Miracle-dz/UniFAR-FTUs huggingface dataset:
All‐trans retinoic acid regulates adhesion mechanism and transmigration of the acute promyelocytic leukaemia cell line NB‐4 under physiologic flow

The success of all‐trans retinoic acid (ATRA) in the therapy of acute promyelocytic leukaemia (APL) has received increased attention. Unfortunately, life‐threatening multiorgan failure commonly occurs, i.e. retinoic acid syndrome, and is thought to be the result of organ infiltration by leukaemic cells. We hypothesized that ATRA‐induced differentiation of APL cells leads to adhesion receptor alterations responsible for leucocyte extravasation from the blood into tissue. Changes in adhesive properties of the APL cell line NB‐4 in response to ATRA were investigated using a parallel plate flow chamber under conditions that recapitulate physiologic flow conditions. Untreated NB‐4 cells initially tether and roll on activated human umbilical vein endothelial cell monolayers using a combination of E‐selectin, P‐selectin and α4 integrin. After ATRA treatment, > 80% of initial NB‐4 cell attachment to endothelial cells was E‐selectin dependent. Stable arrest (firm adherence) of NB‐4 cells on activated endothelium was also altered by ATRA treatment. Untreated NB‐4 cells used α4 integrin to arrest on endothelium, but β2 integrin dependent arrest was induced by ATRA. With the acquisition of β2 integrin function, ATRA‐treated cells acquired the ability to transmigrate through activated endothelium. Thus, ATRA dramatically altered the adhesion phenotype on NB‐4 cells: ATRA induced rolling largely attributable to E‐selectin, abrogated α4 integrin dependent rolling, and promoted acquisition of β2 integrin dependent firm adherence and transmigration. These findings represent novel cellular and differentiation effects of ATRA, and, to our knowledge, are the first demonstration that a therapeutic agent differentially regulates α4 and β2 integrin on the same leucocyte.
A novel clathrin homolog that co‐distributes with cytoskeletal components functions in the trans‐Golgi network

A clathrin homolog encoded on human chromosome 22 (CHC22) displays distinct biochemistry, distribution and function compared with conventional clathrin heavy chain (CHC17), encoded on chromosome 17. CHC22 protein is upregulated during myoblast differentiation into myotubes and is expressed at high levels in muscle and at low levels in non‐muscle cells, relative to CHC17. The trimeric CHC22 protein does not interact with clathrin heavy chain subunits nor bind significantly to clathrin light chains. CHC22 associates with the AP1 and AP3 adaptor complexes but not with AP2. In non‐muscle cells, CHC22 localizes to perinuclear vesicular structures, the majority of which are not clathrin coated. Treatments that disrupt the actin–myosin cytoskeleton or affect sorting in the trans‐Golgi network (TGN) cause CHC22 redistribution. Overexpression of a subdomain of CHC22 induces altered distribution of TGN markers. Together these results implicate CHC22 in TGN membrane traffic involving the cytoskeleton.
Regularisation of images defined on non-flat surfaces. (Régularisation d'images sur des surfaces non-planes)

Nous nous interessons aux approches par EDP pour la regularisation d'images scalaires et multivaluees definies sur des supports non plans et a leurs applications a des problemes de traitement des images. Nous etudions la relation entre les methodes existantes et les comparons en termes de performance et facilite d'implementation. Nous developpons de nouvelles methodes numeriques pour traiter des operateurs de type divergence utilises dans les methodes de regularisation par EDPs sur des surfaces triangulees. Nous generalisons la technique de regularisation du Flot de Beltrami pour le cas des images definies sur des surfaces implicites et explicites. Des implementations sont proposees pour ces methodes, et des experiences sont exposees. Nous montrons aussi une application concrete de ces methodes a un probleme de cartographie retinotopique.
Land Degradation States and Trends in the Northwestern Maghreb Drylands, 1998-2008

States of ecological maturity and temporal trends of drylands in Morocco, Algeria and Tunisia north of 28°N are reported for 1998–2008. The input data were Normalized Difference Vegetation Index databases and corresponding climate fields, at a spatial resolution of 1 km and a temporal resolution of one month. States convey opposing dynamics of human exploitation and ecological succession. They were identified synchronically for the full period by comparing each location to all other locations in the study area under equivalent aridity. Rain Use Efficiency (RUE) at two temporal scales was used to estimate proxies for biomass and turnover rate. Biomass trends were determined for every location by stepwise regression using time and aridity as predictors. This enabled human-induced degradation to be separated from simple responses to interannual climate variation. Some relevant findings include large areas of degraded land, albeit improving over time or fluctuating with climate, but rarely degrading further; smaller, but significant areas of mature and reference vegetation in most climate zones; very low overall active degradation rates throughout the area during the decade observed; biomass accumulation over time exceeding depletion in most zones; and negative feedback between land states and trends suggesting overall landscape persistence. Semiarid zones were found to be the most vulnerable. Those results can be disaggregated by country or province. The combination with existing land cover maps and national forest inventories leads to the information required by the two progress indicators associated with the United Nations Convention to Combat Desertification strategic objective to improve the conditions of ecosystems and with the Sustainable Development Goal Target 15.3 to achieve land degradation neutrality. Beyond that, the results are also useful as a basis for land management and restoration.
Using Zero-Frequency Resonator to Extract Multilingual Intonation Structure

Human uses expressive intonation to convey linguistic and paralinguistic meaning, especially making focal prominence to give emphasis that highlights the focus of speech. Automatic extraction of dynamic intonation feature from a speech corpus and representing it in a continuous form are desired in multilingual speech synthesis. This paper presents a method to extract dynamic prosodic structure from speech signal using zerofrequency resonator to detect glottal cycle epoch and filter both voice amplitude and fundamental frequency (F0) contours. We choose stable voice F0 segments free from micro-prosodic effect to recover relevant F0 trajectory of an utterance, taking into consideration of inter-correlation of micro-prosody with phonetic segments and syllable structure of the utterance, and further filter out long-term global pitch movements. The method is evaluated by objective tests upon multilingual speech corpora including Chinese, Japanese, Korean, and Myanmar. Our experiment results show that the extracted intonation contour can match F0 contour by conventional approach in very high accuracy and the estimated long-term pitch movements demonstrate regular characteristics of intonation across languages. The proposed method is language-independent and robust to noisy speech.
Psychometric functioning, socio‐demographic variability of childhood maltreatment in the general population and its effects of depression

Maltreatment of children is a major public‐health and social‐welfare problem but socio‐demographic variability has received little attention. This work addresses such variability in a general population cohort and associations with depression. Analyses were based on the cross‐sectional SHIP‐LEGEND examination among 2265 adults (29–89 years). Childhood maltreatment was multi‐dimensionally assessed with the German 28‐item Childhood Trauma Questionnaire (CTQ): emotional neglect; emotional abuse; physical neglect; physical abuse; sexual abuse. Non‐linear associations between CTQ responses and age were assessed with fractional polynomials and cubic splines. Scale properties were analysed with confirmatory factor analyses and item response models. Associations between childhood maltreatment domains and depression [Beck Depression Inventory‐II (BDI‐II)] were assessed. The majority (58.9%) reported events indicative of at least mild levels of childhood maltreatment. CTQ subscales showed characteristically different non‐linear associations to age across the five studied domains, indicating methodological issues like recall bias and the influence of seminal events. Psychometric scale properties were acceptable to good for all subscales except for physical neglect. Associations to depression measures varied systematically across socio‐demographic strata. We conclude that socio‐demographic variability is a major issue when studying self‐reported childhood maltreatment in a community sample. This needs to be taken into account for the study of associations to psychiatric key outcomes. Copyright © 2014 John Wiley & Sons, Ltd.
Clonal line of porcine kidney stable cells for assay of Japanese encephalitis virus

have now been serially passed more than 85 times in LE medium plus 5% fetal bovine serum (FBS). From cell stocks grown in 400-ml bottles, 3-oz prescription bottles were seeded with about 2 X 106 cells in 10 ml of LE medium plus 5% FBS and incubated at 37 C. Uniform cell monolayers developed within 24 to 48 hr, at which time they were washed two times with LE medium and inoculated with 0.1 ml of virus diluted in LE medium. Inoculated monolayers were incubated for 60 min at 37 C, after which they were overlaid with approximately 10 ml of LE medium containing 10% FBS and 1.5% agar (Difco). After solidification of the overlay, the assay bottles were incubated, inverted, at 37 C. Plaques first became visible as enlarged rounded cells by 4 days after inoculation. Plaque area increased as adjacent cells developed cytopathogenic effects, and a clearing usually developed in the plaque center. By 8 days after inoculation, plaque numbers leveled off and plaques appeared as shown in Fig. 1. Plaque diameter was 0.1 to 0.2 mm, and plaques were counted with aid of a dissecting microscope at 20 X multiplication. Plaque numbers proved directly proportional to concentration of inoculum (Fig. 2). In hopes of increasing the plaque size by decreasing the viral release time of infected cells (Wallis and Melnick, Virology 16:122, 1962), plaque assays were carried out with varying concentrations of MgCl2. Monolayers were inoculated with mouse salivary gland virus and overlaid with the usual agar medium containing from 0.0 to 47 mm MgCl . 6H20. The incorporation of these additional amounts of MgCl2 into the medium neither decreased the time required for appearance of plaques nor increased the plaque count. Plaque formation was inhibited with 25 mm or more of additional MgCl2 .
Antheridial development in the moss Physcomitrella patens: implications for understanding stem cells in mosses

Stem cells self-renew and produce precursor cells that differentiate to become specialized cell types. Land plants generate several types of stem cells that give rise to most organs of the plant body and whose characters determine the body organization. The moss Physcomitrella patens forms eight types of stem cells throughout its life cycle. Under gametangium-inducing conditions, multiple antheridium apical stem cells are formed at the tip of the gametophore and each antheridium apical stem cell divides to form an antheridium. We found that the gametophore apical stem cell, which typically forms leaf and stem tissues, changes to become a new type of stem cell, which we term the antheridium initial stem cell. This antheridium initial stem cell produces multiple antheridium apical stem cells, resulting in a cluster of antheridia at the tip of gametophore. This is the first report of a land plant stem cell directly producing another type of stem cell during normal development. Notably, the antheridium apical stem cells are distally produced from the antheridium initial stem cell, similar to the root cap stem cells of vascular plants, suggesting the use of similar molecular mechanisms and a possible evolutionary relationship. This article is part of a discussion meeting issue ‘The Rhynie cherts: our earliest terrestrial ecosystem revisited’.
Assessment of the radiation doses to the public from the cesium in oceans after Fukushima Nuclear Accident

A great number of radioactive cesium were released into sea water after Fukushima Accident. We modified the Regional Oceanic Modelling System (ROMS) to reproduce the dispersion process of the cesium in oceans. The simulated water concentration was in good agreement with observation. In order to explore the nuclear impact of these contaminant in ocean, we established a food web model to calculate the concentration in marine organisms and assess the internal dose rate to the public. The estimated internal dose rate is small compared with the recommended limit by International Atomic Energy Agency (IAEA). Then, we employed the Monte Carlo N Particle Transport Code (MCNP) to calculate the transfer coefficient. The external dose rate could be estimated by this coefficient and simulated water concentration.
COACHING DIFFERENCE: A CASE STUDY OF 4 AFRICAN AMERICAN WOMEN STUDENT‐ATHLETES

The purpose of the present investigation was to describe the experiences of African American women student-athletes and the role that coaches play in those experiences. This study profiles 4 women who participated in National Collegiate Athletic Association Division I cross-country, crew, track and field, and volleyball. Using data gathered through the qualitative methods of document analysis, background questionnaires, focus groups, grounded surveys, and in-depth individual interviews, the results of the study are focused on how coaches affect individual student-athletes and, most specifically, a particular segment of the athletic world that tends to be overlooked: the African American woman. Results are organized according to the following themes that emerged through the collection of data: (a) the involvement of coaches in African American women student-athletes' exposure to racism through stereotypes, (b) coaches as significant influences on African American women becoming involved and remaining involved in sport, and (c) power structures in sport and society affecting African American women as a form of institutional racism. A practical applications section follows the results.
Moving to mate: the evolution of separate and combined sexes in multicellular organisms

Which conditions favour the evolution of hermaphroditism or separate sexes? One classical hypothesis states that an organism’s mode of locomotion (if any) when searching for a mate should influence breeding system evolution. We used published phylogenies to reconstruct evolutionary changes in adult mate‐search efficiency and breeding systems among multicellular organisms. Employing maximum‐likelihood analyses, we found that changes in adult mate‐search efficiency are significantly correlated with changes in breeding system, and this result is robust to uncertainties in the phylogenies. These data provide the first statistical support, across a broad range of taxa, for the hypothesis that breeding systems and mate‐search efficiency did not evolve independently. We discuss our results in context with other causal factors, such as inbreeding avoidance and sexual specialization, likely to affect breeding system evolution.
Continuous-Domain Reinforcement Learning Using a Self-Organizing Neural Network

his paper deals with a new algorithm for solving the problems of reinforcement learning in continuous spaces. For continuous states and actions, we use a new method based on self-organizing neural network, DIGNET. Two self-organizing neural network, DIGNETs, are used in this method, which having simple structure, can give an appropriate approximate of state/action space. The network is able to adapt inconsistent nature of reinforcement learning environments fine since the system parameters in DIGNET are self-adjusted in an autonomous way during the learning procedure. Automatic and competitive production and elimination of attraction wells, considering parameters of attraction well, threshold, age and depth, lead to flexibility of proposed algorithm to solve continuous problems and finally, the attraction wells of output DIGNET (action) will concentrate on the areas with high reward, providing an appropriate illustration for a continuous state space. At the end, we also present the results of evaluating proposed method on several problems.
Missing laboratory results data in electronic health databases: implications for monitoring diabetes risk.

AIM Laboratory test (lab) results may be useful to detect incident diabetes in electronic health record and claims-based studies. RESEARCH DESIGN & METHODS Using the Mini-Sentinel distributed database, we assessed the value of lab results added to diagnosis codes and dispensing claims to identify incident diabetes. RESULTS Inclusion of lab results increased the number of diabetes outcomes identified by 21%. In settings where capture of lab results was relatively complete, the absence of lab results was associated with implausibly low rates of the outcome. CONCLUSION Lab results can increase sensitivity of algorithms for detecting diabetes, and missing lab results are associated with much lower rates of diabetes ascertainment regardless of algorithm. Patterns of missing lab results may identify ascertainment bias.
A type 2 neuron model for classification and regression problems

Type 2 fuzzy systems have been under investigation for a while and the projection of type 2 understanding for uncertainty management onto the connectionist models -i.e. neural networks- seems an interesting field of research. This paper considers neurons having multiple bias values defining a new structure that resembles the uncertainty handling capability of type 2 fuzzy models. Such a neuron provides many activation levels that are combined to obtain the neuron response. A neural network with this new model is presented. Several simulation results are shown and the universal approximation property is emphasized.
Identification of Through-Silicon Via (TSV) Failure Points Using the Time Domain Reflectometry (TDR) Method

Time domain reflectometry (TDR) is applied to the failure analysis of through-silicon vias (TSVs). The reflection time of the TDR signal from test-element-group (TEG) chips with TSVs stacked on a silicon interposer is compared to the distance between the failure point and the contact pad derived from a TDR simulation value, using a model which has the same structure as the TEG chips. These results show good agreement between the simulated and the measured results.
Production of tumor necrosis factor and nitric oxide by macrophages infected with live and dead mycobacteria and their suppression by an interleukin-10-secreting recombinant

We have analyzed mycobacterium-induced cytokine secretion in the J774A.1 macrophage-like cell line. Tumor necrosis factor alpha (TNF-alpha) was preferentially induced by live organisms, both slow and rapid growing. Expression of interleukin-10 by a recombinant strain of Mycobacterium smegmatis caused reduced production of TNF-alpha and nitric oxide during the early stages of infection.
M.BssHII, a multispecific cytosine-C5-DNA-methyltransferase with unusual target recognizing properties.

A new multispecific cytosine-C5-DNA-methyltransferase (C5-MTase), M.BssHII, was identified in Bacillus stearothermophilus H3. The M.BssHII gene was cloned and sequenced. The amino acid sequence deduced shows the characteristic building plan of a C5-MTase. By sequencing bisulfite-treated DNA methylated by M.BssHII and by restriction enzyme analysis, we defined the following methylation targets of M.BssHII: ACGCGT/CCGCGG (MluI/SacII), PuGCGCPy (HaeII), PuCCGGPy (Cfr10I) and GCGCGC (BssHII). The relative location of the specificity determinants in the C5-MTase was derived from the analysis of M.BssHII derivatives carrying deletions within the variable region "V" and chimeric C5-Mtases constructed between M.BssHII and the related monospecific enzyme M.phi3TII. Four of the M.BssHII specificities (MluI, SacII, Cfr10I and BssHII) could be associated with amino acid segments within the variable region "V". The determinant for HaeII activity had to be assigned to sequences defining the enzyme core, the first example of a C5-MTase in which a sequence-specific methylation potential is mediated by structures outside of the variable region. Another intriguing result came from the analysis of one particular chimera made between M.BssHII and M.phi3TII. This construct showed a relaxation of the methylation capacity, both with respect to the target recognized and the targeting of methylation within this sequence.
Draft Genome Sequences of Five Pseudomonas fluorescens Subclade I and II Strains, Isolated from Human Respiratory Samples

ABSTRACT We report the draft genomes of five Pseudomonas fluorescens strains, isolated from clinical samples. Phylogenetic analysis places three in subclade I and two in subclade II of the P. fluorescens species complex. The average G+C content and genomic size are 63% and 7.1 Mbp (subclade I) and 59.6% and 6.14 Mbp (subclade II), respectively.
A New Cytochrome Subunit Bound to the Photosynthetic Reaction Center in the Purple Bacterium, Rhodovulum sulfidophilum *

The nucleotide sequence of the pufoperon, which contains the genes encoding the B870 light-harvesting protein and the reaction center complex of the purple photosynthetic bacterium, Rhodovulum sulfidophilum, was determined. The operon, which consisted of six genes, pufQ,pufB, pufA, pufL, pufM, and pufC, is a new variety in photosynthetic bacteria in the sense thatpufQ and pufC coexist. The amino acid sequence of the cytochrome subunit of the reaction center deduced from thepufC sequence revealed that this cytochrome contains only three possible heme-binding motifs; the heme-1-binding motif of the corresponding tetraheme cytochrome subunits was not present. This is the first exception of the “tetraheme” cytochrome family in purple bacteria and green filamentous bacteria. The pufC sequence also revealed that the sixth axial ligands to heme-1 and heme-2 irons were not present in the cytochrome either. This cytochrome was actually detected in membrane preparation as a 43-kDa protein and shown to associate functionally with the photosynthetic reaction center as the immediate electron donor to the photo-oxidized special pair of bacteriochlorophyll. This new cytochrome should be useful for studies on the role of each heme in the cytochrome subunit of the bacterial reaction center and the evolution of proteins in photosynthetic electron transfer systems.