Implementation of a Bayesian design in a dose-escalation study of an experimental agent in healthy volunteers

Summary .   Bayesian decision procedures have recently been developed for dose escalation in phase I clinical trials concerning pharmacokinetic responses observed in healthy volunteers. This article describes how that general methodology was extended and evaluated for implementation in a specific phase I trial of a novel compound. At the time of writing, the study is ongoing, and it will be some time before the sponsor will wish to put the results into the public domain. This article is an account of how the study was designed in a way that should prove to be safe, accurate, and efficient whatever the true nature of the compound. The study involves the observation of two pharmacokinetic endpoints relating to the plasma concentration of the compound itself and of a metabolite as well as a safety endpoint relating to the occurrence of adverse events. Construction of the design and its evaluation via simulation are presented.     

Examining methodology to identify patterns of consulting in primary care for different groups of patients before a diagnosis of cancer: An exemplar applied to oesophagogastric cancer

BackgroundCurrent methods for estimating the timeliness of cancer diagnosis are not robust because dates of key defining milestones, for example first presentation, are uncertain. This is exacerbated when patients have other conditions (multimorbidity), particularly those that share symptoms with cancer. Methods independent of this uncertainty are needed for accurate estimates of the timeliness of cancer diagnosis, and to understand how multimorbidity impacts the diagnostic process.MethodsParticipants were diagnosed with oesophagogastric cancer between 2010 and 2019. Controls were matched on year of birth, sex, general practice and multimorbidity burden calculated using the Cambridge Multimorbidity Score. Primary care data (Clinical Practice Research Datalink) was used to explore population-level consultation rates for up to two years before diagnosis across different multimorbidity burdens. Five approaches were compared on the timing of the consultation frequency increase, the inflection point for different multimorbidity burdens, different aggregated time-periods and sample sizes.ResultsWe included 15,410 participants, of which 13,328 (86.5 %) had a measurable multimorbidity burden. Our new maximum likelihood estimation method found evidence that the inflection point in consultation frequency varied with multimorbidity burden, from 154 days (95 %CI 131.8–176.2) before diagnosis for patients with no multimorbidity, to 126 days (108.5–143.5) for patients with the greatest multimorbidity burden. Inflection points identified using alternative methods were closer to diagnosis for up to three burden groups. Sample size reduction and changing the aggregation period resulted in inflection points closer to diagnosis, with the smallest change for the maximum likelihood method.DiscussionExisting methods to identify changes in consultation rates can introduce substantial bias which depends on sample size and aggregation period. The direct maximum likelihood method was less prone to this bias than other methods and offers a robust, population-level alternative for estimating the timeliness of cancer diagnosis.     

Reoxygenation and Split-Dose Response to Radiation in a Tumour Model with Krogh-Type Vascular Geometry

After a single dose of radiation, transient changes caused by cell death are likely to occur in the oxygenation of surviving cells. Since cell radiosensitivity increases with oxygen concentration, reoxygenation is expected to increase the sensitivity of the cell population to a successive irradiation. In previous papers we proposed a model of the response to treatment of tumour cords (cylindrical arrangements of tumour cells growing around a blood vessel of the tumour). The model included the motion of cells and oxygen diffusion and consumption. By assuming parallel and regularly spaced tumour vessels, as in the Krogh model of microcirculation, we extend our previous model to account for the action of irradiation and the damage repair process, and we study the time course of the oxygenation and the cellular response. By means of simulations of the response to a dose split in two equal fractions, we investigate the dependence of tumour response on the time interval between the fractions and on the main parameters of the system. The influence of reoxygenation on a therapeutic index that compares the effect of a split dose on the tumour and on the normal tissue is also investigated.     

Patient doses and occupational exposure in a hybrid operating room

PurposeThis study aimed to characterize the radiation exposure to patients and workers in a new vascular hybrid operating room during X-ray-guided procedures.MethodsDuring one year, data from 260 interventions performed in a hybrid operating room equipped with a Siemens Artis Zeego angiography system were monitored. The patient doses were analysed using the following parameters: radiation time, kerma-area product, patient entrance reference point dose and peak skin dose. Staff radiation exposure and ambient dose equivalent were also measured using direct reading dosimeters and thermoluminescent dosimeters.ResultsThe radiation time, kerma-area product, patient entrance reference point dose and peak skin dose were, on average, 19:15 min, 67 Gy·cm², 0.41 Gy and 0.23 Gy, respectively. Although the contribution of the acquisition mode was smaller than 5% in terms of the radiation time, this mode accounted for more than 60% of the effective dose per patient. All of the worker dose measurements remained below the limits established by law.ConclusionsThe working conditions in the hybrid operating room HOR are safe in terms of patient and staff radiation protection. Nevertheless, doses are highly dependent on the workload; thus, further research is necessary to evaluate any possible radiological deviation of the daily working conditions in the HOR.     

Variation in female mate preference across a grasshopper hybrid zone

A method for studying variation in female preference among populations free from the confounding effects of variation in male characters is described. This method is applied to sixteen populations in a transect across a hybrid zone in the grasshopper, Chorthippus parallelus. Significant variation in preference is revealed among populations. The pattern of this variation is analysed in the context of the reinforcement model of speciation. While the data do indicate an increased homogamic preference on one side of the zone relative to more distant populations, this pattern cannot be distinguished statistically from an abrupt transition in preference over a distance of less than 1 km. We argue that either of these patterns implies that selection operates on female preferences in the hybrid zone.     

Gene expression divergence and the origin of hybrid dysfunctions

Hybrids between closely related species are often sterile or inviable as a consequence of failed interactions between alleles from the different species. Most genetic studies have focused on localizing the alleles associated with these failed interactions, but the mechanistic/biochemical nature of the failed interactions is poorly understood. This review discusses recent studies that may contribute to our understanding of these failed interactions. We focus on the possible contribution of failures in gene expression as an important contributor to hybrid dysfunctions. Although regulatory pathways that share elements in highly divergent taxa may contribute to hybrid dysfunction, various studies suggest that misexpression may be disproportionately great in regulatory pathways containing rapidly evolving, particularly male-biased, genes. We describe three systems that have been analyzed recently with respect to global patterns of gene expression in hybrids versus pure species, each in Drosophila. These studies reveal that quantitative misexpression of genes is associated with hybrid dysfunction. Misexpression of genes has been documented in sterile hybrids relative to pure species, and variation in upstream factors may sometimes cause the over- or under-expression of genes resulting in hybrid sterility or inviability. Studying patterns of evolution between species in regulatory pathways, such as spermatogenesis, should help in identifying which genes are more likely to be contributors to hybrid dysfunction. Ultimately, we hope more functional genetic studies will complement our understanding of the genetic disruptions leading to hybrid dysfunctions and their role in the origin of species.     

No variation for Wolbachia-induced hybrid breakdown in two populations of a spider mite

Wolbachia are cytoplasmically transmitted bacteria that infect several species of mites. In the two-spotted spider mite Tetranychus urticae Koch this symbiont can induce reproductive incompatibility. Wolbachia-induced reproductive incompatibility is observed in crosses between Wolbachia-infected (W) males and uninfected (U) females. This incompatibility is expressed in F1 broods as male-biased sex ratios, an effect called cytoplasmic incompatibility (CI). However, in the two-spotted spider mite, Wolbachia-induced reproductive incompatibility may extend to the F2: broods of virgin F1 females from U×W crosses sometimes suffer increased mortality rates. This F2 effect is called hybrid breakdown (HB). Several isofemale lines derived from mites collected from rose and cucumber plants had been previously tested for CI. Here we report on the results obtained for HB.     

Glycan structures of ocular surface mucins in man,rabbit and dog display species differences

The composition of the mucus gel of the tear film reflects the competing needs for transparency, stability, hydration, and protection of the ocular surface. Mucins form the macromolecular scaffolding of this hydrated gel, and glycans decorating these glycoproteins represent a rich source of binding ligands that may both modulate microbial binding and regulate the physicochemical characteristics of the gel. This study compares the structure of O-linked glycans derived from the ocular mucins of three species, to determine whether the ocular surface microenvironment dictates the need for a common pattern of O-linked carbohydrate structures. Ocular mucus aspirates were collected from healthy humans, rabbits and dogs. Mucins were purified using standard protocols. O-glycans were released by hydrazinoloysis and subsequently analysed by a combination of HPLC, exoglycosidase digestions and LC–MS/MS. A total of 12 different O-glycans were identified. In human ocular mucin, the majority were negatively charged and terminated in sialic acid, whilst those from rabbit or dog were mainly neutral and terminated in α 1-2 fucose and/or α 1-3 N-acetylgalactosamine. The glycans were short: the most common structures being tetra-, tri- or disaccharides. Less elaborate glycan structures are encountered at the ocular surface than at many other mucosal surfaces. Species-specific glycan expression is a feature of ocular surface mucins, and has implications for their defensive properties where different microbial and environmental challenges are encountered. Louise Royle and Elizabeth Matthews contributed equally to this work.     

Host resistance and pathogen virulence across a plant hybrid zone

Hybridization between locally adapted plant populations has been postulated to have significant evolutionary consequences, and, in particular, may influence host-pathogen interactions with respect to resistance and virulence structure. This study investigated patterns of resistance and virulence in a hybrid zone between ”bog” and ”hill” ecotypes of the native Australian flax, Linum marginale, where the host is subject to attack by the rust pathogen, Melampsora lini. Analysis of the resistance structure of adjoining bog, hill and hybrid populations found that bog plants were generally susceptible to pathogen isolates taken from all these sites, but that hybrids exhibited resistance levels similar to the more resistant hill plants. Similarly, the virulence structure of rust isolates collected from the hybrid population was more similar to that of the hill isolates than the bog. Controlled crosses between bog and hill plants showed that crosses in one direction (bog females×hill males) were much more successful than the other. A multi-year reciprocal transplant study further indicated that bog plants had significantly higher survivorship than hill plants, regardless of site. It is suggested that likelihood of differential gene flow and survivorship for bog and hill plants may at least partially explain the maintenance of a relatively narrow hybrid zone. Received: 5 October 1999 / Accepted: 1 July 1999     

Progress in research and development on hybrid rice: a super-domesticate in China

BACKGROUND: China has been successful in breeding hybrid rice strains, but is now facing challenges to develop new hybrids with high-yielding potential, better grain quality, and tolerance to biotic and abiotic stresses. This paper reviews the most significant advances in hybrid rice breeding in China, and presents a recent study on fine-mapping quantitative trait loci (QTLs) for yield traits. SCOPE: By exploiting new types of male sterility, hybrid rice production in China has become more diversified. The use of inter-subspecies crosses has made an additional contribution to broadening the genetic diversity of hybrid rice and played an important role in the breeding of super rice hybrids in China. With the development and application of indica-inclined and japonica-inclined parental lines, new rice hybrids with super high-yielding potential have been developed and are being grown on a large scale. DNA markers for subspecies differentiation have been identified and applied, and marker-assisted selection performed for the development of restorer lines carrying disease resistance genes. The genetic basis of heterosis in highly heterotic hybrids has been studied, but data from these studies are insufficient to draw sound conclusions. In a QTL study using stepwise residual heterozygous lines, two linked intervals harbouring QTLs for yield traits were resolved, one of which was delimited to a 125-kb region. CONCLUSIONS: Advances in rice genomic research have shed new light on the genetic study and germplasm utilization in rice. Molecular marker-assisted selection is a powerful tool to increase breeding efficiency, but much work remains to be done before this technique can be extended from major genes to QTLs.     

Isolation and characterization of polysaccharides of a hybrid mushroom (backcross mating between PfloVv12 and Volvariella volvacea)

Three polysaccharide fractions (PS-I, PS-II, and PS-III) were isolated from the aqueous extract of a hybrid mushroom obtained through backcross mating of a somatic hybrid mushroom PfloVv12 (Sterile line) with Volvariellavolvacea. PfloVv12 was obtained through protoplast fusion of Pleurotusflorida and V. volvacea. PS-I was identified as 1,6-β glucan. PS-II and PS-III were identified as mannoglucogalactan but differing in molecular weights only. On the basis of total acid hydrolysis, methylation analysis, periodate oxidation, and NMR experiment (¹H, ¹³C, DEPT-135, DQF-COSY, TOCSY, NOESY, ROESY, HMQC, and HMBC) the structures of these polysaccharides were established as;     

Assortative mating across a hybrid zone in Chorthippus parallelus (Orthoptera: Acrididae)

Two subspecies of the grasshopper Chorthippus parallelus meet and form a hybrid zone in the Pyrenees. Both strong hybrid dysfunction and a behavioural difference occur, which would seem to make the zone a suitable candidate for speciation by reinforcement. One of the classic ways of looking for this is to test for increased levels of assortative mating between populations from close to the region of contact. Here we show that, with virgin insects, such assortment decreases as one approaches the centre of the zone in C. parallelus. The pattern is different upon remating, with non-virgins showing a pattern more like that predicted by reinforcement. Overall there is little evidence for reinforcement. We argue that other tests of the model may be more appropriate for stable hybrid zones.     

Bacterial diversity in roots of conventional and genetically modified hybrid maize

Cultivated surfaces of genetically modified (GM) crops increased year by year, becoming in 2012 more extensive in developed than in industrialized countries. Furthermore, it has been postulated that the plant is which leads to the selection of the microorganisms on its root exudates, creating specific conditions which in turn regulate the specific microbial structure of each plant. In this study, our main objective was to examine whether the introduction of transgenic maize herbicide-tolerant plants will impact the microbial structures that inhabit at the rhizosphere and rhizoplane with respect to conventional hybrid maize plants. Bacterial populations were determined (CFU/g) using four different semi-selective media. The bacterial genera isolated from the rhizoplane and rhizosphere were identified by sequencing its 16S ribosomal DNA. Although minor differences were found in bacterial populations, our results indicated that there was not a strong change of the microorganisms populations that interact at the rhizosphere of an either conventional hybrid or genetically modified maize. However, we found some bacteria that were only isolated in the either genetically modified [Chryseobacterium sp. (4.39%) and Micrococcus sp. (3.72%)] or conventional maize [Sphingobium sp. (13.17%) and Microbacterium sp. (14.81%)].     

Modification of a gene encoding hybrid xylanase and its expression in Pichia pastoris

To obtain the protein expression of a hybrid xylanase in yeast, the gene encoding it was modified according to the codon bias of Pichia pastoris and expressed extracellularly in this yeast as an active xylanase, MBtx, exhibited a molecular mass of approximately 35 kDa on SDS–PAGE. The pH behavior of MBtx in terms of both activity and stability was similar to that of Btx, original gene product in Escherichia coli, while a certain difference was observed in optimal temperature for activity and in thermal stability. HPLC analysis revealed the xylan in wheat could be hydrolyzed by MBtx and the major hydrolysis product was xylotriose. These results showed codon usage played a key role in regulating the expression of the hybrid xylanase in P. pastoris and the recombinant hybrid xylanase, MBtx, produced by P. pastoris could be potentially useful in feed industry.     

Degradation of 3-chlorobiphenyl by in vivo constructed hybrid pseudomonads

Abstract 3-Chlorobiphenyl-degrading bacteria were obtained from the mating between Pseudomonas putida strain BN10 and Pseudomonas sp. strain B13. Strains such as BN210 resulted from the transfer of the genes coding the enzyme sequence for the degradation of chlorocatechols from B13 into BN10, whereas B13 derivatives such as B131 have acquired the biphenyl degradation sequence from BN10. During growth of the hybrid strains on 3-chlorobiphenyl 90% chloride was released. Activities of phenylcatechol 2,3-dioxygenase, benzoate dioxygenase, catechol 1,2-dioxygenase, chloromuconate cyloisomerase and 4-carboxymethyl-enebut-2-en-4-olide hydrolase were found in 3-chlorobiphenyl-grown cells. The hybrid strains were found to convert some congeners of the Aroclor 1221 mixture such as mono- and dichloro-substituted biphenyls.     

Flower colour variation across a hybrid zone in Antirrhinum as perceived by bumblebee pollinators

To assess if pollinators’ behaviour could explain the maintenance of hybrid zones between different flower colour morphs, we analyzed flower colour variation in an Antirrhinum hybrid zone using spectrometry and a model of bee perception. Some colours generated by hybridization were not observed in any Antirrhinum species and even appeared to be rare among angiosperms. Variation in flower colours within the hybrid zone was continuous; the most similar colours were predicted not to be discriminated from one another in natural foraging situations. However, when compared at a scale corresponding to bees’ foraging range, some flower colours could be discriminated from all colours displayed by neighbouring plants. This could affect pollinator behaviour and explain lower visitation rates within the centre of the hybrid zone. Behavioural studies involving bumblebees and plant mixtures of parental and hybrid flower colours carefully characterized with appropriate visual models will be necessary to test this hypothesis. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Handling editor: Lars Chittka     

Understanding the genetic and molecular constitutions of heterosis for developing hybrid rice

The wide adoption of hybrid rice has greatly increased rice yield in the last several decades. The utilization of heterosis facilitated by male sterility has been a common strategy for hybrid rice development. Here, we summarize our efforts in the genetic and molecular understanding of heterosis and male sterility together with the related progress from other research groups. Analyses of F1 diallel crosses show that strong heterosis widely exists in hybrids of diverse germplasms, and inter-subsp...