The ABCD of primary biodiversity data access

Abstract

Within the context of the Global Biodiversity Information Facility (GBIF), the Biological Collections Access Service (BioCASe) has been set up to foment data provision by natural history content providers. Products include the BioCASe Protocol and the PyWrapper software, a web service allowing to access rich natural history data using complex schemas like ABCD (Access to Biological Collection Data). New developments include the possibility to produce DarwinCore-Archive files using PyWrapper, in order to facilitate the indexing of large datasets by aggregators such as GBIF. However, BioCASe continues to be committed to distributed data access and continues to provide the possibility to directly query the web service for up-to-date data directly from the provider's database. ABCD provides comprehensive coverage of natural history data, and has been extended to cover DNA collections (ABCD-DNA) and geosciences (ABCD-EFG, the extension for geosciences). BioCASe also developed web portal software that allows to access and display rich data provided by special interest networks. We posit that the XML-based networking approach using a highly standardised data definition such as ABCD continues to be a valuable approach towards mobilising natural history information. Some suggestions are made regarding further improvements of ABCD.     

The UK Nest Record Scheme: its value for science and conservation

Capsule A review of its methodology, analytical procedures and uses.

Aims To provide a comprehensive review of the UK Nest Record Scheme (NRS), its methodology and value to science and conservation.

Methods We reviewed the history of the development and current methodology used in the analysis of NRS data in the scientific literature and unpublished documents and from our personal knowledge.

Results The British Trust for Ornithology's (BTO's) NRS is the largest, longest running and most highly computerized such scheme in the world. Advanced and efficient techniques of data gathering, data capture and analysis are used. It was founded in 1939 to provide information on the breeding biology of birds, but has since developed into a key component of the overall monitoring strategy for birds in the UK. A range of specialized analytical methods is available for NRS data and potential biases need careful treatment. More than 250 scientific publications have used NRS data to describe aspects of basic breeding biology and performance, to study the population dynamics of bird populations and to investigate the demographic causes of bird population declines in the UK.

Conclusions Extensive long-term monitoring schemes, such as the NRS, that collate large historical data sets will become increasingly valuable for monitoring the impact of environmental change. While aspects of the NRS, its recording methods, data capture and analysis can be developed further, the scheme will continue to advance our understanding of both the impacts of new environmental stresses in the UK and the effectiveness of new conservation measures in the wider countryside. This has been amply demonstrated by its use for exploring the impacts of global climate change on the UK's avifauna.     

NFE2L1在食管鳞癌中的表达及临床意义

目的:通过检测食管鳞癌标本中核因子E2相关因子1(NFE2L1)的表达情况,探究NFE2L1在食管鳞癌发生发展中的作用,为食管鳞癌的诊治以及预后评估提供新的思路。方法:收集我校附院2016-2017年经病理组织学检查诊断为食管鳞癌的手术标本40例及其对应的癌旁组织并从NCBI数据库下载GEO测序数据,应用定量PCR、免疫组化和生物信息分析等方法检测分析NFE2L1基因的表达情况。结果:在食管鳞癌组织中,NFE2L1表达阳性31例(77.5%),癌旁组织阳性表达17例(42.5%),两组比较差异显著有统计学意义(P0.001);进一步发现NFE2L1的阳性表达与肿瘤分化程度和淋巴转移相关(P0.05)。但在不同年龄、性别、浸润深度及不同部位之间差异无统计学意义。GEO数据分析结果显示NFE2L1在食管鳞癌组织显著高表达(P0.01),只是未达到显著差异表达的阈值标准(即变化倍数小于2倍)。结论:NFE2L1在食管鳞癌中高表达,表达的高低与食管鳞癌的发生进展密切相关。     

基于BP神经网络和RBF神经网络预测老年痴呆症疾病进展的对比研究

目的:比较反向传播算法(BP)神经网络和径向基函数(RBF)神经网络预测老年痴呆症疾病进展的效果。方法:以老年痴呆症随访数据为研究对象,以性别、年龄、受教育程度、有无高血压、有无高胆固醇、有无心脏病、有无中风史、有无家族史8个指标作为输入变量,以五年随访的MMSE差值为输出变量,构建基于BP神经网络和RBF神经网络的老年痴呆症疾病进展预测模型。结果:与BP神经网络模型相比,RBF神经网络预测的结果更好,能够有效地预测老年痴呆症疾病进展。结论:神经网络模型将老年痴呆症疾病进展预测问题转化为随访数据中相关测量指标与MMSE差值的非线性问题,为复杂的老年痴呆症疾病进展预测提供了新思路。     

Applications and Challenges of Machine Learning Methods in Alzheimer's Disease Multi-Source Data Analysis

BackgroundRecent development in neuroimaging and genetic testing technologies have made it possible to measure pathological features associated with Alzheimer''s disease (AD) in vivo. Mining potential molecular markers of AD from high-dimensional, multi-modal neuroimaging and omics data will provide a new basis for early diagnosis and intervention in AD. In order to discover the real pathogenic mutation and even understand the pathogenic mechanism of AD, lots of machine learning methods have been designed and successfully applied to the analysis and processing of large-scale AD biomedical data.ObjectiveTo introduce and summarize the applications and challenges of machine learning methods in Alzheimer''s disease multi-source data analysis.MethodsThe literature selected in the review is obtained from Google Scholar, PubMed, and Web of Science. The keywords of literature retrieval include Alzheimer''s disease, bioinformatics, image genetics, genome-wide association research, molecular interaction network, multi-omics data integration, and so on.ConclusionThis study comprehensively introduces machine learning-based processing techniques for AD neuroimaging data and then shows the progress of computational analysis methods in omics data, such as the genome, proteome, and so on. Subsequently, machine learning methods for AD imaging analysis are also summarized. Finally, we elaborate on the current emerging technology of multi-modal neuroimaging, multi-omics data joint analysis, and present some outstanding issues and future research directions.     

Nucleosomal Positioning and Genetic Divergence Study Based on DNA Flexibility Map

Abstract

Based on worm like chain model, DNA structural parameters—tilt, roll and rise, derived from crystallographic database have been used to determine the flexibility of DNA that regulates the nucleosomal translational positioning. Theoretically derived data has been compared to the experimental values available in Ioshikhes and Trifonov's database. The methodology has been extended to determine the flexibility of 18S rRNA genome in eukarya, where yeast shows a distinct difference when compared with mammals like human, mouse and rabbit.     

Metastatic Burkitt's Lymphoma Presenting as Diabetes Insipidus

ObjectiveTo present the first reported case of metastatic Burkitt's lymphoma with a single central nervous system (CNS) metastasis to the pituitary stalk.MethodsWe provided details of the case presentation and review the literature.ResultsAlthough other malignancies are known to metastasize to the pituitary, and diabetes insipidus is often the presenting symptom, there has not been a previously reported case of Burkitt's lymphoma with a single CNS metastasis to the pituitary.ConclusionA careful history and an endocrine review of systems may aid early identification of pituitary or central nervous system metastases. (Endocr. Pract. 2013; 19:e102-e104)     

Association of electronic cigarette use with lead,cadmium, barium,and antimony body burden: NHANES 2015-2016

BackgroundExposure of toxic metals from e-cigarette use is a cause for public health concern because youth, young adults, and non-smokers are the target population rapidly adopting e-cigarette use. The purpose of this research is to determine the association of the body burden of heavy metals with e-cigarette use using NHANES (U.S.) 2015–2016 data.MethodsBlood lead (N = 1899) and urinary cadmium, barium, and antimony (N = 1302) data were extracted from NHANES, 2015–2016; geometric means were calculated and bivariate and multivariable linear regression analyses were conducted. Participants were categorized as having neither e-cigarette nor cigarette use; smoking history (including dual use with e-cigarettes); and only e-cigarette (current or former).ResultsIn multivariable analyses adjusted for sex, race/ethnicity, age, and poverty levels, current or former e-cigarette use failed to reach a statistical significance in the association with metals. However, participants with a smoking history were more likely to have higher blood lead and urinary cadmium than participants who neither used e-cigarettes nor cigarettes.ConclusionBlood lead levels, and urinary cadmium, barium, and antimony levels were similar between participants who used e-cigarettes and participants who did not.     

Deep Convolution Neural Network Based System for Early Diagnosis of Alzheimer's Disease

ObjectivesAlzheimer's Disease (AD) is the most general type of dementia. In all leading countries, it is one of the primary reasons of death in senior citizens. Currently, it is diagnosed by calculating the MSME score and by the manual study of MRI Scan. Also, different machine learning methods are utilized for automatic diagnosis but existing has some limitations in terms of accuracy. So, main objective of this paper to include a preprocessing method before CNN model to increase the accuracy of classification.Materials and methodIn this paper, we present a deep learning-based approach for detection of Alzheimer's Disease from ADNI database of Alzheimer's disease patients, the dataset contains fMRI and PET images of Alzheimer's patients along with normal person's image. We have applied 3D to 2D conversion and resizing of images before applying VGG-16 architecture of Convolution neural network for feature extraction. Finally, for classification SVM, Linear Discriminate, K means clustering, and Decision tree classifiers are used.ResultsThe experimental result shows that the average accuracy of 99.95% is achieved for the classification of the fMRI dataset, while the average accuracy of 73.46% is achieved with the PET dataset. On comparing results on the basis of accuracy, specificity, sensitivity and on some other parameters we found that these results are better than existing methods.Conclusionsthis paper, suggested a unique way to increase the performance of CNN models by applying some preprocessing on image dataset before sending to CNN architecture for feature extraction. We applied this method on ADNI database and on comparing the accuracies with other similar approaches it shows better results.     

POLESAT,an innovative e-health geomatic platform in decision-making based on: Geographical approach,medical knowledge visualization and geographic information system & web-mapping architecture

Our goals today, through the updated POLESAT project (version 2), are to improve the usability of the e-health geomatic platform with the help of a geo-medical e-Atlas and an innovative and modern methodology: a graphic language called “medical knowledge visualization”, dynamic and interactive web pages orchestrated by relational management database system, web and map servers.ResultsThis new prototype offers an example of three geo-referenced public hospitals (Dunkerque, Lille and Valenciennes) and its medical information system statistics and associated mapping. The Nord–Pas-de-Calais e-Atlas is displayed and accessible by users thanks to an advanced and secured web-mapping technology.Discussion and conclusionThanks to geographical access with the map, a medical graphic language (by clicking on PiNoKio's anatomy linked to hospital activity) and modern geographic information system architecture, we responded to the first critical assessments. The next version of e-Atlas will evolve into a whole open source environment and will be the subject of a future campaign whose goal will be a programmed medical choice.     

Two Robin Populations

Capsule This study is the first ever documented evidence of an interglacial refugium during the Last Interglacial for birds in Anatolia and suggests the need of a re-examination of the effects of the Last Interglacial on the geographic distribution and genetic structure of species.

Aims We tested whether, in accordance with the ‘refugia within refugia’ model, multiple refugia existed for Kruper's Nuthatch Sitta krueperi during the Last Glacial Maximum or the species survived along the coastal belt of Anatolia through the Late Quaternary glacial–interglacial cycles.

Methods An ecological niche model was developed to predict the geographic distribution of Kruper's Nuthatch under reconstructed past (the Last Interglacial and the Last Glacial Maximum), present, and projected future bioclimatic conditions. Also, robust coalescent-based analyses were used to assess demographic events over the history of Kruper's Nuthatch.

Results Kruper's Nuthatch survived the Last Glacial Maximum almost along the coastal belt of Anatolia, but not in multiple refugia, and surprisingly, contrary to expectations, it survived the Last Interglacial in southern Anatolia, but not along the coastal belt of Anatolia.

Conclusion A kind of the ‘refugia within refugia’ model (i.e. the ‘refugium within refugium’ model) was supported because range shifts took place within Anatolia (itself also a refugium) for Kruper's Nuthatch.     

How to evaluate and improve the quality and credibility of an outcomes database: validation and feedback study on the UK Cardiac Surgery Experience

ObjectivesTo assess the quality and completeness of a database of clinical outcomes after cardiac surgery and to determine whether a process of validation, monitoring, and feedback could improve the quality of the database.DesignStratified sampling of retrospective data followed by prospective re-sampling of database after intervention of monitoring, validation, and feedback.SettingTen tertiary care cardiac surgery centres in the United Kingdom.InterventionValidation of data derived from a stratified sample of case notes (recording of deaths cross checked with mortuary records), monitoring of completeness and accuracy of data entry, feedback to local data managers and lead surgeons.ResultsThe database was incomplete, with a mean (SE) of 24.96% (0.09%) of essential data elements missing, whereas only 1.18% (0.06%) were missing in the patient records (P<0.0001). Intervention was associated with (a) significantly less missing data (9.33% (0.08%) P<0.0001); (b) marginal improvement in reliability of data and mean (SE) overall centre reliability score (0.53 (0.15) v 0.44 (0.17)); and (c) improved accuracy of assigned Parsonnet risk scores (κ 0.84 v 0.70). Mortality scores (actual minus risk adjusted mortality) for all participating centres fell within two standard deviations of the mean score.ConclusionA short period of independent validation, monitoring, and feedback improved the quality of an outcomes database and improved the process of risk adjustment, but with substantial room for further improvement. Wider application of this approach should increase the credibility of similar databases before their public release.

What is already know in this topic

Release of healthcare outcomes into the public domain has altered referral patterns and has led to improvement in some centres and elimination of othersThe tacit assumption is that such outcomes data are accurate and can be relied on by the public and by healthcare providers to guide improvements

What this study adds

Sampling of a published national cardiac surgery database in England revealed it to be both incomplete and unreliable in its ability to yield accurate, risk adjusted outcomes dataAn independent short process of monitoring, validation, and feedback improved the quality of the databaseSuch databases probably require an ongoing process of monitoring in order to allow data of adequate quality to be generated for the purpose of improving healthcare outcomes     

脑卒中昏迷患者气管切开后并发肺部感染的病原菌分布及预防对策

目的:探讨脑卒中昏迷患者气管切开后并发肺部感染的病原菌分布及危险因素,并提出预防措施。方法:回顾性分析2016年1月至2017年2月我院收治的脑卒中昏迷患者96例,分析脑卒中昏迷患者肺部感染发生率及病原菌分布情况,同时采用单因素和多因素logistic回归分析肺部感染的危险因素,从而提出相应的预防措施。结果:96例脑卒中昏迷患者气管切开术后肺部感染的发生率为48.96%(47/96);共分离培养病原菌104株,包括革兰阴性菌69株(66.35%)、革兰阳性菌20株(19.23%)和真菌15株(14.42%);单因素分析结果显示,脑卒中昏迷患者气管切开术后肺部感染与年龄、基础疾病、气管切开时间、卧床时间、使用广谱抗菌药物、吸烟史、人工气道、吸痰次数及雾化吸入次数密切相关(P0.05),而与患者性别、体重、脑卒中类型无关(P0.05);多因素logistic回归分析结果显示,年龄45岁、合并患有基础疾病、气管切开时间5 d、使用广谱抗菌药物、吸烟史及建立人工气道均为脑卒中昏迷患者气管切开术后肺部感染的危险因素(P0.05),ROC分析结果为:气管切开时间的临界点(阈值C)是4.3天,其灵敏度和特异度将分别为0.851和0.918。结论:脑卒中昏迷患者气管切开后并发肺部感染的病原菌以革兰阴性菌为主,年龄45岁、合并患有基础疾病、气管切开时间5 d、使用广谱抗菌药物、吸烟史及建立人工气道能够导致脑卒中昏迷患者气管切开术后发生肺部感染,并且气管切开时间超过4.3天,脑卒中昏迷患者肺部感染的风险将大大增加,应根据病原学特征及其危险因素,采取针对性措施,降低肺部感染的发病风险。     

Solitary subcutaneous hydatid cyst: Review of the literature and report of a new case in the deltoid region

BackgroundSolitary subcutaneous hydatid cyst is not frequent and the only symptom is generally a silent growing mass. Total excision remains the mainstay of treatment. Aim of the study was to present a case surgically treated and perform a statistical analysis reviewing previous published works in order to define a correct approach to diagnosis and treatment.Methods264 documents from Medline database were considered for primary subcutaneous hydatid cyst cases. Data concerning geographic region, gender, age, job, location, evolving time, history and physical, mobility, diameter, laboratory, imaging, locularity (uni- or multilocular cyst), fine-needle aspiration, preoperative diagnosis, neoadjuvant chemotherapy, treatment, spillage, adjuvant therapy, follow-up and recurrences were ordered in a database and analysed performing t-test, Fisher's test and Pearson's test.Results23 cases, included ours, resulted suitable for our study. Lower extremities were involved in most cases (60.9%) and the thigh represented the most common site (34.8%), whereas upper extremities were the rarest location (8.7%). Patients with head and neck located cysts were younger than those with upper extremities cysts (P = 0.037). Patients who underwent multiple imaging approach received a significantly correct first diagnosis (P = 0.001) and ultrasonography, unlike other techniques, appeared to be essential (P = 0.013).Case reportA 68-year-old man who lived and worked in his farm in Sicily (Italy) presented with a 30-year-growing mass in the deltoid region measuring 10 cm. Ultrasonography and magnetic resonance imaging strongly suggested hydatid cyst. Therefore the cyst was excised and pathology confirmed the diagnosis.ConclusionSolitary subcutaneous hydatid cyst must always be considered in the differential diagnosis of silent growing mass in soft tissues. History and physical associated with ultrasound and magnetic resonance imaging are sufficient to achieve a correct preoperative diagnosis.     

Association of newborn blood lead concentration with neurodevelopment outcome in early infancy

BackgroundIn utero exposure to toxic metal substances can cause severe neurodevelopmental deficits in developing fetus and infant.MethodsWe evaluated the association of newborn umbilical cord blood lead concentration with early neurodevelopmental performance (cognitive, receptive language, expressive language, fine motor, gross motor and social-emotional development). The Bayley Scale of Infants Developments-III (BSID-III) was used to perform neurodevelopment outcomes at an average age of 6.5 months. In this prospective study, total of 167 mother-child pairs were enrolled from Western Rajasthan, India. Association between risk factors of lead contamination and newborn umbilical cord blood lead levels was observed. Multivariate regression was performed to see the association of cord blood lead level with infant neurodevelopment outcome.ResultsThe obtained newborn umbilical cord blood lead concentration 5.0–10.5 μg/dL was negatively associated with the sub-scale score of gross motor development (β-coefficient with 95 % CI; −0.29 (−5.0–0.11), p = 0.04). However, no associations were found with the score of cognitive, language, gross motor, and social-emotional development. The umbilical cord blood lead concentration <5.0 μg/dL was also not associated with the BSID-III scores. The mother's regular intake of calcium supplements during the antenatal period was significantly associated with a lower umbilical cord blood lead level (p-value 0.031).ConclusionThe data suggest that newborn umbilical cord blood lead concentration 0.5–10.5 μg/dL has a negative association with early gross motor development during infancy.     

Effects of total dissolved solids on growth and mortality predict distributions of stream macroinvertebrates

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Evolution And Historical Reductionism

Abstract

In response to Hoebel's criticism (1980) of the use of a dialectical model to interpret Cheyenne history, this article examines Hoebel's own views on kinship, politics, and social change. It is argued that Hoebel confuses descent with residence, and is committed to a methodology which necessarily gives inconclusive results. Most importantly, it is argued that Hoebel's theoretical perspective, characterized as “historical reductionism,” imposes a rigidly normative structure onto a society that was undergoing radical social change in the nineteenth century.     

IDO1 and IDO2 Non-Synonymous Gene Variants: Correlation with Crohn's Disease Risk and Clinical Phenotype

BackgroundCrohn''s disease (CD) is a chronic inflammatory disease of the gastrointestinal tract. Genetic polymorphisms can confer CD risk and influence disease phenotype. Indoleamine 2,3 dioxygenase-1 (IDO1) is one of the most over-expressed genes in CD and mediates potent anti-inflammatory effects via tryptophan metabolism along the kynurenine pathway. We aimed to determine whether non-synonymous polymorphisms in IDO1 or IDO2 (a gene paralog) are important either as CD risk alleles or as modifiers of CD phenotype.MethodsUtilizing a prospectively collected database, clinically phenotyped CD patients (n = 734) and non-IBD controls (n = 354) were genotyped for established IDO1 and IDO2 non-synonymous single nucleotide polymorphisms (SNPs) and novel genetic variants elucidated in the literature. Allelic frequencies between CD and non-IBD controls were compared. Genotype-phenotype analysis was conducted. IDO1 enzyme activity was assessed by calculating the serum kynurenine to tryptophan ratio (K/T).ResultsIDO1 SNPs were rare (1.7% non-IBD vs 1.1% CD; p = NS) and not linked to Crohn''s disease diagnosis in this population. IDO1 SNPs did however associate with a severe clinical course, presence of perianal disease, extraintestinal manifestations and a reduced serum K/T ratio during active disease suggesting lower IDO1 function. IDO2 minor allele variants were common and one of them, rs45003083, associated with reduced risk of Crohn''s disease (p = 0.025). No IDO2 SNPs associated with a particular Crohn''s disease clinical phenotype.ConclusionsThis work highlights the functional importance of IDO enzymes in human Crohn''s disease and establishes relative rates of IDO genetic variants in a US population.     

Roles of maternal HDL during pregnancy

BackgroundHigh density lipoproteins (HDL) were first linked to cardiovascular disease (CVD) over 30 years ago when an inverse relationship was shown between CVD and HDL-cholesterol levels. It is now apparent that HDL composition and function, not cholesterol levels, are the pertinent measurements describing HDL's role in various disease processes, especially those with subclinical or overt inflammation.Scope of reviewPregnancy is also an inflammatory state. When inflammation becomes excessive during pregnancy, there is an increased risk for adverse outcomes that affect the health of the mother and fetus, including preterm birth and preeclampsia. Though studies on HDL during pregnancy are limited, recent evidence demonstrates that HDL composition and function change during pregnancy and in women with adverse outcomes.General significanceIn this review, we will discuss how HDL may play a role in maintaining a healthy pregnancy and how impairments in function could lead to pregnancies with adverse outcomes.