Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation

The oligonucleotide specificity for microarray hybridization can be predicted by its sequence identity to non-targets, continuous stretch to non-targets, and/or binding free energy to non-targets. Most currently available programs only use one or two of these criteria, which may choose ‘false’ specific oligonucleotides or miss ‘true’ optimal probes in a considerable proportion. We have developed a software tool, called CommOligo using new algorithms and all three criteria for selection of optimal oligonucleotide probes. A series of filters, including sequence identity, free energy, continuous stretch, GC content, self-annealing, distance to the 3′-untranslated region (3′-UTR) and melting temperature (T(m)), are used to check each possible oligonucleotide. A sequence identity is calculated based on gapped global alignments. A traversal algorithm is used to generate alignments for free energy calculation. The optimal T(m) interval is determined based on probe candidates that have passed all other filters. Final probes are picked using a combination of user-configurable piece-wise linear functions and an iterative process. The thresholds for identity, stretch and free energy filters are automatically determined from experimental data by an accessory software tool, CommOligo_PE (CommOligo Parameter Estimator). The program was used to design probes for both whole-genome and highly homologous sequence data. CommOligo and CommOligo_PE are freely available to academic users upon request

Neutral beam current drive in a tokamak

Neutral beam current drive (NBCD) on the EAST tokamak is studied by using Monte-Carlo simulation. The electron shielding effect to the fast ion current is taken into account by using a fitting formula applicable to general tokamak equilibria and arbitrary collisionality regime. The net currents driven by the beam are off-axis although the fast ion currents are on-axis. This is found to be due to the electron shielding effect being strong near the magnetic axis. We also investigate the dependence of NBCD efficiency on the plasma density. The results indicate that the NBCD efficiency decreases with the increase in plasma density. A simple semi-analytic estimation of the dependence of NBCD efficiency on the density is proposed and is in reasonable agreement with the results directly obtained in the simulations

Rural Financial Reform in China: Progress Made and the Path Forward

Significant progress has been made in reforming China's rural financial system. Nevertheless, the current institutions are unable to meet the multilayered and diversified demands for rural financial services. Establishing a comprehensive and efficient rural credit system to support the dynamic commercial sector of the rural economy, small-scale farming and small and medium-size enterprises is the major challenge in China. This article identifies bottlenecks and suggests policies to develop a well-functioning and sustainable agricultural and rural financial system that would address the diverse needs of the rural and agriculture sectors. To preview the policy recommendations, attention should be given first to legislation and supervision, and then to the corporate governance structure of financial institutions

Intestinal flora and linear growth in children

The gut microbiota plays a critical role in human growth and development as well as the regulation of human pathophysiological processes. According to research, the gut microbiota controls the host's growth and development in areas such as nutrition, metabolism, endocrine hormones, and immune modulation. The human gut microbiota has an important role in child and adolescent growth, especially when nutritional conditions are poor. In this review, we focus on recent findings about the gut microbiota's influence on child growth, including the relationship between the gut microbiota and linear growth during pregnancy, infancy, childhood, and adolescence. Furthermore, we also review some mechanisms by which intestinal flora influence the host's linear growth. Although the data supports a link between intestinal flora and linear development in children, our review has limitations that prohibit us from fully verifying the causal relationship between gut flora and linear development in children. Improving the gut microbiota, in conjunction with renutrition techniques, has the potential to ameliorate the growth and development impairments currently associated with chronic illness and malnutrition in children

Response of radial growth to warming and CO2 enrichment in southern Northeast China: a case of Pinus tabulaeformis

The southern part of northeast China has experienced a marked warming and drying climate. We provide dendrochronological evidence for atmospheric CO2 fertilization and the impacts of warming on Chinese pine (Pinus tabulaeformis) growth. The results of this study show that increased temperature has a negative effect on pine growth during a major part of the growing season and a weakly positive effects on growth during the remaining portion of the year. The monthly temperatures explain ca. 20 % of the total variance in the annual radial growth of Chinese pine from 1901 to 2009. An increase of approximately 3–5 °C is the maximum that Chinese pine can tolerate in this region with an annual rainfall of 500–700 mm. Our results suggest a that there is a proportional response to warming only up to a maximum of 1 °C warming, and indicate the complexities of succession in forest ecosystems in terms of adaptation and evolution in local pine populations under a rapid warming condition. In addition, increasing atmospheric CO2 concentrations have a positive effect on tree growth. This effect can be detected with conventional dendrochronological methods

Extension of summer (June–August) temperature records for northern Inner Mongolia (1715–2008), China using tree rings

This paper presents a spatially and temporally improved reconstruction of mean summer (June–August) temperature derived from tree-ring width data of Dahurian larch (Larix gmelinii Rupr.) from the northern Great Xing'an Mountains, Northeast China. Three new chronologies were added to the original 2011 reconstruction, and the reconstruction extended back to AD 1715. The reconstruction was generated using a simple linear regression method, verified by independent meteorological data, and accounts for 47.0% of the actual temperature variance during the common period (1957–2008). The reconstruction captures decadal and century-scale regional temperature variability, such as cold decades (1940s, 1930s, 1790s, 1950s and 1850s), warm decades (2000s, 1870s, 1750s, 1980s and 1840s), a cold half-century (ca. 1750–1799), and a warm half-century (ca. 1900–1949). It also reveals slightly higher frequency of cold years (20.4%) than warm years (18.0%), and a recent warming trend. Compared to the original 2011 reconstruction, this reconstruction has lower inter-annual temperature variability, high explained variance and high representativeness of regional climate. The reconstruction also correlates with the East Asian Monsoon and the Pacific Ocean signals, and indicates the feasibility of using tree rings from high latitude Northeast China to reconstruct summer temperature in permafrost forest environments

Tree-ring based precipitation variability since AD 1828 in northwestern Liaoning, China

A 183-year record of total precipitation from September to current July was reconstructed using tree rings from Chinese pine (Pinus tabulaeformis) to explore regional moisture variations in northwestern Liaoning province. The reconstruction accounts for 35.4% of the total variance of the instrumental precipitation from 1957 to 2010. The reconstruction shows eleven persistent dry periods (e.g. 1856–1866, 1886–1891, 1898–1905), and eleven persistent wet periods (e.g. 1835–1855, 1867–1878, 1892–1897). Spectral analysis of the reconstruction shows several significant spectral peaks in the ca. 2–4-year periodicity band, suggesting inter-annual variability of El Niño-Southern Oscillation (ENSO). The precipitation reconstruction shows correlations related to the East Asian Monsoon and possible teleconnection of regional moisture variations to Pacific Ocean signals, such as El Niño and La Niña

Association of urban forest landscape characteristics with biomass and soil carbon stocks in Harbin City, Northeastern China

Background Urban forests help in mitigating carbon emissions; however, their associations with landscape patterns are unclear. Understanding the associations would help us to evaluate urban forest ecological services and favor urban forest management via landscape regulations. We used Harbin, capital city of the northernmost province in China, as an example and hypothesized that the urban forests had different landscape metrics among different forest types, administrative districts, and urban–rural gradients, and these differences were closely associated with forest carbon sequestration in the biomass and soils. Methods We extracted the urban forest tree coverage area on the basis of 2 GF-1 remote sensing images and object-oriented based classification method. The analysis of forest landscape patterns and estimation of carbon storage were based on tree coverage data and 199 plots. We also examined the relationships between forest landscape metrics and carbon storage on the basis of forest types, administrative districts, ring roads, and history of urban settlements by using statistical methods. Results The small patches covering an area of less than 0.5 ha accounted for 72.6% of all patches (average patch size, 0.31 ha). The mean patch size (AREA_MN) and largest patch index (LPI) were the highest in the landscape and relaxation forest and Songbei District. The landscape shape index (LSI) and number of patches linearly decreased along rural-urban gradients (p < 0.05). The tree biomass carbon storage varied from less than 10 thousand tons in the urban center (first ring road region and 100-year regions) to more than 100 thousand tons in the rural regions (fourth ring road and newly urbanized regions). In the same urban–rural gradients, soil carbon storage varied from less than five thousand tons in the urban centers to 73–103 thousand tons in the rural regions. The association analysis indicated that the total forest area was the key factor that regulates total carbon storage in trees and soils. However, in the case of carbon density (ton ha−1), AREA_MN was strongly associated with tree biomass carbon, and soil carbon density was negatively related to LSI (p < 0.01) and AREA_MN (p < 0.05), but positively related to LPI (p < 0.05). Discussion The urban forests were more fragmented in Harbin than in other provincial cities in Northeastern China, as shown by the smaller patch size, more complex patch shape, and larger patch density. The decrease in LSI along the rural-urban gradients may contribute to the forest carbon sequestrations in downtown regions, particularly underground soil carbon accumulation, and the increasing patch size may benefit tree carbon sequestration. Our findings help us to understand how forest landscape metrics are associated with carbon storage function. These findings related to urban forest design may maximize forest carbon sequestration services and facilitate in precisely estimating the forest carbon sink