The Tyne Digital Library - Part 2 Maps and Images

In this section, you will find maps showing various important aspects of the River Tyne catchment area. All the maps are drawn based on Ordnance Survey data made available via the Digimap service. For the land cover maps of the catchment area, four variants are provided. Please note that the full details of the intext citations quoted in some of the following maps can be found in the full bibliographic listing.

The Tyne Digital Library - Part 1 Introduction

The Tyne Digital Library (TDL) provides access to scholarly materials (e.g. papers, book chapters, bibliographic reference lists), databases of hydrological and physical information, maps of key physiographic and environmental data, and electronic journal articles, for students undertaking GEOG3023 River Basin Management. In addition, the TDL utilises technological innovations that enhance services for accessing this information.

Collection of the Tyne Digital Library

The Tyne Digital Library (TDL) provides access to scholarly materials (e.g. papers, book chapters, bibliographic reference lists), databases of hydrological and physical information, maps of key physiographic and environmental data, and electronic journal articles, for students undertaking GEOG3023 River Basin Management. In addition, the TDL utilises technological innovations that enhance services for accessing this information.

Brumadoite, a new copper tellurate hydrate, from Brumado, Bahia, Brazil

Brumadoite, ideally Cu(2)Te(6+)O(4)(OH)(4)center dot 5H(2)O, is a new mineral from Pedra Preta mine, Serra das Eguas, Brumado, Bahia, Brazil. It occurs as microcrystalline aggregates both on and, rarely, pseudomorphous after coarse-grained magnesite, associated with mottramite and quartz. Crystals are platy, subhedral, 1-2 mu m in size. Brumadoite is blue (near RHS 114B), has a pale blue streak and a vitreous lustre. It is transparent to translucent and does not fluoresce. The empirical formula is (Cu(2.90)Pb(0.04)Ca(0.01))(Sigma 2.95) (Te(0.93)(6+)Si(0.05))(Sigma 0.98)O(3.92)(OH)(3.84)center dot 5.24H(2)O. Infrared spectra clearly show both (OH) and H(2)O. Microchemical spot tests using a KI Solution show that brumadoite has tellurium in the 6(+) state. The mineral is monoclinic, P2(1)/m or P2(1). Unit-cell parameters refined from X-ray powder data are a 8.629(2) angstrom, b 5.805(2) angstrom, c 7.654(2) angstrom, beta 103.17(2)degrees, V 373.3(2) angstrom(3), Z = 2. The eight strongest X-ray powder-diffraction lines [d in angstrom, (l),(hkl)] are: 8.432,(100),(100); 3.162,(66),((2) over bar 02); 2.385,(27),(220); 2.291,((1) over bar 12),(22); 1.916,(11),(312); 1.666,(14),((4) over bar 22,114); 1.452,(10), (323, 040); 1.450,(10),(422,403). The name is for the type locality, Brumado, Bahia, Brazil. The new mineral species has been approved by the CNMNC (IMA 2008-028).

Genomic organization and transcription analysis of the 195-bp satellite DNA in Trypanosoma cruzi

The 195-bp satellite DNA is the most abundant Trypanosoma cruzi repetitive sequence. Here we show by RNA blotting and RT-PCR that 195 SAT is intensely transcribed. We observed a positive correlation between the level of satellite RNA and the abundance of the satellite copies in the genome of T cruzi strains and that the satellite expression is not developmentally regulated. By analyzing CL Brener individual reads, we estimated that 195 SAT corresponds to approximately 5% of the CL Brener genome. 195 SAT elements were found in only 37 annotated contigs, indicating that a large number of satellite copies were not incorporated into the assembled data. The assembled satellite units are distributed in non-syntenic regions with Trypanosoma brucei and Leishmania major genomes, enriched with surface proteins, retroelements, RHS and hypothetical proteins. Satellite repeats were not observed in annotated subtelomeric regions. We report that 12 satellite sequences are truncated by the retroelement VIPER. (C) 2008 Elsevier B.V. All rights reserved.

Highly polymorphic in silico-derived microsatellite loci in the potato-infecting fungal pathogen Rhizoctonia solani anastomosis group 3 from the Colombian Andes

Fourteen polymorphic microsatellite DNA markers derived from the draft genome sequence of Rhizoctonia solani anastomosis group 3 (AG-3), strain Rhs 1AP, were designed and characterized from the potato-infecting soil fungus R. solani AG-3. All loci were polymorphic in two field populations collected from Solanum tuberosum and S. phureja in the Colombian Andes. The total number of alleles per locus ranged from two to seven, while gene diversity (expected heterozygosity) varied from 0.11 to 0.81. Considering the variable levels of genetic diversity observed, these markers should be useful for population genetic analyses of this important dikaryotic fungal pathogen on a global scale.

Skeletal and dental components of Class II correction with the bionator and removable headgear splint appliances

The purpose of this study was to differentiate the dentoalveolar and skeletal effects to better understand orthodontic treatment. We evaluated the treatment changes associated with the bionator and the removable headgear splint (RHS). Methods: The sample comprised 51 consecutively treated Class II patients from 1 office who had all been successfully treated with either a bionator (n = 17) or an RHS appliance (n = 17). Class II patients waiting to start treatment later served as controls (n = 17). A modified version of the Johnston pitchfork analysis was used to quantify the dentoalveolar and skeletal contributions to the anteroposterior correction at the levels of the molars and the incisors. Results: Both appliances significantly improved anteroposterior molar relationships (2.15 mm for the bionator, 2.27 mm for the RHS), primarily by dentoalveolar modifications (1.49 and 2.36 mm for the bionator and the RHS, respectively), with greater maxillary molar distalization in the RHS group. Overjet relationships also improved significantly compared with the controls (3.11 and 2.12 mm for the bionator and the RHS, respectively), due primarily to retroclination of the maxillary incisors (2.2 and 2.38 mm for the bionator and the RHS, respectively). The differences between overall corrections and dentoalveolar modifications for both molar and overjet relationships were explained by skeletal responses, with the bionator group showing significantly greater anterior mandibular displacement than the RHS group. Conclusions: The bionator and the RHS effectively corrected the molar relationships and overjets of Class II patients primarily by dentoalveolar changes. (Am J Orthod Dentofacial Orthop 2008; 134: 732-41)

Metabolic responses to glucoprivation induced by 2-deoxy-D-glucose in Brycon cephalus (Teleostei, Characidae)

The effects of functional cytoglucopenia provoked by 2-deoxy-D-glucose (2-DG) were studied in adult Brycon cephalus, an omnivorous fish from the Amazon Basin in Brazil. Glycogen content in liver and muscle as well as plasmatic glucose, free fatty acids (FFA), insulin, and glucagon were measured. After 48 h fasting, an intraperitoneal saline injection (NaCl 0.6 g/100 ml) was administered to control fish, whereas the experimental group received 2-DG, dissolved in saline, in the dosage of 80 mg/kg (0.487 mmol/kg) or 150 mg/kg (0.914 mmol/kg) body weight; injection volume was 5 ml in all treatments. Blood and tissue samples were taken immediately before, and 2, 8, 10, and 24 h after administration of the drug or saline. Fish injected with both doses of 2-DG showed a marked increase in glycemia levels. Liver and muscle glycogen decreased after 2-DG administration and reached their lowest values 10-24 h after injection, while in control animals no significant changes were observed. Elevation in plasma glucagon was observed only in response to the maximum dosage of 2-DG administered, especially 10 h and 24 h post-injection. Plasma insulin levels were lower in animals treated with the glucose analogue but only statistically significant 24 h after drug administration. In conclusion, the administration of the non-metabolizable glucose analogue 2-DG in B. cephalus is a stimulus to generate responses towards an increase in the glucose available to tissues, which is a characteristic of a fasting situation. All the above data support the interest of 2-DG administration as a model to study carbohydrate metabolism adjustment mechanisms in fish.

Metabolic changes in Brycon cephalus (Teleostei, Characidae) during post-feeding and fasting

Metabolic changes during the transition from post-feeding to fasting were studied in Brycon cephalus, an omnivorous teleost from the Amazon Basin in Brazil. Body weight and somatic indices (liver and digestive tract), glycogen and glucose content in liver and muscle, as well as plasma glucose, free fatty acids (FFA), insulin and glucagon levels of B. cephalus, were measured at 0, 12, 24, 48, 72, 120, 168 and 336 h after the last feeding. At time 0 h (the moment of food administration, 09.00 h) plasma levels of insulin and glucagon were already high, and relatively high values were maintained until 24 h post-feeding. Glycemia was 6.42 +/- 0.82 mM immediately after food ingestion and 7.53 +/- 1.12 MM at 12 h. Simultaneously, a postprandial replenishment of liver and muscle glycogen reserves was observed. Subsequently, a sharp decrease of plasma insulin occurred, from 7.19 +/- 0.83 ng/ml at 24 h of fasting to 5.27 +/- 0.58 ng/ml at 48 h. This decrease coincided with the drop in liver glucose and liver glycogen, which reached the lowest value at 72 h of fasting (328.56 +/- 192.13 and 70.33 +/- 14.13 mumol/g, respectively). Liver glucose increased after 120 h and reached a peak 168 h post-feeding, which suggests that hepatic gluconeogenesis is occurring. Plasma FFA levels were low after 120 and 168 h and increased again at 336 h of fasting. During the transition from post-feeding to fast condition in B. cephalus, the balance between circulating insulin and glucagon quickly adjust its metabolism to the ingestion or deprivation of food. (C) 2002 Elsevier B.V. All rights reserved.

Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics

Background: Proteinaceous toxins are observed across all levels of inter-organismal and intra-genomic conflicts. These include recently discovered prokaryotic polymorphic toxin systems implicated in intra-specific conflicts. They are characterized by a remarkable diversity of C-terminal toxin domains generated by recombination with standalone toxin-coding cassettes. Prior analysis revealed a striking diversity of nuclease and deaminase domains among the toxin modules. We systematically investigated polymorphic toxin systems using comparative genomics, sequence and structure analysis. Results: Polymorphic toxin systems are distributed across all major bacterial lineages and are delivered by at least eight distinct secretory systems. In addition to type-II, these include type-V, VI, VII (ESX), and the poorly characterized "Photorhabdus virulence cassettes (PVC)", PrsW-dependent and MuF phage-capsid-like systems. We present evidence that trafficking of these toxins is often accompanied by autoproteolytic processing catalyzed by HINT, ZU5, PrsW, caspase-like, papain-like, and a novel metallopeptidase associated with the PVC system. We identified over 150 distinct toxin domains in these systems. These span an extraordinary catalytic spectrum to include 23 distinct clades of peptidases, numerous previously unrecognized versions of nucleases and deaminases, ADP-ribosyltransferases, ADP ribosyl cyclases, RelA/SpoT-like nucleotidyltransferases, glycosyltranferases and other enzymes predicted to modify lipids and carbohydrates, and a pore-forming toxin domain. Several of these toxin domains are shared with host-directed effectors of pathogenic bacteria. Over 90 families of immunity proteins might neutralize anywhere between a single to at least 27 distinct types of toxin domains. In some organisms multiple tandem immunity genes or immunity protein domains are organized into polyimmunity loci or polyimmunity proteins. Gene-neighborhood-analysis of polymorphic toxin systems predicts the presence of novel trafficking-related components, and also the organizational logic that allows toxin diversification through recombination. Domain architecture and protein-length analysis revealed that these toxins might be deployed as secreted factors, through directed injection, or via inter-cellular contact facilitated by filamentous structures formed by RHS/YD, filamentous hemagglutinin and other repeats. Phyletic pattern and life-style analysis indicate that polymorphic toxins and polyimmunity loci participate in cooperative behavior and facultative 'cheating' in several ecosystems such as the human oral cavity and soil. Multiple domains from these systems have also been repeatedly transferred to eukaryotes and their viruses, such as the nucleo-cytoplasmic large DNA viruses. Conclusions: Along with a comprehensive inventory of toxins and immunity proteins, we present several testable predictions regarding active sites and catalytic mechanisms of toxins, their processing and trafficking and their role in intra-specific and inter-specific interactions between bacteria. These systems provide insights regarding the emergence of key systems at different points in eukaryotic evolution, such as ADP ribosylation, interaction of myosin VI with cargo proteins, mediation of apoptosis, hyphal heteroincompatibility, hedgehog signaling, arthropod toxins, cell-cell interaction molecules like teneurins and different signaling messengers.

Revisão sistemática das escalas utilizadas para avaliação funcional na doença de Pompe

OBJETIVO: Identificar as escalas utilizadas para avaliação funcional na doença de Pompe (DP) e descrever seu nível de evidência e recomendação. FONTES DE DADOS: Revisão sistemática sobre as escalas de avaliação funcional na DP. Pesquisa realizada nos bancos de dados Medline, Lilacs, Registro Cochrane de Ensaios Controlados Central (CCTR) e SciELO com artigos (exceto artigos de revisão) publicados entre 2000 e 2010. As palavras-chave utilizadas nos idiomas português e inglês foram: doença de depósito de glicogênio tipo II, atividades cotidianas, avaliação. Os artigos foram classificados em nível de evidência e recomendação. SÍNTESE DOS DADOS: Foram incluídos 14 estudos que avaliaram desde recém-nascidos a adultos (amostra total=449). Foram encontradas as seguintes escalas na literatura: Pediatric Evaluation of Disability Inventory (PEDI) e sua forma adaptada para DP (Pompe-PEDI), Alberta Infant Motor Scale (AIMS), Rotterdam Handiscap Scale (RHS), Functional Independence Measure (FIM), Gross Motor Function Measure (GMFM) e Peabody Developmental Motor Scales (PDMS-II). A maioria dos estudos apresentou nível de evidência III, por serem não randomizados. Grau de recomendação das escalas: C para AIMS e Pompe-PEDI; D para GMFM e PDMS-II; E para RHS e FIM. CONCLUSÕES: A maioria das escalas utilizadas para avaliação funcional na DP apresenta baixo nível de evidência e recomendação. As que apresentam melhor grau de recomendação (C) são as escalas AIMS e Pompe-PEDI aplicadas em Pediatria.

Radio halos in a mass-selected sample of galaxy clusters

A fraction of galaxy clusters host Mpc-scale Radio Halos (RH), generated by ultrarelativistic electrons in the magnetized intra cluster medium (ICM). In the current view they trace turbulent regions in merging clusters, where relativistic particles are trapped and accelerated. This model has clear expectations about the statistical properties of RHs. To test these expectations large mass-selected samples of galaxy clusters with adequate radio and X-ray data are necessary. We used the Planck SZ cluster catalogue as suitable starting point of our investigation, selecting clusters with M500>6x10^14 Msun at 0.08RHs are exclusively found in merging systems.

Laboratory study on the optical properties of absorbing atmospheric aerosols and field applications

The interaction between aerosols and sun light plays an important role in the radiative balance of Earth’s atmosphere. This interaction is obtained by measuring the removal (extinction), redistribution (scattering), and transformation into heat (absorption) of light by the aerosols; i.e. their optical properties. Knowledge of these properties is crucial for our understanding of the atmospheric system. rn Light absorption by aerosols is a major contributor to the direct and indirect effects on our climate system, and an accurate and sensitive measurement method is crucial to further our understanding. A homebuilt photoacoustic sensor (PAS), measuring at a 532nm wavelength, was fully characterized and its functionality validated for measurements of absorbing aerosols. The optical absorption cross-sections of absorbing polystyrene latex spheres, to be used as a standard for aerosol absorption measurements, were measured and compared to literature values. Additionally, a calibration method using absorbing aerosol of known complex refractive index was presented.rn A new approach to retrieve the effective broadband refractive indices (mbroad,eff) of aerosol particles by a white light aerosol spectrometer (WELAS) optical particle counter (OPC) was achieved. Using a tandem differential mobility analyzer (DMA)-OPC system, the nbroad,eff are obtained for both laboratory and field applications. This method was tested in the laboratory using substances with a wide range of optical properties and it was used in ambient measurements to retrieve the nbroad,eff of biomass burning aerosols in a nationwide burning event in Israel. The retrieved effective broadband refractive indices for laboratory generated scattering aerosols were: ammonium sulfate (AS), glutaric acid (GA), and sodium chloride, all within 4% of literature values. For absorbing substances, nigrosine and various mixtures of nigrosine with AS and GA were measured, as well as a lightly absorbing substance, Suwannee river fulvic acid (SRFA). For the ambient measurements, the calibration curves generated from this method were to follow the optical evolution of biomass burning (BB) aerosols. A decrease in the overall aerosol absorption and scattering for aged aerosols during the day after the fires compared to the smoldering phase of the fires was found. rn The connection between light extinction of aerosols, their chemical composition and hygroscopicity for particles with different degrees of absorption was studied. The extinction cross-section (σext) at 532nm for different mobility diameters was measured at 80% and 90% relative humidity (RH), and at an RH<10%. The ratio of the humidified aerosols to the dry ones, fRHext(%RH,Dry), is presented. For purely scattering aerosols, fRHext(%RH,Dry) is inversely proportional with size; this dependence was suppressed for lightly absorbing ones. In addition, the validity of the mixing rules for water soluble absorbing aerosols is explored. The difference between the derived and calculated real parts of the complex RIs were less than 5.3% for all substances, wavelengths, and RHs. The obtained imaginary parts for the retrieved and calculated RIs were in good agreement with each other, and well within the measurement errors of retrieval from pulsed CRD spectroscopy measurements. Finally, a core-shell structure model is also used to explore the differences between the models, for substances with low growth factors, under these hydration conditions. It was found that at 80% RH and for size parameters less than 2.5, there is less than a 5 % difference between the extinction efficiencies calculated with both models. This difference is within measurement errors; hence, there is no significant difference between the models in this case. However, for greater size parameters the difference can be up to 10%. For 90% RH the differences below a size parameter of 2.5 were up to 7%.rn Finally, the fully characterized PAS together with a cavity ring down spectrometer (CRD), were used to study the optical properties of soot and secondary organic aerosol (SOA) during the SOOT-11 project in the AIDA chamber in Karlsruhe, Germany. The fresh fractal-like soot particles were allowed to coagulate for 28 hours before stepwise coating them with SOA. The single scattering albedo for fresh fractal-like soot was measured to be 0.2 (±0.03), and after allowing the soot to coagulate for 28 hours and coating it with SOA, it increased to 0.71(±0.01). An absorption enhancement of the coated soot of up to 1.71 (±0.03) times from the non-coated coagulated soot was directly measured with the PAS. Monodisperse measurements of SOA and soot coated with SOA were performed to derive the complex refractive index (m) of both aerosols. A complex refractive index of m = 1.471(±0.008) + i0.0(±0.002) for the SOA-αO3 was retrieved. For the compact coagulated soot a preliminary complex refractive index of m = 2.04(+0.21/-0.14) + i0.34(+0.18/-0.06) with 10nm(+4/-6) coating thickness was retrieved.rn These detail properties can be use by modelers to decrease uncertainties in assessing climatic impacts of the different species and to improve weather forecasting.rn