A simulation approach for power calculation in large cohort studies based on multistate models

Realistic power calculations for large cohort studies and nested case control studies are essential for successfully answering important and complex research questions in epidemiology and clinical medicine. For this, we provide a methodical framework for general realistic power calculations via simulations that we put into practice by means of an R‐based template. We consider staggered recruitment and individual hazard rates, competing risks, interaction effects, and the misclassification of covariates. The study cohort is assembled with respect to given age‐, gender‐, and community distributions. Nested case‐control analyses with a varying number of controls enable comparisons of power with a full cohort analysis. Time‐to‐event generation under competing risks, including delayed study‐entry times, is realized on the basis of a six‐state Markov model. Incidence rates, prevalence of risk factors and prefixed hazard ratios allow for the assignment of age‐dependent transition rates given in the form of Cox models. These provide the basis for a central simulation‐algorithm, which is used for the generation of sample paths of the underlying time‐inhomogeneous Markov processes. With the inclusion of frailty terms into the Cox models the Markov property is specifically biased. An “individual Markov process given frailty” creates some unobserved heterogeneity between individuals. Different left‐truncation‐ and right‐censoring patterns call for the use of Cox models for data analysis. p‐values are recorded over repeated simulation runs to allow for the desired power calculations. For illustration, we consider scenarios with a “testing” character as well as realistic scenarios. This enables the validation of a correct implementation of theoretical concepts and concrete sample size recommendations against an actual epidemiological background, here given with possible substudy designs within the German National Cohort.     

厚壳贻贝whirlin类贝壳基质蛋白的重组表达与功能分析

贝壳历来是生物工程和材料学研究的重要对象。贝壳中的贝壳基质蛋白质在贝壳的形成与发育过程中具有重要的调控作用。Whirlin类蛋白质(Whirlin-like protein,WLP)是一种从厚壳贻贝(Mytilus coruscus)中鉴定的新型贝壳基质蛋白质。序列分析结果显示,该蛋白质含有PDZ(postsynaptic density/Discs large/Zonula occludens)结构域,而该结构域对贝壳生物矿化的影响目前尚无报道。为深入了解WLP在贝壳形成中对碳酸钙晶体的影响,在序列分析基础上,采用密码子优化结合原核重组表达,获得其重组表达产物后,开展了重组WLP对碳酸钙晶体形貌及晶型的影响研究,结晶速度抑制以及碳酸钙晶体结合分析。分析结果表明,重组WLP能诱导文石型碳酸钙晶体的形貌和方解石型碳酸钙晶体的晶型发生改变;同时重组WLP对碳酸钙晶体具有结合作用,且能抑制碳酸钙晶体的结晶速度。上述结果表明,WLP对贝壳的形成及发育具有重要影响,并可能在贝壳肌棱柱层的形成中发挥了重要作用。     

DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000.     

Allometric growth and adaptive value of exaggerated body parts in the larvae of Gratiana spadicea (Klug) (Coleoptera: Chrysomelidae)

1. Larvae of tortoise beetles present exaggerated body parts in association with an abdominal shield, which is made of faeces and exuviae that are deposited on the urogomphi throughout ontogeny. Growth trajectories and scaling relationships of these functional structures associated with the shield, if any, are unknown. 2. This study of Gratiana spadicea first tested, under field conditions, whether there is adaptive value associated with the shield regarding protection against predation and sunlight. Then, under laboratory conditions, the growth trajectory and allometric relationships among body parts were investigated, including scoli, individual and apparent furcae, and shield. The influence of food deprivation on the development of these structures was also determined. 3. Findings from previous studies were confirmed, suggesting that the adaptive value assigned to the shield is related to protection against predators. The present study demonstrated for the first time that the shield acts as a parasol in cassidines, decreasing the exposure of their larval body to sunlight. The scoli and apparent furca are exaggerated structures of G. spadicea, the development of which involves allometric growth and greater energetic investment (positive allometry) during ontogeny. There was proportionally less energetic investment for somatic construction of individual furca (negative allometry) due to the accumulation of the exuviae. 4. The possible consequences, in terms of developmental costs and survivorship benefits associated with the evolution of such exaggerated structures, are discussed.     

Induced defenses of loblolly pine, Pinus taeda: potential impact on Dendroctonus frontalis within-tree mortality

Loblolly pine (Pinus taeda L.) produces an induced defensive hypersensitive response in inner bark colonized by the southern pine beetle, Dendroctonus frontalis Zimm. (Coleoptera: Scolytidae), and its associated fungi. Adult beetles forced to colonize the induced response tissue in a laboratory study constructed galleries that were the same length as adults boring in normal phloem. However, each female laid fewer eggs in the induced tissue. Larval and pupal mortality were also higher in this tissue when compared to surrounding phloem. Beetles colonizing trees in response to pheromone baits constructed less gallery and laid fewer eggs in induced tissue than in surrounding normal phloem. These results suggest that the lesions produced by the induced defense system in conifers may not only contain the growth of fungi inoculated into trees during the attack phase of beetle colonization, but may also affect survival of bark beetle progeny.

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Résumé Une réaction hypersensible de défense a été induite dans les couches profondes de l'écorce de P. taeda colonisée par D. frontalis et le champignon qui lui est associé. Au laboratoire, des adultes, contraints de coloniser les tissus où une réaction hypersensible e été induite, ont foré des galeries de même longueur que celles creusées dans du phloème sain. Cependant les femelles ont pondu moins d'oeufs dans les tissus induits; les mortalités larvaires et nymphales étaient aussi plus fortes dans ce tissu que dans le phloème voisin. Les scolytes, ayant colonisé les arbres après attraction par des pièges à phéromones, forent moins de galeries et pondent moins d'oeufs dans le tissu induit que dans le phloème sain voisin. Ces résultats suggèrent que les lésions, provoquées par le système de défense induit des conifères, peuvent non seulement limiter la croissance du champignon inoculé dans l'arbre au cours de la colonisation des scolytes, mais aussi affecter la survie des descendants dans l'écorce.

     

Stronger dung removal in forests compared with grassland is driven by trait composition and biomass of dung beetles

1. Ecosystem processes depend on the biomass of the involved organisms, but their functional diversity may play an additional role. In particular, the exclusion of key functional groups through habitat disturbance may lead to the breakdown of ecosystem functions. Dung removal is an important process contributing to nutrient cycling and thus productivity in grazed ecosystems. 2. This study investigated the role of different functional groups of dung beetles in dung removal in different habitats within a wood-pasture in two different seasons. An experimental setting with 12 blocks and 108 dung pads was used to investigate short-term dung removal over 1 week of exposure. 3. Dung removal was most strongly affected by habitat type, with almost 40% lower levels in grassland than in adjacent forest and forest gaps. Of all assemblage characteristics, total biomass of tunneller species was the strongest predictor of dung removal, whereas functional diversity showed no significant effect. In accordance with the dung removal pattern at habitat type level, densities of large tunnellers were suppressed in grassland compared with forest. 4. It is concluded that dung removal is habitat-specific and large tunnellers play a disproportionate role in this important ecosystem function in temperate forests.     

Larva and pupa of Cyphopisthes descarpentriesi Paulian (Coleoptera: Scarabaeoidea: Ceratocanthidae) and their phylogenetic implications

Abstract Pupae and mature larvae of the Australian ceratocanthid beetle, Cyphopisthes descarpentriesi Paulian 1977, are described and extensively illustrated. This is the sixth species of the family for which immature stages are known and the first from the Australian region. Unlike other ceratocanthid larvae described before, those of Cyphopisthes Gestro lack stridulatory teeth on the middle and hind legs and any trace of a frontoclypeal suture on the cranium. Reduced one-segmented labial palpi in Cyphopisthes are unique in Scarabaeoidea. Monophyly of the family is not corroborated by larval characters. Absence of spiracular closing apparatus in larvae is reported in the family for the first time. Like pupae of Ceratocanthus White and Germarostes Paulian, those of Cyphopisthes have thoracic projections, but their shape and location are different. Spiracles are found on abdominal segments 2−4 of pupa; that on segment 2 differs in colour and location from the others.     

Effects of a juvenile hormone analogue on the eggs, post-embryonic development, metamorphosis and diapause induction of the Colorado potato beetle, Leptinotarsa decemlineata

The effect of a juvenile hormone analogue, S-71639, was tested on the eggs, four larval instars and adults of the Colorado potato beetle, Leptinotarsa decemlineata Say, by topical application or after treatment of the foodplant. The last larval instar is very sensitive to S-71639. Treatment of this instar delayed the onset of pupation and prevented adult emergence. Treated animals showed severe abnormalities, but they were not immediately killed at the doses used in this study. Treatment of larvae also interfered with the photoperiodic induction of diapause. Adults, kept under diapausing conditions, started to lay eggs after treatment with S-71639. The ovicidal effect of the compound was rather weak. The implications for practical use of S-71639 in control of the Colorado potato beetle are being discussed.

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Résumé L'effet d'un analogue de l'hormone juvénile, S-71639, a été testé sur les oeufs, les quatre stades larvaires et les adultes du doryphore, Leptinotarsa decemlineata Say, par application topique ou après traitement de la plante-hôte. Le dernier stade larvaire est très sensible au S-71639. Le traitement de ce stade retarde le début de la métamorphose et empêche l'émergence adulte. Les animaux traités montrent de graves anomalies, mais ne sont pas immédiatement tués par les doses utilisées dans cette étude. Le traitement des larves perturbe aussi l'induction photopériodique de la diapause. Les adultes placés dans des conditions de diapause, commencent à pondre après traitement au S-71639. L'effet ovicide de la substance est plutôt faible. Les implications pour l'utilisation pratique du S-71639 dans la lutte contre le doryphore sont discutées.

     

The effect of glucosinolates on responses of young Phyllotreta nemorum larvae to non-host plants

All recorded host plants of Phyllotreta nemorum L. (Coleoptera: Chrysomelidae) contain glucosinolates and belong to the plant families Brassicaceae (Cruciferae), Resedaceae and Capparaceae. The acceptability of 56 plant species from 28 other plant families (non-hosts) for young larvae has been studied in the laboratory. None of these species were fully acceptable for initiations of leaf mines when intact untreated leaves were presented, and only one species, Malva silvestris L. (Malvaceae), was partially acceptable. The acceptability of some species increased when leaf discs were presented instead of intact leaves; but the highest percentages of mine initiations occurred in leaf discs treated with the glucosinolate, sinigrin. A stimulatory effect of sinigrin could be demonstrated in experiments with 7 plant species: Papaver dubium L., Papaver rhoeas L., Fumaria officinalis L., Malva silvestris L., Pisum sativum L., Campanula latifolia L. and Lactuca sativa L. The majority of species remained unacceptable even after treatment with glucosinolates.The main causes for these differences between plant species are supposed to be differences in contents of deterrents and/or other stimulants for mine initiation. These possibilities are discussed in relation to the content of allelochemicals in acceptable plants and the position of these plants in botanical classifications.

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Zusammenfassung Phyllotreta nemorum L. ist ein oligophager Erdfloh, der an Cruciferen und anderen Glukosinolat-haltigen Pflanzenarten gebunden ist. Die Imagines fressen Löcher in die Blätter und die Weibchen legen ihre Eier in den Boden. Die Larven sind Blattminierer. Nach dem Schlüpfen im Boden klettern sie an die Pflanzen hoch, und die Einbohrung und der Anfang der Minierung erfolgt in eines der unteren Blätter der Wirtspflanze.Die Wirkung von Glukosinolaten auf die Einbohrung von Junglarven in Pflanzenarten, die keine natürliche Inhalt von Glukosinolaten haben, ist in Laborexperimenten untersucht worden. 56 Pflanzenarten aus 28 Familien wurden präsentiert teils als unbehandelte Blätter und teils als Glukosinolatbehandelte Blattscheiben. Unbehandelte Blätter von nicht-Glukosinolathaltigen Arten waren immer unbefriedigend für die Larven. Nur in eine Art, Malva silvestris L. war die Frequenz der Einbohrung ein bisschen höher als 10%. Eine signifikante Erhöherung der Anzahl eingebohrten Larven nach der Sinigrin-behandlung erfolgte in 7 Pflanzenarten: Papaver dubium L., P. rhoeas L., Fumaria officinalis L., Malva silvestris L., Pisum sativum L., Campanula latifolia L. und Lactuca sativa L. Doch blieben die meisten Pflanzenarten (84%) auch nach der Sinigrin-Behandlung unbesiedelt.Pflanzenarten, die nach der Sinigrin-Behandlung nicht besiedelt werden enthalten vielleicht frasshemmende Stoffe, oder ihnen fehlen noch weitere Frass-stimulierende Stoffe. Diese Möglichkeiten werden diskutiert in Zusammenhang mit den Inhalt von Allelochemikalien in besiedelten Pflanzenarten und mit ihrer taxonomischer Position.

     

Batch production and growth kinetics of hybridomas

Batch cultures of mouse-mouse hybridoma cell lines were carried out and their growth and production kinetics investigated. Three main cell specific production patterns (expressed as pg IgG/cell x hour) were found, which can be used as a classification system for hybridoma cell lines (groups I–III). Cells showing the highest IgG-production at the beginning of the batch culture (during the lag and the onset of the log-phase) were classified as either group I and II. The difference was that cell lines of group II showed a second high cell specific production at the onset of the stationary and death phases. Cell lines of group III had a quite constant production of antibodies during their growth; but IgG secretion completely stopped after the beginning of the stationary phase. The implications of these three production patterns on the design of a production process are discussed.