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article

6-BA and NAA effect on ‘Galaxy’ fruit growth, abscission and quality: a comparison between the Po Valley and the South Tyrol producing areas

A. M. Bregoli, C. Fabbroni, V. Raimondi, P. Brunner, more

Erwerbs-Obstbau > 2007 > 49 > 3 > 97-100

The present study concerned the fruit thinning efficacy of the cytokinin 6-benzyladenine (6-BA) at 150 ppm alone or in combination with the naphthalene acetic acid (NAA) at 15 ppm, on ‘Galaxy’ trees grown in two orchards, one in South Tyrol and the other in Emilia-Romagna area. Applications were carried out at different fruit sizes (5–7, 10–12, 14–16 mm of the king fruit diameter, KF Ø). In warm climatic...

article

Determination of some galactic constants using planetary nebulae

A. Ali, M.A. Sharaf

New Astronomy > 1998 > 3 > 7 > 419-425

In this paper, Planetary Nebulae (PNe) are considered as a stellar system by which we succeed in determining the following Galactic constants: the Galactic pole coordinates (α _p , δ _p ), which are used for coordinate transformation in Galactic astronomy, the velocity and apex of the solar motion as an important kinematical parameter for stellar groups, Oorts's first constant (A) and...

article

Metal‐poor stars observed with the automated planet finder telescope. III. CEMP‐no stars are the descendant of population III stars

Nour Aldein Almusleh, Ali Taani, Sergen Özdemir, Maria Rah, more

Astronomische Nachrichten > 342 > 4 > 625 - 632

This study reports a probabilistic insight into the stellar‐mass and supernovae (SNe) explosion energy of five CEMP‐no stars' possible progenitors. As such, a direct comparison between the abundance ratios [X/Fe] of the light‐elements and the predicted nucleosynthetic yields of SN of high‐mass metal‐free stars has been performed. This comparison suggests that the possible progenitors have a stellar‐mass...

article

TACITuS: transcriptomic data collector, integrator, and selector on big data platform

Salvatore Alaimo, Antonio Di Maria, Dennis Shasha, Alfredo Ferro, more

BMC Bioinformatics > 2019 > 20 > 9 > 1-11

Background Several large public repositories of microarray datasets and RNA-seq data are available. Two prominent examples include ArrayExpress and NCBI GEO. Unfortunately, there is no easy way to import and manipulate data from such resources, because the data is stored in large files, requiring large bandwidth to download and special purpose data manipulation tools to extract subsets relevant for...

article

Bioinformatics Tools and Workflow to Select Blood Biomarkers for Early Cancer Diagnosis: An Application to Pancreatic Cancer

Yves Vandenbrouck, David Christiany, Florence Combes, Valentin Loux, more

PROTEOMICS > 19 > 21-22 > n/a - n/a

Secretome proteomics for the discovery of cancer biomarkers holds great potential to improve early cancer diagnosis. A knowledge‐based approach relying on mechanistic criteria related to the type of cancer should help to identify candidates from available “omics” information. With the aim of accelerating the discovery process for novel biomarkers, a set of tools is developed and made available via...

article

Kinematics of Open Star Clusters Based on the Data of the New Version of the “Homogeneous Catalog of Open Cluster Parameters”

A. V. Loktin, M. E. Popova

Astrophysical Bulletin > 2019 > 74 > 3 > 270-276

We investigate some aspects of Galactic disc kinematics based on the data on open clusters from the current version of “The Homogeneous Catalog of the Main Parameters of Open Star Clusters” and from Gaia DR2. Based on the radial velocity and proper motion data for the clusters we determine the angular velocity of the Sun in the Galaxy as Ω₀ = 25.6 ± 1.2 km s^-1 kpc^-1. A new approximation of the Galactic...

article

Gould Belt members in X-ray RAVE: cross-matching RAVE stars with 3XMM point sources

B. Coşkunoğlu, O. Plevne, M. T. Özkan

Astrophysics and Space Science > 2019 > 364 > 1 > 1-9

In this paper the results of matching the RAdial Velocity Experiment (RAVE), a spectroscopic Southern hemisphere survey ( 9<IDENIS<12 $9 < I_{\mathrm{DENIS}} < 12$), and XMM-Newton Serendipitous Source Catalogue (3XMM) are presented. The latest data releases of RAVE and XMM were matched and a X-ray RAVE catalogue of 1071 stars was obtained. Then the catalogue was checked for possible Gould...

article

SyNDI: synchronous network data integration framework

Erno Lindfors, Jesse C. J. van Dam, Carolyn Ming Chi Lam, Niels A. Zondervan, more

BMC Bioinformatics > 2018 > 19 > 1 > 1-15

Background Systems biology takes a holistic approach by handling biomolecules and their interactions as big systems. Network based approach has emerged as a natural way to model these systems with the idea of representing biomolecules as nodes and their interactions as edges. Very often the input data come from various sorts of omics analyses. Those resulting networks sometimes describe a wide range...

article

On the Distribution of Radio Pulsars Above the Galaxy Plane

A. A. Loginov, I. F. Malov

Bulletin of the Lebedev Physics Institute > 2018 > 45 > 7 > 218-222

A mechanism of pulsar accumulation over the galaxy plane, caused by deceleration in the gravitational field and stopping at a certain distance of z from the plane is proposed. For pulsars with velocities close to the average observed velocity of about 300 km/s, the consideration of kinematics of such motion estimates the age of stopped pulsars of the order of ten millions years and the average distance...

article

sRNAPipe: a Galaxy-based pipeline for bioinformatic in-depth exploration of small RNAseq data

Romain Pogorelcnik, Chantal Vaury, Pierre Pouchin, Silke Jensen, more

Mobile DNA > 2018 > 9 > 1 > 1-6

Background The field of small RNA is one of the most investigated research areas since they were shown to regulate transposable elements and gene expression and play essential roles in fundamental biological processes. Small RNA deep sequencing (sRNA-seq) is now routinely used for large-scale analyses of small RNA. Such high-throughput sequencing typically produces several millions reads. Results...

article

SAMSA2: a standalone metatranscriptome analysis pipeline

Samuel T. Westreich, Michelle L. Treiber, David A. Mills, Ian Korf, more

BMC Bioinformatics > 2018 > 19 > 1 > 1-11

Background Complex microbial communities are an area of growing interest in biology. Metatranscriptomics allows researchers to quantify microbial gene expression in an environmental sample via high-throughput sequencing. Metatranscriptomic experiments are computationally intensive because the experiments generate a large volume of sequence data and each sequence must be compared with reference sequences...

article

New Asymptotic Giant Branch Carbon Stars in the Galactic Halo

N. Mauron, K. S. Gigoyan, G. R. Kostandyan

Astrophysics > 2018 > 61 > 1 > 83-90

For the first time the data on the eight confirmed or candidate carbon (C) stars found mainly from objective-prism plates are presented. By using the Catalina database of lightcurves, we find that all these stars are pulsating, allowing a distance to be estimated through the K-band Period-Luminosity (PL) relation. This relation does not depend on spectral type (M or C) and distances are reliable even...

article

Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and Apodemus B chromosomes

Alexey I. Makunin, Marija Rajičić, Tatyana V. Karamysheva, Svetlana A. Romanenko, more

Chromosoma > 2018 > 127 > 3 > 301-311

Supernumerary chromosomes sporadically arise in many eukaryotic species as a result of genomic rearrangements. If present in a substantial part of species population, those are called B chromosomes, or Bs. This is the case for 70 mammalian species, most of which are rodents. In humans, the most common types of extra chromosomes, sSMCs (small supernumerary marker chromosomes), are diagnosed in approximately...

article

A-GAME: improving the assembly of pooled functional metagenomics sequence data

Matteo Chiara, Antonio Placido, Ernesto Picardi, Luigi Ruggiero Ceci, more

BMC Genomics > 2018 > 19 > 1 > 1-10

Background Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such “functional metagenomics” experiments, inserts, selected on the basis of activity assays, are sequenced with high throughput sequencing technologies. Assembly is followed by gene prediction,...

article

Near-infrared study of open clusters Teutsch 10 and Teutsch 25

D. Bisht, Shashikiran Ganesh, R.K.S. Yadav, Alok Durgapal, more

Advances in Space Research > 2018 > 61 > 1 > 571-580

The astrophysical parameters have been estimated for two unstudied open star clusters Teutsch 10 and Teutsch 25 using the Two Micron All Sky Survey (2MASS) database. Radius is estimated as 4.5 arcmin for both clusters using radial density profiles. We have estimated proper motion values in both RA and DEC directions as 2.28±0.3 and -0.38±0.11 mas yr⁻¹ for Teutsch 10 and 0.48±0.3 and 3.35±0.16 mas yr...

article

Create, run, share, publish, and reference your LC–MS, FIA–MS, GC–MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics

Yann Guitton, Marie Tremblay-Franco, Gildas Le Corguillé, Jean-François Martin, more

The International Journal of Biochemistry & Cell Biology > 2017 > 93 > C > 89-101

Metabolomics is a key approach in modern functional genomics and systems biology. Due to the complexity of metabolomics data, the variety of experimental designs, and the multiplicity of bioinformatics tools, providing experimenters with a simple and efficient resource to conduct comprehensive and rigorous analysis of their data is of utmost importance. In 2014, we launched the Workflow4Metabolomics...

article

Strategies for analyzing bisulfite sequencing data

Katarzyna Wreczycka, Alexander Gosdschan, Dilmurat Yusuf, Björn Grüning, more

Journal of Biotechnology > 2017 > 261 > C > 105-115

DNA methylation is one of the main epigenetic modifications in the eukaryotic genome; it has been shown to play a role in cell-type specific regulation of gene expression, and therefore cell-type identity. Bisulfite sequencing is the gold-standard for measuring methylation over the genomes of interest. Here, we review several techniques used for the analysis of high-throughput bisulfite sequencing...

article

Workflows for microscopy image analysis and cellular phenotyping

Thomas Wollmann, Holger Erfle, Roland Eils, Karl Rohr, more

Journal of Biotechnology > 2017 > 261 > C > 70-75

In large scale biological experiments, like high-throughput or high-content cellular screening, the amount and the complexity of images to be analyzed are steadily increasing. To handle and process these images, well defined image processing and analysis steps need to be performed by applying dedicated workflows. Multiple software tools have emerged with the aim to facilitate creation of such workflows...

article

RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation

Rolf Backofen, Jan Engelhardt, Anika Erxleben, Jörg Fallmann, more

Journal of Biotechnology > 2017 > 261 > C > 76-84

The importance of RNA-based regulation is becoming more and more evident. Genome-wide sequencing efforts have shown that the majority of the DNA in eukaryotic genomes is transcribed. Advanced high-throughput techniques like CLIP for the genome-wide detection of RNA–protein interactions have shown that post-transcriptional regulation by RNA-binding proteins matches the complexity of transcriptional...

article

The dark matter distribution of NGC 5921

Israa Abdulqasim Mohammed Ali, Norsiah Hashim, Zamri Zainal Abidin

Indian Journal of Physics > 2018 > 92 > 4 > 409-415

We used the neutral atomic hydrogen data of the Very Large Array for the spiral galaxy NGC 5921 with z = 0.0045 at the distance of 22.4 Mpc, to investigate the nature of dark matter. The investigation was based on two theories, namely, dark matter and Modified Newtonian Dynamics (MOND). We presented the kinematic analysis of the rotation curve with two models of dark matter, namely, the Burkert and...

INFONA - science communication portal

Search results

6-BA and NAA effect on ‘Galaxy’ fruit growth, abscission and quality: a comparison between the Po Valley and the South Tyrol producing areas

Determination of some galactic constants using planetary nebulae

Metal‐poor stars observed with the automated planet finder telescope. III. CEMP‐no stars are the descendant of population III stars

TACITuS: transcriptomic data collector, integrator, and selector on big data platform

Bioinformatics Tools and Workflow to Select Blood Biomarkers for Early Cancer Diagnosis: An Application to Pancreatic Cancer

Kinematics of Open Star Clusters Based on the Data of the New Version of the “Homogeneous Catalog of Open Cluster Parameters”

Gould Belt members in X-ray RAVE: cross-matching RAVE stars with 3XMM point sources

SyNDI: synchronous network data integration framework

On the Distribution of Radio Pulsars Above the Galaxy Plane

sRNAPipe: a Galaxy-based pipeline for bioinformatic in-depth exploration of small RNAseq data

SAMSA2: a standalone metatranscriptome analysis pipeline

New Asymptotic Giant Branch Carbon Stars in the Galactic Halo

Low-pass single-chromosome sequencing of human small supernumerary marker chromosomes (sSMCs) and Apodemus B chromosomes

A-GAME: improving the assembly of pooled functional metagenomics sequence data

Near-infrared study of open clusters Teutsch 10 and Teutsch 25

Create, run, share, publish, and reference your LC–MS, FIA–MS, GC–MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics

Strategies for analyzing bisulfite sequencing data

Workflows for microscopy image analysis and cellular phenotyping

RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation

The dark matter distribution of NGC 5921

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