Miracle-dz/UniFAR-FTUs huggingface dataset:
FANCI and FANCD2 have common as well as independent functions during the cellular replication stress response

Abstract Fanconi anemia (FA) is an inherited cancer predisposition syndrome characterized by cellular hypersensitivity to DNA interstrand crosslinks (ICLs). To repair these lesions, the FA proteins act in a linear hierarchy: following ICL detection on chromatin, the FA core complex monoubiquitinates and recruits the central FANCI and FANCD2 proteins that subsequently coordinate ICL removal and repair of the ensuing DNA double-stranded break by homology-dependent repair (HDR). FANCD2 also functions during the replication stress response by mediating the restart of temporarily stalled replication forks thereby suppressing the firing of new replication origins. To address if FANCI is also involved in these FANCD2-dependent mechanisms, we generated isogenic FANCI-, FANCD2- and FANCI:FANCD2 double-null cells. We show that FANCI and FANCD2 are partially independent regarding their protein stability, nuclear localization and chromatin recruitment and contribute independently to cellular proliferation. Simultaneously, FANCD2—but not FANCI—plays a major role in HDR-mediated replication restart and in suppressing new origin firing. Consistent with this observation, deficiencies in HDR-mediated DNA DSB repair can be overcome by stabilizing RAD51 filament formation in cells lacking functional FANCD2. We propose that FANCI and FANCD2 have partially non-overlapping and possibly even opposing roles during the replication stress response.
Biallelic genome modification in F0 Xenopus tropicalis embryos using the CRISPR/Cas system

Gene inactivation is an important tool for correlation of phenotypic and genomic data, allowing researchers to infer normal gene function based on the phenotype when the gene is impaired. New and better approaches are needed to overcome the shortfalls of existing methods for any significant acceleration of scientific progress. We have adapted the CRISPR/Cas system for use in Xenopus tropicalis and report on the efficient creation of mutations in the gene encoding the enzyme tyrosinase, which is responsible for oculocutaneous albinism. Biallelic mutation of this gene was detected in the F0 generation, suggesting targeting efficiencies similar to that of TALENs. We also find that off‐target mutagenesis seems to be negligible, and therefore, CRISPR/Cas may be a useful system for creating genome modifications in this important model organism. genesis 51:827–834. © 2013 Wiley Periodicals, Inc.
Capacity analysis for Gaussian channels with memoryless nonlinear hardware

This paper presents the analysis of the impact of circuit nonlinearities on the transmission rate of a communication system. We consider a general transmission model that includes transmitter- and receiver-side nonlinearities, environmental thermal noise and receiver chain noise. Using this model we establish lower and upper bounds for the capacity of nonlinear additive white Gaussian noise channels in various thermal noise and receiver noise regimes.
Establishment and Characterization of a Bank of Cytotoxic T Lymphocytes for Immunotherapy of Epstein-Barr Virus-Associated Diseases

Adoptive immunotherapy using Epstein-Barr virus (EBV)-specific cytotoxic T lymphocytes (CTL) generated ex vivo can be an effective treatment of EBV-positive posttransplantation lymphoproliferative disease (PTLD). We describe the establishment of a cryopreserved repository of allogeneic virus-specific CTL lines, to our knowledge the first of its kind in the world. CTL lines were grown by weekly stimulation with autologous EBV immortalized lymphoblastoid cell lines (LCLs) from 96 EBV-seropositive blood donors. Analysis of 60 CTL lines grown continuously for 7 to 10 weeks showed an average proportional weekly increase in cell numbers of 1.4, with an overall increase ranging from 1.1 to 83.4. The greatest increase occurred during the early culture period. After four rounds of stimulation, killing of autologous LCLs was generally high (mean 48%); however, most lines required 9 or 10 stimulations to reduce the killing of nonspecific targets. Overall, 79% of CTLs generated showed acceptable levels of specific killing. Phenotypically, the CTL lines consisted of TCR&agr;β+, CD8+ T cells (medians 97% and 90% respectively) with a minority population of CD4+ T cells (median 2%). Most cells expressed the activation and differentiation markers, HLA-DR, CD26, CD45RO, CD69, and CD150. Favorable results have been obtained in an open trial using partially HLA-matched, allogeneic CTLs from this bank to treat PTLD patients. This now represents a single resource that can provide therapeutic CTLs rapidly on a countrywide basis, superseding the time-consuming, expensive practice of generating autologous CTLs from each patient requiring treatment. Additionally, other patient groups, such as those with EBV-positive Hodgkin disease, may benefit from CTL treatment.
Lexicon-based sentiment analysis by mapping conveyed sentiment to intended sentiment

As consumers nowadays generate increasingly more content describing their experiences with, e.g., products and brands in various languages, information systems monitoring a universal, language-independent measure of people's intended sentiment are crucial for today's businesses. In order to facilitate sentiment analysis of user-generated content, we propose to map sentiment conveyed by unstructured natural language text to universal star ratings, capturing intended sentiment. For these mappings, we consider a monotonically increasing step function, a naive Bayes method, and a support vector machine. We demonstrate that the way in which natural language reveals intended sentiment differs across our datasets of Dutch and English texts. Additionally, the results of our experiments on modelling the relation between conveyed sentiment and intended sentiment suggest that language-specific sentiment scores can separate universal classes of intended sentiment from one another to a limited extent.
Drug-induced hypereosinophilia related to tocilizumab therapy for rheumatoid arthritis.

Giacomo Maria Guidelli, Marco Bardelli, Enrico Selvi, Mauro Galeazzi and Renato De Stefano Section of Rheumatology, Department of Medicine, Surgery and Neuroscience, Policlinico Le Scotte, Siena, Italy Revised version accepted 24 June 2015 Correspondence to: Giacomo Maria Guidelli, Section of Rheumatology, Department of Medicine, Surgery and Neuroscience, Policlinico Le Scotte Siena, Italy. E-mail: giacoguidelli@hotmail.com
A Meshless Algorithm to Model Field Evaporation in Atom Probe Tomography

Abstract An alternative approach for simulating the field evaporation process in atom probe tomography is presented. The model uses the electrostatic Robin’s equation to directly calculate charge distribution over the tip apex conducting surface, without the need for a supporting mesh. The partial ionization state of the surface atoms is at the core of the method. Indeed, each surface atom is considered as a point charge, which is representative of its evaporation probability. The computational efficiency is ensured by an adapted version of the Barnes–Hut N-body problem algorithm. Standard desorption maps for cubic structures are presented in order to demonstrate the effectiveness of the method.
Intrinsic risk factors for falls by community-based seniors: implications for prevention

Research suggests that a combination of factors put seniors at risk of falling. The Guidelines for the Prevention of Falls in Older Persons (American Geriatric Society, British Geriatrics Society and American Academy of Orthopaedic Surgeons Panel on Falls Prevention 2001) classified risk factors as either intrinsic (occurring in one’s own body) or extrinsic (occurring in one’s environment) and identified 11 intrinsic factors as most common based on bivariate analyses: muscle weakness; history of falls; gait deficit; balancing deficit; use of assistive devices; visual deficits; arthritis; impairment in doing daily activities; depression; cognitive impairment; and being older than 80 years of age. The US Department of Health and Human Services (2004) identified fear of falling as one of the most common risk factors for falls among community-based seniors and recommended using the Fall Efficacy Scale (FES) to measure fear of falling. This study examines the 1-year prevalence of falls among community-based seniors and uses multifactorial analysis to identify intrinsic risk factors that predict falls.
Application of an extended spectral FDTD method for the analysis of periodic structures with lumped elements

In this paper, a novel FDTD method is presented for calculating the dispersion diagram of periodic structures that include lumped passive circuit elements. By combining the FDTD method with periodic boundary conditions (PBCs) and the uniaxial perfect matched layer (UPML), the analysis of periodic structures is reduced to that of a unit cell. The usefulness of the method is demonstrated through the analysis of a negative refractive index material based on a structure that combines lumped and distributed transmission line elements. Numerical results verify the validity of the method.
Antigen-Specific Effector CD4 T Lymphocytes School Lamina Propria Dendritic Cells To Transfer Innate Tolerance

Dendritic cells (DCs) have been shown to play a major role in oral tolerance, and this function has been associated with their ability to produce anti-inflammatory cytokines and to induce suppressive regulatory T cells. In this study, we demonstrate that upon oral administration of Ag, lamina propia (LP) DCs engage specific T cells and acquire a novel mechanism by which they transfer tolerance against diverse T cell specificities. Indeed, when Ig-myelin oligodendrocyte glycoprotein (MOG) carrying the MOG35–55 epitope was orally administered into either T cell–sufficient or –deficient mice, only the T cell–sufficient hosts yielded CD8α+ and CD8α− LP DCs that were able to transfer tolerance to a variety of MHC class II–restricted effector T cells. Surprisingly, these LP DCs upregulated programmed cell death ligand 1 during the initial interaction with MOG-specific T cells and used this inhibitory molecule to suppress activation of T cells regardless of Ag specificity. Furthermore, oral Ig-MOG was able to overcome experimental autoimmune encephalomyelitis induced with CNS homogenate, indicating that the DCs are able to modulate disease involving diverse T cell specificities. This previously unrecognized attribute potentiates DCs against autoimmunity.
Longitudinal multiparameter assay of lymphocyte interactions from onset by microfluidic cell pairing and culture

Significance Many immune responses are mediated by direct cell–cell interactions and develop over multiple timescales. A mechanistic understanding of how diverse outcomes arise during these interactions entails identifying the relationships between various responses occurring at different stages by correlated measurements. Typical approaches that rely on population-wide correlations, however, reveal these connections broadly and mask the fine details that might be discernible only at the single-cell level. Here, we present a microfluidics-based cell–cell interaction assay that allows defined generation, real-time imaging, and longitudinal assay of lymphocyte interactions, thereby permitting direct correlative studies within each single cell. Our studies using this platform indicate a possible role for the strength of calcium signaling in selective regulation of cytotoxicity and interferon-gamma production of natural killer cells. Resolving how the early signaling events initiated by cell–cell interactions are transduced into diverse functional outcomes necessitates correlated measurements at various stages. Typical approaches that rely on bulk cocultures and population-wide correlations, however, only reveal these relationships broadly at the population level, not within each individual cell. Here, we present a microfluidics-based cell–cell interaction assay that enables longitudinal investigation of lymphocyte interactions at the single-cell level through microfluidic cell pairing, on-chip culture, and multiparameter assays, and allows recovery of desired cell pairs by micromanipulation for off-chip culture and analyses. Well-defined initiation of interactions enables probing cellular responses from the very onset, permitting single-cell correlation analyses between early signaling dynamics and later-stage functional outcomes within same cells. We demonstrate the utility of this microfluidic assay with natural killer cells interacting with tumor cells, and our findings suggest a possible role for the strength of early calcium signaling in selective coordination of subsequent cytotoxicity and IFN-gamma production. Collectively, our experiments demonstrate that this new approach is well-suited for resolving the relationships between complex immune responses within each individual cell.
GAMMA RAYS INDUCED PROTEIN VARIATIONS IN M 4 GENERATION OF BLACK GRAM ( VIGNA MUNGO L.)

Effects of various doses (45 krad, 55 krad and 65 krad) of gamma rays on proteins of black gram (Vigna mungo L.) in M 4 generation were investigated using Sodium dodecyl sulphate-poly acrylamide gel electrophoresis (SDS-PAGE) analysis. Higher doses of gamma rays resulted in reduced seed germination and affected further plant growth. SDS-PAGE results indicated differences in the protein banding patterns in 45 krad, 55 krad and 65 krad irradiated black gram samples. Absence of protein bands and appearance of new protein bands in M 4 generation black gram indicate the gamma rays-induced genomic lesions corresponding to these missing protein bands which could not be repaired even after M 4 generation and was quite stably inherited in M 4 generation. This study provides the useful information for the use of these black gram mutant lines in future breeding programme and further agronomic and nutritional study is needed for the analysis of the mutants. Keywords : Black gram; gamma irradiation; SDS-PAGE; Vigna mungo.
Représentation et classification de structures spatiales - Application à la reconnaissance de paysages agricoles. (Representation and classification of spatial structures : recognition of landscap patterns)

Dans cette these, nous nous interessons a la representation et a la classification de structures spatiales dans le cadre de la reconnaissance de modeles de paysages agricoles sur des images satellites. Nous avons defini, lors d'une phase d'acquisition des connaissances, des modeles de paysages agricoles sous forme de classes dans un systeme de representation des connaissances par objets. Les classes sont reliees entre elles par des relations spatiales qualitatives. Les relations spatiales sont des classes dont les instances lient d'autres classes. Les classes de relations sont organisees dans une hierarchie ayant une structure de treillis permettant de representer la specialisation, l'implication, la disjonction et la conjonction de relations. Nous avons choisi un treillis de Galois qui permet de mettre en evidence le lien entre relations et conditions necessaires a la verification des relations sur l'image. Grâce a cette structure, nous avons propose un algorithme de recherche de l'ensemble minimum des conditions qui permet de reduire le nombre d’operations sur les images. Des algorithmes ont ete aussi proposes pour representer les proprietes mathematiques des relations. Nous proposons d'ajouter au langage quatre facettes permettant de representer la quantification des relations spatiales. Nous avons modifie l'operation qui associe un modele a une entite pour prendre en compte la quantification des relations dans la classification des structures spatiales. Le systeme de reconnaissance a ete implante dans le langage YAFOOL et mis en œuvre sur des cartes de la region lorraine.
Liver microsomes and S9 from rainbow trout (Oncorhynchus mykiss): Comparison of basal‐level enzyme activities with rat and determination of xenobiotic intrinsic clearance in support of bioaccumulation assessment

Metabolism plays an important role in bioaccumulation of xenobiotics in fish. The applicability of trout liver microsomes and S9 fraction in bioaccumulation assessment of xenobiotics in fish was investigated in the present study. Basal‐level activities of 7‐ethoxyresorufin‐O‐dealkylase, testosterone 6β‐hydroxylase, glutathione‐S‐transferase, and uridine 5′‐diphospho‐glucuronosyl‐transferase in trout liver microsomes and S9 were significantly lower than those in rat liver microsomes and S9. The in vitro–to–in vivo scaling factors, which are the values of liver microsomal and S9 protein contents per unit weight of trout liver, were determined to be 38.4 ±5.1 (mean ± standard deviation throughout) and 95.9 ±11.9 mg/g, respectively. Intrinsic clearance (CLint) values for a number of reference compounds obtained from trout liver S9 were lower than those from trout liver microsomes. After correction with the scaling factors, trout liver microsomes and S9 provided equivalent prediction of trout hepatic clearance (CLH) using the well‐stirred liver model, but their CLH values were significantly lower than those obtained from freshly isolated trout hepatocytes. Consequently, trout liver microsomes and S9 showed poorer prediction of the bioconcentration factors of the reference compounds compared with trout hepatocytes. Unit conversion revealed that CLint values obtained from trout liver microsomes and S9 were 6.3 to 22.4% of those from trout hepatocytes, which explained, to a large extent, the differences in their CLH and bioconcentration factor prediction.
Multifocal septic arthritis and osteomyelitis caused by group A Streptococcus in a patient receiving immunomodulating therapy with etanercept.

A 12-year-old girl with juvenile rheumatoid arthritis presented with signs of infection of the proximal interphalangeal joint of her left great toe 1 week after a flu-like illness. Several joints and one bone were subsequently found to be infected with group A beta-hemolytic streptococci. Despite appropriate antibiotic therapy, synovial fluid cultures remained positive for 2 weeks. We believe that the antiinflammatory medications, including etanercept (a tumor necrosis factor antagonist), used to treat this patient's arthritis contributed to the severity and unusual course of her infection.
Blind soft-output decoding of space-time trellis coded transmissions over time-varying Rayleigh fading channels

We present a joint channel estimation and decoding method for space-time trellis codes (STTC) transmitted over an unknown flat fading multiple-input multiple-output (MIMO) channel. In a blind context, i.e. when pilot symbols are not available, we will show that the probability density function (pdf) of the MIMO channel becomes multimodal due to phase ambiguities. To address this problem, a combined state-space model for the time-varying MIMO channel and the STTC is introduced. The proposed algorithm then uses a Gaussian mixture approach to perform joint channel estimation and soft-output detection. We compare our method to several well known algorithms obtained by collapsing the Gaussian mixture to a single Gaussian distribution. A comparison with sequential Monte Carlo methods is also included. Numerical simulations show that the performances of the proposed blind STTC decoder are close to decoding with perfect channel state information (CSI). As a useful application of the proposed soft-output algorithm, we provide an example of blind iterative decoding of concatenated space-time codes.
Direct isolation of atypical thermophilic Campylobacter species from human feces on selective agar medium

Campylobacter upsaliensis is the name which has been proposed for a new group of thermophilic campylobacter strains which differ from C. jejuni and C. coli in having a negative or weak catalase reaction. Primary isolation of these strains from human feces has been achieved only by use of filtration techniques. We report here direct isolation of strains corresponding to C. upsaliensis from stools of six children. The strains were isolated on a newly described campylobacter-selective medium. The strains were oxidase positive, hippurate negative, nitrate positive, negative for H2S in triple sugar iron, and susceptible to cephalothin (30-micrograms disk) and nalidixic acid (30-micrograms disk), and they grew at 37 and 43 degrees C, but not at 25 degrees C. The selective medium used was a blood-free, charcoal-based medium consisting of Columbia agar base, activated charcoal, cefoperazone (32 micrograms/ml), vancomycin (20 micrograms/ml), and cycloheximide (100 micrograms/ml). The medium supported the growth of the weakly reacting or catalase-negative strains, with colony counts equivalent to those obtained on antibiotic-free horse blood agar. These strains could not be isolated directly from stool on Skirrow medium, and colony counts confirmed that this medium could not support a low inoculum of these organisms. The clinical significance of these strains is unknown. We conclude that C. upsaliensis can be isolated directly from stool by using a selective medium, without the need for filtration.
Development of an Attitudes toward Health Care Teams Scale

The authors describe the development and psychometric testing across three study phases of an Attitudes Toward Health Care Teams Scale. The measure contains two subscales: Quality of Care/Process (14 items) and Physician Centrality (6 items). The Quality of Care/Process subscale measures team members’ perceptions of the quality of care delivered by health care teams and the quality of teamwork to accomplish this. The Physician Centrality subscale measures team members’attitudes toward physicians’authority in teams and their control over information about patients. Tests of reliability and validity demonstrate that each subscale is a strong measure of its respective underlying concept. The measure has potential for use as a research tool and as a pre-and posttest tool for educational interventions with teams and for evaluating clinically based team training programs for medical and health professions students and residents.
Spectrophotometric Assay of Gene Expression : Serratia marcescens Pigmentation

Studies of the physiology of unicellular organisms often involve assays for gene expression in conjunction with changes in growth or environmental conditions. We have exploited the property of pigment production by the nonpathogenic bacterium Serratia marcescens to design a simple assay for gene expression that is easily and inexpensively adaptable to the teaching biology laboratory. Our assay uses a spectrophotometer to simultaneously measure bacterial growth and expression of the red, cell-associated pigment prodigiosin. This work defines a unit value for prodigiosin expression and characterizes pigmentation through variations in cell density, growth temperature and growth medium. Spontaneous pigmentation mutants of S. marcescens, which can be easily isolated due to variations in colony color, may be quantitatively assayed for prodigiosin expression throughout the population growth cycle.