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Analysis matrix data collection

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https://www.readbyqxmd.com/read/29776336/phylogenomic-analysis-of-apoidea-sheds-new-light-on-the-sister-group-of-bees
#1
Manuela Sann, Oliver Niehuis, Ralph S Peters, Christoph Mayer, Alexey Kozlov, Lars Podsiadlowski, Sarah Bank, Karen Meusemann, Bernhard Misof, Christoph Bleidorn, Michael Ohl
BACKGROUND: Apoid wasps and bees (Apoidea) are an ecologically and morphologically diverse group of Hymenoptera, with some species of bees having evolved eusocial societies. Major problems for our understanding of the evolutionary history of Apoidea have been the difficulty to trace the phylogenetic origin and to reliably estimate the geological age of bees. To address these issues, we compiled a comprehensive phylogenomic dataset by simultaneously analyzing target DNA enrichment and transcriptomic sequence data, comprising 195 single-copy protein-coding genes and covering all major lineages of apoid wasps and bee families...
May 18, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29773972/genetic-diversity-and-structure-of-tea-plant-in-qinba-area-in-china-by-three-types-of-molecular-markers
#2
Yu Zhang, Xiaojuan Zhang, Xi Chen, Wang Sun, Jiao Li
Background: Qinba area has a long history of tea planting and is a northernmost region in China where Camellia sinensis L. is grown. In order to provide basic data for selection and optimization of molecular markers of tea plants. 118 markers, including 40 EST-SSR, 40 SRAP and 38 SCoT markers were used to evaluate the genetic diversity of 50 tea plant ( Camellia sinensis. ) samples collected from Qinb. tea germplasm, assess population structure. Results: In this study, a total of 414 alleles were obtained using 38 pairs of SCoT primers, with an average of 10...
2018: Hereditas
https://www.readbyqxmd.com/read/29769455/tenascin-c-a-potential-biomarker-for-predicting-the-severity-of-coronary-atherosclerosis
#3
Wen Gao, Jian Li, Huanchun Ni, Haiming Shi, Zhiyong Qi, Shouguo Zhu, Chuanming Hao, Qionghong Xie, Xinping Luo, Kun Xie
AIMS: Coronary artery disease (CAD) is the leading cause of mortality and morbidity worldwide and one of the greatest threats to public health. Tenascin C (TNC) is an extracellular matrix glycoprotein that is found in low concentrations in normal tissues and is enhanced by a range of cardiovascular pathologies. This study aimed to evaluate the value of TNC in assessing the severity of atherosclerosis measured by the Gensini score. METHODS: A total of 157 patients with chest pains who underwent selective coronary angiography for suspected coronary atherosclerosis were enrolled...
May 17, 2018: Journal of Atherosclerosis and Thrombosis
https://www.readbyqxmd.com/read/29762685/urine-multi-drug-screening-with-gc-ms-or-lc-ms-ms-using-salle-hybrid-ppt-spe
#4
Junhui Lee, Jiwon Park, Ahra Go, Heesung Moon, Sujin Kim, Sohee Jung, Wonjoon Jeong, Heesun Chung
To intoxicated patients in the emergency room, toxicological analysis can be considerably helpful for identifying the involved toxicants. In order to develop a urine multi-drug screening (UmDS) method, gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS-MS) were used to determine targeted and unknown toxicants in urine. A GC-MS method in scan mode was validated for selectivity, limit of detection (LOD) and recovery. An LC-MS-MS multiple reaction monitoring (MRM) method was validated for lower LOD, recovery and matrix effect...
May 14, 2018: Journal of Analytical Toxicology
https://www.readbyqxmd.com/read/29758290/proteome-response-of-dental-pulp-cells-to-exogenous-fgf8
#5
Rozaliya Tsikandelova, Petko Mladenov, Sébastien Planchon, Silvia Kalenderova, Maria Dragneva, Zornitsa Mihaylova, Pavel Stanimirov, Vanyo Mitev, Jenny Renaut, Nikolay Ishkitiev
FGF8 specifies early tooth development by directing the migration of the early tooth founder cells to the site of tooth emergence. To date the effect of the FGF8 in adult dental pulp has not been studied. We have assessed the regenerative potential of FGF8 by evaluating changes in the proteome landscape of dental pulp following short- and long-term exposure to recombinant FGF8 protein. In addition, we carried out qRT PCR analysis to determine extracellular/adhesion gene marker expression and assessed cell proliferation and mineralization in response to FGF8 treatment...
May 11, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29750737/inter-and-intraindividual-variation-of-methylphenidate-concentrations-in-serum-and-saliva-of-patients-with-attention-deficit-hyperactivity-disorder
#6
Joshua Preiskorn, Sophie Studer, Reinhold Rauh, Richard Lukačin, Christoph Geffert, Christian Fleischhaker, Hans-Willi Clement, Eberhard Schulz, Monica Biscaldi
BackgroundTherapeutic drug monitoring (TDM) is becoming increasingly important in psychiatric therapy; especially in children. However, for several reasons, it cannot yet be implemented as a daily routine in clinical or outpatient settings. To evaluate new, non-invasive procedures; blood and saliva (oral fluid) samples were collected from patients with attention-deficit/hyperactivity disorder (ADHD) who were also being administered methylphenidate (MPH). The study's main purposes were to correlate MPH concentrations in serum and saliva between subjects; and to analyze intraindividual variation of serum concentration...
May 3, 2018: Therapeutic Drug Monitoring
https://www.readbyqxmd.com/read/29743718/expressional-analysis-of-disease-relevant-signalling-pathways-in-primary-tumours-and-metastasis-of-head-and-neck-cancers
#7
Dorothee Goesswein, Negusse Habtemichael, Aslihan Gerhold-Ay, Johanna Mazur, Désirée Wünsch, Shirley K Knauer, Julian Künzel, Christoph Matthias, Sebastian Strieth, Roland H Stauber
Head and neck squamous cell carcinoma (HNSCC) often metastasize to lymph nodes resulting in poor prognosis for patients. Unfortunately, the underlying molecular mechanisms contributing to tumour aggressiveness, recurrences, and metastasis are still not fully understood. However, such knowledge is key to identify biomarkers and drug targets to improve prognosis and treatments. Consequently, we performed genome-wide expression profiling of 15 primary HNSSCs compared to corresponding lymph node metastases and non-malignant tissue of the same patient...
May 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29738072/combined-inflammation-and-metabolism-biomarker-indices-of-robust-and-impaired-physical-function-in-older-adults
#8
Xintong Zuo, Alison Luciano, Carl F Pieper, James R Bain, Virginia B Kraus, William E Kraus, Miriam C Morey, Harvey J Cohen
OBJECTIVES: To determine whether combinations of inflammatory markers are related to physical function. DESIGN AND SUBJECTS: secondary analysis of baseline of three observational studies of community-dwelling older adults MEASUREMENTS: The baseline data from 3 cohorts of older adults with different health and disease status were employed. Twenty markers of inflammation and metabolism were individually assessed for correlation with usual gait speed and were separated into robust and impairment quartiles...
May 8, 2018: Journal of the American Geriatrics Society
https://www.readbyqxmd.com/read/29735443/-differential-diagnosis-of-hepatocellular-carcinoma-and-hepatic-hemangiomas-based-on-radiomic-features-of-gadoxetate-disodium-enhanced-magnetic-resonance-imaging
#9
Mao-Dong Chen, Jing Zhang, Gui-Xiang Yang, Jie-Min Lin, Yan-Qiu Feng
OBJECTIVE: To evaluate the feasibility of using radiomic features for differential diagnosis of hepatocellular carcinoma (HCC) and hepatic cavernous hemangioma (HHE). METHODS: Gadoxetate disodium-enhanced magnetic resonance imaging data were collected from a total of 135 HCC and HHE lesions. The radiomic texture features of each lesion were extracted on the hepatobiliary phase images, and the performance of each feature was assessed in differentiation and classification of HCC and HHE...
April 20, 2018: Nan Fang Yi Ke da Xue Xue Bao, Journal of Southern Medical University
https://www.readbyqxmd.com/read/29720269/acidic-preconditioning-of-endothelial-colony-forming-cells-ecfc-promote-vasculogenesis-under-proinflammatory-and-high-glucose-conditions-in-vitro-and-in-vivo
#10
Hebe Agustina Mena, Paula Romina Zubiry, Blandine Dizier, Mirta Schattner, Catherine Boisson-Vidal, Soledad Negrotto
BACKGROUND: We have previously demonstrated that acidic preconditioning of human endothelial colony-forming cells (ECFC) increased proliferation, migration, and tubulogenesis in vitro, and increased their regenerative potential in a murine model of hind limb ischemia without baseline disease. We now analyze whether this strategy is also effective under adverse conditions for vasculogenesis, such as the presence of ischemia-related toxic molecules or diabetes, one of the main target diseases for cell therapy due to their well-known healing impairments...
May 2, 2018: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/29713469/metabolomic-analysis-of-longissimus-from-underperforming-piglets-relative-to-piglets-with-normal-preweaning-growth
#11
Timothy G Ramsay, Margo J Stoll, Amy E Shannon, Le Ann Blomberg
Background: Recent increases in intra-litter variability in weaning weight have raised swine production costs. A contributor to this variability is the normal birth weight pig that grows at a slower rate than littermates of similar birth weight. The goal of this study was to interrogate biochemical profiles manifested in skeletal muscle originating from slow growing (SG) and faster growing littermates (control), with the aim of identifying differences in metabolic pathway utilization between skeletal muscle of the SG pig relative to its littermates...
2018: Journal of Animal Science and Biotechnology
https://www.readbyqxmd.com/read/29704703/quality-assurance-of-the-clinical-learning-environment-in-austria-construct-validity-of-the-clinical-learning-environment-supervision-and-nurse-teacher-scale-cles-t-scale
#12
Gerhard Mueller, Demetrius Mylonas, Petra Schumacher
BACKGROUND: Within nursing education, the clinical learning environment is of a high importance in regards to the development of competencies and abilities. The organization, atmosphere, and supervision in the clinical learning environment are only a few factors that influence this development. In Austria there is currently no valid instrument available for the evaluation of influencing factors. OBJECTIVES: The aim of the study was to test the construct validity with principal component analysis as well as the internal consistency of the German Clinical Learning Environment, Supervision and Teacher Scale (CLES+T scale) in Austria...
April 21, 2018: Nurse Education Today
https://www.readbyqxmd.com/read/29688321/comparison-and-evaluation-of-integrative-methods-for-the-analysis-of-multilevel-omics-data-a-study-based-on-simulated-and-experimental-cancer-data
#13
Bettina M Pucher, Oana A Zeleznik, Gerhard G Thallinger
Integrative analysis aims to identify the driving factors of a biological process by the joint exploration of data from multiple cellular levels. The volume of omics data produced is constantly increasing, and so too does the collection of tools for its analysis. Comparative studies assessing performance and the biological value of results, however, are rare but in great demand. We present a comprehensive comparison of three integrative analysis approaches, sparse canonical correlation analysis (sCCA), non-negative matrix factorization (NMF) and logic data mining MicroArray Logic Analyzer (MALA), by applying them to simulated and experimental omics data...
April 23, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29685704/assessment-of-reamer-irrigator-aspirator-system-ria-filtrate-for-its-osteoinductive-potential-in-a-validated-animal-model
#14
Alex R Wessel, Brett D Crist, James P Stannard, Gregory J Della Rocca, Aaron M Stoker, Chantelle C Bozynski, Cristi R Cook, Keiichi Kuroki, Carin E Ahner, James L Cook
PURPOSE: Previous studies indicate that Reamer Irrigator Aspirator (RIA) filtrate contains proteins that have the potential to stimulate bone healing. This study aimed to determine the osteoinductive capabilities of RIA filtrate in a validated in vivo model. METHODS: With Institutional Review Board approval, RIA filtrates from 9 patients were collected. The filtrate was processed to remove cells and inorganic particles. A portion of each sample was set aside for protein analysis while the remainder was lyophilized and prepared for implantation...
April 17, 2018: Injury
https://www.readbyqxmd.com/read/29677186/morphophysiological-changes-in-the-splenic-extracellular-matrix-of-leishmania-infantum-naturally-infected-dogs-is-associated-with-alterations-in-lymphoid-niches-and-the-cd4-t-cell-frequency-in-spleens
#15
Aurea Virginia Andrade da Silva, Fabiano Borges Figueiredo, Rodrigo Caldas Menezes, Arthur Augusto Mendes-Junior, Luisa Helena Monteiro de Miranda, Elisa Cupolillo, Renato Porrozzi, Fernanda Nazaré Morgado
The spleen is one of the main affected organs in canine visceral leishmaniasis (CVL). Disorganization of the splenic white pulp (SWP) has been associated with immunosuppression and disease progression. This study aims to assess structural and cellular changes in the splenic extracellular matrix of dogs with CVL, correlating these changes with the parasite load and clinical signs. Splenic fragments were collected from 41 naturally infected animals for parasite load quantification by quantitative PCR, histopathological analysis and immunohistochemistry for CD3+, CD4+, and CD8+ T cells; CD21+ B cells; Ki-67+, IFN-γ+, and IL-10+ cells; and the MMP-9 and ADAM-10 enzymes...
April 20, 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29670452/floristic-affinities-of-the-lowland-savannahs-of-belize-and-southern-mexico
#16
Idalia Arely Canché-Estrada, Juan Javier Ortiz-Díaz, Juan Tun-Garrido
Environmental heterogeneity of Belize and southern Mexico savannahs as well as their geographical location suggest that these plant communities share floristic elements, making them conducive to a phytogeographical analysis. The aim of this study was to analyse the floristic affinities of nine savannahs of Belize and southern Mexico and to explain the similarities and differences amongst them. A binary data matrix containing 915 species was built based on the authors' own collections and on nine floristic lists already published...
2018: PhytoKeys
https://www.readbyqxmd.com/read/29659648/single-gene-prognostic-signatures-for-advanced-stage-serous-ovarian-cancer-based-on-1257-patient-samples
#17
Fan Zhang, Kai Yang, Kui Deng, Yuanyuan Zhang, Weiwei Zhao, Huan Xu, Zhiwei Rong, Kang Li
OBJECTIVE: We sought to identify stable single-gene prognostic signatures based on a large collection of advanced stage serous ovarian cancer (AS-OvCa) gene expression data and explore their functions. METHODS: The empirical Bayes (EB) method was used to remove the batch effect and integrate 8 ovarian cancer datasets. Univariate Cox regression was used to evaluate the association between gene and overall survival (OS). The Database for Annotation, Visualization and Integrated Discovery (DAVID) tool was used for the functional annotation of genes for Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways...
April 16, 2018: Molecular omics
https://www.readbyqxmd.com/read/29655430/use-of-dielectric-barrier-discharge-ionization-to-minimize-matrix-effects-and-expand-coverage-in-pesticide-residue-analysis-by-liquid-chromatography-mass-spectrometry
#18
Felipe J Lara-Ortega, José Robles-Molina, Sebastian Brandt, Alexander Schütz, Bienvenida Gilbert-López, Antonio Molina-Díaz, Juan F García-Reyes, Joachim Franzke
Although electrospray ionization (ESI) remains the gold standard ionization source for LC-MS, it exhibits two main limitations: the occurrence of matrix effects and the limited ionization coverage towards nonpolar compounds. Dielectric barrier discharge ionization (DBDI) has gained attraction in recent years as a versatile ionization method in different applications and formats. Here, we report a thorough evaluation of DBDI as ionization interface for LC-MS, which reveals attractive advantages over ESI and atmospheric pressure chemical ionization (APCI) provided its singular ionization mechanism versatility...
August 22, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29652600/social-network-analysis-for-assessing-college-aged-adults-health-a-systematic-review
#19
Megan S Patterson, Patricia Go Odson
OBJECTIVE: Social network analysis (SNA) is a useful, emerging method for studying health. College students are especially prone to social influence when it comes to health. This review aimed to identify network variables related to college student health and determine how SNA was used in the literature. PARTICIPANTS: A systematic review of relevant literature was conducted in October 2015. METHODS: Studies employing egocentric or whole network analysis to study college student health were included...
April 13, 2018: Journal of American College Health: J of ACH
https://www.readbyqxmd.com/read/29649471/principal-coordinate-analysis-assisted-chromatographic-analysis-of-bacterial-cell-wall-collection-a-robust-classification-approach
#20
Keshav Kumar, Felipe Cava
In the present work, Principal coordinate analysis (PCoA) is introduced to develop a robust model to classify the chromatographic data sets of peptidoglycan sample. PcoA captures the heterogeneity present in the data sets by using the dissimilarity matrix as input. Thus, in principle, it can even capture the subtle differences in the bacterial peptidoglycan composition and can provide a more robust and fast approach for classifying the bacterial collection and identifying the novel cell wall targets for further biological and clinical studies...
April 9, 2018: Analytical Biochemistry
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