Structural variants (SVs) are the hidden architecture of the human genome, and are critical for us to understand diseases, evolution, and so on. The development of both sequencing technologies and... Show moreStructural variants (SVs) are the hidden architecture of the human genome, and are critical for us to understand diseases, evolution, and so on. The development of both sequencing technologies and computational tools greatly facilitates the detection of SVs, while misinterpreting or even missing complex ones. Detecting and characterizing complex events is a typical field requiring multiple disciplines, i.e., domain knowledge and computer science algorithms. In this thesis, we introduce novel algorithms to detect and validate com- plex events, and assess the reproducibility of current SV detection pipelines for clinical and research settings. Show less
This paper presents new experimental results obtained from 88 Mandarin speaking children (2; 11 – 4; 09; M = 3; 11; SD = 0; 6; 44 girls) in their acquisition of shenme ‘a/some’, a prototypical... Show moreThis paper presents new experimental results obtained from 88 Mandarin speaking children (2; 11 – 4; 09; M = 3; 11; SD = 0; 6; 44 girls) in their acquisition of shenme ‘a/some’, a prototypical superweak Negative Polarity Item (NPI) that survives in nonveridical contexts only (cf. Lin Jing et al. 2014). The existence of NPIs like shenme leads to a learnability problem. Without being confronted with negative evidence, such as corrective feedback or explicit instructions on shenme’s ungrammaticality in contexts that are not nonveridical, how can children detect shenme’s distributional constraint? By analysing children’s performance in an elicited imitation task, this paper investigates the learnability of the superweak NPI in Mandarin Chinese. The results suggest a learning process in which Mandarin children initially analyse shenme as a mere wh-quantifier and reanalyse it as a referentially deficient quantifier later on. The wh-analysis gives rise to a distribution of shenme in wh-questions only, whereas the non-referential analysis generates shenme’s distribution in the whole array of nonveridical contexts. The investigation of the acquisition of the Mandarin NPI shenme shows that children are able to acquire distributionally constrained items in the absence of negative evidence: they start out with a strict assumption (i.e. the wh-analysis) and switch to a less strict and generalising analysis (i.e. the non-referential analysis) later on. Show less
Despite intense efforts over the past 50 years to develop a vaccine, there is currently no licensed malaria vaccine available. The limited success in inducing sufficient protection against malaria... Show moreDespite intense efforts over the past 50 years to develop a vaccine, there is currently no licensed malaria vaccine available. The limited success in inducing sufficient protection against malaria with subunit-vaccines has renewed an interest in whole-parasite vaccination strategies. While live-vaccines are hard to formulate and administer, they have been shown to confer long-lasting sterile immunity in humans. The aim of the work described in this thesis was to genetically engineer and characterize growth- and virulence-attenuated blood stage parasites (GAPBS) in the rodent malaria model, P. berghei. Specifically, the identification of GAPBS that produce only short-lived, low-level infections that can provoke strong and long-lasting protective immunity. The thesis describes improved methods to produce and screen potential GAPBS, specifically transfection methods to generate GAPBS and methods to analyze their blood stage growth-characteristics. In addition, we report the generation and characterization of a number of novel GAPBS that are virulence-attenuated and produce self-resolving infections in mice. These GAPBS are useful tools to better understand the induction of protective immunity against Plasmodium blood stages and may help to create an effective and broad acting antimalarial vaccine. Show less
In the past thirty years, Frans Zwarts has written several papers providing crucial insight in licensing contexts for Negative Polarity Items (NPIs), presenting a more nuanced picture than Ladusaw... Show moreIn the past thirty years, Frans Zwarts has written several papers providing crucial insight in licensing contexts for Negative Polarity Items (NPIs), presenting a more nuanced picture than Ladusaw’s (1979) downward entailing (DE) requirement. Zwarts demonstrated (1981) that a number of Dutch NPIs appear only in a subset of DE-contexts, and proposed (1995) non-veridicality as a logico-semantic property that licenses so-called superweak NPIs. Such superweak NPIs, however, have hardly been attested. We show that Mandarin shenme (‘a (thing)’) is a prototypical superweak NPI. We explain its ungrammaticality in veridical contexts by arguing that shenme exhibits a lexical referential deficiency. Acquisitional data, furthermore, suggest that children initially analyze shenme as a WH-quantifier but acquire the referential deficiency underlying its NPI status after the age of four. Show less
In the past thirty years, Frans Zwarts has written several papers providing crucial insight in licensing contexts for Negative Polarity Items (NPIs), presenting a more nuanced picture than Ladusaw... Show moreIn the past thirty years, Frans Zwarts has written several papers providing crucial insight in licensing contexts for Negative Polarity Items (NPIs), presenting a more nuanced picture than Ladusaw’s (1979) downward entailing (DE) requirement. Zwarts demonstrated (1981) that a number of Dutch NPIs appear only in a subset of DE-contexts, and proposed (1995) non-veridicality as a logico-semantic property that licenses so-called superweak NPIs. Such superweak NPIs, however, have hardly been attested. We show that Mandarin shenme (‘a (thing)’) is a prototypical superweak NPI. We explain its ungrammaticality in veridical contexts by arguing that shenme exhibits a lexical referential deficiency. Acquisitional data, furthermore, suggest that children initially analyze shenme as a WH-quantifier but acquire the referential deficiency underlying its NPI status after the age of four. Show less
The problem of motion detection has received considerable attention due to the explosive growth of its applications in video analysis and surveillance systems. While the previous approaches can... Show moreThe problem of motion detection has received considerable attention due to the explosive growth of its applications in video analysis and surveillance systems. While the previous approaches can produce good results, the accurate detection of motion remains a challenging task due to the difficulties raised by illumination variations, occlusion, camouflage, sudden motions appearing in burst, dynamic texture, and environmental changes such as weather conditions, sunlight changes during a day, and so on. In this paper, a novel per-pixel motion descriptor is proposed for motion detection in video sequences which outperforms the current methods in the literature particularly in severe scenarios. The proposed descriptor is based on two complementary three-dimensional discrete wavelet transforms (3D-DWT) and a 3D wavelet leader. In this approach, a feature vector is extracted for each pixel by applying a novel 3D wavelet-based motion descriptor. Then, the extracted features are clustered by the well-known K-means algorithm. The experimental results demonstrate the effectiveness of the proposed method compared to the state-of-the-art approaches in several public benchmark datasets. The application of the proposed method and additional experimental results for several challenging datasets are available online. Show less
This paper investigates three verbs expressing necessity in the three West Germanic languages: Dutch hoeven, English need, and German brauchen. These three verbs are all categorized as negative... Show moreThis paper investigates three verbs expressing necessity in the three West Germanic languages: Dutch hoeven, English need, and German brauchen. These three verbs are all categorized as negative polarity items (NPIs). However, there are differences in their distribution as NPIs, which posit German brauchen between English need and Dutch hoeven. By analyzing two factors that may influence acquisition, namely, opacity and input frequency, this paper moreover presents a similar pattern for the acquisition of these NPIs: The Dutch NPI hoeven emerges earlier in child language than its German counterpart, which in turn arises earlier than the English NPI need. Show less
Intravascular ultrasound (IVUS) is recommended in guiding coronary intervention. The segmentation of coronary lumen and external elastic membrane (EEM) borders in IVUS images is a key step, but the... Show moreIntravascular ultrasound (IVUS) is recommended in guiding coronary intervention. The segmentation of coronary lumen and external elastic membrane (EEM) borders in IVUS images is a key step, but the manual process is time-consuming and error-prone, and suffers from inter-observer variability. In this paper, we propose a novel perceptual organisation-aware selective transformer framework that can achieve accurate and robust segmentation of the vessel walls in IVUS images. In this framework, temporal context-based feature encoders extract efficient motion features of vessels. Then, a perceptual organisation-aware selective transformer module is proposed to extract accurate boundary information, supervised by a dedicated boundary loss. The obtained EEM and lumen segmentation results will be fused in a temporal constraining and fusion module, to determine the most likely correct boundaries with robustness to morphology. Our proposed methods are extensively evaluated in non-selected IVUS sequences, including normal, bifurcated, and calcified vessels with shadow artifacts. The results show that the proposed methods outperform the state-of-the-art, with a Jaccard measure of 0.92 for lumen and 0.94 for EEM on the IVUS 2011 open challenge dataset. This work has been integrated into a software QCU-CMS1 to automatically segment IVUS images in a user-friendly environment. Show less
Papaver species P. setigerum, P. rhoeas, and P. somniferum accumulates different levels of morphine and noscapine. Here, the authors report the improved genome assembly of P. somniferum and de novo... Show morePapaver species P. setigerum, P. rhoeas, and P. somniferum accumulates different levels of morphine and noscapine. Here, the authors report the improved genome assembly of P. somniferum and de novo assembly of the other two species, and reveal the evolution of the benzylisoquinoline alkaloids biosynthetic pathway.For millions of years, plants evolve plenty of structurally diverse secondary metabolites (SM) to support their sessile lifestyles through continuous biochemical pathway innovation. While new genes commonly drive the evolution of plant SM pathway, how a full biosynthetic pathway evolves remains poorly understood. The evolution of pathway involves recruiting new genes along the reaction cascade forwardly, backwardly, or in a patchwork manner. With three chromosome-scale Papaver genome assemblies, we here reveal whole-genome duplications (WGDs) apparently accelerate chromosomal rearrangements with a nonrandom distribution towards SM optimization. A burst of structural variants involving fusions, translocations and duplications within 7.7 million years have assembled nine genes into the benzylisoquinoline alkaloids gene cluster, following a punctuated patchwork model. Biosynthetic gene copies and their total expression matter to morphinan production. Our results demonstrate how new genes have been recruited from a WGD-induced repertoire of unregulated enzymes with promiscuous reactivities to innovate efficient metabolic pathways with spatiotemporal constraint. Show less
Capuccini, B.; Lin, J.; Talavera-Lopez, C.; Khan, S.M.; Sodenkamp, J.; Spaccapelo, R.; Langhorne, J. 2016
Drawing from the literature on behavioral spillover effects, the work-home resources model and research on helping at work, we investigate how help provision at work spills over to influence the... Show moreDrawing from the literature on behavioral spillover effects, the work-home resources model and research on helping at work, we investigate how help provision at work spills over to influence the provision of spousal support at home by examining a resource generation mechanism and a resource depletion mechanism. Across two experience-sampling studies, we collected data from employees and their spouses multiple times per day in different domains for ten workdays. Results from our two-study examination supported both the resource generation mechanism and the resource depletion mechanism. On days when employees helped colleagues more, they reported higher positive affect, which led to higher support provision to their spouses; meanwhile, higher levels of helping translated in less time for the family, which led to lower support provided to spouses. In Study 2, we tested and found that prosocial motivation enhanced the resource-generating effect of help provision. Theoretical and practical implications are discussed. Show less
