Experimenting with infinite groups, I

A group is termed parafree if it is residually nilpotent and has the same nilpotent quotients as a given free group. Since free groups are residually nilpotent, they are parafree. Nonfree parafree groups abound and they all have many properties in common with free groups. Finitely presented parafree groups have solvable word problems, but little is known about the conjugacy and isomorphism problems. The conjugacy problem plays an important part in determining whether an automorphism is inner, which we term the inner automorphism problem. We will attack these and other problems about parafree groups experimentally, in a series of papers, of which this is the first and which is concerned with the isomorphism problem. The approach that we take here is to distinguish some parafree groups by computing the number of epimorphisms onto selected finite groups. It turns out, rather unexpectedly, that an understanding of the quotients of certain groups leads to some new results about equations in free and relatively free groups. We touch on this only lightly here but will discuss this in more depth in a future paper.

Seizure detection algorithm for neonates based on wave-sequence analysis

Objective: The description and evaluation of the performance of a new real-time seizure detection algorithm in the newborn infant. Methods: The algorithm includes parallel fragmentation of EEG signal into waves; wave-feature extraction and averaging; elementary, preliminary and final detection. The algorithm detects EEG waves with heightened regularity, using wave intervals, amplitudes and shapes. The performance of the algorithm was assessed with the use of event-based and liberal and conservative time-based approaches and compared with the performance of Gotman's and Liu's algorithms. Results: The algorithm was assessed on multi-channel EEG records of 55 neonates including 17 with seizures. The algorithm showed sensitivities ranging 83-95% with positive predictive values (PPV) 48-77%. There were 2.0 false positive detections per hour. In comparison, Gotman's algorithm (with 30 s gap-closing procedure) displayed sensitivities of 45-88% and PPV 29-56%; with 7.4 false positives per hour and Liu's algorithm displayed sensitivities of 96-99%, and PPV 10-25%; with 15.7 false positives per hour. Conclusions: The wave-sequence analysis based algorithm displayed higher sensitivity, higher PPV and a substantially lower level of false positives than two previously published algorithms. Significance: The proposed algorithm provides a basis for major improvements in neonatal seizure detection and monitoring. Published by Elsevier Ireland Ltd. on behalf of International Federation of Clinical Neurophysiology.

Better prediction of protein contact number using a support vector regression analysis of amino acid sequence

Background: Protein tertiary structure can be partly characterized via each amino acid's contact number measuring how residues are spatially arranged. The contact number of a residue in a folded protein is a measure of its exposure to the local environment, and is defined as the number of C-beta atoms in other residues within a sphere around the C-beta atom of the residue of interest. Contact number is partly conserved between protein folds and thus is useful for protein fold and structure prediction. In turn, each residue's contact number can be partially predicted from primary amino acid sequence, assisting tertiary fold analysis from sequence data. In this study, we provide a more accurate contact number prediction method from protein primary sequence. Results: We predict contact number from protein sequence using a novel support vector regression algorithm. Using protein local sequences with multiple sequence alignments (PSI-BLAST profiles), we demonstrate a correlation coefficient between predicted and observed contact numbers of 0.70, which outperforms previously achieved accuracies. Including additional information about sequence weight and amino acid composition further improves prediction accuracies significantly with the correlation coefficient reaching 0.73. If residues are classified as being either contacted or non-contacted, the prediction accuracies are all greater than 77%, regardless of the choice of classification thresholds. Conclusion: The successful application of support vector regression to the prediction of protein contact number reported here, together with previous applications of this approach to the prediction of protein accessible surface area and B-factor profile, suggests that a support vector regression approach may be very useful for determining the structure-function relation between primary sequence and higher order consecutive protein structural and functional properties.

Gyracanthides hawkinsi sp nov (Acanthodii, Gyracanthidae) from the Lower Carboniferous of Queensland, Australia, with a review of gyracanthid taxa

A new species of Gyracanthides from the mid-Visean Ducabrook Formation of Middle Paddock site, near Springsure in the Drummond Basin, central Queensland, is based on isolated three-dimensionally preserved elements. The specimens comprise paired and unpaired spines and pectoral girdle elements, procoracoids and scapulocoracoids, and include growth series. The morphology, especially of the shoulder girdle bones and the form and tubercular ornamentation of the paired fin spines, is used to distinguish the new taxon. These characters also help differentiate the numerous described gyracanthid species. Aspects of palaeobiology including possible sexual dimorphism are explored. A hypothetical reconstruction of the fish is based on our interpretation of the articulation of isolated elements combined with examination of wear patterns on fin spines. Gyracanthides hawkinsi sp. nov. is compared with other Australian taxa as well as with gyracanthids from North America, Europe, Russia, Iran, Africa and Antarctica, some of which are tentatively reassigned here to the Gondwanan genus Gyracanthides.

SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms

Background: This paper describes SeqDoC, a simple, web-based tool to carry out direct comparison of ABI sequence chromatograms. This allows the rapid identification of single nucleotide polymorphisms (SNPs) and point mutations without the need to install or learn more complicated analysis software. Results: SeqDoC produces a subtracted trace showing differences between a reference and test chromatogram, and is optimised to emphasise those characteristic of single base changes. It automatically aligns sequences, and produces straightforward graphical output. The use of direct comparison of the sequence chromatograms means that artefacts introduced by automatic base-calling software are avoided. Homozygous and heterozygous substitutions and insertion/deletion events are all readily identified. SeqDoC successfully highlights nucleotide changes missed by the Staden package 'tracediff' program. Conclusion: SeqDoC is ideal for small-scale SNP identification, for identification of changes in random mutagenesis screens, and for verification of PCR amplification fidelity. Differences are highlighted, not interpreted, allowing the investigator to make the ultimate decision on the nature of the change.

Gnathostome microremains from the lower Devonian Jawf Formation, Saudi Arabia

Calcareotis horizons in the Qasr and Hammamiyat members (Lower Devonian, ?Pragian and lower Emsian) of file Jawf Formation, northwestern Saudi Arabia, yielded a rich assemblage of microremains from acanthodian, placoderm. chondrichthyan, and sarcopterygian vertebrates. The most abundant elements are scales from acanthodians Nostolepis spp., Milesacanthus ancestralis n. sp., Canadatepis? sp., and Gomphonchus? fromensis. scales and dermal bone fragments from acanthothoracid and ?rhenanid placoderms, and teeth from onychodontids. Rarer occurrences include ?chondrichthyan scales of several different morphotypes, and petalichthid and ?ptyctodontid placoderm elements. The Qasr Member assemblage shows a close resemblance to slightly older faunas front the Lochkovian of Brittany and Spain. The Hammamiyat Member microvertebrate fauna shows closest affinity with that of the stratigraphically lower Qasr Member, with similarities also to coeval faunas from southeastern Australia, late Emsian/Eifelian faunas from west-central Europe, and the Givetian Aztec Siltstone fauna from Antarctica.

STAR: predicting recombination sites from amino acid sequence

Background: Designing novel proteins with site-directed recombination has enormous prospects. By locating effective recombination sites for swapping sequence parts, the probability that hybrid sequences have the desired properties is increased dramatically. The prohibitive requirements for applying current tools led us to investigate machine learning to assist in finding useful recombination sites from amino acid sequence alone. Results: We present STAR, Site Targeted Amino acid Recombination predictor, which produces a score indicating the structural disruption caused by recombination, for each position in an amino acid sequence. Example predictions contrasted with those of alternative tools, illustrate STAR'S utility to assist in determining useful recombination sites. Overall, the correlation coefficient between the output of the experimentally validated protein design algorithm SCHEMA and the prediction of STAR is very high (0.89). Conclusion: STAR allows the user to explore useful recombination sites in amino acid sequences with unknown structure and unknown evolutionary origin. The predictor service is available from http://pprowler.itee.uq.edu.au/star.

Thermal evolution of the ore-hosting Isa Superbasin: Central and Northern Lawn Hill Platform

Hydrocarbon migration pathways and organic mineral matter associations were used to identify brine pathways in Paleoproterozic to early Mesoproterozoic rocks from the Lawn Hill platform, Mount Isa. Several types of organic matter are identified, and their thermal imprints are used to reconstruct the thermal history of the northern to central parts of the Isa superbasin. Three major thermal hydrothermal episodes are recognized from the organic maturation studies. Isotherm plots on a 175-km-long structural-sedimentological north-south section of the Isa superbasin highlight specific fault systems that acted as hot fluid conduits during the geologic history of the basin. Some of these systems indicate continuing activity into the south Nicholson basin, supported by the presence of low reflectance (type B) bitumen. This bitumen has not been overprinted by later hydrothermal episodes and therefore represents the latest thermal event. Along the north-south profile a general southward increase in temperature is evident. The lowest temperatures are recorded in proximity to the basin margin on the southern flank of the Murphy inlier. Thermal processes and their sequence of events in the basin are recorded by organic maturation, subsequent hydrocarbon generation, its migration and destruction coincident with transport and precipitation of minerals. As some timing and trapping mechanisms for minerals may have analogues with hydrocarbon entrapment, relative timing of processes leading to organic maturation, hydrocarbon generation and migration are utilized in this study to enhance understanding of ore-grade mineralization. In the Proterozoic successions of the Mount Isa basin multiple hydrocarbon generation events are recognized. These events record the transient passage of potential metal-bearing fluids rather than background conductive heat flow from the basement. Such hydrothermal fluids are responsible for inverse maturation profiles in the vicinity of the Termite Range fault and extreme maturation (reflectance values) up to 6 percent Ro at the Grevillea prospect. At Century, intermediate Ro values of

Timing and chemistry of fluid-flow events in the Lawn Hill Platform, Northern Australia

Mudrocks and carbonates of the Isa superbasin in the Lawn Hill platform in northern Australia host major base metal sulfide mineralization, including the giant strata-bound Century Zn-Pb deposit. Mineral paragenesis, stable isotope, and K-Ar dating studies demonstrate that long-lived structures such as the Termite Range fault acted as hot fluid conduits several times during the Paleoproterozoic and Mesoproterozoic in response to major tectonic events. Illite and chlorite crystallinity studies suggest the southern part of the platform has experienced higher temperatures (up to 300 degrees C) than similar stratigraphic horizons in the north. The irregular downhole variation of illite crystallinity values provides further information oil the thermal regime in the basin and shows that clay formation was controlled not only by temperature increase with depth but also by high water/rock ratios along relatively permeable zones. K-Ar dating of illite, in combination with other data, may indicate three major thermal events in the central and northern Lawn Hill platform Lit 1500, 1440 to 1400, and 1250 to 1150 Ma. This study did not detect the earlier Century base metal mineralizing event at 1575 Ma. 1500 Ma ages are recorded only in the south and correspond to the age of the Late Isan orogeny and deposition of the Lower Roper superbasin. They may reflect exhumation of a provenance region. The 1440 to 1300 Ma ages are related to fault reactivation and a thermal pulse at similar to 1440 to 1400 Ma possibly accompanied by fluid flow, with subsequent enhanced cooling possibly due to thermal relaxation or further crustal exhumation. The youngest thermal and/or fluid-flow event at 1250 to 1150 Ma is recorded mainly to the cast of the Tern-lite Range fault and may be related to the assembly of the Rodinian supercontinent. Fluids in equilibrium with illite that formed over a range of temperatures, at different times in different parts of the platform. have relatively uniform oxygen isotope compositions and more variable hydrogen isotope compositions (delta O-18 = 3.5-9.7 parts per thousand V-SMOW; delta D = -94 to -36 parts per thousand V-SMOW). The extent of the 180 enrichment and the variably depleted hydrogen isotope compositions suggest the illite interacted with deep-basin hypersaline brines that were composed of evaporated seawater and/or highly evolved meteoric water. Siderite is the most abundant iron-rich gangue phase in the Century Zn-Pb deposit, which is surrounded by all extensive ferroan carbonate alteration halo. Modeling suggests that the ore siderite formed at temperatures of 120 degrees to 150 degrees C, whereas siderite and ankerite in the alteration halo formed at temperatures of 150 degrees to 180 degrees C. The calculated isotopic compositions of the fluids are consistent with O-18-rich basinal brines and mixed inorganic and organic carbon Sources (6180 = 3-10 parts per thousand V-SMOW, delta C-13 = -7 to -3 parts per thousand V-PDB). in the northeast Lawn Hill platform carbonate-rich rocks preserve marine to early diagenetic carbon and oxygen isotope compositions, whereas ferroan carbonate cements in siltstones and shales in the Desert Creek borehole are O-18 and C-13 depleted relative to the sedimentary carbonates. The good agreement between temperature estimates from illite crystallinity and organic reflectance (160 degrees-270 degrees C) and inverse correlation with carbonate delta O-18 values indicates that organic maturation and carbonate precipitation in the northeast Lawn Hill platform resulted from interaction with the 1250 to 1150 Ma fluids. The calculated isotopic compositions of the fluid are consistent with evolved basinal brine (delta O-18 = 5.1-9.4 parts per thousand V-SMOW; delta C-13 = -13.2 to -3.7 parts per thousand V-PDB) that contained a variable organic carbon component from the oxidation and/or hydrolysis of organic matter in the host sequence. The occurrence of extensive O-18- and C-13-depleted ankerite and siderite alteration in Desert Creek is related to the high temperature of the 1250 to 1150 Ma fluid-flow event in the northeast Lawn Hill platform, in contrast to the lower temperature fluids associated with the earlier Century Zn-Pb deposit in the central Lawn Hill platform.

Aquatic invertebrates in final void water bodies at an open-cut coal mine in central Queensland

We describe the diversity of aquatic invertebrates colonising water-filled final voids produced by an open-cut coal mine near Moura, central Queensland. Ten disused pits that had been filled with water from < 1 year to 22 years prior to the survey and three nearby 'natural' water bodies were sampled in December 1998 and again in March 1999. All invertebrates collected were identified to family with the exception of oligochaetes, cladocerans, ostracods and copepods, which were identified to these coarser taxonomic levels. Sixty-two taxa were recorded from > 20 000 individuals. The greatest familial richness was displayed by the Insecta (33 families) followed by the mites (Acari) with 12 families. While natural water bodies held the greatest diversity, several mine pits were almost as rich in families. Classification analyses showed that natural sites tended to cluster together, but the groupings did not clearly exclude pit sites. Mining pits that supported higher diversity tended to be older and had lower salinity (< 2000 mu S/cm); however, salinity in all water bodies varied with rainfall conditions. We conclude that ponds formed in final voids at this mine have the potential to provide habitat for many invertebrate taxa typical of lentic inland water bodies in central Queensland.

Volcanic setting of the Bajo de la Alumbrera porphyry Cu-Au deposit, Farallon Negro Volcanics, Northwest Argentina

The late Miocene Farallon Negro volcanics, comprising basaltic to rhyodacitic volcano-sedimentary rocks, host the Bajo de la Alumbrera porphyry copper-gold deposit in northwest Argentina. Early studies of the geology of the district have underpinned the general model for porphyry ore deposits where hydrothermal alteration and mineralization develop in and around porphyritic intrusions emplaced at shallow depths (2.5-3.5 km) into stratovolcanic assemblages. The Farallon Negro succession is dominated by thick sequences of volcano-sedimentary breccias, with lavas forming a minor component volumetrically. These volcaniclastic rocks conformably overlie crystalline basement-derived sedimentary rocks deposited in a developing foreland basin southeast of the Puna-Altiplano plateau. Within the Farallon Negro volcanics, volcanogenic accumulations evolved from early mafic to intermediate and silicic compositions. The younger and more silicic rocks are demonstrably coeval and comagmatic with the earliest group of mineralized porphyritic intrusions at Bajo de la Alumbrera. Our analysis of the volcanic stratigraphy and facies architecture of the Farallon Negro volcanics indicates that volcanic eruptions evolved from effusive to mixed effusive and explosive styles, as magma compositions changed to more intermediate and silicic compositions. Air early phase of mafic to intermediate voleanism was characterized by small synsedimentary intrusions with peperitic contacts, and lesser lava units scattered widely throughout the district, and interbedded with thick and extensive successions of coarse-grained sedimentary breccias. These sedimentary breccias formed from numerous debris- and hyperconcentrated flow events. A later phase of silicic volcanism included both effusive eruptions, forming several areally restricted lavas, and explosive eruptions, producing more widely dispersed (up to 5 kin) tuff units, some tip to 30-m thickness in proximal sections. Four key features of the volcanic stratigraphy suggest that the Farallon Negro volcanics need not simply record the construction of a large steep-sided polygenetic stratovolcano: (1) sheetlike, laterally continuous debris-flow and other coarse-grained sedimentary deposits are dominant, particularly in the lower sections; (2) mafic-intermediate composition lavas are volumetrically minor; (3) peperites are present throughout the sequence; and (4) fine-grained lacustrine sandstone-siltstone sequences occur in areas previously thought to be proximal to the summit region of the stratovolcano. Instead, the nature, distribution, and geometry of volcanic and volcaniclastic facies suggest that volcanism occurred as a relatively low relief, multiple-vent volcanic complex at the eastern edge of a broad, > 200-km-wide late Miocene volcanic belt and oil ail active foreland sedimentary basin to the Puna-Altiplano. Volcanism that occurred synchronously with the earliest stages of porphyry-related mineralization at Bajo de la Alumbrera apparently developed in an alluvial to ring plain setting that was distal to larger volcanic edifices.

Palynostratigraphy of Ordovician strata, Canning Basin, Western Australia. Part One: acritarchs and prasinophytes

This paper is the initial part of a comprehensive bipartite monograph of palynomorphs (viz., acritarchs, prasinophyte phycomata, and chitinozoans) that are represented profusely in marine lower Palaeozoic strata of the Canning Basin, Western Australia. The prime aim is to establish a palynologically based zonal scheme for the Ordovician sequence as represented in five cored boreholes drilled through the Lower to Middle Ordovician strata of the central-northeastern Canning Basin. These strata embrace the Oepikodus communis through Phragmodus-Plectodina conodont zonal interval and comprise (in ascending order) the Willara, Goldwyer, and Nita formations, of inferred early Arenig to Llanvirn age. All three formations contain moderately diverse and variably preserved palynomorphs. The palynomorph taxa, detailed systematically in the current Part One of this monograph, comprise 66 species of acritarchs and six of prasinophytes. Of these, two species of prasinophytes and 11 of acritarchs are newly established: Cymatiosphaera meandrica and Pterospermella franciniae; Aremoricanium hyalinum, A. solaris, Baltisphaeridium tenuicomatum, Gorgonisphaeridium crebrum, Lophosphaeridium aequalium, L. aspersum, Micrhystridium infrequens, Pylantios hadrus, Sertulidium amplexum, Striatotheca indistincta, and Tribulidium globosum. Pylantios (typified by P. hadrus), Sertulidium (typified by S. amplexum), and Tribulidium (typified by T globosum); are defined as new acritarch genera. Three new combinations are instituted: Baltisphaeridium pugiatum (PLAYFORD & MARTIN 1984), Polygonium canningianum (COMRAZ & PENIGUEL 1972), and Sacculidium furtivum (PLAYFORD & MARTIN 1984); and Ammonidium macilentum PLAYFORD & MARTIN 1984 and Sacculidium furtivum (PLAYFORD & MARTIN 1984) are emended. An appreciable number of palynomorph species are not formally named owing to lack of sufficient or adequately preserved specimens; others are compared but not positively identified with previously instituted species. The ensuing Part Two of this study will complete the systematic-descriptive documentation, i.e., chitinozoans, and evaluate the Canning Basin palynoflora in terms of its chronological and stratigraphic-correlative significance.