The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci

For the ∼1% of the human genome in the ENCODE regions, only about half of the transcriptionally active regions (TARs) identified with tiling microarrays correspond to annotated exons. Here we categorize this large amount of “unannotated transcription.” We use a number of disparate features to classify the 6988 novel TARs—array expression profiles across cell lines and conditions, sequence composition, phylogenetic profiles (presence/absence of syntenic conservation across 17 species), and locations relative to genes. In the classification, we first filter out TARs with unusual sequence composition and those likely resulting from cross-hybridization. We then associate some of those remaining with proximal exons having correlated expression profiles. Finally, we cluster unclassified TARs into putative novel loci, based on similar expression and phylogenetic profiles. To encapsulate our classification, we construct a Database of Active Regions and Tools (DART.gersteinlab.org). DART has special facilities for rapidly handling and comparing many sets of TARs and their heterogeneous features, synchronizing across builds, and interfacing with other resources. Overall, we find that ∼14% of the novel TARs can be associated with known genes, while ∼21% can be clustered into ∼200 novel loci. We observe that TARs associated with genes are enriched in the potential to form structural RNAs and many novel TAR clusters are associated with nearby promoters. To benchmark our classification, we design a set of experiments for testing the connectivity of novel TARs. Overall, we find that 18 of the 46 connections tested validate by RT-PCR and four of five sequenced PCR products confirm connectivity unambiguously.

Introducing a new MRI classification of lumbar spinal stenosis based on cross-sectional morphology of the dural sac : 37

Introduction: Measures of the degree of lumbar spinal stenosis (LSS) such as antero-posterior diameter of the canal, and dural sac cross sectional area vary, and do not correlate with symptoms or results of surgery. We created a grading system, comprised of seven categories, based on the morphology of the dural sac and its contents as seen on T2 axial images. The categories take into account the ratio of rootlet/ CSF content. Grade A indicates no significant compression, grade D is equivalent to a total myelograhic block. We compared this classification with commonly used criteria of severity of stenosis. Methods: Fifty T2 axial MRI images taken at disc level from 27 symptomatic LSS patients undergoing decompressive surgery were classified twice by two radiologists and three spinal surgeons working at different institutions and countries. Dural sac cross-sectional surface area and AP diameter of the canal were measured both at disc and pedicle level from DICOM images using OsiriX software. Intraand inter-observer reliability were assessed using Cohen's, Fleiss' kappa statistics, and t test. Results: For the morphological grading the average intra-and inter observer kappas were 0.76 and 0.69+, respectively, for physicians working in the study originating country. Combining all observers the kappa values were 0.57 ± 0.19. and 0.44 ± 0.19, respectively. AP diameter and dural sac cross-sectional area measurements showed no statistically significant differences between observers. No correlation between morphological grading and AP diameter or dural sac crosssectional areawas observed in 13 (26%) and 8 cases (16%), respectively. Discussion: The proposed morphological grading relies on the identification of the dural sac and CSF better seen on full MRI series. This was not available to the external observers, which might explain the lower overall kappa values. Since no specific measurement tools are needed the grading suits everyday clinical practice and favours communication of degree of stenosis between practising physicians. The absence of a strict correlation with the dural sac surface suggests that measuring the surface alone might be insufficient in defining LSS as it is essentially a mismatch between the spinal canal and its contents. This grading is now adopted in our unit and further studies concentrating on relation between morphology, clinical symptoms and surgical results are underway.

The AO comprehensive classification of pediatric long-bone fractures: a web-based multicenter agreement study.

The first AO comprehensive pediatric long-bone fracture classification system has been proposed following a structured path of development and validation with experienced pediatric surgeons. A Web-based multicenter agreement study involving 70 surgeons in 15 clinics and 5 countries was conducted to assess the reliability and accuracy of this classification when used by a wide range of surgeons with various levels of experience. Training was provided at each clinic before the session. Using the Internet, participants could log in at any time and classify 275 supracondylar, radius, and tibia fractures at their own pace. The fracture diagnosis was made following the hierarchy of the classification system using both clinical terminology and codes. kappa coefficients for the single-surgeon diagnosis of epiphyseal, metaphyseal, or diaphyseal fracture type were 0.66, 0.80, and 0.91, respectively. Median accuracy estimates for each bone and type were all greater than 80%. Depending on their experience and specialization, surgeons greatly varied in their ability to classify fractures. Pediatric training and at least 2 years of experience were associated with significant improvement in reliability and accuracy. Kappa coefficients for diagnosis of specific child patterns were 0.51, 0.63, and 0.48 for epiphyseal, metaphyseal, and diaphyseal fractures, respectively. Identified reasons for coding discrepancies were related to different understandings of terminology and definitions, as well as poor quality radiographic images. Results supported some minor adjustments in the coding of fracture type and child patterns. This classification system received wide acceptance and support among the surgeons involved. As long as appropriate training could be performed, the system classification was reliable, especially among surgeons with a minimum of 2 years of clinical experience. We encourage broad-based consultation between surgeons' international societies and the use of this classification system in the context of clinical practice as well as prospectively for clinical studies.

Use of patients’ classification instruments: analysis of the brazilian production of knowledge

Objective To analyze the production of scientific knowledge about the use of patients’ classification instruments in care and management practice in Brazil. Method Integrative literature review with databases search in: Latin American and Caribbean Literature on Health Sciences (LILACS), Medical Literature Analysis and Retrieval System on-line (MEDLINE), Cumulative Index to Nursing and Allied Health Literature (CINAHL) and SCOPUS, between January 2002 through December 2013. Results 1,194 studies were found, 31 met the inclusion criteria. We observed a higher number of studies in the category care plans and workload (n=15), followed by the category evaluation of psychometric properties (n=14). Conclusion Brazilian knowledge production has not yet investigated some purposes of using instruments for classifying patients in professional nursing practice. The identification of unexplored areas can guide future research on the topic.


Leaf consumption and duration of instars of the cassava defoliator Erinnyis ello (L., 1758) (Lepidoptera, Sphingidae)

The objectives of this research were to evaluate leaf consumption and the developmental time of the larvae of Erynnyis ello (L., 1758) (Lepidoptera, Sphingidae) reared on cassava, in order to obtain information for the integrated management of this pest. The larvae were reared on excised cassava leaves in Petri dishes and later in gerbox, and kept in chambers at 24 ± 2 ºC and 75 ± 10% RH. The total leaf area consumed by the larva to complete its development was 589.67 cm²; each of the five instars consumed, respectively: 1.89 cm²; 5.74 cm²; 17.48 cm²; 76.66 cm²; and 487.90 cm². The consumption by the first three instars was insignificant, and did not reach 5% altogether; the 4th represented 13%; the 5th presented a consumption significantly higher, about 82.7%. The total time for the larval development was 22.61 days, and the duration for each of the five larval instar was, respectively: 4.35; 3.19; 3.32; 4.52; and 4.94 days. The pre-pupal period lasted 2.29 days. Since the highest consumption is by the 5th instar larva, the control should be applied before this age to avoid heavier damages to the cassava crop.

Assessment of a new MRI classification of spinal stenosis based on cross-sectional morphology of the dural sac : FM2

Introduction: Quantitative measures of degree of lumbar spinal stenosis (LSS) such as antero-posterior diameter of the canal or dural sac cross sectional area vary widely and do not correlate with clinical symptoms or results of surgical decompression. In an effort to improve quantification of stenosis we have developed a grading system based on the morphology of the dural sac and its contents as seen on T2 axial images. The grading comprises seven categories ranging form normal to the most severe stenosis and takes into account the ratio of rootlet/CSF content. Material and methods: Fifty T2 axial MRI images taken at disc level from twenty seven symptomatic lumbar spinal stenosis patients who underwent decompressive surgery were classified into seven categories by five observers and reclassified 2 weeks later by the same investigators. Intra- and inter-observer reliability of the classification were assessed using Cohen's and Fleiss' kappa statistics, respectively. Results: Generally, the morphology grading system itself was well adopted by the observers. Its success in application is strongly influenced by the identification of the dural sac. The average intraobserver Cohen's kappa was 0.53 ± 0.2. The inter-observer Fleiss' kappa was 0.38 ± 0.02 in the first rating and 0.3 ± 0.03 in the second rating repeated after two weeks. Discussion: In this attempt, the teaching of the observers was limited to an introduction to the general idea of the morphology grading system and one example MRI image per category. The identification of the dimension of the dural sac may be a difficult issue in absence of complete T1 T2 MRI image series as it was the case here. The similarity of the CSF to possibly present fat on T2 images was the main reason of mismatch in the assignment of the cases to a category. The Fleiss correlation factors of the five observers are fair and the proposed morphology grading system is promising.

The In Vitro Mass-Produced Model Mycorrhizal Fungus, Rhizophagus irregularis, Significantly Increases Yields of the Globally Important Food Security Crop Cassava.

The arbuscular mycorrhizal symbiosis is formed between arbuscular mycorrhizal fungi (AMF) and plant roots. The fungi provide the plant with inorganic phosphate (P). The symbiosis can result in increased plant growth. Although most global food crops naturally form this symbiosis, very few studies have shown that their practical application can lead to large-scale increases in food production. Application of AMF to crops in the tropics is potentially effective for improving yields. However, a main problem of using AMF on a large-scale is producing cheap inoculum in a clean sterile carrier and sufficiently concentrated to cheaply transport. Recently, mass-produced in vitro inoculum of the model mycorrhizal fungus Rhizophagus irregularis became available, potentially making its use viable in tropical agriculture. One of the most globally important food plants in the tropics is cassava. We evaluated the effect of in vitro mass-produced R. irregularis inoculum on the yield of cassava crops at two locations in Colombia. A significant effect of R. irregularis inoculation on yield occurred at both sites. At one site, yield increases were observed irrespective of P fertilization. At the other site, inoculation with AMF and 50% of the normally applied P gave the highest yield. Despite that AMF inoculation resulted in greater food production, economic analyses revealed that AMF inoculation did not give greater return on investment than with conventional cultivation. However, the amount of AMF inoculum used was double the recommended dose and was calculated with European, not Colombian, inoculum prices. R. irregularis can also be manipulated genetically in vitro, leading to improved plant growth. We conclude that application of in vitro R. irregularis is currently a way of increasing cassava yields, that there is a strong potential for it to be economically profitable and that there is enormous potential to improve this efficiency further in the future.

Classification of cell death: recommendations of the Nomenclature Committee on Cell Death 2009

Different types of cell death are often defined by morphological criteria, without a clear reference to precise biochemical mechanisms. The Nomenclature Committee on Cell Death (NCCD) proposes unified criteria for the definition of cell death and of its different morphologies, while formulating several caveats against the misuse of words and concepts that slow down progress in the area of cell death research. Authors, reviewers and editors of scientific periodicals are invited to abandon expressions like 'percentage apoptosis' and to replace them with more accurate descriptions of the biochemical and cellular parameters that are actually measured. Moreover, at the present stage, it should be accepted that caspase-independent mechanisms can cooperate with (or substitute for) caspases in the execution of lethal signaling pathways and that 'autophagic cell death' is a type of cell death occurring together with (but not necessarily by) autophagic vacuolization. This study details the 2009 recommendations of the NCCD on the use of cell death-related terminology including 'entosis', 'mitotic catastrophe', 'necrosis', 'necroptosis' and 'pyroptosis'.

Minimal data requirements for a continuous monitoring of the quality of care using the DRG classification.

The DRG classification provides a useful tool for the evaluation of hospital care. Indicators such as readmissions and mortality rates adjusted for the hospital Casemix could be adopted in Switzerland at the price of minor additions to the hospital discharge record. The additional information required to build patients histories and to identify the deaths occurring after hospital discharge is detailed.

A methodology for the classification of convective structures using meteorological radar: Application to heavy rainfall events on the Mediterranean coast of the Iberian Peninsula

During the period 1996-2000, forty-three heavy rainfall events have been detected in the Internal Basins of Catalonia (Northeastern of Spain). Most of these events caused floods and serious damage. This high number leads to the need for a methodology to classify them, on the basis of their surface rainfall distribution, their internal organization and their physical features. The aim of this paper is to show a methodology to analyze systematically the convective structures responsible of those heavy rainfall events on the basis of the information supplied by the meteorological radar. The proposed methodology is as follows. Firstly, the rainfall intensity and the surface rainfall pattern are analyzed on the basis of the raingauge data. Secondly, the convective structures at the lowest level are identified and characterized by using a 2-D algorithm, and the convective cells are identified by using a 3-D procedure that looks for the reflectivity cores in every radar volume. Thirdly, the convective cells (3-D) are associated with the 2-D structures (convective rainfall areas). This methodology has been applied to the 43 heavy rainfall events using the meteorological radar located near Barcelona and the SAIH automatic raingauge network.

ITMIG consensus statement on the use of the WHO histological classification of thymoma and thymic carcinoma: refined definitions, histological criteria, and reporting.

INTRODUCTION: The 2004 version of the World Health Organization classification subdivides thymic epithelial tumors into A, AB, B1, B2, and B3 (and rare other) thymomas and thymic carcinomas (TC). Due to a morphological continuum between some thymoma subtypes and some morphological overlap between thymomas and TC, a variable proportion of cases may pose problems in classification, contributing to the poor interobserver reproducibility in some studies. METHODS: To overcome this problem, hematoxylin-eosin-stained and immunohistochemically processed sections of prototypic, "borderland," and "combined" thymomas and TC (n = 72) were studied by 18 pathologists at an international consensus slide workshop supported by the International Thymic Malignancy Interest Group. RESULTS: Consensus was achieved on refined criteria for decision making at the A/AB borderland, the distinction between B1, B2, and B3 thymomas and the separation of B3 thymomas from TCs. "Atypical type A thymoma" is tentatively proposed as a new type A thymoma variant. New reporting strategies for tumors with more than one histological pattern are proposed. CONCLUSION: These guidelines can set the stage for reproducibility studies and the design of a clinically meaningful grading system for thymic epithelial tumors.

Classification of acid sulphate soils of Finland according to Soil Taxonomy and the FAO/Unesco legend

Selostus: Suomen happamien sulfaattimaiden kansainvälinen luokittelu

CD34/QBEND10 immunostaining in bone marrow biopsies: an additional parameter for the diagnosis and classification of myelodysplastic syndromes.

CD34/QBEND10 immunostaining has been assessed in 150 bone marrow biopsies (BMB) including 91 myelodysplastic syndromes (MDS), 16 MDS-related AML, 25 reactive BMB, and 18 cases where RA could neither be established nor ruled out. All cases were reviewed and classified according to the clinical and morphological FAB criteria. The percentage of CD34-positive (CD34 +) hematopoietic cells and the number of clusters of CD34+ cells in 10 HPF were determined. In most cases the CD34+ cell count was similar to the blast percentage determined morphologically. In RA, however, not only typical blasts but also less immature hemopoietic cells lying morphologically between blasts and promyelocytes were stained with CD34. The CD34+ cell count and cluster values were significantly higher in RA than in BMB with reactive changes (p<0.0001 for both), in RAEB than in RA (p=0.0006 and p=0.0189, respectively), in RAEBt than in RAEB (p=0.0001 and p=0.0038), and in MDS-AML than in RAEBt (p<0.0001 and p=0.0007). Presence of CD34+ cell clusters in RA correlated with increased risk of progression of the disease. We conclude that CD34 immunostaining in BMB is a useful tool for distinguishing RA from other anemias, assessing blast percentage in MDS cases, classifying them according to FAB, and following their evolution.

Genesis and classification of Oxisols in a highland toposequence of the upper Jequitinhonha Valley (MG)

The Brazilian System of Soil Classification (SiBCS) is a taxonomic system, open and in permanent construction, as new knowledge on Brazilian soils is obtained. The objective of this study was to characterize the chemical, physical, morphological, micro-morphological and mineralogical properties of four pedons of Oxisols in a highland toposequence in the upper Jequitinhonha Valley, emphasizing aspects of their genesis, classification and landscape development. The pedons occupy the following slope positions: summit - Red Oxisol (LV), mid slope (upper third) - Yellow-Red Oxisol (LVA), lower slope (middle third)- Yellow Oxisol (LA) and bottom of the valley (lowest third) - "Gray Oxisol" ("LAC"). These pedons were described and sampled for characterization in chemical and physical routine analyses. The total Fe, Al and Mn contents were determined by sulfuric attack and the Fe, Al and Mn oxides in dithionite-citrate-bicarbonate and oxalate extraction. The mineralogy of silicate clays was identified by X ray diffraction and the Fe oxides were detected by differential X ray diffraction. Total Ti, Ga and Zr contents were determined by X ray fluorescence spectrometry. The "LAC" is gray-colored and contains significant fragments of structure units in the form of a dense paste, characteristic of a gleysoil, in the horizons A and BA. All pedons are very clayey, dystrophic and have low contents of available P and a pH of around 5. The soil color was related to the Fe oxide content, which decreased along the slope. The decrease of crystalline and low- crystalline Fe along the slope confirmed the loss of Fe from the "LAC". Total Si increased along the slope and total Al remained constant. The clay fraction in all pedons was dominated by kaolinite and gibbsite. Hematite and goethite were identified in LV, low-intensity hematite and goethite in LVA, goethite in LA. In the "LAC", no hematite peaks and goethite were detected by differential X ray diffraction. The micro-morphology indicated prevalence of granular microstructure and porosity with complex stacking patterns.. The soil properties in the toposequence converged to a single soil class, the Oxisols, derived from the same source material. The landscape evolution and genesis of Oxisols of the highlands in the upper Jequitinhonha Valley are related to the evolution of the drainage system and the activity of excavating fauna.

Highlands of the upper Jequitinhonha valley, Brazil: I - characterization and classification

In the upper Jequitinhonha valley, state of Minas Gerais, Brazi, there are large plane areas known as "chapadas", which are separated by areas dissected by tributaries of the Jequitinhonha and Araçuaí rivers. These dissected areas have a surface drainage system with tree, shrub, and grass vegetation, more commonly known as "veredas", i.e., palm swamps. The main purpose of this study was to characterize soil physical, chemical and morphological properties of a representative toposequence in the watershed of the Vereda Lagoa do Leandro, a swamp near Minas Novas, MG, on "chapadas", the highlands of the Alto Jequitinhonha region Different soil types are observed in the landscape: at the top - Typic Haplustox (LVA), in the middle slope - Xanthic Haplustox (LA), at the footslope - Xanthic Haplustox, gray color, here called "Gray Haplustox" ("LAC") and, at the bottom of the palm swamp - Typic Albaquult (GXbd). These soils were first morphologically described; samples of disturbed and undisturbed soils were collected from all horizons and subhorizons, to evaluate their essential physical and chemical properties, by means of standard determination of Fe, Al, Mn, Ti and Si oxides after sulfuric extraction. The contents of Fe, Al and Mn, extracted with dithionite-citrate-bicarbonate and oxalate treatments, were also determined. In the well-drained soils of the slope positions, the typical morphological, physical and chemical properties of Oxisols were found. The GXbd sample, from the bottom of the palm swamp, is grayish and has high texture gradient (B/A) and massive structure. The reduction of the proportion of crystalline iron compounds and the low crystallinity along the slope confirmed the loss of iron during pedogenesis, which is reflected in the current soil color. The Si and Al contents were lowest in the "LAC" soil. There was a decrease of the Fe2O3/TiO2 ratio downhill, indicating progressive drainage restriction along the toposequence. The genesis and all physical and chemical properties of the soils at the footslope and the bottom of the palm swamp of the "chapadas" of the Alto Jequitinhonha region are strongly influenced by the occurrence of ground water on the surface or near the surface all year long, at present and/or in the past. Total concentrations of iron oxides, Fe d and Fe o in soils of the toposequence studied are related to the past and/or present soil colors and drainage conditions.