Conditions in subjects with rheumatic diseases: pulmonary manifestations of vasculitides

Pulmonary involvement is a common complication of vasculitides, especially small vessel vasculitides. This review provides an overview of vasculitic manifestations of the lung as well as of other organs involved in vasculitides. Furthermore, it provides the diagnostic procedures required to asses a patient with vasculitic lung involvement and gives an overview of current treatment strategies.     

Optimisation of skin phototype classification

Understanding individuals' skin pigmentation and photosensitivity is important in judging risk of skin cancer and response to certain treatment modalities. However, individuals with darkly pigmented skin are poorly represented in the widely used Fitzpatrick skin phototype (FST) system. Moreover, the FST system is prone to misuse, as it relies on subjective patient and clinician assessment of skin type, and does not clearly differentiate pigmentation from photosensitivity. By evaluating the key literature surrounding the FST system, its criticisms and proposed alternatives, this review serves to understand how skin phototype classification can be optimised.     

Implications from a 28S rRNA gene fragment for the phylogenetic relationships of halichondrid sponges (Porifera: Demospongiae)

Halichondrida is a pivotal demosponge order of which the classification underwent major changes in the recent history. The monophyly of this order and its intra-ordinal phylogeny cannot be reliably determined on the basis of morphology. Here we present a 28Sr RNA gene tree of selected halichondrids, which supports the hypothesis of halichondrid non-monophyly and elucidates further inter-ordinal relationships. We enlarged the analysis by previously published sequences, discuss how previous analyses suffer from taxon bias and analyse the resulting phylogenetic implications. Most halichondrid families (in particular Axinellidae und Dictyonellidae) cluster polyphyletic and the molecular classification of several genera does not agree with the current (morphological) system.     

双歧杆菌属天然质粒系统分类

【背景】以往双歧杆菌质粒分类学研究较少,双歧杆菌属质粒系统分类方法缺失。【目的】建立双歧杆菌属天然质粒系统分类和鉴定方法,促进质粒在双歧杆菌生物学研究中的理解和应用。【方法】利用质粒复制起始蛋白进化树和基因组共线性分析方法,对目前所有已测序的双歧杆菌属天然质粒进行系统分类研究。【结果】双歧杆菌所有已知天然质粒可以划分为6个不同类型的质粒家族和3个独特的复合质粒,家族Ⅲ和家族Ⅵ质粒可进一步划分为不同的亚型类群。家族Ⅲ质粒是双歧杆菌属天然质粒的主要类型和优势家族。家族Ⅵ质粒成员亚型分类最丰富。在质粒家族水平,2种方法的分类结果完全一致。【结论】本文揭示了所有分析质粒之间的系统分类关系,建立了双歧杆菌属天然质粒系统的分类标准、方法和体系,可为今后双歧杆菌天然质粒分类和鉴定提供重要的理论参考和分类依据。     

Classification, disease, and diagnosis

Classification shapes medicine and guides its practice. Understanding classification must be part of the quest to better understand the social context and implications of diagnosis. Classifications are part of the human work that provides a foundation for the recognition and study of illness: deciding how the vast expanse of nature can be partitioned into meaningful chunks, stabilizing and structuring what is otherwise disordered. This article explores the aims of classification, their embodiment in medical diagnosis, and the historical traditions of medical classification. It provides a brief overview of the aims and principles of classification and their relevance to contemporary medicine. It also demonstrates how classifications operate as social framing devices that enable and disable communication, assert and refute authority, and are important items for sociological study.     

The classification of wetlands: integration of top-down and bottom-up approaches and their significance for ecosystem service determination

The typology of wetlands provides important information for both water resource managers and conservation planners. One of the most important aims of allocating wetlands to a certain type or class is to provide information about the ecosystem services that the wetland provides. There are two main approaches towards wetland classification. Firstly, there are top-down approaches whereby wetlands are divided into several categories based on a conceptual understanding of how the wetland functions (mostly with regards to water flows). Secondly there are bottom-up approaches whereby the classification of wetlands is based on the collection of data in the wetland that is then subjected to various clustering techniques (mostly with regards to biodiversity). The most utilized system of top-down classification assigns wetlands into hydrogeomorphic units, which function as a single unit in terms of hydrology and geomorphology. This type of classification is most useful for water resource planning, as it provides information about how the wetland is connected to the drainage network and what are the water inflows, throughflows and outflows of the wetland. The bottom-up classification approach typically focusses on the classification of wetland habitats rather than complete wetlands, where wetland habitat represents a spatial unit delineated on the basis of vegetation, embedded within the (complete) hydrogeomorphic unit, and defined as an area of wetland that is homogeneous in terms of opportunities for plant growth. At a broad scale, most ecosystem services can be superficially derived from the hydrogeomorphic unit type and the way water moves through a wetland, but habitat units and the plant species that define them would have a specific effect on the delivery of ecosystem services, for example, with different assemblages providing different resistance to flow. Some types of ecosystem services are exclusively linked to specific wetland habitats, especially provisioning services. For this reason, it is proposed that a combined approach of hydrogeomorphic classification together with a vegetation map, offers the maximum information value for ecosystem service determination. In order to account for the potential pitfall of “double counting” when combining the top-down and bottom-up approaches, each service needs to be considered individually with reference to the degree to which a service is either: (a) primarily determined by HGM class/attributes and modified by the vegetation class/attributes; or (b) primarily determined by the vegetation class/attributes.     

Autoantibodies to endothelial cell surface ATP synthase, the endogenous receptor for hsp60, might play a pathogenic role in vasculatides

Background

Heat shock protein (hsp) 60 that provides “danger signal” binds to the surface of resting endothelial cells (EC) but its receptor has not yet been characterized. In mitochondria, hsp60 specifically associates with adenosine triphosphate (ATP) synthase. We therefore examined the possible interaction between hsp60 and ATP synthase on EC surface.

Methodology/Principal Findings

Using Far Western blot approach, co-immunoprecipitation studies and surface plasmon resonance analyses, we demonstrated that hsp60 binds to the β-subunit of ATP synthase. As a cell surface-expressed molecule, ATP synthase is potentially targeted by anti-EC-antibodies (AECAs) found in the sera of patients suffering vasculitides. Based on enzyme-linked immunosorbent assay and Western blotting techniques with F1-ATP synthase as substrate, we established the presence of anti-ATP synthase antibodies at higher frequency in patients with primary vasculitides (group I) compared with secondary vasculitides (group II). Anti-ATP synthase reactivity from group I patients was restricted to the β-subunit of ATP synthase, whereas those from group II was directed to the α-, β- and γ-subunits. Cell surface ATP synthase regulates intracellular pH (pHi). In low extracellular pH medium, we detected abnormal decreased of EC pHi in the presence of anti-ATP synthase antibodies, irrespective of their fine reactivities. Interestingly, soluble hsp60 abrogated the anti-ATP synthase-induced pHi down-regulation.

Conclusions/Significance

Our results indicate that ATP synthase is targeted by AECAs on the surface of EC that induce intracellular acidification. Such pathogenic effect in vasculitides can be modulated by hsp60 binding on ATP synthase which preserves ATP synthase activity.     

What you should know about PR3-ANCA. Evidence for the role of T cells in the pathogenesis of systemic vasculitis

The pathogenesis of systemic vasculitis is complex and is likely to involve many mechanisms. There is a growing body of evidence that T cells may contribute to the pathogenesis of anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitides. Predominantly, T cells and monocytes are found in inflammatory infiltrates in patients with Wegener's granulomatosis (WG). The production of ANCA appears to be T-cell-dependent. T lymphocytes from the peripheral blood of patients with ANCA-associated vasculitis have been shown to proliferate in response to proteinase 3 (PR3). These and other findings outlined in this review indicate T-cell involvement, although further studies are still needed to elucidate the exact contribution of T cells to the pathogenesis of systemic vasculitis.     

Anti-neutrophil cytoplasm antibody associated vasculitis

Anti-neutrophil cytoplasm antibody associated vasculitides are autoimmune diseases that require treatment with powerful immunosuppressants in order to avert life threatening complications, principally renal failure and lung haemorrhage. Their pathogenesis remains unclear but the circulating autoantibodies are almost certainly instrumental in mediating vascular inflammation. Recent insights into leukocyte-autoantibody interactions support this assertion and may direct future therapeutic strategies, perhaps circumventing some of the toxicity associated with currently used drugs.     

What you should know about PR3-ANCA: Evidence for the role of T cells in the pathogenesis of systemic vasculitis

The pathogenesis of systemic vasculitis is complex and is likely to involve many mechanisms. There is a growing body of evidence that T cells may contribute to the pathogenesis of anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitides. Predominantly, T cells and monocytes are found in inflammatory infiltrates in patients with Wegener's granulomatosis (WG). The production of ANCA appears to be T-cell-dependent. T lymphocytes from the peripheral blood of patients with ANCA-associated vasculitis have been shown to proliferate in response to proteinase 3 (PR3). These and other findings outlined in this review indicate T-cell involvement, although further studies are still needed to elucidate the exact contribution of T cells to the pathogenesis of systemic vasculitis.     

The value of protein structure classification information—Surveying the scientific literature

The Structural Classification of Proteins (SCOP) and Class, Architecture, Topology, Homology (CATH) databases have been valuable resources for protein structure classification for over 20 years. Development of SCOP (version 1) concluded in June 2009 with SCOP 1.75. The SCOPe (SCOP–extended) database offers continued development of the classic SCOP hierarchy, adding over 33,000 structures. We have attempted to assess the impact of these two decade old resources and guide future development. To this end, we surveyed recent articles to learn how structure classification data are used. Of 571 articles published in 2012–2013 that cite SCOP, 439 actually use data from the resource. We found that the type of use was fairly evenly distributed among four top categories: A) study protein structure or evolution (27% of articles), B) train and/or benchmark algorithms (28% of articles), C) augment non‐SCOP datasets with SCOP classification (21% of articles), and D) examine the classification of one protein/a small set of proteins (22% of articles). Most articles described computational research, although 11% described purely experimental research, and a further 9% included both. We examined how CATH and SCOP were used in 158 articles that cited both databases: while some studies used only one dataset, the majority used data from both resources. Protein structure classification remains highly relevant for a diverse range of problems and settings. Proteins 2015; 83:2025–2038. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.     

Effects of different experimental conditions on the PrPSc core generated by protease digestion: implications for strain typing and molecular classification of CJD

The discovery of molecular subtypes of the pathological prion protein PrPSc has provided the basis for a novel classification of human transmissible spongiform encephalopathies (TSEs) and a potentially powerful method for strain typing. However, there is still a significant disparity regarding the understanding and nomenclature of PrPSc types. In addition, it is still unknown whether a specific PrPSc type is associated with each TSE phenotypic variant. In sporadic Creutzfeldt-Jakob disease (sCJD), five disease phenotypes are known, but only two major types of PrPSc, types 1 and 2, have been consistently reproduced. We further analyzed PrPSc properties in sCJD and variant CJD using a high resolution gel electrophoresis system and varying experimental conditions. We found that pH varies among CJD brain homogenates in standard buffers, thereby influencing the characteristics of protease-treated PrPSc. We also show that PrPSc type 1 and type 2 are heterogeneous species which can be further distinguished into five molecular subtypes that fit the current histopathological classification of sCJD variants. Our results shed light on previous disparities in PrPSc typing, provide a refined classification of human PrPSc types, and support the notion that the pathological TSE phenotype is related to PrPSc structure.     

Low persistence of a monocarpic invasive plant in historical sites biases our perception of its actual distribution

AIM: As accurate and up-to-date distribution data for plant species are rarely available, cumulative records over long periods of time are frequently used for mapping distributions, without taking into account that species do not persist in their historical localities forever. However, persistence is highly relevant in changing modern landscapes, especially for invasive species that dynamically spread in unstable human-made habitats. We studied how an invasive species, Heracleum mantegazzianum, persists at sites once colonized and how its ability to persist affects its distribution. LOCATION: The Czech Republic. METHODS: We visited 521 localities of H. mantegazzianum occurrence reported in the literature and herbaria to determine whether the species still occurs at these sites. By using G-tests and classification trees, we explored the roles of various factors affecting its persistence at a site. RESULTS: Of the total number of 521 historical sites at which the species has occurred since the end of the 19th century, it persists at only 124 (23.8%). The persistence rate differs with respect to habitat type and is highest in meadows and forest margins. Analysis using classification trees indicated that the factors that best explain persistence are: type of habitat (with meadow and forest margins over-represented); urbanity (with a higher persistence outside urban areas); proximity to the place of the species' introduction into the country; metapopulation connectivity; and distance to the nearest neighbouring population. MAIN CONCLUSIONS: The use of cumulative historical records as a measure of species distribution, which is common in invasion literature, can seriously overestimate the actual distribution of alien plant species with low persistence. In the case of alien species such as H. mantegazzanium, which is non-clonal and reproduces only by seed, estimates of distribution and spread based on historical data are informative about potentially suitable habitat but may be unreliable as indicators of current occurrence and invasion dynamics.     

Classification and quantification of green in the expanding urban and semi-urban complex: Application of detailed field data and IKONOS-imagery

Urban land cover is expanding rapidly worldwide. This major phenomenon is often accompanied by an expansion of a green component. Urban green can itself be considered as a most important but often ignored land cover category. With this study we investigate how IKONOS data can be used more exhaustively for the detection and more importantly the quantification of urban green, compared to state-of-the art investigations. This paper demonstrates how a combination of specific techniques, including pansharpening, the use of vegetation indices and object detection can enhance the possibilities to map vegetated elements and even estimate volumes of woody patches in the southern fringe of Roeselare (Belgium). The values of the soil adjusted MSAVI index are found to be related to the increase in volume of the trees (coniferous and deciduous). To analyze the vegetation in more detail, we use an object-oriented classification with MSAVI to exclude the sealed areas from the further analysis. With a rule set of segmentation and classification steps, the vegetation is defined on a higher level. Especially textural measures are of importance to separate grass from high vegetation.     

A phytoplankton trophic index to assess the status of lakes for the Water Framework Directive

Despite improvements in wastewater treatment systems, the impact of anthropogenic nutrient sources remains a key issue for the management of European lakes. The Water Framework Directive (WFD) provides a mechanism through which progress can be made on this issue. The Directive requires a classification of the ecological status of phytoplankton, which includes an assessment of taxonomic composition. In this paper, we present a composition metric, the plankton trophic index, that was developed in the WISER EU FP7 project and demonstrate how it has been used to compare national phytoplankton classification systems in Northern and Central Europe. The metric was derived from summer phytoplankton data summarised by genus from 1,795 lakes, covering 20 European countries. We show that it is significantly related to total phosphorus concentrations, but that it is also sensitive to alkalinity, lake size and climatic variables. Through the use of country-specific reference values for the index, we demonstrate that it is significantly related to other national phytoplankton assessment systems and illustrate for a single European (intercalibration) lake type how it was used to intercalibrate WFD boundaries from different countries.     

Management of the medial canthal tendon in nasoethmoid orbital fractures: the importance of the central fragment in classification and treatment

The medial canthal tendon and the fragment of bone on which it inserts ("central" fragment) are the critical factors in the diagnosis and treatment of nasoethmoid orbital fractures. The status of the tendon, the tendon-bearing bone segment, and the fracture pattern define a clinically useful classification system. Three patterns of fracture are appreciated: type I--single-segment central fragment; type II--comminuted central fragment with fractures remaining external to the medial canthal tendon insertion; and type III--comminuted central fragment with fractures extending into bone bearing the canthal insertion. Injuries are further classified as unilateral and bilateral and by their extension into other anatomic areas. The fracture pattern determines exposure and fixation. Inferior approaches alone are advised for unilateral single-segment injuries that are nondisplaced superiorly. Superior and inferior approaches are required for displaced unilateral single-segment injuries, for bilateral single-segment injuries, and for all comminuted fractures. Complete interfragment wiring of all segments is stabilized by junctional rigid fixation. All comminuted fractures require transnasal wiring of the bones of the medial orbital rim (medial canthal tendon-bearing or "central" bone fragment). If the fracture does not extend through the canthal insertion, the canthus should not be detached to accomplish the reduction.     

Classification of human placental villi

Summary The classification of human placental villi was reviewed on the basis of material prepared by means of special methods. The material from in situ normal-term placentae was biopsied by aspiration into glutaraldehyde. The classification was made on the basis of light-microscopic observations of semithin sections, reconstructions from serial sections, and scanning-electron micrographs. The peripheral villous tree is roughly divided into stem (ramuli), intermediate and terminal villi. The intermediate villi may be further subdivided as mature and immature types, which are found between the stem and terminal villi. Some of the terminal villi possess a local specialization described as the neck region. The histological characteristics and the branching pattern of each type are described, and the basis of the proposed classification is discussed.The authors wish to acknowledge the technical help of Mrs. Elke Böhm