Determination of window size for analyzing DNA sequences

Summary DNA sequences are generally not random sequences. To show such nonrandomness visually, DNA sequence data are often plotted as moving averages for a certain length of window slid along a sequence. Here a simple algorithm is presented for determining the window size and for finding a nonrandom region of sequence.     

半干旱区湿地-干草原交错带边界判定及其变化

鉴于目前国内对于半干旱区及小尺度上湿地-干草原交错带边界界定的研究较少,利用交错带对其周围环境变化具有提前指示作用的原理,以宁夏盐池四儿滩湿地为例,首先探讨游动分割窗技术在半干旱区湿地-干草原交错带边界判定中的可行性,其次再对2006年—2010年湿地-干草原交错带的宽度和边界进行判定,通过交错带的宽度和边界变化并结合交错带内植被的变化情况,综合对整个湿地生态系统的健康状况和湿地退化进行研究。结果表明:研究的尺度大小以及交错带过渡性是否明显将决定适宜窗口宽度的大小,这点在选择最小适宜窗口宽度时体现更为显著;降雨量是决定该区交错带的位置与宽度的最主要因素,但降雨量并不是决定该区交错带内植被变化状况的最主要因素,交错带距湿地核心区的距离是影响交错带内物种丰富度指数变化的最主要因素;由于保护区的成立,四儿滩湿地在2006年—2007年间,交错带宽度变大,湿地状况转好,2008年—2010年,由于铁路建设,湿地遭到破坏,交错带萎缩,湿地出现退化现象。湿地-干草原交错带作为一个敏感地带,它的变化情况可以对整个湿地生态系统的变化情况作出一定的提前预示;在半干旱区湿地的健康评价和退化研究中,通过交错带的变化来反映整个湿地生态系统的健康情况是一种可行的思路和方法。     

阿替普酶联合依达拉奉治疗急性缺血性卒中的疗效及神经功能缺损与时间窗的关系研究

目的:探讨阿替普酶联合依达拉奉治疗急性缺血性卒中的疗效及神经功能缺损与时间窗的关系。方法:选取大连医科大学附属大连市中心医院于2016年3月~2018年10月间收治的急性缺血性卒中患者117例,根据随机数字表法将患者分为对照组(n=58,阿替普酶治疗)和研究组(n=59,阿替普酶联合依达拉奉治疗),比较两组患者临床疗效、神经功能缺损情况、基质金属蛋白酶-9(MMP-9)、白介素-6(IL-6)水平、头颅CT梗死面积,观察两组治疗期间不良反应发生情况。结果:研究组的总有效率为84.75%(50/59),高于对照组的63.79%(37/58)(P<0.05)。两组患者治疗2周后MMP-9、IL-6、美国国立卫生研究院卒中量表(NIHSS)评分均较治疗前降低,且研究组低于对照组(P<0.05)。研究组治疗24h、48h、72h的头颅CT梗死面积小于对照组(P<0.05)。治疗后研究组发病72h内、发病48h内患者NIHSS评分、头颅CT梗死面积高于发病24h内,且发病72h内高于发病48h内(P<0.05)。两组患者不良反应发生率比较无差异(P>0.05)。结论:阿替普酶联合依达拉奉治疗急性缺血性卒中,疗效确切,可有效改善患者过氧化损伤,降低细胞因子水平,且越早的时间窗内接受治疗的患者,其神经功能缺损、脑梗死面积改善效果越好。     

斑块边缘效应的定量评价及其生态学意义

边缘效应是生态系统 (斑块 )边缘和生态过渡区所呈现出的生态效应。但由于景观性质、研究目标和斑块形状的变化 ,边缘效应影响的范围和程度差异较大。核心斑块与周边景观之间的相似性既可以增强边缘效应 ,也可以减弱边缘效应。正确理解和确定边缘效应的影响范围和程度直接关系到对野外环境观测数据的科学使用。许多情况下 ,由于未能正确认识一个生态系统(斑块 )的边缘效应 ,时常会将在边缘效应地区获得的数据与系统内部核心区的观测数据混淆使用 ,得出一些不科学的结论。边缘效应的定量评价对于进行科学的野外环境观测 ,及其在自然保护区功能区设计和生物多样性保护中具有重要意义。但如何定量评价生态系统 (斑块 )的边缘效应目前还缺乏科学有效的方法。从分析边缘效应的概念和影响因子出发 ,结合地理信息系统 ,提出了开展定量评价斑块边缘效应的方法 ,并探讨了定量研究边缘效应的生态学意义。     

Long‐term research avoids spurious and misleading trends in sustainability attributes of no‐till

Agricultural management recommendations based on short‐term studies can produce findings inconsistent with long‐term reality. Here, we test the long‐term environmental sustainability and profitability of continuous no‐till agriculture on yield, soil water availability, and N₂O fluxes. Using a moving window approach, we investigate the development and stability of several attributes of continuous no‐till as compared to conventional till agriculture over a 29‐year period at a site in the upper Midwest, US. Over a decade is needed to detect the consistent effects of no‐till. Both crop yield and soil water availability required 15 years or longer to generate patterns consistent with 29‐year trends. Only marginal trends for N₂O fluxes appeared in this period. Relative profitability analysis suggests that after initial implementation, 86% of periods between 10 and 29 years recuperated the initial expense of no‐till implementation, with the probability of higher relative profit increasing with longevity. Importantly, statistically significant but misleading short‐term trends appeared in more than 20% of the periods examined. Results underscore the importance of decadal and longer studies for revealing consistent dynamics and emergent outcomes of no‐till agriculture, shown to be beneficial in the long term.     

Proteins searching for their target on DNA by one-dimensional diffusion: overcoming the “speed-stability” paradox

The sequence dependence of DNA-protein interactions that allows proteins to find the correct reaction site also slows down the 1D diffusion of the protein along the DNA molecule, leading to the so-called “speed-stability paradox,” wherein fast diffusion along the DNA molecule is seemingly incompatible with stable targeting of the reaction site. Here, we develop diffusion-reaction models that use discrete and continuous Gaussian random 1D diffusion landscapes with or without a high-energy cut-off, and two-state models with a transition to and from a “searching” mode in which the protein diffuses rapidly without recognizing the target. We show the conditions under which such considerations lead to a predicted speed-up of the targeting process, and under which the presence of a “searching” mode in a two-state model is nearly equivalent to the existence of a high-energy cut-off in a one-state model. We also determine the conditions under which the search is either diffusion-limited or reaction-limited, and develop quantitative expressions for the rate of successful targeting as a function of the site-specific reaction rate, the roughness of the DNA-protein interaction potential, and the presence of a “searching” mode. In general, we find that a rough landscape is compatible with a fast search if the highest energy barriers can be avoided by “hopping” or by the protein transitioning to a lower-energy “searching” mode. We validate these predictions with the results of Brownian dynamics, kinetic Metropolis, and kinetic Monte Carlo simulations of the diffusion and targeting process, and apply these concepts to the case of T7 RNA polymerase searching for its target site on T7 DNA.     

Early-life exposure to a herbicide has enduring effects on pathogen-induced mortality

Exposure to stressors at formative stages in the development of wildlife and humans can have enduring effects on health. Understanding which, when and how stressors cause enduring health effects is crucial because these stressors might then be avoided or mitigated during formative stages to prevent lasting increases in disease susceptibility. Nevertheless, the impact of early-life exposure to stressors on the ability of hosts to resist and tolerate infections has yet to be thoroughly investigated. Here, we show that early-life, 6-day exposure to the herbicide atrazine (mean ± s.e.: 65.9±3.48 µg l⁻¹) increased frog mortality 46 days after atrazine exposure (post-metamorphosis), but only when frogs were challenged with a chytrid fungus implicated in global amphibian declines. Previous atrazine exposure did not affect resistance of infection (fungal load). Rather, early-life exposure to atrazine altered growth and development, which resulted in exposure to chytrid at more susceptible developmental stages and sizes, and reduced tolerance of infection, elevating mortality risk at an equivalent fungal burden to frogs unexposed to atrazine. Moreover, there was no evidence of recovery from atrazine exposure. Hence, reducing early-life exposure of amphibians to atrazine could reduce lasting increases in the risk of mortality from a disease associated with worldwide amphibian declines. More generally, these findings highlight that a better understanding of how stressors cause enduring effects on disease susceptibility could facilitate disease prevention in wildlife and humans, an approach that is often more cost-effective and efficient than reactive medicine.     

The effect of harvest date and harvest method on the combustion characteristics of Miscanthus × giganteus

Miscanthus × giganteus is an energy crop with many attributes that make it a potential biofuel feedstock. This study examined the chemical composition of M. × giganteus stems cut at different dates throughout the spring harvest window (January, February and March) and either left in a swath or left flat in a thin layer on the ground and compared the composition to that of the standing crop collected on the same date in April (control). The research then examined the effect of cutting date on the chemical composition of whole plant M. × giganteus biomass (leaf and stem). The parameters examined in both parts of this experiment were lower heating value on a wet basis (LHV_WB), ash, chlorine, potassium, nitrogen, sulphur, carbon and hydrogen content. The range of values recorded for the parameters from both aspects of this trial were LHV_WB 4.84–11.87 MJ kg^?1; ash 1.44–1.97%; Cl 0.07–0.23%; K 0.15–0.32%; N 0.28–0.39%; S 0.13–0.19%; C 46.75–50.00%; H 5.76–6.09%. The length of time that the M. × giganteus remained in the field after cutting affected the LHV_WB (increased with time) of the stem biomass material. Cutting the biomass and leaving it in the field lowered the ash, Cl and C content of the stem material compared to that of the control which was cut and collected on the same date. No differences were observed for the other parameters. Date of harvest affected the LHV_WB, Cl and C content which all improved with later cutting dates. Thus, combustion quality can be improved by delaying the harvest date or by cutting the crop and leaving it in the field for a period prior to collection. Choosing the correct combination of time and harvest method can therefore improve biomass fuel quality.     

The leg strength of two commercial strains of meat chicken subjected to different incubation profiles

Lower egg shell temperatures (EST) during the first 2 weeks of incubation, notionally known as Slow start incubation, extended the standing time of a 5-week-old fast feathering meat chicken parent line. This study was designed to evaluate the effect of Slow start incubation on the standing ability of commercial meat chickens. Eggs from two strains of meat chickens, Strains 1 and 2, were incubated using either the Slow start incubation, (the initial EST was 36.75°C followed by a gradual increase in EST, reaching 37.8°C at day 16 of incubation), or Control incubation (EST 37.75°C to 38°C from the start of incubation until day 18 of incubation). Eggs were observed every 6 h from 468 h until 516 h of incubation to identify chick hatch window. At 516 h of incubation all chicks were taken out of the incubator (take-off). Chicks from each Strain and incubation treatment were randomly selected for assessment of chick weight, chick length, yolk sac weight, serum Ca and P, and femoral bone ash (BA). All unhatched eggs were inspected to determine the stage of embryo failure. Remaining chicks were grown for 5 weeks in floorpens. Weekly feed intake (FI), chick weight and feed conversion ratio (FCR) were determined. At 35 days of age the standing ability of visibly male birds was assessed in a latency-to-lie test. Compared to the Control, Slow start incubation delayed the average hatch time of both strains by ∼13 h, and reduced hatchability with 4.6% live but unhatched chicks, which was most evident in Strain 2. Significant differences due to main effects only were observed at take-off. Strain 1 chicks were significantly heavier and longer with higher serum Ca but significantly lower BA and serum P than Strain 2. Slow start incubation generated significantly heavier chicks that were shorter, but had significantly heavier yolk sacs, lower serum Ca but higher serum P than Control incubated chicks. During the 1^st week post hatch Strain 1 Control incubated chicks had significantly higher FI and higher FCR than all other Strain and incubation treatments. At 35 days of age Slow start incubated birds of both Strains stood significantly longer than those from the Control incubation. This experiment clearly demonstrated the ability of Slow start incubation of commercial meat chickens to improve their leg strength.