Browsing by Author "Li, Jing"

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  • Application of GIS and RS in Abandoned Land Surveying: A Case Study in Shandong, China
    Li, Jing; Liu, Zishang; Li, Wenyu (2014)
    For the acute contradiction between land and people, cherishing and reasonable using per inch land is a persistent national policy in China, whereas land damage is unavoidable in mining, construction and other activity. There is still a lot of abandoned land unused and with no obligator in China, which will have to be the government’s responsibility to survey, plan how to use them and to complete recovering them. For the abandoned land damage always occurred minimally 25 years ago, it is hard to find their information which is truly needed to make clear how much, when and where to reclaim them. Focus on that problem, we proposed a method to find and capture the abandoned land information, which is based on social surveying methods, but featured with GIS and RS. The method was used in Shandong Province. Result showed there are totally 15,751 units and 76,088 ha abandoned land, distributed in 15 cities. Among that, subsided land, digging land and occupied land are 23,981ha, 4154ha and 4,471ha respectively. The conclusion is that based on social survey data, GIS overlapping analysis function and RS method are effective to identified the location, specific damaged time, land use status and so on. As the project is just on the beginning stage, there are still further study on the monitoring and evaluation of self-rehabilitation status of abandoned land.
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    Black-White Disparity in Student Loan Debt More Than Triples After Graduation
    Scott-Clayton, Judith; Li, Jing (The Brookings Institution, 2016-10-20)
    The moment they earn their bachelor’s degrees, black college graduates owe $7,400 more on average than their white peers ($23,400 versus $16,000, including non-borrowers in the averages). But over the next few years, the black-white debt gap more than triples to a whopping $25,000. Differences in interest accrual and graduate school borrowing lead to black graduates holding nearly $53,000 in student loan debt four years after graduation—almost twice as much as their white counterparts. While previous work has documented racial disparities in student borrowing, delinquencies, and defaults, in this report we provide new evidence that racial gaps in total debt are far larger than even recent reports have recognized, far larger now than in the past, and correlated with troubling trends in the economy and in the for-profit sector. The authors conclude with a discussion of policy implications.
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    Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
    Menden, Michael P.; Wang, Dennis; Mason, Mike J.; Szalai, Bence; Bulusu, Krishna C.; Guan, Yuanfang; Yu, Thomas; Kang, Jaewoo; Jeon, Minji; Wolfinger, Russ; Nguyen, Tin; Zaslavskiy, Mikhail; Jang, In Sock; Ghazoui, Zara; Ahsen, Mehmet Eren; Vogel, Robert; Neto, Elias Chaibub; Norman, Thea; Tang, Eric K. Y.; Garnett, Mathew J.; Di Veroli, Giovanni Y.; Fawell, Stephen; Stolovitzky, Gustavo; Guinney, Justin; Dry, Jonathan R.; Saez-Rodriguez, Julio; Abante, Jordi; Abecassis, Barbara Schmitz; Aben, Nanne; Aghamirzaie, Delasa; Aittokallio, Tero; Akhtari, Farida S.; Al-lazikani, Bissan; Alam, Tanvir; Allam, Amin; Allen, Chad; de Almeida, Mariana Pelicano; Altarawy, Doaa; Alves, Vinicius; Amadoz, Alicia; Anchang, Benedict; Antolin, Albert A.; Ash, Jeremy R.; Romeo Aznar, Victoria; Ba-alawi, Wail; Bagheri, Moeen; Bajic, Vladimir; Ball, Gordon; Ballester, Pedro J.; Baptista, Delora; Bare, Christopher; Bateson, Mathilde; Bender, Andreas; Bertrand, Denis; Wijayawardena, Bhagya; Boroevich, Keith A.; Bosdriesz, Evert; Bougouffa, Salim; Bounova, Gergana; Brouwer, Thomas; Bryant, Barbara; Calaza, Manuel; Calderone, Alberto; Calza, Stefano; Capuzzi, Stephen; Carbonell-Caballero, Jose; Carlin, Daniel; Carter, Hannah; Castagnoli, Luisa; Celebi, Remzi; Cesareni, Gianni; Chang, Hyeokyoon; Chen, Guocai; Chen, Haoran; Chen, Huiyuan; Cheng, Lijun; Chernomoretz, Ariel; Chicco, Davide; Cho, Kwang-Hyun; Cho, Sunghwan; Choi, Daeseon; Choi, Jaejoon; Choi, Kwanghun; Choi, Minsoo; De Cock, Martine; Coker, Elizabeth; Cortes-Ciriano, Isidro; Cserzo, Miklos; Cubuk, Cankut; Curtis, Christina; Van Daele, Dries; Dang, Cuong C.; Dijkstra, Tjeerd; Dopazo, Joaquin; Draghici, Sorin; Drosou, Anastasios; Dumontier, Michel; Ehrhart, Friederike; Eid, Fatma-Elzahraa; ElHefnawi, Mahmoud; Elmarakeby, Haitham A.; van Engelen, Bo; Engin, Hatice Billur; de Esch, Iwan; Evelo, Chris; Falcao, Andre O.; Farag, Sherif; Fernandez-Lozano, Carlos; Fisch, Kathleen; Flobak, Asmund; Fornari, Chiara; Foroushani, Amir B. K.; Fotso, Donatien Chedom; Fourches, Denis; Friend, Stephen; Frigessi, Arnoldo; Gao, Feng; Gao, Xiaoting; Gerold, Jeffrey M.; Gestraud, Pierre; Ghosh, Samik; Gillberg, Jussi; Godoy-Lorite, Antonia; Godynyuk, Lizzy; Godzik, Adam; Goldenberg, Anna; Gomez-Cabrero, David; Gonen, Mehmet; de Graaf, Chris; Gray, Harry; Grechkin, Maxim; Guimera, Roger; Guney, Emre; Haibe-Kains, Benjamin; Han, Younghyun; Hase, Takeshi; He, Di; He, Liye; Heath, Lenwood S.; Hellton, Kristoffer H.; Helmer-Citterich, Manuela; Hidalgo, Marta R.; Hidru, Daniel; Hill, Steven M.; Hochreiter, Sepp; Hong, Seungpyo; Hovig, Eivind; Hsueh, Ya-Chih; Hu, Zhiyuan; Huang, Justin K.; Huang, R. Stephanie; Hunyady, Laszlo; Hwang, Jinseub; Hwang, Tae Hyun; Hwang, Woochang; Hwang, Yongdeuk; Isayev, Olexandr; Walk, Oliver Bear Don't; Jack, John; Jahandideh, Samad; Ji, Jiadong; Jo, Yousang; Kamola, Piotr J.; Kanev, Georgi K.; Karacosta, Loukia; Karimi, Mostafa; Kaski, Samuel; Kazanov, Marat; Khamis, Abdullah M.; Khan, Suleiman Ali; Kiani, Narsis A.; Kim, Allen; Kim, Jinhan; Kim, Juntae; Kim, Kiseong; Kim, Kyung; Kim, Sunkyu; Kim, Yongsoo; Kim, Yunseong; Kirk, Paul D. W.; Kitano, Hiroaki; Klambauer, Gunter; Knowles, David; Ko, Melissa; Kohn-Luque, Alvaro; Kooistra, Albert J.; Kuenemann, Melaine A.; Kuiper, Martin; Kurz, Christoph; Kwon, Mijin; van Laarhoven, Twan; Laegreid, Astrid; Lederer, Simone; Lee, Heewon; Lee, Jeon; Lee, Yun Woo; Leppaho, Eemeli; Lewis, Richard; Li, Jing; Li, Lang; Liley, James; Lim, Weng Khong; Lin, Chieh; Liu, Yiyi; Lopez, Yosvany; Low, Joshua; Lysenko, Artem; Machado, Daniel; Madhukar, Neel; De Maeyer, Dries; Malpartida, Ana Belen; Mamitsuka, Hiroshi; Marabita, Francesco; Marchal, Kathleen; Marttinen, Pekka; Mason, Daniel; Mazaheri, Alireza; Mehmood, Arfa; Mehreen, Ali; Michaut, Magali; Miller, Ryan A.; Mitsopoulos, Costas; Modos, Dezso; Van Moerbeke, Marijke; Moo, Keagan; Motsinger-Reif, Alison; Movva, Rajiv; Muraru, Sebastian; Muratov, Eugene; Mushthofa, Mushthofa; Nagarajan, Niranjan; Nakken, Sigve; Nath, Aritro; Neuvial, Pierre; Newton, Richard; Ning, Zheng; De Niz, Carlos; Oliva, Baldo; Olsen, Catharina; Palmeri, Antonio; Panesar, Bhawan; Papadopoulos, Stavros; Park, Jaesub; Park, Seonyeong; Park, Sungjoon; Pawitan, Yudi; Peluso, Daniele; Pendyala, Sriram; Peng, Jian; Perfetto, Livia; Pirro, Stefano; Plevritis, Sylvia; Politi, Regina; Poon, Hoifung; Porta, Eduard; Prellner, Isak; Preuer, Kristina; Angel Pujana, Miguel; Ramnarine, Ricardo; Reid, John E.; Reyal, Fabien; Richardson, Sylvia; Ricketts, Camir; Rieswijk, Linda; Rocha, Miguel; Rodriguez-Gonzalvez, Carmen; Roell, Kyle; Rotroff, Daniel; de Ruiter, Julian R.; Rukawa, Ploy; Sadacca, Benjamin; Safikhani, Zhaleh; Safitri, Fita; Sales-Pardo, Marta; Sauer, Sebastian; Schlichting, Moritz; Seoane, Jose A.; Serra, Jordi; Shang, Ming-Mei; Sharma, Alok; Sharma, Hari; Shen, Yang; Shiga, Motoki; Shin, Moonshik; Shkedy, Ziv; Shopsowitz, Kevin; Sinai, Sam; Skola, Dylan; Smirnov, Petr; Soerensen, Izel Fourie; Soerensen, Peter; Song, Je-Hoon; Song, Sang Ok; Soufan, Othman; Spitzmueller, Andreas; Steipe, Boris; Suphavilai, Chayaporn; Tamayo, Sergio Pulido; Tamborero, David; Tang, Jing; Tanoli, Zia-ur-Rehman; Tarres-Deulofeu, Marc; Tegner, Jesper; Thommesen, Liv; Tonekaboni, Seyed Ali Madani; Tran, Hong T.; De Troyer, Ewoud; Truong, Amy; Tsunoda, Tatsuhiko; Turu, Gabor; Tzeng, Guang-Yo; Verbeke, Lieven; Videla, Santiago; Vis, Daniel; Voronkov, Andrey; Votis, Konstantinos; Wang, Ashley; Wang, Hong-Qiang Horace; Wang, Po-Wei; Wang, Sheng; Wang, Wei; Wang, Xiaochen; Wang, Xin; Wennerberg, Krister; Wernisch, Lorenz; Wessels, Lodewyk; van Westen, Gerard J. P.; Westerman, Bart A.; White, Simon Richard; Willighagen, Egon; Wurdinger, Tom; Xie, Lei; Xie, Shuilian; Xu, Hua; Yadav, Bhagwan; Yau, Christopher; Yeerna, Huwate; Yin, Jia Wei; Yu, Michael; Yu, MinHwan; Yun, So Jeong; Zakharov, Alexey; Zamichos, Alexandros; Zanin, Massimiliano; Zeng, Li; Zenil, Hector; Zhang, Frederick; Zhang, Pengyue; Zhang, Wei; Zhao, Hongyu; Zhao, Lan; Zheng, Wenjin; Zoufir, Azedine; Zucknick, Manuela (Springer Nature, 2019-06-17)
    The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca's large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.
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    COVID-19 Seroprevalence in Canada Modelling Waning and Boosting COVID-19 Immunity in Canada a Canadian Immunization Research Network Study
    Dick, David W.; Childs, Lauren M.; Feng, Zhilan; Li, Jing; Röst, Gergely; Buckeridge, David L.; Ogden, Nick H.; Heffernan, Jane M. (MDPI, 2021-12-23)
    COVID-19 seroprevalence changes over time, with infection, vaccination, and waning immunity. Seroprevalence estimates are needed to determine when increased COVID-19 vaccination coverage is needed, and when booster doses should be considered, to reduce the spread and disease severity of COVID-19 infection. We use an age-structured model including infection, vaccination and waning immunity to estimate the distribution of immunity to COVID-19 in the Canadian population. This is the first mathematical model to do so. We estimate that 60–80% of the Canadian population has some immunity to COVID-19 by late Summer 2021, depending on specific characteristics of the vaccine and the waning rate of immunity. Models results indicate that increased vaccination uptake in age groups 12–29, and booster doses in age group 50+ are needed to reduce the severity COVID-19 Fall 2021 resurgence.
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    Genome sequences of wild and domestic bactrian camels
    Jirimutu; Wang, Zhen; Ding, Guohui; Chen, Gangliang; Sun, Yamin; Sun, Zhihong; Zhang, Heping; Wang, Lei; Hasi, Surong; Zhang, Yan; Li, Jianmei; Shi, Yixiang; Xu, Ze; He, Chuan; Yu, Siriguleng; Li, Shengdi; Zhang, Wenbin; Batmunkh, Mijiddorj; Ts, Batsukh; Narenbatu; Unierhu; Bat-Ireedui, Shirzana; Gao, Hongwei; Baysgalan, Banzragch; Li, Qing; Jia, Zhiling; Turigenbayila; Subudenggerile; Narenmanduhu; Wang, Zhaoxia; Wang, Juan; Pan, Lei; Chen, Yongcan; Ganerdene, Yaichil; Dabxilt; Erdemt; Altansha; Altansukh; Liu, Tuya; Cao, Minhui; Aruuntsever; Bayart; Hosblig; He, Fei; Zha-ti, A.; Zheng, Guangyong; Qiu, Feng; Sun, Zikui; Zhao, Lele; Zhao, Wenjing; Liu, Baohong; Li, Chao; Chen, Yunqin; Tang, Xiaoyan; Guo, Chunyan; Liu, Wei; Ming, Liang; Temuulen; Cui, Aiying; Li, Yi; Gao, Junhui; Li, Jing; Wurentaodi; Niu, Shen; Sun, Tao; Zhai, Zhengxiao; Zhang, Min; Chen, Chen; Baldan, Tunteg; Bayaer, Tuman; Li, Yixue; Meng, He (Springer Nature, 2012-11)
    Bactrian camels serve as an important means of transportation in the cold desert regions of China and Mongolia. Here we present a 2.01 Gb draft genome sequence from both a wild and a domestic bactrian camel. We estimate the camel genome to be 2.38 Gb, containing 20,821 protein-coding genes. Our phylogenomics analysis reveals that camels shared common ancestors with other even-toed ungulates about 55-60 million years ago. Rapidly evolving genes in the camel lineage are significantly enriched in metabolic pathways, and these changes may underlie the insulin resistance typically observed in these animals. We estimate the genome-wide heterozygosity rates in both wild and domestic camels to be 1.0 x 10(-3). However, genomic regions with significantly lower heterozygosity are found in the domestic camel, and olfactory receptors are enriched in these regions. Our comparative genomics analyses may also shed light on the genetic basis of the camel's remarkable salt tolerance and unusual immune system.
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    A Geometrically nonlinear curved beam theory and its finite element formulation
    Li, Jing (Virginia Tech, 2000-12-05)
    This thesis presents a geometrically exact curved beam theory, with the assumption that the cross-section remains rigid, and its finite element formulation/implementation. The theory provides a theoretical view and an exact and efficient means to handle a large range of nonlinear beam problems. A geometrically exact curved/twisted beam theory, which assumes that the beam cross-section remains rigid, is re-examined and extended using orthonormal reference frames starting from a 3-D beam theory. The relevant engineering strain measures at any material point on the current beam cross-section with an initial curvature correction term, which are conjugate to the first Piola-Kirchhoff stresses, are obtained through the deformation gradient tensor of the current beam configuration relative to the initially curved beam configuration. The Green strains and Eulerian strains are explicitly represented in terms of the engineering strain measures while other stresses, such as the Cauchy stresses and second Piola-Kirchhoff stresses, are explicitly represented in terms of the first Piola-Kirchhoff stresses and engineering strains. The stress resultant and couple are defined in the classical sense and the reduced strains are obtained from the three-dimensional beam model, which are the same as obtained from the reduced differential equations of motion. The reduced differential equations of motion are also re-examined for the initially curved/twisted beams. The corresponding equations of motion include additional inertia terms as compared to previous studies. The linear and linearized nonlinear constitutive relations with couplings are considered for the engineering strain and stress conjugate pair at the three-dimensional beam level. The cross-section elasticity constants corresponding to the reduced constitutive relations are obtained with the initial curvature correction term. For the finite element formulation and implementation of the curved beam theory, some basic concepts associated with finite rotations and their parametrizations are first summarized. In terms of a generalized vector-like parametrization of finite rotations under spatial descriptions (i.e., in spatial forms), a unified formulation is given for the virtual work equations that leads to the load residual and tangent stiffness operators. With a proper explanation, the case of the non-vectorial parametrization can be recovered if the incremental rotation is parametrized using the incremental rotation vector. As an example for static problems, taking advantage of the simplicity in formulation and clear classical meanings of rotations and moments, the non-vectorial parametrization is applied to implement a four-noded 3-D curved beam element, in which the compound rotation is represented by the unit quaternion and the incremental rotation is parametrized using the incremental rotation vector. Conventional Lagrangian interpolation functions are adopted to approximate both the reference curve and incremental rotation of the deformed beam. Reduced integration is used to overcome locking problems. The finite element equations are developed for static structural analyses, including deformations, stress resultants/couples, and linearized/nonlinear bifurcation buckling, as well as post-buckling analyses of arches subjected to conservative and non-conservative loads. Several examples are used to test the formulation and the Fortran implementation of the element.
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    Hepatic Metabolic, Inflammatory, and Stress-Related Gene Expression in Growing Mice Consuming a Low Dose of Trans-10, cis-12-Conjugated Linoleic Acid
    Li, Jing; Viswanadha, Srikant; Loor, Juan J. (Hindawi, 2012-09-02)
    Dietary trans-10, cis-12-conjugated linoleic acid (trans-10, cis-12-CLA) fed to obese and nonobese rodents reduces body fat but leads to greater liver mass due to steatosis. The molecular mechanisms accompanying such responses remain largely unknown. Our study investigated the effects of chronic low trans-10, cis-12-CLA supplementation on hepatic expression of 39 genes related to metabolism, inflammation, and stress in growing mice. Feeding a diet supplemented with 0.3% trans-10, cis-12-CLA (wt/wt basis) for 6 weeks increased liver mass and concentration of long-chain fatty acids (LCFAs) in liver, while adipose tissue mass decreased markedly. These changes were accompanied by greater expression of genes involved in LCFA uptake (Cd36), lipogenesis, and triacylglycerol synthesis (Acaca, Gpam, Scd, Pck1, Plin2). Expression of these genes was in line with upregulation of the lipogenic transcription factor Srebf1. Unlike previous studies where higher >0.50% of the diet) doses of trans-10, cis-12-CLA were fed, we found greater expression of genes associated with VLDL assembly/secretion (Mttp, Cideb), ketogenesis (Hmgcs2, Bdh1), and LCFA oxidation (Acox1, Pdk4) in response to trans-10, cis-12-CLA. Dietary CLA, however, did not affect inflammation- and stress-related genes. Results suggested that a chronic low dose of dietary CLA increases liver mass and lipid accumulation due to activation of lipogenesis and insufficient induction of LCFA oxidation and VLDL assembly/secretion.
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    Inverse Problems in Structural Mechanics
    Li, Jing (Virginia Tech, 2005-12-01)
    This dissertation deals with the solution of three inverse problems in structural mechanics. The first one is load updating for finite element models (FEMs). A least squares fitting is used to identify the load parameters. The basic studies are made for geometrically linear and nonlinear FEMs of beams or frames by using a four-noded curved beam element, which, for a given precision, may significantly solve the ill-posed problem by reducing the overall number of degrees of freedom (DOF) of the system, especially the number of the unknown variables to obtain an overdetermined system. For the basic studies, the unknown applied load within an element is represented by a linear combination of integrated Legendre polynomials, the coefficients of which are the parameters to be extracted using measured displacements or strains. The optimizer L-BFGS-B is used to solve the least squares problem. The second problem is the placement optimization of a distributed sensing fiber optic sensor for a smart bed using Genetic Algorithms (GA), where the sensor performance is maximized. The sensing fiber optic cable is represented by a Non-uniform Rational B-Splines (NURBS) curve, which changes the placement of a set of infinite number of the infinitesimal sensors to the placement of a set of finite number of the control points. The sensor performance is simplified as the integration of the absolute curvature change of the fiber optic cable with respect to a perturbation due to the body movement of a patient. The smart bed is modeled as an elastic mattress core, which supports a fiber optic sensor cable. The initial and deformed geometries of the bed due to the body weight of the patient are calculated using MSC/NASTRAN for a given body pressure. The deformation of the fiber optic cable can be extracted from the deformation of the mattress. The performance of the fiber optic sensor for any given placement is further calculated for any given perturbation. The third application is stiffened panel optimization, including the size and placement optimization for the blade stiffeners, subject to buckling and stress constraints. The present work uses NURBS for the panel and stiffener representation. The mesh for the panel is generated using DistMesh, a triangulation algorithm in MATLAB. A NASTRAN/MATLAB interface is developed to automatically transfer the data between the analysis and optimization processes respectively. The optimization consists of minimizing the weight of the stiffened panel with design variables being the thickness of the plate and height and width of the stiffener as well as the placement of the stiffeners subjected to buckling and stress constraints under in-plane normal/shear and out-plane pressure loading conditions.
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    Ion transport and storage of ionic liquids in ionic polymer conductor network composites
    Liu, Yang; Liu, Sheng; Lin, Junhong; Wang, Dong; Jain, Vaibhav; Montazami, Reza; Heflin, James R.; Li, Jing; Madsen, Louis A.; Zhang, Q. M. (AIP Publishing, 2010-05-01)
    We investigate ion transport and storage of ionic liquids in ionic polymer conductor network composite electroactive devices. Specifically, we show that by combining the time domain electric and electromechanical responses, one can gain quantitative information on transport behavior of the two mobile ions in ionic liquids (i.e., cation and anion) in these electroactive devices. By employing a two carrier model, the total excess ions stored and strains generated by the cations and anions, and their transport times in the nanocomposites can be determined, which all depend critically on the morphologies of the conductor network nanocomposites. (C) 2010 American Institute of Physics. [doi:10.1063/1.3432664]
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    Mid-latitudinal habitable environment for marine eukaryotes during the waning stage of the Marinoan snowball glaciation
    Song, Huyue; An, Zhihui; Ye, Qin; Stueken, Eva E.; Li, Jing; Hu, Jun; Algeo, Thomas J.; Tian, Li; Chu, Daoliang; Song, Haijun; Xiao, Shuhai; Tong, Jinnan (Nature Portfolio, 2023-04)
    Based on geochemical and paleontological data, this study shows that habitable open-oceans extended to mid-latitude coastal oceans during the waning stage of the Marinoan snowball Earth, offering refugia for benthic photosynthetic eukaryotes During the Marinoan Ice Age (ca. 654-635 Ma), one of the 'Snowball Earth' events in the Cryogenian Period, continental icesheets reached the tropical oceans. Oceanic refugia must have existed for aerobic marine eukaryotes to survive this event, as evidenced by benthic phototrophic macroalgae of the Songluo Biota preserved in black shales interbedded with glacial diamictites of the late Cryogenian Nantuo Formation in South China. However, the environmental conditions that allowed these organisms to thrive are poorly known. Here, we report carbon-nitrogen-iron geochemical data from the fossiliferous black shales and adjacent diamictites of the Nantuo Formation. Iron-speciation data document dysoxic-anoxic conditions in bottom waters, whereas nitrogen isotopes record aerobic nitrogen cycling perhaps in surface waters. These findings indicate that habitable open-ocean conditions were more extensive than previously thought, extending into mid-latitude coastal oceans and providing refugia for eukaryotic organisms during the waning stage of the Marinoan Ice Age.
  • Mining disturbances in Virginia's southwestern coalfield, 1984-2011
    Li, Jing; Donovan, Patricia F.; Zipper, Carl E.; Wynne, Randolph H.; Oliphant, Adam J. (2015-06-01)
    Coal mining has been taking place in southwestern Virginia's Appalachian coalfield for more than a century, and surface mining has been a common method of coal extraction since the 1960s. Coal surface mining creates a significant landscape disturbance that is visible from space during the period of active mining. Researcher's have constructed a surface-mining disturbance history for Virginia's Appalachian coalfield that extends from the early 1980s through 2011. A series of multispectral images of the region produced by Landsat satellites and extending from 1984 through 2011 was obtained and analyzed. The automated analysis generated a geospatial data file that identifies surface mined areas spatially and by year of initial disturbance as detected during that period. The classification accuracy was found to be 93.5 percent. A manuscript describing the analysis methods, and interpreting and discussing results, has been published by Environmental Monitoring and Assessment. The citation is, Li, J., Zipper, C.E., Donovan, P.F., Wynne, R.H., and Oliphant, A.J., 2015, Reconstruction disturbance history for an intensively mined region by time-series analysis of Landsat imagery, Environmental Monitoring and Assessment, vol. 187:557. DOI: 10.1007/s10661-015-4766-1 and can be accessed at: http://link.springer.com/article/10.1007/s10661-015-4766-1 .
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    Modeling the waning and boosting of immunity from infection or vaccination
    Carlsson, Rose-Marie; Childs, Lauren M.; Feng, Zhilan; Glasser, John W.; Heffernan, Jane M.; Li, Jing; Röst, Gergely (2020-07-21)
    Immunity following natural infection or immunization may wane, increasing susceptibility to infection with time since infection or vaccination. Symptoms, and concomitantly infectiousness, depend on residual immunity. We quantify these phenomena in a model population composed of individuals whose susceptibility, infectiousness, and symptoms all vary with immune status. We also model age, which affects contact, vaccination and possibly waning rates. The resurgences of pertussis that have been observed wherever effective vaccination programs have reduced typical disease among young children follow from these processes. As one example, we compare simulations with the experience of Sweden following resumption of pertussis vaccination after the hiatus from 1979 to 1996, reproducing the observations leading health authorities to introduce booster doses among school-aged children and adolescents in 2007 and 2014, respectively. Because pertussis comprises a spectrum of symptoms, only the most severe of which are medically attended, accurate models are needed to design optimal vaccination programs where surveillance is less effective. (C) 2020 The Authors. Published by Elsevier Ltd.
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    Transcriptional profile of isoproterenol-induced cardiomyopathy and comparison to exercise-induced cardiac hypertrophy and human cardiac failure
    Galindo, Cristi L.; Skinner, Michael A.; Errami, Mounir; Olson, L Danielle; Watson, David A.; Li, Jing; McCormick, John F.; McIver, Lauren J.; Kumar, Neil M.; Pham, Thinh Q.; Garner, Harold R. (2009-12-09)
    Background Isoproterenol-induced cardiac hypertrophy in mice has been used in a number of studies to model human cardiac disease. In this study, we compared the transcriptional response of the heart in this model to other animal models of heart failure, as well as to the transcriptional response of human hearts suffering heart failure. Results We performed microarray analyses on RNA from mice with isoproterenol-induced cardiac hypertrophy and mice with exercise-induced physiological hypertrophy and identified 865 and 2,534 genes that were significantly altered in pathological and physiological cardiac hypertrophy models, respectively. We compared our results to 18 different microarray data sets (318 individual arrays) representing various other animal models and four human cardiac diseases and identified a canonical set of 64 genes that are generally altered in failing hearts. We also produced a pairwise similarity matrix to illustrate relatedness of animal models with human heart disease and identified ischemia as the human condition that most resembles isoproterenol treatment. Conclusion The overall patterns of gene expression are consistent with observed structural and molecular differences between normal and maladaptive cardiac hypertrophy and support a role for the immune system (or immune cell infiltration) in the pathology of stress-induced hypertrophy. Cross-study comparisons such as the results presented here provide targets for further research of cardiac disease that might generally apply to maladaptive cardiac stresses and are also a means of identifying which animal models best recapitulate human disease at the transcriptional level.