基于扩展起始节点和加权融合策略预测肺癌风险致病基因

肺癌风险致病基因预测有助于了解疾病发病机制、提高临床治疗效果.目前,以重启游走为框架的风险致病基因预测算法,普遍存在起始节点少、节点转移概率相同、信息源单一的问题.为此,本文提出一种基于扩展起始节点和加权融合策略的风险致病基因预测算法(命名为AFMFSC),并在肺癌中验证算法有效性.首先,基于增广模糊测量思想,计算疾病表型近似基因间的增广功能相似得分,从中选出重要基因与致病基因作为扩展起始节点;其次,采用节点拓扑相似度转移矩阵及基因表达差异相关性转移矩阵,分别在蛋白质网络中重启随机游走,并将两种结果加权融合排序;最后,通过富集分析排名靠前基因,得到有显著意义的风险致病基因.AFMFSC算法预测的73个肺癌风险致病基因,均与肺癌发生、发展有密切联系,生物学意义显著.与其他排序算法相比,AFMFSC算法的Top 1%、Top 5%和AUC值比较大,平均排名和受拓扑特性偏差影响程度小;融合策略排名性能优于单一转移矩阵或普通邻接矩阵游走排名.AFMFSC算法不仅能准确有效地预测肺癌风险致病基因,而且可推广预测其他疾病风险致病基因,为探索癌症致病机理提供新视角及依据.     

Low‐Temperature Growth of Hard Carbon with Graphite Crystal for Sodium‐Ion Storage with High Initial Coulombic Efficiency: A General Method

Practical application of hard carbon materials in sodium‐ion batteries (SIBs) is largely limited by their low initial coulombic efficiency (ICE), which may be improved by increasing the graphitization degree. However, biomass‐derived hard carbon is usually nongraphitizable and extremely difficult to graphitize by direct heating even at 3000 °C. Herein, a general strategy is reported for fabricating hard carbon materials with graphite crystals at 1300 °C promoted by external graphite that serves as a crystal template for the growth of graphite crystals. The graphite crystals enable the contacted pseudographitic domains with a high‐level ordered structure, large domain size, and low defects, leading to an enhanced ICE. The obtained hard carbon materials with graphite crystals, using the carbonized eggshell membranes, and sucrose‐derived microsphere as precursors, achieve very high ICE of 89% and 91% with reversible capacity of 310 and 301 mA h g^?1, respectively. Therefore, using external graphite to promote high‐level ordering pseudographitic domains at low temperature is quite useful to improve ICE for SIB applications.     

Species Dynamics During Early Secondary Forest Succession: Recruitment, Mortality and Species Turnover

The "Initial Floristic Composition" hypothesis is applied to secondary tropical rain forest succession in abandoned agricultural fields with light previous land-use and close to seed sources. This hypothesis predicts that both pioneer and shade-tolerant species colonize a site directly after abandonment, and as the canopy closes, the recruitment of pioneers sharply declines, while recruitment of shade-tolerant species continues. It also predicts higher mortality among pioneers. Consequently, recruited and dead trees are expected to differ in species composition, with highest species richness for the recruits. During 18 mo, we monitored recruitment and mortality of trees with height ≥ 1.5 m in eight plots in abandoned cornfields with initial fallow age of 1–5 yr, in SE Mexico. Shade-tolerant species established in the first years of succession, albeit in low numbers. As predicted, recruited and dead trees differed in species richness and composition, and in shade-tolerant frequency. In contrast to our expectations, over 50 percent of recruits were from pioneer species, as high stand-level mortality opened new opportunities for continued pioneer colonization. Species turnover starts very early in succession but is not always a gradual and continuous process, complicating prevailing succession models. The strong spatial and temporal variability of succession emphasizes the need to monitor these dynamics in permanent plots across a range of initial stand ages, with multiple plots in a given age class.     

Teleconnection between the early immigration of brown planthopper (Nilaparvata lugens Stål) and ENSO indices: implication for its medium- and long-term forecast

Teleconnection between the early immigration of brown planthopper (BPH) and El Nino/Southern Oscillation (ENSO) indices from January of two years previously to the current June was investigated to make long-term forecast. The teleconnection results were as follows: ENSO indices which were significantly correlated with the early immigration of BPH were primarily sea surface temperature anomalies (SSTA) in N3, N4 and N3.4 regions, accounting for 71.8% of the total. Significant ENSO indices from two years and one year before the immigration events had a proportion of about 84%, while those in the current year only accounted for 16.7%. There was significantly negative correlation between the early immigration of BPH and SSTA in each Nino region from two years before to the previous spring, whereas there was significantly positive correlation between these two factors during the period from the previous winter to the current spring. The significant correlation between the early immigration of BPH and SSTA in each Nino region in the last summer and autumn did not show any obvious tendencies. The relationship between the southern oscillation index (SOI) and the early immigration of BPH was opposite to that between the immigration and SSTA in each Nino region. The above mentioned significant ENSO indices were used as key factors to build forecasting models for the early immigration of BPH by step-wise multiple linear regression analysis. Finally, 12 integrated forecasting models were obtained, which could make predictions 3–27 months ahead and had a predictive accuracy of 88.9%.     

Effect of five diatomaceous earth formulations against Tribofium castaneum （Coleoptera： Tenebrionidae）, Oryzaephflus surinamensis （Coleoptera： Silvanidae） and Rhyzopertha dominica （Coleoptera： Bostrychidae）

Laboratory bioassays were conducted to determine the effect of food source on the survival of Tribolium castaneum Herbst, Oryzaephilus surinamensis L. and Rhyzopertha dominica F., after exposure to five diatomaceous earth （DE） formulations： Protect-It, Insecto, Perma-GuardTM, Dryacide and SilicoSec. Adults of these species were exposed to DEs at the rate of 0.5 mg/cm^2 for 1 day on filter paper inside plastic Petri dishes. After exposure, the initial mortality was counted and live individuals of the three species were held for a week in glass vials containing 50 mg wheat flour, rice and whole wheat, respectively. In the second experiment, after 1 day exposure to DEs, beetles were transferred to Petri dishes without food and held for a week to determine if the presence of food source would decrease the mortality of beetles. Experiments were carried out at 27℃ and 55% RH in the dark. The initial mortality in both of the experiments reached 100% for the three species exposed to Protect-It and in the case ofR. dominica and O. surinamensis exposed to Dryacide. In contrast, low level of mortality （〈 10%） was observed for T. castaneum exposed to Perma-GuardTM and Insecto. The mortality after the post-treatment period on food was decreased for the three species exposed to Perma-GuardTM and in the case of T. castaneum and R. dominica exposed to Insecto and SilicoSec. Adults of O. surinamensis were the most susceptible followed by R. dominica and 100% adult mortality was obtained, whereas T. castaneum were the least susceptible beetles to DEs. Protect-It and Dryacide were the most efficient DE formulations and can be used effectively in a stored grain integrated pest management program.     

Monthly change of community structure of zoobenthos in Xiangxi Bay after impoundment of the Three Gorges Teservoir, China

Xiangxi Bay, a typical bay of the Three Gorges Reservoir (TGR) in China, was formed in June 2003 after the impoundment of the TGR. We investigated the community structure of zoobenthos in Xiangxi Bay from August 2003 to August 2004. Benthic abundance and biomass were calculated per unit area of sediment. A total of 26 taxa were identified. They included two families of Lamellibranchia (7.7% of the total taxa number), two families of Oligochaeta (50%), Chironomidae (38.5%), and one other animal (3.8%). The average density and biomass were 276 ind./m² and 0.301 g/m², respectively. Oligochaetes and chironomids constituted the major groups, and Limnodrilus hoffmeisteri, Procladius sp., Branchiura sowerbyi, Tubificidae sp1. and Polypedilum scalaenum group sp. were the common taxa in this reservoir system. Among them, L. hoffmeisteri and Procladius sp. were the dominant species, and contributed 37.0% and 28.3% of the total density, respectively. The standing crop of zoobenthos in Xiangxi Bay was relative low, compared with other similar reservoirs. Our studies demonstrate that the standing crop increased gradually with time. The total density and biomass in August 2004 were 8.8 and 14.3 times those of the initial impoundment, separately. Oligochaetes did not become the sole dominant group, indicating that the sediment loading in Xiangxi Bay may be not serious. __________ Translated from Acta Hydrobiologica Sinica, 2006, 30(1): 64–69 [译自: 水生生物学报]     

Temporal variation in abundance of male and female spruce budworms at combinatory associations of light traps and pheromone traps

A 3‐year study (2014–2016) was conducted at Rocky Harbour near the west coast of Newfoundland, Canada, to record the abundance and phenology of adult spruce budworms captured at traps, using a factorial design (light traps and pheromone traps deployed contiguously or segregated spatially). Budworms were most abundant and occurred seasonally earlier in 2014 than in 2015 and 2016; these findings held generally true for males and females. The geographic setting of Newfoundland (large island isolated from the mainland by an oceanic barrier of >100 km across) provides an ideal location to discriminate local flight from long‐range immigrations; in our study, however, immigrations cannot be ruled out for any single day of trapping due to broad overlap in emergence patterns at Rocky Harbour relative to forest stands with known populations of budworms on the mainland. Based on moderate daily variation in adult abundance, however, major immigration events (defined as external deposition of budworms with large numerical amplitude) likely did not take place at Rocky Harbor between 2014 and 2016. Males were more abundant at light traps coupled with pheromone traps, whereas abundance of males at pheromone traps was similar with or without contiguous light traps. This outcome may be mediated by lower range of attraction for light traps (usually <100 m) and (generally assumed to be several hundreds of meters). Females were equally abundant at light traps with or without pheromone traps. As expected, males were captured earlier in the season at pheromone traps than at light traps, and females occurred later in the season due to protandry. The onset of flight observed at light traps or pheromone traps in 2015 and 2016 occurred 10–15 days later than simulated predictions; caution is thus warranted as to conclusions derived on computer modeling of adult emergence.     

Influence of oocyte collection technique on initial chromatin configuration, meiotic competence, and male pronucleus formation after intracytoplasmic sperm injection (ICSI) of equine oocytes

There is a great variability in the success of horse oocyte maturation and fertilization among laboratories. This study was conducted to determine if the meiotic and developmental competence of horse oocytes could be dependent on the method of oocyte collection, i.e., aspiration of follicular fluid with a vacuum apparatus, or opening follicles and scraping the granulosa layer. Horse oocytes were recovered from abattoir ovaries by aspiration or scraping and classified as having compact (Cp), expanded (Ex), or partial (P) cumuli. In Experiment 1 (Part A in May and Part B in October), oocytes were fixed immediately after collection to assess whether the collection method influenced the initial chromatin configuration of oocytes. In Experiment 2, in vitro maturation rates of oocytes recovered by aspiration or scraping were compared. In Experiment 3, oocytes were matured in vitro and submitted to intracytoplasmic sperm injection (ICSI). Initial chromatin configuration differed according to collection method in that there was a significantly higher prevalence of diffuse chromatin within the germinal vesicle in oocytes recovered by scraping than in oocytes recovered by aspiration (29/87, 33% and 28/166, 17%, respectively; P < 0.01). Maturation of oocytes to metaphase II did not significantly differ between scraped and aspirated oocytes (56/101, 55.4 % vs. 65/106, 61.4%, respectively). The overall pronucleus formation rate after ICSI of oocytes recovered by scraping was not significantly different than that of oocytes recovered by aspiration (50/99, 52.6% vs. 50/85, 68.5 %, respectively); however, the rate of abnormal fertilization was significantly higher for oocytes collected by aspiration (14/73, 19% vs. 6/94, 6%, respectively; P <0.05). These results demonstrate that the collection method affects the population of recovered oocytes and may contribute to differences in results observed among laboratories working with horse oocytes.     

Fate of Legionella pneumophila in macrophages of C57BL/6 chronic granulomatous disease mice

We compared the intracellular survival and growth of Legionella pneumophila Philadelphia-1 in peritoneal macrophages obtained from A/J, C57BL/6, and X-linked chronic granulomatous disease (CGD) mice produced from C57BL/6 strain. The initial killing was observed in A/J and C57BL/6 macrophages at 2, 4 and 6 hr after in vitro phagocytosis, but not in the CGD macrophages. Thereafter, there was a 10-fold increase of CFU in A/J macrophages. The bacteria, however, did not proliferate in C57BL/6 and CGD macrophages at 24 or 48 hr after in vitro phagocytosis. These results suggest that effector molecules for the initial killing are a superoxide anion and its metabolites, and Lgn1 gene product inhibits the intracellular growth of L. pneumophila independently of NADPH oxidase.     

Modelling Diurnal Courses of Photosynthesis and Transpiration of Leaves on the Basis of Stomatal and Non-Stomatal Responses,Including Photoinhibition

A mathematical model for photoinhibition of leaf photosynthesis was developed by formalising the assumptions that (1) the rate of photoinhibition is proportional to irradiance; and (2) the rate of recovery, derived from the formulae for a pseudo first-order process, is proportional to the extent of inhibition. The photoinhibition model to calculate initial photo yield is integrated into a photosynthesis-stomatal conductance (g _s) model that combines net photosynthetic rate (P _N), transpiration rate (E), and g _s, and also the leaf energy balance. The model was run to simulate the diurnal courses of P _N, E, g _s, photochemical efficiency, i.e., ratio of intercellular CO₂ concentration and CO₂ concentration over leaf surface (C _i/C _s), and leaf temperature (T ₁) under different irradiances, air temperature, and humidity separately with fixed time courses of others. When midday depression occurred under high temperature, g _s decreased the most and E the least. The duration of midday depression of g _s was the longest and that in E the shortest. E increased with increasing vapour pressure deficit (VPD) initially, but when VPD exceeded a certain value, it decreased with increasing VPD; this was caused by a rapid decrease in g _s. When air temperature exceeded a certain value, an increase in solar irradiance raised T ₁ and the degree of midday depression. High solar radiation caused large decrease in initial photon efficiency (). P _N, E, and g _s showed reasonable decreases under conditions causing photoinhibition compared with non-photoinhibition condition under high irradiance. The T ₁ under photoinhibition was higher than that under non-photoinhibition conditions, which was evident under high solar irradiance around noon. The decrease in C _i/C _s at midday implies that stomatal closure is a factor causing midday depression of photosynthesis.