Focus: A Multifaceted Battle Against Cancer: Extracting Knowledge from Chemical Imaging Data Using Computational Algorithms for Digital Cancer Diagnosis

Fourier transform infrared (FTIR) spectroscopic imaging is an emerging microscopy modality for clinical histopathologic diagnoses as well as for biomedical research. Spectral data recorded in this modality are indicative of the underlying, spatially resolved biochemical composition but need computerized algorithms to digitally recognize and transform this information to a diagnostic tool to identify cancer or other physiologic conditions. Statistical pattern recognition forms the backbone of these recognition protocols and can be used for highly accurate results. Aided by biochemical correlations with normal and diseased states and the power of modern computer-aided pattern recognition, this approach is capable of combating many standing questions of traditional histology-based diagnosis models. For example, a simple diagnostic test can be developed to determine cell types in tissue. As a more advanced application, IR spectral data can be integrated with patient information to predict risk of cancer, providing a potential road to precision medicine and personalized care in cancer treatment. The IR imaging approach can be implemented to complement conventional diagnoses, as the samples remain unperturbed and are not destroyed. Despite high potential and utility of this approach, clinical implementation has not yet been achieved due to practical hurdles like speed of data acquisition and lack of optimized computational procedures for extracting clinically actionable information rapidly. The latter problem has been addressed by developing highly efficient ways to process IR imaging data but remains one that has considerable scope for progress. Here, we summarize the major issues and provide practical considerations in implementing a modified Bayesian classification protocol for digital molecular pathology. We hope to familiarize readers with analysis methods in IR imaging data and enable researchers to develop methods that can lead to the use of this promising technique for digital diagnosis of cancer.     

Functional classifications of coastal barrier island vegetation

Abstract. Due to the complexity of coastal barrier vegetation, it is useful to apply a functional-type approach to assess the response of barrier island vegetation to climate change. In this paper, a simple clustering analysis is applied to a group of 19 plant associations, based on six plant attributes and six environmental constraints. This analysis results in the suggestion that the main division of the vegetation types at Virginia Coast Reserve is between herbaceous and woody types, which differs from the existing classification which recognizes three groups: xeric-mesic herbaceous, woody and hydric-halophytic herbaceous. Considerations about grouping plant functional types are also addressed in this paper. At a global scale, inclusion of barrier plant functional types may not be so important for the climate-change response of vegetation, but it may be necessary to consider these important systems for spatially explicit modelling of landscape responses.     

Morphological and morphometrical analysis of Heterodera spp. populations in Jordan

Phenotypic diversity of five Jordanian populations of cyst nematodes, Heterodera spp. collected from five regions from Jordan (Ar-Ramtha, Madaba, Dana, Al-Karak, and Jerash) was investigated. Soil samples were collected from one representative field in each region. Morphological and morphometrical characteristics revealed that Heterodera latipons is dominated in cereal fields at Ar-Ramtha, Madaba, Dana and Al-Karak regions and Heterodera schachtii in Jerash. Cysts populations from all cereal fields had bifenestrate vulval cone and a strong underbridge. Wherever, cysts of the cabbage population had ambifenestrate vulval cone with long vulval slit. The bullae were absent in Ar-Ramtha, Madaba and Dana populations, but present in Al-Karak and Jerash. Based on 12 morphometrical characters, the first three functions in canonical discriminant analysis accounted 99.3% of the total variation. Distance from dorsal gland duct opening to stylet base, underbridge length, a = L/W (body length/midbody width) and length of hyaline tail tip had strong and significant contributions in the first function. While the second function was strongly influenced by length of hyaline tail, fenestral length, fenestral width and tail length. However, the third canonical discriminate function was found to be influenced by stylet length, fenestral length, a = L/W (body length/midbody width) and underbridge width. The graphical representation of the distribution of the samples showed that the first canonical discriminant function clearly separated H. schachtii from Jerash from other populations. Whereas, H. latipons collected from Madaba and Dana were clearly separated in the second function. The results indicated that differences at morphological and morphometrical levels revealed diverse populations of Heterodera spp. in Jordan.     

EMAP-Wetlands: A sampling design with global application

The U.S. Environmental Protection Agency (EPA) initiated the Environmental Monitoring and Assessment Program (EMAP) in 1988. The wetland component (EMAP-Wetlands) is designed to provide quantitative assessments of the current status and long-term trends in the ecological condition of wetland resources. EMAP-Wetlands will develop a wetland monitoring network and will identify and evaluate indicators that describe and quantify wetland condition. The EMAP-Wetlands network will represent a probability sample of the total wetland resource. The EMAP sample is based on a triangular grid of approximately 12,600 sample points in the conterminous U.S. The triangular grid adequately samples wetland resources that are common and uniformly distributed in a region, such as the prairie pothole wetlands of the Midwest. However, the design is flexible and allows the base grid density to be increased to adequately sample wetland resources, such as the coastal wetlands of the Gulf of Mexico, which are distributed linearly along the coast. The Gulf sample network required a 49-fold increase in base grid density. EMAP-Wetlands aggregates the 56 U.S. Fish and Wildlife Service's (FWS) National Wetland Inventory (NWI) categories (Cowardin et al. 1979) into 12 functionally similar groups (Leibowitz et al. 1991). Both the EMAP sample design and aggregated wetland classes are suitable for global inventory and assessment of wetlands.The research described in this report has been funded by the U.S. Environmental Protection Agency. This document has been prepared at the EPA Environmental Research Laboratory in Corvallis, OR, through contract No. 68-C8-0006 to Man Tech Environmental Technology, Inc. This paper has been subjected to the Agency's peer and administrative review and approved for publication. Mention of trade names or commercial products does not constitute endorsement or recommendation for use.     

Genomic factors responsible for abnormal morphology of pollen tubes in the interspecific cross Nicotiana tabacum ×N. rustica

Nicotiana tabacum shows unilateral pollen-pistil incongruity with N. rustica. If N. tabacum is pollinated with N. rustica, growth of the pollen tube is arrested in the middle of the style, and abundant callose deposition, tube swelling and tube winding are observed. An attempt was made to clarify the genomic factors responsible for this pollen-pistil incongruity. N. tabacum was pollinated with N. paniculata or N. undulata, progenitors of amphidiploid N. rustica. When pollinated with N. undulata, growth of the pollen tube was arrested in the middle of the style and showed abnormal morphology similar to that with N. rustica, but when pollinated with N. paniculata the pollen tube reached near the base of the style and was almost normal in appearance. These observations suggest that the factors responsible for the pollen tube abnormality of N. rustica are derived from the N. undulata genome.We also used N. sylvestris, N. glutinosa and N. otophora as pistilar parents and N. rustica or its progenitors as pollen parents to examine the genomic factors of the pistilate parents. The pollen tube features of these three species in the pistils of N. sylvestris were similar to those in the pistil of N. tabacum. Received: 25 October 1999 / Revision accepted: 2 February 2000     

On the diploidization mechanism of the genus Aegilops: meiotic behaviour of interspecific hybrids

Chromosomal pairing of the three diploid hybrids Aegilops uniaristata × Ae. tauschii (ND), Ae. umbellulata × Ae. tauschii (UD) and Ae. comosa × Ae. uniaristata (MN), and a triploid hybrid Ae. cylindrica × Ae. caudata (DCC), was analyzed by electron microscopy in surface-spread-prophase-I nuclei and compared with light-microscopic observations of metaphase-I cells after C-banding and fluorescence in situhybridization. All hybrids showed extensive synapsis and complex multivalents in which up to 14 chromosomes were involved. In the diploid hybrids most metaphase-I chromosomal associations were between homoeologs, their frequencies being dependent on the relationship between the donor genomes. Despite the different overall bound-arm frequencies displayed by ND and MN hybrids at metaphase-I, chromosomes bearing rDNA sequences showed similar mean cell chromosomal association frequencies. In the triploid hybrid preferential associations involving C genomes were predominant. These observations are discussed in relation to the mechanism of diploidization showed by allotetraploid Aegilops species. Received: 13 January 1999 / Accepted: 12 March 1999     

Interspecific competition between two species of the bean weevil

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Contributions from the Entomological Laboratory, Kyoto University, No. 110.     

Analysis of Profiles Based on Ordinal Classification Functions and Rank Tests

In this article a test for the comparison of K groups of independent profiles is suggested. It is based on rank tests, in which the criterion is obtained by using a suitably chosen ordinal classification function. This function represents a specific view on the profiles. The test, which is easy to use, can be regarded as a generalisation of other well known tests and can be applied within a variety of situations. The relationships to other procedures for the analysis of profiles are described. Some properties are discussed.     

Novel summary metrics for insular biotic assemblages based on taxonomy and phylogeny: Biogeographical,palaeogeographical and possible conservational applications

Using the land‐bound vertebrates on the marine islands as model organisms, two metrics are presented that permit quantitative and succinct synopses of the ‘evolutionary maturity’ of the hosted faunal assemblages. In turn, these reflect the geo‐physical settings and geological developments of the substrates. The assemblage lineage‐taxonomy spectrum (ALTS) is based on the constituent lineages’ taxonomic distinctiveness and diversity. Individual lineages within assemblages can in most cases be assigned to one of six categories, LT1?LT6: LT1 is a non‐endemic taxon, whereas LT6 comprises multiple endemic genera from a family that arose elsewhere. If required, the scheme can be expanded: LT9 is an endemic order. The data can then be combined to provide an assemblage spectrum, for example, 00:08:38:30:08:15[ 13 ]. Here, the first six values denote the number of lineages assigned to each category expressed as percentages of the overall total, with the sum of the processed lineages listed as the seventh (in brackets and bold). The ALTS metric highlights efficiently the key features of a marine island's biological assemblage. Notably, the contrast between spectra for suites on geologically and geo‐physically varied island types can be striking, for instance the squamate suite on the young, proximate orogenic margin island of Taiwan is coded 78:16:05:00:00:00[ 37 ] whereas the one on the distantly located, Late Eocene composite terrane island of New Caledonia is 00:11:00:11:33:44[ 9 ]. To overcome the subjectivity that is inherent in assigning supraspecific ranks, an alternative assemblage lineage‐age spectrum (ALAS) is also introduced that makes use of the binary logarithm values of the colonization times of the island lineages (0–2, 2–4, … , 32–64, >64 Ma). It is represented using a seven‐plus‐two‐number code, for instance Madagascar's squamates are 00:06:00:00:19:62:12[ 19 ( 16 )]; most colonizations took place in the Palaeogene (66–23 Ma); there are 19 lineages, but only 16 are presently age‐dated. In addition to marine‐island biogeography studies, the ALTS–ALAS spectrum approach is potentially useful for encapsulating biotas in other sorts of insular setting (e.g. lakes, mountain tops), and for evaluating palaeogeographical models. Furthermore, it may help emphasize the conservation value of an island's faunal assemblage.     

Typologie des rivières oligotrophes du massif Ardennais (Belgique) par l'analyse multivariée de relevés de diatomées benthiques

Typology of oligotrophic streams of the Ardenne (Belgium) by multivariate analysis of benthic diatoms records.During three years, samples of water and algae has been taken in 72 stations distributed on the river system of the northern part of the Ardennes. 357 taxa of diatoms have been identified. Principal component analysis and cluster analysis, applied to diatoms counts, allowed to classify the records in a table comparable to phytosociological tables. A continuum in the data is an indication of the progressive modification of the communities according to the physico-chemical characteristics of the water. Ten diatoms assemblages have been described and this typology has been compared to some algal associations defined in the literature. In natural environments, these 10 assemblages are strictly correlated with the nature of the geological substrate and the physico-chemical characteristics of the water. The sensibility of the oligotrophic streams is revealed by the speedy changes in the communities after following a small modification of the environmental factors (seasonal variations or light eutrophication).

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Typologie des rivières oligotrophes du massif Ardennais (Belgique) par l'analyse multivariée de relevés de diatomées benthiques