The Köppen climate classification as a diagnostic tool for general circulation models

Koppen climate classification was applied to the output of atmospheric general circulation models and coupled atmosphere-ocean circulation models. The classification was used to validate model control runs of the present climate and to analyse greenhouse gas warming simulations The most prominent results of the global warming con~putationsw ere a retreat of regions of permafrost and the increase of areas with tropical rainy climates and dry climates.

Evaluation of diagnostic molecular markers for DUS phenotypic assessment in the cereal crop, barley (Hordeum vulgare ssp. vulgare L.)

The deployment of genetic markers is of interest in crop assessment and breeding programmes, due to the potential savings in cost and time afforded. As part of the internationally recognised framework for the awarding of Plant Breeders’ Rights (PBR), new barley variety submissions are evaluated using a suite of morphological traits to ensure they are distinct, uniform and stable (DUS) in comparison to all previous submissions. Increasing knowledge of the genetic control of many of these traits provides the opportunity to assess the potential of deploying diagnostic/perfect genetic markers in place of phenotypic assessment. Here, we identify a suite of 25 genetic markers assaying for 14 DUS traits, and implement them using a single genotyping platform (KASPar). Using a panel of 169 UK barley varieties, we show that phenotypic state at three of these traits can be perfectly predicted by genotype. Predictive values for an additional nine traits ranged from 81 to 99 %. Finally, by comparison of varietal discrimination based on phenotype and genotype resulted in correlation of 0.72, indicating that deployment of molecular markers for varietal discrimination could be feasible in the near future. Due to the flexibility of the genotyping platform used, the genetic markers described here can be used in any number or combination, in-house or by outsourcing, allowing flexible deployment by users. These markers are likely to find application where tracking of specific alleles is required in breeding programmes, or for potential use within national assessment programmes for the awarding of PBRs.

PCR-based markers diagnostic for spring and winter seasonal growth habit in barley

Toward the ultimate goal of replacing field-based evaluation of seasonal growth habit, we describe the design and validation of a multiplex polymerase chain reaction assay diagnostic for allelic status at the barley (Hordeum vulgare ssp. vulgare L.) vernalization locus, VRN-H1 By assaying for the presence of all known insertion–deletion polymorphisms thought to be responsible for the difference between spring and winter alleles, this assay directly tests for the presence of functional polymorphism at VRN-H1 Four of the nine previously recognized VRN-H1 haplotypes (including both winter alleles) give unique profiles using this assay. The remaining five spring haplotypes share a single profile, indicative of function-altering deletions spanning, or adjacent to, the putative “vernalization critical” region of intron 1. When used in conjunction with a previously published PCR-based assay diagnostic for alleles at VRN-H2, it was possible to predict growth habit in all the 100 contemporary UK spring and winter lines analyzed in this study. This assay is likely to find application in instances when seasonal growth habit needs to be determined without the time and cost of phenotypic assessment and during marker-assisted selection using conventional and multicross population analysis.

Gene expression changes in phosphorus deficient potato (Solanum tuberosum L.) leaves and the potential for diagnostic gene expression markers

Background: There are compelling economic and environmental reasons to reduce our reliance on inorganic phosphate (Pi) fertilisers. Better management of Pi fertiliser applications is one option to improve the efficiency of Pi fertiliser use, whilst maintaining crop yields. Application rates of Pi fertilisers are traditionally determined from analyses of soil or plant tissues. Alternatively, diagnostic genes with altered expression under Pi limiting conditions that suggest a physiological requirement for Pi fertilisation, could be used to manage Pifertiliser applications, and might be more precise than indirect measurements of soil or tissue samples. Results: We grew potato (Solanum tuberosum L.) plants hydroponically, under glasshouse conditions, to control their nutrient status accurately. Samples of total leaf RNA taken periodically after Pi was removed from the nutrient solution were labelled and hybridised to potato oligonucleotide arrays. A total of 1,659 genes were significantly differentially expressed following Pi withdrawal. These included genes that encode proteins involved in lipid, protein, and carbohydrate metabolism, characteristic of Pi deficient leaves and included potential novel roles for genes encoding patatin like proteins in potatoes. The array data were analysed using a support vector machine algorithm to identify groups of genes that could predict the Pi status of the crop. These groups of diagnostic genes were tested using field grown potatoes that had either been fertilised or unfertilised. A group of 200 genes could correctly predict the Pi status of field grown potatoes. Conclusions: This paper provides a proof-of-concept demonstration for using microarrays and class prediction tools to predict the Pi status of a field grown potato crop. There is potential to develop this technology for other biotic and abiotic stresses in field grown crops. Ultimately, a better understanding of crop stresses may improve our management of the crop, improving the sustainability of agriculture.

Northern Hemisphere atmospheric blocking as simulated by 15 atmospheric general circulation models in the period 1979-1988 (Results from an AMIP diagnostic subproject)

As a part of the Atmospheric Model Intercomparison Project (AMIP), the behaviour of 15 general circulation models has been analysed in order to diagnose and compare the ability of the different models in simulating Northern Hemisphere midlatitude atmospheric blocking. In accordance with the established AMIP procedure, the 10-year model integrations were performed using prescribed, time-evolving monthly mean observed SSTs spanning the period January 1979–December 1988. Atmospheric observational data (ECMWF analyses) over the same period have been also used to verify the models results. The models involved in this comparison represent a wide spectrum of model complexity, with different horizontal and vertical resolution, numerical techniques and physical parametrizations, and exhibit large differences in blocking behaviour. Nevertheless, a few common features can be found, such as the general tendency to underestimate both blocking frequency and the average duration of blocks. The problem of the possible relationship between model blocking and model systematic errors has also been assessed, although without resorting to ad-hoc numerical experimentation it is impossible to relate with certainty particular model deficiencies in representing blocking to precise parts of the model formulation.

An environmental uncertainty-based diagnostic reference tool for evaluating the performance of supply chain value streams

This research has responded to the need for diagnostic reference tools explicitly linking the influence of environmental uncertainty and performance within the supply chain. Uncertainty is a key factor influencing performance and an important measure of the operating environment. We develop and demonstrate a novel reference methodology based on data envelopment analysis (DEA) for examining the performance of value streams within the supply chain with specific reference to the level of environmental uncertainty they face. In this paper, using real industrial data, 20 product supply value streams within the European automotive industry sector are evaluated. Two are found to be efficient. The peer reference groups for the underperforming value streams are identified and numerical improvement targets are derived. The paper demonstrates how DEA can be used to guide supply chain improvement efforts through role-model identification and target setting, in a way that recognises the multiple dimensions/outcomes of the supply chain process and the influence of its environmental conditions. We have facilitated the contextualisation of environmental uncertainty and its incorporation into a specific diagnostic reference tool.

Translation and usability of autism screening and diagnostic tools for autism spectrum conditions in India

There is a critical need for screening and diagnostic tools (SDT) for autism spectrum conditions (ASC) in regional languages in South Asia. To address this, we translated four widely used SDT (Social Communication Disorder Checklist, Autism Spectrum Quotient, Social Communication Questionnaire, and Autism Diagnostic Observation Schedule) into Bengali and Hindi, two main regional languages (∼ 360 million speakers), and tested their usability in children with and without ASC. We found a significant difference in scores between children with ASC (n = 45 in Bengali, n = 40 in Hindi) and typically developing children (n = 43 in Bengali, n = 42 in Hindi) on all SDTs. These results demonstrate that these SDTs are usable in South Asia, and constitute an important resource for epidemiology research and clinical diagnosis in the region.

Diagnostic tool to analyse colour-magnitude diagrams of poorly populated stellar concentrations

The dynamical processes that lead to open cluster disruption cause its mass to decrease. To investigate such processes from the observational point of view, it is important to identify open cluster remnants (OCRs), which are intrinsically poorly populated. Due to their nature, distinguishing them from field star fluctuations is still an unresolved issue. In this work, we developed a statistical diagnostic tool to distinguish poorly populated star concentrations from background field fluctuations. We use 2MASS photometry to explore one of the conditions required for a stellar group to be a physical group: to produce distinct sequences in a colour-magnitude diagram (CMD). We use automated tools to (i) derive the limiting radius; (ii) decontaminate the field and assign membership probabilities; (iii) fit isochrones; and (iv) compare object and field CMDs, considering the isochrone solution, in order to verify the similarity. If the object cannot be statistically considered as a field fluctuation, we derive its probable age, distance modulus, reddening and uncertainties in a self-consistent way. As a test, we apply the tool to open clusters and comparison fields. Finally, we study the OCR candidates DoDz 6, NGC 272, ESO 435 SC48 and ESO 325 SC15. The tool is optimized to treat these low-statistic objects and to separate the best OCR candidates for studies on kinematics and chemical composition. The study of the possible OCRs will certainly provide a deep understanding of OCR properties and constraints for theoretical models, including insights into the evolution of open clusters and dissolution rates.

Alternative diagnostic diagrams and the `forgotten` population of weak line galaxies in the SDSS

A numerous population of weak line galaxies (WLGs) is often left out of statistical studies on emission-line galaxies (ELGs) due to the absence of an adequate classification scheme, since classical diagnostic diagrams, such as [O iii]/H beta versus [N ii]/H alpha (the BPT diagram), require the measurement of at least four emission lines. This paper aims to remedy this situation by transposing the usual divisory lines between star-forming (SF) galaxies and active galactic nuclei (AGN) hosts and between Seyferts and LINERs to diagrams that are more economical in terms of line quality requirements. By doing this, we rescue from the classification limbo a substantial number of sources and modify the global census of ELGs. More specifically, (1) we use the Sloan Digital Sky Survey Data Release 7 to constitute a suitable sample of 280 000 ELGs, one-third of which are WLGs. (2) Galaxies with strong emission lines are classified using the widely applied criteria of Kewley et al., Kauffmann et al. and Stasinska et al. to distinguish SF galaxies and AGN hosts and Kewley et al. to distinguish Seyferts from LINERs. (3) We transpose these classification schemes to alternative diagrams keeping [N ii]/H alpha as a horizontal axis, but replacing H beta by a stronger line (H alpha or [O ii]), or substituting the ionization-level sensitive [O iii]/H beta ratio with the equivalent width of H alpha (W(H alpha)). Optimized equations for the transposed divisory lines are provided. (4) We show that nothing significant is lost in the translation, but that the new diagrams allow one to classify up to 50 per cent more ELGs. (5) Introducing WLGs in the census of galaxies in the local Universe increases the proportion of metal-rich SF galaxies and especially LINERs. In the course of this analysis, we were led to make the following points. (i) The Kewley et al. BPT line for galaxy classification is generally ill-used. (ii) Replacing [O iii]/H beta by W(H alpha) in the classification introduces a change in the philosophy of the distinction between LINERs and Seyferts, but not in its results. Because the W(H alpha) versus [N ii]/H alpha diagram can be applied to the largest sample of ELGs without loss of discriminating power between Seyferts and LINERs, we recommend its use in further studies. (iii) The dichotomy between Seyferts and LINERs is washed out by WLGs in the BPT plane, but it subsists in other diagnostic diagrams. This suggests that the right wing in the BPT diagram is indeed populated by at least two classes, tentatively identified with bona fide AGN and `retired` galaxies that have stopped forming stars and are ionized by their old stellar populations.

Consensus Statement: Chromosomal Microarray Is a First-Tier Clinical Diagnostic Test for Individuals with Developmental Disabilities or Congenital Anomalies

Chromosomal microarray (CMA) is increasingly utilized for genetic testing of individuals with unexplained developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), or multiple congenital anomalies (MCA). Performing CMA and G-banded karyotyping on every patient substantially increases the total cost of genetic testing. The International Standard Cytogenomic Array (ISCA) Consortium held two international workshops and conducted a literature review of 33 studies, including 21,698 patients tested by CMA. We provide an evidence-based summary of clinical cytogenetic testing comparing CMA to G-banded karyotyping with respect to technical advantages and limitations, diagnostic yield for various types of chromosomal aberrations, and issues that affect test interpretation. CMA offers a much higher diagnostic yield (15%-20%) for genetic testing of individuals with unexplained DD/ID, ASD, or MCA than a G-banded karyotype (similar to 3%, excluding Down syndrome and other recognizable chromosomal syndromes), primarily because of its higher sensitivity for submicroscopic deletions and duplications. Truly balanced rearrangements and low-level mosaicism are generally not detectable by arrays, but these are relatively infrequent causes of abnormal phenotypes in this population (<1%). Available evidence strongly supports the use of CMA in place of G-banded karyotyping as the first-tier cytogenetic diagnostic test for patients with DD/ID, ASD, or MCA. G-banded karyotype analysis should be reserved for patients with obvious chromosomal syndromes (e.g., Down syndrome), a family history of chromosomal rearrangement, or a history of multiple miscarriages.

Genotoxic effects of X-rays on keratinized mucosa cells during panoramic dental radiography

Objectives: The aim of this study was to evaluate the genotoxic effects of X-rays on epithelial gingival cells during panoramic dental radiography using a differentiated protocol for the micronucleus test. Methods: 40 healthy individuals who underwent this procedure for diagnostic purposes on request from their dentists agreed to participate in this study. All of them answered a questionnaire before the examination. Epithelial gingival cells were obtained from the keratinized mucosa of the upper dental arcade by gentle scraping with a cervical brush immediately before exposure and 10 days later. Cytological preparations were stained according to the Feulgen-Rossenbeck reaction, counterstained with fast green 1% for 1 min and analysed under a light microscope. Micronuclei, nuclear projections (broken eggs) and degenerative nuclear alterations (pyknosis, karyolysis, karyorrhexis and condensed chromatin) were scored. Results: The frequency of micronuclei was significantly higher after exposure (P < 0.05), as were frequencies of nuclear alterations indicate of apoptosis (P < 0.001). Conclusions: These results indicate that X-ray radiation emitted during panoramic dental radiography induces a genotoxic effect on epithelial gingival cells that increases the frequency of chromosomal damage and nuclear alterations indicative of apoptosis.

Cathepsin L-like genes of Trypanosoma vivax from Africa and South America - characterization, relationships and diagnostic implications

We characterized sequences from genes encoding cathepsin L-like (CatL-like) cysteine proteases from African and South American isolates of Trypanosoma vivax and T. vivax-like organisms, and evaluated their suitability as genetic markers for population structure analysis and diagnosis. Phylogenetic analysis of sequences corresponding to CatL-like catalytic domains revealed substantial polymorphism, and clades of sequences (TviCatL1-9) were separated by large genetic distances. TviCatL1-4 sequences were from cattle isolates from West Africa (Nigeria and Burkina Faso) and South America (Brazil and Venezuela), which belonged to the same T. vivax genotype. T. vivax-like genotypes from East Africa showed divergent sequences, including TviCatL5-7 for isolates from Mozambique and TviCatL8-9 for an isolate from Kenya. Phylogenetic analysis of CatL-like gene data supported the relationships among trypanosome species reflected in the phylogenies based on the analysis of small subunit (SSU) of ribosomal RNA gene sequence data. The discovery of different CatL-like sequences for each genotype, defined previously by ribosomal DNA data, indicate that these sequences provide useful targets for epidemiological and population genetic studies. Regions in CatL-like sequences shared by all T. vivax genotypes but not by other trypanosomes allowed the establishment of a specific and sensitive diagnostic PCR for epidemiological studies in South America and Africa. (C) 2008 Elsevier Ltd. All rights reserved.

The monoclonal antibody against the major diagnostic antigen of Paracoccidioides brasiliensis mediates immune protection in infected BALB/c mice challenged intratracheally with the fungus

The protective role of specific antibodies against Paracoccidioides brasiliensis is controversial. In the present study, we analyzed the effects of monoclonal antibodies on the major diagnostic antigen (gp43) using in vitro and in vivo P. brasiliensis infection models. The passive administration of some monoclonal antibodies (MAbs) before and after intratracheal or intravenous infections led to a reduced fungal burden and decreased pulmonary inflammation. The protection mediated by MAb 3E, the most efficient MAb in the reduction of fungal burden, was associated with the enhanced phagocytosis of P. brasiliensis yeast cells by J774.16, MH-S, or primary macrophages. The ingestion of opsonized yeast cells led to an increase in NO production by macrophages. Passive immunization with MAb 3E induced enhanced levels of gamma interferon in the lungs of infected mice. The reactivity of MAb 3E against a panel of gp43-derived peptides suggested that the sequence NHVRIPIGWAV contains the binding epitope. The present work shows that some but not all MAbs against gp43 can reduce the fungal burden and identifies a new peptide candidate for vaccine development.