bluuebunny/crossref_metadata_2025_split huggingface dataset:
Th1, Th17, and Treg Responses are Differently Modulated by TNF-α Inhibitors and Methotrexate in Psoriasis Patients
Authors: Furiati Sandro C. , Catarino Jonatas S. , Silva Marcos V. , Silva Rafaela F. , Estevam Rayane B. , Teodoro Reginaldo B. , Pereira Sanivia L. , Ataide Meire , Rodrigues Virmondes , Rodrigues Denise B. R. 
Published: May 2019

AbstractPsoriasis is a chronic, recurrent, immune-mediated, hyperproliferative inflammatory skin disease. The role of the adaptive immune system, particularly of Th1 and Th17 lymphocytes, has been regarded as prominent in the immunopathogenesis of psoriasis, as well as decreased Tregs function. Immunobiological drugs were administered in therapeutic pulses and a few studies evaluate their effects on the immune repertoire. The aim of this study was to evaluate the adaptive immune profile of patients with severe psoriasis under immunobiological treatment in two time points. Thirty-two psoriasis patients and 10 control patients were evaluated. In the group of psoriasis patients, 10 patients were on anti-TNF and 14 patients on methotrexate treatment, while 8 individuals were not treated. IL-17, IFN-γ, TNF-α, IL-6, IL-2, and IL-10 were analyzed. CD4 T cell intracellular cytokines were analyzed. It was observed that stimulation could significantly increase the production of IL-17, IFN-γ, TNF-α, and IL-10 only before anti-TNF pulse therapy. The activation of Th1 and Treg cells after stimulation was significantly higher before anti-TNF pulse. Patients on methotrexate or anti-TNF therapy produced significantly lower levels of TNF-α, IL-10, and IL-6. Furthermore, these patients showed a significant decrease in the activated CD4+ T cells. The treatment with immunomodulator or methotrexate modulates the activation of CD4+ T cells, and anti-TNF treatment appears to have a modulating effect on the activation and production of Th1, Th17, and Treg cells.
Plk1 Mediates Paxillin Phosphorylation (Ser-272), Centrosome Maturation, and Airway Smooth Muscle Layer Thickening in Allergic Asthma
Authors: Rezey Alyssa C. , Gerlach Brennan D. , Wang Ruping , Liao Guoning , Tang Dale D. 
Published: May 2019

AbstractAllergic asthma is characterized by airway smooth muscle layer thickening, which is largely attributed to cell division that requires the formation of centrosomes. Centrosomes play a pivotal role in regulating bipolar spindle formation and cell division. Before mitosis, centrosomes undergo maturation characterized by expansion of pericentriolar material proteins, which facilitates spindle formation and mitotic efficiency of many cell types. Although polo-like kinase 1 (Plk1) has been implicated in centrosome maturation, the mechanisms by which Plk1 regulates the cellular process are incompletely elucidated. Here, we identified paxillin as a new Plk1-interacting protein in human airway smooth muscle cells. We unexpectedly found that phosphorylated paxillin (Ser-272) was localized in centrosomes of human smooth muscle cells, which regulated centrosome maturation and spindle assembly. Plk1 knockdown inhibited paxillin Ser-272 phosphorylation, centrosome maturation, and cell division. Furthermore, exposure to allergens enhanced airway smooth muscle layer and paxillin phosphorylation at this residue in mice, which was reduced by smooth muscle conditional knockout of Plk1. These findings suggest that Plk1 regulates centrosome maturation and cell division in part by modulating paxillin phosphorylation on Ser-272. Furthermore, Plk1 contributes to the pathogenesis of allergen-induced thickening of the airway smooth muscle layer by affecting paxillin phosphorylation at this position.
Fish diversity of the largest deltaic formation in the Americas - a description of the fish fauna of the Parnaíba Delta using DNA Barcoding
Authors: Guimarães-Costa Aurycéia J. , Machado Fabíola S. , Oliveira Rory R. S. , Silva-Costa Vinícius , Andrade Marcelo C. , Giarrizzo Tommaso , Saint-Paul Ulrich , Sampaio Iracilda , Schneider Horacio 
Published: May 2019

AbstractDeltas are dynamic and productive systems of enormous ecological significance, encompassing unique and biologically diverse wetland habitats. Here, we present the first data on the molecular diversity of the fish fauna of the Parnaíba Delta, the largest deltaic formation of the Americas. Partial sequences (626 bp) of the mitochondrial COI gene (Cytochrome c oxidase subunit I) were used to barcode 402 individuals, representing 128 species, belonging to 98 genera, 57 families, 17 orders and two classes. The most abundant orders were the Perciformes, Siluriformes, Gobiiformes, and Pleuronectiformes. The Neighbor-Joining (NJ), Bayesian Inference (BI), and BIN analyses produced 103 molecular clusters, while the Automatic Barcode Gap Discovery (ABGD) and Maximum Likelihood (ML) approaches revealed 102 clusters. The mean conspecific, congeneric and confamilial genetic distances were 0.33%, 14.37%, and 18.60%, respectively. Intraspecific divergence ranged from 0.0% to 1.4%, and all species presented barcode gaps, with the exception of two clusters of Cathorops spixii (OTU 96 and OTU 103), which were separated by a low interspecific distance (1.2%), which overlaps the maximum intraspecific genetic distance (1.4%). The barcode data provide new insights into the fish diversity of the Parnaíba Delta, which will be important for the development of further research on this fauna.
Imaging of dehydration in particulate matter using Raman line-focus microscopy
Authors: Okeyo Peter Ouma , Ilchenko Oleksii , Slipets Roman , Larsen Peter Emil , Boisen Anja , Rades Thomas , Rantanen Jukka 
Published: May 2019

AbstractCrystalline solids can incorporate water molecules into their crystal lattice causing a dramatic impact on their properties. This explains the increasing interest in understanding the dehydration pathways of these solids. However, the classical thermal analytical techniques cannot spatially resolve the dehydration pathway of organic hydrates at the single particle level. We have developed a new method for imaging the dehydration of organic hydrates using Raman line-focus microscopy during heating of a particle. Based on this approach, we propose a new metastable intermediate of theophylline monohydrate during the three-step dehydration process of this system and further, we visualize the complex nature of the three-step dehydration pathway of nitrofurantoin monohydrate to its stable anhydrous form. A Raman line-focus mapping option was applied for fast simultaneous mapping of differently sized and shaped particles of nitrofurantoin monohydrate, revealing the appearance of multiple solid-state forms and the non-uniformity of this particle system during the complex dehydration process. This method provides an in-depth understanding of phase transformations and can be used to explain practical industrial challenges related to variations in the quality of particulate materials.
The Effects of Regular Exercise on Circulating Cardiovascular-related MicroRNAs
Authors: Barber Jacob L. , Zellars Kia N. , Barringhaus Kurt G. , Bouchard Claude , Spinale Francis G. , Sarzynski Mark A. 
Published: May 2019

AbstractThe purpose of the present study was to examine the effects of regular exercise on the abundance of targeted circulating microRNAs (miRNAs). The present analysis examined 20 previously sedentary adults from the HERITAGE Family Study who completed 20 weeks of endurance exercise training. The expression of 53 miRNAs related to cardiovascular disease were measured in serum collected at baseline and post-training by performing RT-qPCR on the Human Cardiovascular Disease miRNA array (Qiagen, Germany). The effect of regular exercise on circulating miRNAs was assessed using paired t-tests of baseline and post-training expression levels. A false discovery rate threshold of 5% was used to determine significance. Regular exercise resulted in significantly decreased mean serum expression of nine miRNAs (miR-486-5p, let-7b-5p, miR-29c-3p, let-7e-5p, miR-93-5p, miR-7-5p, miR-25-3p, miR-92a-3p, and miR-29b-3p; fold change range: 0.64–83, p = 0.0002–0.01) and increased mean expression of five miRNAs (miR-142-3p, miR-221-3p, miR-126-3p, miR-146a-5p, and miR-27b-3p; fold change range: 1.41–3.60, p = 0.001–0.006). Enrichment analysis found that these 14 miRNAs target genes related to over 345 different biological pathways. These results provide further evidence of the effects of regular exercise on the circulating miRNA profile.
Systematic analysis of TruSeq, SMARTer and SMARTer Ultra-Low RNA-seq kits for standard, low and ultra-low quantity samples
Authors: Palomares Marie-Ange , Dalmasso Cyril , Bonnet Eric , Derbois Céline , Brohard-Julien Solène , Ambroise Christophe , Battail Christophe , Deleuze Jean-François , Olaso Robert 
Published: May 2019

AbstractHigh-throughput RNA-sequencing has become the gold standard method for whole-transcriptome gene expression analysis, and is widely used in numerous applications to study cell and tissue transcriptomes. It is also being increasingly used in a number of clinical applications, including expression profiling for diagnostics and alternative transcript detection. However, despite its many advantages, RNA sequencing can be challenging in some situations, for instance in cases of low input amounts or degraded RNA samples. Several protocols have been proposed to overcome these challenges, and many are available as commercial kits. In this study, we systematically test three recent commercial technologies for RNA-seq library preparation (TruSeq, SMARTer and SMARTer Ultra-Low) on human biological reference materials, using standard (1 mg), low (100 ng and 10 ng) and ultra-low (<1 ng) input amounts, and for mRNA and total RNA, stranded and unstranded. The results are analyzed using read quality and alignment metrics, gene detection and differential gene expression metrics. Overall, we show that the TruSeq kit performs well with an input amount of 100 ng, while the SMARTer kit shows decreased performance for inputs of 100 and 10 ng, and the SMARTer Ultra-Low kit performs relatively well for input amounts <1 ng. All the results are discussed in detail, and we provide guidelines for biologists for the selection of an RNA-seq library preparation kit.
Discrepancies between observed data and predictions from mathematical modelling of the impact of screening interventions on Chlamydia trachomatis prevalence
Authors: Smid Joost , Althaus Christian L. , Low Nicola 
Published: May 2019

AbstractMathematical modelling studies of C. trachomatis transmission predict that interventions to screen and treat chlamydia infection will reduce prevalence to a greater degree than that observed in empirical population-based studies. We investigated two factors that might explain this discrepancy: partial immunity after natural infection clearance and differential screening coverage according to infection risk. We used four variants of a compartmental model for heterosexual C. trachomatis transmission, parameterized using data from England about sexual behaviour, C. trachomatis testing, diagnosis and prevalence, and Markov Chain Monte Carlo methods for statistical inference. In our baseline scenario, a model in which partial immunity follows natural infection clearance and the proportion of tests done in chlamydia-infected people decreases over time fitted the data best. The model predicts that partial immunity reduced susceptibility to reinfection by 68% (95% Bayesian credible interval 46–87%). The estimated screening rate was 4.3 (2.2–6.6) times higher for infected than for uninfected women in 2000, decreasing to 2.1 (1.4–2.9) in 2011. Despite incorporation of these factors, the model still predicted a marked decline in C. trachomatis prevalence. To reduce the gap between modelling and data, advances are needed in knowledge about factors influencing the coverage of chlamydia screening, the immunology of C. trachomatis and changes in C. trachomatis prevalence at the population level.
Circulating Microbiota-Based Metagenomic Signature for Detection of Hepatocellular Carcinoma
Authors: Cho Eun Ju , Leem Sangseob , Kim Sun Ah , Yang Jinho , Lee Yun Bin , Kim Soon Sun , Cheong Jae Youn , Cho Sung Won , Kim Ji Won , Kim Sung-Min , Yoon Jung-Hwan , Park Taesung 
Published: May 2019

AbstractCirculating microbial dysbiosis is associated with chronic liver disease including nonalcoholic steatohepatitis and alcoholic liver disease. In this study, we evaluated whether disease-specific alterations of circulating microbiome are present in patients with cirrhosis and hepatocellular carcinoma (HCC), and their potential as diagnostic biomarkers for HCC. We performed cross-sectional metagenomic analyses of serum samples from 79 patients with HCC, 83 with cirrhosis, and 201 matching healthy controls, and validated the results in the same number of subjects. Serum bacterial DNA was analyzed using high-throughput pyrosequencing after amplification of the V3–V4 hypervariable regions of 16S rDNA. Blood microbial diversity was significantly reduced in HCC, compared with cirrhosis and control. There were significant differences in the relative abundances of several bacterial taxa that correlate with the presence of HCC, thus defining a specific blood microbiome-derived metagenomic signature of HCC. We identified 5 microbial gene markers-based model which distinguished HCC from controls with an area under the receiver-operating curve (AUC) of 0.879 and a balanced accuracy of 81.6%. In the validation, this model accurately distinguished HCC with an AUC of 0.875 and an accuracy of 79.8%. In conclusion, circulating microbiome-based signatures may be potential biomarkers for the detection HCC.
Common cuckoo females may escape male sexual harassment by color polymorphism
Authors: Lee Jin-Won , Kim Hae-Ni , Yoo Sohyeon , Yoo Jeong-Chil 
Published: May 2019

AbstractSexual conflict over mating rate is widely regarded as a selective force on the evolution of female-limited color polymorphism in invertebrates, such as damselflies and butterflies. However, evidence confirming its use in higher vertebrates remains limited. The common cuckoo,Cuculus canorus, is an avian brood parasite that does not provide parental care and represents a rare example of female-limited polymorphism in higher vertebrates. Specifically, males exhibit a monomorphic gray morph, while females are either gray or rufous colored, like juveniles. To test a prediction from the hypothesis that the rufous plumage of female cuckoos may help avoid excessive sexual harassment by males (the harassment avoidance hypothesis), we investigate color morph preference in male cuckoos. Mate choice experiments using playbacks of female calls with decoys mimicking both color morphs indicated that the attracted males immediately copulated with decoys without courtship displays, recognizing both color morphs as a sexual partner. However, the males attempted to copulate more frequently and excessively with the gray morph, which is consistent with the prediction from the harassment avoidance hypothesis. We propose that the absence of parental care augments sexual conflict over mating in cuckoos, resulting in the unusual evolution of female-limited polymorphism in this higher vertebrate.
Histopathology and expression of the chemokines CXCL10, CXCL13, and CXCR3 and the endogenous TLR-4 ligand S100A8/A9 in lymph nodes of patients with adult-onset Still’s disease
Authors: Kim Hyoun-Ah , Kim Yon Hee , Jeon Yoon Kyung , Yang Woo-Ick , Kwon Ji Eun , Han Jae Ho 
Published: May 2019

AbstractAdult-onset Still’s disease (AOSD) is a rare systemic inflammatory disease manifesting with a persistent high-spiking fever, a typical rash, and lymphadenopathy. Endogenous factors related to interleukin-1, such as S100A8/A9 and several chemokines including CXCL10, CXCR3, and CXCL13, potentially play roles in its pathogenesis. We describe the histopathological features and chemokine expression pattern in lymph nodes (LNs) of patients with AOSD. Formalin-fixed, paraffin-embedded excisional LN tissues from 48 patients with AOSD were histologically reviewed. CXCL10, CXCR3, CXCL13, and S100A8/A9 expression was evaluated immunohistochemically. The pathology of LN was characterized by paracortical hyperplasia with proliferation of histiocyte, immunoblast, CD8-positive lymphoid cell and blood vessel. Most cases required differential diagnosis from dermatopathic lymphadenitis (n = 16, 33.3%), T cell lymphoma (n = 11, 22.9%), and histiocytic necrotizing lymphadenitis (HNL) (n = 9, 18.8%). The expression levels of CXCL10 and CXCR3 were higher in patients with AOSD than in those with T cell lymphoma, HNL, tuberculous lymphadenitis, and reactive hyperplasia. It is important to recognize the aforementioned histopathologic findings of nodal involvement of AOSD because improper diagnosis and treatment can be avoided. Immunohistochemical staining for chemokines, CXCL10 and CXCR3, may aid in differentiating AOSD from other mimickers.
A sulfur and nitrogen cycle informed model to simulate nitrate treatment of reservoir souring
Authors: Jahanbani Veshareh Moein , Nick Hamidreza M. 
Published: May 2019

AbstractNitrate treatment has been widely used in various seawater injection projects to treat biologic sulfate reduction or reservoir souring. To design a promising nitrate treatment plan, it is essential to have a comprehensive understanding of reactions that represent the microbial communities of the reservoir and mechanisms through which the souring process is inhibited. We employ a new approach of evaluating different reaction pathways to design reaction models that reflect governing microbial processes in a set of batch and flow experiments. Utilizing the designed models, we suggest dissimilatory nitrate reduction to ammonium is the main reaction pathway. Additionally, we illustrate nitrite inhibition is the major mechanism of nitrate treatment process; independent of nitrate reduction being autotrophic or heterotrophic. We introduce an inhibitory nitrate injection concentration that can inhibit souring regardless of nitrite inhibition effect and the distance between injection and production wells. Furthermore, we demonstrate that the ratio of the nitrite-nitrate reduction rate can be used to estimate nitrate treatment effectiveness. Our findings in regard to importance of nitrite inhibition mechanism and the inhibitory nitrate concentration are in accordance with the field observations.
The Cdh5-CreERT2 transgene causes conditional Shb gene deletion in hematopoietic cells with consequences for immune cell responses to tumors
Authors: He Qi , Li Xiujuan , Singh Kailash , Luo Zhengkang , Meija-Cordova Mariela , Jamalpour Maria , Lindahl Björn , Kriz Vitezslav , Vuolteenaho Reetta , Ulvmar Maria , Welsh Michael 
Published: May 2019

AbstractThe tamoxifen-responsive conditional Cdh5-CreERT2 is commonly used for endothelial cell specific conditional deletion of loxP-flanked gene sequences. To address the role of endothelial cell Shb gene for B16F10 melanoma immune responses, tamoxifen-injected Cdh5-CreERT2/WT and Cdh5-CreERT2/Shbflox/flox mice received subcutaneous tumor cell injections. We observed a decrease of tumor myeloid cell Shb mRNA in the tamoxifen treated Cdh5-CreERT2/Shbflox/flox mice, which was not present when the mice had undergone a preceding bone marrow transplantation using wild type bone marrow. Differences in CD4+/FoxP3+ Tregs were similarly abolished by a preceding bone marrow transplantation. In ROSA26-mTmG mice, Cdh5-CreERT2 caused detectable floxing in certain bone marrow populations and in spleen cells. Floxing in bone marrow could be detected two months after tamoxifen treatment. In the spleen, however, floxing was undetectable two months after tamoxifen treatment, suggesting that Cdh5-CreERT2 is operating in a non-renewable population of hematopoietic cells in this organ. These data suggest that conditional gene deletion in hematopoietic cells is a potential confounder in experiments attempting to assess the role of endothelial specific effects. A cautious approach to achieve an endothelial-specific phenotype would be to adopt a strategy that includes a preceding bone marrow transplantation.
Refining the Genomic Region Containing a Major Locus Controlling Fruit Maturity in Peach
Authors: Elsadr H. , Sherif S. , Banks T. , Somers D. , Jayasankar S. 
Published: May 2019

AbstractMaturity date (MD), defined as the duration between the first calendar day of the year and maturity, and fruit development period (FDP), defined as the duration between full bloom and maturity, are highly variable in peach [Prunus persica(L.) Batsch]. There is a need to discover molecular markers associated with these traits in order to enhance the efficiency and reliability of breeding for extending the harvest season in peach. An association mapping population consisting of 132 peach accessions was phenotypically evaluated for MD and FDP, and genotypically characterized using the genotyping-by-sequencing (GBS) approach. The phenotypic and genotypic data collected were used to conduct a genome-wide association study (GWAS). The GWAS identified three SNPs on chromosome 4 that are significantly associated with both FDP and MD. These three SNPs covered a region of 43,067 bp; we referred to this region as the MD/FDP locus. Seven genes were identified in the MD/FDP locus. One or more of these genes is believed to regulate some aspect of maturity in peach. The data reported here is expected to aid in marker-assisted seedling selection (MASS) targeted towards widening peach germplasm for maturity, particularly early maturity.
BioTimer assay as complementary method to vortex-sonication-vortex technique for the microbiological diagnosis of implant associated infections
Authors: Rosa Luigi , Lepanto Maria Stefania , Cutone Antimo , Berlutti Francesca , De Angelis Massimiliano , Vullo Vincenzo , Mastroianni Claudio Maria , Valenti Piera , Oliva Alessandra 
Published: May 2019

AbstractTo enumerate bacteria adherent to medical devices, Vortex-Sonication-Vortex Method (VSVM) and BioTimer Assay (BTA) have been applied. VSVM counts detached microorganisms whereas BTA enumerates adherent microorganisms through microbial metabolism. However, the limitation of VSVM consists in incomplete detachment of adherent microorganisms while BTA is unable to identify microbial genera and species. Herein, the combined use of VSVM and BTA for the diagnosis and enumeration of adherent microorganisms causing implant-associated-infections (IAIs) is reported. Over 2016–2018, 46 patients with IAIs were enrolled and their 82 explanted devices were submitted firstly to VSVM and then to BTA. VSVM plus BTA detected microorganisms in 39/46 patients (84.7%) compared with 32/46 (69.5%) and 31/46 (67.3%) by VSVM and BTA alone, respectively. Likely, combined methods led to microorganism detection in 54/82 devices (65.9%) compared with each method alone [43/82 (52.4%), 44/82 (53.6%) for VSVM and BTA, respectively]. The combination of both methods (concordance 75.6%) raised the sensitivity of microbial analysis in IAIs compared with either VSVM or BTA alone, thus representing a simple and accurate way for the identification and enumeration of microorganisms adherent on devices. Moreover, BTA reagent applied in a new apparatus allowed also the enumeration of the microorganisms adherent on different segments of cardiac electrodes, thus contributing to define IAIs pathogenesis.