Basics of Multivariate Analysis in Neuroimaging Data

Multivariate analysis techniques for neuroimaging data have recently received increasing attention as they have many attractive features that cannot be easily realized by the more commonly used univariate, voxel-wise, techniques^1,5,6,7,8,9. Multivariate approaches evaluate correlation/covariance of activation across brain regions, rather than proceeding on a voxel-by-voxel basis. Thus, their results can be more easily interpreted as a signature of neural networks. Univariate approaches, on the other hand, cannot directly address interregional correlation in the brain. Multivariate approaches can also result in greater statistical power when compared with univariate techniques, which are forced to employ very stringent corrections for voxel-wise multiple comparisons. Further, multivariate techniques also lend themselves much better to prospective application of results from the analysis of one dataset to entirely new datasets. Multivariate techniques are thus well placed to provide information about mean differences and correlations with behavior, similarly to univariate approaches, with potentially greater statistical power and better reproducibility checks. In contrast to these advantages is the high barrier of entry to the use of multivariate approaches, preventing more widespread application in the community. To the neuroscientist becoming familiar with multivariate analysis techniques, an initial survey of the field might present a bewildering variety of approaches that, although algorithmically similar, are presented with different emphases, typically by people with mathematics backgrounds. We believe that multivariate analysis techniques have sufficient potential to warrant better dissemination. Researchers should be able to employ them in an informed and accessible manner. The current article is an attempt at a didactic introduction of multivariate techniques for the novice. A conceptual introduction is followed with a very simple application to a diagnostic data set from the Alzheimer s Disease Neuroimaging Initiative (ADNI), clearly demonstrating the superior performance of the multivariate approach.     

Declines of zoonotic agents in liquid livestock wastes stored in batches on-farm

AIM: To measure the decline rates of zoonotic agents introduced into liquid livestock wastes in on-farm storage tanks. METHODS AND RESULTS: Salmonella spp., Escherichia coli O157, Campylobacter jejuni, Listeria monocytogenes and Cryptosporidium parvum, propagated in laboratory-controlled conditions, were inoculated into 35,000-l volumes of fresh livestock wastes (pig slurries, cattle slurries and dirty waters). D-values for bacteria were six to 44 days, and for C. parvum were 133 to 345 days. Campylobacter jejuni declined significantly more rapidly than the other bacterial pathogens, while E. coli O157 declined significantly more slowly. On average, bacterial declines were not affected by the season of waste deposition and storage or by the dry matter content of the wastes, but were more rapid in dirty waters than in pig slurries. The physiciochemical composition of wastes in each category varied significantly. CONCLUSIONS: Zoonotic agents can survive for several months during storage of liquid livestock wastes. Livestock wastes should be batch-stored and not subjected to continuous additions. SIGNIFICANCE AND IMPACT OF THE STUDY: This study indicates that batches of liquid livestock waste, if contaminated with bacterial pathogens, should be stored for 6 months to reduce contamination levels. Alternative strategies for reducing C. parvum levels in liquid livestock wastes should be explored.     

The conversion of the corn/soybean ecosystem to no-till agriculture may result in a carbon sink

Mitigating or slowing an increase in atmospheric carbon dioxide concentration ([CO₂]) has been the focus of international efforts, most apparent with the development of the Kyoto Protocol. Sequestration of carbon (C) in agricultural soils is being advocated as a method to assist in meeting the demands of an international C credit system. The conversion of conventionally tilled agricultural lands to no till is widely accepted as having a large-scale sequestration potential. In this study, C flux measurements over a no-till corn/soybean agricultural ecosystem over 6 years were coupled with estimates of C release associated with agricultural practices to assess the net biome productivity (NBP) of this no-till ecosystem. Estimates of NBP were also calculated for the conventionally tilled corn/soybean ecosystem assuming net ecosystem exchange is C neutral. These measurements were scaled to the US as a whole to determine the sequestration potential of corn/soybean ecosystems, under current practices where 10% of agricultural land devoted to this ecosystem is no-tilled and under a hypothetical scenario where 100% of the land is not tilled. The estimates of this analysis show that current corn/soybean agriculture in the US releases ∼7.2 Tg C annually, with no-till sequestering ∼2.2 Tg and conventional-till releasing ∼9.4 Tg. The complete conversion of land area to no till might result in 21.7 Tg C sequestered annually, representing a net C flux difference of ∼29 Tg C. These results demonstrate that large-scale conversion to no-till practices, at least for the corn/soybean ecosystem, could potentially offset ca. 2% of annual US carbon emissions.     

Environmental (in)dependence of a hybrid zone: Insights from molecular markers and ecological niche modeling in a hybrid zone of Origanum (Lamiaceae) on the island of Crete

The role of environment and the relative significance of endogenous versus exogenous selection in shaping hybrid zones have been crucial issues in the studies of hybridization. Recent advances in ecological niche modeling (ENM) offer new methodological tools, especially in combination with the genotyping of individuals in the hybrid zone. Here, we study the hybrid zone between the widely known spices Origanum onites and Origanum vulgare ssp. hirtum in Crete. We analyze the genetic structure of both parental taxa and their hybrid Origanum × intercendens using AFLP markers on 15 sympatric and 12 allopatric populations and employ ecological niche modeling and niche similarity tests to study their niche patterns. We complement these analyses with seed viability measurements. Our study revealed that the hybridizing taxa O. onites and O. vulgare ssp. hirtum and the resulting genotypic classes showed geographical and environmental niche similarities based on the predictions of ENMs and the subsequent similarity tests. The occurrence of the hybrid zone is not directly dependent on environmental factors which favor the fitness of the hybrid compared to the parental taxa, but rather on aspects such as historical factors and management practices, which may contribute to the localization and maintenance of the contact zone between parental species. Our results suggest that if a minimum required niche differentiation between genotypic classes is not achieved, environmental dependence might not have a prominent role on the outcome of the hybridization.     

综合性医院临床科室目标管理效益效率分析

目的 通过对临床科室综合目标管理效益效率考核实施情况进行分析,评价考核方法及考核成效,为医院改进相关考核工作提供参考。方法 科学确立考核指标,并应用横向比较法实证分析安徽医科大学第二附属医院2012年各临床科室综合目标管理效益效率考核实施情况。结果 确立以门诊人次、出院人次、手术台次、净收益、每医生实际占用总床日等为核心指标的测算方案,对12个内科科室、10个外科科室进行测算并获得排名,结果基本客观公正地反映了科室效益效率情况。结论 采用横向比较方法对上述指标进行评价能有效反映效益效率考核要求,一定程度上克服科室之间不能直接比较的困难。该评价方法及测算过程简单实用,易于操作,在医院综合目标管理体系效益效率考核中有着一定的应用价值。

     

Patient ratings of chewing ability from a randomised crossover trial: lingualised vs. first premolar/canine-guided occlusion for complete dentures

Background: Complex procedures involving a facebow transfer and the use of lingualised teeth are deemed to have a positive influence on the chewing ability with complete dentures. Objectives: To determine if patients’ ratings of their ability to chew depend on the method of complete denture fabrication. Methods: Edentulous patients (n = 20) participated in a within‐subject crossover trial. Each patient received two sets of new complete dentures. One pair was manufactured based on intraoral tracing of centric relation and facebow transfer; semi‐anatomical teeth with lingualised occlusion denture (LOD) were chosen. The second pair was made using a simplified procedure without facebow transfer; jaw relations were recorded with wax occlusion rims, and anatomical teeth with a first premolar/canine‐guidance (CGD) were selected. The dentures were delivered in randomised order, and each was worn for 3 months. Three months after delivery, patients’ ratings of each new prosthesis were recorded on visual analogue scales for their ability to chew seven index foods. Repeated measurements analysis of variance was performed to investigate possible carry‐over effects accounting for confounding by treatment period. Results: When comparing the two treatments, participants rated their ability to chew in general, to masticate carrots, hard sausage, steak and raw apple in particular, was significantly better with the CGD (anatomical teeth) than with the LOD (p < 0.05). Conclusion: Comprehensive methods for the fabrication of complete dentures including semi‐anatomical lingualised teeth and a full registration do not seem to influence the perceived chewing ability, when compared with more simple procedures. Chewing ability for tough foods appears to benefit from the use of anatomical teeth.     

Downregulation of microRNA‐15a‐3p is correlated with clinical outcome and negatively regulates cancer proliferation and migration in human osteosarcoma

In this study, we investigated the expression, correlation to clinical outcomes and biological functions of microRNA‐15a‐3p (miR‐15a‐3p) in human osteosarcoma. MiR‐15a‐3p expressions in osteosarcoma cell lines and clinical tissues of osteosarcoma patients were measured by qPCR. Relevance of endogenous miR‐15a‐3p to osteosarcoma patients' clinicopathological factors or overall survival was statistically analyzed. In addition, the independence of miR‐15a‐3p predicting cancer patients' overall survival was analyzed by Cox regression method. Furthermore, in osteosarcoma cell lines, Saos‐2 and HOS cells, miR‐15a‐3p was overexpressed through stable lentiviral transduction. The functional regulations of miR‐15a‐3p overexpression on cancer ell proliferation and migration were then analyzed. MiR‐15a‐3p was significantly downregulated in osteosarcoma cell lines and human osteosarcoma tumors. Downregulation of endogenous miR‐15a‐3p in osteosarcoma tumors was significantly associated with cancer patient's poor clinical outcomes and low survival rate. Also, endogenous miR‐15a‐3p was confirmed to be an independent biomarker for predicating cancer patients' survival. In Saos‐2 and HOS cells, lentivirus‐induced miR‐15a‐3p overexpression had significantly tumor suppressing functions, by inhibiting both proliferation and migration. Significant downregulation of miR‐15a‐3p in osteosarcoma may be an independent biomarker to predicting cancer patients' poor prognosis. Overexpression miR‐15a‐3p may be an efficient functional meaning to suppress osteosarcoma development.     

Apolipoprotein A-V is a potential target for treating coronary artery disease: evidence from genetic and metabolomic analyses

Triglyceride (TG)-lowering LPL variants in combination with genetic LDL-C-lowering variants are associated with reduced risk of coronary artery disease (CAD). Genetic variation in the APOA5 gene encoding apolipoprotein A-V also strongly affects TG levels, but the potential clinical impact and underlying mechanisms are yet to be resolved. Here, we aimed to study the effects of APOA5 genetic variation on CAD risk and plasma lipoproteins through factorial genetic association analyses. Using data from 309,780 European-ancestry participants from the UK Biobank, we evaluated the effects of lower TG levels as a result of genetic variation in APOA5 and/or LPL on CAD risk with or without a background of reduced LDL-C. Next, we compared lower TG levels via APOA5 and LPL variation with over 100 lipoprotein measurements in a combined sample from the Netherlands Epidemiology of Obesity study (N = 4,838) and the Oxford Biobank (N = 6,999). We found that lower TG levels due to combined APOA5 and LPL variation and genetically-influenced lower LDL-C levels afforded the largest reduction in CAD risk (odds ratio: 0.78 (0.73–0.82)). Compared to patients with genetically-influenced lower TG via LPL, genetically-influenced lower TG via APOA5 had similar and independent, but notably larger, effects on the lipoprotein profile. Our results suggest that lower TG levels as a result of APOA5 variation have strong beneficial effects on CAD risk and the lipoprotein profile, which suggest apo A-V may be a potential novel therapeutic target for CAD prevention.