4,523 research outputs found
The Human Phenotype Ontology in 2024: phenotypes around the world.
The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs
Structuring the State’s Voice of Contention in Harmonious Society: How Party Newspapers Cover Social Protests in China
During the Chinese Communist Party’s (CCP) campaign of building a ‘harmonious society’, how do the official newspapers cover the instances of social contention on the ground? Answering this question will shed light not only on how the party press works but also on how the state and the society interact in today’s China. This thesis conceptualises this phenomenon with a multi-faceted and multi-levelled notion of ‘state-initiated contentious public sphere’ to capture the complexity of mediated relations between the state and social contention in the party press. Adopting a relational approach, this thesis analyses 1758 news reports of ‘mass incident’ in the People’s Daily and the Guangming Daily between 2004 and 2020, employing cluster analysis, qualitative comparative analysis, and social network analysis. The thesis finds significant differences in the patterns of contentious coverage in the party press at the level of event and province and an uneven distribution of attention to social contention across incidents and regions. For ‘reported regions’, the thesis distinguishes four types of coverage and presents how party press responds differently to social contention in different scenarios at the provincial level. For ‘identified incidents’, the thesis distinguishes a cumulative type of visibility based on the quantity of coverage from a relational visibility based on the structure emerging from coverage and explains how different news-making rationales determine whether instances receive similar amounts of coverage or occupy similar positions within coverage. Eventually, by demonstrating how the Chinese state strategically uses party press to respond to social contention and how social contention is journalistically placed in different positions in the state’s eyes, this thesis argues that what social contention leads to is the establishment of complex state-contention relations channelled through the party press
The Human Phenotype Ontology in 2024: phenotypes around the world
\ua9 The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs
Sound Event Detection by Exploring Audio Sequence Modelling
Everyday sounds in real-world environments are a powerful source of information by which humans can interact with their environments. Humans can infer what is happening around them by listening to everyday sounds. At the same time, it is a challenging task for a computer algorithm in a smart device to automatically recognise, understand, and interpret everyday sounds. Sound event detection (SED) is the process of transcribing an audio recording into sound event tags with onset and offset time values. This involves classification and segmentation of sound events in the given audio recording. SED has numerous applications in everyday life which include security and surveillance, automation, healthcare monitoring, multimedia information retrieval, and assisted living technologies. SED is to everyday sounds what automatic speech recognition (ASR) is to speech and automatic music transcription (AMT) is to music. The fundamental questions in designing a sound recognition system are, which portion of a sound event should the system analyse, and what proportion of a sound event should the system process in order to claim a confident detection of that particular sound event. While the classification of sound events has improved a lot in recent years, it is considered that the temporal-segmentation of sound events has not improved in the same extent. The aim of this thesis is to propose and develop methods to improve the segmentation and classification of everyday sound events in SED models. In particular, this thesis explores the segmentation of sound events by investigating audio sequence encoding-based and audio sequence modelling-based methods, in an effort to improve the overall sound event detection performance. In the first phase of this thesis, efforts are put towards improving sound event detection by explicitly conditioning the audio sequence representations of an SED model using sound activity detection (SAD) and onset detection. To achieve this, we propose multi-task learning-based SED models in which SAD and onset detection are used as auxiliary tasks for the SED task. The next part of this thesis explores self-attention-based audio sequence modelling, which aggregates audio representations based on temporal relations within and between sound events, scored on the basis of the similarity of sound event portions in audio event sequences. We propose SED models that include memory-controlled, adaptive, dynamic, and source separation-induced self-attention variants, with the aim to improve overall sound recognition
NURSING AND MIDWIFERY STUDENTS’ LENS: CONNECTING THEORETICAL KNOWLEDGE WITH CLINICAL PRACTICE: AN INTERPRETATIVE PHENOMENOLOGICAL STUDY
Aim: To explore and critically analyse the strategies employed by final-year BSc pre-registration nursing and midwifery students at an inner London university to connect theoretical knowledge with clinical practice, to promote their learning and professional development. Background: Navigating the theory-practice gap has been a significant challenge for nursing and midwifery students. While there are many perspectives from academics and clinicians, how theoretical knowledge is connected with clinical practice is rarely discussed and studied from the students’ perspectives. Design: Interpretative phenomenological analysis was used to understand nursing and midwifery students' experiences in connecting theoretical knowledge with clinical practice. Rather than attempting to establish objective truth, this thesis focused on participants’ subjective experiences. Method: This study employed a qualitative research design. The data was obtained using semi-structured interviews and analysed using an inductive approach. The study population included (n=12) pre-registration nursing and midwifery students enrolled on a Bachelor of Science programs. Findings: Four themes emerged (1) Complexity of embodied knowledge; (2) Sensing the meaning of personal and professional learning; (3) Demographic attributes and self-understanding; (4) Sense-making of COVID-19. Conclusion: The process by which pre-registration nursing and midwifery students connect theoretical knowledge with clinical practice is complex and multifaceted. It intersects with other factors and cannot be understood in isolation. This interconnectedness necessitates a thorough examination of all the variables involved
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Cancer Care in Pandemic Times: Building Inclusive Local Health Security in Africa and India
This is a book about improving cancer care in Africa and India that is a child of its pandemic times. It has been collaboratively researched and written by colleagues in Kenya, Tanzania, India and the UK, working within a cross-country, multidisciplinary research project, Innovation for Cancer Care in Africa (ICCA). Since this was a health-focused research project, ICCA researchers during the pandemic not only continued to work on the cancer research project but were also called upon by their governments to respond to immediate pandemic needs. In combining these two concerns, for improving cancer care and responding to pandemic needs, our original project aims have been challenged, deepened and reworked. ICCA’s initial collaborative research focus included—against the grain of most global health literature—the potential role of enhanced local production of essential healthcare supplies for improving cancer care in African countries. The pandemic experience has strikingly validated these earlier findings on the importance of industrial development for health care. The pandemic crystallised for researchers and policymakers an often overlooked phenomenon: global health security is built on the foundations of strong local health security. We argue in this book that new analytical thinking from social scientists and others is required on how to build local health security. We use the “lens” of original research on cancer care in East Africa and India to build up an understanding of the scope for the development of stronger synergies between local health industries and health care, in order to strengthen local health security and develop tools for policy making. The rethinking and reimagining presented here is required for different African countries, for India and the wider world, and this research on cancer care has taught us that this imperative goes much wider than infectious diseases
Development of variable and robust brain wiring patterns in the fly visual system
Precise generation of synapse-specific neuronal connections are crucial for establishing a robust and functional brain. Neuronal wiring patterns emerge from proper spatiotemporal regulation of axon branching and synapse formation during development. Several neuropsychiatric and neurodevelopmental disorders exhibit defects in neuronal wiring owing to synapse loss and/or dys-regulated axon branching. Despite decades of research, how the two inter-dependent cellular processes: axon branching and synaptogenesis are coupled locally in the presynaptic arborizations is still unclear.
In my doctoral work, I investigated the possible role of EGF receptor (EGFR) activity in coregulating axon branching and synapse formation in a spatiotemporally restricted fashion, locally in the medulla innervating Dorsal Cluster Neuron (M- DCN)/LC14 axon terminals. In this work I have explored how genetically encoded EGFR randomly recycles in the axon branch terminals, thus creating an asymmetric, non-deterministic distribution pattern. Asymmetric EGFR activity in the branches acts as a permissive signal for axon branch pruning. I observed that the M-DCN branches which stochastically becomes EGFR ‘+’ during development are synaptogenic, which means they can recruit synaptic machineries like Syd1 and Bruchpilot (Brp). My work showed that EGFR activity has a dual role in establishing proper M-DCN wiring; first in regulating primary branch consolidation possibly via actin regulation prior to synaptogenesis. Later in maintaining/protecting the levels of late Active Zone (AZ) protein Brp in the presynaptic branches by suppressing basal autophagy level during synaptogenesis. When M-DCNs lack optimal EGFR activity, the basal autophagy level increases resulting in loss of Brp marked synapses which is causal to increased exploratory branches and post-synaptic target loss. Lack of EGFR activity affects the M-DCN wiring pattern that makes adult flies more active and behave like obsessive compulsive in object fixation assay. In the second part of my doctoral work, I have asked how non-genetic factors like developmental temperature affects adult brain wiring. To test that, I increased or decreased rearing temperature which is known to inversely affect pupal developmental rate. We asked if all the noisy cellular processes of neuronal assembly: filopodial dynamics, axon branching, synapse formation and postsynaptic connections scale up or down accordingly. I observed that indeed all the cellular processes slow down at lower developmental temperature and vice versa, which changes the DCN wiring pattern accordingly. Interestingly, behavior of flies adapts to their developmental temperature, performing best at the temperature they have been raised at. This shows that optimal brain function is an adaptation of robust brain wiring patterns which are specified by noisy developmental processes.
In conclusion, my doctoral work helps us better understand the developmental regulation of axon branching and synapse formation for establishing precise brain wiring pattern. We need all the cell intrinsic developmental processes to be highly regulated in space and time. It is infact a combinatorial effect of such stochastic processes and external factors that contribute to the final outcome, a functional and robust adult brain
The use of proxies in designing for and with autistic children: supporting friendship as a case study
Participatory Design (PD) is an approach for designing new technologies which involves end users in the design process. It is generally accepted that involving users in the design process gives them a sense of ownership over the final product which enhances its usability and acceptance by the target population. Employing a PD approach can introduce multiple challenges especially when working with autistic children. Many approaches for involving autistic children and children with special needs were developed to address these challenges. However, these frameworks introduce their own limitations as well. There is an ethical dilemma to consider in the involvement of autistic children in the design process. Although we established the ethical benefit of involving children, we did not address the ethical issues that will result from involving them in these research projects. Among other issues, the nature of design workshops we as a community currently run require working with unfamiliar researchers and communicating with them while social and communication differences are one of the main diagnostic criteria for autism. When designing for autistic children and other vulnerable populations an alternative (or most often an additional) approach is designing with proxies. Proxies for the child can be one of several groups of other stakeholders, such as: teachers, parents and siblings. Each of these groups may inform the design process, from their particular perspective, and as proxies for the target group of autistic children. Decisions need to be made about what stages in the design process are suited to their participation, and the role they play in each case. For this reason, we explore the role of teachers, parents, autistic adults and neurotypical children as proxies in the design process.
To explore the roles of proxies we chose friendship between autistic and neurotypical children as the context we are designing for. We are interested in understanding the nature of children's friendships and the potential for technology to support them. Although children themselves are the ones who experience friendship and challenges around its development and peer interaction, they might find it difficult to articulate the challenges they face. Furthermore, it is unrealistic to expect children to identify strategies to help them overcome the challenges with friendship development that they are facing as it assumes children have the social skills to come up with these strategies in the first place. Hence, it is necessary in this context to consider proxies who can identify challenges and suggest ways to overcome them
Talking about personal recovery in bipolar disorder: Integrating health research, natural language processing, and corpus linguistics to analyse peer online support forum posts
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
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