Browsing by Author "Jiang, Wei"

Now showing 1 - 5 of 5
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    CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed
    (American Chemical Society, 2024) Hwang, Wonmuk; Austin, Steven L.; Blondel, Arnaud; Boittier, Eric D.; Boresch, Stefan; Buck, Matthias; Buckner, Joshua; Caflisch, Amedeo; Chang, Hao-Ting; Cheng, Xi; Choi, Yeol Kyo; Chu, Jhih-Wei; Crowley, Michael F.; Cui, Qiang; Damjanovic, Ana; Deng, Yuqing; Devereux, Mike; Ding, Xinqiang; Feig, Michael F.; Gao, Jiali; Glowacki, David R.; Gonzales, James E., II; Hamaneh, Mehdi Bagerhi; Harder, Edward D.; Hayes, Ryan L.; Huang, Jing; Huang, Yandong; Hudson, Phillip S.; Im, Wonpil; Islam, Shahidul M.; Jiang, Wei; Jones, Michael R.; Käser, Silvan; Kearns, Fiona L.; Kern, Nathan R.; Klauda, Jeffery B.; Lazaridis, Themis; Lee, Jinhyuk; Lemkul, Justin A.; Liu, Xiaorong; Luo, Yun; MacKerell, Alexander D., Jr.; Major, Dan T.; Meuwly, Markus; Nam, Kwangho; Nilsson, Lennart; Ovchinnikov, Victor; Paci, Emanuele; Park, Soohyung; Pastor, Richard W.; Pittman, Amanda R.; Post, Carol Beth; Prasad, Samarjeet; Pu, Jingzhi; Qi, Yifei; Rathinavelan, Thenmalarchelvi; Roe, Daniel R.; Roux, Benoit; Rowley, Christopher N.; Shen, Jana; Simmonett, Andrew C.; Sodt, Alexander J.; Töpfer, Kai; Upadhyay, Meenu; van der Vaart, Arjan; Vazquez-Salazar, Luis Itza; Venable, Richard M.; Warrensford, Luke C.; Woodcock, H. Lee; Wu, Yujin; Brooks, Charles L., III; Brooks, Bernard R.; Karplus, Martin; Chemistry and Chemical Biology, School of Science
    Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.
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    COVID-19 Epidemic Peer Support and Crisis Intervention Via Social Media
    (Springer Nature, 2020-05-06) Cheng, Pu; Xia, Guohua; Pang, Peng; Wu, Bo; Jiang, Wei; Li, Yong-Tong; Wang, Mei; Ling, Qi; Chang, Xiaoying; Wang, Jinghan; Dai, Xiaocheng; Lin, Xiaojin; Bi, Xiaoting; Psychiatry, School of Medicine
    This article describes a peer support project developed and carried out by a group of experienced mental health professionals, organized to offer peer psychological support from overseas to healthcare professionals on the frontline of the COVID-19 outbreak in Wuhan, China. This pandemic extremely challenged the existing health care systems and caused severe mental distress to frontline healthcare workers. The authors describe the infrastructure of the team and a novel model of peer support and crisis intervention that utilized a popular social media application on smartphone. Such a model for intervention that can be used elsewhere in the face of current global pandemic, or future disaster response.
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    Satellite observations reveal decreasing soil erosion in Northeast Inner Mongolia, China, over the past four decades
    (Frontiers Media, 2022) Jiang, Wei; Pang, Zhiguo; Lv, Juan; Ju, Hongrun; Li, Lin; Fu, June; Earth and Environmental Sciences, School of Science
    Knowledge regarding the soil erosion change patterns in Northeast Inner Mongolia (NIM) is essential for ecological security and sustainable development. Multisource satellite remote sensing with auxiliary data, including meteorology, land use, vegetation coverage, and digital elevation, was collected to establish a distributed soil erosion model to quantify the soil erosion intensity in Northeast Inner Mongolia. The results showed that soil erosion in Northeast Inner Mongolia, China, decreased by 100,654 km2 from 1978 to 2018. The area change rates of the mild, moderate, strong, intensive and severe soil erosion intensities were −48.91%, −41.41%, 32.63%, −91.15%, and −91.14%, respectively. The decrease in soil erosion was mainly located in the Hulunbuir and Tongliao regions. Our findings from satellite observations provide information about the soil erosion intensity and spatial distribution required for policy-making and the management of soil erosion prevention in Northeast Inner Mongolia.
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    Splenic-vasculature involvement is associated with poor prognosis in resected distal pancreatic cancer
    (Oxford University Press, 2020-11-24) Yin, Feng; Saad, Mohammed; Lin, Jingmei; Jackson, Christopher R.; Ren, Bing; Lawson, Cynthia; Karamchandani, Dipti M.; Bernabeu, Belen Quereda; Jiang, Wei; Dhir, Teena; Zheng, Richard; Schultz, Christopher W.; Zhang, Dongwei; Thomas, Courtney L.; Zhang, Xuchen; Lai, Jinping; Schild, Michael; Zhang, Xuefeng; Xie, Hao; Liu, Xiuli; Pathology and Laboratory Medicine, School of Medicine
    Background: Distal pancreatic carcinoma is one of the most lethal cancers largely due to its high incidence of distant metastasis. This study aims to assess the prognostic value of splenic-vasculature involvement in resected distal pancreatic carcinoma. Methods: In this retrospective study, we collected the clinicopathologic information of 454 patients with pancreatic cancer and performed univariate and multivariate analyses to identify factors associated with progression-free survival (PFS) and overall survival (OS), with an emphasis on the prognostic value of splenic-artery and -vein involvement. Results: Univariate analysis revealed that larger tumor size, non-intraductal papillary mucinous neoplasm (non-IPMN)-associated adenocarcinoma, poor differentiation, stage pT3, nodal metastasis, lymphovascular invasion, perineural invasion, and pathologic and radiographic evidence of splenic-vein invasion were significantly associated with shorter PFS and OS (all P < 0.05). Multivariate analysis confirmed non-IPMN-associated adenocarcinoma, stage pT3, stage pN1-2, and post-operative adjuvant chemotherapy as independent risk factors for both PFS and OS, and larger tumor size and radiographic evidence of splenic-artery invasion as predictors of PFS only. Conclusion: Guidelines should be developed for a uniform approach with regard to the examination and reporting of the status of the splenic vasculature when dealing with distal-pancreatic-cancer specimens.
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    Validation of American Joint Committee on Cancer 8th edition of TNM staging in resected distal pancreatic cancer
    (Baishideng, 2020-06-09) Yin, Feng; Saad, Mohammed; Xie, Hao; Lin, Jingmei; Jackson, Christopher R.; Ren, Bing; Lawson, Cynthia; Karamchandani, Dipti M.; Bernabeu, Belen Quereda; Jiang, Wei; Dhir, Teena; Zheng, Richard; Schultz, Christopher W.; Zhang, Dongwei; Thomas, Courtney L.; Zhang, Xuchen; Lai, Jinping; Schild, Michael; Zhang, Xuefeng; Liu, Xiuli; Medicine, School of Medicine
    BACKGROUND In order to improve risk stratification and clinical management of the pancreatic ductal adenocarcinoma (PDAC), the American Joint Committee on Cancer (AJCC) has published its eighth edition staging manual. Some major changes have been introduced in the new staging system for both T and N categories. Given the rarity of resectable disease, distal pancreatic cancer is likely underrepresented in the published clinical studies, and how the impact of the staging system actually reflects on to clinical outcomes remain unclear. AIM To validate the AJCC 8th edition of TNM staging in distal PDAC. METHODS A retrospective cohort study was performed in seven academic medical centers in the United States. Clinicopathological prognostic factors associated with progression-free survival (PFS) and overall survival (OS) were evaluated through univariate and multivariate analyses. RESULTS Overall, 454 patients were enrolled in the study, and were divided into 2 subgroups: Invasive intraductal papillary mucinous neoplasms (IPMN) (115 cases) and non-IPMN associated adenocarcinoma (339 cases). Compared to invasive IPMN, non-IPMN associated adenocarcinomas are more common in relatively younger patients, have larger tumor size, are more likely to have positive lymph nodes, and are associated with a higher tumor (T) stage and nodal (N) stage, lymphovascular invasion, perineural invasion, tumor recurrence, and a worse PFS and OS. The cohort was predominantly categorized as stage 3 per AJCC 7th edition staging manual, and it’s more evenly distributed based on 8th edition staging manual. T and N staging of both 7th and 8th edition sufficiently stratify PFS and OS in the entire cohort, although dividing into N1 and N2 according to the 8th edition does not show additional stratification. For PDAC arising in IPMN, T staging of the 7th edition and N1/N2 staging of the 8th edition appear to further stratify PFS and OS. For PDAC without an IPMN component, T staging from both versions fails to stratify PFS and OS. CONCLUSION The AJCC 8th edition TNM staging system provides even distribution for the T staging, however, it does not provide better risk stratification than previous staging system for distal pancreatic cancer.