ALBERT

Description: The objectives of this study were to estimate the effects of temperature on cardiovascular mortality in 26 regions in the south and west of China from 2008 to 2011, and to identify socioeconomic and demographic factors contributing to such inter-region variation in the temperature effect. A separate Poisson generalized additive model (GAM) was fitted to estimate percent changes in cardiovascular mortality at low and high temperatures on a daily basis for each region. The model used the smooth functions to model the nonlinear effects of temperature and humidity and to control for the seasonal factor using the calendar time variable. Given variation in the magnitude of the temperature effect on cardiovascular mortality, we employed a Bayesian network (BN) to identify potential region-specific socioeconomic and demographic factors that may explain the variation. In most regions, an increasing trend in high or low temperature was associated with an increase in cardiovascular mortality, with variation in the magnitude of the temperature effects across regions. Three factors, including per capita years of education (as an indicator of economic status), percentage of the population over 65 years of age and percentage of women had direct impact on cold-related cardiovascular mortality. Number of hospital beds (as an indicator of the availability of medical resources), percentage of population engaged in industrial occupations, and percentage of women showed direct impact on heat-related cardiovascular mortality. Due to the socioeconomic and demographic inequalities between regions, the development of customized prevention and adaptation programs to address the low/high temperatures in vulnerable regions should be prioritized.

Description: Background: Pooling is a cost effective way to collect data for genetic association studies, particularly for rare genetic variants. It is of interest to estimate the haplotype frequencies, which contain more information than single locus statistics. By viewing the pooled genotype data as incomplete data, the expectation- maximization (EM) algorithm is the natural algorithm to use, but it is computationally intensive. A recent proposal to reduce the computational burden is to make use of database information to form a list of frequently occurring haplotypes, and to restrict the haplotypes to come from this list only in implementing the EM algorithm. There is, however, the danger of using an incorrect list, and there may not be enough database information to form a list externally in some applications. Results: We investigate the possibility of creating an internal list from the data at hand. One way to form such a list is to collapse the observed total allele frequencies to ``zero" or ``at least one", which is shown to have the desirable effect of amplifying the haplotype frequencies. To improve coverage, we propose ways to add and remove haplotypes from the list, and a benchmarking method to determine the frequency threshold for removing haplotypes. Simulation results show that the EM estimates based on a suitably augmented and trimmed collapsed data list (ATCDL) perform satisfactorily. In two scenarios involving 25 and 32 loci respectively, the EM-ATCDL estimates outperform the EM estimates based on other lists as well as the collapsed data maximum likelihood estimates. Conclusions: The proposed augmented and trimmed CD list is a useful list for the EM algorithm to base upon in estimating the haplotype distributions of rare variants. It can handle more markers and larger pool size than existing methods, and the resulting EM-ATCDL estimates are more efficient than the EM estimates based on other lists.

Description: Intermittent operation can improve the coefficient of performance (COP) of a ground source heat pump (GSHP) system. In this paper, an analytical solution to analyze the geo-temperature restoration performance under intermittent operation of borehole heat exchanger (BHE) fields is established. For this purpose, the moving finite line source model is combined with the g-function and the superposition principle. The model takes into account the heat transfer along the borehole, thermal interference between BHEs, and the influence of groundwater flow. The accuracy of the model is validated through comparison with an experiment carried out under intermittent operation. The model makes it possible to analyze the geo-temperature restoration performance and its influencing factors, such as BHE spacing, heat flow rate, operation mode, and groundwater flow. The main conclusions of this work are as follows. The heat transfer along the borehole should be considered when analyzing the geo-temperature restoration performance. When the BHE spacing increases, the soil temperature change decreases and the heat recovery improves. Therefore, adequate borehole separation distance is essential in the case of a multiple BHE system with unbalanced load. The presence of groundwater flow is associated with interference between the BHEs, which should not be ignored. In the case of long-term operation, the groundwater flow is beneficial to the geo-temperature recovery process, even for downstream BHEs. Finally, a greater groundwater flux leads to a better geo-temperature recovery.

Description: Background: Differentiation and copy number of repetitive sequences affect directly chromosome structure which contributes to reproductive isolation and speciation. Comparative cytogenetic mapping has been verified an efficient tool to elucidate the differentiation and distribution of repetitive sequences in genome. In present study, the distinct chromosomal structures of five Cucumis species were revealed through genomic in situ hybridization (GISH) technique and comparative cytogenetic mapping of major satellite repeats. Results: Chromosome structures of five Cucumis species were investigated using GISH and comparative mapping of specific satellites. Southern hybridization was employed to study the proliferation of satellites, whose structural characteristics were helpful for analyzing chromosome evolution. Preferential distribution of repetitive DNAs at the subtelomeric regions was found in C. sativus, C hystrix and C. metuliferus, while majority was positioned at the pericentromeric heterochromatin regions in C. melo and C. anguria. Further, comparative GISH (cGISH) through using genomic DNA of other species as probes revealed high homology of repeats between C. sativus and C. hystrix. Specific satellites including 45S rDNA, Type I/II, Type III, Type IV, CentM and telomeric repeat were then comparatively mapped in these species. Type I/II and Type IV produced bright signals at the subtelomeric regions of C. sativus and C. hystrix simultaneously, which might explain the significance of their amplification in the divergence of Cucumis subgenus from the ancient ancestor. Unique positioning of Type III and CentM only at the centromeric domains of C. sativus and C. melo, respectively, combining with unique southern bands, revealed rapid evolutionary patterns of centromeric DNA in Cucumis. Obvious interstitial telomeric repeats were observed in chromosomes 1 and 2 of C. sativus, which might provide evidence of the fusion hypothesis of chromosome evolution from x = 12 to x = 7 in Cucumis species. Besides, the significant correlation was found between gene density along chromosome and GISH band intensity in C. sativus and C. melo. Conclusions: In summary, comparative cytogenetic mapping of major satellites and GISH revealed the distinct differentiation of chromosome structure during species formation. The evolution of repetitive sequences was the main force for the divergence of Cucumis species from common ancestor.

Description: Background: Polyploid species contribute to Oryza diversity. However, the mechanisms underlying gene and genome evolution in Oryza polyploids remain largely unknown. The allotetraploid Oryza minuta, which is estimated to have formed less than one million years ago, along with its putative diploid progenitors (O. punctata and O. officinalis), are quite suitable for the study of polyploid genome evolution using a comparative genomics approach. Results: Here, we performed a comparative study of a large genomic region surrounding the Shattering4 locus in O. minuta, as well as in O. punctata and O. officinalis. Duplicated genomes in O. minuta have maintained the diploid genome organization, except for several structural variations mediated by transposon movement. Tandem duplicated gene clusters are prevalent in the Sh4 region, and segmental duplication followed by random deletion is illustrated to explain the gene gain-and-loss process. Both copies of most duplicated genes still persist in O. minuta. Molecular evolution analysis suggested that these duplicated genes are equally evolved and mostly manipulated by purifying selection. However, cDNA-SSCP analysis revealed that the expression patterns were dramatically altered between duplicated genes: nine of 29 duplicated genes exhibited expression divergence in O. minuta. We further detected one gene silencing event that was attributed to gene structural variation, but most gene silencing could not be related to sequence changes. We identified one case in which DNA methylation differences within promoter regions that were associated with the insertion of one hAT element were probably responsible for gene silencing, suggesting a potential epigenetic gene silencing pathway triggered by TE movement. Conclusions: Our study revealed both genetic and epigenetic mechanisms involved in duplicated gene silencing in the allotetraploid O. minuta.