12,752 research outputs found
The Type 2 Diabetes Knowledge Portal: an open access genetic resource dedicated to type 2 diabetes and related traits
Associations between human genetic variation and clinical phenotypes have become a foundation of biomedical research. Most repositories of these data seek to be disease-agnostic and therefore lack disease-focused views. The Type 2 Diabetes Knowledge Portal (T2DKP) is a public resource of genetic datasets and genomic annotations dedicated to type 2 diabetes (T2D) and related traits. Here, we seek to make the T2DKP more accessible to prospective users and more useful to existing users. First, we evaluate the T2DKP's comprehensiveness by comparing its datasets with those of other repositories. Second, we describe how researchers unfamiliar with human genetic data can begin using and correctly interpreting them via the T2DKP. Third, we describe how existing users can extend their current workflows to use the full suite of tools offered by the T2DKP. We finally discuss the lessons offered by the T2DKP toward the goal of democratizing access to complex disease genetic results
An advanced deep learning models-based plant disease detection: A review of recent research
Plants play a crucial role in supplying food globally. Various environmental factors lead to plant diseases which results in significant production losses. However, manual detection of plant diseases is a time-consuming and error-prone process. It can be an unreliable method of identifying and preventing the spread of plant diseases. Adopting advanced technologies such as Machine Learning (ML) and Deep Learning (DL) can help to overcome these challenges by enabling early identification of plant diseases. In this paper, the recent advancements in the use of ML and DL techniques for the identification of plant diseases are explored. The research focuses on publications between 2015 and 2022, and the experiments discussed in this study demonstrate the effectiveness of using these techniques in improving the accuracy and efficiency of plant disease detection. This study also addresses the challenges and limitations associated with using ML and DL for plant disease identification, such as issues with data availability, imaging quality, and the differentiation between healthy and diseased plants. The research provides valuable insights for plant disease detection researchers, practitioners, and industry professionals by offering solutions to these challenges and limitations, providing a comprehensive understanding of the current state of research in this field, highlighting the benefits and limitations of these methods, and proposing potential solutions to overcome the challenges of their implementation
a systematic review
Funding Information: This study is part of an interdisciplinary research project, funded by the Special Research Fund (Bijzonder Onderzoeksfonds) of Ghent University.Introduction: Ontologies are a formal way to represent knowledge in a particular field and have the potential to transform the field of health promotion and digital interventions. However, few researchers in physical activity (PA) are familiar with ontologies, and the field can be difficult to navigate. This systematic review aims to (1) identify ontologies in the field of PA, (2) assess their content and (3) assess their quality. Methods: Databases were searched for ontologies on PA. Ontologies were included if they described PA or sedentary behavior, and were available in English language. We coded whether ontologies covered the user profile, activity, or context domain. For the assessment of quality, we used 12 criteria informed by the Open Biological and Biomedical Ontology (OBO) Foundry principles of good ontology practice. Results: Twenty-eight ontologies met the inclusion criteria. All ontologies covered PA, and 19 included information on the user profile. Context was covered by 17 ontologies (physical context, n = 12; temporal context, n = 14; social context: n = 5). Ontologies met an average of 4.3 out of 12 quality criteria. No ontology met all quality criteria. Discussion: This review did not identify a single comprehensive ontology of PA that allowed reuse. Nonetheless, several ontologies may serve as a good starting point for the promotion of PA. We provide several recommendations about the identification, evaluation, and adaptation of ontologies for their further development and use.publishersversionpublishe
Novel 129Xe Magnetic Resonance Imaging and Spectroscopy Measurements of Pulmonary Gas-Exchange
Gas-exchange is the primary function of the lungs and involves removing carbon dioxide from the body and exchanging it within the alveoli for inhaled oxygen. Several different pulmonary, cardiac and cardiovascular abnormalities have negative effects on pulmonary gas-exchange. Unfortunately, clinical tests do not always pinpoint the problem; sensitive and specific measurements are needed to probe the individual components participating in gas-exchange for a better understanding of pathophysiology, disease progression and response to therapy.
In vivo Xenon-129 gas-exchange magnetic resonance imaging (129Xe gas-exchange MRI) has the potential to overcome these challenges. When participants inhale hyperpolarized 129Xe gas, it has different MR spectral properties as a gas, as it diffuses through the alveolar membrane and as it binds to red-blood-cells. 129Xe MR spectroscopy and imaging provides a way to tease out the different anatomic components of gas-exchange simultaneously and provides spatial information about where abnormalities may occur.
In this thesis, I developed and applied 129Xe MR spectroscopy and imaging to measure gas-exchange in the lungs alongside other clinical and imaging measurements. I measured 129Xe gas-exchange in asymptomatic congenital heart disease and in prospective, controlled studies of long-COVID. I also developed mathematical tools to model 129Xe MR signals during acquisition and reconstruction. The insights gained from my work underscore the potential for 129Xe gas-exchange MRI biomarkers towards a better understanding of cardiopulmonary disease. My work also provides a way to generate a deeper imaging and physiologic understanding of gas-exchange in vivo in healthy participants and patients with chronic lung and heart disease
Inferior Alveolar Canal Automatic Detection with Deep Learning CNNs on CBCTs: Development of a Novel Model and Release of Open-Source Dataset and Algorithm
Featured Application Convolutional neural networks can accurately identify the Inferior Alveolar Canal, rapidly generating precise 3D data. The datasets and source code used in this paper are publicly available, allowing the reproducibility of the experiments performed. Introduction: The need of accurate three-dimensional data of anatomical structures is increasing in the surgical field. The development of convolutional neural networks (CNNs) has been helping to fill this gap by trying to provide efficient tools to clinicians. Nonetheless, the lack of a fully accessible datasets and open-source algorithms is slowing the improvements in this field. In this paper, we focus on the fully automatic segmentation of the Inferior Alveolar Canal (IAC), which is of immense interest in the dental and maxillo-facial surgeries. Conventionally, only a bidimensional annotation of the IAC is used in common clinical practice. A reliable convolutional neural network (CNNs) might be timesaving in daily practice and improve the quality of assistance. Materials and methods: Cone Beam Computed Tomography (CBCT) volumes obtained from a single radiological center using the same machine were gathered and annotated. The course of the IAC was annotated on the CBCT volumes. A secondary dataset with sparse annotations and a primary dataset with both dense and sparse annotations were generated. Three separate experiments were conducted in order to evaluate the CNN. The IoU and Dice scores of every experiment were recorded as the primary endpoint, while the time needed to achieve the annotation was assessed as the secondary end-point. Results: A total of 347 CBCT volumes were collected, then divided into primary and secondary datasets. Among the three experiments, an IoU score of 0.64 and a Dice score of 0.79 were obtained thanks to the pre-training of the CNN on the secondary dataset and the creation of a novel deep label propagation model, followed by proper training on the primary dataset. To the best of our knowledge, these results are the best ever published in the segmentation of the IAC. The datasets is publicly available and algorithm is published as open-source software. On average, the CNN could produce a 3D annotation of the IAC in 6.33 s, compared to 87.3 s needed by the radiology technician to produce a bidimensional annotation. Conclusions: To resume, the following achievements have been reached. A new state of the art in terms of Dice score was achieved, overcoming the threshold commonly considered of 0.75 for the use in clinical practice. The CNN could fully automatically produce accurate three-dimensional segmentation of the IAC in a rapid setting, compared to the bidimensional annotations commonly used in the clinical practice and generated in a time-consuming manner. We introduced our innovative deep label propagation method to optimize the performance of the CNN in the segmentation of the IAC. For the first time in this field, the datasets and the source codes used were publicly released, granting reproducibility of the experiments and helping in the improvement of IAC segmentation
Knowledge Graph Building Blocks: An easy-to-use Framework for developing FAIREr Knowledge Graphs
Knowledge graphs and ontologies provide promising technical solutions for
implementing the FAIR Principles for Findable, Accessible, Interoperable, and
Reusable data and metadata. However, they also come with their own challenges.
Nine such challenges are discussed and associated with the criterion of
cognitive interoperability and specific FAIREr principles (FAIR + Explorability
raised) that they fail to meet. We introduce an easy-to-use, open source
knowledge graph framework that is based on knowledge graph building blocks
(KGBBs). KGBBs are small information modules for knowledge-processing, each
based on a specific type of semantic unit. By interrelating several KGBBs, one
can specify a KGBB-driven FAIREr knowledge graph. Besides implementing semantic
units, the KGBB Framework clearly distinguishes and decouples an internal
in-memory data model from data storage, data display, and data access/export
models. We argue that this decoupling is essential for solving many problems of
knowledge management systems. We discuss the architecture of the KGBB Framework
as we envision it, comprising (i) an openly accessible KGBB-Repository for
different types of KGBBs, (ii) a KGBB-Engine for managing and operating FAIREr
knowledge graphs (including automatic provenance tracking, editing changelog,
and versioning of semantic units); (iii) a repository for KGBB-Functions; (iv)
a low-code KGBB-Editor with which domain experts can create new KGBBs and
specify their own FAIREr knowledge graph without having to think about semantic
modelling. We conclude with discussing the nine challenges and how the KGBB
Framework provides solutions for the issues they raise. While most of what we
discuss here is entirely conceptual, we can point to two prototypes that
demonstrate the principle feasibility of using semantic units and KGBBs to
manage and structure knowledge graphs
Semi-Supervised Medical Image Segmentation with Co-Distribution Alignment
Medical image segmentation has made significant progress when a large amount
of labeled data are available. However, annotating medical image segmentation
datasets is expensive due to the requirement of professional skills.
Additionally, classes are often unevenly distributed in medical images, which
severely affects the classification performance on minority classes. To address
these problems, this paper proposes Co-Distribution Alignment (Co-DA) for
semi-supervised medical image segmentation. Specifically, Co-DA aligns marginal
predictions on unlabeled data to marginal predictions on labeled data in a
class-wise manner with two differently initialized models before using the
pseudo-labels generated by one model to supervise the other. Besides, we design
an over-expectation cross-entropy loss for filtering the unlabeled pixels to
reduce noise in their pseudo-labels. Quantitative and qualitative experiments
on three public datasets demonstrate that the proposed approach outperforms
existing state-of-the-art semi-supervised medical image segmentation methods on
both the 2D CaDIS dataset and the 3D LGE-MRI and ACDC datasets, achieving an
mIoU of 0.8515 with only 24% labeled data on CaDIS, and a Dice score of 0.8824
and 0.8773 with only 20% data on LGE-MRI and ACDC, respectively.Comment: Paper appears in Bioengineering 2023, 10(7), 86
Molecular Research in Rice: Agronomically Important Traits 2.0
This volume presents recent research achievements concerning the molecular genetic basis of agronomic traits in rice. Rice (Oryza sativa L.) is the most important food crop in the world, being a staple food for more than half of the world’s population. Recent improvements in living standards have increased the worldwide demand for high-yielding and high-quality rice cultivars. To develop novel cultivars with superior agronomic performance, we need to understand the molecular basis of agronomically important traits related to grain yield, grain quality, disease resistance, and abiotic stress tolerance. Decoding the whole rice genome sequence revealed that ,while there are more than 37,000 genes in the ~400 Mbp rice genome, there are only about 3000 genes whose molecular functions are characterized in detail. We collected in this volume the continued research efforts of scholars that elucidate genetic networks and the molecular mechanisms controlling agronomically important traits in rice
Activity Recognition From Newborn Resuscitation Videos
Objective: Birth asphyxia is one of the leading causes of neonatal deaths. A
key for survival is performing immediate and continuous quality newborn
resuscitation. A dataset of recorded signals during newborn resuscitation,
including videos, has been collected in Haydom, Tanzania, and the aim is to
analyze the treatment and its effect on the newborn outcome. An important step
is to generate timelines of relevant resuscitation activities, including
ventilation, stimulation, suction, etc., during the resuscitation episodes.
Methods: We propose a two-step deep neural network system, ORAA-net, utilizing
low-quality video recordings of resuscitation episodes to do activity
recognition during newborn resuscitation. The first step is to detect and track
relevant objects using Convolutional Neural Networks (CNN) and post-processing,
and the second step is to analyze the proposed activity regions from step 1 to
do activity recognition using 3D CNNs. Results: The system recognized the
activities newborn uncovered, stimulation, ventilation and suction with a mean
precision of 77.67 %, a mean recall of 77,64 %, and a mean accuracy of 92.40 %.
Moreover, the accuracy of the estimated number of Health Care Providers (HCPs)
present during the resuscitation episodes was 68.32 %. Conclusion: The results
indicate that the proposed CNN-based two-step ORAAnet could be used for object
detection and activity recognition in noisy low-quality newborn resuscitation
videos. Significance: A thorough analysis of the effect the different
resuscitation activities have on the newborn outcome could potentially allow us
to optimize treatment guidelines, training, debriefing, and local quality
improvement in newborn resuscitation.Comment: 10 page
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