Miracle-dz/UniFAR-FTUs huggingface dataset:
Strong genetic structure over the American continents and transoceanic dispersal in the mangrove genus Rhizophora (Rhizophoraceae) revealed by broad-scale nuclear and chloroplast DNA analysis.

UNLABELLED PREMISE OF THE STUDY The global distribution of mangroves is attributed to interactions between long-distance propagule dispersal and geographical barriers, which are manifest in genetic structuring. Uncovering this genetic structure thus provides a window into the ecological, evolutionary, and phylogeographic history of mangroves. We used cpDNA and nuclear microsatellites to evaluate transbarrier (transoceanic and transisthmian) linkages in the genus Rhizophora in the Atlantic East Pacific (AEP) and South Pacific region. • METHODS Leaf samples of 756 individuals of Rhizophora mangle, R. racemosa, R. ×harrisonii, and R. samoensis from 36 populations across the AEP supplied material from which we used the cpDNA haplotypes and nine microsatellite markers for population analyses. • KEY RESULTS Clear genetic differentiation of cpDNA haplotypes was found between the Pacific and Atlantic populations in R. mangle and R. racemosa, supporting the hypothesis of the Central American Isthmus as a barrier to gene flow. Both cpDNA and microsatellite analyses support the hypothesis of recent and frequent transatlantic propagule dispersal for R. mangle. Finally, we provide strong evidence for genetic similarity of Pacific R. mangle and R. samoensis suggesting trans-Pacific dispersal of R. mangle. • CONCLUSION The American continents are strong geographical barriers to dispersal of Rhizophora, to the point where the Pacific and Atlantic populations are distinct genealogical units, supporting the recommendation to treat the populations as separate conservation and management units. Trans-Pacific propagule dispersal of Rhizophora has occurred; R. mangle and R. samoensis might be the same species and this question should be resolved with further taxonomic study.
Perceptual asynchrony for motion

Psychophysical experiments show that two different visual attributes, color and motion, processed in different areas of the visual brain, are perceived at different times relative to each other (Moutoussis and Zeki, 1997a). Here we demonstrate psychophysically that two variants of the same attribute, motion, which have the same temporal structure and are processed in the same visual areas, are also processed asynchronously. When subjects were asked to pair up–down motion of dots in one half of their hemifield with up-right motion in the other, they perceived the two directions of motion asynchronously, with the advantage in favor of up-right motion; when they were asked to pair the motion of white dots moving against a black background with that of red dots moving against an equiluminant green background, they perceived the luminant motion first, thus demonstrating a perceptual advantage of luminant over equiluminant motion. These results were not affected by motion speed or perceived motion “streaks. ” We thus interpret these results to reflect the different processing times produced by luminant and equiluminant motion stimuli or by different degrees of motion direction change, thus adding to the evidence that processing time within the visual system is a major determinant of perceptual time.
Social networks and the implementation of environmental technology

A study of 83 firms in the North American electronics industry that have implemented environmentally "clean" process technology found that social networks have a significant positive impact on implementation success. This paper presents evidence that some types of social networks influence implementation success more than others. More specifically, interfirm networks composed of both suppliers and competitors were significantly correlated with the routinization and incorporation of alternative technical solutions to reducing ozone depleting chlorofluorocarbons (CFCs). This only held in situations where the complexity of the implementation was relatively high. Intrafirm and local social networks were not significant. The utilization of a network of publicly accessible sources of information and expertise had a negative impact. Brief case studies from field research are provided to help explain these results.
DNA methylation signatures in cord blood of ICSI children

Abstract STUDY QUESTION Does ICSI induce specific DNA methylation changes in the resulting offspring? SUMMARY ANSWER Although several thousand analyzed CpG sites (throughout the genome) displayed significant between-group methylation differences, both ICSI and spontaneously conceived children varied within the normal range of methylation variation. WHAT IS KNOWN ALREADY Children conceived by ART have increased risks for medical problems at birth and to the extent of present knowledge also in later life (i.e. impaired metabolic and cardiovascular functions). One plausible mechanism mediating these ART effects are epigenetic changes originating in the germ cells and/or early embryos and persisting during further development. STUDY DESIGN, SIZE, DURATION We compared the cord blood methylomes and candidate gene methylation patterns of newborns conceived through ICSI or spontaneously. PARTICIPANTS/MATERIALS, SETTING, METHODS Umbilical cord bloods were obtained from healthy newborn singletons conceived spontaneously (53 samples), through ICSI (89) or IVF (34). Bisulfite-converted DNA samples of 48 ICSI and 46 control pregnancies were used for genome-wide analyses with Illumina's 450K methylation arrays. Candidate genes from the methylation screen were analyzed in all three groups by bisulfite pyrosequencing. MAIN RESULTS AND THE ROLE OF CHANCE Altogether, 4730 (0.11%) of 428 227 analyzed CpG sites exhibited significant between-group methylation differences, but all with small (β < 10%) or very small (β < 1%) effect size. ICSI children showed a significantly decreased DNA methylation age at birth, lagging approximately half a week behind the controls. ART-susceptible CpGs were enriched in CpG islands with low methylation values (0–20%) and in imprinting control regions (ICRs). Eighteen promoter regions (six in microRNA and SNORD RNA genes), four CpG islands (three in genes including one long non-coding RNA), and two ICRs contained multiple significant sites. Three differentially methylated regions were studied in more detail by bisulfite pyrosequencing. ATG4C and SNORD114-9 could be validated in an independent ICSI group, following adjustment for maternal age and other confounding factors. ATG4C was also significant in the IVF group. LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION The observed epigenetic effects are small and there are numerous potential confounding factors such as parental age and infertility. Although our study meets current standards for epigenetic screens, sample size is still two orders of magnitude below that of genome-wide association studies. WIDER IMPLICATIONS OF THE FINDINGS Our study suggests an impact of ICSI on the offspring's epigenome(s), which may contribute to phenotypic variation and disease susceptibility in ART children. Epigenetic regulation of gene expression by different classes of non-coding RNAs may be a key mechanism for developmental programming through ART. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by a research grant (no. 692185) from the European Union (ERA of ART). There are no competing interests.
A Dairy Bacterium Displays InVitro Probiotic Properties for the Pharyngeal Mucosa by Antagonizing Group A Streptococci and Modulating the Immune Response

ABSTRACT The probiotic approach represents an alternative strategy in the prevention and treatment of infectious diseases, not only at the intestinal level but also at other sites of the body where the microbiota plays a role in the maintenance of physiological homeostasis. In this context, we evaluated in vitro the potential abilities of probiotic and dairy bacteria in controlling Streptococcus pyogenes infections at the pharyngeal level. Initially, we analyzed bacterial adhesion to FaDu hypopharyngeal carcinoma cells and the ability to antagonize S. pyogenes on FaDu cell layers and HaCat keratinocytes. Due to its promising adhesive and antagonistic features, we studied the dairy strain Lactobacillus helveticus MIMLh5, also through in vitro immunological experiments. First, we performed quantification of several cytokines and measurement of NF-κB activation in FaDu cells. MIMLh5 efficiently reduced the induction of interleukin-6 (IL-6), IL-8, and tumor necrosis factor alpha (TNF-α), in a dose-dependent manner. After stimulation of cells with IL-1β, active NF-κB was still markedly lowered. Nevertheless, we observed an increased secretion of IL-6, gamma interferon (IFN-γ), and granulocyte-macrophage colony-stimulating factor (GM-CSF) under these conditions. These effects were associated with the ability of MIMLh5 to enhance the expression of the heat shock protein coding gene hsp70. In addition, MIMLh5 increased the GM-CSF/G-CSF ratio. This is compatible with a switch of the immune response toward a TH1 pathway, as supported by our observation that MIMLh5, once in contact with bone marrow-derived dendritic cells, triggered the secretion of TNF-α and IL-2. In conclusion, we propose MIMLh5 as a potential probiotic bacterium for the human pharynx, with promising antagonistic and immunomodulatory properties.
Prevalence, Risk Factors, and Strategies for Controlling Mastitis in Heifers During the Periparturient Period

Intramammary infections (IMIs) in unbred and pregnant dairy heifers were once thought to be very infrequent. However, during the last 2 decades, several studies have shown that IMIs in heifers occur frequently during the prepartum and peripartum periods. Many of these infections can persist for long periods of time, may be associated with elevated somatic cell counts (SCC), and may impair mammary development and affect milk production after calving. The purpose of this communication is to review literature published on the prevalence of mastitis in heifers, potential risk factors associated with heifer mastitis, and to describe results of different approaches that have been taken to control mastitis in heifers.
Growth of a tropical marine yeast Yarrowia lipolytica NCIM 3589 on bromoalkanes: relevance of cell size and cell surface properties

Yarrowia lipolytica 3589, a tropical marine yeast, grew aerobically on a broad range of bromoalkanes varying in carbon chain length and differing in degree and position of bromide group. Amongst the bromoalkanes studied, viz. 2‐bromopropane (2‐BP), 1‐bromobutane (1‐BB), 1,5‐dibromopentane (1,5‐DBP) and 1‐bromodecane (1‐BD), the best utilized was 1‐BD, with a maximal growth rate (μmax) of 0.055 h−1 and an affinity ratio (μmax/Ks) of 0.022. Utilization of these bromoalkanes as growth substrates was associated with a concomitant release of bromide (8202.9 µm) and cell mass (36 × 109 cells/ml), occurring maximally on 1‐BD. Adherence of yeast cells to these hydrophobic bromoalkanes was observed microscopically, with an increase in cell size and surface hydrophobicity. The maximal cell diameter was for 1‐BD (4.66 µm), resulting in an increase in the calculated cell surface area (68.19 µm2) and sedimentation velocity (1.31 µm/s). Cell surface hydrophobicity values by microbial adhesion to solvents (MATS) analysis for yeasts grown on bromoalkanes and glucose were significantly high, i.e. >80%. Similarly, water contact angles also indicate that the cell surface of yeast cells grown in glucose possess a relatively more hydrophilic cell surface (θ = 49.1°), whereas cells grown in 1‐BD possess a more hydrophobic cell surface (θ = 90.7°). No significant change in emulsification activity or surface tension was detected in the cell‐free supernatant. Thus adherence to the bromoalkane droplets by an increase in cell size and surface hydrophobicity leading to debromination of the substrate might be the strategy employed in bromoalkane utilization and growth by Y. lipolytica 3589. Copyright © 2011 John Wiley & Sons, Ltd.
Accurate classification of schizophrenia patients based on novel resting-state fMRI features

There is a growing interest in automatic classification of mental disorders such as schizophrenia based on neuroimaging data. Most previous studies considered structural MRI, diffusion tensor imaging and task-based fMRI for this purpose. However, resting-state fMRI data has not been used much to evaluate discrimination of schizophrenia patients from healthy controls. Resting data are of great interest, since they are relatively easy to collect, and not confounded by behavioral performance on a task. In this study, we extract two types of features from resting-state fMRI data: functional network connectivity features that capture internetwork connectivity patterns and autoconnectivity features capturing temporal connectivity of each brain network. Autoconnectivity is a novel concept we have recently proposed. We used minimum redundancy maximum relevancy to select features. Classification results using support vector machine shows that combining these two types of features can improve the classification on a large resting fMRI dataset consisting of 195 patients with schizophrenia and 175 healthy controls. We achieved the accuracy of 85% which is very promising.
Increased translocations and aneusomy in chromosomes 8 and 21 among workers exposed to benzene.

Chromosome aberrations in peripheral blood lymphocytes have been used for many years to monitor human populations exposed to potential carcinogens. Recent reports have confirmed the validity of this approach by demonstrating that elevated levels of chromosome aberrations in lymphocytes are associated with subsequent increased cancer risk, especially for increased mortality from hematological malignancies including acute myeloid leukemia (AML). We postulated that this approach could be improved in two ways: (a) by detecting oncogenic disease-specific aberrations; and (b) by using chromosome painting so that many more metaphases could be analyzed. Numerical and structural aberrations in chromosomes 8 and 21 are commonly observed in AML. In the present study, we painted chromosomes 8 and 21 in lymphocyte metaphases from 43 healthy workers exposed to benzene, an established cause of AML, and from 44 matched controls. To examine dose-response relationships the workers were divided into two groups at the median exposure level, a lower-exposed group (< or = 31 ppm; n = 21), and a higher-exposed group (> 31 ppm; n = 22). Benzene exposure was associated with significant increases in hyperdiploidy of chromosomes 8 (1.2, 1.5, and 2.4 per 100 metaphases; P < 0.0001) and 21 (0.9, 1.1, and 1.9 per 100 metaphases; P < 0.0001). Translocations between chromosomes 8 and 21 were increased up to 15-fold in highly exposed workers (0.01, 0.04, and 0.16 per 100 metaphases; P < 0.0001). In one highly exposed individual, these translocations were reciprocal and were detectable by reverse transcriptase-PCR. These data indicate a potential role for t(8;21) in benzene-induced leukemogenesis and are consistent with the hypothesis that detection of specific chromosome aberrations may be a powerful approach to identify populations at increased risk of leukemia.
Prospectively Isolated Human Bone Marrow Cell‐Derived MSCs Support Primitive Human CD34‐Negative Hematopoietic Stem Cells

Hematopoietic stem cells (HSCs) are maintained in a specialized bone marrow (BM) niche, which consists of osteoblasts, endothelial cells, and a variety of mesenchymal stem/stromal cells (MSCs). However, precisely what types of MSCs support human HSCs in the BM remain to be elucidated because of their heterogeneity. In this study, we succeeded in prospectively isolating/establishing three types of MSCs from human BM‐derived lineage‐ and CD45‐negative cells, according to their cell surface expression of CD271 and stage‐specific embryonic antigen (SSEA)−4. Among them, the MSCs established from the Lineage−CD45−CD271+SSEA‐4+ fraction (DP MSC) could differentiate into osteoblasts and chondrocytes, but they lacked adipogenic differentiation potential. The DP MSCs expressed significantly higher levels of well‐characterized HSC‐supportive genes, including IGF‐2, Wnt3a, Jagged1, TGFβ3, nestin, CXCL12, and Foxc1, compared with other MSCs. Interestingly, these osteo‐chondrogenic DP MSCs possessed the ability to support cord blood‐derived primitive human CD34‐negative severe combined immunodeficiency‐repopulating cells. The HSC‐supportive actions of DP MSCs were partially carried out by soluble factors, including IGF‐2, Wnt3a, and Jagged1. Moreover, contact between DP MSCs and CD34‐positive (CD34+) as well as CD34‐negative (CD34−) HSCs was important for the support/maintenance of the CD34+/− HSCs in vitro. These data suggest that DP MSCs might play an important role in the maintenance of human primitive HSCs in the BM niche. Therefore, the establishment of DP MSCs provides a new tool for the elucidation of the human HSC/niche interaction in vitro as well as in vivo. Stem Cells 2015;33:1554–1565
Incidence and Risks of Liver Resection: An All-Inclusive French Nationwide Study

Objective:To evaluate at a national level the incidence of liver resection, postoperative mortality, and variables that predict this outcome. Background:Data on indications of and results of liver resection are mainly derived from high-volume centers. Nationwide data are lacking. Methods:French health care databases were screened to identify all patients who had undergone elective hepatectomy between 2007 and 2010. The patients' age, address, associated conditions, indication and extent of hepatic (or extrahepatic) surgery and the hospital type, location, and hepatectomy caseload were retrieved. Logistic regression was used to measure the influence of these parameters on in-hospital and 90-day mortality rates. The model, created using patients operated on in 2007 and 2009, was tested in those operated on in 2008 and 2010. Results:Overall, 28,708 hepatectomies were performed. The annual incidence (13.2 per 105 adult inhabitants) varied between regions, but the extremal quotient was limited to 2.2 because 15% of the operations took place outside the patients' home region. Hospitals performed a median of 4 resections per year but 53% of all resections were performed in institutions with a volume of more than 50 per year. Treatment for primary tumors and major resections correlated with hepatectomy caseload. In-hospital and 90-day mortality were 3.4% and 5.8%, respectively. The area under the receiver operating characteristic curve of the prognostic model was 0.78/0.77 in the training and validation sample. Conclusions:There were significant disparities in practice. In-hospital mortality underestimated true, postoperative mortality by more than 50%. The model created may be useful for more efficient regionalization of care and patient counseling.
Face detection in the near-IR spectrum

Face detection is an important prerequisite step for successful face recognition. Face detection methods reported in the literature are far from perfect and deteriorate ungracefully where lighting conditions cannot be controlled. We propose a method that could potentially outperform state-of-the-art face detection methods in environments with dynamic lighting conditions. The approach capitalizes upon our near-IR skin and face detection methods reported elsewhere. It ascertains the existence of a face within a skin region by finding the eyes and eyebrows. The eye-eyebrow pairs are determined by extracting appropriate features from multiple near-IR bands. In this paper we introduce a novel feature extraction method we call dynamic integral projection. The method is relatively simple but highly effective because the processing is constrained within the skin region and aided by the near-IR phenomenology.
Th17 cells in neuromyelitis optica spectrum disorder: a review

Neuromyelitis optica spectrum disorder (NMOSD) has been identified as a central nervous system (CNS) autoimmune inflammatory disorder, which has been recognized as a B cell-mediated humoral immune disease. However, cases have been reported indicating that some of the neuromyelitis optica (NMO) patients have been resistant to B cell-related treatments. Recently, more and more evidence has shown that T cell-mediated immunity may take part in the pathogenesis of NMOSD, especially in the Th17 phenotype. In our PUBMED search, we used the following keywords: Th17 cell, Th17 cell-related cytokines, T cells, B cells, B cell-related productions, NMO, NMOSD, recurrent/bilateral optic neuritis, recurrent transverse myelitis and longitudinally extensive transverse myelitis. We systemically reviewed the role of Th17 cells and Th17 cell-related cytokines in NMOSD. We found that Th17 cells and Th17-related cytokines, such as IL-6, IL-1β, IL-17, IL-21, IL-22, IL-23 and TGF-β, are not only directly involved in the pathogenesis but also collaborated with B cells and B cell-related antibody production to induce CNS lesions. Th17 cell-related therapy has also been reviewed in this article, and the data suggested that Th17 may be a new therapeutic target of NMOSD.
Connexin43 phosphorylation by PKC and MAPK signals VEGF-mediated gap junction internalization

Phosphorylation on well-recognized, regulatory connexin43 amino acid residues by a series of kinases serves as an early molecular signal that triggers not only inhibition of gap junction (GJ)–mediated cell-to-cell communication but also GJ internalization. The findings contribute to the newly evolving dynamic picture of GJs.
Improvement in Detection of Differential Item Functioning Using a Mixture Item Response Theory Model

Usually, methods for detection of differential item functioning (DIF) compare the functioning of items across manifest groups. However, the manifest groups with respect to which the items function differentially may not necessarily coincide with the true source of the bias. It is expected that DIF detection under a model that includes a latent DIF variable is more sensitive to this source of bias. In a simulation study, it is shown that a mixture item response theory model, which includes a latent grouping variable, performs better in identifying DIF items than DIF detection methods using manifest variables only. The difference between manifest and latent DIF detection increases as the correlation between the manifest variable and the true source of the DIF becomes smaller. Different sample sizes, relative group sizes, and significance levels are studied. Finally, an empirical example demonstrates the detection of heterogeneity in a minority sample using a latent grouping variable. Manifest and latent DIF detection methods are applied to a Vocabulary test of the General Aptitude Test Battery (GATB).