Sustainable Agriculture and Advances of Remote Sensing (Volume 2)

Agriculture, as the main source of alimentation and the most important economic activity globally, is being affected by the impacts of climate change. To maintain and increase our global food system production, to reduce biodiversity loss and preserve our natural ecosystem, new practices and technologies are required. This book focuses on the latest advances in remote sensing technology and agricultural engineering leading to the sustainable agriculture practices. Earth observation data, in situ and proxy-remote sensing data are the main source of information for monitoring and analyzing agriculture activities. Particular attention is given to earth observation satellites and the Internet of Things for data collection, to multispectral and hyperspectral data analysis using machine learning and deep learning, to WebGIS and the Internet of Things for sharing and publication of the results, among others

Novel molecular techniques for diagnostics and cancer biology

Molecular biology is reliant on a large set of increasingly complex methods. The development of high-throughput DNA sequencing almost 20 years ago kicked off a revolution in method development due to its incredible versatility. Besides determining the genomic DNA sequence itself, sequencing has been used to profile gene expression, investigate binding of proteins to DNA and RNA, trace cell lineages, screen for genes involved in biological processes, assay 3D organization of chromatin, and much more. Most of these methods have been immensely useful in cancer biology, helping us to understand the mechanisms of this complex disease and find new ways to battle it. But sequencing is not necessary if the mere presence or absence of a nucleic acid is impotant. In order to be able to rapidly diagnose viral diseases, crucial during pandemics such as the recent COVID-19, simpler methods are more useful. Various nucleic acid detection methods have been developed for molecular diagnostics, which can provide an answer within minutes. In this thesis, the fields of high-throughput sequencing, cancer biology, and molecular viral diagnostics are reviewed, since the work presented here consists of three projects dealing with these different topics. In Paper I, we present a novel method for detecting low frequency variants in DNA. Such variants are important in applications such as genetic heterogeneity or minimal residual disease in cancer. However, their detection is hampered by the errors in sequencing data. To circumvent this, one approach is to attach double-stranded unique molecular identifier sequences (dsUMIs) to the ends of each DNA fragment before sequencing. This allows to compare reads originating from the same original molecule and form consensus sequences, removing most errors in the process. However, protocols that achieve this are challenging to perform. We developed a novel, simplified library preparation approach called one pot double-stranded UMI sequencing (OPUSeq) that adds dsUMIs to DNA in the same reaction as the PCR. We demonstrate that OPUSeq efficiently removes errors in sequencing data and can be used to detect variants down to 0.01% variant allele frequency. Using OPUSeq, we also found a novel type of artifact that arises when fragmentase enzyme mix is used in library preparation. In Paper II, we investigated the existence of genetic factors that regulate cell state plasticity in cancer. Cancer cells are known to be capable of phenotypic cell state transitions that help them evade treatment. In certain cancer cell line models, such as the chronic myeloid leukemia (CML) K562, the cells are observed to adopt and switch between different states even in the absence of any specific stimuli. As our model system, we used the heterogeneous expression of CD24 protein in K562 as a marker for differential cell states. We designed two orthogonal genome-wide CRISPR-Cas9 knockout screening approaches to look for genes which regulate the spontaneous transitions between CD24-positive and CD24-negative states. We performed both screens and combined the data to produce a list of 49 plasticity regulator candidate genes. We further showed that seven of these genes are differentially expressed between CML patients exhibiting early molecular response to imatinib and those who do not, indicating a connection between plasticity and drug resistance. Finally, we validate one of the plasticity impeding candidates, ALDOB, by generating a single knockout model and demonstrating the increased ability of these cells to undergo state transitions. In Paper III, we present a protocol for detection of SARS-CoV-2 RNA in unextracted patient samples using reverse transcription loop mediated isothermal amplification (RT-LAMP) with non-commercial enzymes. This protocol provides an alternative diagnostic method for situations where RT-LAMP and RNA extraction reagents are scarce. First, we showed how reverse transcriptases (RT) and strand-displacing polymerases necessary for RT-LAMP can be expressed and purified in-house. We tested different enzymes and LAMP primer sets and optimized the reaction conditions. Benchmarking showed that our in-house mix performs similarly to or even better than commercial alternatives. Finally, we tested our protocol on heat-inactivated, unextracted nasopharyngeal samples from patients and found that it exhibited good specificity as well as good sensitivity in samples with moderate to high viral load

A Multiple 'Omics' Approach to Study the Interaction between the Vitis Vinifera Transcriptome and Epigenome and the Barossa Valley Terroir

The local growing conditions have a significant impact in grapevine (Vitis vinifera) phenotype of as well as in its epigenome. Little is known about how grapevine responds to the local environment through epigenetic modifications and any effect on gene expression in field-grown plants. Here, we characterized the leaf methylome and transcriptome of 198 Shiraz vines cultivated across twenty-two vineyards, covering six sub-regions of the Barossa Wine Zone in Australia. Samples clustered for both DNA methylation and gene expression depending on the sub-region of their origin. In addition, we identified genes with DNA methylation and expression significantly associated to measured environmental variables. Planting year and annual rainfall were the variables showing a higher influence both on DNA methylation and gene expression. Plants use long-distance signaling mechanisms to coordinate developmental and environmental cues between organs and tissues. Studies have begun to unravel the molecular nature of systemic signaling and RNA transcripts have emerged as key players by acting as mobile messengers. Along with DNA methylation and chromatin modifications, non-coding RNAs are a molecular mechanism for the epigenetic regulation of gene expression. Recent evidence in model plants suggests that dicistronic tRNA-like structures can act as mobile signals for mRNA transcripts to move between distant tissues, potentially acting as signals for development or changes in environmental conditions. However, it is not clear the extent to which dicistronic transcripts of tRNA and mRNAs are expressed in field-grown plants, or the factors that contribute to their expression. We identified and analysed the expression of tRNA-mRNA dicistronic transcripts in leaves and berries from the twenty-two vineyards, using a novel pipeline developed to identify dicistronic transcripts from high-throughput short-read RNA sequencing data. Of the 124 tRNA genes that were expressed in both tissues, we detected 18 tRNA genes forming part of 19 dicistronic tRNA-mRNA molecules. We found that the presence and abundance of dicistronic molecules was tissue specific, and that each the sub-region displayed a distinct expression profile for dicistronic tRNA-mRNA transcripts. In this work we propose that DNA methylation can reflect the local growing conditions in grapevine, as a mechanism of response to its environment. We also detected the presence of dicistronic tRNA-mRNAs, which might act as signaling molecules between distant tissues. Both responses to the growing environment are especially relevant in long-lived woody plants, potentially giving them the necessary plasticity to adapt to local conditions. As grapevine is also an economically important fruit crop, understanding its response to the environment could give us a better inside of the possible mechanisms behind the expression of terroir in grapevine.Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 202

Evolutionary design of deep neural networks

Mención Internacional en el título de doctorFor three decades, neuroevolution has applied evolutionary computation to the optimization of the topology of artificial neural networks, with most works focusing on very simple architectures. However, times have changed, and nowadays convolutional neural networks are the industry and academia standard for solving a variety of problems, many of which remained unsolved before the discovery of this kind of networks. Convolutional neural networks involve complex topologies, and the manual design of these topologies for solving a problem at hand is expensive and inefficient. In this thesis, our aim is to use neuroevolution in order to evolve the architecture of convolutional neural networks. To do so, we have decided to try two different techniques: genetic algorithms and grammatical evolution. We have implemented a niching scheme for preserving the genetic diversity, in order to ease the construction of ensembles of neural networks. These techniques have been validated against the MNIST database for handwritten digit recognition, achieving a test error rate of 0.28%, and the OPPORTUNITY data set for human activity recognition, attaining an F1 score of 0.9275. Both results have proven very competitive when compared with the state of the art. Also, in all cases, ensembles have proven to perform better than individual models. Later, the topologies learned for MNIST were tested on EMNIST, a database recently introduced in 2017, which includes more samples and a set of letters for character recognition. Results have shown that the topologies optimized for MNIST perform well on EMNIST, proving that architectures can be reused across domains with similar characteristics. In summary, neuroevolution is an effective approach for automatically designing topologies for convolutional neural networks. However, it still remains as an unexplored field due to hardware limitations. Current advances, however, should constitute the fuel that empowers the emergence of this field, and further research should start as of today.This Ph.D. dissertation has been partially supported by the Spanish Ministry of Education, Culture and Sports under FPU fellowship with identifier FPU13/03917. This research stay has been partially co-funded by the Spanish Ministry of Education, Culture and Sports under FPU short stay grant with identifier EST15/00260.Programa Oficial de Doctorado en Ciencia y Tecnología InformáticaPresidente: María Araceli Sanchís de Miguel.- Secretario: Francisco Javier Segovia Pérez.- Vocal: Simon Luca

Front Lines of Thoracic Surgery

Front Lines of Thoracic Surgery collects up-to-date contributions on some of the most debated topics in today's clinical practice of cardiac, aortic, and general thoracic surgery,and anesthesia as viewed by authors personally involved in their evolution. The strong and genuine enthusiasm of the authors was clearly perceptible in all their contributions and I'm sure that will further stimulate the reader to understand their messages. Moreover, the strict adhesion of the authors' original observations and findings to the evidence base proves that facts are the best guarantee of scientific value. This is not a standard textbook where the whole discipline is organically presented, but authors' contributions are simply listed in their pertaining subclasses of Thoracic Surgery. I'm sure that this original and very promising editorial format which has and free availability at its core further increases this book's value and it will be of interest to healthcare professionals and scientists dedicated to this field

Neuroimaging of fetal cell therapy in Parkinson’s disease

Parkinson’s disease is the second most common neurodegenerative disease characterised by the elevated formation of α-synuclein-immunopositive intraneuronal proteinaceous inclusions (Lewy pathology) and the progressive loss of neuromelanin-laden dopaminergic cells of the substantia nigra pars compacta, resulting in the loss of striatal dopaminergic terminals and emergence of cardinal motor features including bradykinesia, rigidity, tremor and postural instability. Dopaminomimetic agents provide effective symptomatic relief in the early stages of illness, yet due to the inherently progressive nature of the disease and the induction of debilitating side effects their efficacy is eventually lost. Cellular restorative strategies involving intrastriatal transplantation of human fetal ventral mesencephalic (hfVM) tissue gained traction from the early 1990’s, when several multi-disciplinary teams reported drastic motoric improvements concomitant with graft-derived dopaminergic re-innervation. However, outcomes of double-blind randomised controlled trials and the presentation of novel dyskinetic movements persisting in the “off-state” called for substantial revision of cell delivery strategies. The current thesis utilises positron emission tomography to examine the effects of hfVM implantation under the Transeuro protocol on dopaminergic ([18F]FDOPA, [11C]PE2I) and serotonergic ([11C]DASB) systems in patients with Parkinson’s disease and elucidate the neural underpinnings of its clinical impact. The main findings are; 1) implanted hfVM tissue led to increases in putamenal dopamine synthesis and storage capacity, dopamine and serotonin transporter density as compared to non-transplanted patients; 2) modification to surgical procedures provided inhomogenous and inconsistent re-innervation; 3) hfVM transplantation was associated with clinical improvements in measures of bradykinesia, rigidity and tremor; 4) graft-related changes in posterior putamenal dopamine and serotonin transporter density predicted symptomatic relief of bradykinesia and tremor; 5) heterogeneity of posterior putamenal re-innervation may impact upon potential clinical benefit; 6) graft-induced dyskinesia was associated with greater post-operative increases in dopamine transporter expression in the anterior putamen; 7) there was no evidence that graft-induced dyskinesia was related to serotonergic hyperinnervation. The novel findings presented in this thesis have major implications for cell-based restorative strategies beyond the hfVM era and will likely foster informed [re]consideration of many aspects of therapeutic delivery and trial design. For its ability to provide mechanistic insight in vivo, neuroimaging may continue to play a central role in the optimisation of future interventions.Open Acces

Special Topics in Cardiac Surgery

This book considers mainly the current perioperative care, as well as progresses in new cardiac surgery technologies. Perioperative strategies and new technologies in the field of cardiac surgery will continue to contribute to improvements in postoperative outcomes and enable the cardiac surgical society to optimize surgical procedures. This book should prove to be a useful reference for trainees, senior surgeons and nurses in cardiac surgery, as well as anesthesiologists, perfusionists, and all the related health care workers who are involved in taking care of patients with heart disease which require surgical therapy. I hope these internationally cumulative and diligent efforts will provide patients undergoing cardiac surgery with meticulous perioperative care methods

New nuclear medicine techniques for the assessment of myocardial viability

Een dotterbehandeling of een bypassoperatie heeft alleen zin als er nog voldoende hartspierweefsel over is dat zich kan herstellen. Momenteel wordt de vitaliteit van de hartspier voor de ingreep nog onderzocht met een PET-scan, maar deze techniek is duur en maar in een paar ziekenhuizen in Nederland aanwezig. Riemer Slart constateert in zijn proefschrift dat een goedkopere scan het succes van een bypass of dotteren ook kan voorspellen.