Estimating the proportion cured of cancer: Some practical advice for users

BackgroundCure models can provide improved possibilities for inference if used appropriately, but there is potential for misleading results if care is not taken. In this study, we compared five commonly used approaches for modelling cure in a relative survival framework and provide some practical advice on the use of these approaches.Patients and methodsData for colon, female breast, and ovarian cancers were used to illustrate these approaches. The proportion cured was estimated for each of these three cancers within each of three age groups. We then graphically assessed the assumption of cure and the model fit, by comparing the predicted relative survival from the cure models to empirical life table estimates.ResultsWhere both cure and distributional assumptions are appropriate (e.g., for colon or ovarian cancer patients aged <75 years), all five approaches led to similar estimates of the proportion cured. The estimates varied slightly when cure was a reasonable assumption but the distributional assumption was not (e.g., for colon cancer patients ≥75 years). Greater variability in the estimates was observed when the cure assumption was not supported by the data (breast cancer).ConclusionsIf the data suggest cure is not a reasonable assumption then we advise against fitting cure models. In the scenarios where cure was reasonable, we found that flexible parametric cure models performed at least as well, or better, than the other modelling approaches. We recommend that, regardless of the model used, the underlying assumptions for cure and model fit should always be graphically assessed.     

北京雾灵山自然保护区冬春季地面活动鸟兽红外相机初步调查

为了解北京雾灵山自然保护区野生动物资源现状,于2014年11月至2015年4月,在保护区内放置30台红外相机开展调查。结果共记录鸟类5目14科27种,兽类4目8科10种,其中勺鸡(Pucrasia macrolopha)、红角鸮(Otus sunia)、纵纹腹小鸮(Athene noctua)和中华斑羚(Naemorhedus griseus)为国家Ⅱ级重点保护野生动物。鸟类物种数月变化剧烈。相对丰富度最高的6种动物为狍(Capreolus pygargus)(60.19)、红嘴蓝鹊(Urocissa erythrorhyncha)(34.14)、星鸦(Nucifraga caryocatactes)(27.78)、岩松鼠(Sciurotamias davidianus)(23.34)、松鸦(Garrulus glandarius)(23.34)、中华斑羚(21.99)。对狍、岩松鼠、中华斑羚进行日活动节律分析,狍属晨昏活动型;中华斑羚有两个活动高峰;岩松鼠的日活动高峰集中在晨间,为单峰型。本研究提供了北京雾灵山部分鸟兽资源的最新动态现状及活动节律信息,同时表明红外相机在拍摄地栖性鸟类、大中型兽类、夜行性动物方面具有优势,而对于非地栖鸟类和小型兽类,红外相机有一定局限性。本研究为应用红外相机技术开展森林野生动物多样性监测提供了经验。     

5种甘草属植物花序和种子生产的位置效应及繁殖资源分配模式初步研究

以种植于新疆石河子的光果甘草( Glycyrrhiza glabra Linn.)、胀果甘草( G. inflata Batal.)、乌拉尔甘草( G. uralensis Fisch.)、黄甘草( G. eurycarpa P. C. Li)和蜜腺甘草( G. glabra var. glandulosa X. Y. Li)为研究对象,对植株不同部位的花序数量、花序正常发育率、每花序单花数量和果穗干质量,以及植株不同部位和花序不同部位的生物量投入比、座果率、结籽率、种子投影面积和种子千粒质量进行测定;在此基础上,对供试5种甘草属( Glycyrrhiza Linn.)植物的繁殖资源分配模式和种子生产策略进行分析。结果表明：同一植株内,光果甘草、乌拉尔甘草、黄甘草和蜜腺甘草的花序数量、花序正常发育率、每花序单花数量和果穗干质量从植株下部到上部总体上依次递减,而胀果甘草植株不同部位间这4项指标总体上无显著差异。同一植株内,胀果甘草植株中部的生物量投入比和座果率均较高,但其生物量投入比、座果率和结籽率在植株不同部位间均无显著差异;而供试另4种植物的生物量投入比、座果率和结籽率从植株下部到上部总体上依次递减。同一花序内,胀果甘草花序中部的生物量投入比明显高于花序上部和下部,座果率从花序下部到上部依次递减,结籽率则在花序不同部位间无显著差异,而供试另4种植物的生物量投入比、座果率和结籽率从花序下部到上部总体上依次递减。供试5种植物的种子投影面积和种子千粒质量在植株不同部位间和花序不同部位间均无显著差异。综合研究结果显示：在资源竞争、结构效应和花粉限制的影响下,供试5种甘草属植物存在2种不同的资源分配模式和种子生产格局。其中,光果甘草、乌拉尔甘草、黄甘草和蜜腺甘草通过减少对晚发育的花或果实的资源投入来保障早发育的花或果实获得较多的资源,达到繁殖成功的目的;而胀果甘草则采取对花和果实随机败育的方式减小资源竞争的压力,这2种繁殖资源分配模式和种子生产策略对提高甘草属植物的繁殖成功率具有重要作用。     

Tailoring of recombinant FDH: effect of histidine tag location on solubility and catalytic properties of Chaetomium thermophilum formate dehydrogenase (CtFDH)

Abstract

Several protein expression systems can be used to get enzymes in required quantities and study their functions. Incorporating a polyhistidine tag is a beneficial way of getting various enzymes such as FDHs for industrial applications. The NAD⁺ dependent formate dehydrogenase from Chaetomium thermophilum (CtFDH) can be utilized for interconversion of formate to carbon dioxide coupled with the conversion of NAD⁺ to NADH. In this study, N-terminal His tagged CtFDH (N-CtFDH) and C-terminal His tagged CtFDH (C-CtFDH) was constructed to learn the effect of His tag location on the activity and kinetic parameters of the enzyme. The solubility of proteins was not affected by tag position, however, an interference on the N-terminal region caused a deterioration in specific activity and the kinetic ability of enzyme. The obtained results indicated that the C-terminus of the enzyme is an appropriate region for tag engineering. The C-CtFDH has an approximately three-fold larger specific activity and two-fold higher catalytic efficiency than N-CtFDH. The results suggest that insertion of a His-tag at the N-terminal or C-terminal end of CtFDH has different effects on the protein and the N-terminal fragment of the protein is crucial for the function of CtFDH.     

利用红外相机调查祁连山国家公园(青海片区)兽类和鸟类多样性

2017年5-9月,采用红外相机调查祁连山国家公园(青海片区)兽类和鸟类多样性。共布设154个相机位点,累计12 096个相机日,共获得9 675张有效独立照片,鉴定23种野生兽类和50种野生鸟类物种,分别隶属5目10科和9目19科,另记录到家畜5种。相对多度指数最高的前五种野生动物依次为岩羊(Pseudois rnayaur)(18.23)、喜马拉雅旱獭(Marmota himalayarea)(15.98)、灰尾兔(Lepus oiostolus)(5.06)、红嘴山鸦(Pyrrhocorax pyrrhocorax)(3.39)、高原鼠兔(Ochotona curzoniae)(2.49)。中国特有物种有荒漠猫(Felis bieti)、白唇鹿(Ceryus albirostris)、西藏马鹿(Cervus wallichii)、藏原羚(Procapra picticaudata)、红耳鼠兔(Ochotana erythrotis)、蓝马鸡(Crossoptilon auritum)和地山雀(Pseudopocdoces humilis)7种。国家Ⅰ级重点保护野生动物有4种,国家Ⅱ级重点保护野生动物有20种;被中国脊椎动物红色名录评估为极危、濒危、易危、近危的物种分别有1种、6种、3种、14种。红外相机调查结果反映出祁连山国家公园(青海片区)兽类和鸟类现状,为祁连山国家公园体制试点生物多样性保护和管理提供基础数据。     

Grassland harvesting alters ant community trophic structure: An isotopic study in tallgrass prairies

Disturbances have long been recognized as important forces for structuring natural communities but their effects on trophic structure are not well understood, particularly in terrestrial systems. This is in part because quantifying trophic linkages is a challenge, especially for small organisms with cryptic feeding behaviors such as insects, and often relies on conducting labor‐intensive feeding trials or extensive observations in the field. In this study, we used stable isotopes of carbon and nitrogen to examine how disturbance (annual biomass harvesting) in tallgrass prairies affected the trophic position, trophic range, and niche space of ants, a widespread grassland consumer. We hypothesized that biomass harvest would remove important food and nesting resources of insects thus affecting ant feeding relationships and trophic structure. We found shifts in the feeding relationships inferred by isotopic signatures with harvest. In particular, these shifts suggest that ants within harvest sites utilized resources at lower trophic levels (possibly plant‐based resources or herbivores), expanded trophic breadth, and occupied different niche spaces. Shifts in resource use following harvest could be due to harvest‐mediated changes in both the plant and arthropod communities that might affect the strength of competition or alter plant nitrogen availability. Because shifts in resource use alter the flow of nutrients across the food web, disturbance effects on ants could have ecosystem‐level consequences through nutrient cycling.     

Changes in retention behavior of fluorescently labeled proteins during ion-exchange chromatography caused by different protein surface labeling positions

Confocal laser scanning microscopy (CLSM) is a method allowing in situ visualization of protein transport in porous chromatography resins. CLSM requires labeling a protein with a fluorescent probe. Recent work has shown that conjugation of the protein with fluorescent probes can lead to significant changes in the retention time of the protein-dye conjugate with respect to the unlabeled protein. In this study, we show that common labeling procedures result in a heterogeneous mixture of different variants and that attachment location of the fluorescent probe on the protein surface can have a strong effect on the retention of protein-dye conjugate. Lysozyme was labeled with Cy5 and BODIPY-FL succinimidyl esters, followed by chromatographic separation of the different lysozyme-dye conjugates and subsequent determination of the label position using MALDI-TOF-MS. Finally, homogenously labeled lysozyme-dye conjugates were used in CLSM experimentation and compared to published results arising from heterogeneously labeled feedstocks. The results confirm that the attachment location of the fluorescent probe has a strong effect on chromatographic retention behavior. When addressing the binding affinities of the different labeled protein fractions, it was found that native lysozyme was able to displace lysozyme-dye conjugates when the fluorescent label was attached to lysine-33, but not when attached to lysine-97. Finally, it could be shown that when superimposing the single profiles of the three major fractions obtained during a labeling procedure a qualitative picture of the net profile is obtained.     

DFT study of alpha- and beta-D-allopyranose at the B3LYP/6-311++G ** level of theory

One hundred and two conformations of alpha- and beta-D-allopyranose, the C-3 substituted epimer of glucopyranose, were geometry optimized using the density functional, B3LYP, and the basis set, 6-311++G **. Full geometry optimization was performed on different ring geometries and on the hydroxymethyl rotamers (gg/gt/tg). Analytically derived Hessians were used to calculate zero point energy, enthalpy, and entropy. The lowest energy and free energy conformation found is the alpha-tg(g-)-4C1-c conformation, which is only slightly higher in electronic (approximately 0.2 kcal/mol) and free energy than the lowest energy alpha-D-glucopyranose. The in vacuo calculations showed a small (approximately 0.3 kcal/mol) energetic preference for the alpha- over the beta-anomer for allopyranose in the 4C1 conformation, whereas in the 1C4 conformation a considerable (approximately 1.6 kcal/mol) energetic preference for the beta- over the alpha-anomer for allopyranose was encountered. The results are compared to previous aldohexose calculations in vacuo. Boat and skew forms were found that remained stable upon gradient optimization although many starting boat conformations moved to other skew forms upon optimization. As found for glucose, mannose, and galactose the orientation and interaction of the hydroxyl groups make the most significant contributions to the conformation/energy relationship in vacuo. A comparison of different basis sets and density functionals is made in the Discussion section, confirming the appropriateness of the level of theory used here.     

Ecological application of wavelet analysis in the scaling of spatial distribution patterns of Ceratoides ewersmanniana

Ecological experiments are usually conducted on small scales, but the ecological and environmental issues are usually on large scales. Hence, there is a clear need of scaling. Namely, when we deal with patterns and processes on larger scales, a special connection needs to be established on the small scales that we are familiar with. Here we presented a wavelet analysis method that could build relationships between spatial distribution patterns on different scales. With this method, we also studied how spatial heterogeneity and distribution patterns changed with the scale. We investigated the distribution and the habitat of C. ewersmanniana in two plots (200 m × 200 m; the distance between these two plots is 15 km) at Mosuowan desert. The results demonstrated that spatial heterogeneity and distribution patterns were incorporated into larger scales when the wavelet scale varied from one (5 m) to four (20 m). However, if the wavelet scale was above five (25 m), the spatial distribution patterns varied placidly, the oscillation frequency of landforms stabilized at 110 m, and the dynamic quantity period of C. ewersmanniana stabilized at 115–125 m. We also identified signal mutation points with wavelet analysis and verified the heterogeneity degree of local space with position variance. We found that position variance decomposed the distribution patterns on large scales into small sampling plots, and the position with the largest variance also had the strongest heterogeneity. In a word, the wavelet analysis method could scale-up spatial distribution patterns and habitat heterogeneity. With this method and other methods derived from this one, such as wavelet scale, wavelet variance, position variance and extremely direct-viewing graphs, wavelet analysis could be widely applied in solving the scaling problem in ecological and environmental studies.