3,470 research outputs found

    Inter-individual variation of the human epigenome & applications

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    Long-Molecule Assessment of Ribosomal DNA and RNA

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    The genes encoding ribosomal RNA and their transcriptional products are essential for life, however, remain poorly understood. Even with the advent of long-range sequencing methodologies, rDNA loci are difficult to study and remain obscure, prompting the consideration of alternative methods to probing this critical region of the genome. The research outlined in this thesis utilises molecular combing, a fibre stretching technique, to isolate DNA molecules measuring more than 5 Mbp in length. The capture of DNA molecules of this size should assist in exploring the architecture of entire rDNA clusters at the single-molecule level. Combining molecular combing with SNP targeting probes, this study aims to distinguish and assess the arrangement of rDNA promoter variants which have been shown to exhibit dramatically different environmental sensitivity. Additionally, through the application of Oxford Nanopore Technologies direct RNA sequencing, the work here has demonstrated the capture of near full-length rRNA primary transcripts, which will allow for assessing post-transcriptional modification across the length of multiple coding subunits within a single molecule, for the first time. Furthermore, an exploration of RNA modification profiles across sample types representative of different developmental stages has been conducted. This study predicts many sites to be differentially modified across these different developmental conditions, several of which are known to be important for, if not crucial in ribosome biogenesis and function. The work outlined in this thesis provides a framework for future studies to conduct long-molecule, genetic, and epitranscriptome profiling of this vital region of the genome, and its dynamic response to a changing environment

    LIPIcs, Volume 251, ITCS 2023, Complete Volume

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    LIPIcs, Volume 251, ITCS 2023, Complete Volum

    Effects of municipal smoke-free ordinances on secondhand smoke exposure in the Republic of Korea

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    ObjectiveTo reduce premature deaths due to secondhand smoke (SHS) exposure among non-smokers, the Republic of Korea (ROK) adopted changes to the National Health Promotion Act, which allowed local governments to enact municipal ordinances to strengthen their authority to designate smoke-free areas and levy penalty fines. In this study, we examined national trends in SHS exposure after the introduction of these municipal ordinances at the city level in 2010.MethodsWe used interrupted time series analysis to assess whether the trends of SHS exposure in the workplace and at home, and the primary cigarette smoking rate changed following the policy adjustment in the national legislation in ROK. Population-standardized data for selected variables were retrieved from a nationally representative survey dataset and used to study the policy action’s effectiveness.ResultsFollowing the change in the legislation, SHS exposure in the workplace reversed course from an increasing (18% per year) trend prior to the introduction of these smoke-free ordinances to a decreasing (−10% per year) trend after adoption and enforcement of these laws (β2 = 0.18, p-value = 0.07; β3 = −0.10, p-value = 0.02). SHS exposure at home (β2 = 0.10, p-value = 0.09; β3 = −0.03, p-value = 0.14) and the primary cigarette smoking rate (β2 = 0.03, p-value = 0.10; β3 = 0.008, p-value = 0.15) showed no significant changes in the sampled period. Although analyses stratified by sex showed that the allowance of municipal ordinances resulted in reduced SHS exposure in the workplace for both males and females, they did not affect the primary cigarette smoking rate as much, especially among females.ConclusionStrengthening the role of local governments by giving them the authority to enact and enforce penalties on SHS exposure violation helped ROK to reduce SHS exposure in the workplace. However, smoking behaviors and related activities seemed to shift to less restrictive areas such as on the streets and in apartment hallways, negating some of the effects due to these ordinances. Future studies should investigate how smoke-free policies beyond public places can further reduce the SHS exposure in ROK

    Proceedings of SIRM 2023 - The 15th European Conference on Rotordynamics

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    It was our great honor and pleasure to host the SIRM Conference after 2003 and 2011 for the third time in Darmstadt. Rotordynamics covers a huge variety of different applications and challenges which are all in the scope of this conference. The conference was opened with a keynote lecture given by Rainer Nordmann, one of the three founders of SIRM “Schwingungen in rotierenden Maschinen”. In total 53 papers passed our strict review process and were presented. This impressively shows that rotordynamics is relevant as ever. These contributions cover a very wide spectrum of session topics: fluid bearings and seals; air foil bearings; magnetic bearings; rotor blade interaction; rotor fluid interactions; unbalance and balancing; vibrations in turbomachines; vibration control; instability; electrical machines; monitoring, identification and diagnosis; advanced numerical tools and nonlinearities as well as general rotordynamics. The international character of the conference has been significantly enhanced by the Scientific Board since the 14th SIRM resulting on one hand in an expanded Scientific Committee which meanwhile consists of 31 members from 13 different European countries and on the other hand in the new name “European Conference on Rotordynamics”. This new international profile has also been emphasized by participants of the 15th SIRM coming from 17 different countries out of three continents. We experienced a vital discussion and dialogue between industry and academia at the conference where roughly one third of the papers were presented by industry and two thirds by academia being an excellent basis to follow a bidirectional transfer what we call xchange at Technical University of Darmstadt. At this point we also want to give our special thanks to the eleven industry sponsors for their great support of the conference. On behalf of the Darmstadt Local Committee I welcome you to read the papers of the 15th SIRM giving you further insight into the topics and presentations

    Talking about personal recovery in bipolar disorder: Integrating health research, natural language processing, and corpus linguistics to analyse peer online support forum posts

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    Background: Personal recovery, ‘living a satisfying, hopeful and contributing lifeeven with the limitations caused by the illness’ (Anthony, 1993) is of particular value in bipolar disorder where symptoms often persist despite treatment. So far, personal recovery has only been studied in researcher-constructed environments (interviews, focus groups). Support forum posts can serve as a complementary naturalistic data source. Objective: The overarching aim of this thesis was to study personal recovery experiences that people living with bipolar disorder have shared in online support forums through integrating health research, NLP, and corpus linguistics in a mixed methods approach within a pragmatic research paradigm, while considering ethical issues and involving people with lived experience. Methods: This mixed-methods study analysed: 1) previous qualitative evidence on personal recovery in bipolar disorder from interviews and focus groups 2) who self-reports a bipolar disorder diagnosis on the online discussion platform Reddit 3) the relationship of mood and posting in mental health-specific Reddit forums (subreddits) 4) discussions of personal recovery in bipolar disorder subreddits. Results: A systematic review of qualitative evidence resulted in the first framework for personal recovery in bipolar disorder, POETIC (Purpose & meaning, Optimism & hope, Empowerment, Tensions, Identity, Connectedness). Mainly young or middle-aged US-based adults self-report a bipolar disorder diagnosis on Reddit. Of these, those experiencing more intense emotions appear to be more likely to post in mental health support subreddits. Their personal recovery-related discussions in bipolar disorder subreddits primarily focussed on three domains: Purpose & meaning (particularly reproductive decisions, work), Connectedness (romantic relationships, social support), Empowerment (self-management, personal responsibility). Support forum data highlighted personal recovery issues that exclusively or more frequently came up online compared to previous evidence from interviews and focus groups. Conclusion: This project is the first to analyse non-reactive data on personal recovery in bipolar disorder. Indicating the key areas that people focus on in personal recovery when posting freely and the language they use provides a helpful starting point for formal and informal carers to understand the concerns of people diagnosed with bipolar disorder and to consider how best to offer support

    Understanding Agreement and Disagreement in Listeners’ Perceived Emotion in Live Music Performance

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    Emotion perception of music is subjective and time dependent. Most computational music emotion recognition (MER) systems overlook time- and listener-dependent factors by averaging emotion judgments across listeners. In this work, we investigate the influence of music, setting (live vs lab vs online), and individual factors on music emotion perception over time. In an initial study, we explore changes in perceived music emotions among audience members during live classical music performances. Fifteen audience members used a mobile application to annotate time-varying emotion judgments based on the valence-arousal model. Inter-rater reliability analyses indicate that consistency in emotion judgments varies significantly across rehearsal segments, with systematic disagreements in certain segments. In a follow-up study, we examine listeners' reasons for their ratings in segments with high and low agreement. We relate these reasons to acoustic features and individual differences. Twenty-one listeners annotated perceived emotions while watching a recorded video of the live performance. They then reflected on their judgments and provided explanations retrospectively. Disagreements were attributed to listeners attending to different musical features or being uncertain about the expressed emotions. Emotion judgments were significantly associated with personality traits, gender, cultural background, and music preference. Thematic analysis of explanations revealed cognitive processes underlying music emotion perception, highlighting attributes less frequently discussed in MER studies, such as instrumentation, arrangement, musical structure, and multimodal factors related to performer expression. Exploratory models incorporating these semantic features and individual factors were developed to predict perceived music emotion over time. Regression analyses confirmed the significance of listener-informed semantic features as independent variables, with individual factors acting as moderators between loudness, pitch range, and arousal. In our final study, we analyzed the effects of individual differences on music emotion perception among 128 participants with diverse backgrounds. Participants annotated perceived emotions for 51 piano performances of different compositions from the Western canon, spanning various era. Linear mixed effects models revealed significant variations in valence and arousal ratings, as well as the frequency of emotion ratings, with regard to several individual factors: music sophistication, music preferences, personality traits, and mood states. Additionally, participants' ratings of arousal, valence, and emotional agreement were significantly associated to the historical time periods of the examined clips. This research highlights the complexity of music emotion perception, revealing it to be a dynamic, individual and context-dependent process. It paves the way for the development of more individually nuanced, time-based models in music psychology, opening up new avenues for personalised music emotion recognition and recommendation, music emotion-driven generation and therapeutic applications

    Using hydrological models and digital soil mapping for the assessment and management of catchments: A case study of the Nyangores and Ruiru catchments in Kenya (East Africa)

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    Human activities on land have a direct and cumulative impact on water and other natural resources within a catchment. This land-use change can have hydrological consequences on the local and regional scales. Sound catchment assessment is not only critical to understanding processes and functions but also important in identifying priority management areas. The overarching goal of this doctoral thesis was to design a methodological framework for catchment assessment (dependent upon data availability) and propose practical catchment management strategies for sustainable water resources management. The Nyangores and Ruiru reservoir catchments located in Kenya, East Africa were used as case studies. A properly calibrated Soil and Water Assessment Tool (SWAT) hydrologic model coupled with a generic land-use optimization tool (Constrained Multi-Objective Optimization of Land-use Allocation-CoMOLA) was applied to identify and quantify functional trade-offs between environmental sustainability and food production in the ‘data-available’ Nyangores catchment. This was determined using a four-dimension objective function defined as (i) minimizing sediment load, (ii) maximizing stream low flow and (iii and iv) maximizing the crop yields of maize and soybeans, respectively. Additionally, three different optimization scenarios, represented as i.) agroforestry (Scenario 1), ii.) agroforestry + conservation agriculture (Scenario 2) and iii.) conservation agriculture (Scenario 3), were compared. For the data-scarce Ruiru reservoir catchment, alternative methods using digital soil mapping of soil erosion proxies (aggregate stability using Mean Weight Diameter) and spatial-temporal soil loss analysis using empirical models (the Revised Universal Soil Loss Equation-RUSLE) were used. The lack of adequate data necessitated a data-collection phase which implemented the conditional Latin Hypercube Sampling. This sampling technique reduced the need for intensive soil sampling while still capturing spatial variability. The results revealed that for the Nyangores catchment, adoption of both agroforestry and conservation agriculture (Scenario 2) led to the smallest trade-off amongst the different objectives i.e. a 3.6% change in forests combined with 35% change in conservation agriculture resulted in the largest reduction in sediment loads (78%), increased low flow (+14%) and only slightly decreased crop yields (3.8% for both maize and soybeans). Therefore, the advanced use of hydrologic models with optimization tools allows for the simultaneous assessment of different outputs/objectives and is ideal for areas with adequate data to properly calibrate the model. For the Ruiru reservoir catchment, digital soil mapping (DSM) of aggregate stability revealed that susceptibility to erosion exists for cropland (food crops), tea and roadsides, which are mainly located in the eastern part of the catchment, as well as deforested areas on the western side. This validated that with limited soil samples and the use of computing power, machine learning and freely available covariates, DSM can effectively be applied in data-scarce areas. Moreover, uncertainty in the predictions can be incorporated using prediction intervals. The spatial-temporal analysis exhibited that bare land (which has the lowest areal proportion) was the largest contributor to erosion. Two peak soil loss periods corresponding to the two rainy periods of March–May and October–December were identified. Thus, yearly soil erosion risk maps misrepresent the true dimensions of soil loss with averages disguising areas of low and high potential. Also, a small portion of the catchment can be responsible for a large proportion of the total erosion. For both catchments, agroforestry (combining both the use of trees and conservation farming) is the most feasible catchment management strategy (CMS) for solving the major water quantity and quality problems. Finally, the key to thriving catchments aiming at both sustainability and resilience requires urgent collaborative action by all stakeholders. The necessary stakeholders in both Nyangores and Ruiru reservoir catchments must be involved in catchment assessment in order to identify the catchment problems, mitigation strategies/roles and responsibilities while keeping in mind that some risks need to be shared and negotiated, but so will the benefits.:TABLE OF CONTENTS DECLARATION OF CONFORMITY........................................................................ i DECLARATION OF INDEPENDENT WORK AND CONSENT ............................. ii LIST OF PAPERS ................................................................................................. iii ACKNOWLEDGEMENTS ..................................................................................... iv THESIS AT A GLANCE ......................................................................................... v SUMMARY ............................................................................................................ vi List of Figures......................................................................................................... x List of Tables........................................................................................................... x ABBREVIATION..................................................................................................... xi PART A: SYNTHESIS 1. INTRODUCTION ............................................................................................... 1 1.1 Catchment management ...................................................................................1 1.2 Tools to support catchment assessment and management ..............................4 1.3 Catchment management strategies (CMSs)......................................................9 1.4 Concept and research objectives.......................................................................11 2. MATERIAL AND METHODS................................................................................15 2.1. STUDY AREA ..................................................................................................15 2.1.1. Nyangores catchment ...................................................................................15 2.1.2. Ruiru reservoir catchment .............................................................................17 2.2. Using SWAT conceptual model and land-use optimization ..............................19 2.3. Using soil erosion proxies and empirical models ..............................................21 3. RESULTS AND DISCUSSION..............................................................................24 3.1. Assessing multi-metric calibration performance using the SWAT model...........25 3.2. Land-use optimization using SWAT-CoMOLA for the Nyangores catchment. ..26 3.3. Digital soil mapping of soil aggregate stability ..................................................28 3.4. Spatio-temporal analysis using the revised universal soil loss equation (RUSLE) 29 4. CRITICAL ASSESSMENT OF THE METHODS USED ......................................31 4.1. Assessing suitability of data for modelling and overcoming data challenges...31 4.2. Selecting catchment management strategies based on catchment assessment . 35 5. CONCLUSION AND RECOMMENDATIONS ....................................................36 6. REFERENCES ............................ .....................................................................38 PART B: PAPERS PAPER I .................................................................................................................47 PAPER II ................................................................................................................59 PAPER III ...............................................................................................................74 PAPER IV ...............................................................................................................8

    Advances and Applications of DSmT for Information Fusion. Collected Works, Volume 5

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    This fifth volume on Advances and Applications of DSmT for Information Fusion collects theoretical and applied contributions of researchers working in different fields of applications and in mathematics, and is available in open-access. The collected contributions of this volume have either been published or presented after disseminating the fourth volume in 2015 in international conferences, seminars, workshops and journals, or they are new. The contributions of each part of this volume are chronologically ordered. First Part of this book presents some theoretical advances on DSmT, dealing mainly with modified Proportional Conflict Redistribution Rules (PCR) of combination with degree of intersection, coarsening techniques, interval calculus for PCR thanks to set inversion via interval analysis (SIVIA), rough set classifiers, canonical decomposition of dichotomous belief functions, fast PCR fusion, fast inter-criteria analysis with PCR, and improved PCR5 and PCR6 rules preserving the (quasi-)neutrality of (quasi-)vacuous belief assignment in the fusion of sources of evidence with their Matlab codes. Because more applications of DSmT have emerged in the past years since the apparition of the fourth book of DSmT in 2015, the second part of this volume is about selected applications of DSmT mainly in building change detection, object recognition, quality of data association in tracking, perception in robotics, risk assessment for torrent protection and multi-criteria decision-making, multi-modal image fusion, coarsening techniques, recommender system, levee characterization and assessment, human heading perception, trust assessment, robotics, biometrics, failure detection, GPS systems, inter-criteria analysis, group decision, human activity recognition, storm prediction, data association for autonomous vehicles, identification of maritime vessels, fusion of support vector machines (SVM), Silx-Furtif RUST code library for information fusion including PCR rules, and network for ship classification. Finally, the third part presents interesting contributions related to belief functions in general published or presented along the years since 2015. These contributions are related with decision-making under uncertainty, belief approximations, probability transformations, new distances between belief functions, non-classical multi-criteria decision-making problems with belief functions, generalization of Bayes theorem, image processing, data association, entropy and cross-entropy measures, fuzzy evidence numbers, negator of belief mass, human activity recognition, information fusion for breast cancer therapy, imbalanced data classification, and hybrid techniques mixing deep learning with belief functions as well
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