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  • 1
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    Online Resource
    The east–west division of changing precipitation in Nepal
    Wiley ; 2020
    In:  International Journal of Climatology Vol. 40, No. 7 ( 2020-06-15), p. 3348-3359
    Details
    In: International Journal of Climatology, Wiley, Vol. 40, No. 7 ( 2020-06-15), p. 3348-3359
    Abstract: Changes to precipitation patterns and extremes over the Nepalese Himalayas were examined using a high‐resolution, station‐based daily dataset, Asian Precipitation‐Highly Resolved Observational Data Integration Towards Evaluation (0.05° × 0.05° APHRODITE) from 1951 to 2007. The annual statistics of extreme precipitation across Nepal show a significant increase since the end of the 20th century. However, seasonal mean precipitation shows a remarkable decrease in western Nepal, particularly since 1980, forming an east–west division in the precipitation change. This decreasing trend of precipitation led to a reduction to the dry‐season stream flow of Karnali River, the major river in western Nepal. At the same time, the increasing extreme precipitation produced greater threat of flash flood in Nepal. This east–west division of the precipitation trend agrees with the second leading mode of the mean precipitation variability, which was traced to the interannual variability of the Indian Ocean sea surface temperature that showed a slowdown of warming. Similar to the APHRODITE trends, precipitation simulated by the fifth phase of the Coupled Model Intercomparison Project (CMIP5) models depicted the decreasing historical trend in western Nepal, but future projections reverse that trend towards an all‐Nepal increase. CMIP5 future climate projections depict continual warming in the Indian Ocean, potentially reversing the historical decreasing trends of precipitation in western Nepal.
    Type of Medium: Online Resource
    ISSN: 0899-8418 , 1097-0088
    URL: Issue
    URL: Article
    DOI: 10.1002/joc.v40.7
    DOI: 10.1002/joc.6401
    RVK:
    RA 1000
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 1491204-1
    detail.hit.zdb_id: 1000947-4
    SSG: 14
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  • 2
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    LMNglyPred: prediction of human N -linked glycosylation sites using embeddings from a pre-trained protein language model
    Oxford University Press (OUP) ; 2023
    In:  Glycobiology Vol. 33, No. 5 ( 2023-06-03), p. 411-422
    Details
    In: Glycobiology, Oxford University Press (OUP), Vol. 33, No. 5 ( 2023-06-03), p. 411-422
    Abstract: Protein N-linked glycosylation is an important post-translational mechanism in Homo sapiens, playing essential roles in many vital biological processes. It occurs at the N-X-[S/T] sequon in amino acid sequences, where X can be any amino acid except proline. However, not all N-X-[S/T] sequons are glycosylated; thus, the N-X-[S/T] sequon is a necessary but not sufficient determinant for protein glycosylation. In this regard, computational prediction of N-linked glycosylation sites confined to N-X-[S/T] sequons is an important problem that has not been extensively addressed by the existing methods, especially in regard to the creation of negative sets and leveraging the distilled information from protein language models (pLMs). Here, we developed LMNglyPred, a deep learning-based approach, to predict N-linked glycosylated sites in human proteins using embeddings from a pre-trained pLM. LMNglyPred produces sensitivity, specificity, Matthews Correlation Coefficient, precision, and accuracy of 76.50, 75.36, 0.49, 60.99, and 75.74 percent, respectively, on a benchmark-independent test set. These results demonstrate that LMNglyPred is a robust computational tool to predict N-linked glycosylation sites confined to the N-X-[S/T] sequon.
    Type of Medium: Online Resource
    ISSN: 1460-2423
    URL: Article
    DOI: 10.1093/glycob/cwad033
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1478140-2
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  • 3
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    Improving protein succinylation sites prediction using embeddings from protein language model
    Springer Science and Business Media LLC ; 2022
    In:  Scientific Reports Vol. 12, No. 1 ( 2022-10-08)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2022-10-08)
    Abstract: Protein succinylation is an important post-translational modification (PTM) responsible for many vital metabolic activities in cells, including cellular respiration, regulation, and repair. Here, we present a novel approach that combines features from supervised word embedding with embedding from a protein language model called ProtT5-XL-UniRef50 (hereafter termed, ProtT5) in a deep learning framework to predict protein succinylation sites. To our knowledge, this is one of the first attempts to employ embedding from a pre-trained protein language model to predict protein succinylation sites. The proposed model, dubbed LMSuccSite, achieves state-of-the-art results compared to existing methods, with performance scores of 0.36, 0.79, 0.79 for MCC, sensitivity, and specificity, respectively. LMSuccSite is likely to serve as a valuable resource for exploration of succinylation and its role in cellular physiology and disease.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-022-21366-2
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2615211-3
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  • 4
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    A dosimetric study of volumetric modulated arc therapy planning techniques for treatment of low-risk prostate cancer in patients with bilateral hip prostheses
    Georg Thieme Verlag KG ; 2014
    In:  South Asian Journal of Cancer Vol. 03, No. 01 ( 2014-01), p. 018-021
    Details
    In: South Asian Journal of Cancer, Georg Thieme Verlag KG, Vol. 03, No. 01 ( 2014-01), p. 018-021
    Abstract: Background and Purpose: Recently, megavoltage (MV) photon volumetric modulated arc therapy (VMAT) has gained widespread acceptance as the technique of choice for prostate cancer patients undergoing external beam radiation therapy. However, radiation treatment planning for patients with metallic hip prostheses composed of high-Z materials can be challenging due to (1) presence of streak artifacts from prosthetic hips in computed tomography dataset, and (2) inhomogeneous dose distribution within the target volume. The purpose of this study was to compare the dosimetric quality of VMAT techniques in the form of Rapid Arc (RA) for treating low-risk prostate cancer patient with bilateral prostheses. Materials and Methods: Three treatment plans were created using RA techniques utilizing 2 arcs (2-RA), 3 arcs (3-RA), and 4 arcs (4-RA) for 6 MV photon beam in Eclipse treatment planning system. Each plan was optimized for total dose of 79.2 Gy prescribed to the planning target volume (PTV) over 44 fractions. All three RA plans were calculated with anisotropic analytical algorithm. Results : The mean and maximum doses to the PTV as well as the homogeneity index among all three RA plans were comparable. The plan conformity index was highest in the 2-Arc plan (1.19) and lowest in the 4-Arc plan (1.10). In comparison to the 2-RA technique, the 4-RA technique reduced the doses to rectum by up to 18.8% and to bladder by up to 7.8%. In comparison to the 3-RA technique, the 4-RA technique reduced the doses to rectum by up to 14.6% and to bladder by up to 3.5%. Conclusion: Based on the RA techniques investigated for a low-risk prostate cancer patient with bilateral prostheses, the 4-RA plan produced lower rectal and bladder dose and better dose conformity across the PTV in comparison with the 2-RA and 3-RA plans.
    Type of Medium: Online Resource
    ISSN: 2278-330X , 2278-4306
    URL: Article
    DOI: 10.4103/2278-330X.126506
    Language: English
    Publisher: Georg Thieme Verlag KG
    Publication Date: 2014
    detail.hit.zdb_id: 2719571-5
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  • 5
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    Treatment planning study comparing proton therapy, RapidArc and IMRT for a synchronous bilateral lung cancer case
    International Journal of Cancer Therapy and Oncology ; 2014
    In:  International Journal of Cancer Therapy and Oncology Vol. 2, No. 2 ( 2014-05-14), p. 020216-
    Details
    In: International Journal of Cancer Therapy and Oncology, International Journal of Cancer Therapy and Oncology, Vol. 2, No. 2 ( 2014-05-14), p. 020216-
    Type of Medium: Online Resource
    ISSN: 2330-4049
    URL: Journal
    URL: Article
    DOI: 10.14319/ijcto
    DOI: 10.14319/ijcto.0202.16
    Language: Unknown
    Publisher: International Journal of Cancer Therapy and Oncology
    Publication Date: 2014
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  • 6
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    Dose-to-medium vs. dose-to-water: Dosimetric evaluation of dose reporting modes in Acuros XB for prostate, lung and breast cancer
    International Journal of Cancer Therapy and Oncology ; 2014
    In:  International Journal of Cancer Therapy and Oncology Vol. 2, No. 4 ( 2014-12-13), p. 020421-
    Details
    In: International Journal of Cancer Therapy and Oncology, International Journal of Cancer Therapy and Oncology, Vol. 2, No. 4 ( 2014-12-13), p. 020421-
    Type of Medium: Online Resource
    ISSN: 2330-4049
    URL: Journal
    URL: Article
    DOI: 10.14319/ijcto
    DOI: 10.14319/ijcto.0204.21
    Language: Unknown
    Publisher: International Journal of Cancer Therapy and Oncology
    Publication Date: 2014
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  • 7
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    Evaluation of hybrid inverse planning and optimization (HIPO) algorithm for optimization in real‐time, high‐dose‐rate (HDR) brachytherapy for prostate
    Wiley ; 2013
    In:  Journal of Applied Clinical Medical Physics Vol. 14, No. 4 ( 2013-07), p. 96-107
    Details
    In: Journal of Applied Clinical Medical Physics, Wiley, Vol. 14, No. 4 ( 2013-07), p. 96-107
    Abstract: The purpose of this study is to investigate the effectiveness of the HIPO planning and optimization algorithm for real‐time prostate HDR brachytherapy. This study consists of 20 patients who underwent ultrasound‐based real‐time HDR brachytherapy of the prostate using the treatment planning system called Oncentra Prostate (SWIFT version 3.0). The treatment plans for all patients were optimized using inverse dose‐volume histogram–based optimization followed by graphical optimization (GRO) in real time. The GRO is manual manipulation of isodose lines slice by slice. The quality of the plan heavily depends on planner expertise and experience. The data for all patients were retrieved later, and treatment plans were created and optimized using HIPO algorithm with the same set of dose constraints, number of catheters, and set of contours as in the real‐time optimization algorithm. The HIPO algorithm is a hybrid because it combines both stochastic and deterministic algorithms. The stochastic algorithm, called simulated annealing, searches the optimal catheter distributions for a given set of dose objectives. The deterministic algorithm, called dose‐volume histogram–based optimization (DVHO), optimizes three‐dimensional dose distribution quickly by moving straight downhill once it is in the advantageous region of the search space given by the stochastic algorithm. The PTV receiving 100% of the prescription dose ( ) was 97.56% and 95.38% with GRO and HIPO, respectively. The mean dose ( ) and minimum dose to 10% volume ( ) for the urethra, rectum, and bladder were all statistically lower with HIPO compared to GRO using the student pair t ‐test at 5% significance level. HIPO can provide treatment plans with comparable target coverage to that of GRO with a reduction in dose to the critical structures. PACS number: 87.55.‐X
    Type of Medium: Online Resource
    ISSN: 1526-9914 , 1526-9914
    URL: Article
    DOI: 10.1120/jacmp.v14i4.4198
    Language: English
    Publisher: Wiley
    Publication Date: 2013
    detail.hit.zdb_id: 2010347-5
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  • 8
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    Evaluation of Acuros XB algorithm based on RTOG 0813 dosimetric criteria for SBRT lung treatment with RapidArc
    Wiley ; 2014
    In:  Journal of Applied Clinical Medical Physics Vol. 15, No. 1 ( 2014-01), p. 118-129
    Details
    In: Journal of Applied Clinical Medical Physics, Wiley, Vol. 15, No. 1 ( 2014-01), p. 118-129
    Abstract: The Radiation Therapy Oncology Group (RTOG) 0813 protocol requires the use of dose calculation algorithms with tissue heterogeneity corrections to compute dose on stereotactic body radiation therapy (SBRT) non‐small cell lung cancer (NSCLC) plans. A new photon dose calculation algorithm called Acuros XB (AXB) has recently been implemented in the Eclipse treatment planning system (TPS). The main purpose of this study was to compare the dosimetric results of AXB with that of anisotropic analytical algorithm (AAA) for RTOG 0813 parameters. Additionally, phantom study was done to evaluate the dose prediction accuracy of AXB and AAA beyond low‐density medium of different thicknesses by comparing the calculated results with the measurements. For the RTOG dosimetric study, 14 clinically approved SBRT NSCLC cases were included. The planning target volume (PTV) ranged from 3.2‐43.0 cc. RapidArc treatment plans were generated in the Eclipse TPS following RTOG 0813 dosimetric criteria, and treatment plans were calculated using AAA with heterogeneity correction (AAA plans). All the AAA plans were then recalculated using AXB with heterogeneity correction (AXB plans) for identical beam parameters and same number of monitor units. The AAA and AXB plans were compared for following RTOG 0813 parameters: ratio of prescription isodose volume to PTV (R100%), ratio of 50% prescription isodose volume to PTV (R50%), maximal dose 2 cm from the PTV in any direction as a percentage of prescription dose , and the percentage of ipsilateral lung receiving dose equal to or larger than 20 Gy . The phantom study showed that the results of AXB had better agreement with the measurements, and the difference ranged from to 2.8%. The AAA results showed larger disagreement with the measurements, with differences from 4.1% to 12.5% for field size and from 1.4% to 6.8% for field size . The results from the RTOG SBRT lung cases showed that, on average, the AXB plans produced lower values for R100%, R50%, and by 4.96%, 1.15%, and 1.60%, respectively, but higher of ipsilateral lung by 1.09% when compared with AAA plans. In the set of AAA plans, minor deviation was seen for R100% (six cases), R50% (nine cases), (four cases), and (one case). Similarly, the AXB plans also showed minor deviation for R100% (one case), R50% (eight cases), (three cases), and (one case). The dosimetric results presented in the current study show that both the AXB and AAA can meet the RTOG 0813 dosimetric criteria. PACS number: 87.55.D‐, 87.55.dk, 87.55.kd, 87.55.km
    Type of Medium: Online Resource
    ISSN: 1526-9914 , 1526-9914
    URL: Article
    DOI: 10.1120/jacmp.v15i1.4474
    Language: English
    Publisher: Wiley
    Publication Date: 2014
    detail.hit.zdb_id: 2010347-5
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  • 9
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    Integrating Embeddings from Multiple Protein Language Models to Improve Protein O-GlcNAc Site Prediction
    MDPI AG ; 2023
    In:  International Journal of Molecular Sciences Vol. 24, No. 21 ( 2023-11-06), p. 16000-
    Details
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 24, No. 21 ( 2023-11-06), p. 16000-
    Abstract: O-linked β-N-acetylglucosamine (O-GlcNAc) is a distinct monosaccharide modification of serine (S) or threonine (T) residues of nucleocytoplasmic and mitochondrial proteins. O-GlcNAc modification (i.e., O-GlcNAcylation) is involved in the regulation of diverse cellular processes, including transcription, epigenetic modifications, and cell signaling. Despite the great progress in experimentally mapping O-GlcNAc sites, there is an unmet need to develop robust prediction tools that can effectively locate the presence of O-GlcNAc sites in protein sequences of interest. In this work, we performed a comprehensive evaluation of a framework for prediction of protein O-GlcNAc sites using embeddings from pre-trained protein language models. In particular, we compared the performance of three protein sequence-based large protein language models (pLMs), Ankh, ESM-2, and ProtT5, for prediction of O-GlcNAc sites and also evaluated various ensemble strategies to integrate embeddings from these protein language models. Upon investigation, the decision-level fusion approach that integrates the decisions of the three embedding models, which we call LM-OGlcNAc-Site, outperformed the models trained on these individual language models as well as other fusion approaches and other existing predictors in almost all of the parameters evaluated. The precise prediction of O-GlcNAc sites will facilitate the probing of O-GlcNAc site-specific functions of proteins in physiology and diseases. Moreover, these findings also indicate the effectiveness of combined uses of multiple protein language models in post-translational modification prediction and open exciting avenues for further research and exploration in other protein downstream tasks. LM-OGlcNAc-Site’s web server and source code are publicly available to the community.
    Type of Medium: Online Resource
    ISSN: 1422-0067
    URL: Article
    DOI: 10.3390/ijms242116000
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2019364-6
    SSG: 12
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  • 10
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    Experimental Study: Deep Learning-Based Fall Monitoring among Older Adults with Skin-Wearable Electronics
    MDPI AG ; 2023
    In:  Sensors Vol. 23, No. 8 ( 2023-04-14), p. 3983-
    Details
    In: Sensors, MDPI AG, Vol. 23, No. 8 ( 2023-04-14), p. 3983-
    Abstract: Older adults are more vulnerable to falling due to normal changes due to aging, and their falls are a serious medical risk with high healthcare and societal costs. However, there is a lack of automatic fall detection systems for older adults. This paper reports (1) a wireless, flexible, skin-wearable electronic device for both accurate motion sensing and user comfort, and (2) a deep learning-based classification algorithm for reliable fall detection of older adults. The cost-effective skin-wearable motion monitoring device is designed and fabricated using thin copper films. It includes a six-axis motion sensor and is directly laminated on the skin without adhesives for the collection of accurate motion data. To study accurate fall detection using the proposed device, different deep learning models, body locations for the device placement, and input datasets are investigated using motion data based on various human activities. Our results indicate the optimal location to place the device is the chest, achieving accuracy of more than 98% for falls with motion data from older adults. Moreover, our results suggest a large motion dataset directly collected from older adults is essential to improve the accuracy of fall detection for the older adult population.
    Type of Medium: Online Resource
    ISSN: 1424-8220
    URL: Article
    DOI: 10.3390/s23083983
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2052857-7
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