An SVM method using evolutionary information for the identification of allergenic proteins

This study presents an allergenic protein prediction system that appears to be capable of producing high sensitivity and specificity. The proposed system is based on support vector machine (SVM) using evolutionary information in the form of an amino acid position specific scoring matrix (PSSM). The performance of this system is assessed by a 10-fold cross-validation experiment using a dataset consisting of 693 allergens and 1041 non-allergens obtained from Swiss-Prot and Structural Database of Allergenic Proteins (SDAP). The PSSM method produced an accuracy of 90.1% in comparison to the methods based on SVM using amino acid, dipeptide composition, pseudo (5-tier) amino acid composition that achieved an accuracy of 86.3, 86.5 and 82.1% respectively. The results show that evolutionary information can be useful to build more effective and efficient allergen prediction systems.     

Classification of hospital pathways in the management of cancer: Application to lung cancer in the region of burgundy

Context: The evaluation of national cancer plans is an important aspect of their implementation. For this evaluation, the principal actors in the field (doctors, nurses, etc.) as well as decision-makers must have access to information that is reliable, synthetic and easy to interpret, and which reflects the implementation process in the field. We propose here a methodology to make this type of information available in the context of reducing inequalities with regard to access to healthcare for patients with lung cancer in the region of Burgundy. Methods: We used the national medico-administrative DRG-type database, which gathers together all hospital stays. By using this database, it was possible to identify and reconstruct the care management history of these patients. That is, by linking together all attended hospitals, sorted chronologically. Eligible patients were at least 18 years old, whatever the gender and had undergone surgery for their lung cancer. They had to be residents of Burgundy at the time of the first operation between 2006 and 2008. Patient's pathway was defined as the sequence of all attended hospitals (hospital stays) during the year of follow up linked together using an anonymised patient identifier. We then constructed a pathway typology of pathway using an unsupervised clustering method, and conducted a spatial analysis of this typology. Results: Between 2006 and 2008, we selected 495 patients in the 4 administrative departments of the Burgundy region. They accounted for a total of 3821 stays during the year of follow-up. There were 393 men (79%) and the mean age was 64 (95% confidence interval: 63–65) years. We reconstructed 94 pathways (about five per patient). Here, neighbourhood's cares accounted for 41% of them, while 44% included a surgical intervention outside the region of Burgundy. We constructed a pathway typology with five classes. Spatial analysis showed that the vast majority of initial surgeries took place in the major regional centres. Conclusion: The construction of a pathway typology leads to better understanding of the reasoning that lies behind the movements of patients. It opens the way for analysis of the collaboration between the different healthcares establishments attended, which should bring to light associations that need to be developed.     

Systematics,biological knowledge and environmental conservation

Systematics and taxonomy are essential: they respectively elucidate life's history, and organize and verify biological knowledge. This knowledge is built of interrelated concepts which are ultimately accounted for by biological specimens. Such knowledge is essential to decide how much and what biodiversity survives human onslaughts. The preservation of specimens in natural history collections is the essential part of the process which builds and maintains biological knowledge. These collections and the human expertise essential to interpret specimens are the taxonomic resources which maintain accurate and verifiable concepts of biological entities. Present and future knowledge of the complexities and diversity of the biosphere depends on the integrity of taxonomic resources, vet widespread ignorance and disregard for their fundamental value has created a global crisis. Preservation of specimens in natural history collections is chronically neglected and support to study and manage collections is very insufficient. The knowledge held by experienced taxonomists is not being passed on to younger recruits. Neglect of collections has destroyed countless specimens and threatens millions more. These threats to taxonomic resources not only impinge on systematics but all biology: this tragedy jeopardizes the integrity of biological knowledge. The consequences for environmental conservation and therefore humanity are also of dire severity and the biodiversity crisis adds unprecedented weight to the barely recognized crisis in taxonomy and systematics.Where correspondence should     

新一代植物志：iFlora

进入21世纪,随着分子生物学及计算机信息等技术的快速发展,人们认知自然的手段和方式发生了根本性的变化。在现有电子植物志（eFlora）的基础上,融入新一代测序技术、DNA条形码数据、地理信息数据和计算机信息技术等新元素的新一代植物志（iFlora）应运而生。iFlora是通过系列关键技术的集成和攻关,构建便捷、准确识别植物和掌握相关数字化信息的新一代植物志（或智能装备）,它将极大地促进植物分类学和系统发育、演化生物学、生态学、生物地理学和保护生物学等相关学科的发展,有效地服务于生物多样性保护和生物资源可持续利用、国家生态安全和社会公共教育等,并进一步提升公众对生物多样性的认识。iFlora的实施,将为培育和拓展物种识别圈（taxasphere）和生物文化圈（bioliterate world）做出应有的贡献,并可能成为引领国际植物学发展新的生长点。     

中国西部地区土地利用/土地覆盖近期动态分析

在野外调查和资料收集的基础上 ,利用遥感 (RS)和地理信息系统 (GIS)技术 ,对中国西部地区 12个省 (直辖市 ) 1995年和2 0 0 0年的 6种土地利用 /覆盖类型的遥感数据进行了制图及其叠加分析。结果表明 :(1)对 1330 0个土地利用 /覆盖类型的图斑判读中 ,平均正确率 92 .92 %。同时对西部各省级土地利用 /土地覆被动态及更新成果进行的准确程度检查中 ,共获取全部 6个一级类型的动态图斑 13874 6个。地类更新平均准确率 97.71% ,勾绘图斑界线的准确率 99.85 %。 (2 )制图区域国土面积近 6 73万 km2 ,占全国土地面积的 70 %。其中 ,耕地面积 5年来增加了 12 0 .6 5万 hm2 ,比 1995年增长了 2 .4 1% ;林地面积 5年来减少了 6 1.5 0万 hm2 ,比 1995年减少了 0 .6 1% ;草地面积减少了 119.6 5万 hm2 ,比 1995年减少了 0 .5 9% ;城镇建设用地和水域面积 5年来分别增加了 19.2 5万 hm2和 17.0 4万 hm2 ,比 1995年增加了 1.36 %和 1.4 4 %。另外 ,作为西部地区主要生态环境问题之一的土地沙漠化和土地盐碱化 ,由于近年来的连续干旱以及油田开发等人为干扰的加剧 ,5 a来不可利用地面积扩大了 2 4 .2 8万 hm2 ,其中草地沙化面积占到 2 6 .94 %。     

基于专家数据库的人体信息诊疗仪的研制

本文介绍了我们研制的一种基于电脑专家数据库的人体信息诊疗仪。融合了先进的激光技术、电子技术、计算机技术和人体信息诊疗学于一体。该仪器由两部分组成：（1）可自动诊断的电脑专家数据库;（2）半导体激光针灸部分。     

Novel polymorphisms of SIX4 gene and their association with body measurement traits in Qinchuan cattle

Sine oculis homeobox homolog 4 (SIX4) gene belongs to the sine oculis/SIX gene family, which includes six members in vertebrates. SIX4 gene plays a crucial role in skeletal myogenesis, and its genetic variations or deficiency may cause hypopituitarism, suggesting that SIX4 gene is a potential candidate gene affecting body measurement traits (BMTs) in animals. Herein, the objectives of this study were to identify genetic polymorphisms of bovine SIX4 gene and to analyze potential association between single nucleotide polymorphisms (SNPs) and body measurement traits in Qinchuan cattle. In the present study, we investigated polymorphisms of SIX4 gene in 426 Qinchuan cattle using DNA sequencing and polymerase chain reaction–restriction fragment length polymorphisms. Three novel SNPs were identified within bovine SIX4 gene. Associations between body measurement traits and SIX4 gene polymorphisms were investigated, and significant statistical associations were found between polymorphisms of these three SNPs and body measurement traits (P < 0.05). Hence, based on results obtained from this study, we conjectured that SIX4 gene may have potential effects on body measurement traits in Qinchuan cattle population and could be used for marker-assisted selection.     

An informational diversity framework,illustrated with sexually deceptive orchids in early stages of speciation

Reconstructing evolutionary history for emerging species complexes is notoriously difficult, with newly isolated taxa often morphologically cryptic and the signature of reproductive isolation often restricted to a few genes. Evidence from multiple loci and genomes is highly desirable, but multiple inputs require ‘common currency’ translation. Here we deploy a Shannon information framework, converting into diversity analogue, which provides a common currency analysis for maternally inherited haploid and bi‐parentally inherited diploid nuclear markers, and then extend that analysis to construction of minimum‐spanning networks for both genomes. The new approach is illustrated with a quartet of cryptic congeners from the sexually deceptive Australian orchid genus Chiloglottis, still in the early stages of speciation. Divergence is more rapid for haploid plastids than for nuclear markers, consistent with the effective population size differential (N_ep < N_en), but divergence patterns are broadly correlated for the two genomes. There are nevertheless intriguing discrepancies between the emerging plastid and nuclear signals of early phylogenetic radiation of these taxa, and neither pattern is entirely consistent with the available information on the sexual cues used by the orchids to lure the pollinators enforcing reproductive isolation. We describe possible extensions of this methodology to multiple ploidy levels and other types of markers, which should increase the range of application to any taxonomic assemblage in the very early stages of reproductive isolation and speciation.     

The utility of deformable image registration for small artery visualisation in contrast-enhanced whole body MR angiography

PurposeAn investigation was carried out into the effect of three image registration techniques on the diagnostic image quality of contrast-enhanced magnetic resonance angiography (CE-MRA) images.MethodsWhole-body CE-MRA data from the lower legs of 27 patients recruited onto a study of asymptomatic atherosclerosis were processed using three deformable image registration algorithms. The resultant diagnostic image quality was evaluated qualitatively in a clinical evaluation by four expert observers, and quantitatively by measuring contrast-to-noise ratios and volumes of blood vessels, and assessing the techniques' ability to correct for varying degrees of motion.ResultsThe first registration algorithm (‘AIR’) introduced significant stenosis-mimicking artefacts into the blood vessels' appearance, observed both qualitatively (clinical evaluation) and quantitatively (vessel volume measurements). The two other algorithms (‘Slicer’ and ‘SEMI’), based on the normalised mutual information (NMI) concept and designed specifically to deal with variations in signal intensity as found in contrast-enhanced image data, did not suffer from this serious issue but were rather found to significantly improve the diagnostic image quality both qualitatively and quantitatively, and demonstrated a significantly improved ability to deal with the common problem of patient motion.ConclusionsThis work highlights both the significant benefits to be gained through the use of suitable registration algorithms and the deleterious effects of an inappropriate choice of algorithm for contrast-enhanced MRI data. The maximum benefit was found in the lower legs, where the small arterial vessel diameters and propensity for leg movement during image acquisitions posed considerable problems in making accurate diagnoses from the un-registered images.