Review and simulation of homoplasy and collision in AFLP

In this paper we give a short review of the problems of homoplasy and collision in AFLP, and describe a software tool that we developed to illustrate these problems. AFLP is a DNA fingerprinting technique, producing profiles of bands, the result of the separation of DNA fragments by length on a gel or microcapillary system. The profiles are usually interpreted as binary band absence/presence patterns. We focus on two major problems: (1) Within a profile two or more fragments of the same length but of different genomic origin may have been selected, colliding into a single band. This collision problem, akin to the birthday problem, may be surprisingly large. (2) In a pair of profiles two equally long fragments of different genomic origin may have been selected, appearing as identical bands in the two profiles. This is called homoplasy. Both problems are quantified by modeling AFLP as a random sampling technique of fragment lengths. AFLP may be used in phylogenetic studies to estimate the pairwise genetic similarity of individuals. Similarity coefficients like Dice and Jaccard coefficients overestimate the true genetic similarity because of homoplasy, with increasing bias for higher numbers of bands per profile. Corrected estimators are described, which do not suffer from bias. The ideas are illustrated using a new software tool. Data from studies on Arabidopsis and tomato serve as examples. Finally, we make some recommendations with respect to the use of AFLP

On some surprising statistical properties of a DNA fingerprinting technique called AFLP

AFLP is a widely used DNA fingerprinting technique, resulting in band absence - presence profiles, like a bar code. Bands represent DNA fragments, sampled from the genome of an individual plant or other organism. The DNA fragments travel through a lane of an electrophoretic gel or microcapillary system, and are separated by length, with shorter fragments traveling further. Multiple individuals are simultaneously fingerprinted on a gel. One of the applications of AFLP is the estimation of genetic similarity between individuals, e.g. in diversity and phylogenetic studies. In that case, profiles of two individuals are compared, and the fraction of shared (comigrating) bands is calculated, e.g. using the Dice similarity coefficient. Two comigrating bands may share the same fragment, but band sharing could also be due to chance, if two equally sized, but different fragments are amplified. This is called homoplasy. Homoplasy biases similarity coefficients. Homoplasy could also occur within a lane, if two different fragments of equal length are amplified, resulting in a single band. We call this collision. The main objective of this thesis is the study of collision and homoplasy in AFLP. The length distribution of AFLP fragments plays an important role. This distribution is highly skewed with more abundant short fragments. By simulation the expected similarity for unrelated genotypes is calculated. As much as 40% of the bands may be shared by chance in case of profiles with 120 bands. The collision problem is analogous to the birthday problem, which has a surprising solution. The collision problem is even more extreme, making it even more surprising. Profiles with only 19 bands contain collision(s) with probability 1/2. These findings have consequences for practice. In some cases it is better to prevent the occurrence of collisions by decreasing the number of bands, in other cases a correction for homoplasy and collision is preferred. Modified similarity coefficients are proposed, that estimate the fraction of homologous fragments, correcting for homoplasy and collision. Partially related to homoplasy and collision, we study the codominant scoring of AFLP in association panels. Examples of AFLP in lettuce and tomato serve as illustrations

Use of the Bradley-Terry model to assess uncertainty in an error matrix from a hierarchical segmentation of an ASTER image

Remotely sensed images are increasingly being used for collection of spatial information. A wide development in sensor systems has occurred during the last decades, resulting in improved spatial, temporal, and spectral resolution. The collection of data by remote sensing is generally more efficient and cheaper than by direct observation and measurement on the ground, although still of a varying quality. Data collected by sensors may be affected by atmospheric factors between sensors and the values reflected on the earth's surface, local impurities on the earth's surface, technical deficiencies of sensors and other factors. In addition, only the reflection of the sensor's signal or of the sunlight on the earth's surface is being measured, and no direct measurements are made. Consequently, the quality of maps produced by remote sensing needs to be assessed

Efficacy of management and monitoring methods to prevent post-harvest losses caused by rodents

The presence of pest rodents around food production and storage sites is one of many underlying problems contributing to food contamination and loss, particularly influencing food and nutrition security in low-income countries. By reducing both pre- and post-harvest losses by rodents, millions of food-insecure people would benefit. As there are limited quantitative data on post-harvest rice losses due to rodents, our objectives were to assess stored rice losses in local households from eight rural communities and two rice milling factories in Bangladesh and to monitor the effect of different rodent control strategies to limit potential losses. Four treatments were applied in 2016 and 2017, (i) untreated control, (ii) use of domestic cats, (iii) use of rodenticides, (iv) use of snap-traps. In total, over a two-year period, 210 rodents were captured from inside people’s homes, with Rattus rattus trapped most often (n = 91), followed by Mus musculus (n = 75) and Bandicota bengalensis (n = 26). In the milling stations, 68 rodents were trapped, of which 21 were M. musculus, 19 R. rattus, 17 B. bengalensis, 8 Rattus exulans, and 3 Mus terricolor. In 2016, losses from standardised baskets of rice within households were between 13.6% and 16.7%. In 2017, the losses were lower, ranging from 0.6% to 2.2%. Daily rodent removal by trapping proved to be most effective to diminish stored produce loss. The effectiveness of domestic cats was limited

Ісламський фактор в міжнародних економічних відносинах: приклад ЄС і Турції

В роботі представлена спроба цілісного вивчення впливу культурних, соціальних, економічних і політичних факторів на процеси взаємовідносин Туреччини і ЄС, що дозволяє надати більш об'ємне й глибоке уявлення про соціально-політичні процеси в Туреччині і ЄС в контексті їх еволюції. Дана оцінка сучасного стану мусульманської діаспори в країнах ЄС з подальшою систематизацією даних. Зроблена авторська порівняльна характеристика процесів євроінтеграції України (у якої є свій «ісламський» фактор) і Туреччини і її систематизаці

When nudgees become nudgers: exploring the use of self-nudging to promote fruit intake

The current study explored (1) the immediate and prolonged effects of self-nudges promoting fruit intake in the home environment, (2) whether the effect of self-nudges on fruit intake persists after self-nudges are no longer used (i.e. a temporal spillover effect) and (3) whether self-nudges can install healthy eating habits that, in turn, explain the temporal spillover effect. Participants (N = 331) were randomly assigned to either a control or self-nudge condition in which they had to choose a self-nudge promoting fruit consumption for 8 weeks. Thereafter, participants were asked to remove the self-nudge for 1 week to assess a possible temporal spillover effect. Results showed a positive effect of the self-nudges on fruit consumption right after implementation that continued during the 8 weeks in which the self-nudge was implemented, which was accompanied by an increase in fruit intake habit strength. However, a mixed picture emerged regarding the temporal spillover effect and no support was found for a mediation effect of habit strength. Although this study is only a first exploration of self-nudging to increase healthy food consumption, results indicate that self-nudging may be a promising extension of traditional nudging that can influence behaviour beyond out-of-home settings.Prevention, Population and Disease management (PrePoD

Time- and momentum-resolved photoemission studies using time-of-flight momentum microscopy at a free-electron laser

Time-resolved photoemission with ultrafast pump and probe pulses is an emerging technique with wide application potential. Real-time recording of nonequilibrium electronic processes, transient states in chemical reactions, or the interplay of electronic and structural dynamics offers fascinating opportunities for future research. Combining valence-band and core-level spectroscopy with photoelectron diffraction for electronic, chemical, and structural analyses requires few 10 fs soft X-ray pulses with some 10 meV spectral resolution, which are currently available at high repetition rate free-electron lasers. We have constructed and optimized a versatile setup commissioned at FLASH/PG2 that combines free-electron laser capabilities together with a multidimensional recording scheme for photoemission studies. We use a full-field imaging momentum microscope with time-of-flight energy recording as the detector for mapping of 3D band structures in (kx, ky, E) parameter space with unprecedented efficiency. Our instrument can image full surface Brillouin zones with up to 7 Å−1 diameter in a binding-energy range of several eV, resolving about 2.5 × 105 data voxels simultaneously. Using the ultrafast excited state dynamics in the van der Waals semiconductor WSe2 measured at photon energies of 36.5 eV and 109.5 eV, we demonstrate an experimental energy resolution of 130 meV, a momentum resolution of 0.06 Å−1, and a system response function of 150 fs