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"Lin, Yuan-Chi"
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The AT-hook is an evolutionarily conserved auto-regulatory domain of SWI/SNF required for cell lineage priming
The SWI/SNF ATP-dependent chromatin remodeler is a master regulator of the epigenome, controlling pluripotency and differentiation. Towards the C-terminus of the catalytic subunit of SWI/SNF is a motif called the AT-hook that is evolutionary conserved. The AT-hook is present in many chromatin modifiers and generally thought to help anchor them to DNA. We observe however that the AT-hook regulates the intrinsic DNA-stimulated ATPase activity aside from promoting SWI/SNF recruitment to DNA or nucleosomes by increasing the reaction velocity a factor of 13 with no accompanying change in substrate affinity (K
M
). The changes in ATP hydrolysis causes an equivalent change in nucleosome movement, confirming they are tightly coupled. The catalytic subunit’s AT-hook is required in vivo for SWI/SNF remodeling activity in yeast and mouse embryonic stem cells. The AT-hook in SWI/SNF is required for transcription regulation and activation of stage-specific enhancers critical in cell lineage priming. Similarly, growth assays suggest the AT-hook is required in yeast SWI/SNF for activation of genes involved in amino acid biosynthesis and metabolizing ethanol. Our findings highlight the importance of studying SWI/SNF attenuation versus eliminating the catalytic subunit or completely shutting down its enzymatic activity.
This study demonstrates that an evolutionary conserved, autoregulatory ‘AT-hook’ domain of SWI/SNF regulates gene transcription and enhancer activation by modulating SWI/SNF intrinsic catalytic activity and is critical for cell lineage priming.
Journal Article
Metabolomics-Based Liquid Biopsy for Predicting Clinically Significant Prostate Cancer
Prostate cancer (PC) remains a major cause of cancer deaths in men. The serum biomarker prostate-specific antigen (PSA) lacks specificity in distinguishing clinically significant PC (sPC) from insignificant PC (isPC), leading to overdiagnosis and overtreatment. Although magnetic resonance imaging (MRI) improves detection, it is expensive, is time-consuming, and may involve inter-reader discrepancies. Recently, metabolomics, which has a high analytical sensitivity and broad molecular-feature coverage, has emerged as a promising tool to risk-stratify PC. This review examined studies of blood and urine metabolomics for sPC biomarker identification. Significant metabolite changes in sPC patients often involved fatty acid metabolism, sphingolipid metabolism, glycolysis, the citric acid cycle, purine/pyrimidine metabolism, and tyrosine/phenylalanine metabolism. Specifically, more than one study reported increased lactate and phenylalanine levels, along with decreased tyrosine, xanthine, and histidine levels, in sPC patients. Several metabolic panels outperformed serum PSA in predicting sPC, particularly when combined with clinical factors. Among these, two urine-based tests may have higher accuracy in predicting sPC than most current commercially available assays. However, direct comparison between studies may be inappropriate due to methodological heterogeneity, the variability in biospecimen types, inconsistent use of digital rectal examinations, and different sPC definitions and predictive endpoints. Most relevant studies were of small sample size or lacked external validation. Despite these challenges, metabolomics-based liquid biopsies show strong potential for improving sPC detection. Future research should focus on protocol standardization, MRI integration, absolute metabolite quantification, and validation in large and independent cohorts to enhance model credibility.
Journal Article
An analysis on the preliminary benefits of aquaculture smart aeration control
Aquaculture in Taiwan is characterised by high breeding densities of up to five times higher than the normal breeding densities. Pollution in the breeding environment and its adjacent waters have exacerbated the occurrence of disease outbreaks in fish, shrimp and shellfish, which greatly impacted the economy. Therefore, the parameters pertaining to water quality status, especially dissolved oxygen are particularly important. In addition to the rising cost of labour, land, infrastructure and other materials, the capital needed to engage in aquaculture has risen, whereas the profits have decreased. This limits the growth of aquaculture and fisheries. To overcome this problem, it is essential to shift towards efficient and ecologically precise smart aquaculture. The application of industrialised and smart systems in the vertical diffusion and in‐depth integration of aquaculture facilitates decision‐making, improves the level of intelligence in breeding, and enhance aquaculture's contribution to Taiwan's economy. The preliminary analysis results have confirmed that the smart aeration control system can instantly identify signal anomalies and trigger field equipment regulations depending on the varied degrees of anomaly andcould maintain field water quality stability by using less energy and manpower costs.
Journal Article
An Embedding Strategy Using Q-Ary Convolutional Codes for Large and Small Payloads
Matrix embedding (ME) code is a commonly used steganography technique, which uses linear block codes to improve embedding efficiency. However, its main disadvantage is the inability to perform maximum likelihood decoding due to the high complexity of decoding large ME codes. As such, it is difficult to improve the embedding efficiency. The proposed q-ary embedding code can provide excellent embedding efficiency and is suitable for various embedding rates (large and small payloads). This article discusses that by using perforation technology, a convolutional code with a high embedding rate can be easily converted into a convolutional code with a low embedding rate. By keeping the embedding rate of the (2, 1) convolutional code unchanged, convolutional codes with different embedding rates can be designed through puncturing.
Journal Article
Prediction of clinically significant prostate cancer through urine metabolomic signatures: A large-scale validated study
Purpose
Currently, there are no accurate markers for predicting potentially lethal prostate cancer (PC) before biopsy. This study aimed to develop urine tests to predict clinically significant PC (sPC) in men at risk.
Methods
Urine samples from 928 men, namely, 660 PC patients and 268 benign subjects, were analyzed by gas chromatography/quadrupole time-of-flight mass spectrophotometry (GC/Q-TOF MS) metabolomic profiling to construct four predictive models. Model I discriminated between PC and benign cases. Models II, III, and GS, respectively, predicted sPC in those classified as having favorable intermediate risk or higher, unfavorable intermediate risk or higher (according to the National Comprehensive Cancer Network risk groupings), and a Gleason sum (GS) of ≥ 7. Multivariable logistic regression was used to evaluate the area under the receiver operating characteristic curves (AUC).
Results
In Models I, II, III, and GS, the best AUCs (0.94, 0.85, 0.82, and 0.80, respectively; training cohort, N = 603) involved 26, 24, 26, and 22 metabolites, respectively. The addition of five clinical risk factors (serum prostate-specific antigen, patient age, previous negative biopsy, digital rectal examination, and family history) significantly improved the AUCs of the models (0.95, 0.92, 0.92, and 0.87, respectively). At 90% sensitivity, 48%, 47%, 50%, and 36% of unnecessary biopsies could be avoided. These models were successfully validated against an independent validation cohort (N = 325). Decision curve analysis showed a significant clinical net benefit with each combined model at low threshold probabilities. Models II and III were more robust and clinically relevant than Model GS.
Conclusion
This urine test, which combines urine metabolic markers and clinical factors, may be used to predict sPC and thereby inform the necessity of biopsy in men with an elevated PC risk.
Journal Article
Nucleosome mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains
The ISWI chromatin remodelers interact with extranucleosomal DNA to mediate nucleosome positioning. A new study now shows that the conserved SLIDE domain in the Isw2 subunit, which binds linker DNA, facilitates unidirectional linker DNA movement into nucleosomes. These findings suggest that the SLIDE domain functions in conjunction with the ATPase domain to mobilize nucleosomes.
The ISWI family of ATP-dependent chromatin remodelers represses transcription by changing nucleosome positions. ISWI regulates nucleosome positioning by requiring a minimal length of extranucleosomal DNA for moving nucleosomes. ISW2 from
Saccharomyces cerevisiae
, a member of the ISWI family, has a conserved domain called SLIDE (SANT-like ISWI domain) that binds to extranucleosomal DNA ~19 base pairs from the edge of nucleosomes. Loss of SLIDE binding does not perturb binding of the ATPase domain or the initial movement of DNA inside of nucleosomes. Not only is extranucleosomal DNA required to help recruit ISW2, but also the interactions of the SLIDE domain with extranucleosomal DNA are functionally required to move nucleosomes.
Journal Article
Eight-Scale Image Contrast Enhancement Based on Adaptive Inverse Hyperbolic Tangent Algorithm
The Eight-Scale parameter adjustment is a natural extension of Adaptive Inverse Hyperbolic Tangent (AIHT) algorithm. It has long been known that the Human Vision System (HVS) heavily depends on detail and edge in the understanding and perception of scenes. The main goal of this study is to produce a contrast enhancement technique to recover an image from blurring and darkness, and at the same time to improve visual quality. Eight-scale coefficient adjustments can provide a further local refinement in detail under the AIHT algorithm. The proposed Eight-Scale Adaptive Inverse Hyperbolic Tangent (8SAIHT) method uses the sub-band to calculate the local mean and local variance before the AIHT algorithm is applied. This study also shows that this approach is convenient and effective in the enhancement processes for various types of images. The 8SAIHT is also capable of adaptively enhancing the local contrast of the original image while simultaneously extruding more on object details.
Journal Article
A Study of Digital Image Enlargement and Enhancement
Most image enlargement techniques suffer the problem of zigzagged edges and jagged images following enlargement. Humans are sensitive to the edges of objects; if the edges in the image are sharp, the visual is considered to be high quality. To solve this problem, this paper presents a new and effective method for image enlargement and enhancement based on adaptive inverse hyperbolic tangent (AIHT) algorithm. Conventional image enlargement and enhancement methods enlarge the image using interpolation, and subsequently enhance the image without considering image features. However, this study presents the method based on Adaptive Inverse Hyperbolic Tangent algorithm to enhance images according to image features before enlarging the image. Experimental results indicate that the proposed algorithm is capable of adaptively enhancing the image and extruding object details, thereby improving enlargements by smoothing the edge of the objects in the image.
Journal Article
Application of Artificial Immune System Approach in MRI Classification
Numerous scholars have submitted the theory and research of artificial immune systems (AISs) in recent years. Although AIS has been used in various fields, applying the AIS to medical images is very rare. The purpose of this study is using the clonal selection algorithm (CSA) of artificial immune systems for classifying the brain MRI, and displaying a single organism image which can finally offer faster organism reference information to a doctor; hence reducing the time to ascertain large number of images, so that the doctor can diagnose the nidus more efficiently and accurately. In order to verify the feasibility and efficiency of this method, we adopt statistical theory for manifold assessment and compare with the perceptron network of double layers, FCM method. The result proves that the method of this study is both feasible and useful.
Journal Article