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利用机器学习预测县级白尾鹿慢性消耗性疾病

Predicting chronic wasting disease in white-tailed deer at the county scale using machine learning

Nature 等信源发布 2024-06-22 14:57

可切换为仅中文


AbstractContinued spread of chronic wasting disease (CWD) through wild cervid herds negatively impacts populations, erodes wildlife conservation, drains resource dollars, and challenges wildlife management agencies. Risk factors for CWD have been investigated at state scales, but a regional model to predict locations of new infections can guide increasingly efficient surveillance efforts.

摘要慢性消耗性疾病(CWD)通过野生鹿群的持续传播对种群产生负面影响,侵蚀野生动物保护,消耗资源美元,并对野生动物管理机构提出挑战。CWD的风险因素已经在州范围内进行了调查,但预测新感染地点的区域模型可以指导越来越有效的监测工作。

We predicted CWD incidence by county using CWD surveillance data depicting white-tailed deer (Odocoileus virginianus) in 16 eastern and midwestern US states. We predicted the binary outcome of CWD-status using four machine learning models, utilized five-fold cross-validation and grid search to pinpoint the best model, then compared model predictions against the subsequent year of surveillance data.

我们使用描述美国东部和中西部16个州的白尾鹿(Odocoileus virginianus)的CWD监测数据预测了各县的CWD发病率。我们使用四个机器学习模型预测了CWD状态的二元结果,利用五重交叉验证和网格搜索来确定最佳模型,然后将模型预测与随后一年的监测数据进行了比较。

Cross validation revealed that the Light Boosting Gradient model was the most reliable predictor given the regional data. The predictive model could be helpful for surveillance planning. Predictions of false positives emphasize areas that warrant targeted CWD surveillance because of similar conditions with counties known to harbor CWD.

交叉验证表明,鉴于区域数据,光增强梯度模型是最可靠的预测因子。预测模型可能有助于监测规划。假阳性预测强调了需要有针对性的CWD监测的地区,因为与已知存在CWD的县的情况相似。

However, disagreements in positives and negatives between the CWD Prediction Web App predictions and the on-the-ground surveillance data one year later underscore the need for state wildlife agency professionals to use a layered modeling approach to ensure robust surveillance planning. The CWD Prediction Web App is at https://cwd-predict.streamlit.app/..

然而,CWD预测网络应用程序预测与一年后的地面监测数据之间在正面和负面方面存在分歧,这突显了国家野生动物管理局专业人员需要使用分层建模方法来确保稳健的监测规划。CWD预测Web应用程序位于https://cwd-predict.streamlit.app/..

IntroductionChronic wasting disease (CWD) is a transmissible spongiform encephalopathy that infects members of the Cervidae family1. The disease stems from the misfolding of prion proteins, leading to neurodegeneration, weight loss, altered behavior, and eventual death2. Since first detected in the 1960s, CWD continues to spread through wild and captive cervids across North America3.

引言慢性消耗性疾病(CWD)是一种传染性海绵状脑病,感染Cervidae家族成员1。该疾病源于朊病毒蛋白的错误折叠,导致神经变性,体重减轻,行为改变和最终死亡2。自20世纪60年代首次发现以来,CWD继续通过北美的野生和圈养鹿传播3。

To date, 34 United States (US) state wildlife agencies and four Canadian provincial wildlife agencies have detected CWD in at least one wild cervid herd3.Wildlife agencies in North America have established surveillance programs to detect CWD in wild cervid populations4. Such programs focus on identifying locations most likely to harbor CWD and provide the best opportunity to manage the disease while prevalence is low5; however, these programs constitute an enormous monetary and human resource cost to agencies6.

迄今为止,34个美国(美国)州野生动物机构和四个加拿大省级野生动物机构已经在至少一个野生鹿群中检测到CWD。北美的野生动物机构已经建立了监测计划,以检测野生鹿群中的CWD。这些计划的重点是确定最有可能窝藏CWD的地点,并在患病率较低的情况下提供管理疾病的最佳机会5;然而,这些计划对机构构成了巨大的货币和人力资源成本6。

Accordingly, post hoc evaluation of existing surveillance data has focused on pinpointing variables in association with the emergence and spread of CWD to further inform the next year of surveillance7.Anthropogenic factors such as transport and captivity5,8, 9 of cervids and natural movements8 of cervids can contribute to initial introduction of CWD.

因此,对现有监测数据的事后评估侧重于确定与CWD的出现和传播相关的变量,以进一步为下一年的监测提供信息7。人为因素,如cervids的运输和捕获5,8,9以及cervids的自然运动8可能有助于CWD的初步引入。

Persistence of prions in the environment10, soil types11, baiting and feeding12, forest cover13, water14, cervid density15, and natural movements8 contribute to disease spread. Authority for non-imperiled terrestrial wildlife, including most deer species, resides with state and provincial governments16,17; as a result, management and surveillance efforts for CWD are highly variable between jurisdictions.Important and complex questions are driving rapid development, refinement, and use of technology in ecology18,19.

朊病毒在环境中的持久性10,土壤类型11,诱饵和饲养12,森林覆盖13,水14,cervid密度15和自然运动8有助于疾病传播。包括大多数鹿类在内的非濒危陆地野生动物管理局由州和省政府负责16,17;因此,CWD的管理和监督工作在不同司法管辖区之间差异很大。重要而复杂的问题正在推动生态学技术的快速发展,完善和使用18,19。

Among these technologi.

在这些技术中。

Table 1 Definitions of variables in the Orthogonal Dataset, borrowed with permission33.Full size tableFigure 1The known status of chronic wasting disease (CWD) in wild white-tailed deer by county in the 2019–20 season according to the results of surveillance testing by US state wildlife agencies33. CWD Detected represents counties where governing wildlife officials confirmed at least one CWD-positive case in wild, white-tailed deer in the 2019–20 season.

表1正交数据集中变量的定义,借用了许可33。全尺寸表图1根据美国国家野生动物管理局33的监测测试结果,2019-20赛季各县野生白尾鹿慢性消耗性疾病(CWD)的已知状态33。检测到的CWD代表了管理野生动物官员在2019-20年季节在野生白尾鹿中确认至少一例CWD阳性病例的县。

CWD Not Detected represents counties where governing wildlife officials conducted CWD testing in 2019–20 in wild, white-tailed deer, but did not confirm CWD in any subject. Not Considered represents counties that did not exist in the Pooled Dataset33. Map was created in QGIS (version 3.32.2-Lima)60.Full size imageThe Balanced Orthogonal Dataset consisted of a subset of 158 counties depicting conditions in the 2019–20 season-year.

未检测到的CWD代表了2019-20年野生动物管理官员在野生白尾鹿中进行CWD测试的县,但没有确认任何主题的CWD。未考虑代表汇总数据集中不存在的县33。地图是在QGIS(版本3.32.2-Lima)60中创建的。全尺寸图像平衡正交数据集由158个县的子集组成,描绘了2019-20赛季的情况。

Of the 158 counties, 50% (79/158) represented CWD-positive counties and 50% (79/158) represented randomly selected CWD-non detect counties. All counties in the Balanced Orthogonal Dataset contained values for hunter harvest (although that value could have been zero). [Note that of the 85 total positive counties available in the Orthogonal Dataset, six counties in the US state of Mississippi were excluded from the Balanced Dataset due to missing Total_harvest values.] The Training Dataset consisted of 126 (80%) records randomly selected from the Balanced Orthogonal Dataset while the Testing Dataset consisted of the remaining 32 (20%) records of the Balanced Orthogonal Dataset.

在158个县中,50%(79/158)代表CWD阳性县,50%(79/158)代表随机选择的CWD未检测县。平衡正交数据集中的所有县都包含猎人收获的值(尽管该值可能为零)。[请注意,在正交数据集中可用的85个总阳性县中,由于缺少total\u harvest值,美国密西西比州的6个县被排除在平衡数据集中。]训练数据集由126个(80%)记录组成从平衡正交数据集中随机选择,而测试数据集由平衡正交数据集的其余32个(20%)记录组成。

Summary statistics for each variable in the Pooled, Orthogonal, Balanced Orthogonal, Training, and Testing Datasets are provided in the Supplement.The Balanced Orthogonal Dataset set contained non-linear data and outliers,.

补充资料中提供了汇总,正交,平衡正交,训练和测试数据集中每个变量的汇总统计数据。平衡正交数据集包含非线性数据和异常值,。

Table 2 The confusion matrix of the best Light Gradient Boosting (LGB) model when CWD Prediction Web App predictions were compared against on-the-ground surveillance in white-tailed deer in the season-year 2020–21.Full size tableThe CWD Prediction Web App had 70 TPs for the 2020–21 season-year, 66 of which constituted counties already known to be CWD-positive in white-tailed deer from the 2019–20 surveillance data.

表2最佳光梯度增强(LGB)模型的混淆矩阵,当CWD预测网络应用程序的预测与2020-21赛季白尾鹿的地面监测进行比较时。全尺寸表CWD预测网络应用程序在2020-21赛季有70个TP,其中66个构成了2019-20年监测数据中已知白尾鹿CWD阳性的县。

The remaining four TPs depicted counties that indeed turned positive in white-tailed deer for the first time in the 2020–21 season-year, just as the model predicted (Dakota county, Minnesota; Shawano, Washington, and Wood counties, Wisconsin). The CWD Prediction Web App had 325 FPs relative to surveillance data from the 2020–21 season-year.The CWD Prediction Web App had 946 TNs for the 2020–21 season-year.

剩下的四个TPs描述了在2020-21个季节年份,白尾鹿的数量确实首次呈阳性的县,正如模型预测的那样(明尼苏达州达科塔县;华盛顿州沙瓦诺县和威斯康星州伍德县)。相对于2020-21赛季的监测数据,CWD预测Web应用程序的FPs为325 FPs。CWD预测Web应用程序在2020-21赛季有946个TNs。

The CWD Prediction Web App had 15 FNs for the 2020–21 season-year, 13 of which were counties the CWD Prediction Web App knew were positive from the 2019–20 but incorrectly assigned to be negative in the 2020–21 season-year. The remaining two counties (Wyandot county, Ohio; Lauderdale county, Tennessee) were negative in 2019–20 and detected a positive in 2020–21, but the CWD Prediction Web App did not successfully predict that transition in CWD-status.

CWD预测网络应用程序在2020-21赛季有15个FN,其中13个是CWD预测网络应用程序知道的2019-20赛季为正值的县,但在2020-21赛季被错误地分配为负值。其余两个县(俄亥俄州怀安多县;田纳西州劳德代尔县)在2019-20年呈阴性,2020-21年呈阳性,但CWD预测网络应用程序未能成功预测CWD状态的转变。

The CWD Prediction Web App is at https://cwd-predict.streamlit.app/. The code is available at https://github.com/sohel10/lgbm.DiscussionDespite the governing autonomy of management agencies, free-ranging wildlife spans jurisdictional boundaries. Consequently, wildlife agencies across North America would benefit from cooperative efforts designed to understand shared risk factors of disease.

CWD预测Web应用程序位于https://cwd-predict.streamlit.app/.代码位于https://github.com/sohel10/lgbm.DiscussionDespite管理机构的管理自主权,自由放养的野生动物跨越了管辖范围。因此,北美各地的野生动物机构将受益于旨在了解疾病共同风险因素的合作努力。

Our study was the first to use regional data that represent a single species exposed to diverse management goals, herd dyn.

我们的研究是第一个使用区域数据的研究,这些数据代表了暴露于不同管理目标的单一物种,即群体dyn。

Data availability

数据可用性

The data are publicly available at https://doi.org/10.7298/7txw-2681.2. The CWD Prediction Web App is at https://cwd-predict.streamlit.app/.

这些数据可以在https://doi.org/10.7298/7txw-2681.2.CWD预测Web应用程序位于https://cwd-predict.streamlit.app/.

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QGIS.org, QGIS Geographic Information System. QGIS Association. http://www.qgis.org (2024).Download referencesAcknowledgementsWe thank W. Kozlowski, J. Peaslee, M. Cosgrove, J. Dennison, T. DeRosia, C. Faller, D. Howlett, M. Keightley, E. Kessel, J. Kessler, E. Larson, M. McCord, A. Nolder, D.

QGIS.org,QGIS地理信息系统。QGIS协会。http://www.qgis.org(2024年)。下载参考文献致谢我们感谢W.Kozlowski,J.Peaslee,M.Cosgrove,J.Dennison,T.DeRosia,C.Faller,D.Howlett,M.Keightley,E.Kessel,J.Kessler,E.Larson,M.McCord,A.Nolder,D。

Stanfield, S. Stura, J. Sweaney, G. Timko, B. Wallingford, B. Wojcik, C. Yoest, A. J. Riggs, and 5 anonymous individuals, Arkansas Game and Fish Commission Wildlife Management Division staff and F23AF01862-00, Georgia Wildlife Resources Division, Indiana Department of Natural Resources Division of Fish and Wildlife, Iowa DNR Wildlife Bureau staff, Minnesota DNR staff, Mississippi Department of Wildlife, Fisheries, and Parks staff, New York State Department of Environmental Conservation Wildlife Health Unit staff, the North Carolina Wildlife Resources Commission staff, Ohio DNR Division of Wildlife staff.

Stanfield、S.Stura、J.Sweeney、G.Timko、B.Wallingford、B.Wojcik、C.Yoest、A.J.Riggs和5名匿名人士、阿肯色州狩猎和鱼类委员会野生动物管理司工作人员和F23AF01862-00、佐治亚州野生动物资源司、印第安纳州自然资源部鱼类和野生动物司、爱荷华州DNR野生动物局工作人员、明尼苏达州DNR工作人员、密西西比州野生动物、渔业和公园部工作人员、纽约州环境保护部野生动物健康股工作人员、北卡罗来纳州野生动物资源委员会工作人员、俄亥俄州DNR野生动物司工作人员。

Data collection was funded in part by Arkansas’s Wildlife Restoration funds, ‘State Wildlife Health’; Florida’s State Game Trust Fund Deer Management Program; Georgia’s Wildlife and Sport Fish Restoration Program; Indiana DNR and Fish and Wildlife F18AF00484, W38R05 White-tailed Deer Management, F20AF10029-00, Monitoring Wildlife Populations and Health W-51-R-01, F21AF02467-01, Monitoring Wildlife Populations and Health W-51-R-02; Iowa’s Fish and Wildlife Trust Fund and U.

数据收集部分由阿肯色州野生动物恢复基金“州立野生动物健康”资助;佛罗里达州游戏信托基金鹿管理计划;乔治亚州野生动物和运动鱼类恢复计划;印第安纳州DNR和鱼类及野生动物F18AF00484,W38R05白尾鹿管理,F20AF10029-00,监测野生动物种群和健康W-51-R-01,F21AF02467-01,监测野生动物种群和健康W-51-R-02;爱荷华州鱼类和野生动物信托基金和美国。

S. Fish and Wildlife Service Wildlife and Sport Fish Restoration Program; Maryland’s award of the U. S. Fish and Wildlife Service Wildlife and Sport Fish Restoration Program, W 61-R-29; Minnesota DNR; New York’s Wildlife Health Unit and New York’s award for Federal Aid Wildlife Restoration Grant W-178-R; North Carolina’s award for Federal Aid in Wildlife Restoration; Tennessee’s award for the Wil.

S、 鱼类和野生动物服务野生动物和运动鱼类恢复计划;马里兰州美国鱼类和野生动物管理局野生动物和运动鱼类恢复计划奖,W 61-R-29;明尼苏达州DNR;纽约野生动物健康部门和纽约联邦援助野生动物恢复奖W-178-R;北卡罗莱纳州野生动物恢复联邦援助奖;田纳西州Wil奖。

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PubMed Google ScholarContributionsConceptualization: MSA; BJH; KLS. Funding: JGB; JG; BJH; CSJ; KLS. Literature review: BJH; MSA; RCA; KLS. Wrote software: MSA; BJH. Conducted the analysis: MSA; BJH. Provided data and applied agency expertise CRM; JRB; BC; CHK; TMH; JNC; KMBW; EM; CC; LMO; JKT; MC; WTM; CS; KPH; AES; LAM; MC; RTM; JS; MJT; JDK; DMG; DJS.

PubMed谷歌学术贡献概念:MSA;BJH公司;吉隆坡。资金来源:日本国债;JG;BJH公司;CSJ;吉隆坡。文献综述:BJH;MSA;RCA;吉隆坡。编写软件:MSA;BJH公司。进行了分析:MSA;BJH公司。提供数据和应用机构专业知识CRM;JRB;不列颠哥伦比亚省;CHK公司;TMH;JNC;KMBW;EM;抄送;LMO;JKT;MC;WTM;CS;KPH;不良事件;林;MC;RTM;JS;美赞臣;JDK公司;DMG;DJ。

Wrote the draft: BJH; MSA. All authors provided critical edits and gave approval for submission.Corresponding authorCorrespondence to.

写了草稿:BJH;MSA。所有作者都提供了重要的编辑并批准了提交。对应作者对应。

Md Sohel Ahmed.Ethics declarations

医学博士Sohel Ahmed。道德宣言

Competing interests

相互竞争的利益

MSA, BJH, RCA, JGB, JG, NAH, CGC, CRM, JRB, BC, CHK, TMH, JNC, KMBW, EM, CC, LMO, JKT, MC, WTM, KPH, AES, LAM, CS, MC, RTM, JS, MJT, JDK, DMG, DJS, and KLS declare no competing interests. A portion of this work was completed when CIM was a consultant at Desert Centered Ecology, LLC; CSJ was a consultant at Christopher S.

MSA、BJH、RCA、JGB、JG、NAH、CGC、CRM、JRB、BC、CHK、TMH、JNC、KMBW、EM、CC、LMO、JKT、MC、WTM、KPH、AES、LAM、CS、MC、RTM、JS、MJT、JDK、DMG、DJS和KLS声明没有利益冲突。这项工作的一部分是在CIM担任沙漠中心生态有限责任公司顾问时完成的;CSJ是克里斯托弗S的顾问。

Jennelle; and FHH was a consultant at Florian H. Hodel..

詹内尔;FHH是Florian H.Hodel的顾问。。

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Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.

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The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.

本文中的图像或其他第三方材料包含在文章的知识共享许可中,除非在材料的信用额度中另有说明。。

To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/..

要查看此许可证的副本,请访问http://creativecommons.org/licenses/by/4.0/..

Reprints and permissionsAbout this articleCite this articleAhmed, M.S., Hanley, B.J., Mitchell, C.I. et al. Predicting chronic wasting disease in white-tailed deer at the county scale using machine learning.

转载和许可本文引用本文Ahmed,M.S.,Hanley,B.J.,Mitchell,C.I.等人使用机器学习预测县范围内白尾鹿的慢性消耗性疾病。

Sci Rep 14, 14373 (2024). https://doi.org/10.1038/s41598-024-65002-7Download citationReceived: 31 October 2023Accepted: 15 June 2024Published: 22 June 2024DOI: https://doi.org/10.1038/s41598-024-65002-7Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard.

Sci Rep 1414373(2024)。https://doi.org/10.1038/s41598-024-65002-7Download引文接收日期:2023年10月31日接收日期:2024年6月15日发布日期:2024年6月22日OI:https://doi.org/10.1038/s41598-024-65002-7Share本文与您共享以下链接的任何人都可以阅读此内容:获取可共享链接对不起,本文目前没有可共享的链接。复制到剪贴板。

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主题

Ecological epidemiologySoftwareStatistics

生态流行病学软件统计

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