Splitting statistical potentials into meaningful scoring functions: testing the prediction of near-native structures from decoy conformations

Background: Recent advances on high-throughput technologies have produced a vast amount of protein sequences, while the number of high-resolution structures has seen a limited increase. This has impelled the production of many strategies to built protein structures from its sequence, generating a considerable amount of alternative models. The selection of the closest model to the native conformation has thus become crucial for structure prediction. Several methods have been developed to score protein models by energies, knowledge-based potentials and combination of both.Results: Here, we present and demonstrate a theory to split the knowledge-based potentials in scoring terms biologically meaningful and to combine them in new scores to predict near-native structures. Our strategy allows circumventing the problem of defining the reference state. In this approach we give the proof for a simple and linear application that can be further improved by optimizing the combination of Zscores. Using the simplest composite score () we obtained predictions similar to state-of-the-art methods. Besides, our approach has the advantage of identifying the most relevant terms involved in the stability of the protein structure. Finally, we also use the composite Zscores to assess the conformation of models and to detect local errors.Conclusion: We have introduced a method to split knowledge-based potentials and to solve the problem of defining a reference state. The new scores have detected near-native structures as accurately as state-of-art methods and have been successful to identify wrongly modeled regions of many near-native conformations.

City of Missouri Valley, Auditor of State's Report on Reaudit, For the Period July 1, 2003 through June 30, 2004

Other Audit Reports - Reaudit

Structural characterization of rockfall sources in Yosemite Valley from remote sensing data and field surveys

Yosemite Valley poses significant rockfall hazard and related risk due to its glacially steepened walls and approximately 4 million visitors annually. To assess rockfall hazard, it is necessary to evaluate the geologic structure that contributes to the destabilization of rockfall sources and locate the most probable future source areas. Coupling new remote sensing techniques (Terrestrial Laser Scanning, Aerial Laser Scanning) and traditional field surveys, we investigated the regional geologic and structural setting, the orientation of the primary discontinuity sets for large areas of Yosemite Valley, and the specific discontinuity sets present at active rockfall sources. This information, combined with better understanding of the geologic processes that contribute to the progressive destabilization and triggering of granitic rock slabs, contributes to a more accurate rockfall susceptibility assessment for Yosemite Valley and elsewhere.

Buried Valley Aquifers of Iowa, 2004

Buried Valley Aquifers of Iowa in 2004

Splitting rivers at their seams: bifurcations and avulsion

River bifurcations are critical but poorly understood elements of many geomorphological systems. They are integral elements of alluvial fans, braided rivers, fluvial lowland plains, and deltas and control the partitioning of water and sediment through these systems. Bifurcations are commonly unstable but their lifespan varies greatly. In braided rivers bars and channels migrate, split and merge at annual or shorter timescales, thereby creating and abandoning bifurcations. This behaviour has been studied mainly by geomorphologists and fluid dynamicists. Bifurcations also exist during avulsion, the process of a river changing course on a floodplain or in a delta, which may take 102103 years and has been studied mainly by sedimentologists. This review synthesizes our current understanding of bifurcations and brings together insights from different research communities and different environmental settings. We consider the causes and initiation of bifurcations and avulsion, the physical mechanisms controlling bifurcation and avulsion evolution, mathematical and numerical modelling of these processes, and the possibility of stable bifurcations. We end the review with some open questions. Copyright (c) 2012 John Wiley & Sons, Ltd.

Phlebotomines (Diptera, Psychodidae) in the Ribeira Valley Speleological Province - 1. Parque Estadual Intervales, state of São Paulo, Brazil

The identification of the sandfly fauna and investigation of some ecological aspects of its populations in areas frequented by tourists of the PEI, an Atlantic forest reserve with many caves, were the objective of this study. Captures were undertaken monthly from January 2001 to December 2002, with automatic light traps installed in 13 ecotopes, including caves, forests, domiciliary and peridomiciliary environments, and by aspiration in armadillo burrows. Additionally, although not at regular intervals, Shannon traps were installed in forests and anthropic environments, aspirations were made on cave walls, among roots and fallen leaves, and some insects were captured while biting researchers. A total of 891 sandflies belonging to 21 species were captured. Six hundred specimens representing 19 species were captured with light traps, 215 in anthropic (2.24 insects/trap) and 385 in extra-domiciliary (1.46 insects/trap) environments. Brumptomyia troglodytes was the most abundant species (the Standardised Index of Species Abundance = 0.705). Pintomyia monticola predominated in the Shannon traps and showed anthropophilic and diurnal activity. Psathyromyia pascalei predominated in the aspirations; the largest number being in armadillo burrows. Eleven species were captured in caves; although some might be troglophiles, the majority used these ecotopes as resting places. Nyssomyia intermedia, Nyssomyia neivai and Migonemyia migonei, implicated in the transmission of cutaneous leishmaniasis in the Southeastern Brazilian region, were all found, though in such low densities as to suggest minimal risk of the disease in the PEI.

Phlebotomines (Diptera, Psychodidae) in the Speleological Province of the Ribeira Valley: 2. Parque Estadual do Alto Ribeira (PETAR), São Paulo State, Brazil

The Parque Estadual do Alto Ribeira (PETAR) with about 250 caves, in an Atlantic forest reserve, is an important ecotourist attraction in the Ribeira Valley, an endemic area of American cutaneous leishmaniasis (ACL). With the purpose of investigating Leishmania vector species bothersome to humans the sandfly fauna was identified and some of its ecological aspects in the Santana nucleus, captures were undertaken monthly with automatic light traps in 11 ecotopes, including caves, forests, a camping site and domiciliary environments, and on black and white Shannon traps, from January/2001 to December/2002. A total of 2,449 sandflies representing 21 species were captured. The highest values of abundance obtained in the captures with automatic light traps were for Psathyromyia pascalei and Psychodopygus ayrozai. A total of 107 specimens representing 13 species were captured on black (12 species) and white (6 species) Shannon traps set simultaneously. Psychodopygus geniculatus females predominated on the black (43.75%), and Psathyromyia lanei and Ps. ayrozai equally (32.4%) on the white. Nyssomyia intermedia and Nyssomyia neivai, both implicated in the transmission of ACL in the Brazilian Southeastern region, were also captured. Ny. intermedia predominated in the open camping area. Low frequencies of phlebotomines were observed in the caves, where Evandromyia edwardsi predominated Lutzomyia longipalpis, the main vector of the American visceral leishmaniasis, was aslo present. This is its most southernly reported occurrence in the Atlantic forest.

Phlebotomines (Diptera, Psychodidae) in the Speleological Province of the Ribeira Valley: 3. Serra district - area of hostels for tourists who visit the Parque Estadual do Alto Ribeira (PETAR), state of São Paulo, Brazil

Phlebotomines (Diptera, Psychodidae) in the Speleological Province of the Ribeira Valley: 3. Area of hostels for tourists who visit the Parque Estadual do Alto Ribeira (PETAR), state of São Paulo, Brazil. The study characterizes some ecological aspects of the phlebotomine fauna in an endemic area of cutaneous leishmaniasis (CL) situated in the Serra district, Iporanga municipality where the hostels for tourists visiting the PETAR are located. Captures were undertaken on a smallholding and a small farm situated near the hostels, monthly between January/2001 and December/2003 with automatic light traps (ALT) in pigsty, hen-house and veranda of a domicile at the two sites, and in peridomicile of the small farm also with black/white Shannon traps. With the ALT a total of 87,224 phlebotomines representing 19 species and also two hybrids of Nyssomyia intermedia (Lutz & Neiva) and Nyssomyia neivai (Pinto) and two anomalous specimens were captured. The standardized index species abundance was for Ny. intermedia = 1.0 and Ny. neivai = 0.935. The highest frequencies of the smallholding occurred in the pigsty, the Williams' mean/capture for Ny. intermedia being 63.7 specimens and for Ny. neivai 29.2, and on the small farm, in the hen-house, Ny. intermedia 402.6 and Ny. neivai 116.2. A total of 863 phlebotomines (Ny. intermedia: 75.4%; Ny. neivai: 24.3%) were captured with black/white Shannon traps; females of both species being predominant in the white trap. The high frequencies of Ny. intermedia and Ny. neivai, both implicated in CL transmission, indicate the areas presenting risk of the disease.

A new species of Eupithecia Curtis (Lepidoptera, Geometridae) from the Azapa Valley, northern Chile

A new species of Eupithecia Curtis (Lepidoptera, Geometridae) from the Azapa Valley, northern Chile. Male and female adults of a new species of Eupithecia Curtis from the Arica Province, Chile are described and illustrated. The species is compared with E. yubitzae Vargas & Parra, 2004, from the same locality, and E. galapagosata Landry & Rindge 1995, from the Galapagos Islands, Ecuador.

First remarks on the nesting biology of Hypodynerus andeus (Packard) (Hymenoptera, Vespidae, Eumeninae) in the Azapa valley, northern Chile

First remarks on the nesting biology of Hypodynerus andeus (Packard) (Hymenoptera, Vespidae, Eumeninae) in the Azapa valley, northern Chile. Some aspects about the nesting biology of the potter wasp Hypodynerus andeus (Packard, 1869) are reported for the first time. Observations were carried out at the Azapa valley, coastal desert of northern Chile. A total of sixty nests were collected and examined, each composed by 1-14 cells, most of them found attached to concrete lamp posts. The only preys recorded in the cells were Geometridae (Lepidoptera) caterpillars and the presence of the parasitoid Anthrax sp. (Diptera, Bombyliidae) was also recorded. A number of arthropods belonging to different groups, mainly spiders, were found occupying empty nests.

Tertiary Himalayan structures and metamorphism in the Kulu Valley (Mandi-Khoksar transect of the Western Himalaya) - Shikar-Beh-nappe and crystalline nappe

The Crystalline Nappe of the High Himalayan Crystalline has been examined along the Kulu Valley and its vicinity (Mandi-Khoksar transect). This nappe was believed to have undergone deformation related only to its transport towards the SW essentially during the `'Main Central Thrust event''. New data has led to the conclusion that during the Himalayan orogeny, two distinctive phases, related to two opposite transport directions, characterize the evolution of this part of the chain, before the creation of the late NE-vergent backfolding. The first phase corresponds to an early NE-vergent folding and thrusting, creating the Tandi Syncline and the NE-oriented Shikar Beh Nappe stack, with a displacement amplitude of about 50 km. Two schistosities, together with a strong stretching lineation are developed at a deep tectonic level under amphibolite facies conditions (kyanite-staurolite-garnet-two mica schists). At a higher tectonic level and in the southern part of the section (Tandy Syncline and southern Kulu Valley between Kulu and Mandi) one or two schistosities are developed in the greenschist facies grade rocks (garnet-biotite and biotite schists). These structures and the associated Barrovian type metamorphism are all related to the NE-verging Shikar Beh Nappe. The creation of the NE-verging Shikar Beh Nappe may be explained by the reactivation of a SW dipping listric normal fault of the N Indian flexural passive margin, during the early stages of the Himalayan orogeny. In the second phase, the still hot metamorphic rocks of the Shikar Beh Nappe were folded and thrust towards the SW (mainly along the MBT and the MCT with a displacement in excess of 100 km) onto the cold, low-grade metamorphic rocks of the Larji-Kulu-Rampur Window or, near Mandi, on the non-metamorphic sandstones of the Ganges Molasse (Siwaliks). Sense of shear criteria and a strong NE-SW stretching-lineation indicate that the Crystalline Nappe has been overthrusted towards the SW. Thermometry on synkinematically crystallised garnet-biotite and garnet-hornblende pairs reveals the lower amphibolite facies temperature conditions related to the Crystalline Nappe formation. From the muscovite and biotite Rb-Sr cooling ages, the Shikar Beh Nappe emplacement occurred before 32 Ma and the southwestward thrusting of the Crystalline Nappe began before 21 Ma. Our model involving two opposite directions of thrusting goes against the conventional idea of only one main SW-oriented transport direction in the High Himalayan Crystalline Nappes.

Survey of potential sharpshooter and spittlebug vectors of Xylella fastidiosa to grapevines at the São Francisco River Valley, Brazil

Survey of potential sharpshooter and spittlebug vectors of Xylella fastidiosa to grapevines at the São Francisco River Valley, Brazil. Pierce's disease of grapevines, caused by Xylella fastidiosa, is a serious problem in some regions of North America, not yet reported in Brazil. In this study, a survey of potential sharpshooter (Hemiptera, Cicadellidae, Cicadellinae) and spittlebug (Hemiptera, Cercopidae) vectors of X. fastidiosa was conducted in vineyards at the São Francisco River Valley, a major grape growing region in Brazil. Four vineyards of Vitis vinifera L. were sampled fortnightly from June/2005 to June/2007, using yellow sticky cards, each placed at two different heights (45 cm aboveground and 45 cm above the crop canopy) in 10 sampling localities. A total of 4,095 specimens of sharpshooters were collected, nearly all from 3 Proconiini species, Homalodisca spottii Takiya, Cavichioli & McKamey, 2006 (96.8% of the specimens), Tapajosa fulvopunctata (Signoret, 1854) (3.1%), and Tretogonia cribrata Melichar, 1926 (1 specimen). Hortensia similis (Walker, 1851) (2 specimens) was the only Cicadellini species. Only 1 cercopid specimen, belonging to Aeneolamia colon (Germar, 1821), was trapped. Even though they are not considered potential Xylella vectors, 2 Gyponini leafhoppers were collected: Curtara samera DeLong & Freytag, 1972 (11 specimens) and Curtara inflata DeLong & Freytag, 1976 (1 specimen). Homalodisca spottii was observed feeding and mating on green branches of grapevines, in addition to egg masses. Because of its prevalence on the crop canopy, occurrence throughout the year (with peaks from February to August), and ability to colonize grapevines, H. spottii could be an important vector if a X. fastidiosa strain pathogenic to grapevines becomes introduced at the São Francisco River Valley.