal and Personalized Health Monitoring is presented.