A new pattern-based method for identifying recent HIV-1 infections from the viral <Emphasis Type="Italic">env</Emphasis> sequence

The long asymptomatic stage of HIV infection poses a great challenge in identifying recent HIV infections. This is a bottleneck for monitoring HIV epidemic trends and evaluating the effectiveness of national AIDS control programs. Several serological methods were used to address this issue with some success. Because of high false-positive rates in patients with advanced infection or in ART treatment, UNAIDS still hesitates to recommend their use in routine surveillance. We developed a new pattern-based method for measuring intra-patient viral genetic diversity for determination of recent infections and estimation of population incidence. This method is verified by using several datasets (424 subtype B and 77 CRF07_BC samples) with clearly identified HIV-1 infection times. Pattern-based diversities of recent infections are significantly lower than that of chronic ones. With larger window periods varying from 200 to 350 days, a higher accuracy (90%–95%) not affected by advanced disease nor ART treatment could be obtained. The pattern-based genetic method is supplementary to the existing serology-based assays, both of which could be suitable for use in low and high epidemic regions, respectively.     

Investigating Changes in Land Use Cover and Associated Environmental Parameters in Taihu Lake in Recent Decades Using Remote Sensing and Geochemistry

Humans have had a significant impact on the terrestrial pedosphere through activities such as agriculture and urbanization. The effects of human activities on land use and the related environmental changes were investigated through point and areal studies surrounding Meiliang Bay, which is an open area of extreme eutrophication in Taihu Lake, China. This study used remote sensing and environmental-tracer profiles [total nitrogen (TN), total phosphorus (TP), total organic carbon (TOC), grain size, and geochemical parameters] to determine the causes of changes in land use and the associated environmental parameters. The results of LUCCs (Land use/cover changes) indicate that over the past three decades, total farmland decreased by 862.49 km², with an annual decrement rate of 28.75 km²/year, and total urbanized land increased by 859.71 km², with an annual growth rate of 28.66 km²/year. The geochemical results indicate that the trophic state of Taihu Lake was persistently intensifying and that the TN, TP, and TOC concentrations increased twofold, threefold, and twofold, respectively, from 1949 to 2010. The sources of TN, TP, and TOC were highly similar after 1975. However, before 1974, TN and TP originated from different sources than TOC. The grassland and woodland around the lake retain nutrients and sand from the land of study area. The increase in urbanized land and tertiary industries significantly increased the sediment concentrations of TN, TP, and TOC after 1980.     

社群大小的年变化、气候和人类活动对神农架自然保护区川金丝猴日移动距离的影响

作者于2001年4月至2003年1月研究了社群大小的年变化、气候和人类活动对神农架自然保护区千家坪地区一群川金丝猴(Rhinopithecusroxellana)日移动距离的影响。对该群金丝猴进行了8个季节的跟踪研究,每季连续跟踪30d。用社群直线距离法确定猴群的日移动距离,同时调查社群大小,记录人为活动和气象因子。研究结果显示:(1)两年间猴群的个体数增加了14%,但其日移动距离没有明显变化,说明社群大小的年变化对日移动距离没有影响。(2)猴群在人为活动影响下的日移动距离比没有人为活动影响时长。(3)多变量回归分析显示,各个季节中,猴群的日移动距离与一天中晴和有云但无降水所占时间的比例没有相关性;与春季和冬季日降雨或雪所占时间的比例呈负相关,但与夏季和秋季的没有相关性,说明降水缩短了冬春季猴群的日移动距离,这可能与川金丝猴的繁殖有关。人为活动对猴群是不利的;冬春季的长时间降水可能是川金丝猴的灾害性天气。     

Photoregulation of thrombin aptamer activity using Bhc caging strategy

Thrombin aptamer was attempted to cage with Bhc (6-bromo-7-hydroxycoumarin-4-ylmethyl) group for controlling its specific affinity to target molecular through photolysis. By multiple-caging strategy, aptamer could be rendered biologically inert and partially restored with subsequently illumination. This provides a convenient method for photoregulating aptamer activity with exact spatiotemporal resolution.     

MBA: a literature mining system for extracting biomedical abbreviations

Background  

The exploding growth of the biomedical literature presents many challenges for biological researchers. One such challenge is from the use of a great deal of abbreviations. Extracting abbreviations and their definitions accurately is very helpful to biologists and also facilitates biomedical text analysis. Existing approaches fall into four broad categories: rule based, machine learning based, text alignment based and statistically based. State of the art methods either focus exclusively on acronym-type abbreviations, or could not recognize rare abbreviations. We propose a systematic method to extract abbreviations effectively. At first a scoring method is used to classify the abbreviations into acronym-type and non-acronym-type abbreviations, and then their corresponding definitions are identified by two different methods: text alignment algorithm for the former, statistical method for the latter.     

CAPE promotes the expansion of human umbilical cord blood-derived hematopoietic stem and progenitor cells in vitro

Due to the low number of collectable stem cells from single umbilical cord blood(UCB)unit,their initial uses were limited to pediatric therapies.Clinical applications of UCB hematopoietic stem and progenitor cells(HSPCs)would become feasible if there were a culture method that can effectively expand HSPCs while maintaining their self-renewal capacity.In recent years,numerous attempts have been made to expand human UCB HSPCs in vitro.In this study,we report that caffeic acid phenethyl ester(CAPE),a small molecule from honeybee extract,can promote in vitro expansion of HSPCs.Treatment with CAPE increased the percentage of HSPCs in cultured mononuclear cells.Importantly,culture of CD34+HSPCs with CAPE resulted in a significant increase in total colony-forming units and high proliferative potential colony-forming units.Burst-forming unit-erythroid was the mostly affected colony type,which increased more than 3.7-fold in 1μg mL 1CAPE treatment group when compared to the controls.CAPE appears to induce HSPC expansion by upregulating the expression of SCF and HIF1-α.Our data suggest that CAPE may become a potent medium supplement for in vitro HSPC expansion.     

Effect of Boundary Condition and Periodical Extension on Transmission Characteristics of Terahertz Filters with Periodical Hole Array Structure Fabricated on Aluminum Slab

Terahertz (THz) filters based on extraordinary optical transmission from periodical hole array structures fabricated on aluminum slab have been experimentally investigated by using THz time-domain spectroscopy. The incident THz pulses with frequency from 0.1 to 2.7 THz could be partly filtered, and the central peak was at ～0.26. The high frequency signal could be observed to decrease, especially for the frequency above ～1 THz. Moreover, the transmission peak from small-size sample with less hole arrays shifts to high frequency at ～0.53 THz due to both the effects of boundary condition and insufficient periodical extension. Furthermore, finite element method with surface plasmon polariton theory is employed to analyze this extraordinary optical transmission and filter phenomena.     

Chronotype and sleep duration are associated with stimulant consumption and BMI among Chinese undergraduates

The study sought to identify the association between stimulant consumption and social jetlag, chronotype as well as sleep duration among undergraduate students. A cross-sectional survey was conducted in the university town in Chongqing, China. Data were collected on 977 participants, age 20.06 (SD = 1.25) years old, using the Munich Chronotype Questionnaire (MCTQ) to measure social jetlag, chronotype and average sleep duration. A self-reported questionnaire was used to collect the information: BMI, demographic data, outdoor activity time, smoking status, alcohol consumption, coffee consumption and sugar-sweetened beverage consumption. The positive significant association was found between late chronotype and alcohol consumption (OR = 1.26, 95% CI [1.05–1.52]), being a current smoker (OR = 1.62, 95% CI [1.26–2.07]) and sugar-sweetened beverage consumption (OR = 1.42, 95% CI [1.17–1.72]). Average sleep duration was negatively associated with BMI (OR = 0.84, 95% CI [0.71–0.98]). Social jetlag did not find any association between stimulant consumption and BMI in the adjusted model. The results showed that Chinese undergraduate students had a negative significant association between average sleep duration and BMI, and late chronotype might affect the stimulant consumption among the group. This study may provide some implications for health management of obesity among undergraduate students in China.