Genetic Networks of Complex Disorders: from a Novel Search Engine for PubMed Article Database

Finding genetic risk factors of complex disorders may involve reviewing hundreds of genes or thousands of research articles iteratively, but few tools have been available to facilitate this procedure. In this work, we built a novel publication search engine that can identify target-disorder specific, genetics-oriented research articles and extract the genes with significant results. Preliminary test results showed that the output of this engine has better coverage in terms of genes or publications, than other existing applications. We consider it as an essential tool for understanding genetic networks of complex disorders

Evolutionary Design of Artificial Neural Networks Using a Descriptive Encoding Language

Automated design of artificial neural networks by evolutionary algorithms (neuroevolution) has generated much recent research both because successful approaches will facilitate wide-spread use of intelligent systems based on neural networks, and because it will shed light on our understanding of how "real" neural networks may have evolved. The main challenge in neuroevolution is that the search space of neural network architectures and their corresponding optimal weights can be high-dimensional and disparate, and therefore evolution may not discover an optimal network even if it exists. In this dissertation, I present a high-level encoding language that can be used to restrict the general search space of neural networks, and implement a problem-independent design system based on this encoding language. I show that this encoding scheme works effectively in 1) describing the search space in which evolution occurs; 2) specifying the initial configuration and evolutionary parameters; and 3) generating the final neural networks resulting from the evolutionary process in a human-readable manner. Evolved networks for ``n-partition problems'' demonstrate that this approach can evolve high-performance network architectures, and show by example that a small parsimony factor in the fitness measure can lead to the emergence of modular networks. Further, this approach is shown to work for encoding recurrent neural networks for a temporal sequence generation problem, and the trade-offs between various recurrent network architectures are systematically compared via multi-objective optimization. Finally, it is shown that this system can be extended to address reinforcement learning problems by evolving architectures and connection weights in a hierarchical manner. Experimental results support the conclusion that hierarchical evolutionary approaches integrated in a system having a high-level descriptive encoding language can be useful in designing modular networks, including those that have recurrent connectivity

Socio-economic factors associated with mental health outcomes during the COVID-19 pandemic in South Korea

BackgroundIndividuals are at an increased risk of adverse mental health outcomes during the COVID-19 pandemic. To reduce the impact on mental health outcomes that were induced by national-level policies, which may influence an individual at the community level, exploring the comprehensive relations between individual and environmental factors are needed. The aim is to examine socio-ecological factors associated with mental health outcomes, including depressive and anxiety symptoms, with the perspective of support to provide interventions that help the community during future disease outbreaks.MethodFrom 5 November to 20 November 2020, a cross-sectional and population-based study was conducted to assess the socio-ecological factors of mental health outcomes during the COVID-19 pandemic. A total of 1,000 participants, aged 20–69 years, in Chungnam Region, South Korea, were included in this study. Multiple linear regression models were used to examine the association between socio-ecological factors and mental health outcomes. The primary outcomes were individuals' mental health outcomes which are measured by PHQ-9 and GAD-7 scores.ResultsOf the 1,000 participants, the average PHQ-9 was 4.39, and GAD-7 was 3.21 during the COVID-19 pandemic. Specifically, the participants with moderate or severe levels of PHQ-9 and GAD-7 were 12.6 and 6.8%, respectively. Higher levels of depressive and anxiety symptoms were associated with participants who were single, reported a lower household income, had decreased support from friends or family, and increased stress from the workplace or home. In subgroup analyses by age, gender, and household income, a similar trend was reported in individual and interpersonal-level factors. There were significant associations between regional-level factors, including gross regional domestic product (GRDP), mental health institutions, psychiatrists, nurse-to-population ratios, and individuals' mental health outcomes.ConclusionThe management of depressive and anxiety symptoms of individuals during the pandemic was better explained by individual and interpersonal characteristics rather than regional-level factors, highlighting the need for more policies aimed at these lower levels

Phylogenetically informed logic relationships improve detection of biological network organization

Background: A "phylogenetic profile" refers to the presence or absence of a gene across a set of organisms, and it has been proven valuable for understanding gene functional relationships and network organization. Despite this success, few studies have attempted to search beyond just pairwise relationships among genes. Here we search for logic relationships involving three genes, and explore its potential application in gene network analyses. Results: Taking advantage of a phylogenetic matrix constructed from the large orthologs database Roundup, we invented a method to create balanced profiles for individual triplets of genes that guarantee equal weight on the different phylogenetic scenarios of coevolution between genes. When we applied this idea to LAPP, the method to search for logic triplets of genes, the balanced profiles resulted in significant performance improvement and the discovery of hundreds of thousands more putative triplets than unadjusted profiles. We found that logic triplets detected biological network organization and identified key proteins and their functions, ranging from neighbouring proteins in local pathways, to well separated proteins in the whole pathway, and to the interactions among different pathways at the system level. Finally, our case study suggested that the directionality in a logic relationship and the profile of a triplet could disclose the connectivity between the triplet and surrounding networks. Conclusion: Balanced profiles are superior to the raw profiles employed by traditional methods of phylogenetic profiling in searching for high order gene sets. Gene triplets can provide valuable information in detection of biological network organization and identification of key genes at different levels of cellular interaction

Carpal Tunnel Syndrome Caused by Space Occupying Lesions

PURPOSE: To evaluate the diagnosis and treatment of the carpal tunnel syndrome (CTS) due to space occupying lesions (SOL). MATERIALS and METHODS: Eleven patients and 12 cases that underwent surgery for CTS due to SOL were studied retrospectively. We excluded SOL caused by bony lesions, such as malunion of distal radius fracture, volar lunate dislocation, etc. the average age was 51 years. There were 3 men and 8 women. Follow-up period was 12 to 40 months with an average of 18 months. the diagnosis of CTS was made clinically and electrophysiologically. in patients with swelling or tenderness on the area of wrist flexion creases, magnetic resonance imaging (MRI) and/or computed tomogram (CT) were additionally taken as well as the carpal tunnel view. We performed conventional open transverse carpal ligament release and removal of SOL. RESULTS: the types of lesion confirmed by pathologic examination were; tuberculosis tenosynovitis in 3 cases, nonspecific tenosynovitis in 2 cases, and gout in one case. Other SOLs were tumorous condition in five cases, and abnormal palmaris longus hypertrophy in 1 case. Tumorous conditions were due to calcifying mass in 4 cases and ganglion in 1 case. Following surgery, all cases showed alleviation of symptom without recurrence or complications. CONCLUSION: in cases with swelling or tenderness on the area of wrist flexion creases, it is important to obtain a carpal tunnel view, and MRI and/or CT should be supplemented in order to rule out SOLs around the carpal tunnel, if necessary.ope

Small non-coding RNA profiling and the role of piRNA pathway genes in the protection of chicken primordial germ cells

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.Background Genes, RNAs, and proteins play important roles during germline development. However, the functions of non-coding RNAs (ncRNAs) on germline development remain unclear in avian species. Recent high-throughput techniques have identified several classes of ncRNAs, including micro RNAs (miRNAs), small-interfering RNAs (siRNAs), and PIWI-interacting RNAs (piRNAs). These ncRNAs are functionally important in the genome, however, the identification and annotation of ncRNAs in a genome is challenging. The aim of this study was to identify different types of small ncRNAs particularly piRNAs, and the role of piRNA pathway genes in the protection of chicken primordial germ cells (PGCs). Results At first, we performed next-generation sequencing to identify ncRNAs in chicken PGCs, and we performed ab initio predictive analysis to identify putative piRNAs in PGCs. Then, we examined the expression of three repetitive sequence-linked piRNAs and 14 genic-transcript-linked piRNAs along with their linked genes using real-time PCR. All piRNAs and their linked genes were highly expressed in PGCs. Subsequently, we knocked down two known piRNA pathway genes of chicken, PIWI-like protein 1 (CIWI) and 2 (CILI), in PGCs using siRNAs. After knockdown of CIWI and CILI, we examined their effects on the expression of six putative piRNA-linked genes and DNA double-strand breakage in PGCs. The knockdown of CIWI and CILI upregulated chicken repetitive 1 (CR1) element and RAP2B, a member of RAS oncogene family, and increased DNA double-strand breakage in PGCs. Conclusions Our results increase the understanding of PGC-expressed piRNAs and the role of piRNA pathway genes in the protection of germ cells