Dataset Papers in Science The latest articles from Hindawi Publishing Corporation © 2014 , Hindawi Publishing Corporation . All rights reserved. MicroRNA Gene Interaction in Amyotrophic Lateral Sclerosis Dataset Mon, 30 Jun 2014 11:48:49 +0000 All microRNAs (miRNAs) in amyotrophic lateral sclerosis (ALS) study were collected from public databases such as miRBase, mir2Disease, and Human miRNA and Disease Database (HMDD). These miRNA datasets were used for target identification; these sets of miRNAs were expressed in brain specific parts of brain such as midbrain, cerebellum, frontal cortex, and hippocampus. Gene’s information and sequences were collected from NCBI and KEGG databases. All miRNAs were used for target prediction against 35 ALS associated genes. Three programs were used for target identification, namely, miRanda, TargetScan, and PicTar. The dataset contained information about miRNA targets sites identified by each program. Intersection studies of three programs such as miRanda versus TargetScan, miRanda versus PicTar, and TargetScan versus PicTar were carried out with all datasets. Target sites identified by each program were further explored for distribution of target sites across 35 genes in 5′ UTR, CDS, and 3′ UTR for miRNAs expressed in midbrain, cerebellum, frontal cortex, and hippocampus as predicted. Dataset was also used for calculation of multiplicity and coopretivity; this information was then used for construction of complex gene-microRNA interaction map. Santosh Shinde and Utpal Bhadra Copyright © 2014 Santosh Shinde and Utpal Bhadra. All rights reserved. Mapping the Slums of Dhaka from 2006 to 2010 Wed, 25 Jun 2014 00:00:00 +0000 Background. Rapid urban growth in low and middle income countries is frequently characterized by informal developments. The resulting social segregation and slums show disparities in health outcomes for the populations of the world’s megacities. To address these challenges, information on the spatial distribution of slums is necessary, yet the data are rarely available. The goal of this study was to use a remote sensing based approach to map urban slums in Dhaka, the second fastest growing megacity in the world. Methods. Slums were mapped through the visual interpretation of Quickbird satellite imagery between the years 2006 and 2010. Ancillary references included the 2005 census and mapping of slums, Google Earth, and geolocated photographs. The 2006 slums were first delineated and filtered in GIS to avoid small, isolated slums. For 2010, changes to the 2006 slums were defined over the latter’s polygons to retain border consistency. Conclusions. The dataset presented here can be considered a stepping stone for further research on slums and urban expansion in Dhaka. The slum distribution dataset is useful to be pooled with other data to reveal trends of informal settlement growth for local health policy advice in Dhaka. Oliver Gruebner, Jonathan Sachs, Anika Nockert, Michael Frings, Md. Mobarak Hossain Khan, Tobia Lakes, and Patrick Hostert Copyright © 2014 Oliver Gruebner et al. All rights reserved. Dataset for Modelling Reaction Mechanisms Using Density Functional Theory: Mechanism of ortho-Hydroxylation by High-Valent Iron-Oxo Species Sun, 08 Jun 2014 00:00:00 +0000 Modelling reaction mechanisms using density functional theory is one of the popular routes to underpin the course of a chemical reaction. Although numerous publications have come out in this area, the pitfall of modelling such reactions and explicitly publishing the entire data set (structures, energies, coordinates, spin densities, etc.) which lead to the conclusions are scarce. Here we have attempted to set a trend wherein all the computed data to underpin the reaction mechanism of ortho-hydroxylation of aromatic compounds by high-valent iron-oxo complexes (–OOH, =O, and =O) are collected. Since the structure, energetics and other details of the calculations can be employed in future to probe/understand the reactivity pattern of such species, establishing the data set is justified. Here by analysing the presented results we also discuss in brief the presented results. Azaj Ansari and Gopalan Rajaraman Copyright © 2014 Azaj Ansari and Gopalan Rajaraman. All rights reserved. The In Vitro Susceptibility of Biofilm Forming Medical Device Related Pathogens to Conventional Antibiotics Sun, 01 Jun 2014 10:56:18 +0000 Minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and minimum biofilm eradication concentration (MBEC) and kill kinetics were established for vancomycin, rifampicin, trimethoprim, gentamicin, and ciprofloxacin against the biofilm forming bacteria Staphylococcus epidermidis (ATCC 35984), Staphylococcus aureus (ATCC 29213), Methicillin Resistant Staphylococcus aureus (MRSA) (ATCC 43300), Pseudomonas aeruginosa (PAO1), and Escherichia coli (NCTC 8196). MICs and MBCs were determined via broth microdilution in 96-well plates. MBECs were studied using the Calgary Biofilm Device. Values obtained were used to investigate the kill kinetics of conventional antimicrobials against a range of planktonic and biofilm microorganisms over a period of 24 hours. Planktonic kill kinetics were determined at 4xMIC and biofilm kill kinetics at relative MBECs. Susceptibility of microorganisms varied depending on antibiotic selected and phenotypic form of bacteria. Gram-positive planktonic isolates were extremely susceptible to vancomycin (highest MBC: 7.81 mg L−1: methicillin sensitive and resistant S. aureus) but no MBEC value was obtained against all biofilm pathogens tested (up to 1000 mg L−1). Both gentamicin and ciprofloxacin displayed the broadest spectrum of activity with MIC and MBCs in the mg L−1 range against all planktonic isolates tested and MBEC values obtained against all but S. epidermidis (ATCC 35984) and MRSA (ATCC 43300). Garry Laverty, Mahmoud Y. Alkawareek, and Brendan F. Gilmore Copyright © 2014 Garry Laverty et al. All rights reserved. New Distributional Data of Butterflies in the Middle of the Mediterranean Basin: An Area Very Sensitive to Expected Climate Change Mon, 12 May 2014 11:40:11 +0000 Butterflies are known to be very sensitive to environmental changes. Species distribution is modified by climate warming with latitudinal and altitudinal range shifts, but also environmental perturbations modify abundance and species composition of communities. Changes can be detected and described when large datasets are available, but unfortunately only for few Mediterranean countries they were created. The butterfly fauna of the Mediterranean Basin is very sensitive to climate warming and there is an urgent need of large datasets to investigate and mitigate risks such as local extinctions or new pest outbreaks. The fauna of Calabria, the southernmost region of peninsular Italy, is composed also of European species having here their southern range. The aim of this dataset paper is to increase and update the knowledge of butterfly distribution in a region very sensitive to climate warming that can become an early-warning area. Stefano Scalercio Copyright © 2014 Stefano Scalercio. All rights reserved. Subtracted Transcriptome Profile of Tiger Shrimp (Penaeus monodon) That Survived WSSV Challenge Thu, 08 May 2014 10:10:31 +0000 There is increased interest in the development of virus-resistant or improved shrimp stock because production is currently hindered by outbreaks and limited understanding of shrimp defense. Recent advancement now allows for high-throughput molecular studies on shrimp immunity. We used next-generation sequencing (NGS) coupled with suppression subtractive hybridization (SSH) to generate a transcriptome database of genes from tiger shrimp that survived White spot syndrome virus (WSSV) challenge. A total of 9,597 unique sequences were uploaded to NCBI Sequence Read Archive with accession number SRR577080. Sixty-five unique sequences, 6% of the total, were homologous to genes of Penaeus monodon. Genes that were initially related to bacterial infection and environmental stress such as 14-3-3 gene, heat shock protein 90, and calreticulin were also found including a few full-length gene sequences. Initial analysis of the expression of some genes was done. Hemocyanin, ferritin, and fortilin-binding protein exhibited differential expression between survivor and control tiger shrimps. Furthermore, candidate microsatellite markers for brood stock selection were mined and tested. Four trinucleotide and one dinucleotide microsatellites were successfully amplified. The study highlights the advantage of the NGS platform coupled with SSH in terms of gene discovery and marker generation. Benedict A. Maralit, Minerva Fatimae H. Ventolero, Mary Beth B. Maningas, Edgar C. Amar, and Mudjekeewis D. Santos Copyright © 2014 Benedict A. Maralit et al. All rights reserved. Multiple Ion Cluster Source for the Generation of Magnetic Nanoparticles: Investigation of the Efficiency as a Function of the Working Parameters for the Case of Cobalt Tue, 29 Apr 2014 07:25:41 +0000 We present dataset of Co nanoparticles production using a Multiple Ion Cluster Source (MICS). We study the evolution of the mean size and deposition rate of Co nanoparticles as a function of the power and argon flux applied to the Co magnetron, the aggregation length of the Co magnetron and the total argon flux. The results show the strong influence of these parameters on the mean size of the nanoparticles and the efficiency of the process as well as on the atomic deposition rate. In particular, it is shown that nanoparticles of mean size ranging from 4 to 14 nm can be produced and that the influence of the working parameters on the production of magnetic nanoparticles is more complex than for the case of noble metal presented previously. Daniel Llamosa Perez, Lidia Martínez, and Yves Huttel Copyright © 2014 Daniel Llamosa Perez et al. All rights reserved. A Dataset of Experimental HLA-B*2705 Peptide Binding Affinities Sun, 27 Apr 2014 13:18:45 +0000 T-cell epitopes form the basis of many vaccines, diagnostics, and reagents. Current methods for the in silico identification of T-cell epitopes rely, in the main, on the accurate quantitative prediction of peptide-Major Histocompatibility Complex (pMHC) affinity using data-driven computational approaches. Here, we describe a dataset of experimentally determined pMHC binding affinities for the problematic human class I allele HLA-B*2705. Using an in-house, FACS-based, MHC stabilization assay, we measured binding of 223 peptides. This dataset includes both nonbinding and binding peptides, with measured affinities (expressed as of the half-maximal binding level) ranging from 1.2 to 7.4. This dataset should provide a useful independent benchmark for new and existing methods for predicting peptide binding to HLA-B*2705. Valerie A. Walshe, Channa K. Hattotuwagama, Irini A. Doytchinova, and Darren R. Flower Copyright © 2014 Valerie A. Walshe et al. All rights reserved. FTIR Spectra of n-Octanol in Liquid and Solid States Wed, 23 Apr 2014 13:50:59 +0000 The investigation of the temperature dependence of FTIR spectrum of n-octanol in the temperature range from −150°C to 50°C is presented. The observed changes in the registered spectra during gradual heating of the sample were analysed. The structure transformation at the phase transition from solid to liquid phase is detected. A. Vasileva, P. Golub, I. Doroshenko, V. Pogorelov, V. Sablinskas, V. Balevicius, and J. Ceponkus Copyright © 2014 A. Vasileva et al. All rights reserved. Morphological Characterisation of Some Important Indian Garcinia Species Wed, 23 Apr 2014 13:45:38 +0000 The genus Garcinia has over 200 species distributed in the tropics of the world. About 35 species occur in India, many of which are endemic and economically important with immense medicinal properties. However, lack of awareness, coupled with habitat destruction, leads to genetic erosion of this forest resource and many species are threatened. The Indian Institute of Spices Research (IISR), Calicut, has Garcinia genetic resources’ collection of 15 species of Western Ghats and Eastern Himalaya species. The morphological characterisation of the species of these two different eco systems indicates that there are variations within the species of the same ecosystem while there are similarities in the species of two different ecosystems. Utpala Parthasarathy and O. P. Nandakishore Copyright © 2014 Utpala Parthasarathy and O. P. Nandakishore. All rights reserved. DNA Microarray Assay Helps to Identify Functional Genes Specific for Leukemia Stem Cells Wed, 04 Sep 2013 08:35:57 +0000 Chronic myeloid leukemia (CML) is a myeloproliferative disease derived from an abnormal hematopoietic stem cell (HSC) and is consistently associated with the formation of Philadelphia (Ph) chromosome. Tyrosine kinase inhibitors (TKIs) are highly effective in treating chronic phase CML but do not eliminate leukemia stem cells (LSCs), which are believed to be related to disease relapse. Therefore, one major challenge in the current CML research is to understand the biology of LSCs and to identify the molecular difference between LSCs and its normal stem cell counterparts. Comparing the gene expression profiles between LSCs and normal HSCs by DNA microarray assay is a systematic and unbiased approach to address this issue. In this paper, we present a DNA microarray dataset for CML LSCs and normal HSCs to show that the microarray assay will benefit the current and future studies of the biology of CML stem cells. Haojian Zhang and Shaoguang Li Copyright © 2013 Haojian Zhang and Shaoguang Li. All rights reserved. Molecular Data for the Sea Turtle Population in Brazil Thu, 22 Aug 2013 08:00:21 +0000 We report here a dataset comprising nine nuclear markers for the Brazilian population of Cheloniidae turtles: hawksbills (Eretmochelys imbricata), loggerheads (Caretta caretta), olive ridleys (Lepidochelys olivacea), and green turtles (Chelonia mydas). Because hybridization is a common phenomenon between the four Cheloniidae species nesting on the Brazilian coast, we also report molecular markers for the hybrids E. imbricata × C. caretta, C. caretta × L. olivacea, and E. imbricata × L. olivacea and for one hybrid E. imbricata × C. mydas and one between three species C. mydas × E. imbricata × C. caretta. The data was used in previous studies concerning (1) the description of frequent hybrids C. caretta × E. imbricata in Brazil, (2) the report of introgression in some of these hybrids, and (3) population genetics. As a next step for the study of these hybrids and their evolution, genome-wide studies will be performed in the Brazilian population of E. imbricata, C. caretta, and their hybrids. Sibelle Torres Vilaça and Fabricio Rodrigues dos Santos Copyright © 2013 Sibelle Torres Vilaça and Fabricio Rodrigues dos Santos. All rights reserved. Investigation of the Working Parameters of a Single Magnetron of a Multiple Ion Cluster Source: Determination of the Relative Influence of the Parameters on the Size and Density of Nanoparticles Sun, 18 Aug 2013 10:51:35 +0000 Multiple Ion Cluster Source (MICS) is the new optimized route of a standard technique based on a sputtering gas aggregation source, the Ion Cluster Source. The single magnetron used in the standard Ion Cluster Source is replaced by three magnetrons inside the aggregation zone, and they are controlled individually in order to fabricate nanoparticles with the desired and tunable chemical composition. Apart from the working parameters of each magnetron, it is also reported that the relation between the working parameters of individual magnetrons is of prime importance for the control of both the size and density of the nanoparticles. The influences of fluxes of the sputtering gas applied to each magnetron, the total gas flux in the aggregation zone, the position in the aggregation zone of Ag magnetron, and the relative position of the magnetrons in the aggregation zone have been studied through the operation of one of the magnetrons loaded with a silver target. Manuel Ruano, Lidia Martínez, and Yves Huttel Copyright © 2013 Manuel Ruano et al. All rights reserved. Rainfall, Soil Water Content, and Groundwater Levels at the Riverlands Nature Reserve (South Africa) Sun, 16 Jun 2013 08:05:43 +0000 Quantified medium- and long-term hydrological datasets are scarce in South Africa, yet they are essential to gain understanding of natural systems, contribute to ecosystem conservation, and ultimately quantify water balance processes accurately. A hydrological experiment was carried out at Riverlands Nature Reserve (Western Cape, South Africa) in order to quantify the components of the soil water balance at experimental sites occupied by endemic and invasive vegetation. In two separate follow-up projects, five-year time series were collected in three treatments, namely, endemic fynbos vegetation, bare soil, and land invaded by Acacia saligna. Rainfall was recorded daily with a manual rain gauge. Groundwater levels were logged hourly at 14 boreholes. Volumetric soil water contents and soil temperatures were logged hourly at different depths in the soil profile. Groundwater levels and soil water contents responded to rainfall with very clear seasonal trends. The data can be applied in water balance and evapotranspiration studies, unsaturated flux studies, soil temperature profile studies, and rainfall-groundwater level response analysis and for calibrating and validating a wide range of hydrological models. Nebo Jovanovic, Richard D. H. Bugan, and Sumaya Israel Copyright © 2013 Nebo Jovanovic et al. All rights reserved. Temperature Evolution of Cluster Structures in Ethanol Sun, 02 Jun 2013 09:30:42 +0000 The dependence of FTIR spectrum of pure ethanol on the temperature was investigated. The measurements were performed for frozen (the minimum temperature −180°C) and liquid ethanol (the maximum temperature 40°C). All changes in IR spectrum of ethanol during gradual warming were detected and analyzed. On the bases of preset observations, the conclusions concerning the evolution of cluster structures in ethanol during transition from solid (frozen) state to liquid state were made. P. Golub, I. Doroshenko, V. Pogorelov, V. Sablinskas, V. Balevicius, and J. Ceponkus Copyright © 2013 P. Golub et al. All rights reserved. A Benchmark Dataset Comprising Partition and Distribution Coefficients of Linear Peptides Thu, 16 May 2013 11:30:17 +0000 Peptides have a dominant role in biology; yet the study of their physical properties is at best sporadic. Peptide quantitative structure-activity relationship (QSAR) lags far behind the QSAR analysis of drug-like organic small molecules. Traditionally, QSAR has focussed on experimentally determined partition coefficients as the main descriptor of hydrophobicity. A partition coefficient () is the ratio between the concentrations of an uncharged chemical substance in two immiscible phases: most typically water and an organic solvent, usually 1-octanol. A distribution coefficient () is the equivalent ratio for charged molecules. We report here a compilation of partition and distribution coefficients for linear peptides compiled from literature reports, suitable for the development and benchmarking of peptide and prediction algorithms. Matthew N. Davies and Darren R. Flower Copyright © 2013 Matthew N. Davies and Darren R. Flower. All rights reserved. Judd-Ofelt Calculations for Nd3+-Doped Fluorozirconate-Based Glasses and Glass Ceramics Thu, 11 Apr 2013 09:04:44 +0000 A Judd-Ofelt analysis is performed to calculate the optical properties of Nd3+ ions embedded in a fluorozirconate glass matrix. The changes in the Judd-Ofelt parameters were determined as a function of the size of BaCl2 nanocrystals grown inside the matrix. From these data, the radiative decay rates and the branching ratios of every transition in the energy range from 25.000 cm−1 to the ground state are calculated. This was accomplished for samples containing nanocrystals with average sizes ranging from 10 to 40 nm. U. Skrzypczak, C. Pfau, C. Bohley, G. Seifert, and S. Schweizer Copyright © 2013 U. Skrzypczak et al. All rights reserved. Bending Angle and Temperature Climatologies from Global Positioning System Radio Occultations Wed, 27 Mar 2013 12:19:15 +0000 The Global Positioning System (GPS) Radio Occultation (OR) technique provides estimates of atmospheric density, temperature, and water vapour content with high vertical resolution, global coverage, and high accuracy. We have used data acquired using this technique in the period 1995–2009 to create a reference climatology of radio occultation bending angle and atmospheric temperature which are used for meteorological studies. The bending angle is interesting because it is a direct measurement and independent of models. It is given with one-degree spatial resolution and 50-meter vertical sampling. In addition, we give the temperature climatology with one-degree spatial resolution and 100-meter vertical sampling. This dataset can be used for several applications including weather forecast, physics of atmosphere, and climate changes. Since the GPS signal is not affected by clouds and the acquisitions are evenly distributed in the globe, the dataset is well suited for studying extreme events (such as convective systems and tropical cyclones) and remote areas. R. Biondi and T. Neubert Copyright © 2013 R. Biondi and T. Neubert. All rights reserved. Global Speleothem Oxygen Isotope Measurements Since the Last Glacial Maximum Tue, 26 Mar 2013 08:45:53 +0000 This synthesis of thirty-six sites (sixty cores with over 27 000 measurements) located around the world facilitates scientific research on the climate of the last 21 000 years ago obtained from oxygen isotope ( or delta-O-18) measurements. Oxygen isotopes in speleothem calcite record the influence of ambient temperature and the isotopic composition of the source water, the latter providing evidence of hydrologic variability and change. Compared to paleoclimate proxies from sedimentary archives, the age uncertainty is unusually small, around +/−100 years for the last 21 000-year interval. Using data contributed to the World Data Center (WDC) for Paleoclimatology, we have created consistently formatted data files for individual sites as well as composite dataset of annual to millennial resolution. These individual files also contain the chronology information about the sites. The data are useful in understanding hydrologic variability at local and regional scales, such as the Asian summer monsoon and the Intertropical Convergence Zone (as discussed in the underlying source publications), and should also be useful in understanding large-scale aspects of hydrologic change since the Last Glacial Maximum (LGM). A. M. Shah, C. Morrill, E. P. Gille, W. S. Gross, D. M. Anderson, B. A. Bauer, R. Buckner, and M. Hartman Copyright © 2013 A. M. Shah et al. All rights reserved. Optical Constants of - and -Zinc(II)-Phthalocyanine Films Sun, 24 Feb 2013 15:00:01 +0000 We present a dataset of the optical constants of α- and β-zinc(II)-phthalocyanine (ZnPc). They were determined accurately from transmission and differential reflectance spectra, with the surface roughness taken into account. For this purpose, thin films were prepared on quartz glass substrates via physical vapor deposition and characterized by ultraviolet-visible (UV-Vis) spectroscopy before as well as after a well-defined annealing process. Kramers-Kronig consistency of the optical constants obtained was checked by means of a numerical algorithm. Michael Kozlik, Sören Paulke, Marco Gruenewald, Roman Forker, and Torsten Fritz Copyright © 2013 Michael Kozlik et al. All rights reserved. Extending MapMan Ontology to Tobacco for Visualization of Gene Expression Wed, 20 Feb 2013 15:31:22 +0000 Microarrays are a large-scale expression profiling method which has been used to study the transcriptome of plants under various environmental conditions. However, manual inspection of microarray data is difficult at the genome level because of the large number of genes (normally at least 30 000) and the many different processes that occur within any given plant. MapMan software, which was initially developed to visualize microarray data for Arabidopsis, has been adapted to other plant species by mapping other species onto MapMan ontology. This paper provides a detailed procedure and the relevant computing codes to generate a MapMan ontology mapping file for tobacco (Nicotiana tabacum L.) using potato and Arabidopsis as intermediates. The mapping file can be used directly with our custom-made NimbleGen oligoarray, which contains gene sequences from both the tobacco gene space sequence and the tobacco gene index 4 (NTGI4) collection of ESTs. The generated dataset will be informative for scientists working on tobacco as their model plant by providing a MapMan ontology mapping file to tobacco, homology between tobacco coding sequences and that of potato and Arabidopsis, as well as adapting our procedure and codes for other plant species where the complete genome is not yet available. Maurice H. T. Ling, Roel C. Rabara, Prateek Tripathi, Paul J. Rushton, and Xijin Ge Copyright © 2013 Maurice H. T. Ling et al. All rights reserved. First Y-Short Tandem Repeat Categorical Dataset for Clustering Applications Sun, 17 Feb 2013 11:58:13 +0000 The Y-chromosome short tandem repeat (Y-STR) data are mainly collected for a performance benchmarking result in clustering methods. There are six Y-STR dataset items, divided into two categories: Y-STR surname and Y-haplogroup data presented here. The Y-STR data are categorical, unique, and different from the other categorical data. They are composed of a lot of similar and almost similar objects. This characteristic of the Y-STR data has caused certain problems of the existing clustering algorithms in clustering them. Ali Seman, Zainab Abu Bakar, and Mohamed Nizam Isa Copyright © 2013 Ali Seman et al. All rights reserved. A Microarray Dataset of Genes Expressed by the R28 Retinal Precursor Cell Line Thu, 14 Feb 2013 15:34:11 +0000 The R28 rat retinal progenitor cell line was developed from postnatal day six rat retina immortalized with the 12S E1A gene of adenovirus. R28 cells have been distributed to over 100 laboratories worldwide, with over 60 publications on topics that include in vitro toxicology, cellular physiology, gene expression analysis, and experimental transplantation. In this paper, we present a microarray dataset of R28 cells that describes the presence or absence of 8799 genes and ESTs that may be relevant to current and future studies of R28 retinal precursor cells. Gail M. Seigel and Richard J. Salvi Copyright © 2013 Gail M. Seigel and Richard J. Salvi. All rights reserved. Long-Term Aerosol Climate Data Record Derived from Operational AVHRR Satellite Observations Thu, 14 Feb 2013 15:08:50 +0000 Aerosol optical thickness (AOT) was retrieved using the Advanced Very High Resolution Radiometer (AVHRR) PATMOS-x Level-2b gridded radiances and the two-channel algorithm of the National Climatic Data Center (NCDC). The primary retrieval product is AOT at 0.63 μm channel. AOT is also retrieved at 0.83 μm or 1.61 μm channel for consistent check. The retrieval was made during day time, under clear sky and snow-free conditions, and over the global oceans. The spatial resolution is degree grid and the temporal resolution is both daily and monthly. The resultant AVHRR AOT climate data record (CDR) spans from August 1981 to December 2009 and provides the longest aerosol CDR currently available from operational satellites. This dataset is useful in studying aerosol climate forcing, monitoring long-term aerosol trends, and evaluating global air pollution and aerosol transport models over the global ocean. P. K. Chan, X.-P. Zhao, and A. K. Heidinger Copyright © 2013 P. K. Chan et al. All rights reserved. Detection of Introns in Eukaryotic Small Subunit Ribosomal RNA Gene Sequences Wed, 06 Feb 2013 16:19:26 +0000 The gene encoding SSU-rRNA sequences is the tool of choice for phylogenetic analyses and environmental biodiversity analyses of bacteria, Archaea but also unicellular Eukaryota. In Eukaryota, gene sequences may often be interrupted by long or several introns. Searching in GenBank release 188, we found descriptions of 3638 such sequences. Using a database of 180 000 SSU-rRNA sequences well annotated for taxonomy and a C++ program written for that purpose, we computed the presence of 18 691 introns (among which the 3638 described introns). Filtering on length and sequence quality, 3646 sequences were retained. These introns were clustered; clusters were analyzed for the presence of single or multiple clades at various levels of taxonomic depth, allowing future analyses of horizontal transfers. Various analyses of the results are provided as tabulated files as well as FASTA files of described or computed introns. Each sequence is annotated for cellular location (nuclear, chloroplast, and mitochondria), positions at which they were found in the SSU-rRNA sequences and taxonomy as provided by GenBank. Dipankar Bachar, Laure Guillou, and Richard Christen Copyright © 2013 Dipankar Bachar et al. All rights reserved. Rodent Carcinogenicity Dataset Thu, 17 Jan 2013 09:49:18 +0000 The rodent carcinogenicity dataset was compiled from the Carcinogenic Potency Database (CPDBAS) and was applied for the classification of quantitative structure-activity relationship (QSAR) models for the prediction of carcinogenicity based on the counter-propagation artificial neural network (CP ANN) algorithm. The models were developed within EU-funded project CAESAR for regulatory use. The dataset contains the following information: common information about chemicals (ID, chemical name, and their CASRN), molecular structure information (SDF files and SMILES), and carcinogenic (toxicological) properties information: carcinogenic potency (TD50_Rat_mg; carcinogen/noncarcinogen) and structural alert (SA) for carcinogenicity based on mechanistic data. Molecular structure information was used to get chemometrics information to calculate molecular descriptors (254 MDL and 784 Dragon descriptors), which were further used in predictive QSAR modeling. The dataset presented in the paper can be used in future research in oncology, ecology, or chemicals' risk assessment. Natalja Fjodorova and Marjana Novič Copyright © 2013 Natalja Fjodorova and Marjana Novič. All rights reserved. Efficacy and Safety of Botulinum Toxin A for Treating Bladder Hyperactivity in Children and Adolescents with Neuropathic Bladder Secondary to Myelomeningocele Thu, 17 Jan 2013 08:10:23 +0000 We verified the efficacy and safety of botulinum toxin A (BTX-A) in treating bladder overactivity in children with neurogenic bladder (NB) secondary to myelomeningocele (MMC). Forty-seven patients (22, females; 25, males; age range, 5–17 years; mean age, 10.7 years) with poorly compliant/overactive neurogenic bladder on clean intermittent catheterization (CIC) and resistance or noncompliant to anticholinergics were injected with 200 IU of BTX-A intradetrusor. All patients experienced a significant 66.45% average increase of leak point volume (Wilcoxon paired rank test = 7.169 e-10) and a significant 118.57% average increase of specific bladder capacity at 20 cm H2O (Wilcoxon paired rank test = 2.466 e-12). Ten patients who presented with concomitant uni/bilateral grade II–IV vesicoureteral reflux were treated at the same time with Deflux. No patient presented with major perioperative or postoperative problems. Twenty-two patients needed a second and 18 a third injection of BTX-A after 6–9 months for the reappearance of symptoms. After a mean follow-up of 5.7 years, 38 out of 47 patients achieved dryness between CICs, and 9 patients improved their incontinence but still need pads. Our conclusion is that BTX-A represents a viable alternative to more invasive procedure in treatment of overactive NB secondary to MMC. Antonio Marte, Micaela Borrelli, Maurizio Prezioso, Lucia Pintozzi, and Pio Parmeggiani Copyright © 2013 Antonio Marte et al. All rights reserved. Alterations of Hormone-Sensitive Adenylyl Cyclase System in the Tissues of Rats with Long-Term Streptozotocin Diabetes and the Influence of Intranasal Insulin Thu, 27 Dec 2012 08:20:17 +0000 One of the causes of complications in type 1 diabetes mellitus (T1DM) is the changes in adenylyl cyclase (AC) signaling system, identified on the early stages of the disease. However, the most significant disturbances in this system occur on the later stages of T1DM, which ultimately leads to severe complications, but functional state of the AC system in late T1DM is poorly understood. The aim of this work was to study alterations in AC system sensitive to biogenic amines and polypeptide hormones in the heart, brain, and testes of male rats with long-term, 7-month, streptozotocin T1DM and to assess the influence on them of 135-day therapy with intranasal insulin. It was shown that AC effects of -adrenergic agonists in the heart, serotonin receptor agonists and PACAP-38 in the brain, chorionic gonadotropin and PACAP-38 in the testes, and somatostatin in all investigated tissues in long-term T1DM were drastically decreased. The treatment with intranasal insulin (0.48 IU/day) significantly restored these effects. The results were obtained suggesting that long-term T1DM induces significant alterations in hormone-sensitive AC system in the heart, brain, and testes that are much more pronounced, compared with short-term T1DM, and include a large number of hormonal regulations. Alexander O. Shpakov, Kira V. Derkach, Irina V. Moyseyuk, and Oksana V. Chistyakova Copyright © 2013 Alexander O. Shpakov et al. All rights reserved. Solubility Data of Comonomer Pairs Relevant to Aqueous-Phase Study in the Emulsion Copolymerization Wed, 12 Dec 2012 11:37:25 +0000 In emulsion copolymerizations, the two monomers might not be equally incorporated in the copolymers. Besides copolymerization in the particles, also copolymerization in the aqueous phase can take place which affects the formation of oligomeric radicals responsible for the entry of radicals into the particles. In describing copolymerization in emulsion polymerization, one can use the normal reactivity ratios in combination with the monomer feed ratios in the phase at hand (either water phase or particle phase). Most of the research works done were focused on the feed ratio of the monomers in the particle phase. This is because of the interest in the final product. But in case of water-soluble monomers, where significant amount of polymerization already occurs in the water phase, feed ratios of monomers in the water phase have to be known. Even for less water-soluble monomers, the feed ratios in the aqueous phase are important to know, related to entry of radicals. Therefore, to calculate feed ratios in water phase, solubilities of mixtures of monomers in this phase have been measured by using a UV-Vis technique. It is shown that the solubility of one monomer is influenced by the presence of another monomer. Pooja Daswani and Alex van Herk Copyright © 2013 Pooja Daswani and Alex van Herk. All rights reserved. A 10-Year Dataset of Basic Meteorology and Soil Properties in Central Sudan Wed, 07 Nov 2012 10:24:59 +0000 Meteorological data and soil data have been collected at a site in the central Sudan from 2002 to 2012. The site is a sparse savanna in the semiarid region of Sudan. In addition to basic meteorological variables, soil properties (temperature, water content, and heat flux) and radiation (global radiation, net radiation, and photosynthetic active radiation) were measured. The dataset has a temporal resolution of 30 minutes and provides general data for calibration and validation of ecosystem models and remote-sensing-based assessments, and it is relevant for studies of ecosystem properties and processes. Jonas Ardö Copyright © 2013 Jonas Ardö. All rights reserved.