On the hierarchical classification of G Protein-Coupled Receptors

Motivation: G protein-coupled receptors (GPCRs) play an important role in many physiological systems by transducing an extracellular signal into an intracellular response. Over 50% of all marketed drugs are targeted towards a GPCR. There is considerable interest in developing an algorithm that could effectively predict the function of a GPCR from its primary sequence. Such an algorithm is useful not only in identifying novel GPCR sequences but in characterizing the interrelationships between known GPCRs. Results: An alignment-free approach to GPCR classification has been developed using techniques drawn from data mining and proteochemometrics. A dataset of over 8000 sequences was constructed to train the algorithm. This represents one of the largest GPCR datasets currently available. A predictive algorithm was developed based upon the simplest reasonable numerical representation of the protein's physicochemical properties. A selective top-down approach was developed, which used a hierarchical classifier to assign sequences to subdivisions within the GPCR hierarchy. The predictive performance of the algorithm was assessed against several standard data mining classifiers and further validated against Support Vector Machine-based GPCR prediction servers. The selective top-down approach achieves significantly higher accuracy than standard data mining methods in almost all cases

X-ray Astronomy in the Laboratory with a Miniature Compact Object Produced by Laser-Driven Implosion

Laboratory spectroscopy of non-thermal equilibrium plasmas photoionized by intense radiation is a key to understanding compact objects, such as black holes, based on astronomical observations. This paper describes an experiment to study photoionizing plasmas in laboratory under well-defined and genuine conditions. Photoionized plasma is here generated using a 0.5-keV Planckian x-ray source created by means of a laser-driven implosion. The measured x-ray spectrum from the photoionized silicon plasma resembles those observed from the binary stars Cygnus X-3 and Vela X-1 with the Chandra x-ray satellite. This demonstrates that an extreme radiation field was produced in the laboratory, however, the theoretical interpretation of the laboratory spectrum significantly contradicts the generally accepted explanations in x-ray astronomy. This model experiment offers a novel test bed for validation and verification of computational codes used in x-ray astronomy.Comment: 5 pages, 4 figures are included. This is the original submitted version of the manuscript to be published in Nature Physic

South African National Survey of Arachnida (SANSA) : review of current knowledge, constraints and future needs for documenting spider diversity (Arachnida : Araneae)

Biodiversity is one of the most important concepts in contemporary biology, with a broad range of applications. In November 1995, South Africa ratified the Convention on Biological Diversity (CBD). Signatories are obligated to develop a strategic plan for the conservation and sustainable use of biodiversity. To meet the requirements of the CBD, the South African National Survey of Arachnida (SANSA) was initiated in 1997. This national project has several aims: to document and describe the arachnid fauna of South Africa; to consolidate all the available data on South African arachnids into one relational database and to make this biodiversity information available to science; and to address issues concerning their conservation and sustainable use. Extensive sampling took place and the SANSA database contains a wealth of biodiversity data that are used to provide answers to ecological questions. Presently 71 spider families, 471 genera and 2170 species are known from South Africa, representing approximately 4.8% of the world fauna. This paper presents the current state of spider biodiversity information and how it is managed. It demonstrates the importance of running a national inventory; emphasises the significance of using a good database application; and the importance of capacity development to improve the quality and integration of biodiversity information. Further, it shows the role SANSA has played in unifying and strengthening arachnid research, with the major thrust to discover the spider diversity in South Africa. We discuss the present status of knowledge, constraints to improving this, and the future directions for research. SANSA has provided the foundations for a more integrative approach to spider diversity research. Future research should build on this legacy by linking taxonomic diversity with that of functional diversity, predicting the response of this diversity to global change drivers. Functional approaches will link these studies to ecosystem processes. Global collaborative studies at several sites following standardised sampling protocols and focused research questions would add value to the SANSA collection and the importance of spiders for the health of ecosystems.http://www.tandfonline.com/loi/ttrs202016-10-31hb201

The faunistic diversity of spiders (Arachnida : Araneae) of the South African grassland biome

As part of the South African National Survey of Arachnida (SANSA), all available information on spider species distribution in the South African Grassland Biome was compiled. A total of 11 470 records from more than 900 point localities were sampled in the South African Grassland Biome until the end of 2011, representing 58 families, 275 genera and 792 described species. A further five families (Chummidae, Mysmenidae, Orsolobidae, Symphytognathidae and Theridiosomatidae) have been recorded from the biome but are only known from undescribed species. The most frequently recorded families are the Gnaphosidae (2504 records), Salticidae (1500 records) and Thomisidae (1197 records). The last decade has seen an exponential growth in the knowledge of spiders in South Africa, but there are certainly many more species that still have to be discovered and described. The most species-rich families are the Salticidae (112 spp.), followed by the Gnaphosidae (88 spp.), Thomisidae (72 spp.) and Araneidae (52 spp.). A rarity index, taking into account an endemicity index and an abundance index, was determined to give a preliminary indication of the conservation importance of each species. The endemicity index indicates that 58 species are endemic to the biome, while 38 species could be considered to be introduced, cosmopolitan, or having a distribution extending beyond the Afrotropical Region. Levels of endemism are highest for mygalomorph trapdoor spiders (7.14–50%) and selected araneomorph families with restricted dispersal capabilities (i.e. Archaeidae, Sicariidae and Scytodidae). A brief review of the published data of surveys from the biome and the patterns of spider assemblage structure in each is presented, together with information on the most species-rich spider families occurring in the biome.The Agricultural Research Council (ARC) and the South African National Biodiversity Institute (SANBI). Threatened Species Programme are thanked for generously funding SANSA Phase II. The National Research Foundation (NRF). SHF acknowledges financial assistance from the DST-NRF Centre of Excellence for Invasion Biology.http://www.tandfonline.com/loi/ttrs20hb2013ab201

South African National Survey of Arachnida: A checklist of the spiders (Arachnida, Araneae) of the Tswalu Kalahari Reserve in the Northern Cape province, South Africa

One of the aims of South African National Survey of Arachnida (SANSA) is to survey protected areas to obtain species-specific information and compile inventories to determine species distribution patterns and evaluate their conservation status for Red Data assessments. The aim of this study, the first in a series of surveys of the Diamond Route Reserves, was to compile the first checklist of the spider species in the Northern Cape at the Tswalu Kalahari Reserve. Spiders were collected during three survey periods (2005−2013) using different collecting methods to sample both the ground and field layers. In total, 32 families represented by 108 genera and 136 species have been collected so far. The most species-rich families are the Salticidae (20 spp.) and Thomisidae (18 spp.), followed by the Gnaphosidae and Araneidae (11 spp. each), while nine families are represented by singletons. The free-living wandering spiders represent 97 spp., while 39 spp. are web-builders. Information on spider guilds, endemicity value and conservation status are provided. The Tswalu Kalahari Reserve protects approximately 6.1% of the total South African spider fauna, while 24.3% of the species found in the reserve are South African endemics, of which 5.9% are Northern Cape endemics. Approximately 6.0% of the species sampled are possibly new to science or represent new records for South Africa. Conservation implications: The Tswalu Kalahari Reserve falls within the Savanna Biome in the Northern Cape province. Only one spider species was previously known from the reserve; a further 135 spp. are reported for the first time, with 5.9% of the species being Northern Cape endemics and 24.3% South African endemics. Approximately 6.0% of the species may be new to science or represent new records for South Africa

The promise of the affordable artist's studio: Governing creative spaces in London

The role of artists' organisations in populating and popularising postindustrial urban areas is well documented. However, what are less apparent are analyses of how spaces of artistic production are organised and governed in these areas. This paper explores, via an analysis of organisational documents and practices, the techniques used by London-based affordable studio providers to imagine, calculate, and make material low-cost workspace for artists. The argument made is that the negotiation of competing agendas around the production of cultural, economic, and social benefit by affordable studio providers has led to the emergence of a specific form of affordable studio. This analysis will thus show how configurations of creative space emerge from mundane techniques of measurement and governance. © 2013 Pion and its Licensors

The Seoul National University AGN Monitoring Project. II. BLR Size and Black Hole Mass of Two AGNs

Active galactic nuclei (AGNs) show a correlation between the size of the broad line region and the monochromatic continuum luminosity at 5100 Å, allowing black hole mass estimation based on single-epoch spectra. However, the validity of the correlation is yet to be clearly tested for high-luminosity AGNs. We present the first reverberation mapping results of the Seoul National University AGN Monitoring Project (SAMP), which is designed to focus on luminous AGNs for probing the high end of the size–luminosity relation. We report time lag measurements of two AGNs, namely, 2MASS J10261389+5237510 and SDSS J161911.24+501109.2, using the light curves obtained over an ∼1000 days period with an average cadence of 10 and 20 days, respectively, for photometry and spectroscopy monitoring. Based on a cross-correlation analysis and Hβ line width measurements, we determine the Hβ lag as and days in the observed frame, and black hole mass as and , respectively, for 2MASS J1026 and SDSS J1619

The diversity of South African spiders (Arachnida: Araneae) : documenting a national survey

Die Suid-Afrikaanse Nasionale Opname van Arachnida (SANSA) is in 1997 deur die Landbounavorsingsraad (LNR) geïnisieer met die primêre doelwit om die Arachnidafauna van Suid-Afrika op nasionale vlak te dokumenteer. Tydens die tweede fase van die projek, genaamd SANSA II, het die Suid-Afrikaanse Nasionale Biodiversiteitsinstituut (SANBI) deur hul program vir bedreigde spesies van 2006 tot 2010, in vennootskap met die LNR by die projek aangesluit. Gedurende die vier jaar lange projek is daar gepoog om alle beskikbare spinnekopdata in een databasis te konsolideer. Hierdie data is gebruik om die ruimtelike dekking van spesies te bepaal en vas te stel waar gapings in die data bestaan om sodoende prioriteitsareas te identifiseer vir meer gefokuste opnames. Uitgebreide versameltogte deur SANSA-veldwerkbestuurders is gedurende die vier jaar onderneem. Inligting oor spesies is aangevul deur byvangste van ander navorsingsprojekte, studenteprojekte, en deur openbare deelname. Al die pogings het waardevolle inligting voorsien oor die teenwoordigheid en verspreiding van spinnekoppe. Die inligting is gebruik om die Eerste atlas van spinnekopspesies van Suid-Afrika saam te stel, insluitende kaarte om die verspreiding van elke spesie aan te dui, sowel as inligting oor die vlakke van endemisme vir elke spesie. Tans is daar 71 spinnekopfamilies, 471 genera en 2028 spesies in Suid-Afrika bekend. Die derde fase van SANSA is in 2011 van stapel gestuur en verskeie aksies soos die saamstel van ’n rooidatalys van spesies, ‘n reeks handboeke vir al die biome, die publikasie van die atlas, en die beskrywing van nuwe spesies is onderweg.The South African National Survey of Arachnida (SANSA) was initiated in 1997 by the Agricultural Research Council (ARC), with the main aim of documenting the Arachnid fauna of South Africa at a national level. Through their Endangered Species Programme, the South African National Biodiversity Institute (SANBI) came on board for the project’s second phase, called SANSA II, from 2006 to 2010, in partnership with the ARC. During this four-year project an attempt was made to consolidate all available data on South African spiders into one database. This data was used to determine the spatial coverage of the already available data, and to determine where ‘gaps’ in the data lie to identify priority areas for focused field work. Due to extensive collecting done by SANSA field work managers, specimen bycatches from other research projects, student projects, and through public participation in collecting specimens, more than 40 degree square grids were sampled in previously poorly sampled areas. This effort has provided valuable material that has improved our knowledge of the distribution of species, and provided specimens for future taxonomic studies. All this data was used to compile the First Atlas of the Spider Species of South Africa, including georeferenced locality data, distribution maps and information on the level of endemicity of each species. Following SANSA II, 71 spider families, 471 genera and 2028 species are presently known in South Africa. The third phase of SANSA started in 2011 and several actions, such as Red Listing of species, a handbook series for all the biomes, publication of the atlas, and description of new species are underway.Scan this QR code with your smart phone or mobile device to read online.A.D.S. (Landbounavorsingsraad) was die projekleier van SANSA en kurator van die Nasionale Versameling van Arachnida; A.v.d.B. (Landbounavorsingsraad) het gehelp met die saamstel van hierdie artikel en is betrokke by verskeie opnames in agro-ekosisteme; R.L. (Landbounavorsingsraad) is verantwoodelik vir opnames in die Noord-Kaap; C.H. (Universiteit van die Vrystaat) is die hulpprojekleier van SANSA en was verantwoordelik vir koördinering van versamelritte; S.F. (Universiteit van Venda) was verantwoordelik vir opnames in die savannabioom; L.L. (Nasionale Museum) het data verskaf vanaf die Nasionale Museum en was betrokke by opnames in die graslandbioom.Finansiële steun en beskikbaarstelling van infrastruktuur deur die Landbounavorsingsraad word met dank erken. Befondsing is verkry vanaf die Suid-Afrikaanse Biodiversiteitsinstituut se program vir bedreigde spesies, asook van die NRF deur hul Thuthuka-program.http://www.satnt.ac.zaam2013ab201

TRH: Pathophysiologic and clinical implications

Thyrotropin releasing hormone is thought to be a tonic stimulator of the pituitary TSH secretion regulating the setpoint of the thyrotrophs to the suppressive effect of thyroid hormones. The peptide stimulates the release of normal and elevated prolactin. ACTH and GH may increase in response to exogenous TRH in pituitary ACTH and GH hypersecretion syndromes and in some extrapituitary diseases. The pathophysiological implications of extrahypothalamic TRH in humans are essentially unknown. The TSH response to TRH is nowadays widely used as a diganostic amplifier in thyroid diseases being suppressed in borderline and overt hyperthyroid states and increased in primary thyroid failure. In hypothyroid states of hypothalamic origin, TSH increases in response to exogenous TRH often with a delayed and/or exaggerated time course. But in patients with pituitary tumors and suprasellar extension TSH may also respond to TRH despite secondary hypothyroidism. This TSH increase may indicate a suprasellar cause for the secondary hypothyroidism, probably due to portal vessel occlusion. The TSH released in these cases is shown to be biologically inactive

Water volume differentially modifies copepod predatory strengths on two prey types

Predatory interaction strengths are highly context-dependent, and in temporary aquatic ecosystems, may be affected by water volume changes. We examine the influence of water volume on Lovenula raynerae (Copepoda) functional responses towards two temporary pond prey types. Daphnia prey risk was not affected by increasing water volume, whereas for Culex prey risk was reduced. Accordingly, water volume changes through the hydroperiod may have species-specific effects on prey, with implications for population persistence under environmental change