DPRP: a database of phenotype-specific regulatory programs derived from transcription factor binding data

Gene expression profiling has been extensively used in the past decades, resulting in an enormous amount of expression data available in public databases. These data sets are informative in elucidating transcriptional regulation of genes underlying various biological and clinical conditions. However, it is usually difficult to identify transcription factors (TFs) responsible for gene expression changes directly from their own expression, as TF activity is often regulated at the posttranscriptional level. In recent years, technical advances have made it possible to systematically determine the target genes of TFs by ChIP-seq experiments. To identify the regulatory programs underlying gene expression profiles, we constructed a database of phenotype-specific regulatory programs (DPRP, http://syslab.nchu.edu.tw/DPRP/) derived from the integrative analysis of TF binding data and gene expression data. DPRP provides three methods: the Fisher's Exact Test, the Kolmogorov-Smirnov test and the BASE algorithm to facilitate the application of gene expression data for generating new hypotheses on transcriptional regulatory programs in biological and clinical studies

DPRP: A Database of Phenotype-Specific Regulatory Programs Derived from Transcription Factor Binding Data

Gene expression profiling has been extensively used in the past decades, resulting in an enormous amount of expression data available in public databases. These data sets are informative in elucidating transcriptional regulation of genes underlying various biological and clinical conditions. However, it is usually difficult to identify transcription factors (TFs) responsible for gene expression changes directly from their own expression, as TF activity is often regulated at the posttranscriptional level. In recent years, technical advances have made it possible to systematically determine the target genes of TFs by ChIP-seq experiments. To identify the regulatory programs underlying gene expression profiles, we constructed a database of phenotype-specific regulatory programs (DPRP, http://syslab.nchu.edu.tw/DPRP/) derived from the integrative analysis of TF binding data and gene expression data. DPRP provides three methods: the Fisher’s Exact Test, the Kolmogorov–Smirnov test and the BASE algorithm to facilitate the application of gene expression data for generating new hypotheses on transcriptional regulatory programs in biological and clinical studies

Digital Storytelling Framework to Assist Young Children in Understanding Dementia

A digital storytelling tool is one of the interactive technologies that can help youngsters better comprehend Dementia. Dementia makes it difficult for older people to maintain their daily routines. They have difficulties in effectively communicating with those around them. Similarly, children whose grandparents have Dementia will struggle to understand their grandparents' situation. It will also negatively influence children's relationships with their grandparents. Learning through interactive digital storytelling will affect younger people's entertainment experiences, which may help them better comprehend Dementia. As a result, the children's relationships with their grandparents may be strengthened. This study aims to present the framework of digital storytelling in helping young children understand more about Dementia. The framework was developed in a step-by-step procedure that included analyzing and synthesizing current applications and relevant research, constructing the framework, and having it confirmed by experts. Researchers and developers may use the framework as a guideline to build meaningful digital storytelling features

Numerical modeling of unsaturated layered soil for rainfall-induced shallow landslides

In this paper, a pioneer study on numerical modeling of rainfall-induced shallow landslides in unsaturated layered soil using the variably saturated flow equation is presented. To model the shallow landslides, the infinite slope stability analysis coupled with the hydrological model with the consideration of the fluctuation of time-dependent pore water pressure and Gardner equation for soil water characteristic curve was developed. A linearization process for the nonlinear Richards equation to deal with groundwater flow in unsaturated layered soil is derived using the Gardner model. To solve one-dimensional flow in the unsaturated zone of layered soil profiles, flux conservation and the continuity of pressure potential at the interface between two consecutive layers are considered in the numerical discretization of the finite difference method. The validity of the proposed model is established in three numerical problems by comparing the results with the analytical and other numerical solutions. Application examples have also been conducted. Obtained results demonstrate that the fluctuation of pore water pressure in unsaturated layered soil dominates slope stability of landslides and the lowest factor of safety may occur at the interface between two consecutive layers. The findings observed in this study are a fundamental contribution to environmental protection engineering for landslides in areas with higher occurrence and vulnerability to extreme precipitation

Pleural Effusion after Percutaneous Radiofrequency Ablation for Hepatic Malignancies

AbstractBackground and AimsRadiofrequency ablation (RFA) can play an important role in the treatment of primary or metastatic liver tumors. Currently, percutaneous RFA is generally regarded as a safe, effective, and minimally invasive procedure. This study aimed to evaluate the presence and course of pleural effusion after monopolar RFA.MethodsFrom October 2008 to July 2013, a total of 54 patients (28 male and 26 female, mean age 65.2) treated with monopolar RFA were included in our study. 47 patients were diagnosed with hepatocellular carcinoma, 4 patients with hepatic metastasis, and 3 patients had other diagnoses. There were a total of 115 sessions of treatment and 199 liver tumors to be treated (1.73 ± 1.02 tumors treated per session). The tumor size ranged from 0.8 cm to 5.0 cm (mean 2.31 cm, standard deviation 1.04 cm). Thereafter, a follow-up ultrasound was performed within 24 hours subsequent to ablation to evaluate the presence of pleural effusion. The degree of pleural effusion was assessed by chest X-ray.ResultsFifteen (13.0%) treatment sessions in 14 patients showed right-sided pleural effusion after ablations. One patient had a large amount of effusion, while other patients manifested a minimal to small amount of effusion. There were 5 patients that experienced delayed resolution of pleural effusion; one patient (0.87%) had a minimal amount of pleural effusion even after one month. Overall, there was no pneumothorax, or periprocedural morality. Age, gender, tumor numbers, tumor sizes, and complete ablation of target tumors were similar among groups presenting with or without pleural effusion. Tumor locations associated with S78 segments abutting the diaphragm or right lobe of the liver were not associated with development of pleural effusion. Only the duration of ablation time had a marginal trend toward significance (p = 0.051).ConclusionsThe transient appearance of right-sided pleural effusion after percutaneous RFA for hepatic malignancies was not infrequent. However, refractory pleural effusion was rare

MVA2023 Small Object Detection Challenge for Spotting Birds: Dataset, Methods, and Results

Small Object Detection (SOD) is an important machine vision topic because (i) a variety of real-world applications require object detection for distant objects and (ii) SOD is a challenging task due to the noisy, blurred, and less-informative image appearances of small objects. This paper proposes a new SOD dataset consisting of 39,070 images including 137,121 bird instances, which is called the Small Object Detection for Spotting Birds (SOD4SB) dataset. The detail of the challenge with the SOD4SB dataset is introduced in this paper. In total, 223 participants joined this challenge. This paper briefly introduces the award-winning methods. The dataset, the baseline code, and the website for evaluation on the public testset are publicly available.Comment: This paper is included in the proceedings of the 18th International Conference on Machine Vision Applications (MVA2023). It will be officially published at a later date. Project page : https://www.mva-org.jp/mva2023/challeng

Comparison of coplanar and noncoplanar intensity-modulated radiation therapy and helical tomotherapy for hepatocellular carcinoma

<p>Abstract</p> <p>Background</p> <p>To compare the differences in dose-volume data among coplanar intensity modulated radiotherapy (IMRT), noncoplanar IMRT, and helical tomotherapy (HT) among patients with hepatocellular carcinoma (HCC) and portal vein thrombosis (PVT).</p> <p>Methods</p> <p>Nine patients with unresectable HCC and PVT underwent step and shoot coplanar IMRT with intent to deliver 46 - 54 Gy to the tumor and portal vein. The volume of liver received 30Gy was set to keep less than 30% of whole normal liver (V30 < 30%). The mean dose to at least one side of kidney was kept below 23 Gy, and 50 Gy as for stomach. The maximum dose was kept below 47 Gy for spinal cord. Several parameters including mean hepatic dose, percent volume of normal liver with radiation dose at X Gy (Vx), uniformity index, conformal index, and doses to organs at risk were evaluated from the dose-volume histogram.</p> <p>Results</p> <p>HT provided better uniformity for the planning-target volume dose coverage than both IMRT techniques. The noncoplanar IMRT technique reduces the V10 to normal liver with a statistically significant level as compared to HT. The constraints for the liver in the V30 for coplanar IMRT vs. noncoplanar IMRT vs. HT could be reconsidered as 21% vs. 17% vs. 17%, respectively. When delivering 50 Gy and 60-66 Gy to the tumor bed, the constraints of mean dose to the normal liver could be less than 20 Gy and 25 Gy, respectively.</p> <p>Conclusion</p> <p>Noncoplanar IMRT and HT are potential techniques of radiation therapy for HCC patients with PVT. Constraints for the liver in IMRT and HT could be stricter than for 3DCRT.</p

miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions

MicroRNAs (miRNAs) are small non-coding RNA molecules capable of negatively regulating gene expression to control many cellular mechanisms. The miRTarBase database (http://mirtarbase.mbc.nctu.edu.tw/) provides the most current and comprehensive information of experimentally validated miRNA-target interactions. The database was launched in 2010 with data sources for >100 published studies in the identification of miRNA targets, molecular networks of miRNA targets and systems biology, and the current release (2013, version 4) includes significant expansions and enhancements over the initial release (2010, version 1). This article reports the current status of and recent improvements to the database, including (i) a 14-fold increase to miRNA-target interaction entries, (ii) a miRNA-target network, (iii) expression profile of miRNA and its target gene, (iv) miRNA target-associated diseases and (v) additional utilities including an upgrade reminder and an error reporting/user feedback system

Phytochemicals as antibiotic alternatives to promote growth and enhance host health

There are heightened concerns globally on emerging drug-resistant superbugs and the lack of new antibiotics for treating human and animal diseases. For the agricultural industry, there is an urgent need to develop strategies to replace antibiotics for food-producing animals, especially poultry and livestock. The 2nd International Symposium on Alternatives to Antibiotics was held at the World Organization for Animal Health in Paris, France, December 12-15, 2016 to discuss recent scientific developments on strategic antibiotic-free management plans, to evaluate regional differences in policies regarding the reduction of antibiotics in animal agriculture and to develop antibiotic alternatives to combat the global increase in antibiotic resistance. More than 270 participants from academia, government research institutions, regulatory agencies, and private animal industries from >25 different countries came together to discuss recent research and promising novel technologies that could provide alternatives to antibiotics for use in animal health and production; assess challenges associated with their commercialization; and devise actionable strategies to facilitate the development of alternatives to antibiotic growth promoters (AGPs) without hampering animal production. The 3-day meeting consisted of four scientific sessions including vaccines, microbial products, phytochemicals, immune-related products, and innovative drugs, chemicals and enzymes, followed by the last session on regulation and funding. Each session was followed by an expert panel discussion that included industry representatives and session speakers. The session on phytochemicals included talks describing recent research achievements, with examples of successful agricultural use of various phytochemicals as antibiotic alternatives and their mode of action in major agricultural animals (poultry, swine and ruminants). Scientists from industry and academia and government research institutes shared their experience in developing and applying potential antibiotic-alternative phytochemicals commercially to reduce AGPs and to develop a sustainable animal production system in the absence of antibiotics.Fil: Lillehoj, Hyun. United States Department of Agriculture. Agricultural Research Service; ArgentinaFil: Liu, Yanhong. University of California; Estados UnidosFil: Calsamiglia, Sergio. Universitat Autònoma de Barcelona; EspañaFil: Fernandez Miyakawa, Mariano Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Patobiología; ArgentinaFil: Chi, Fang. Amlan International; Estados UnidosFil: Cravens, Ron L.. Amlan International; Estados UnidosFil: Oh, Sungtaek. United States Department of Agriculture. Agricultural Research Service; ArgentinaFil: Gay, Cyril G.. United States Department of Agriculture. Agricultural Research Service; Argentin