Current Classification Schemes Research Articles

Species diversity and phylogeny of fleas of small terrestrial mammals in the forests of the Central Highlands of Madagascar.

Fleas are holometabolous insects forming the order of Siphonaptera. Some studies have been carried out on biology and systematic of Malagasy fleas, but little is known about their phylogenetic relationships. In this study, we focused on flea species occurring in the forests of the Central Highlands and also, on the determination of their phylogenetic relationships. Three families, five genera and thirteen species were identified. The family Pulicidae includes four species (Centetipsylla madagascariensis Rothschild, Synopsyllus fonquerniei Wagner Roubaud, S. estradei Klein and S. robici Klein); Leptopsyllidae has eight species (Paractenopsyllus vauceli Klein, P. petiti Klein, P. viettei Klein, P. grandidieri Klein, P. goodmani Duchemin, P. rouxi Duchemin, P. raxworthyi Duchemin Ratovonjato and Tsaractenus rodhaini Duchemin), and Ctenophtalmidae one species (Dinopsyllus brachypecten Smit). All are endemic to Madagascar and each differs geographically. Flea phylogenetic relationships were inferred using four molecular markers (ITS2, mtCOII, 16SrRNA and 12S rRNA) and using Neighbor-Joining, Maximum Parsimony and Bayesian methods with addition of Genbank sequences of exotic species. The Family Pulicidae was monophyletic while the families Leptopsyllidae and Ctenophtalmidae were paraphyletic. Malagasy fleas are homogeneous and all species adhere to current classification schemes.

Rates of Amyloid Imaging Positivity in Patients With Primary Progressive Aphasia

The ability to predict the pathology underlying different neurodegenerative syndromes is of critical importance owing to the advent of molecule-specific therapies. To determine the rates of positron emission tomography (PET) amyloid positivity in the main clinical variants of primary progressive aphasia (PPA). This prospective clinical-pathologic case series was conducted at a tertiary research clinic specialized in cognitive disorders. Patients were evaluated as part of a prospective, longitudinal research study between January 2002 and December 2015. Inclusion criteria included clinical diagnosis of PPA; availability of complete speech, language, and cognitive testing; magnetic resonance imaging performed within 6 months of the cognitive evaluation; and PET carbon 11-labeled Pittsburgh Compound-B or florbetapir F 18 brain scan results. Of 109 patients referred for evaluation of language symptoms who underwent amyloid brain imaging, 3 were excluded because of incomplete language evaluations, 5 for absence of significant aphasia, and 12 for presenting with significant initial symptoms outside of the language domain, leaving a cohort of 89 patients with PPA. Clinical, cognitive, neuroimaging, and pathology results. Twenty-eight cases were classified as imaging-supported semantic variant PPA (11 women [39.3%]; mean [SD] age, 64 [7] years), 31 nonfluent/agrammatic variant PPA (22 women [71.0%]; mean [SD] age, 68 [7] years), 26 logopenic variant PPA (17 women [65.4%]; mean [SD] age, 63 [8] years), and 4 mixed PPA cases. Twenty-four of 28 patients with semantic variant PPA (86%) and 28 of 31 patients with nonfluent/agrammatic variant PPA (90%) had negative amyloid PET scan results, while 25 of 26 patients with logopenic variant PPA (96%) and 3 of 4 mixed PPA cases (75%) had positive scan results. The amyloid positive semantic variant PPA and nonfluent/agrammatic variant PPA cases with available autopsy data (2 of 4 and 2 of 3, respectively) all had a primary frontotemporal lobar degeneration and secondary Alzheimer disease pathologic diagnoses, whereas autopsy of 2 patients with amyloid PET-positive logopenic variant PPA confirmed Alzheimer disease. One mixed PPA patient with a negative amyloid PET scan had Pick disease at autopsy. Primary progressive aphasia variant diagnosis according to the current classification scheme is associated with Alzheimer disease biomarker status, with the logopenic variant being associated with carbon 11-labeled Pittsburgh Compound-B positivity in more than 95% of cases. Furthermore, in the presence of a clinical syndrome highly predictive of frontotemporal lobar degeneration pathology, biomarker positivity for Alzheimer disease may be associated more with mixed pathology rather than primary Alzheimer disease.

Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation.

β-lactamases, the enzymes responsible for resistance to β-lactam antibiotics, are widespread among prokaryotic genera. However, current β-lactamase classification schemes do not represent their present diversity. Here, we propose a workflow to identify and classify β-lactamases. Initially, a set of curated sequences was used as a model for the construction of profiles Hidden Markov Models (HMM), specific for each β-lactamase class. An extensive, nonredundant set of β-lactamase sequences was constructed from 7 different resistance proteins databases to test the methodology. The profiles HMM were improved for their specificity and sensitivity and then applied to fully assembled genomes. Five hierarchical classification levels are described, and a new class of β-lactamases with fused domains is proposed. Our profiles HMM provide a better annotation of β-lactamases, with classes and subclasses defined by objective criteria such as sequence similarity. This classification offers a solid base to the elaboration of studies on the diversity, dispersion, prevalence, and evolution of the different classes and subclasses of this critical enzymatic activity.

Classifying aerosol type using in situ surface spectral aerosol optical properties

Abstract. Knowledge of aerosol size and composition is important for determining radiative forcing effects of aerosols, identifying aerosol sources and improving aerosol satellite retrieval algorithms. The ability to extrapolate aerosol size and composition, or type, from intensive aerosol optical properties can help expand the current knowledge of spatiotemporal variability in aerosol type globally, particularly where chemical composition measurements do not exist concurrently with optical property measurements. This study uses medians of the scattering Ångström exponent (SAE), absorption Ångström exponent (AAE) and single scattering albedo (SSA) from 24 stations within the NOAA/ESRL Federated Aerosol Monitoring Network to infer aerosol type using previously published aerosol classification schemes.Three methods are implemented to obtain a best estimate of dominant aerosol type at each station using aerosol optical properties. The first method plots station medians into an AAE vs. SAE plot space, so that a unique combination of intensive properties corresponds with an aerosol type. The second typing method expands on the first by introducing a multivariate cluster analysis, which aims to group stations with similar optical characteristics and thus similar dominant aerosol type. The third and final classification method pairs 3-day backward air mass trajectories with median aerosol optical properties to explore the relationship between trajectory origin (proxy for likely aerosol type) and aerosol intensive parameters, while allowing for multiple dominant aerosol types at each station.The three aerosol classification methods have some common, and thus robust, results. In general, estimating dominant aerosol type using optical properties is best suited for site locations with a stable and homogenous aerosol population, particularly continental polluted (carbonaceous aerosol), marine polluted (carbonaceous aerosol mixed with sea salt) and continental dust/biomass sites (dust and carbonaceous aerosol); however, current classification schemes perform poorly when predicting dominant aerosol type at remote marine and Arctic sites and at stations with more complex locations and topography where variable aerosol populations are not well represented by median optical properties. Although the aerosol classification methods presented here provide new ways to reduce ambiguity in typing schemes, there is more work needed to find aerosol typing methods that are useful for a larger range of geographic locations and aerosol populations.

A distinct clinicopathological variant of focal cortical dysplasia IIId characterized by loss of layer 4 in the occipital lobe in 12 children with remote hypoxic-ischemic injury.

In 2011, the International League Against Epilepsy (ILAE) proposed a consensus classification system of focal cortical dysplasia (FCD) to distinguish clinicopathological subtypes, for example, "isolated" FCD type Ia-c and IIa-b, versus "associated" FCD type IIIa-d. The histopathological differentiation of FCD type I and III variants remains, however, a challenging issue in everyday practice. We present a unique histopathological pattern in patients with difficult-to-diagnose FCD, which highlights this dilemma, but also helps to refine the current ILAE classification scheme of FCD. We present a retrospective series of 11 male and one female patient with early onset pharmacoresistant epilepsy of the posterior quadrant (mean age at seizure onset = 4.6 years). All surgical specimens were reviewed. Clinical histories were retrieved and extracted from archival patient files. Microscopic inspection revealed abnormalities in cortical architecture with complete loss of layer 4 in all surgical samples of the occipital lobe, as confirmed by semiquantitative measurements (p < 0.01). Clinical history reported early transient hypoxic condition in nine patients (75%). Magnetic resonance imaging (MRI) revealed abnormal signals in the occipital lobe in all patients, and signal changes suggestive of subcortical encephalomalacia were found in seven patients. Surgical treatment achieved favorable seizure control (Engel class I and II) in seven patients with an available follow-up period of 6.1 years. Prominent disorganization of cortical layering and lack of any other microscopically visible principle lesion in the surgical specimen would result in this neuropathological pattern hitherto being classified as FCD ILAE type Ib. However, perinatal hypoxia with distinctive MRI changes suggested primarily a hypoxemic lesion and acquired pathomechanism of neuronal cell loss in the occipital lobe of our patient series. We propose, therefore, classifying this distinctive clinicopathological pattern as a separate variant of FCD ILAE type IIId.

Classification of infectious bursal disease virus into genogroups

Infectious bursal disease virus (IBDV) causes infectious bursal disease (IBD), an immunosuppressive disease of poultry. The current classification scheme of IBDV is confusing because it is based on antigenic types (variant and classical) as well as pathotypes. Many of the amino acid changes differentiating these various classifications are found in a hypervariable region of the capsid protein VP2 (hvVP2), the major host protective antigen. Data from this study were used to propose a new classification scheme for IBDV based solely on genogroups identified from phylogenetic analysis of the hvVP2 of strains worldwide. Seven major genogroups were identified, some of which are geographically restricted and others that have global dispersion, such as genogroup 1. Genogroup 2 viruses are predominately distributed in North America, while genogroup 3 viruses are most often identified on other continents. Additionally, we have identified a population of genogroup 3 vvIBDV isolates that have an amino acid change from alanine to threonine at position 222 while maintaining other residues conserved in this genogroup (I242, I256 and I294). A222T is an important mutation because amino acid 222 is located in the first of four surface loops of hvVP2. A similar shift from proline to threonine at 222 is believed to play a role in the significant antigenic change of the genogroup 2 IBDV strains, suggesting that antigenic drift may be occurring in genogroup 3, possibly in response to antigenic pressure from vaccination.

Turning the tide in myelodysplastic/myeloproliferative neoplasms.

Myelodysplastic syndromes/myeloproliferative neoplasms (MDS/MPN) are aggressive myeloid malignancies recognized as a distinct category owing to their unique combination of dysplastic and proliferative features. Although current classification schemes still emphasize morphology and exclusionary criteria, disease-defining somatic mutations and/or germline predisposition alleles are increasingly incorporated into diagnostic algorithms. The developing picture suggests that phenotypes are driven mostly by epigenetic mechanisms that reflect a complex interplay between genotype, physiological processes such as ageing and interactions between malignant haematopoietic cells and the stromal microenvironment of the bone marrow. Despite the rapid accumulation of genetic knowledge, therapies have remained nonspecific and largely inefficient. In this Review, we discuss the pathogenesis of MDS/MPN, focusing on the relationship between genotype and phenotype and the molecular underpinnings of epigenetic dysregulation. Starting with the limitations of current therapies, we also explore how the available mechanistic data may be harnessed to inform strategies to develop rational and more effective treatments, and which gaps in our knowledge need to be filled to translate biological understanding into clinical progress.

Evaluation of the Latest MODIS GPP Products across Multiple Biomes Using Global Eddy Covariance Flux Data

The latest MODIS GPP (gross primary productivity) product, MOD17A2H, has great advantages over the previous version, MOD17A2, because the resolution increased from 1000 m to 500 m. In this study, MOD17A2H GPP was assessed using the latest eddy covariance (EC) flux data (FLUXNET2015 Dataset) at eighteen sites in six ecosystems across the globe. The sensitivity of MOD17A2H GPP to the meteorology dataset and the fractional photosynthetically- active radiation (FPAR) product was explored by introducing site meteorology observations and improved Global Land Surface Satellite (GLASS) Leaf Area Index (LAI) products. The results showed that MOD17A2H GPP underestimated flux-derived GPP at most sites. Its performance in estimating annual GPP was poor (R2 = 0.62) and even worse over eight days (R2 = 0.52). For the MOD17A2H algorithm, replacing the reanalysis meteorological datasets with the site meteorological measurements failed to improve the estimation accuracies. However, great improvements in estimating the site-based GPP were gained by replacing MODIS FPAR with GLASS FPAR. This indicated that in the existing MOD17A2H product, the errors were originated more from FPAR than the meteorological data. We further examined the potential error contributions from land cover classification and maximum light use efficiency (εmax). It was found that the current land cover classification scheme exhibited frequent misclassification errors. Moreover, the εmax value assigned in MOD17A2H was much smaller than the inferred εmax value. Therefore, the qualities of FPAR and land cover classification datasets should be upgraded, and the εmax value needs to be adjusted to provide more accurate GPP estimates using MOD17A2H for global ecosystems.

Integrated multi-period dynamic inventory classification and control

This paper investigates the dynamic integration and optimization of inventory classification and inventory control decisions to maximize the net present value (NPV) of profit over a planning horizon. A mixed-integer linear programming model is developed by explicitly accounting for various real-world complexities, such as nonstationary demand, arbitrary review period, and limited inventory budget. We apply the model to a 900-SKU experiment and observe an average 7.5% improvement in profit over the traditional ABC approach. A real-world application for a cheese manufacturer provides a nearly 3% improvement in company's profit with a 13% reduction in inventory capital compared to its current eight-class multi-criteria inventory classification scheme. Comprehensive computational experiments are performed to examine the individual and interactive effects of various parameters on the inventory performance. Results show that it is critical for a company to manage its inventory both dynamically in the face of nonstationary demand and holistically by integrating SKU classification and policy setting. Our work provides a practical decision-support tool that simultaneously optimizes multi-period inventory classification and control decisions under nonstationary demand. It contributes to the inventory management literature by bridging two distinct streams of inventory research, inventory classification and inventory optimization, within a practical inventory modeling framework. Our study also offers several managerial implications for manufacturers and distributors managing finished goods inventory.

Revising the shock classification of meteorites

AbstractThe current shock classification scheme of meteorites assigns shock levels of S1 (unshocked) to S6 (very strongly shocked) using shock effects in rock‐forming minerals such as olivine and plagioclase. The S6 stage (55–90 GPa; 850–1750 °C) relies solely on localized effects in or near melt zones, the recrystallization of olivine, or the presence of mafic high‐pressure phases such as ringwoodite. However, high whole rock temperatures and the presence of high‐pressure phases that are unstable at those temperatures and pressures of zero GPa (e.g., ringwoodite) are two criteria that exclude each other. Each type of high‐pressure phase provides a minimum shock pressure during elevated pressure conditions to allow the formation of this phase, and a maximum temperature of the whole rock after decompression to allow the preservation of this phase. Rocks classified as S6 are characterized not by the presence but by the absence of those thermally unstable high‐pressure phases. High‐pressure phases in or attached to shock melt zones form mainly during shock pressure decline. This is because shocked rocks (&lt;60 GPa) experience a shock wave with a broad isobaric pressure plateau only during low velocity (&lt;4.5 km s−1) impacts, which rarely occur on small planetary bodies; e.g., the Moon and asteroids. The mineralogy of shock melt zones provides information on the shape and temporal duration of the shock wave but no information on the general maximum shock pressure in the whole rock.

High-grade Neuroendocrine Carcinoma of the Lung With Carcinoid Morphology: A Study of 12 Cases.

Twelve lung neuroendocrine tumors with morphologic features of carcinoid tumors but with mitotic count >10/2 mm are reported. There were 7 males and 5 females, with age ranging from 56 to 78 years. Four cases were from never-smokers. All tumors showed architectural and cytomorphologic features of carcinoid tumor, including organoid nesting, insular, trabecular, or acinar growth, and tumor cells with low nucleocytoplasmic ratio, abundant cytoplasm, ovoid to round nuclei, and salt and pepper chromatin. Angulated or confluent nesting, insular or lobular growth pattern was also seen. Nuclear irregularities and anisonucleosis were focally present. Mitotic count ranged from 11 to 61/2 mm. Punctate-type necrosis was present in 8 tumors. Anaplastic cytology, large infarct-type necrosis, desmoplasia, or marked inflammatory infiltrate was not found in any of the tumors. One tumor occurred in the background of diffuse idiopathic pulmonary neuroendocrine hyperplasia. All tumors were treated by resection, and all but 1 patient subsequently developed metastasis, and 7 died of the tumor. For metastatic tumors, 4 patients were treated by platinum-based chemotherapy with no apparent response, whereas 3 other patients were treated by combined capecitabine and temozolomide-novel chemotherapy for well-differentiated neuroendocrine tumor/carcinoid tumor-2 of them responded. This subset of tumor would be classified as large cell neuroendocrine carcinoma according to the current WHO classification scheme, but their clinical and pathologic features appear to have more in common with the carcinoid tumor group than large cell neuroendocrine carcinoma, therefore, identification of this subset may be relevant for further therapeutic management.

‘Non-classical’ HER2 FISH results in breast cancer: a multi-institutional study

The 2013 CAP/ASCO HER2 Testing Guidelines Update modified HER2 FISH categories such that some cases with ‘monosomy’, ‘co-amplification/polysomy’, low-level increased HER2 signals or clustered heterogeneity now are considered amplified or equivocal. This study examines the frequency and clinico-pathologic characteristics of breast cancers with equivocal or ‘non-classical’ HER2 FISH results. Breast cancers (2001–2014) with HER2 FISH results, HER2 immunohistochemistry, ER, grade, and age from three institutions (Stanford, UCSF, UWMC) were collected. HER2 FISH was interpreted using the updated recommendations. Amplified cases with non-classical results were grouped into the following categories: (1) ‘monosomy’ (ratio ≥2.0, mean HER2/cell<4.0); (2) ‘co-amplified’ (ratio<2.0, mean HER2/cell ≥6.0); (3) ‘low amplified’ (ratio ≥2.0, mean HER2/cell 4.0–5.9). Heterogeneous cases with clustered HER2-positive cells were also included. Of 8068 cases, 5.2% were equivocal and 4.6% had a ‘non-classical’ HER2 amplified result; 1.4% ‘monosomy’, 0.8% ‘co-amplified’, 2.1% ‘low amplified’, and 0.3% clustered heterogeneity. These cancers had a high frequency of ER positive (80.4%), Nottingham grade 3 (52.1%) results. The highest percentage of grade 3 cancers (66.7%) and positive HER2 immunohistochemistry (31.7%) was in the ‘co-amplified’ group. The ‘monosomy’ group had the highest percent grade 1 cancers (13.3%) and was most frequently HER2 immunohistochemistry negative (30.1%). Equivocal cases had very similar characteristics to the ‘low-amplified’ category. Cases with non-classical HER2 amplification or equivocal results are typically ER positive, higher grade cancers. ‘Co-amplified’ cases have the highest frequencies of aggressive characteristics and ‘monosomy’ cases the highest frequencies of lower risk features. With little clinical outcomes data currently available on these non-classical HER2 results, these results support the current classification scheme for HER2 FISH, with case-by-case correlation with additional clinical-pathologic factors when evaluating whether to offer HER2-targeted therapies in these non-classical cases.

Morphological Distribution of the Anterior Inferior Iliac Spine in Patients With and Without Hip Impingement: Reliability, Validity, and Relationship to the Intraoperative Assessment

Background: Subspinous impingement of the anterior inferior iliac spine (AIIS) on the femoral head-neck junction is increasingly recognized as a source of hip impingement. A classification system of AIIS morphology has previously been proposed that correlates with reduced hip motion and may predispose patients to subspinous hip impingement. Purpose: To examine the morphological distribution of AIIS types in patients with and without diagnosed hip impingement and correlate AIIS morphology to intraoperative findings at the time of surgery. Study Design: Cross-sectional study; Level of evidence, 3. Methods: Three-dimensional reconstructed pelvic computed tomography scans were generated for a stratified sample of 449 hips in patients without a history of hip pain or hip impingement and 59 hips in patients with a diagnosis of hip impingement. Three blinded assessors classified the AIIS for each hip twice. The morphological distribution between symptomatic and asymptomatic patients was compared, controlling for age, sex, and affected side. Within the symptomatic cohort, AIIS morphology was compared with the intraoperative assessment of a low-lying AIIS using the Fisher exact test. Results: The intraobserver reliability of the classification system in our cohort was substantial (κ = 0.68-0.77). The interobserver reliability was moderate (κ = 0.50). The morphological distribution between symptomatic and asymptomatic patients was similar, with 75% of patients in the asymptomatic group and 80% of the patients in the symptomatic group having a type 2 or type 3 AIIS. When matched for age, sex, and affected side, there was no significant difference in the assessed classification type between the groups (P = .55). Within the symptomatic group, there was no significant correlation between the surgeon assessment of a low-lying AIIS and a type 2 or type 3 radiographic classification (P = .10). The positive predictive value of a type 2 or type 3 AIIS classification for hip impingement symptoms was 10%, and the negative predictive value was 91%. Conclusion: These findings suggest that a high percentage of patients with AIIS morphology associated with subspinous impingement are, in fact, asymptomatic. The current radiographic classification scheme should not be used exclusively for clinical decision making.

Long-Run Dynamics of the U.S. Patent Classification System

Almost by definition, radical innovations create a need to revise existing classification systems. As a result, the evolution of technological classification systems reflects technological evolution. We present three sets of findings regarding classification volatility in the U.S. Patent Classification System. First, we study the evolution of the number of distinct classes. Reconstructed time series based on the current classification scheme are very different from historical data. This suggests that using the current classification to analyze the past produces a distorted view of the evolution of the system. Second, we study the relative sizes of classes. The size distribution is exponential so classes can be of quite different sizes, but the largest classes are not necessarily the oldest. To explain this pattern with a simple stochastic growth model, we introduce the assumption that classes have a regular chance to be split. Third, we study reclassification. The share of patents that are in a different class now than they were at birth can be quite high. Reclassification mostly occurs across classes belonging to the same 1-digit NBER category, but not always. We also document that reclassified patents tend to be more cited than non-reclassified ones, even after controlling for grant year and class of origin. More generally we argue that classification changes and patent reclassification are quite common, reveal interesting information about technological evolution, and must be taken into account when using classification as a basis for forecasting.

Neuroendocrine tumors of the lung: the current classification and pathology diagnosis algorithm

Bronchopulmonary neuroendocrine tumors (NET) comprise one of the most common categories within the heterogeneous group of human neuroendocrine neoplasms. Tumors of this type often occur in practical pathology diagnosis; however, their classification and histological grading are not the same as for the gastrointestinal and pancreatic NET. Terminology of lung NET is still based on using the term «carcinoid». In the recent World Health Organization classification of lung tumors published in 2015, all NETs of this localization for the first time were presented in one single chapter. According to the current classification scheme the group of neuroendocrine proliferation processes consists of carcinoid tumors (including typical carcinoid and atypical carcinoid), large-cell neuroendocrine carcinoma and small cell lung carcinoma, along with diffuse idiopathic pulmonary neuroendocrine cell hyperplasia as a pre-invasive lesion with a potential toward the development of carcinoids. Each tumor category has characteristic morphological and immunohistochemical features, which are the key diagnostic criteria of these tumors. Histology parameters for grading have remained unchanged in new edition. However, uncertainties remain in relation to the role of Ki-67 in tumor grading in resection specimens and small samples. This review outlines the main key questions in the field of classification and pathology diagnosis of lung NET, the answers to which are still inconclusive. Thus additional research is required to improve our understanding on NET of this localization.

Reconciling Mining with the Conservation of Cave Biodiversity: A Quantitative Baseline to Help Establish Conservation Priorities.

Caves pose significant challenges for mining projects, since they harbor many endemic and threatened species, and must therefore be protected. Recent discussions between academia, environmental protection agencies, and industry partners, have highlighted problems with the current Brazilian legislation for the protection of caves. While the licensing process is long, complex and cumbersome, the criteria used to assign caves into conservation relevance categories are often subjective, with relevance being mainly determined by the presence of obligate cave dwellers (troglobites) and their presumed rarity. However, the rarity of these troglobitic species is questionable, as most remain unidentified to the species level and their habitats and distribution ranges are poorly known. Using data from 844 iron caves retrieved from different speleology reports for the Carajás region (South-Eastern Amazon, Brazil), one of the world's largest deposits of high-grade iron ore, we assess the influence of different cave characteristics on four biodiversity proxies (species richness, presence of troglobites, presence of rare troglobites, and presence of resident bat populations). We then examine how the current relevance classification scheme ranks caves with different biodiversity indicators. Large caves were found to be important reservoirs of biodiversity, so they should be prioritized in conservation programs. Our results also reveal spatial autocorrelation in all the biodiversity proxies assessed, indicating that iron caves should be treated as components of a cave network immersed in the karst landscape. Finally, we show that by prioritizing the conservation of rare troglobites, the current relevance classification scheme is undermining overall cave biodiversity and leaving ecologically important caves unprotected. We argue that conservation efforts should target subterranean habitats as a whole and propose an alternative relevance ranking scheme, which could help simplify the assessment process and channel more resources to the effective protection of overall cave biodiversity.

A word from the editors

Two years have passed since the first issue of “Stochastics and Dynamics” appeared in March 2001. It was a good start for a new journal on a not so new subject in a new millenium. Due to personal reasons Ludwig Arnold (Bremen) has resigned from the Editorin-Chief position by the end of 2002, and Manfred Denker (Gottingen) took over in January 2003. This occasion is well suited to reflecting past and future of the journal, where we stand and in which direction we should move. There is no doubt that the combination of stochastics and dynamics is a field of research in its own right which has all the features such a field should have: its own examples and paradigms, its theorems, its specific methods and significant applications. It has developed into various branches, like SDE’s, stochasticity in dynamics, or random structures in dynamics, to name some. Other subjects with a natural intertwining of stochastics and dynamics are listed throughout the current classification scheme like, for example, in 28, 34, 35, 37, 47, 58, 60, 62, 70, 74, 76, 80. It is this description we will focus on in the future. An important aspect of the editorial work has been to include contributions to research in applied fields. We especially mention the September 2002 issue on stochastic climate models which grew out of Ludwig Arnold’s interest in the field and two conferences on the subject in Chorin (Germany). All this will be preserved. On the other hand, we believe it is necessary to broaden the scope of the journal to include more trend-setting articles and to incorporate the full spectrum of research as described above. Moreover, the journal should serve the needs of the community as a genuine board of information exchange in the area. In order to come closer to this goal, a new Advisory Board has been created to advise and inform the Editors about new trends and important directions in the field. Its three members will guarantee that the journal will be able to incorporate new scientific developments. The Editorial Board has been changed only slightly — which reflects the continuity of the editorial policy. Survey articles are important means for trend-setting and orientation. This needs to be done on an irregular basis. Also, the publication of important contributions to conferences which to a large part are devoted to stochastics and dynamics are very welcome.

Redefining the invertebrate RNA virosphere.

Current knowledge of RNA virus biodiversity is both biased and fragmentary, reflecting a focus on culturable or disease-causing agents. Here we profile the transcriptomes of over 220 invertebrate species sampled across nine animal phyla and report the discovery of 1,445 RNA viruses, including some that are sufficiently divergent to comprise new families. The identified viruses fill major gaps in the RNA virus phylogeny and reveal an evolutionary history that is characterized by both host switching and co-divergence. The invertebrate virome also reveals remarkable genomic flexibility that includes frequent recombination, lateral gene transfer among viruses and hosts, gene gain and loss, and complex genomic rearrangements. Together, these data present a view of the RNA virosphere that is more phylogenetically and genomically diverse than that depicted in current classification schemes and provide a more solid foundation for studies in virus ecology and evolution.

Investigation of shear wave velocity depth variability, site classification, and liquefaction vulnerability identification using a near-surface Vs model of Christchurch, New Zealand

Following the companion work of McGann et al. [1], several applications of a regional surficial shear wave velocity (Vs) model developed for Christchurch, New Zealand are examined. Comparisons of time-averaged Vs over various profile depths are used to characterize the inherent depth variability of the soils in the region. The degree of correlation between 30m shear wave velocity (Vs30) and average velocity over shallower profile depths (Vsz) exhibited by the current model is compared to similar correlations developed for other locations, and consideration is given to differences between the four primary surficial geologic units present in the majority of the Christchurch urban area. The effects of the observed Vs depth variability on expected seismic response are assessed through the consideration of transfer functions developed for 30m typical Vs profiles for eight subregions of Christchurch. The regional Vs model is also used to develop site classification maps for Christchurch using current New Zealand and international site classification schemes, and these maps are used to comment on the applicability of these conventional schemes to the soil profiles typical to the region. Models of 5m shear wave velocity (Vs5) filtered by average soil behaviour type index are used to examine the relationship between Vs5 and observations of liquefaction-related surface damage made following the 22 February 2011 Christchurch earthquake. It is shown that when properly filtered to remove regions with soils that are less susceptible (or not susceptible) to liquefaction due to soil composition, there is a good correlation between Vs5 and severity of liquefaction-related damage.

The future of transposable element annotation and their classification in the light of functional genomics - what we can learn from the fables of Jean de la Fontaine?

Transposable element (TE) science has been significantly influenced by the pioneering ideas of David Finnegan near the end of the last century, as well as by the classification systems that were subsequently developed. Today, whole genome TE annotation is mostly done using tools that were developed to aid gene annotation rather than to specifically study TEs. We argue that further progress in the TE field is impeded both by current TE classification schemes and by a failure to recognize that TE biology is fundamentally different from that of multicellular organisms. Novel genome wide TE annotation methods are helping to redefine our understanding of TE sequence origins and evolution. We briefly discuss some of these new methods as well as ideas for possible alternative classification schemes. Our hope is to encourage the formation of a society to organize a larger debate on these questions and to promote the adoption of standards for annotation and an improved TE classification.