A database of multi-year (2004-2010) quality-assured surface solar hourly irradiation measurements for the Egyptian territory

A database containing the global and diffuse components of the surface solar hourly irradiation measured from 1 January 2004 to 31 December 2010 at eight stations of the Egyptian Meteorological Authority is presented. For three of these sites (Cairo, Aswan, and El-Farafra), the direct component is also available. In addition, a series of meteorological variables including surface pressure, relative humidity, temperature, wind speed and direction is provided at the same hourly resolution at all stations. The details of the experimental sites and instruments used for the acquisition are given. Special attention is paid to the quality of the data and the procedure applied to flag suspicious or erroneous measurements is described in details. Between 88 and 99% of the daytime measurements are validated by this quality control. Except at Barrani where the number is lower (13500), between 20000 and 29000 measurements of global and diffuse hourly irradiation are available at all sites for the 7-year period. Similarly, from 9000 to 13000 measurements of direct hourly irradiation values are provided for the three sites where this component is measured. With its high temporal resolution this consistent irradiation and meteorological database constitutes a reliable source to estimate the potential of solar energy in Egypt. It is also adapted to the study of high-frequency atmospheric processes such as the impact of aerosols on atmospheric radiative transfer. In the next future, it is planned to complete regularly the present 2004-2010 database.

The MEDESS-GIB drifters database

On September 9th 2014, an intensive drifter deployment was carried out in the Strait of Gibraltar. In the frame of the EU MED Program MEDESS-4MS, the MEDESS-GIB experiment consisted of the deployment of 35 satellite tracked drifters, mostly of CODE-type, equipped with temperature sensor sampling at a rate of 30 minutes. Drifters were distributed along and on both sides of the Strait of Gibraltar. The MEDESS-GIB deployment plan was designed as to ensure quasi-synoptic spatial coverage. To this end, 4 boats covering an area of about 680 NM2 in 6 hours were coordinated. As far as authors know, this experiment is the most important exercise in the area in terms of number of drifters released. Collected satellite-tracked data along drifter trajectories have been quality controlled and processed to build the here presented MEDESS-GIB data set.

Global macrozoobenthos production and energy budget data base V150731, with link to database

I developed a new model for estimating annual production-to-biomass ratio P/B and production P of macrobenthic populations in marine and freshwater habitats. Self-learning artificial neural networks (ANN) were used to model the relationships between P/B and twenty easy-to-measure abiotic and biotic parameters in 1252 data sets of population production. Based on log-transformed data, the final predictive model estimates log(P/B) with reasonable accuracy and precision (r2 = 0.801; residual mean square RMS = 0.083). Body mass and water temperature contributed most to the explanatory power of the model. However, as with all least squares models using nonlinearly transformed data, back-transformation to natural scale introduces a bias in the model predictions, i.e., an underestimation of P/B (and P). When estimating production of assemblages of populations by adding up population estimates, accuracy decreases but precision increases with the number of populations in the assemblage.

Availability of sequences of aquatic and terrestrial taxa in genetic databases (GenBank and BOLD - the Barcode of Life Database) in 2010, 2012 and 2016

Correct species identifications are of tremendous importance for invasion ecology, as mistakes could lead to misdirecting limited resources against harmless species or inaction against problematic ones. DNA barcoding is becoming a promising and reliable tool for species identifications, however the efficacy of such molecular taxonomy depends on gene region(s) that provide a unique sequence to differentiate among species and on availability of reference sequences in existing genetic databases. Here, we assembled a list of aquatic and terrestrial non-indigenous species (NIS) and checked two leading genetic databases for corresponding sequences of six genome regions used for DNA barcoding. The genetic databases were checked in 2010, 2012, and 2016. All four aquatic kingdoms (Animalia, Chromista, Plantae and Protozoa) were initially equally represented in the genetic databases, with 64, 65, 69, and 61% of NIS included, respectively. Sequences for terrestrial NIS were present at rates of 58 and 78% for Animalia and Plantae, respectively. Six years later, the number of sequences for aquatic NIS increased to 75, 75, 74, and 63% respectively, while those for terrestrial NIS increased to 74 and 88% respectively. Genetic databases are marginally better populated with sequences of terrestrial NIS of plants compared to aquatic NIS and terrestrial NIS of animals. The rate at which sequences are added to databases is not equal among taxa. Though some groups of NIS are not detectable at all based on available data - mostly aquatic ones - encouragingly, current availability of sequences of taxa with environmental and/or economic impact is relatively good and continues to increase with time.

Accession clause of TPP : Is it really open?

One of the most important policy questions relating to the future impact of the Trans-Pacific Partnership on the global and regional economy is whether other countries in the region, particularly China, will join the partnership. While several commentators have made some observations regarding the future prospects of TPP expansion, little scholarly analysis has been conducted. To go beyond the speculation of a certain country's accession to TPP, we first attempt to generalize the issue before moving on to a specific question. We conduct a comparative analysis of a large number of regional trade agreements for a better understanding of the parameters of RTAs that are critical for membership expansion. This general framework enables us to conduct a systematic examination of specific membership expansion cases, such as China's membership in TPP. The paper also proposes a necessary "accession practice" that truly facilitates new members' participation.

HispaVeg: a new online vegetation plot database for Spain

We describe a new online database, named HispaVeg, which currently holds data from 2663 vegetation plots of Spanish woodlands, scrublands and grasslands. Unlike other similar databases, a detailed description of the structure is stored with the floristic data of each plot (i.e., number and physiognomy of the vertical layers, cover values for each layer).Most of the vegetation plots are large rectangles (400 to 2000 square meters) with an average of 34 species per plot. The survey dates range from 1956 to present, with most of the records between 1964 and 1994. The elevation of the plots ranges from 0 to 2880, with most of the plots between 300 and 1500 m. HispaVeg is freely available to the scientific community. Users can query the online database, view printable reports for each plot and download spreadsheet-like raw data for subsets of vegetation plots.

Self Learning and self evaluation exercises database in basic mechanics: a theoretical-practical approach

In the School of Mines of the Technical University of Madrid (UPM) the first course of different degrees has been implemented and adapted to the European Higher Educational Area (EHEA). In all of the degrees there is a first semester course which gathers all the contents of basic mechanics: from the first kinematics concepts to the rigid solid plane motion Before the Bologna process took place, the authors had established the final assessment of the theoretical contents through open questions of theoretical-practical character In the present work, the elaboration of a wide database containing theoretical-practical questions that students can access on line is presented. The questions are divided in thirteen different questionnaires composed of a number of questions randomly chosen from a certain group in the database. Each group corresponds to a certain learning objective that the student knows. After answering the questionnaire and checking the grade assigned according to the performance of the student, the pupils can see the correct response displayed on the screen and widely explained by the professors. This represents a 10% of the final grade. As the student can access the questionnaires as many times as they want, the main goal is the self-assessment of each learning objective and therefore, getting the students involved in their own learning process so they can decide how much time they need to acquire the required level.

Expanding the functional human mitochondrial DNA database by the establishment of primate xenomitochondrial cybrids

The nuclear and mitochondrial genomes coevolve to optimize approximately 100 different interactions necessary for an efficient ATP-generating system. This coevolution led to a species-specific compatibility between these genomes. We introduced mitochondrial DNA (mtDNA) from different primates into mtDNA-less human cells and selected for growth of cells with a functional oxidative phosphorylation system. mtDNA from common chimpanzee, pigmy chimpanzee, and gorilla were able to restore oxidative phosphorylation in the context of a human nuclear background, whereas mtDNA from orangutan, and species representative of Old-World monkeys, New-World monkeys, and lemurs were not. Oxygen consumption, a sensitive index of respiratory function, showed that mtDNA from chimpanzee, pigmy chimpanzee, and gorilla replaced the human mtDNA and restored respiration to essentially normal levels. Mitochondrial protein synthesis was also unaltered in successful “xenomitochondrial cybrids.” The abrupt failure of mtDNA from primate species that diverged from humans as recently as 8–18 million years ago to functionally replace human mtDNA suggests the presence of one or a few mutations affecting critical nuclear–mitochondrial genome interactions between these species. These cellular systems provide a demonstration of intergenus mtDNA transfer, expand more than 20-fold the number of mtDNA polymorphisms that can be analyzed in a human nuclear background, and provide a novel model for the study of nuclear–mitochondrial interactions.

A very limited number of keywords (main patterns) describes all sequences of the human variable heavy (VH) and κ (Vκ) domains

Sequences of the variable heavy (VH) and κ (Vκ) domains of Ig structures were divided into 21 fragments that correspond to strands, loops, or parts of these structural units of the variable domains. Amino acid sequences of fragments (termed “words”) were collected from the 1,172 human heavy and 668 human κ chains available in the Kabat database. Statistical analysis of words of 17 fragments was performed (fragments that comprise the complementary determining regions′ fragments will not be discussed in this paper). The number of different words (those with different residues in at least one position) ranged, for various fragments, from 11 to 75 in the κ chains, and from 23 to 189 in the heavy chains. The main result of this study is that very few keywords, or main patterns of words, were necessary to describe over 90% of the sequences (no more than two keywords per fragment in the κ and no more than five per fragment in the heavy chains). No identical keywords were found for different fragments of the variable domains. Keywords of aligned fragments of the VH and Vκ domains were different in all but two instances. Thus, knowing the keywords, one can determine whether any given small part of a sequence belongs to a heavy or κ chain and predict its precise localization in the sequence. In addition, by using all of the keywords obtained through analysis of the Kabat database, it was possible to describe completely the sequences of the human VH and Vκ germ-line segments.

STRBase: a short tandem repeat DNA database for the human identity testing community

The National Institute of Standards and Technology (NIST) has compiled and maintained a Short Tandem Repeat DNA Internet Database (http://www.cstl.nist.gov/biotech/strbase/) since 1997 commonly referred to as STRBase. This database is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. STRBase consolidates and organizes the abundant literature on this subject to facilitate on-going efforts in DNA typing. Observed alleles and annotated sequence for each STR locus are described along with a review of STR analysis technologies. Additionally, commercially available STR multiplex kits are described, published polymerase chain reaction (PCR) primer sequences are reported, and validation studies conducted by a number of forensic laboratories are listed. To supplement the technical information, addresses for scientists and hyperlinks to organizations working in this area are available, along with the comprehensive reference list of over 1300 publications on STRs used for DNA typing purposes.

ARED: human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins

The adenylate uridylate-rich elements (AREs) mediate the rapid turnover of mRNAs encoding proteins that regulate cellular growth and body response to exogenous agents such as microbes, inflammatory and environmental stimuli. However, the full repertoire of ARE-containing mRNAs is unknown. Here, we explore the distribution of AREs in human mRNA sequences. Computational derivation of a 13-bp ARE pattern was performed using multiple expectation maximization for motif elicitations (MEME) and consensus analyses. This pattern was statistically validated for the specificity towards the 3′-untranslated region and not coding region. The computationally derived ARE pattern is the basis of a database which contains non-redundant full-length ARE-mRNAs. The ARE-mRNA database (ARED; http://rc.kfshrc.edu.sa/ared) reveals that ARE-mRNAs encode a wide repertoire of functionally diverse proteins that belong to different biological processes and are important in several disease states. Cluster analysis was performed using the ARE sequences to demonstrate potential relationships between the type and number of ARE motifs, and the functional characteristics of the proteins.

Web-based access to mouse models of human cancers: the Mouse Tumor Biology (MTB) Database

The Mouse Tumor Biology (MTB) Database serves as a curated, integrated resource for information about tumor genetics and pathology in genetically defined strains of mice (i.e., inbred, transgenic and targeted mutation strains). Sources of information for the database include the published scientific literature and direct data submissions by the scientific community. Researchers access MTB using Web-based query forms and can use the database to answer such questions as ‘What tumors have been reported in transgenic mice created on a C57BL/6J background?’, ‘What tumors in mice are associated with mutations in the Trp53 gene?’ and ‘What pathology images are available for tumors of the mammary gland regardless of genetic background?’. MTB has been available on the Web since 1998 from the Mouse Genome Informatics web site (http://www.informatics.jax.org). We have recently implemented a number of enhancements to MTB including new query options, redesigned query forms and results pages for pathology and genetic data, and the addition of an electronic data submission and annotation tool for pathology data.

The RDP-II (Ribosomal Database Project)

The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [Nucleic Acids Res. (2000), 28, 173–174], continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 8.0 (June 1, 2000) consisted of 16 277 aligned prokaryotic small subunit (SSU) rRNA sequences while the number of eukaryotic and mitochondrial SSU rRNA sequences in aligned form remained at 2055 and 1503, respectively. The number of prokaryotic SSU rRNA sequences more than doubled from the previous release 14 months earlier, and ~75% are longer than 899 bp. An RDP-II mirror site in Japan is now available (http://wdcm.nig.ac.jp/RDP/html/index.html). RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/). Analysis services include rRNA probe checking, approximate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment polymorphism experiments. The RDP-II email address for questions and comments has been changed from curator@cme.msu.edu to rdpstaff@msu.edu.