NCBI RefSeq: reference sequence standards through 25 years of curation and annotation.

Reference sequences and annotations serve as the foundation for many lines of research today, from organism and sequence identification to providing a core description of the genes, transcripts and proteins found in an organism's genome. Interpretation of data including transcriptomics, proteomics, sequence variation and comparative analyses based on reference gene annotations informs our understanding of gene function and possible disease mechanisms, leading to new biomedical discoveries. The Reference Sequence (RefSeq) resource created at the National Center for Biotechnology Information (NCBI) leverages both automatic processes and expert curation to create a robust set of reference sequences of genomic, transcript and protein data spanning the tree of life.

Investigation of Hafnium Thin Films for Design of TES Microcalorimeters.

Hafnium is a superconductor with a transition temperature slightly above 100 mK. This makes it attractive for such applications as microcalorimeters with high energy resolution. We report the superconducting properties of Hf films of thicknesses ranging from 60 to 115 nm, deposited on Si and AlO substrates by electron beam evaporation.

A Case of Laying Hens Mycosis Caused by .

In this article, we present the first case report of a chicken mycosis caused by occurred on a private farm in the Russian Federation. Lesions on the skin of the legs and scallops were reported. The object of this study was samples of feed and pathological material from sick hens-layers.

Assessment of Irrigation Efficiency by Coupling Remote Sensing and Ground-Based Data: Case Study of Sprinkler Irrigation of Alfalfa in the Saratovskoye Zavolgie Region of Russia.

Nowadays, the leading role of data from sensors to monitor crop irrigation practices is indisputable. The combination of ground and space monitoring data and agrohydrological modeling made it possible to evaluate the effectiveness of crop irrigation. This paper presents some additions to recently published results of field study at the territory of the Privolzhskaya irrigation system located on the left bank of the Volga in the Russian Federation, during the growing season of 2012.

Spatial Interpolation of Gravimetric Soil Moisture Using EM38-mk Induction and Ensemble Machine Learning (Case Study from Dry Steppe Zone in Volgograd Region).

The implementation of the sustainable management of the interaction between agriculture and the environment requires an increasingly deep understanding and numerical description of the soil genesis and properties of soils. One of the areas of application of relevant knowledge is digital irrigated agriculture. During the development of such technologies, the traditional methods of soil research can be quite expensive and time consuming.

A joint NCBI and EMBL-EBI transcript set for clinical genomics and research.

Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, the absence of a standard for clinical reporting and browser display complicates the process of consistent interpretation and reporting. To address these challenges, Ensembl/GENCODE and RefSeq launched a joint initiative, the Matched Annotation from NCBI and EMBL-EBI (MANE) collaboration, to converge on human gene and transcript annotation and to jointly define a high-value set of transcripts and corresponding proteins.

Revision of the banding sequence pool and new data on chromosomal polymorphism in natural populations of Shobanov et Djomin, 1988 (Diptera, Chironomidae).

Quantitative and qualitative analysis of chromosomal polymorphism in 19 natural populations of had been performed. Most studied populations showed a medium level of chromosomal polymorphism: on average 45±3.0% of specimens are heterozygotes with 0.

RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse.

Eukaryotic genomes contain many nongenic elements that function in gene regulation, chromosome organization, recombination, repair, or replication, and mutation of those elements can affect genome function and cause disease. Although numerous epigenomic studies provide high coverage of gene regulatory regions, those data are not usually exposed in traditional genome annotation and can be difficult to access and interpret without field-specific expertise. The National Center for Biotechnology Information (NCBI) therefore provides RefSeq Functional Elements (RefSeqFEs), which represent experimentally validated human and mouse nongenic elements derived from the literature.

Field test of the surface soil moisture mapping using Sentinel-1 radar data.

Soil surface moisture is one of the key parameters for describing the hydrological state and assessing the potential availability of water for irrigated plants. Because the radar backscattering coefficient is sensitive to soil moisture, the application of Sentinel-1 data may support soil surface moisture mapping at high spatial resolution by detecting spatial and temporal changes at the field scale for precision irrigation management. This mapping is required to control soil water erosion and preferential water flow to improve irrigation water efficiency and minimise negative impacts on surface and ground water bodies.

Artificial Dense Lattices of Magnetic Skyrmions.

Multilayer Co/Pt films with perpendicular magnetic anisotropy are irradiated by focused a He ion beam to locally reduce the anisotropy value. The irradiated spots with the diameters of 100 and 200 nm are arranged in square lattices with the periods of 200 and 300 nm. The formation of nonuniform magnetic states within the spots was observed by magnetic force microscopy methods.

Magnetic Force Microscopy of Nanostructured Co/Pt Multilayer Films with Perpendicular Magnetization.

We present the results of magnetic force microscopy investigations of domain structures in multilayer [Co (0.5 nm)/Pt (1 nm)]₅ thin film structures (denoted hereafter as Co/Pt) modified by additional Co capping layers and by ion irradiation. It is demonstrated that a Co capping layer essentially changes the domain structure and decreases the threshold of magnetization reversal, due to the formation of noncollinear magnetization in Co/Pt.

GENES CODING RIBOSOMAL PROTEIN RPL11 AND 5,8S RIBOSOMAL RNA IN SPECIES OF GENUS CHIRONOMUS: NUCLEOTIDE VARIABILITY, DIVERGENCE AND CHROMOSOMAL LOCATION.

Ribosomes of eukaryotic cells contain four rRNA’s (28S, 18S, 5,8S and 5S) and about 80 ribosomal proteins (RP). Whereas the patterns of evolution and chromosomal location of rRNA genes are studied rather extensively in many taxonomic groups, there is only scarce information about evolution of genes coding ribosomal proteins. To obtain more information about evolution of ribosomal protein genes, the study of the nucleotide sequences and chromosomal location of rp111 gene was carried out in 12 species of the genus Chironomus.

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.

Gene: a gene-centered information resource at NCBI.

The National Center for Biotechnology Information's (NCBI) Gene database (www.ncbi.nlm.

RefSeq: an update on mammalian reference sequences.

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of annotated genomic, transcript and protein sequence records derived from data in public sequence archives and from computation, curation and collaboration (http://www.ncbi.nlm.

Evaluation and selection of indicators for land degradation and desertification monitoring: types of degradation, causes, and implications for management.

Indicator-based approaches are often used to monitor land degradation and desertification from the global to the very local scale. However, there is still little agreement on which indicators may best reflect both status and trends of these phenomena. In this study, various processes of land degradation and desertification have been analyzed in 17 study sites around the world using a wide set of biophysical and socioeconomic indicators.

Evaluation and selection of indicators for land degradation and desertification monitoring: methodological approach.

An approach to derive relationships for defining land degradation and desertification risk and developing appropriate tools for assessing the effectiveness of the various land management practices using indicators is presented in the present paper. In order to investigate which indicators are most effective in assessing the level of desertification risk, a total of 70 candidate indicators was selected providing information for the biophysical environment, socio-economic conditions, and land management characteristics. The indicators were defined in 1,672 field sites located in 17 study areas in the Mediterranean region, Eastern Europe, Latin America, Africa, and Asia.

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis.

The genome of the model beetle and pest Tribolium castaneum.

Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes.

[Cytogenetic monitoring of the Usmansky and Hrenovskoy autochtonic pine stands].

The data on the cytogenetic monitoring of the Usmansky and Khrenovskoy autochthonic pine stands (Voronezh Region) allow their status to be rated satisfactory. The indices of the mitotic and nucleolar activity as well as of abnormal mitosis were within the normal variation range for Scotch pine. However, the occurrence of micronuclei (less than 1%) points to pathological processes starting in the stands, which necessitates urgent measures for the conservation of the Usmansky and Khrenovskoy Forests as valuable gene sources.

[Thrombus precursor protein (soluble monomeric protein) in patients with acute coronary syndrome].

The purpose of the study was to determine the level of thrombus precursor protein (TrP) in patients with acute coronary syndrome (ACS). Twenty-six patients with ACS and anginal pain experienced during 2 to 12 hours (7.2 +/- 1.

The genome of the sea urchin Strongylocentrotus purpuratus.

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome.

A genome-wide analysis of biomineralization-related proteins in the sea urchin Strongylocentrotus purpuratus.

Biomineralization, the biologically controlled formation of mineral deposits, is of widespread importance in biology, medicine, and engineering. Mineralized structures are found in most metazoan phyla and often have supportive, protective, or feeding functions. Among deuterostomes, only echinoderms and vertebrates produce extensive biomineralized structures.