The Development of Multi-epitope Vaccines: Epitope Identification, Vaccine Design and Clinical Evaluation

We have developed efficient methods for epitope identification and vaccine design. Our process for epitope selection based on the combined use of motif analyses, binding assays and immunogenicity evaluations is described. We also describe how the projected population coverage and vaccine design can be optimized. Finally, it is discussed how vaccine potency is evaluated by immunogenicity and antigenicity assays.     

典型矿区植被覆盖度时空分布特征及影响因素

植被状况可以直接或间接地反映采煤对生态环境的影响。以长河井工煤矿、离柳井工煤矿、平朔露天煤矿3个典型矿区为研究区域。以Landsat数据为数据源，基于地形调节植被指数的像元二分模型提取植被覆盖度；采用趋势分析、线性回归斜率、稳定性分析方法，分析了3个典型矿区2001-2016年植被覆盖度的时空变化特征；运用"以时间换空间"的方法，采用相关分析方法对植被覆盖度变化的自然影响因素进行了分析。结果表明：（1）近16年3个典型矿区植被覆盖度呈增加趋势，长河、离柳、平朔矿区的增长速率分别为0.09%/10 a、0.10%/10 a、0.08%/10 a（P > 0.05）。（2）空间上，长河、离柳、平朔矿区植被覆盖度变化不明显比例分别占到66.63%，59.90%，62.25%，呈增加趋势的比例仅分别占28.14%、32.55%、27.81%，而呈减少趋势的比例分别占到5.23%、7.55%、9.94%。长河矿区明显改善的区域位于自然植被和耕作区的北部和东北部，离柳矿区明显改善的区域位于以低植被覆盖度为主的北部，平朔矿区明显改善的区域位于复垦的中西部。（3）不区分植被类型时，3个矿区的植被覆盖度变化与高程、高程与温度的交互作用表现出显著相关性（P < 0.01），与各自然因素的相关性总体表现为长河 > 离柳 > 平朔矿区；区分植被类型时，草地与坡度的相关性不显著（P > 0.05），与降雨量、高程存在显著正相关（P < 0.05）；灌木林与温度相关性不显著，与高程和降雨量的交互作用存在显著正相关；旱地与高程、高程与温度的交互作用存在显著相关性；疏林地与坡向、降雨量与坡向坡度的交互作用均没有表现出相关性；有林地与高程降雨量的交互作用表现出显著正相关性。探讨不同植被类型对自然因素的响应，可为矿区植被结构的选择，矿区复垦提供参考依据。     

Societal Risk Perception in Arab Countries: The Case of Kuwait

The study was aimed at examining data on risk perception from an Arab country—Kuwait—in order to support the existence of an Arab group as regards the way hazards are perceived. The data were gathered in 2003 and 2004 on two Kuwaiti samples of young adults and adolescents. The questionnaire used was the one used in studies conducted in Egypt and France. It comprised 141 items. The overall mean value observed in the Kuwaiti sample was close to the one found in the Egyptian sample. The linear association between Kuwaiti and French ratings was moderate (0.70) and of the same magnitude as the one found between Egyptian and French ratings. The association between Kuwaiti and Egyptian ratings was greater (0.90). In 80% of the hazards, the specific differences observed between the Kuwaiti and French ratings were the same as the ones observed between Egyptian and French ratings. The whole set of findings supports the hypothesis that Kuwaitis and Egyptians, despite huge differences in the socioeconomic environments in which they live, perceive societal risks in a common way, a way that is different from the way Western Europeans perceive them.     

Prediction Intervals in Nonlinear Regression

By treating the nonlinear model as if it were linear in the parameterization θ in the neighbourhood of the least squares estimate θ, we construct two-sided nominally-q-prediction intervals by applying the usual linear model theory. The derivation of the truncated series expansion of the expected coverage of the prediction intervals at a feasible value of the parameter vector is described. The quadratic approximation of the expected coverage is then obtained for a two-parameter nonlinear model. Finally we show how we may construct the prediction intervals when a certain type of nonlinear transformation of the parameter vector has been applied.     

Effective aerial monitoring of cyanobacterial harmful algal blooms is dependent on understanding cellular migration

Cyanobacterial harmful algal blooms (CHABs) degrade water quality and may produce toxins. The distribution of CHABs can change rapidly due to variations in population dynamics and environmental conditions. Biological and ecological aspects of CHABs were studied in order to better understand CHABs dynamics. Field experiments were conducted near Hartington, Ontario, Canada in ponds dominated by Microcystis aeruginosa and CHABs floating experiments were conducted at Lake Taihu during the summers of 2015 and 2016. Single colonies composed of hundreds to thousands of cells with an average median of 0.2–0.5 mm in diameter were the basic form assumed by the Microcystis, and this remained the same throughout the growing season. Thorough mixing of the water column followed by calm conditions resulted in over 90% of the cyanobacteria floating after 1 h. Multiple colonies floated on the water surface in four types of assemblages: aggregates, ribbons, patches, and mats. It is the mats that are conventionally considered the blooming stage of cyanobacteria.Presence of CHABs on open water surfaces also depends on environmental influences such as direct and indirect wind effects. For example, field tests revealed that the surface coverage of CHABs can be reduced to half within an hour at wind speeds of 0.5 m/s.Because our findings indicated that blooming involves surface display of cyanobacteria essentially presenting as a two-dimensional plane under defined conditions, the use of surface imagery to quantify CHABs was justified. This is particularly important in light of the fact that traditional detection methods do not provide accurate distribution information. Nor do they portray CHABs events in a real-time manner due to limitations in on-demand surveillance and delays between sample time and analyzed results. Therefore, a new CHAB detection method using small unmanned aerial systems with consumer-grade cameras was developed at a maximum detection altitude of 80 m. When cyanobacteria were floating on the surface, CHABs detection through RGB band cameras and spectral enhancement techniques was efficient and accurate. Small unmanned aerial systems were capable of providing coverage up to 1 km² per mission and the short intervals between sampling and results (approx. 2 h) allowed for the rapid analysis of data and for implementing follow-up monitoring or treatments. This method is very cost-effective at an estimate of as low as $100 CAD per mission with an average cyanobacterial detection accuracy of 86%. Thus, it is a good candidate method to fill the urgent need for CHABs detection, providing cost effective, rapid, and accurate information to improve risk management at a local level as well as to help quickly allocate resources for purposes of mitigation.     

Generalized and species-specific prediction models for aboveground biomass in semi-steppe rangelands

Aims The accurate estimation of aboveground biomass in vegetation is critical for global carbon accounting. Regression models provide an easy estimation of aboveground biomass at large spatial and temporal scales. Yet, only few prediction models are available for aboveground biomass in rangelands, as compared with forests. In addition to the development of prediction models, we tested whether such prediction models vary with plant growth forms and life spans, and with the inclusion of site and/or quadrat-specific factors.     

An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity

Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low‐coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high‐density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low‐density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.     

Fast protein sequencing of monoclonal antibody by real-time digestion on emitter during nanoelectrospray

Growth in the pharmaceutical industry has led to an increasing demand for rapid characterization of therapeutic monoclonal antibodies. The current methods for antibody sequence confirmation (e.g., N-terminal Edman sequencing and traditional peptide mapping methods) are not sufficient; thus, we developed a fast method for sequencing recombinant monoclonal antibodies using a novel digestion-on-emitter technology. Using this method, a monoclonal antibody can be denatured, reduced, digested, and sequenced in less than an hour. High throughput and satisfactory protein sequence coverage were achieved by using a non-specific protease from Aspergillus saitoi, protease XIII, to digest the denatured and reduced monoclonal antibody on an electrospray emitter, while electrospray high voltage was applied to the digestion mixture through the emitter. Tandem mass spectrometry data was acquired over the course of enzyme digestion, generating similar information compared to standard peptide mapping experiments in much less time. We demonstrated that this fast protein sequencing method provided sufficient sequence information for bovine serum albumin and two commercially available monoclonal antibodies, mouse IgG1 MOPC21 and humanized IgG1 NISTmAb. For two monoclonal antibodies, we obtained sequence coverage of 90.5–95.1% for the heavy chains and 98.6–99.1% for the light chains. We found that on-emitter digestion by protease XIII generated peptides of various lengths during the digestion process, which was critical for achieving sufficient sequence coverage. Moreover, we discovered that the enzyme-to-substrate ratio was an important parameter that affects protein sequence coverage. Due to its highly automatable and efficient design, our method offers a major advantage over N-terminal Edman sequencing and traditional peptide mapping methods in the identification of protein sequence, and is capable of meeting an ever-increasing demand for monoclonal antibody sequence confirmation in the biopharmaceutical industry.     

云南中部地区植被覆盖时空变化特征及其影响因素研究

基于MODIS NDVI数据通过像元二分模型提取植被覆盖,利用线性趋势、相关分析方法分析了云南中部地区2000-2016年植被覆盖的时空分布特征与变化趋势,并探讨了气候因子、地形因子、人类活动对其植被覆盖的影响。研究结果为:云南中部地区植被覆盖春季最低(平均58.75%),秋季最高(平均66.30%),大部分地区年植被覆盖度的平均值在50%-70%之间;植被覆盖高值区主要分布在曲靖境内(>80%);滇池周边人口高密度区植被覆盖常年最低(<20%)。近17年来云南中部地区植被覆盖总体呈现增长趋势,年平均增长率0.3%·a^-1,其中秋季增幅最大(0.42%·a^-1)。坡度对植被覆盖影响较大,坡度≤8°地区的植被覆盖明显较低。除了冬季降水量与植被覆盖呈现显著正相关关系,其他季节多呈现负相关关系;气温与植被覆盖多呈现正相关关系,云南中部地区植被覆盖变化主要受气温影响。人类活动对植被覆盖变化影响较大,造林面积变化与植被覆盖趋势变化具有相对一致性,经济发展水平较高的昆明市区植被覆盖为常年最低。     

宁夏东部风沙区沙化草地土壤水分和植被的空间特征

土壤水分作为土壤-植被-大气连续体的关键因子,对沙化草地的演化过程具有重要作用。为探讨宁夏东部风沙区沙化草地土壤水分、物种丰富度指数及植被盖度的空间变异及其相互关系,以哈巴湖自然保护区沙化草地为对象,采用样线法自潜在沙化草地至重度沙化草地进行植被调查和土壤取样,通过经典统计学和地统计学分析,得出以下结果：0—100 m各土层土壤水分含量、植被盖度和物种丰富度指数的分布范围分别为0.82%—28.22%、41.00%—93.00%和0.82—2.80,变异系数范围为0.20—0.48,均属于中等变异。各土层土壤水分和物种丰富度指数表现为中等的空间自相关性,植被盖度则表现为强烈的空间自相关性。Kriging插值结果表明,0—100 cm各土层土壤水分和植被盖度的空间插值图呈条带状和斑块状的梯度变化,物种丰富度呈斑块分布,自潜在沙化草地至重度沙化草地,表现为逐渐降低的趋势。相关分析表明,植被盖度与0—40 cm各土层土壤水分呈显著正相关,与40—100 cm各土层土壤水分呈极显著正相关。宁夏东部风沙区沙化草地土壤水分含量总体较低,由于结构因素和随机因素的共同作用,随草地沙化程度的加重,表现为...