S-PLUS DR1 galaxy clusters and groups catalogue using PzWav

We present a catalogue of 4499 groups and clusters of galaxies from the first data release of the multi-filter (5 broad, 7 narrow) Southern Photometric Local Universe Survey (S-PLUS). These groups and clusters are distributed over 273 deg$^2$ in the Stripe 82 region. They are found using the PzWav algorithm, which identifies peaks in galaxy density maps that have been smoothed by a cluster scale difference-of-Gaussians kernel to isolate clusters and groups. Using a simulation-based mock catalogue, we estimate the purity and completeness of cluster detections: at S/N>3.3 we define a catalogue that is 80% pure and complete in the redshift range 0.1<z<0.4, for clusters with $M_{200} > 10^{14}$ M$_\odot$. We also assessed the accuracy of the catalogue in terms of central positions and redshifts, finding scatter of $\sigma_R=12$ kpc and $\sigma_z=8.8 \times 10^{-3}$, respectively. Moreover, less than 1% of the sample suffers from fragmentation or overmerging. The S-PLUS cluster catalogue recovers ~80% of all known X-ray and Sunyaev-Zel'dovich selected clusters in this field. This fraction is very close to the estimated completeness, thus validating the mock data analysis and paving an efficient way to find new groups and clusters of galaxies using data from the ongoing S-PLUS project. When complete, S-PLUS will have surveyed 9300 deg$^{2}$ of the sky, representing the widest uninterrupted areas with narrow-through-broad multi-band photometry for cluster follow-up studies.Comment: 17 pages, 15 figures, paper accepted for publication by MNRA

Protein kinase A enhances lipopolysaccharide-induced IL-6, IL-8, and PGE2 production by human gingival fibroblasts

<p>Abstract</p> <p>Objective</p> <p>Periodontal disease is accompanied by inflammation of the gingiva and destruction of periodontal tissues, leading to alveolar bone loss in severe clinical cases. Interleukin (IL)-6, IL-8, and the chemical mediator prostaglandin E₂(PGE₂) are known to play important roles in inflammatory responses and tissue degradation.</p> <p>Recently, we reported that the protein kinase A (PKA) inhibitor H-89 suppresses lipopolysaccharide (LPS)-induced IL-8 production by human gingival fibroblasts (HGFs). In the present study, the relevance of the PKA activity and two PKA-activating drugs, aminophylline and adrenaline, to LPS-induced inflammatory cytokines (IL-6 and IL-8) and PGE₂by HGFs were examined.</p> <p>Methods</p> <p>HGFs were treated with LPS from <it>Porphyromonas gingivalis </it>and H-89, the cAMP analog dibutyryl cyclic AMP (dbcAMP), aminophylline, or adrenaline. After 24 h, IL-6, IL-8, and PGE₂levels were evaluated by ELISA.</p> <p>Results</p> <p>H-89 did not affect LPS-induced IL-6 production, but suppressed IL-8 and PGE₂production. In contrast, dbcAMP significantly increased LPS-induced IL-6, IL-8, and PGE₂production. Up to 10 μg/ml of aminophylline did not affect LPS-induced IL-6, IL-8, or PGE₂production, but they were significantly increased at 100 μg/ml. Similarly, 0.01 μg/ml of adrenaline did not affect LPS-induced IL-6, IL-8, or PGE₂production, but they were significantly increased at concentrations of 0.1 and 1 μg/ml. In the absence of LPS, H-89, dbcAMP, aminophylline, and adrenaline had no relevance to IL-6, IL-8, or PGE₂production.</p> <p>Conclusion</p> <p>These results suggest that the PKA pathway, and also PKA-activating drugs, enhance LPS-induced IL-6, IL-8, and PGE₂production by HGFs. However, aminophylline may not have an effect on the production of these molecules at concentrations used in clinical settings (8 to 20 μg/ml in serum). These results suggest that aminophylline does not affect inflammatory responses in periodontal disease.</p

Identification of ovule transcripts from the Apospory-Specific Genomic Region (ASGR)-carrier chromosome

<p>Abstract</p> <p>Background</p> <p>Apomixis, asexual seed production in plants, holds great potential for agriculture as a means to fix hybrid vigor. Apospory is a form of apomixis where the embryo develops from an unreduced egg that is derived from a somatic nucellar cell, the aposporous initial, via mitosis. Understanding the molecular mechanism regulating aposporous initial specification will be a critical step toward elucidation of apomixis and also provide insight into developmental regulation and downstream signaling that results in apomixis. To discover candidate transcripts for regulating aposporous initial specification in <it>P. squamulatum</it>, we compared two transcriptomes derived from microdissected ovules at the stage of aposporous initial formation between the apomictic donor parent, <it>P. squamulatum </it>(accession PS26), and an apomictic derived backcross 8 (BC₈) line containing only the Apospory-Specific Genomic Region (ASGR)-carrier chromosome from <it>P. squamulatum</it>. Toward this end, two transcriptomes derived from ovules of an apomictic donor parent and its apomictic backcross derivative at the stage of apospory initiation, were sequenced using 454-FLX technology.</p> <p>Results</p> <p>Using 454-FLX technology, we generated 332,567 reads with an average read length of 147 base pairs (bp) for the PS26 ovule transcriptome library and 363,637 reads with an average read length of 142 bp for the BC₈ovule transcriptome library. A total of 33,977 contigs from the PS26 ovule transcriptome library and 26,576 contigs from the BC₈ovule transcriptome library were assembled using the Multifunctional Inertial Reference Assembly program. Using stringent <it>in silico </it>parameters, 61 transcripts were predicted to map to the ASGR-carrier chromosome, of which 49 transcripts were verified as ASGR-carrier chromosome specific. One of the alien expressed genes could be assigned as tightly linked to the ASGR by screening of apomictic and sexual F₁s. Only one transcript, which did not map to the ASGR, showed expression primarily in reproductive tissue.</p> <p>Conclusions</p> <p>Our results suggest that a strategy of comparative sequencing of transcriptomes between donor parent and backcross lines containing an alien chromosome of interest can be an efficient method of identifying transcripts derived from an alien chromosome in a chromosome addition line.</p

Profiling of Genes Related to Cross Protection and Competition for NbTOM1 by HLSV and TMV

10.1371/journal.pone.0073725PLoS ONE89-POLN

Effect of clinical signs, endocrinopathies, timing of surgery, hyperlipidemia, and hyperbilirubinemia on outcome in dogs with gallbladder mucocele

Gallbladder mucocele (GBM) is a common extra-hepatic biliary syndrome in dogs with death rates ranging from 7 to 45%. Therefore, the aim of this study was to identify the association of survival with variables that could be utilized to improve clinical decisions. A total of 1194 dogs with a gross and histopathological diagnosis of GBM were included from 41 veterinary referral hospitals in this retrospective study. Dogs with GBM that demonstrated abnormal clinical signs had significantly greater odds of death than subclinical dogs in a univariable analysis (OR, 4.2; 95% CI, 2.14–8.23; P &lt; 0.001). The multivariable model indicated that categorical variables including owner recognition of jaundice (OR, 2.12; 95% CI, 1.19–3.77; P = 0.011), concurrent hyperadrenocorticism (OR 1.94; 95% CI, 1.08–3.47; P = 0.026), and Pomeranian breed (OR, 2.46; 95% CI 1.10–5.50; P = 0.029) were associated with increased odds of death, and vomiting was associated with decreased odds of death (OR, 0.48; 95% CI, 0.30–0.72; P=0.001). Continuous variables in the multivariable model, total serum/plasma bilirubin concentration (OR, 1.03; 95% CI, 1.01– 1.04; P &lt; 0.001) and age (OR, 1.17; 95% CI, 1.08–1.26; P &lt; 0.001), were associated with increased odds of death. The clinical utility of total serum/plasma bilirubin concentration as a biomarker to predict death was poor with a sensitivity of 0.61 (95% CI, 0.54–0.69) and a specificity of 0.63 (95% CI, 0.59–0.66). This study identified several prognostic variables in dogs with GBM including total serum/plasma bilirubin concentration, age, clinical signs, concurrent hyperadrenocorticism, and the Pomeranian breed. The presence of hypothyroidism or diabetes mellitus did not impact outcome in this study

Nitric oxide production by tumour tissue: impact on the response to photodynamic therapy

The role of nitric oxide (NO) in the response to Photofrin-based photodynamic therapy (PDT) was investigated using mouse tumour models characterized by either relatively high or low endogenous NO production (RIF and SCCVII vs EMT6 and FsaR, respectively). The NO synthase inhibitors Nω-nitro- L -arginine (L-NNA) or Nω-nitro- L -arginine methyl ester (L-NAME), administered to mice immediately after PDT light treatment of subcutaneously growing tumours, markedly enhanced the cure rate of RIF and SCCVII models, but produced no obvious benefit with the EMT6 and FsaR models. Laser Doppler flowmetry measurement revealed that both L-NNA and L-NAME strongly inhibit blood flow in RIF and SCCVII tumours, but not in EMT6 and FsaR tumours. When injected intravenously immediately after PDT light treatment, L-NAME dramatically augmented the decrease in blood flow in SCCVII tumours induced by PDT. The pattern of blood flow alterations in tumours following PDT indicates that, even with curative doses, regular circulation may be restored in some vessels after episodes of partial or complete obstruction. Such conditions are conducive to the induction of ischaemia-reperfusion injury, which is instigated by the formation of superoxide radical. The administration of superoxide dismutase immediately after PDT resulted in a decrease in tumour cure rates, thus confirming the involvement of superoxide in the anti-tumour effect. The results of this study demonstrate that NO participates in the events associated with PDT-mediated tumour destruction, particularly in the vascular response that is of critical importance for the curative outcome of this therapy. The level of endogenous production of NO in tumours appears to be one of the determinants of sensitivity to PDT. © 2000 Cancer Research Campaig

Comprehensive Network Analysis of Anther-Expressed Genes in Rice by the Combination of 33 Laser Microdissection and 143 Spatiotemporal Microarrays

Co-expression networks systematically constructed from large-scale transcriptome data reflect the interactions and functions of genes with similar expression patterns and are a powerful tool for the comprehensive understanding of biological events and mining of novel genes. In Arabidopsis (a model dicot plant), high-resolution co-expression networks have been constructed from very large microarray datasets and these are publicly available as online information resources. However, the available transcriptome data of rice (a model monocot plant) have been limited so far, making it difficult for rice researchers to achieve reliable co-expression analysis. In this study, we performed co-expression network analysis by using combined 44 K agilent microarray datasets of rice, which consisted of 33 laser microdissection (LM)-microarray datasets of anthers, and 143 spatiotemporal transcriptome datasets deposited in RicexPro. The entire data of the rice co-expression network, which was generated from the 176 microarray datasets by the Pearson correlation coefficient (PCC) method with the mutual rank (MR)-based cut-off, contained 24,258 genes and 60,441 genes pairs. Using these datasets, we constructed high-resolution co-expression subnetworks of two specific biological events in the anther, “meiosis” and “pollen wall synthesis”. The meiosis network contained many known or putative meiotic genes, including genes related to meiosis initiation and recombination. In the pollen wall synthesis network, several candidate genes involved in the sporopollenin biosynthesis pathway were efficiently identified. Hence, these two subnetworks are important demonstrations of the efficiency of co-expression network analysis in rice. Our co-expression analysis included the separated transcriptomes of pollen and tapetum cells in the anther, which are able to provide precise information on transcriptional regulation during male gametophyte development in rice. The co-expression network data presented here is a useful resource for rice researchers to elucidate important and complex biological events

On the discovery of stars, quasars, and galaxies in the Southern Hemisphere with S-PLUS DR2

This paper provides a catalogue of stars, quasars, and galaxies for the Southern Photometric Local Universe Survey Data Release 2 (S-PLUS DR2) in the Stripe 82 region. We show that a 12-band filter system (5 Sloan-like and 7 narrow bands) allows better performance for object classification than the usual analysis based solely on broad bands (regardless of infrared information). Moreover, we show that our classification is robust against missing values. Using spectroscopically confirmed sources retrieved from the Sloan Digital Sky Survey DR16 and DR14Q, we train a random forest classifier with the 12 S-PLUS magnitudes + 4 morphological features. A second random forest classifier is trained with the addition of the W1 (3.4 μm) and W2 (4.6 μm) magnitudes from the Wide-field Infrared Survey Explorer (WISE). Forty-four per cent of our catalogue have WISE counterparts and are provided with classification from both models. We achieve 95.76 per cent (52.47 per cent) of quasar purity, 95.88 per cent (92.24 per cent) of quasar completeness, 99.44 per cent (98.17 per cent) of star purity, 98.22 per cent (78.56 per cent) of star completeness, 98.04 per cent (81.39 per cent) of galaxy purity, and 98.8 per cent (85.37 per cent) of galaxy completeness for the first (second) classifier, for which the metrics were calculated on objects with (without) WISE counterpart. A total of 2926 787 objects that are not in our spectroscopic sample were labelled, obtaining 335 956 quasars, 1347 340 stars, and 1243 391 galaxies. From those, 7.4 per cent, 76.0 per cent, and 58.4 per cent were classified with probabilities above 80 per cent. The catalogue with classification and probabilities for Stripe 82 S-PLUS DR2 is available for download. © 2021 The Author(s).This work has been supported by a PhD fellowship to the lead author from Fundacao de Amparo à Pesquisa do Estado de Sao Paulo (FAPESP), 2019/01312-2. LN also acknowledges the support of Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior -Brasil (CAPES) -Finance Code 001 and FAPESP through process number 2014/10566-4. LN also thanks the staff of the Astronomy department from the University of Florida, where part of this work was done; Marco Antonio dos Santos and Ulisses Manzo Castello for the technical support; Luis Manrique for the technical support, feedback, and discussions about Machine Learning; Christian Massao Tsujiguchi Takagi and Vin ' icius Amaral Haga for the feedback on the accessibility of the figures in this paper; Gustavo Oliveira Schwarz for building the database. CMdO acknowledges funding from FAPESP through grants 2009/542028 and 2019/26492-3 and funding from the Brazilian National Research Council (CNPq), through grant 309209/2019-6. NSTH acknowledges FAPESP (grants 2017/25835-9 and 2015/22308-2). CQ acknowledges support from FAPESP (grants 2015/11442-0 and 2019/06766-1). AM acknowledges FAPESP scholarship grant 2018/25671-9. CEB acknowledges FAPESP, grant 2016/12331-0. FA-F acknowledges funding for this work from FAPESP grant 2018/20977-2. LSJ acknowledges support from Brazilian agencies FAPESP (2019/10923-5) and CNPq (304819/201794). AAC acknowledges support from Fundacao de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ; grant E26/203.186/2016) and CNPq (grants 304971/2016-2 and 401669/2016-5). EVL acknowledges funding for this work from CNPq grant 169181/2017-0 and CAPES grant 88887.470064/2019-00. MLB acknowledges FAPESP, grants 2018/09165-6 and 2019/23388-0. KMD acknowledges support from FAPERJ (grant E-26/203.184/2017), CNPq (grant 312702/2017-5) and the Serrapilheira Institute (grant Serra-1709-17357). AAC acknowledges support from FAPERJ (grant E26/203.186/2016), CNPq (grants 304971/2016-2 and 401669/2016-5), from the Universidad de Alicante under contract UATALENTO18-02, and from the State Agency for Research of the Spanish MCIU through the `Center of Excellence Severo Ochoa' award to the Instituto de Astrofísica de Andalucía (SEV-2017-0709). ARL acknowledges the financial support from CNPq through the PCI (Programa de Capacitacao Institucional) fellowship. The S-PLUS project, including the T80-South robotic telescope and the S-PLUS scientific survey, was founded as a partnership between FAPESP, the Observatorio Nacional (ON), the Federal University of Sergipe (UFS), and the Federal University of Santa Catarina (UFSC), with important financial and practical contributions from other collaborating institutes in Brazil, Chile (Universidad de La Serena), and Spain (Centro de Estudios de Física del Cosmos de Aragón, CEFCA). We further acknowledge financial support from FAPESP, CNPq, CAPES, FAPERJ, and the Brazilian Innovation Agency (FINEP).Peer reviewe