106 research outputs found
Geometric Data Analysis: Advancements of the Statistical Methodology and Applications
Data analysis has become fundamental to our society and comes in multiple facets and approaches. Nevertheless, in research and applications, the focus was primarily on data from Euclidean vector spaces. Consequently, the majority of methods that are applied today are not suited for more general data types. Driven by needs from fields like image processing, (medical) shape analysis, and network analysis, more and more attention has recently been given to data from non-Euclidean spaces–particularly (curved) manifolds. It has led to the field of geometric data analysis whose methods explicitly take the structure (for example, the topology and geometry) of the underlying space into account.
This thesis contributes to the methodology of geometric data analysis by generalizing several fundamental notions from multivariate statistics to manifolds. We thereby focus on two different viewpoints.
First, we use Riemannian structures to derive a novel regression scheme for general manifolds that relies on splines of generalized BĂ©zier curves. It can accurately model non-geodesic relationships, for example, time-dependent trends with saturation effects or cyclic trends. Since BĂ©zier curves can be evaluated with the constructive de Casteljau algorithm, working with data from manifolds of high dimensions (for example, a hundred thousand or more) is feasible. Relying on the regression, we further develop
a hierarchical statistical model for an adequate analysis of longitudinal data in manifolds, and a method to control for confounding variables.
We secondly focus on data that is not only manifold- but even Lie group-valued, which is frequently the case in applications. We can only achieve this by endowing the group with an affine connection structure that is generally not Riemannian. Utilizing it, we derive generalizations of several well-known dissimilarity measures between data distributions that can be used for various tasks, including hypothesis testing. Invariance under data translations is proven, and a connection to continuous distributions is given for one measure.
A further central contribution of this thesis is that it shows use cases for all notions in real-world applications, particularly in problems from shape analysis in medical imaging and archaeology. We can replicate or further quantify several known findings for shape changes of the femur and the right hippocampus under osteoarthritis and Alzheimer's, respectively. Furthermore, in an archaeological application, we obtain new insights into the construction principles of ancient sundials. Last but not least, we use the geometric structure underlying human brain connectomes to predict cognitive scores. Utilizing a sample selection procedure, we obtain state-of-the-art results
Machine Learning Methods with Noisy, Incomplete or Small Datasets
In many machine learning applications, available datasets are sometimes incomplete, noisy or affected by artifacts. In supervised scenarios, it could happen that label information has low quality, which might include unbalanced training sets, noisy labels and other problems. Moreover, in practice, it is very common that available data samples are not enough to derive useful supervised or unsupervised classifiers. All these issues are commonly referred to as the low-quality data problem. This book collects novel contributions on machine learning methods for low-quality datasets, to contribute to the dissemination of new ideas to solve this challenging problem, and to provide clear examples of application in real scenarios
Recent Advances in Forensic Anthropological Methods and Research
Forensic anthropology, while still relatively in its infancy compared to other forensic science disciplines, adopts a wide array of methods from many disciplines for human skeletal identification in medico-legal and humanitarian contexts. The human skeleton is a dynamic tissue that can withstand the ravages of time given the right environment and may be the only remaining evidence left in a forensic case whether a week or decades old. Improved understanding of the intrinsic and extrinsic factors that modulate skeletal tissues allows researchers and practitioners to improve the accuracy and precision of identification methods ranging from establishing a biological profile such as estimating age-at-death, and population affinity, estimating time-since-death, using isotopes for geolocation of unidentified decedents, radiology for personal identification, histology to assess a live birth, to assessing traumatic injuries and so much more
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CONSTRAINTS OF THE IMAGINATION: HOW PHENOTYPES ARE SHAPED THROUGH GENETICS, THE ENVIRONMENT, AND DEVELOPMENT
Phenotypic constraints are ubiquitous throughout nature, being found throughout all stages of life and at multiple different biological levels including cellular, genetic, environmental, behavioral, evolutionary, and developmental. These constraints have shaped, not only the natural world, but the way that we perceive what is possible, or impossible, an observation made clear by François Jacob in his 1977 paper “Evolution and Tinkering”. This is reflected in the literature, repeatedly, by the regular occurrence of densely packed visualization of phenotypic space that seemingly always have large areas that go unoccupied. Despite constrained regions of space being observable across countless taxa, identifying the mechanisms of those constraints remains elusive. Given that constraints are widespread and have influenced how evolution may work, my aim was to identify mechanisms of constraint throughout multiple biological levels. Chapter one is divided into two parts, sections A and B, but largely focuses on how constraints are influenced by genetics. For this, we investigated crocc2, a protein that encodes for a structural component of the ciliary rootlet which in turn plays a major role as a mechanosensory for nearly all cells. We found dysfunctional crocc2 resulted in both dysmorphic bone development and a decrease in the plastic response potential of zebrafish (section A), as well as altered developmental trajectories in juvenile morphology, presumably due to alterations in cellular polarity and inadequate extracellular communication. Importantly, all results from this chapter point toward crocc2 play a canalizing role in the production of phenotypes at multiple life-history stages. Chapter 2 takes a different approach into understanding constrains by looking at broad ecological alterations and how those alterations may alter morphology of resident taxa. Here, we utilized the heavily altered habitat of the Tocantins River in the Amazon and the existing museum collections to evaluate how select representatives of the cichlid community had responded to such change. We found significant changes in contemporary morphology across all included cichlid species compared to their historical counterparts. These data show that alterations to the environment have resulted in changes to the local resident species, and possibly an alteration to their future evolutionary trajectories. Among the species included, one was found to have the most substantial morphological changes, which is what we followed up in the next chapter. Chapter 3 dug into the morphological changes of Satanoperca, a Geophagine cichlid with a unique feeding mechanism known as winnowing. Winnowing is a poorly understood mechanical process involving substrate manipulation. Given that anthropogenic alterations to local hydrology oft result in changes to the benthic sediment composition, we wanted to know if differing substrates was enough to induce a plastic response in winnowing fishes, and if so which traits were effected. We found significant differences across our experimental populations in both shape and disparity and present evidence in support of wide-spread integration across craniofacial traits. In addition, these data suggest that the novel anatomical structure, the epibranchial lobe, is more modular than other craniofacial traits involved in the winnowing process. Chapters 4 and 5 utilize a unique lineage of fishes, the Bramidae, to understand how developmental and evolutionary constraints are broken to produce morphological novelties. We used a combination of DNA sequences from GenBank and numerous museum specimens to illuminate constraints and determine how constraints are broken to produce complex phenotypic novelties. In Chapter 4, we found that the fanfishes had experienced greater rates of morphological evolution than other members of the Bramidae family, resulting in their occupation of an entirely novel region of phenotypic space. In Chapter 5, we elaborated on this by investigating the developmental processes involved in producing an extreme morphological novelty. The data presented in Chapter 5 provide evidence suggesting that the fanfishes have broken various constraints, resulting in prominent anatomical and morphological changes to accommodate their novel phenotype. In all, my dissertation provides examples of how constraints have shaped the variability that we see throughout life and shows examples of how constraints can be identified, what happens when they are broken, and how they work to control the pace and trajectory of evolutionary processes
Animal Welfare Assessment
This Special Issue provides a collection of recent research and reviews that investigate many areas of welfare assessment, such as novel approaches and technologies used to evaluate the welfare of farmed, captive, or wild animals. Research in this Special Issue includes welfare assessment related to pilot whales, finishing pigs, commercial turkey flocks, and dairy goats; the use of sensors or wearable technologies, such as heart rate monitors to assess sleep in dairy cows, ear tag sensors, and machine learning to assess commercial pig behaviour; non-invasive measures, such as video monitoring of behaviour, computer vision to analyse video footage of red foxes, remote camera traps of free-roaming wild horses, infrared thermography of effort and sport recovery in sport horses; telomere length and regulatory genes as novel biomarkers of stress in broiler chickens; the effect of environment on growth physiology and behaviour of laboratory rare minnows and housing system on anxiety, stress, fear, and immune function of laying hens; and discussions of natural behaviour in farm animal welfare and maintaining health, welfare, and productivity of commercial pig herds
Plant Parasitic Nematodes
Plant-parasitic nematodes (PPNs) are economically important pests for numerous agriculture and forestry crops, representing a significant constraint on global food security and forestry health. Root knot nematodes (Meloidogyne spp.), potato cyst nematodes (Globodera spp.), and root lesion nematodes (Pratylenchus spp.) are some examples of PPNs that are ranked at the top in the list of the most economically and scientifically important species. Current approaches to controlling these PPNs include the use of nematicides, but many pose serious concerns for human health and the environment. To cope with such threats, accurate diagnostic methods for nematode detection and a deep understanding of nematode infection processes, as well as of their intricate relationships with the host plants, are crucial for the development of effective integrated nematode management programs. This Special Issue entitled “Pant Parasitic Nematodes” is a collection of 11 original papers that cover a wide range of topics, including the state of the art of important PPN, and the detection and management of PPNs through sustainable and eco-friendly strategies
High-resolution single-worm transcriptomics and the function of oscillating genes in mouth-form development in Pristionchus pacificus
Development is largely under the control of genes. Specific spatiotemporal gene expression can modify the development and the final phenotype of an organism. To obtain a high-resolution catalog of the developmental transcriptome in Pristionchus pacificus, I developed and implemented a single worm transcriptomic approach for the nematode model organism P. pacificus, and performed temporal transcriptome analysis over the entire postembryonic development with 38 time points. I focused on investigating oscillating gene expression patterns and found that i) nearly 3000 oscillating genes are periodically expressed during postembryonic development, ii) there is an overrepresentation of ancient gene classes among oscillatory genes, and iii) the developmental switch gene eud-1 mediates numerous oscillatory genes including collagens, indicating the potential roles of these oscillating collagens in regulating mouth-form plasticity.
Mouth-form dimorphism in P. pacificus provides an ideal example to study the mechanisms of phenotype plasticity. Many previous studies focused on the regulation of mouth-form development and identified environmental influences, developmental switches, the gene regulatory network involved in mouth-form plasticity, and the associated evolutionary processes. However, the molecular and structural basis of the teeth in P. pacificus remains poorly understood. To address this fundamental question, I used two complementary approaches. First, I performed a large-scale genetic screen and obtained six mutants displaying morphological changes in both stomatal structures and body shape. Using whole genome sequencing and genome editing (CRISPR/Cas9 system) technologies, I identified Ppa-dpy-6, which encodes a mucin-type protein, as the first structural component of the nematode stoma involved in the specification of the cheilostom and cuticle. Second, I investigated the function of two chitin synthase genes (chs) in P. pacificus. Phylogenetic analysis revealed that two chitin synthase genes are highly conserved across nematodes. Mutations in the C- terminus of chs-2 in P. pacificus result in a viable but teethless phenotype. Moreover, animals with this teethless phenotype were observed after injection of the chitin-synthase inhibitor Nikkomycin Z. These results suggest that the conserved Ppa-chs-2 is essential for P. pacificus teeth formation. In addition, such teethless mutants can feed on various bacterial food sources, yet they are incapable of predation
Transcriptome and Genome Analyses Applied to Aquaculture Research
Aquaculture is an important economic activity for food production all around the world that has experienced an exponential growth during the last few decades. However, several weaknesses and bottlenecks still need to be addressed in order to improve the aquaculture productive system. The recent fast development of the omics technologies has provided scientists with meaningful tools to elucidate the molecular basis of their research interests. This reprint compiles different works about the use of transcriptomics and genomics technologies in different aspects of the aquaculture research, such as immunity, stress response, development, sexual dimorphism, among others, in a variety of fish and shellfish, and even in turtles. Different transcriptome (mRNAs and non-coding RNAs (ncRNAs)), genome (Single Nucleotide Polymorphisms (SNPs)), and metatranscriptome analyses were conducted to unravel those different aspects of interest
The Alcohol Hangover
The seeds and fruits (or their parts) of Iberoamerican crops have high nutritional and functional properties which could be utilized in a wide range of foods. The crops included in this book are amaranth (Amaranthus spp.), quinoa (Chenopodium quinoa), kañiwa (Chenopodium pallidicaule), chia (Salvia hispanica L.), Andean maize (Zea mays L.), moringa (Moringa oleifera), yvapuru (Plinia peruviana), kurugua (Sicana odorifera), sacha inchi (Plukenetia huayllabambana), camu camu (Myrciaria dubia), mango (Mangifera indica), tarwi (Lupinus mutabilis), peanut (Arachis hypogaea L.) and taro (Colocasia esculenta), all of them still underutilized. Their cultivation is low; nevertheless, in recent years, the worldwide demand for some of them has increased immensely, resulting in an increase in their production. The ancient Iberoamerican crops have been widely recognized for their nutritional value by food scientists and food producers because they contain high-quality proteins and large quantities of micronutrients such as minerals, vitamins and bioactive compounds. In addition, they are gluten-free, which makes them suitable for people suffering from various gluten intolerances. This book summarizes the large amount of investigations in this field in the last year and provides knowledge within all the relevant areas of food science. The editors hope that this book will contribute to an increased use of these products in human nutrition by consumers worldwide
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