Statistical shape and appearance models for fast and automated estimation of proximal femur fracture load using 2D finite element models

Estimating the risk of osteoporotic fractures is an important diagnostic step that needs to be taken before medicinal treatment. Densitometry-based criteria are normally used in clinical practice for this purpose. However, densitometry-based techniques could not explain all low-energy fractures. As patient-specific finite element (FE) models allow for consideration of other parameters (e.g. load conditions) that are known to be associated with fracture, they are considered promising candidates for more accurate fracture risk estimation. Nevertheless, they are often time consuming, expensive, and complex to build and may need the type of expertise that is not normally available in clinical settings. In this study, we report the development of an automated platform for estimating proximal femur fracture loads using patient-specific 2D FE models generated using dual-energy x-ray absorptiometry (DXA) scans. First, a statistical shape and appearance model (SSAM) is built using DXA scans of patients screened for osteoporosis following a low energy fracture. SSAM is then used together with Active Appearance Models (AAM) for automated segmentation of the proximal femur from new unseen DXA scans. The mean point-to-curve error of the automated procedure, i.e. 1.2–1.4 mm, is shown to be only slightly larger than the intra-observer variability of manual segmentation, i.e. 1.0 mm. Moreover, the developed platform automatically meshes the segmented shape, assigns density-based mechanical properties, assigns loads and boundary conditions, submits the 2D FE model for solution, and performs post-processing of the 2D FE simulation data to determine fracture loads. The fracture loads predicted using the manually generated and automatically generated 2D FE models are shown to be very close with a mean difference of around 8.8%. Repeated measures ANOVA showed no significant differences between the fracture loads calculated using FE models manually generated by three independent observers and those calculated using the automatically generated FE models (p>0.05).     

LipidSeq: a next-generation clinical resequencing panel for monogenic dyslipidemias

We report the design of a targeted resequencing panel for monogenic dyslipidemias, LipidSeq, for the purpose of replacing Sanger sequencing in the clinical detection of dyslipidemia-causing variants. We also evaluate the performance of the LipidSeq approach versus Sanger sequencing in 84 patients with a range of phenotypes including extreme blood lipid concentrations as well as additional dyslipidemias and related metabolic disorders. The panel performs well, with high concordance (95.2%) in samples with known mutations based on Sanger sequencing and a high detection rate (57.9%) of mutations likely to be causative for disease in samples not previously sequenced. Clinical implementation of LipidSeq has the potential to aid in the molecular diagnosis of patients with monogenic dyslipidemias with a high degree of speed and accuracy and at lower cost than either Sanger sequencing or whole exome sequencing. Furthermore, LipidSeq will help to provide a more focused picture of monogenic and polygenic contributors that underlie dyslipidemia while excluding the discovery of incidental pathogenic clinically actionable variants in nonmetabolism-related genes, such as oncogenes, that would otherwise be identified by a whole exome approach, thus minimizing potential ethical issues.     

Prevalence and Risk Factors of Clonorchiasis among Residents of Riverside Areas in Muju-gun,Jeollabuk-do,Korea

We evaluated the status of Clonorchis sinensis infection and potential risk factors among residents of riverside areas (Geumgang) in Muju-gun, Jeollabuk-do (Province), Korea. From January to February 2010, a total of 349 (171 males, 178 females) stool samples were collected and examined by the formalin-ether concentration technique. Also, village residents were interviewed using questionnaires to obtain information about C. sinensis infection-related risk factors. Overall egg-positive rate of C. sinensis was 13.2%. Egg-positive rates were significantly higher in males, farmers, and residents who had lived there more than 20 years, and in residents who had eaten raw freshwater fish than in opposite groups, respectively. However, there was no significant difference between age groups, education levels, cigarette smoking, alcohol drinking, health status, past history of infection, and experience of clonorchiasis medication and examination. Logistic regression analysis was performed to determine risk factors for clonorchiasis. On univariate analysis, the odds ratios for males, farmers, those who had lived there more than 20 years, and who had eaten raw freshwater fish were 2.41, 4.44, 3.16, and 4.88 times higher than those of the opposites, respectively. On multivariate analysis, the odds ratio of residents who had eaten raw freshwater fish was 3.2-fold higher than that of those who had not. These results indicate that residents living in Muju-gun, along the Geum River, Korea, have relatively high C. sinensis egg-positive rates, and the habit of eating raw freshwater fish was the major factor for the maintenance of clonorchiasis.     

Can plants serve as a vector for prions causing chronic wasting disease?

Prions, the causative agent of chronic wasting disease (CWD) enter the environment through shedding of bodily fluids and carcass decay, posing a disease risk as a result of their environmental persistence. Plants have the ability to take up large organic particles, including whole proteins, and microbes. This study used wheat (Triticum aestivum L.) to investigate the uptake of infectious CWD prions into roots and their transport into aerial tissues. The roots of intact wheat plants were exposed to infectious prions (PrP^TSE) for 24 h in three replicate studies with PrP^TSE in protein extracts being detected by western blot, IDEXX and Bio-Rad diagnostic tests. Recombinant prion protein (PrP^C) bound to roots, but was not detected in the stem or leaves. Protease-digested CWD prions (PrP^TSE) in elk brain homogenate interacted with root tissue, but were not detected in the stem. This suggests wheat was unable to transport sufficient PrP^TSE from the roots to the stem to be detectable by the methods employed. Undigested PrP^TSE did not associate with roots. The present study suggests that if prions are transported from the roots to the stems it is at levels that are below those that are detectable by western blot, IDEXX or Bio-Rad diagnostic kits.     

A statistical simulation model for field testing of non‐target organisms in environmental risk assessment of genetically modified plants

Genetic modification of plants may result in unintended effects causing potentially adverse effects on the environment. A comparative safety assessment is therefore required by authorities, such as the European Food Safety Authority, in which the genetically modified plant is compared with its conventional counterpart. Part of the environmental risk assessment is a comparative field experiment in which the effect on non‐target organisms is compared. Statistical analysis of such trials come in two flavors: difference testing and equivalence testing. It is important to know the statistical properties of these, for example, the power to detect environmental change of a given magnitude, before the start of an experiment. Such prospective power analysis can best be studied by means of a statistical simulation model. This paper describes a general framework for simulating data typically encountered in environmental risk assessment of genetically modified plants. The simulation model, available as Supplementary Material, can be used to generate count data having different statistical distributions possibly with excess‐zeros. In addition the model employs completely randomized or randomized block experiments, can be used to simulate single or multiple trials across environments, enables genotype by environment interaction by adding random variety effects, and finally includes repeated measures in time following a constant, linear or quadratic pattern in time possibly with some form of autocorrelation. The model also allows to add a set of reference varieties to the GM plants and its comparator to assess the natural variation which can then be used to set limits of concern for equivalence testing. The different count distributions are described in some detail and some examples of how to use the simulation model to study various aspects, including a prospective power analysis, are provided.     

红火蚁在云南的入侵风险分析

[背景]红火蚁是一种严重威胁公共设施、动植物和人类安全的重要害虫,在国际上被列为极具破坏性和攻击性的入侵生物之一。自2004年在我国大陆广东省首次发现以来,其发生范围急剧扩大,目前已扩散至南方多个省份。[方法]通过分析该虫进入、定殖和扩散的可能性、危害影响和危害管理难度等5个方面,依据国际植物检疫措施标准（ISPM）中的有害生物风险分析原则,利用云南外来入侵有害生物多指标综合评价体系,对红火蚁在云南的入侵风险进行评估。[结果]通过定性和定量风险分析,对其入侵云南的风险做出综合评价,得出风险评估值R=2．25。[结论与意义]红火蚁在云南属高度风险的有害生物,需在云南各口岸进境检疫中实施相应的风险管理,分析结果可为云南省开展红火蚁的检疫防控提供参考。     

Human risk associated with the ingestion of artichokes grown in soils irrigated with water contaminated by potentially toxic elements,Junin, Peru

The contamination of water, air and soil with potentially toxic elements (PTE) compromises the supply of contaminant free food. Vegetables grown in contaminated soils can absorb and accumulate PTE at concentrations that are toxic to human health. In this context, the human risk associated with the intake of artichokes grown in soils irrigated with PTE contaminated water was assessed. 120 samples of surface soil and artichoke heads were collected and the concentrations of Cu, Fe, Pb, Zn and As were determined. The results showed that the concentrations of Cu, Fe and Zn in soil did not exceed the standards of the Ministry of Environment of Peru, but they did exceed those of Pb (125.45 mg kg⁻¹) and As (28.70 mg kg⁻¹). The decreasing order of mean PTE concentration in artichoke heads was Fe > Zn > Cu > Pb > As, exceeding the permissible levels of FAO/WHO CODEX Alimentarius. However, the concentrations of As comply with the maximum limits of inorganic contaminants in vegetables (0.3 mg kg⁻¹) established in the MERCOSUR regulations. The non-carcinogenic and carcinogenic risk of Pb and As indicated that the ingestion of artichoke heads does not represent a health risk.     

Species distribution models for invasive Eurasian watermilfoil highlight the importance of data quality and limitations of discrimination accuracy metrics

AimAvailability of uniformly collected presence, absence, and abundance data remains a key challenge in species distribution modeling (SDM). For invasive species, abundance and impacts are highly variable across landscapes, and quality occurrence and abundance data are critical for predicting locations at high risk for invasion and impacts, respectively. We leverage a large aquatic vegetation dataset comprising point‐level survey data that includes information on the invasive plant Myriophyllum spicatum (Eurasian watermilfoil) to: (a) develop SDMs to predict invasion and impact from environmental variables based on presence–absence, presence‐only, and abundance data, and (b) compare evaluation metrics based on functional and discrimination accuracy for presence–absence and presence‐only SDMs.LocationMinnesota, USA.MethodsEurasian watermilfoil presence–absence and abundance information were gathered from 468 surveyed lakes, and 801 unsurveyed lakes were leveraged as pseudoabsences for presence‐only models. A Random Forest algorithm was used to model the distribution and abundance of Eurasian watermilfoil as a function of lake‐specific predictors, both with and without a spatial autocovariate. Occurrence‐based SDMs were evaluated using conventional discrimination accuracy metrics and functional accuracy metrics assessing correlation between predicted suitability and observed abundance.ResultsWater temperature degree days and maximum lake depth were two leading predictors influencing both invasion risk and abundance, but they were relatively less important for predicting abundance than other water quality measures. Road density was a strong predictor of Eurasian watermilfoil invasion risk but not abundance. Model evaluations highlighted significant differences: Presence–absence models had high functional accuracy despite low discrimination accuracy, whereas presence‐only models showed the opposite pattern.Main conclusionComplementing presence–absence data with abundance information offers a richer understanding of invasive Eurasian watermilfoil''s ecological niche and enables evaluation of the model''s functional accuracy. Conventional discrimination accuracy measures were misleading when models were developed using pseudoabsences. We thus caution against the overuse of presence‐only models and suggest directing more effort toward systematic monitoring programs that yield high‐quality data.     

黄顶菊在中国的潜在适生区

菊科黄菊属植物黄顶菊近年出现在我国华北地区天津市和河北省的衡水、廊坊等地,其入侵范围有不断扩大的趋势.黄顶菊是一种入侵性极高的一年生杂草,对农牧业生态系统有极大的破坏性.为指导黄顶菊的防除和制定相关的控制政策,本研究根据黄顶菊在其原产地南美洲及扩散入侵地的分布资料,采用CLIMEX生态位模型对其在中国的潜在适生分布区域进行预测.结果表明,黄顶菊在中国的潜在适生区域集中分布于东南部的广东、广西、云南、海南、福建、台湾、江西、湖南、贵州、四川、重庆、湖北、安徽、江苏、上海15个省（市、自治区）,其中高风险区域包括广东、广西、台湾、海南、福建、云南、四川、贵州、重庆和西藏局部地区.     

围垦滩涂湿地旱生耐盐植物的入侵和影响

以上海市崇明东滩1998年围垦湿地为例,基于彩红外航片的景观格局分析以及样地群落调查,分析了湿地人工排水后,旱生耐盐植物在湿地原生芦苇群落中的入侵和影响.结果表明：以碱菀为建群种的旱生耐盐植物群落在围垦湿地区从东北向西南扩散,速度达143 m·a^-1,原生芦苇斑块迅速收缩、破碎,缀块密度指数和形状指数分别增长22.7倍和1.3倍;2006和2007年两个生长季后群落中碱菀生物量高达2783.8 g·m^-2,占群落总生物量的98％,重要值达88%;芦苇生物量和重要值则分别下降98％和83%.表明侵入过程与地下0～20 cm土壤水分和土壤盐度密切相关.应深入研究旱生耐盐植物的侵入机制,探讨合理、动态的湿地排水管理策略,以便控制旱生耐盐植物群落的迅速入侵.