Blinded and unblinded sample size reestimation procedures for stepped‐wedge cluster randomized trials

The ability to accurately estimate the sample size required by a stepped‐wedge (SW) cluster randomized trial (CRT) routinely depends upon the specification of several nuisance parameters. If these parameters are misspecified, the trial could be overpowered, leading to increased cost, or underpowered, enhancing the likelihood of a false negative. We address this issue here for cross‐sectional SW‐CRTs, analyzed with a particular linear‐mixed model, by proposing methods for blinded and unblinded sample size reestimation (SSRE). First, blinded estimators for the variance parameters of a SW‐CRT analyzed using the Hussey and Hughes model are derived. Following this, procedures for blinded and unblinded SSRE after any time period in a SW‐CRT are detailed. The performance of these procedures is then examined and contrasted using two example trial design scenarios. We find that if the two key variance parameters were underspecified by 50%, the SSRE procedures were able to increase power over the conventional SW‐CRT design by up to 41%, resulting in an empirical power above the desired level. Thus, though there are practical issues to consider, the performance of the procedures means researchers should consider incorporating SSRE in to future SW‐CRTs.     

Expression of firefly luciferase gene in Erwinia amylovora

In this study we describe an ef?cient stable genetic transformation of the phytopathogenic bacterium Erwinia amylovora using a recombinant expression vector encoding the ?re?y luciferase gene of Photinus pyralis, which is further controlled by IPTG‐inducible promoter. Stably transformed E. amylovora cells maintain the same infectivity as the wild‐type strain and, after induction with IPTG, produce luciferase. Luminescence produced by the action of luciferase on an exogenous substrate was easily detectable by a simple and rapid bioluminescent assay (BL). The transformed E. amylovora strain maintains the same high emission level, even after passage in pears, until about 15 days post‐infection. Our ?ndings therefore show that the luciferase assay can be conveniently used to follow the bacterial movement in plant tissue and its dissemination in controlled environments.     

Some biological aspects and life history strategies of Nile tilapia Oreochromis niloticus (L.) in Lake Victoria, Kenya

The life history characteristics of introduced Nile tilapia (Oreochromis niloticus L.) in Lake Victoria, including, sex ratio, fecundity, reproduction, weight‐length relationship and body condition were studied and compared with those of other populations. Samples were collected by trawling and seining in the Kenyan sector of Lake Victoria between June 1998 and December 2000. Males predominated over females (sex ratio 1.42 : 1 : 00). O. niloticus spawned throughout the year but with a peak between December and June. Length at first maturity was (mean ± SD) 30.81 ± 0.09 for females and 34.5 ± 6 0.48 for males. There was little seasonal variation in relative condition, which ranged from 0.92 to 1.05 in males and 0.94 to 1.07 in females. Gonadosomatic index (GSI) was low during the postspawning period (July to October) and high during the protracted breeding period (December and June). Fecundity ranged from 905 to 7619 oocytes for fish of 28 to 51 cm total length (TL) respectively. The relationships between fecundity (F) and total length (L), weight (W) and ovary weight (OW) were: F = 8.159L^1.53, F = 96.269W^0.4504, F = 1806 + 39.4OW. The slope b of the weight‐length relationship was 3.08–3.32 for males and 3.07–3.22 for females. Growth was allometric in both cases and was significantly different from the expected value of 3. The life history strategy of O. niloticus is discussed in context of environmental changes occurring in the lake.     

Steppe bison hunting in the Gravettian of Buda (lower Bistriţa Valley,eastern Romania)

The rich accumulation of bovid remains found at Buda (Bacău County, eastern Romania) is unique among the Upper Palaeolithic sites in the region. The morphological analysis of postcranial remains, which dominate the assemblage by far, shows they belong to Bison priscus, the steppe bison. The body parts representation is biased towards distal limbs, which also display typical butchery cut marks (resulted from disarticulation or skinning) and bone breakage, suggesting the presence of secondary butchery site where limbs were disarticulated and broken for marrow extraction. The assemblage is dominated by adults, mostly females, and includes few sub-adult individuals and no young juveniles. The large number of bison individuals indicates the found remains are the result of a mass killing event representing at least one hunting episode. Considering the age and sex structure of the population, we estimate that the event can be placed during autumn.     

Reconstruction of lignin and hemicelluloses by aqueous ethanol anti‐solvents to improve the ionic liquid‐acid pretreatment performance of Arundo donax Linn

Ionic liquid (IL)‐acid pretreatment is known to not only enhance the enzymatic hydrolysis efficiency of lignocellulose but also to generate deposits on the surface of fiber by conventional water regeneration, which retard the increment. In this study, ethanol aqueous solution regeneration was developed as a new method to change the substrates characteristics for IL‐acid pretreatment and their effects on the enzymatic hydrolysis were evaluated. Following the IL‐acid reaction, the biomass slurry was subjected to ethanol aqueous solution at various concentration. Results indicated that anti‐solvent choice significantly influenced the reconstruction of both hemicelluloses and lignin as a result of the competition between water and ethanol. The partial removal of hemicelluloses and suitable lignin re‐localization contributed to a more porous structure. Consequently, the cellulose digestibility of aqueous ethanol regenerated samples was dramatically enhanced to ～100% and approximately 11‐ and 2‐fold higher than that of untreated and conventional water regenerated pretreated samples, respectively. A giant leap in the initial rate of enzymatic hydrolysis was also detected in 50% ethanol aqueous solution regenerated samples and only about 10 hr was needed to convert 80% of cellulose to glucose due to the appearance of cellulose II hydrate‐like and more porous structure.     

半干旱黄土丘陵区沙棘优良品种引种选育试验研究

1985-1998年先后在黄土高原半干旱区的陕西吴旗,安塞县进行了沙棘优良品种引种选育试验研究。通过引种国内不同地理种源20余种优良沙棘类型。引进俄罗斯优良沙棘品种,采用家系选择法进行试验研究,初步筛选出生态经济型5种沙棘类型,经济型2种类型。前者生长迅速,树冠好,根系发达,郁闭快,水土保持效益好,且果实较大（果径0.8-0.9cm,百果重20-31g),单株产果量为2-3.5kg,Vc和含油量较高,其生态,经济性状较当地野生沙棘为好。此种类型沙棘适于在黄土丘陵大面积荒沟,荒坡种植,通过引种俄罗斯大果,无刺沙棘为好。此种类型沙棘适于在黄土丘陵大面积荒沟,荒坡种植,通过引种俄罗斯大果,无刺沙棘优良品种与本地野生中国沙棘对比分析看,出,其适应性,抗性较中国沙棘差,经济性状较好,通过试验筛选出2种优良类型,果径为0.9-1.3cm,百果重46-52g,单株产果量2-3.5kg,无刺或少刺,此项研究为在半干旱黄土丘陵区大面积荒山,荒沟建造高产,优质沙棘林,高效,持续发展沙棘产业具重要意义,在引种试验中必须掌握好其关键技术,建立好采穗圃,种子园,并建立一定面积的集约经营的高产,优质沙棘园及良种繁育基地,掌握好抚育管理技术,特别是水,肥管理技术。     

Multiple introductions,admixture and bridgehead invasion characterize the introduction history of Ambrosia artemisiifolia in Europe and Australia

Admixture between differentiated populations is considered to be a powerful mechanism stimulating the invasive success of some introduced species. It is generally facilitated through multiple introductions; however, the importance of admixture prior to introduction has rarely been considered. We assess the likelihood that the invasive Ambrosia artemisiifolia populations of Europe and Australia developed through multiple introductions or were sourced from a historical admixture zone within native North America. To do this, we combine large genomic and sampling data sets analysed with approximate Bayesian computation and random forest scenario evaluation to compare single and multiple invasion scenarios with pre‐ and postintroduction admixture simultaneously. We show the historical admixture zone within native North America originated before global invasion of this weed and could act as a potential source of introduced populations. We provide evidence supporting the hypothesis that the invasive populations established through multiple introductions from the native range into Europe and subsequent bridgehead invasion into Australia. We discuss the evolutionary mechanisms that could promote invasiveness and evolutionary potential of alien species from bridgehead invasions and admixed source populations.     

Unloading of homologous recombination factors is required for restoring double‐stranded DNA at damage repair loci

Cells use homology‐dependent DNA repair to mend chromosome breaks and restore broken replication forks, thereby ensuring genome stability and cell survival. DNA break repair via homology‐based mechanisms involves nuclease‐dependent DNA end resection, which generates long tracts of single‐stranded DNA required for checkpoint activation and loading of homologous recombination proteins Rad52/51/55/57. While recruitment of the homologous recombination machinery is well characterized, it is not known how its presence at repair loci is coordinated with downstream re‐synthesis of resected DNA. We show that Rad51 inhibits recruitment of proliferating cell nuclear antigen (PCNA), the platform for assembly of the DNA replication machinery, and that unloading of Rad51 by Srs2 helicase is required for efficient PCNA loading and restoration of resected DNA. As a result, srs2Δ mutants are deficient in DNA repair correlating with extensive DNA processing, but this defect in srs2Δ mutants can be suppressed by inactivation of the resection nuclease Exo1. We propose a model in which during re‐synthesis of resected DNA, the replication machinery must catch up with the preceding processing nucleases, in order to close the single‐stranded gap and terminate further resection.     

Dorsal rib histology of dinosaurs and a crocodylomorph from western Portugal: Skeletochronological implications on age determination and life history traits

Bone histology is an important tool for uncovering life history traits of extinct animals, particularly those that lack modern analogs, such as the non-avian dinosaurs. In most studies, histological analyses preferentially focus on long bones for understanding growth rates and determining age. Here we show, by analyzing ornithischians (a stegosaur and an ornithopod), saurischians (a sauropod and a theropod), and a crocodile, rib histology is a suitable alternative. The estimated age for all sampled taxa ranges between 14 to 17 years for Lourinhanosaurus antunesi and 27 to 31 years estimated for Draconyx loureiroi. The theropod Baryonyx was skeletally mature around 23–25 years of age but showed unfused neurocentral sutures, a paedomorphic feature possibly related to aquatic locomotion. Our results show that ribs can contain a nearly complete growth record, and reveal important information about individual age, point of sexual maturity, and, in some cases, sex. Because ribs are more available than long bones, this method opens new possibilities for studying rare and incomplete fossils, including holotypes.