Topological side-chain classification of beta-turns: Ideal motifs for peptidomimetic development

beta-turns are important topological motifs for biological recognition of proteins and peptides. Organic molecules that sample the side chain positions of beta-turns have shown broad binding capacity to multiple different receptors, for example benzodiazepines. beta-turns have traditionally been classified into various types based on the backbone dihedral angles (phi 2, psi 2, phi 3 and psi 3). Indeed, 57-68% of beta-turns are currently classified into 8 different backbone families (Type I, Type II, Type I', Type II', Type VIII, Type VIa1, Type VIa2 and Type VIb and Type IV which represents unclassified beta-turns). Although this classification of beta-turns has been useful, the resulting beta-turn types are not ideal for the design of beta-turn mimetics as they do not reflect topological features of the recognition elements, the side chains. To overcome this, we have extracted beta-turns from a data set of non-homologous and high-resolution protein crystal structures. The side chain positions, as defined by C-alpha-C-beta vectors, of these turns have been clustered using the kth nearest neighbor clustering and filtered nearest centroid sorting algorithms. Nine clusters were obtained that cluster 90% of the data, and the average intra-cluster RMSD of the four C-alpha-C-beta vectors is 0.36. The nine clusters therefore represent the topology of the side chain scaffold architecture of the vast majority of beta-turns. The mean structures of the nine clusters are useful for the development of beta-turn mimetics and as biological descriptors for focusing combinatorial chemistry towards biologically relevant topological space.

Specification and validation of process constraints for flexible workflows

Workflow systems have traditionally focused on the so-called production processes which are characterized by pre-definition, high volume, and repetitiveness. Recently, the deployment of workflow systems in non-traditional domains such as collaborative applications, e-learning and cross-organizational process integration, have put forth new requirements for flexible and dynamic specification. However, this flexibility cannot be offered at the expense of control, a critical requirement of business processes. In this paper, we will present a foundation set of constraints for flexible workflow specification. These constraints are intended to provide an appropriate balance between flexibility and control. The constraint specification framework is based on the concept of pockets of flexibility which allows ad hoc changes and/or building of workflows for highly flexible processes. Basically, our approach is to provide the ability to execute on the basis of a partially specified model, where the full specification of the model is made at runtime, and may be unique to each instance. The verification of dynamically built models is essential. Where as ensuring that the model conforms to specified constraints does not pose great difficulty, ensuring that the constraint set itself does not carry conflicts and redundancy is an interesting and challenging problem. In this paper, we will provide a discussion on both the static and dynamic verification aspects. We will also briefly present Chameleon, a prototype workflow engine that implements these concepts. (c) 2004 Elsevier Ltd. All rights reserved.

Volcanic resurfacing and the early terrestrial crust: Zircon U-Pb and REE constraints from the Isua Greenstone Belt, southern West Greenland

The oldest known bona fide succession of elastic metasediments Occurs in the Isua Greenstone Belt. SW Greenland and consists of a variety of mica schists and rare metaconglomerates. The metasediments are in direct contact with a felsic metavolcanic lithology that has previously been dated to 3.71 Ga. Based on trace element geochemical data for 30 metasediments, we selected the six samples with highest Zr concentrations for zircon extraction. These samples all yielded very few or no zircon, Those extracted from mica schists yielded ion probe U/Pb ages between 3.70 and 3,71 Ga. One metaconglomerate sample yielded just a single zircon of 3.74 Ga age. The mica schist hosted zircons have U/Pb ages. Th/U ratios, REE patterns and Eu anomalies indistinguishable from zircon in the adjacent 3.71 Ga felsic metavolcanic unit. Trace element modelling requires the bulk of material in the metasediments to be derived from variably weathered mafic lithologies but some metasediments contain substantial contribution from more evolved source lithologies. The paucity of zircon in the mica schists is thus explained by incorporation of material from largely zircon-free volcanic lithologies. The absence of older zircon in the mica schists and the preponderance of mafic source material imply intense, mainly basaltic resurfacing of the early Earth. The implications of this process are discussed, Thermal considerations suggest that horizontal growth of Hadean crust by addition of mafic ultramafic lavas must have triggered self-reorganisation of the protocrust by remelting. Reworking oft Hadean crust may have been aided by burial of hydrated (weathered) metabasalt due to semi-continuous addition of new voluminous basalt Outpouring,;, This process Causes a bias towards eruption of Zr-saturated partial melts at the surface with O-isotope corn posit ion,, potentially different from the mantle. The oldest zircons hosted in sediments would have been buried to substantial depth or formed in plutons that crystallised at some depth from which it took hundreds of millions of years for them to be exhumed and incorporated into much younger sediments. (C) 2005 Elsevier B.V.All rights reserved.

Matching poultry production with available feed resources: issues and constraints

Corn and soyabeans may not be available in many countries particularly those which do not have sufficient foreign currency or the capacity to grow them. This paper outlines strategies that may be important under these circumstances. Alternative feedstuffs and various feeding systems may be used to support poultry production. Alternative ingredients such as rice bran, pearl millet, cottonseed meal and grain legumes are discussed. Evidence is presented showing that amino acid requirements of layers and broilers may be too generous particularly in countries where climate, management and disease can impose production constraints. The ability of finishing broilers to perform well on very low-energy diets allows the inclusion of alternative feeds and by-products into formulations. Very low protein diets based on cereals and free amino acids can be used for layers without loss of performance. Self-selection of feedstuffs may be an important strategy in reducing feed costs of broilers and layers. The concept of matching production with available feed resources may compromise broiler growth and egg production, but in many countries this may be the most economical choice. Countries in the humid tropics usually have reduced poultry performance. The effects of high temperature and humidity are difficult to overcome. The vexed questions of the escalation in the price of fossil fuel and the outbreak of avian influenza, both seemingly without a solution, are clouds hanging over an otherwise buoyant industry.

Cyclic MrIA: A stable and potent cyclic conotoxin with a novel topological fold that targets the norepinephrine transporter

Conotoxins, disulfide-rich peptides from the venom of cone snails, have created much excitement over recent years due to their potency and specificity for ion channels and their therapeutic potential. One recently identified conotoxin, MrIA, a 13-residue member of the chi-conotoxin family, inhibits the human norepinephrine transporter (NET) and has potential applications in the treatment of pain. In the current study, we show that the, beta-hairpin structure of native MrIA is retained in a synthetic cyclic version, as is biological activity at the NET. Furthermore, the cyclic version has increased resistance to trypsin digestion relative to the native peptide, an intriguing result because the cleavage site for the trypsin is not close to the cyclization site. The use of peptides as drugs is generally hampered by susceptibility to proteolysis, and so, the increase in enzymatic stability against trypsin observed in the current study may be useful in improving the therapeutic potential of MrIA. Furthermore, the structure reported here for cyclic MrIA represents a new topology among a growing number of circular disulfide-rich peptides.

Neuromuscular-skeletal constraints on the acquisition of skill in a discrete torque production task

The organisation of the human neuromuscular-skeletal system allows an extremely wide variety of actions to be performed, often with great dexterity. Adaptations associated with skill acquisition occur at all levels of the neuromuscular-skeletal system although all neural adaptations are inevitably constrained by the organisation of the actuating apparatus (muscles and bones). We quantified the extent to which skill acquisition in an isometric task set is influenced by the mechanical properties of the muscles used to produce the required actions. Initial performance was greatly dependent upon the specific combination of torques required in each variant of the experimental task. Five consecutive days of practice improved the performance to a similar degree across eight actions despite differences in the torques required about the elbow and forearm. The proportional improvement in performance was also similar when the actions were performed at either 20 or 40% of participants' maximum voluntary torque capacity. The skill acquired during practice was successfully extrapolated to variants of the task requiring more torque than that required during practice. We conclude that while the extent to which skill can be acquired in isometric actions is independent of the specific combination of joint torques required for target acquisition, the nature of the kinetic adaptations leading to the performance improvement in isometric actions is influenced by the neural and mechanical properties of the actuating muscles.

Summarizing level-two topological relations in large spatial datasets

Summarizing topological relations is fundamental to many spatial applications including spatial query optimization. In this article, we present several novel techniques to effectively construct cell density based spatial histograms for range (window) summarizations restricted to the four most important level-two topological relations: contains, contained, overlap, and disjoint. We first present a novel framework to construct a multiscale Euler histogram in 2D space with the guarantee of the exact summarization results for aligned windows in constant time. To minimize the storage space in such a multiscale Euler histogram, an approximate algorithm with the approximate ratio 19/12 is presented, while the problem is shown NP-hard generally. To conform to a limited storage space where a multiscale histogram may be allowed to have only k Euler histograms, an effective algorithm is presented to construct multiscale histograms to achieve high accuracy in approximately summarizing aligned windows. Then, we present a new approximate algorithm to query an Euler histogram that cannot guarantee the exact answers; it runs in constant time. We also investigate the problem of nonaligned windows and the problem of effectively partitioning the data space to support nonaligned window queries. Finally, we extend our techniques to 3D space. Our extensive experiments against both synthetic and real world datasets demonstrate that the approximate multiscale histogram techniques may improve the accuracy of the existing techniques by several orders of magnitude while retaining the cost efficiency, and the exact multiscale histogram technique requires only a storage space linearly proportional to the number of cells for many popular real datasets.

Quality of service in flexible workflows through process constraints

Workflow technology has delivered effectively for a large class of business processes, providing the requisite control and monitoring functions. At the same time, this technology has been the target of much criticism due to its limited ability to cope with dynamically changing business conditions which require business processes to be adapted frequently, and/or its limited ability to model business processes which cannot be entirely predefined. Requirements indicate the need for generic solutions where a balance between process control and flexibility may be achieved. In this paper we present a framework that allows the workflow to execute on the basis of a partially specified model where the full specification of the model is made at runtime, and may be unique to each instance. This framework is based on the notion of process constraints. Where as process constraints may be specified for any aspect of the workflow, such as structural, temporal, etc. our focus in this paper is on a constraint which allows dynamic selection of activities for inclusion in a given instance. We call these cardinality constraints, and this paper will discuss their specification and validation requirements.

40Ar/39Ar geochronological constraints on the evolution of lateritic iron deposits in the Quadrilatero Ferrifero, Minas Gerais, Brazil

Weathering profiles overlying the Sapecado, Pico and Andaime iron ore deposits, Quadrilátero Ferrífero (QF), Minas Gerais, Brazil, reach depths of 150–400 m and host world-class supergene iron orebodies. In addition to hosting supergene ore bodies of global economic significance, weathered banded iron-formations at the Quadrilátero Ferrífero and elsewhere (e.g., Carajás, Hamersley) are postulated to underlie some of the most ancient continuously exposed weathering profiles on earth. Laser incremental-heating 40Ar/39Ar results for 69 grains of hollandite-group manganese oxides extracted from 23 samples collected at depths ranging from 5 to 150 m at the Sapecado, Pico and Andaime deposits reveal ages ranging from ca. 62 to 14 Ma. Older Mn-oxides occur near the surface, while younger Mn-oxides occur at depth. However, many samples collected at the weathering–bedrock interface yield ages in the 51–41 Ma range, suggesting that the weathering profiles in the Quadrilátero Ferrífero had already reached their present depth in the Paleogene. The antiquity of the weathering profiles in the Quadrilátero Ferrífero is comparable to the antiquity of dated weathering profiles on banded iron-formations in the Carajás Region (Brazil) and the Hamersley Province, Western Australia. The age versus depth distributions obtained in this study, but not available for other regions containing similar supergene iron deposits, suggest that little further advance of the weathering front has occurred in the Quadrilátero Ferrífero lateritic profiles during the Neogene. The results suggest that weathering in some of these ancient landscapes is not controlled by the steady-state advance of weathering fronts through time, but may reflect climatic and geomorphological conditions prevailing in a remote past. The geochronological results also confirm that the ancient landsurfaces in the Quadrilátero Ferrífero probably remained immune to erosion for tens of millions of years. Deep weathering, mostly in the Paleogene, combined with low erosion rates, account for the abundance and widespread distribution of supergene iron, manganese, and aluminum orebodies in this region.

40Ar/39Ar geochronology constraints on late miocene weathering rates in Minas Gerais, Brazil

Ar-40/Ar-39 incremental heating ages for twenty one grains of cryptomelane, collected at 0, 42, 45, and 60 in depths in the Cachoeira Mine weathering profile, Minas Gerais, permit calculating long-term (10 Ma time scale) weathering rate (saprolitization rate) in SE Brazil. Pure well-crystallized cryptomelane grains with high K contents (3-5 wt.%) yield reliable geochronological results. The Ar-40/Ar-39 plateau ages obtained decrease from the top to the bottom of the profile (12.7 +/- 0.1 to 7.6 +/- 0.1 Ma at surface; 7.6 +/- 0.2 to 6.1 +/- 0.2 Ma at 42 m; and 7.1 +/- 0.2 to 5.9 +/- 0.1 Ma at 45 in; 6.6 +/- 0.1 to 5.2 +/- 0.1 Ma at 60 in), yielding a weathering front propagation rate of 8.9 +/- 1.1 m/m.y. From the geochronological results and the mineral transformations implicit by the current mineralogy in the weathering profiles, it is possible to calculate the saprolitization rate for the Cachoeira Mine lithologies and for adjacent weathering profiles developed on granodiorites and scbists. The measured weathering front propagation rate yields a saprolitization rate of 24.9 +/- 3.1 t/km(2)/yr. This average long-term (> 10 Ma) saprolitization rate is consistent with mass balance calculations results for present saprolitization rates in weathering watersheds. These results are also consistent with longterm saprolitization rates estimated by combining cosmogenic isotope denudation rates with mass balance calculations. (c) 2005 Elsevier B.V All rights reserved.