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  1. Article ; Online: Preoperative overweight and obesity do not cause inferior outcomes following open-wedge high tibial osteotomy: A retrospective cohort study of 123 patients.

    Wu, Cheng-Yi / Huang, Jen-Wei / Lin, Chang-Hao / Chih, Wei-Hsing

    PloS one

    2023  Volume 18, Issue 1, Page(s) e0280687

    Abstract: Open-wedge high tibial osteotomy (OWHTO) is effective in treating medial compartment osteoarthritis. The association between body mass index (BMI) and outcomes following OWHTO is being debated. This study compared radiographic and clinical outcomes ... ...

    Abstract Open-wedge high tibial osteotomy (OWHTO) is effective in treating medial compartment osteoarthritis. The association between body mass index (BMI) and outcomes following OWHTO is being debated. This study compared radiographic and clinical outcomes between patients with preoperative overweight, obesity, and normal BMI following OWHTO for medial compartment osteoarthritis. In total, 123 patients (123 knees) who underwent OWHTO for medial compartment osteoarthritis were enrolled and were divided into normal-BMI (18.5-24.9 kg/m2), overweight (25-29.9 kg/m2), and obese (>30 kg/m2) groups based on body mass index. The numeric rating scale for pain, mechanical tibiofemoral angle (mTFA), tibia tilting angle (TTA), and Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) for function were evaluated preoperatively and at postoperative follow-ups. The improvements of clinical and radiological outcomes in normal-BMI, overweight, and obese groups were not significantly different. The incidence of soft tissue irritation, wound infection, nonunion, and conversion to total knee arthroplasty were not significantly different between groups.The clinical and radiological outcomes in patients with preoperative overweight, obesity, and normal-BMI were not significantly different. Preoperative overweight and obesity thus has no effect on outcomes following OWHTO during the two years follow-up period. These findings cannot be generalized to patients with morbid obesity.
    MeSH term(s) Humans ; Knee Joint/diagnostic imaging ; Knee Joint/surgery ; Osteoarthritis, Knee/diagnostic imaging ; Osteoarthritis, Knee/surgery ; Retrospective Studies ; Overweight/complications ; Tibia/diagnostic imaging ; Tibia/surgery ; Osteotomy/adverse effects ; Obesity/complications ; Obesity/surgery
    Language English
    Publishing date 2023-01-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0280687
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Reductive Degradation of 1,1,1-Trichloroethane with Alkaline Green Tea/Ferrous Ion in Aqueous Phase

    Wu, Siang Chen / Huang, Jen-Wei / Liang, Chenju

    Industrial & engineering chemistry process design and development. 2020 Oct. 20, v. 59, no. 43

    2020  

    Abstract: 1,1,1-Trichloroethane (1,1,1-TCA) is a USEPA Priority Pollutant that has caused serious environmental contamination in the soil and groundwater. This study verified a chemical approach using an alkaline green tea (GT)/Fe²⁺ system at pH 10 to degrade ... ...

    Abstract 1,1,1-Trichloroethane (1,1,1-TCA) is a USEPA Priority Pollutant that has caused serious environmental contamination in the soil and groundwater. This study verified a chemical approach using an alkaline green tea (GT)/Fe²⁺ system at pH 10 to degrade reductively 1,1,1-TCA in an aqueous phase. Evaluation of the effect of GT dosage, Fe²⁺ concentrations, and reaction temperatures on the 1,1,1-TCA degradation through batch-scale experiments revealed that initiation of the degradation process is dependent on the GT/Fe²⁺ dosing ratio, with a minimum polyphenol concentration of 367 mg L–¹ and a polyphenol-to-Fe mass ratio of 0.44. The reductive degradation of 1,1,1-TCA by the alkaline GT/Fe²⁺ system exhibited an initial rapid reaction stage, followed by a slower pseudo-first-order reaction kinetic stage. The highest initial degradation rate and fitted rate constant observed in this study were 0.106 mM h–¹ and 0.046 h–¹, respectively. The polyphenol–Fe complexes, especially epigallocatechin gallate (EGCG) Fe²⁺/Fe³⁺, were expected to trigger the reductive degradation of 1,1,1-TCA via interactions between GT and Fe. Ethane was generated as the major end product through the reductive dehalogenation route with 1,1-dichloroethane and chloroethane as intermediate products. This study demonstrated the potential of the alkaline GT/Fe²⁺ system as a chemical reductive treatment of recalcitrant chlorinated solvents.
    Keywords United States Environmental Protection Agency ; dehalogenation ; epigallocatechin gallate ; ethane ; green tea ; groundwater ; pH ; pollutants ; pollution ; polyphenols ; process design ; soil
    Language English
    Dates of publication 2020-1020
    Size p. 19093-19101.
    Publishing place American Chemical Society
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 1484436-9
    ISSN 1520-5045 ; 0888-5885
    ISSN (online) 1520-5045
    ISSN 0888-5885
    DOI 10.1021/acs.iecr.0c03443
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: TADILOF: Time Aware Density-Based Incremental Local Outlier Detection in Data Streams.

    Huang, Jen-Wei / Zhong, Meng-Xun / Jaysawal, Bijay Prasad

    Sensors (Basel, Switzerland)

    2020  Volume 20, Issue 20

    Abstract: Outlier detection in data streams is crucial to successful data mining. However, this task is made increasingly difficult by the enormous growth in the quantity of data generated by the expansion of Internet of Things (IoT). Recent advances in outlier ... ...

    Abstract Outlier detection in data streams is crucial to successful data mining. However, this task is made increasingly difficult by the enormous growth in the quantity of data generated by the expansion of Internet of Things (IoT). Recent advances in outlier detection based on the density-based local outlier factor (LOF) algorithms do not consider variations in data that change over time. For example, there may appear a new cluster of data points over time in the data stream. Therefore, we present a novel algorithm for streaming data, referred to as time-aware density-based incremental local outlier detection (TADILOF) to overcome this issue. In addition, we have developed a means for estimating the LOF score, termed "approximate LOF," based on historical information following the removal of outdated data. The results of experiments demonstrate that TADILOF outperforms current state-of-the-art methods in terms of AUC while achieving similar performance in terms of execution time. Moreover, we present an application of the proposed scheme to the development of an air-quality monitoring system.
    Language English
    Publishing date 2020-10-15
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2052857-7
    ISSN 1424-8220 ; 1424-8220
    ISSN (online) 1424-8220
    ISSN 1424-8220
    DOI 10.3390/s20205829
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  4. Article ; Online: Finding Possible Promoter Binding Sites in DNA Sequences by Sequential Patterns Mining With Specific Numbers of Gaps.

    Ke, Yu-Hao / Huang, Jen-Wei / Lin, Wei-Chen / Jaysawal, Bijay Prasad

    IEEE/ACM transactions on computational biology and bioinformatics

    2021  Volume 18, Issue 6, Page(s) 2459–2470

    Abstract: Identifying motifs in promoter regions is crucial to our understanding of transcription regulation. Researchers commonly use known promoter features in a variety of species to predict promoter motifs. However the results are not particularly useful. ... ...

    Abstract Identifying motifs in promoter regions is crucial to our understanding of transcription regulation. Researchers commonly use known promoter features in a variety of species to predict promoter motifs. However the results are not particularly useful. Different species rarely have similar features in promoter binding sites. In this study, we adopt sequence analysis techniques to find the possible promoter binding sites among different species. We sought to improve the existing algorithm to suit the task of mining sequential patterns with specific number of gaps. Moreover, we discuss the implementation of proposed method in a distributed environment. The proposed method finds the transcription start sites (TSS) and extracts possible promoter regions from DNA sequences according to TSS. We derived the motifs in the possible promoter regions, while taking into account the number of gaps in the motifs to deal with unimportant nucleotides. The motifs generated from promoter regions using the proposed methodology were shown to tolerate unimportant nucleotides. A comparison with known promoter motifs verified the efficacy of the proposed method.
    MeSH term(s) Algorithms ; Base Sequence/genetics ; Binding Sites/genetics ; Computational Biology/methods ; Data Mining ; Promoter Regions, Genetic/genetics ; Sequence Analysis, DNA/methods
    Language English
    Publishing date 2021-12-08
    Publishing country United States
    Document type Journal Article
    ISSN 1557-9964
    ISSN (online) 1557-9964
    DOI 10.1109/TCBB.2020.2980234
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Mechanism of DNA unwinding by MCM8-9 in complex with HROB.

    Acharya, Ananya / Bret, Hélène / Huang, Jen-Wei / Mütze, Martin / Göse, Martin / Kissling, Vera Maria / Seidel, Ralf / Ciccia, Alberto / Guérois, Raphaël / Cejka, Petr

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 3584

    Abstract: HROB promotes the MCM8-9 helicase in DNA damage response. To understand how HROB activates MCM8-9, we defined their interaction interface. We showed that HROB makes important yet transient contacts with both MCM8 and MCM9, and binds the MCM8-9 ... ...

    Abstract HROB promotes the MCM8-9 helicase in DNA damage response. To understand how HROB activates MCM8-9, we defined their interaction interface. We showed that HROB makes important yet transient contacts with both MCM8 and MCM9, and binds the MCM8-9 heterodimer with the highest affinity. MCM8-9-HROB prefer branched DNA structures, and display low DNA unwinding processivity. MCM8-9 unwinds DNA as a hexamer that assembles from dimers on DNA in the presence of ATP. The hexamer involves two repeating protein-protein interfaces between the alternating MCM8 and MCM9 subunits. One of these interfaces is quite stable and forms an obligate heterodimer across which HROB binds. The other interface is labile and mediates hexamer assembly, independently of HROB. The ATPase site formed at the labile interface contributes disproportionally more to DNA unwinding than that at the stable interface. Here, we show that HROB promotes DNA unwinding downstream of MCM8-9 loading and ring formation on ssDNA.
    MeSH term(s) Minichromosome Maintenance Proteins/metabolism ; Minichromosome Maintenance Proteins/genetics ; Humans ; DNA, Single-Stranded/metabolism ; Protein Binding ; DNA/metabolism ; DNA/chemistry ; DNA-Binding Proteins/metabolism ; Adenosine Triphosphate/metabolism ; Protein Multimerization
    Chemical Substances Minichromosome Maintenance Proteins (EC 3.6.4.12) ; DNA, Single-Stranded ; DNA (9007-49-2) ; DNA-Binding Proteins ; Adenosine Triphosphate (8L70Q75FXE) ; MCM8 protein, human (EC 3.6.4.12) ; MCM9 protein, human (EC 3.6.4.12)
    Language English
    Publishing date 2024-04-27
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-47936-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Time for remodeling: SNF2-family DNA translocases in replication fork metabolism and human disease.

    Joseph, Sarah A / Taglialatela, Angelo / Leuzzi, Giuseppe / Huang, Jen-Wei / Cuella-Martin, Raquel / Ciccia, Alberto

    DNA repair

    2020  Volume 95, Page(s) 102943

    Abstract: Over the course of DNA replication, DNA lesions, transcriptional intermediates and protein-DNA complexes can impair the progression of replication forks, thus resulting in replication stress. Failure to maintain replication fork integrity in response to ... ...

    Abstract Over the course of DNA replication, DNA lesions, transcriptional intermediates and protein-DNA complexes can impair the progression of replication forks, thus resulting in replication stress. Failure to maintain replication fork integrity in response to replication stress leads to genomic instability and predisposes to the development of cancer and other genetic disorders. Multiple DNA damage and repair pathways have evolved to allow completion of DNA replication following replication stress, thus preserving genomic integrity. One of the processes commonly induced in response to replication stress is fork reversal, which consists in the remodeling of stalled replication forks into four-way DNA junctions. In normal conditions, fork reversal slows down replication fork progression to ensure accurate repair of DNA lesions and facilitates replication fork restart once the DNA lesions have been removed. However, in certain pathological situations, such as the deficiency of DNA repair factors that protect regressed forks from nuclease-mediated degradation, fork reversal can cause genomic instability. In this review, we describe the complex molecular mechanisms regulating fork reversal, with a focus on the role of the SNF2-family fork remodelers SMARCAL1, ZRANB3 and HLTF, and highlight the implications of fork reversal for tumorigenesis and cancer therapy.
    MeSH term(s) DNA/metabolism ; DNA Helicases/metabolism ; DNA Repair ; DNA Replication ; DNA-Binding Proteins/metabolism ; Genomic Instability ; Humans ; Transcription Factors/metabolism
    Chemical Substances DNA-Binding Proteins ; HLTF protein, human ; Transcription Factors ; DNA (9007-49-2) ; SMARCAL1 protein, human (EC 2.7.7.-) ; DNA Helicases (EC 3.6.4.-) ; ZRANB3 protein, human (EC 3.6.4.-)
    Language English
    Publishing date 2020-08-15
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 2071608-4
    ISSN 1568-7856 ; 1568-7864
    ISSN (online) 1568-7856
    ISSN 1568-7864
    DOI 10.1016/j.dnarep.2020.102943
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  7. Article: Mechanism of DNA unwinding by hexameric MCM8-9 in complex with HROB.

    Acharya, Ananya / Bret, Hélène / Huang, Jen-Wei / Mütze, Martin / Göse, Martin / Kissling, Vera / Seidel, Ralf / Ciccia, Alberto / Guérois, Raphaël / Cejka, Petr

    Research square

    2023  

    Abstract: The human MCM8-9 helicase functions in concert with HROB in the context of homologous recombination, but its precise function is unknown. To gain insights into how HROB regulates MCM8-9, we first used molecular modeling and biochemistry to define their ... ...

    Abstract The human MCM8-9 helicase functions in concert with HROB in the context of homologous recombination, but its precise function is unknown. To gain insights into how HROB regulates MCM8-9, we first used molecular modeling and biochemistry to define their interaction interface. We show that HROB makes important contacts with both MCM8 and MCM9 subunits, which directly promotes its DNA-dependent ATPase and helicase activities. MCM8-9-HROB preferentially binds and unwinds branched DNA structures, and single-molecule experiments reveal a low DNA unwinding processivity. MCM8-9 unwinds DNA as a hexameric complex that assembles from dimers on DNA in the presence of ATP, which is prerequisite for its helicase function. The hexamer formation thus involves two repeating protein-protein interfaces forming between the alternating MCM8 and MCM9 subunits. One of these interfaces is rather stable and forms an obligate heterodimer, while the other interface is labile and mediates the assembly of the hexamer on DNA, independently of HROB. The ATPase site composed of the subunits forming the labile interface disproportionally contributes to DNA unwinding. HROB does not affect the MCM8-9 ring formation, but promotes DNA unwinding downstream by possibly coordinating ATP hydrolysis with structural transitions accompanying translocation of MCM8-9 on DNA.
    Language English
    Publishing date 2023-06-26
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-3054483/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Mechanism of DNA unwinding by hexameric MCM8-9 in complex with HROB.

    Acharya, Ananya / Bret, Hélène / Huang, Jen-Wei / Mütze, Martin / Göse, Martin / Kissling, Vera / Seidel, Ralf / Ciccia, Alberto / Guérois, Raphaël / Cejka, Petr

    bioRxiv : the preprint server for biology

    2023  

    Abstract: The human MCM8-9 helicase functions in concert with HROB in the context of homologous recombination, but its precise function is unknown. To gain insights into how HROB regulates MCM8-9, we first used molecular modeling and biochemistry to define their ... ...

    Abstract The human MCM8-9 helicase functions in concert with HROB in the context of homologous recombination, but its precise function is unknown. To gain insights into how HROB regulates MCM8-9, we first used molecular modeling and biochemistry to define their interaction interface. We show that HROB makes important contacts with both MCM8 and MCM9 subunits, which directly promotes its DNA-dependent ATPase and helicase activities. MCM8-9-HROB preferentially binds and unwinds branched DNA structures, and single-molecule experiments reveal a low DNA unwinding processivity. MCM8-9 unwinds DNA as a hexameric complex that assembles from dimers on DNA in the presence of ATP, which is prerequisite for its helicase function. The hexamer formation thus involves two repeating protein-protein interfaces forming between the alternating MCM8 and MCM9 subunits. One of these interfaces is rather stable and forms an obligate heterodimer, while the other interface is labile and mediates the assembly of the hexamer on DNA, independently of HROB. The ATPase site composed of the subunits forming the labile interface disproportionally contributes to DNA unwinding. HROB does not affect the MCM8-9 ring formation, but promotes DNA unwinding downstream by possibly coordinating ATP hydrolysis with structural transitions accompanying translocation of MCM8-9 on DNA.
    Language English
    Publishing date 2023-06-12
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.06.12.544631
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: REV1-Polζ maintains the viability of homologous recombination-deficient cancer cells through mutagenic repair of PRIMPOL-dependent ssDNA gaps

    Taglialatela, Angelo / Leuzzi, Giuseppe / Sannino, Vincenzo / Cuella-Martin, Raquel / Huang, Jen-Wei / Wu-Baer, Foon / Baer, Richard / Costanzo, Vincenzo / Ciccia, Alberto

    Molecular cell. 2021 Oct. 07, v. 81, no. 19

    2021  

    Abstract: BRCA1/2 mutant tumor cells display an elevated mutation burden, the etiology of which remains unclear. Here, we report that these cells accumulate ssDNA gaps and spontaneous mutations during unperturbed DNA replication due to repriming by the DNA primase- ...

    Abstract BRCA1/2 mutant tumor cells display an elevated mutation burden, the etiology of which remains unclear. Here, we report that these cells accumulate ssDNA gaps and spontaneous mutations during unperturbed DNA replication due to repriming by the DNA primase-polymerase PRIMPOL. Gap accumulation requires the DNA glycosylase SMUG1 and is exacerbated by depletion of the translesion synthesis (TLS) factor RAD18 or inhibition of the error-prone TLS polymerase complex REV1-Polζ by the small molecule JH-RE-06. JH-RE-06 treatment of BRCA1/2-deficient cells results in reduced mutation rates and PRIMPOL- and SMUG1-dependent loss of viability. Through cellular and animal studies, we demonstrate that JH-RE-06 is preferentially toxic toward HR-deficient cancer cells. Furthermore, JH-RE-06 remains effective toward PARP inhibitor (PARPi)-resistant BRCA1 mutant cells and displays additive toxicity with crosslinking agents or PARPi. Collectively, these studies identify a protective and mutagenic role for REV1-Polζ in BRCA1/2 mutant cells and provide the rationale for using REV1-Polζ inhibitors to treat BRCA1/2 mutant tumors.
    Keywords DNA glycosylases ; DNA replication ; animals ; crosslinking ; etiology ; mutagens ; mutants ; neoplasms ; toxicity ; tumor suppressor proteins ; viability
    Language English
    Dates of publication 2021-1007
    Size p. 4008-4025.e7.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2021.08.016
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  10. Article: Using land-use machine learning models to estimate daily NO2 concentration variations in Taiwan

    Wong, Pei-Yi / Su, Huey-Jen / Lee, Hsiao-Yun / Chen, Yu-Cheng / Hsiao, Ya-Ping / Huang, Jen-Wei / Teo, Tee-Ann / Wu, Chih-Da / Spengler, John D.

    Journal of cleaner production. 2021 Oct. 01, v. 317

    2021  

    Abstract: It is likely that exposure surrogates from monitoring stations with various limitations are not sufficient for epidemiological studies covering large areas. Moreover, the spatiotemporal resolution of air pollution modelling approaches must be improved in ...

    Abstract It is likely that exposure surrogates from monitoring stations with various limitations are not sufficient for epidemiological studies covering large areas. Moreover, the spatiotemporal resolution of air pollution modelling approaches must be improved in order to achieve more accurate estimates. If not, the exposure assessments will not be applicable in future health risk assessments. To deal with this challenge, this study featured Land-Use Regression (LUR) models that use machine learning to assess the spatial-temporal variability of Nitrogen Dioxide (NO₂). Daily average NO₂ data was collected from 70 fixed air quality monitoring stations, belonging to the Taiwanese EPA, on the main island of Taiwan. Around 0.41 million observations from 2000 to 2016 were used for the analysis. Several datasets were employed to determine spatial predictor variables, including the EPA environmental resources dataset, the meteorological dataset, the land-use inventory, the landmark dataset, the digital road network map, the digital terrain model, MODIS Normalized Difference Vegetation Index database, and the power plant distribution dataset. Regarding analyses, conventional LUR and Hybrid Kriging-LUR were performed first to identify important predictor variables. A Deep Neural Network, Random Forest, and XGBoost algorithms were then used to fit the prediction model based on the variables selected by the LUR models. Lastly, data splitting, 10-fold cross validation, external data verification, and seasonal-based and county-based validation methods were applied to verify the robustness of the developed models. The results demonstrated that the proposed conventional LUR and Hybrid Kriging-LUR models captured 65% and 78%, respectively, of NO₂ variation. When the XGBoost algorithm was further incorporated in LUR and hybrid-LUR, the explanatory power increased to 84% and 91%, respectively. The Hybrid Kriging-LUR with XGBoost algorithm outperformed all other integrated methods. This study demonstrates the value of combining Hybrid Kriging-LUR model and an XGBoost algorithm to estimate the spatial-temporal variability of NO₂ exposure. For practical application, the associations of specific land-use/land cover types selected in the final model can be applied in land-use management and in planning emission reduction strategies.
    Keywords air pollution ; air quality ; algorithms ; data collection ; databases ; hybrids ; inventories ; landscapes ; models ; nitrogen dioxide ; population distribution ; power plants ; risk ; roads ; Taiwan
    Language English
    Dates of publication 2021-1001
    Publishing place Elsevier Ltd
    Document type Article
    ISSN 0959-6526
    DOI 10.1016/j.jclepro.2021.128411
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