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Reduced effectiveness of repeat influenza vaccination: distinguishing among within-season waning, recent clinical infection, and subclinical infection. 重复接种流感疫苗的有效性降低:区分季节内减弱、近期临床感染和亚临床感染。
Pub Date : 2024-04-10 DOI: 10.1101/2023.03.12.23287173
Qifang Bi, Barbra A Dickerman, Huong Q Nguyen, Emily T Martin, Manjusha Gaglani, Karen J Wernli, G K Balasubramani, Brendan Flannery, Marc Lipsitch, Sarah Cobey

Studies have reported that prior-season influenza vaccination is associated with higher risk of clinical influenza infection among vaccinees. This effect might arise from incomplete consideration of within-season waning and recent infection. Using data from the US Flu Vaccine Effectiveness (VE) Network (2011-2012 to 2018-2019 seasons), we found that repeat vaccinees were vaccinated earlier in a season by one week. After accounting for waning VE, repeat vaccinees were still more likely to test positive for A(H3N2) (OR=1.11, 95%CI:1.02-1.21) but not for influenza B or A(H1N1). We found that clinical infection influenced individuals' decision to vaccinate in the following season while protecting against clinical infection of the same (sub)type. However, adjusting for recent clinical infections did not strongly influence the estimated effect of prior-season vaccination. In contrast, we found that adjusting for subclinical infection could theoretically attenuate this effect. Additional investigation is needed to determine the impact of subclinical infections on VE.

研究报告称,接种前一季流感疫苗与接种者感染临床流感的风险较高有关。这种影响可能是由于不完全考虑季节内的衰退和最近的感染。使用美国流感疫苗有效性网络(VE)的数据(2011-2012至2018-2019赛季),我们发现重复接种疫苗的人在一个赛季中提前一周接种疫苗。在考虑到VE减弱后,重复接种疫苗的人仍然更有可能检测出A(H3N2)呈阳性(OR=1.11,95%CI:1.02-1.21),但B型流感或A(H1N1)则不然。我们发现,临床感染会影响个人在下一个季节接种疫苗的决定,同时预防相同(亚)类型的临床感染。然而,对最近的临床感染进行调整并没有强烈影响前一季疫苗接种的估计效果。相反,我们发现调整亚临床感染在理论上可以减弱这种影响。需要进一步的调查来确定亚临床感染对VE的影响。
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引用次数: 0
Identification of Novel Genomic Loci for Anxiety and Extensive Genetic Overlap with Psychiatric Disorders. 焦虑症和精神疾病广泛遗传重叠的新基因座的鉴定。
Pub Date : 2024-04-08 DOI: 10.1101/2023.09.01.23294920
Markos Tesfaye, Piotr Jaholkowski, Alexey A Shadrin, Dennis van der Meer, Guy F L Hindley, Børge Holen, Nadine Parker, Pravesh Parekh, Viktoria Birkenæs, Zillur Rahman, Shahram Bahrami, Gleda Kutrolli, Oleksandr Frei, Srdjan Djurovic, Anders M Dale, Olav B Smeland, Kevin S O'Connell, Ole A Andreassen

Background: Anxiety disorders are prevalent and anxiety symptoms co-occur with many psychiatric disorders. We aimed to identify genomic risk loci associated with anxiety, characterize its genetic architecture, and genetic overlap with psychiatric disorders.

Methods: We used the GWAS of anxiety symptoms, schizophrenia, bipolar disorder, major depression, and attention deficit hyperactivity disorder (ADHD). We employed MiXeR and LAVA to characterize the genetic architecture and genetic overlap between the phenotypes. Conditional and conjunctional false discovery rate analyses were performed to boost the identification of genomic loci associated with anxiety and those shared with psychiatric disorders. Gene annotation and gene set analyses were conducted using OpenTargets and FUMA, respectively.

Results: Anxiety was polygenic with 12.9k estimated genetic risk variants and overlapped extensively with psychiatric disorders (4.1-11.4k variants). MiXeR and LAVA revealed predominantly positive genetic correlations between anxiety and psychiatric disorders. We identified 114 novel loci for anxiety by conditioning on the psychiatric disorders. We also identified loci shared between anxiety and major depression (n = 47), bipolar disorder (n = 33), schizophrenia (n = 71), and ADHD (n = 20). Genes annotated to anxiety loci exhibit enrichment for a broader range of biological pathways and differential tissue expression in more diverse tissues than those annotated to the shared loci.

Conclusions: Anxiety is a highly polygenic phenotype with extensive genetic overlap with psychiatric disorders. These genetic overlaps enabled the identification of novel loci for anxiety. The shared genetic architecture may underlie the extensive cross-disorder comorbidity of anxiety, and the identified genetic loci implicate molecular pathways that may lead to potential drug targets.

背景:焦虑症普遍存在,焦虑症状往往与精神疾病同时发生。在这里,我们旨在确定与焦虑相关的基因组风险基因座,描述其遗传结构,以及与精神疾病的遗传重叠。方法:我们使用了焦虑(GAD-2评分)、精神分裂症、双相情感障碍、重度抑郁症和注意力缺陷多动障碍(ADHD)的最大可用GWAS。我们使用MiXeR和LAVA来表征表型之间的遗传结构和遗传重叠。此外,还进行了条件和联合错误发现率分析,以促进对与焦虑相关的基因组基因座和与精神疾病共有的基因座的识别。分别使用OpenTargets和FUMA进行基因注释和基因集分析。结果:焦虑是多基因的,估计有8.4k个遗传风险变异,并与精神疾病广泛重叠(4.1-7.8k个变异)。MiXeR和LAVA都显示焦虑和精神障碍之间主要存在正的遗传相关性。我们通过对精神障碍的条件调节,确定了154个焦虑位点(139个新位点)。我们确定了焦虑与重度抑郁症(n=66)、双相情感障碍(n=19)、精神分裂症(n=51)和多动症(n=37)之间的共同基因座。与共享基因座注释的基因相比,注释到焦虑基因座的基因在更广泛的生物途径中表现出富集,并在更多样的组织中表现出不同的组织表达。结论:焦虑是一种高度多基因表型,与精神疾病有广泛的基因重叠。这些基因重叠使得能够识别焦虑症的新基因座和精神疾病的共享基因座。共享的遗传结构可能是焦虑共病的基础,而已确定的遗传基因座暗示了可能成为潜在药物靶点的分子途径。
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引用次数: 0
Inpatient Skin-to-Skin Care Predicts 12-month Neurodevelopmental Outcomes in Very Preterm Infants. 住院皮肤护理可预测早产儿 12 个月的神经发育结果。
Pub Date : 2024-04-08 DOI: 10.1101/2023.04.06.23288260
Molly F Lazarus, Virginia A Marchman, Edith Brignoni-Pérez, Sarah Dubner, Heidi M Feldman, Melissa Scala, Katherine E Travis

Objective: Limited research links hospital-based experiences of skin-to-skin (STS) care to longer-term neurodevelopmental outcomes in preterm children. The present study examined relations between inpatient STS and neurodevelopmental scores measured at 12 months in a sample of very preterm (VPT) infants.

Study design and methods: From a retrospective study review of medical records of 181 VPT infants (<32 weeks gestational age (GA)) we derived the STS rate, i.e., the total minutes of STS each infant received/day of hospital stay. We used scores on the Capute Scales from routine follow-up care at 12 months as the measure of neurodevelopmental outcome (n=181).

Results: Families averaged approximately 17 minutes/day of STS care (2 days/week, 70 minutes/session), although there was substantial variability. Variation in STS rate was positively associated with outcomes at 12 months corrected age ( r = 0.25, p < .001). STS rate significantly predicted 6.2% unique variance in 12-month neurodevelopmental outcomes, after controlling for GA, socioeconomic status (SES), health acuity, and visitation frequency. A 20-minute increase in STS per day was associated with a 10-point increase (.67 SDs) in neurodevelopmental outcomes at 12 months. SES, GA, and infant health acuity did not moderate these relations.

Conclusion: VPT infants who experienced more STS during hospitalization demonstrated higher scores on 12-month assessments of neurodevelopment. Results provide evidence that STS care may confer extended neuroprotection on VPT infants through the first year of life.

目的:将早产儿在医院接受皮肤接触护理(STS)的经历与神经发育的长期结果联系起来的研究非常有限。本研究以极度早产儿(VPT)为样本,探讨了住院期间皮肤接触护理(STS)与 12 个月时神经发育评分之间的关系:研究设计和方法:对 181 名 VPT 婴儿的医疗记录进行了回顾性研究(结果:家庭平均每天接受约 17 分钟的 STS 护理(每周 2 天,每节课 70 分钟),但差异很大。STS 率的变化与 12 个月矫治后的结果呈正相关(r = 0.25,p .001)。在控制了GA、社会经济地位(SES)、健康敏锐度和探视频率后,STS率可明显预测12个月神经发育结果中6.2%的独特差异。每天增加 20 分钟的 STS 与 12 个月时神经发育结果增加 10 分(0.67 SDs)有关。SES、GA和婴儿健康敏锐度并没有缓和这些关系:结论:住院期间经历更多 STS 的 VPT 婴儿在 12 个月的神经发育评估中得分更高。研究结果证明,STS护理可为VPT婴儿提供持续到出生后第一年的神经保护。
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引用次数: 0
ReMIND: The Brain Resection Multimodal Imaging Database. ReMIND:脑切除多模式成像数据库。
Pub Date : 2024-04-08 DOI: 10.1101/2023.09.14.23295596
Parikshit Juvekar, Reuben Dorent, Fryderyk Kögl, Erickson Torio, Colton Barr, Laura Rigolo, Colin Galvin, Nick Jowkar, Anees Kazi, Nazim Haouchine, Harneet Cheema, Nassir Navab, Steve Pieper, William M Wells, Wenya Linda Bi, Alexandra Golby, Sarah Frisken, Tina Kapur

The standard of care for brain tumors is maximal safe surgical resection. Neuronavigation augments the surgeon's ability to achieve this but loses validity as surgery progresses due to brain shift. Moreover, gliomas are often indistinguishable from surrounding healthy brain tissue. Intraoperative magnetic resonance imaging (iMRI) and ultrasound (iUS) help visualize the tumor and brain shift. iUS is faster and easier to incorporate into surgical workflows but offers a lower contrast between tumorous and healthy tissues than iMRI. With the success of data-hungry Artificial Intelligence algorithms in medical image analysis, the benefits of sharing well-curated data cannot be overstated. To this end, we provide the largest publicly available MRI and iUS database of surgically treated brain tumors, including gliomas (n=92), metastases (n=11), and others (n=11). This collection contains 369 preoperative MRI series, 320 3D iUS series, 301 iMRI series, and 356 segmentations collected from 114 consecutive patients at a single institution. This database is expected to help brain shift and image analysis research and neurosurgical training in interpreting iUS and iMRI.

脑肿瘤的护理标准是将最大限度的安全手术切除作为第一步。神经导航增强了外科医生实现这一目标的能力,但随着手术的进行,由于大脑的变化而失去了有效性。此外,许多胶质瘤很难与邻近的健康脑组织区分开来。术中MRI(iMRI)是一种有用的外科辅助手段,可用于显示残余肿瘤和脑转移。术中超声(iUS)也有类似的目的,同时也更快、更容易融入工作流程。然而,与术中MRI相比,它在肿瘤组织和正常脑组织之间提供了较低的对比度。随着渴望数据的人工智能(AI)/机器学习(ML)算法在推进医学图像分析技术方面的成功,共享精心策划的数据的好处怎么强调都不为过。为此,我们在这里提供了最大的公开可用的手术治疗脑肿瘤的MRI和术中超声成像数据库,包括神经胶质瘤(n=92)、转移瘤(n=11)和其他肿瘤(n=11)。该集合包含369个术前MRI系列、320个3D术中超声系列、301个术中MRI系列和356个分割,这些分割来自单个机构的114名连续患者。我们希望这些数据能成为脑转移和图像分析的计算研究以及术中超声和iMRI解释的神经外科训练的资源。
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引用次数: 0
Pre-stroke physical activity matters for functional limitations: A longitudinal case-control study of 12,860 participants. 中风幸存者的功能限制:中风前的身体活动很重要。
Pub Date : 2024-04-04 DOI: 10.1101/2023.09.14.23295576
Zack van Allen, Dan Orsholits, Matthieu P Boisgontier

Objective: In the chronic phase after a stroke, limitations in activities of daily living (ADLs) and instrumental ADL (IADLs) initially plateau before steadily increasing. The benefits of pre-stroke physical activity on these limitations remain unclear. To clarify this relationship, we examined the effect of physical activity on the long-term evolution of functional limitations in a cohort of stroke survivors and compared it to a cohort of matched stroke-free adults.

Methods: Longitudinal data from 2,143 stroke survivors and 10,717 stroke-free adults aged 50 years and older were drawn from a prospective cohort study based on the Survey of Health, Ageing and Retirement in Europe (2004-2022; 8 data collection waves). Physical activity was assessed in the pre-stroke wave. Functional limitations were assessed in the post-stroke waves. Each stroke survivor was matched with 5 stroke-free adults who had similar propensity scores computed on the basis of key covariates, including baseline age, sex, body mass index, limitations in ADL and IADL, chronic conditions and country of residence, before any of the participants from either cohort had experienced a stroke.

Results: Results showed an interaction between stroke status and physical activity on ADL limitations (b = -0.076; 95% CI = -0.142 to -0.011), with the effect of physical activity being stronger in stroke survivors (b = -0.345, 95% CI = -0.438 to -0.252) than in stroke-free adults (b = -0.269, 95% CI = -0.269 to -0.241).

Conclusion: The beneficial effect of pre-stroke physical activity on ADL limitations after stroke is stronger than its effect in matched stroke-free adults followed for a similar number of years.

Impact: Physical activity, an intervention within the physical therapist's scope of practice, is effective in reducing the risk of functional dependence after stroke. Moreover, pre-stroke levels of physical activity can inform the prognosis of functional dependence in stroke survivors.

背景和目的:在中风后的慢性期,日常生活活动能力(ADL)和工具性ADL(IADL)的限制最初趋于平稳,然后稳步增加。然而,中风前的体育活动水平对这些限制的益处尚不清楚。为了阐明这种关系,本研究比较了体育活动对中风幸存者和无中风对照者I/ADL限制的长期演变的影响。方法:从欧洲健康、老龄化和退休调查(SHARE;2004-2020)中获得2143名中风幸存者和10717名50岁及以上匹配的无中风对照的纵向数据。根据卒中事件前的波动和卒中后慢性期I/ADL限制的数量评估身体活动。每个中风幸存者与5名无中风对照组进行匹配,这些对照组具有相似的倾向得分,这些得分是基于关键协变量计算的。使用根据年龄、性别、教育水平和慢性病数量调整的线性混合效应模型,将卒中前体育活动对卒中幸存者I/ADL限制的影响与其在无卒中对照组中的影响进行比较,在体育活动和I/ADL评估之间具有相似的时滞。结果:在卒中幸存者中,卒中前体育活动对卒中后ADL限制的有益影响明显强于在任何参与者经历卒中之前,与基线年龄、性别、体重指数、I/ADL限制、慢性病和居住国相匹配的无卒中对照组。结论:体育活动是一种有效的预防性干预措施,可以降低中风后功能依赖的风险。此外,卒中前的体力活动水平是卒中后功能依赖预后的一个重要变量。数据:http://www.share-project.org/data-access.htmlhttps://doi.org/10.6103/SHARE.w1.600https://doi.org/10.6103/SHARE.w2.600https://doi.org/10.6103/SHARE.w4.600https://doi.org/10.6103/SHARE.w5.600https://doi.org/10.6103/SHARE.w6.600https://doi.org/10.6103/SHARE.w7.711https://doi.org/10.6103/SHARE.w8.800.Code:https://github.com/matthieuboisgontier/Stroke_Physical-Activity.
{"title":"Pre-stroke physical activity matters for functional limitations: A longitudinal case-control study of 12,860 participants.","authors":"Zack van Allen, Dan Orsholits, Matthieu P Boisgontier","doi":"10.1101/2023.09.14.23295576","DOIUrl":"10.1101/2023.09.14.23295576","url":null,"abstract":"<p><strong>Objective: </strong>In the chronic phase after a stroke, limitations in activities of daily living (ADLs) and instrumental ADL (IADLs) initially plateau before steadily increasing. The benefits of pre-stroke physical activity on these limitations remain unclear. To clarify this relationship, we examined the effect of physical activity on the long-term evolution of functional limitations in a cohort of stroke survivors and compared it to a cohort of matched stroke-free adults.</p><p><strong>Methods: </strong>Longitudinal data from 2,143 stroke survivors and 10,717 stroke-free adults aged 50 years and older were drawn from a prospective cohort study based on the Survey of Health, Ageing and Retirement in Europe (2004-2022; 8 data collection waves). Physical activity was assessed in the pre-stroke wave. Functional limitations were assessed in the post-stroke waves. Each stroke survivor was matched with 5 stroke-free adults who had similar propensity scores computed on the basis of key covariates, including baseline age, sex, body mass index, limitations in ADL and IADL, chronic conditions and country of residence, before any of the participants from either cohort had experienced a stroke.</p><p><strong>Results: </strong>Results showed an interaction between stroke status and physical activity on ADL limitations (b = -0.076; 95% CI = -0.142 to -0.011), with the effect of physical activity being stronger in stroke survivors (b = -0.345, 95% CI = -0.438 to -0.252) than in stroke-free adults (b = -0.269, 95% CI = -0.269 to -0.241).</p><p><strong>Conclusion: </strong>The beneficial effect of pre-stroke physical activity on ADL limitations after stroke is stronger than its effect in matched stroke-free adults followed for a similar number of years.</p><p><strong>Impact: </strong>Physical activity, an intervention within the physical therapist's scope of practice, is effective in reducing the risk of functional dependence after stroke. Moreover, pre-stroke levels of physical activity can inform the prognosis of functional dependence in stroke survivors.</p>","PeriodicalId":18659,"journal":{"name":"medRxiv : the preprint server for health sciences","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10516084/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41140847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Omicron detection with large language models and YouTube audio data. 使用来自社交媒体的无脚本语音样本进行数字奥密克戎检测。
Pub Date : 2024-03-27 DOI: 10.1101/2022.09.13.22279673
James T Anibal, Adam J Landa, Nguyen T T Hang, Miranda J Song, Alec K Peltekian, Ashley Shin, Hannah B Huth, Lindsey A Hazen, Anna S Christou, Jocelyne Rivera, Robert A Morhard, Ulas Bagci, Ming Li, Yael Bensoussan, David A Clifton, Bradford J Wood

Publicly available audio data presents a unique opportunity for the development of digital health technologies with large language models (LLMs). In this study, YouTube was mined to collect audio data from individuals with self-declared positive COVID-19 tests as well as those with other upper respiratory infections (URI) and healthy subjects discussing a diverse range of topics. The resulting dataset was transcribed with the Whisper model and used to assess the capacity of LLMs for detecting self-reported COVID-19 cases and performing variant classification. Following prompt optimization, LLMs achieved accuracies of 0.89, 0.97, respectively, in the tasks of identifying self-reported COVID-19 cases and other respiratory illnesses. The model also obtained a mean accuracy of 0.77 at identifying the variant of self-reported COVID-19 cases using only symptoms and other health-related factors described in the YouTube videos. In comparison with past studies, which used scripted, standardized voice samples to capture biomarkers, this study focused on extracting meaningful information from public online audio data. This work introduced novel design paradigms for pandemic management tools, showing the potential of audio data in clinical and public health applications.

人工智能在临床环境中的成功取决于训练数据的多样性和可用性。在某些情况下,社交媒体数据可以用来平衡有限数量的可访问、精心策划的临床数据,但这种可能性在很大程度上仍未被探索。在这项研究中,我们挖掘了YouTube,以收集在奥密克戎是主要变异株1、2、3期间,新冠肺炎自我检测呈阳性的个体的语音数据,同时还对非奥密克毒株新冠肺炎变异株、其他上呼吸道感染(URI)和健康受试者进行了采样。由此产生的数据集用于训练DenseNet模型,以从语音变化中检测奥密克戎变异株。我们的模型在从健康样本中分离奥密克戎样本时实现了0.85/0.80的特异性/敏感性,在从有症状的非新冠病毒样本中分离奥密克戎样品时实现了0.76/0.70的特异性/敏感性。与过去使用脚本语音样本的研究相比,我们发现利用无脚本语音固有的样本内方差可以增强泛化能力。我们的工作介绍了基于音频的诊断工具的新设计范式,并确立了社交媒体数据训练适合现实世界部署的数字诊断模型的潜力。
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引用次数: 0
Strong Genetic Overlaps Between Dimensional and Categorical Models of Bipolar Disorders in a Family Sample. 家庭样本中双相情感障碍的维度和分类模型之间的强遗传重叠。
Pub Date : 2024-03-26 DOI: 10.1101/2023.06.24.23291169
Alejandro Arbona-Lampaya, Heejong Sung, Alexander D'Amico, Emma E M Knowles, Emily K Besançon, Ally Freifeld, Ley Lacbawan, Fabiana Lopes, Layla Kassem, Antonio E Nardi, Francis J McMahon

Background: Bipolar disorder (BD) presents with a wide range of symptoms that vary among relatives, casting doubt on categorical illness models. To address this uncertainly, we investigated the heritability and genetic relationships between categorical and dimensional models of BD in a family sample.

Methods: Participants in the Amish-Mennonite Bipolar Genetics (AMBiGen) study were assigned categorical mood disorder diagnoses by structured psychiatric interview and completed the Mood Disorder Questionnaire (MDQ), which assesses lifetime history of manic symptoms and associated impairment. Major MDQ dimensions were analyzed by Principal Component Analysis (PCA) in 726 participants. Heritability and genetic overlaps between categorical diagnoses and MDQ-derived dimensions were estimated with SOLAR-ECLIPSE within 432 genotyped participants.

Results: MDQ scores were significantly higher among individuals diagnosed with BD and related disorders, as expected, but varied widely among relatives. PCA suggested a three-component model for the MDQ. Heritability of the MDQ score was 30% (p<0.001), evenly distributed across its three principal components. Strong and significant genetic correlations were found between categorical diagnoses and most MDQ measures.

Limitations: Recruitment through probands with BD resulted in increased prevalence of BD in this sample, limiting generalizability. Unavailable genetic data reduced sample size for some analyses.

Conclusion: heritability and high genetic correlations between categorical diagnoses and MDQ measures support a genetic continuity between dimensional and categorical models of BD.

目的:双相情感障碍(BD)通常表现出广泛的症状,但这种经常致残的障碍的维度和分类模型之间的遗传力和遗传关系几乎没有一致性。方法:Amish Mennonite双极遗传学(AMBiGen)研究的参与者,该研究招募了来自北美洲和南美洲Amish和Mennonite社区的BD和相关疾病家庭,通过结构化的精神病学访谈,被分配了一个分类的情绪障碍诊断,并被要求完成情绪障碍问卷(MDQ),评估主要躁狂症状和相关损伤的终生病史。主成分分析(PCA)用于分析726名参与者的MDQ维度,其中212人对主要情绪障碍进行了分类诊断。SOLAR-ECLIPSE(v9.0.0)用于估计432名基因型参与者的MDQ衍生测量和分类诊断之间的遗传力和遗传重叠。结果:不出所料,在被诊断为BD和相关疾病的个体中,MDQ评分显著更高。主成分分析为MDQ提出了一个三分量模型,与文献一致。MDQ症状评分的遗传性估计为30%(结论:结果支持MDQ作为BD的维度测量。此外,MDQ评分和分类诊断之间的显著遗传性和高遗传相关性表明,主要情绪障碍的维度和分类测量之间存在遗传连续性。
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引用次数: 0
HIV co-infection increases the risk of post-tuberculosis mortality among persons who initiated treatment for drug-resistant tuberculosis. 在接受耐药性结核病治疗的患者中,HIV合并感染增加了结核病后死亡的风险。
Pub Date : 2024-03-26 DOI: 10.1101/2023.05.19.23290190
Argita D Salindri, Maia Kipiani, Nino Lomtadze, Nestani Tukvadze, Zaza Avaliani, Henry M Blumberg, Katherine E Masyn, Richard B Rothenberg, Russell R Kempker, Matthew J Magee

Little is known regarding the relationship between common comorbidities in persons with tuberculosis (TB) (including human immunodeficiency virus [HIV], diabetes, and hepatitis C virus [HCV]) with post-TB mortality. We conducted a retrospective cohort study among persons who initiated treatment for rifampicin-resistant and multi/extensively drug-resistant (RR and M/XDR) TB reported to the country of Georgia's TB surveillance during 2009-2017. Exposures included HIV serologic status, diabetes, and HCV status. Our outcome was all-cause post-TB mortality determined by cross-validating vital status with Georgia's death registry through November 2019. We estimated adjusted hazard rate ratios (aHR) and 95% confidence intervals (CI) of post-TB mortality among participants with and without comorbidities using cause-specific hazard regressions. Among 1032 eligible participants, 34 (3.3%) died during treatment and 87 (8.7%) died post-TB treatment. Among those who died post-TB treatment, the median time to death was 21 months (interquartile range 7-39) post-TB treatment. After adjusting for confounders, the hazard rates of post-TB mortality were higher among participants with HIV co-infection (aHR=3.74, 95%CI 1.77-7.91) compared to those without HIV co-infection. In our cohort, post-TB mortality occurred most commonly in the first three years post-TB treatment. Linkage to care for common TB comorbidities post-treatment may reduce post-TB mortality rates.

背景:我们旨在确定结核病(TB)患者常见的预先存在的合并症(包括人类免疫缺陷病毒(HIV)、糖尿病和丙型肝炎病毒(HCV))与结核病治疗后全因死亡率之间的关系。方法:我们对2009-2017年格鲁吉亚国家接受利福平耐药性和多药/广泛耐药(RR和M/XDR)结核病治疗的患者进行了回顾性队列研究。符合条件的参与者年龄在15岁以上,有新诊断的、实验室确认的耐药结核病,并接受二线治疗。暴露包括HIV血清学状态、糖尿病和HCV状态。主要结果是通过与格鲁吉亚国家死亡登记处交叉验证截至2019年11月的生命状态来确定结核病治疗后的死亡率。我们使用病因特异性风险回归估计了患有和不患有合并症的参与者的结核病后死亡率的危险率比(HR)和95%置信区间(CI)。结果:在纳入我们分析的1032名符合条件的患者中,34名(3.3%)参与者在治疗期间死亡,87名(8.7%)参与者在结核病治疗后死亡。在结核病治疗后死亡的患者中,中位死亡时间为结核病治疗结束后21个月(IQR 7-39)。在校正了潜在的混杂因素后,与未合并感染艾滋病毒的参与者相比,合并感染艾滋病毒参与者在结核病治疗后的死亡率危险率更高(校正后的危险比[aHR]=3.74,95%CI 1.77-7.91)。结论:在我们的队列中,结核病后死亡率最常见于结核病治疗结束后的前三年。额外的结核病后护理和随访,特别是在患有结核病和合并症(尤其是艾滋病毒合并感染)的患者中,可以降低结核病治疗后的死亡率。
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引用次数: 0
Identifying bias in models that detect vocal fold paralysis from audio recordings using explainable machine learning and clinician ratings. 使用可解释的机器学习和临床医生评分,识别从录音中检测声带麻痹的模型中的偏差。
Pub Date : 2024-03-20 DOI: 10.1101/2020.11.23.20235945
Daniel M Low, Vishwanatha Rao, Gregory Randolph, Phillip C Song, Satrajit S Ghosh

Introduction: Detecting voice disorders from voice recordings could allow for frequent, remote, and low-cost screening before costly clinical visits and a more invasive laryngoscopy examination. Our goals were to detect unilateral vocal fold paralysis (UVFP) from voice recordings using machine learning, to identify which acoustic variables were important for prediction to increase trust, and to determine model performance relative to clinician performance.

Methods: Patients with confirmed UVFP through endoscopic examination (N=77) and controls with normal voices matched for age and sex (N=77) were included. Voice samples were elicited by reading the Rainbow Passage and sustaining phonation of the vowel "a". Four machine learning models of differing complexity were used. SHapley Additive explanations (SHAP) was used to identify important features.

Results: The highest median bootstrapped ROC AUC score was 0.87 and beat clinician's performance (range: 0.74 - 0.81) based on the recordings. Recording durations were different between UVFP recordings and controls due to how that data was originally processed when storing, which we can show can classify both groups. And counterintuitively, many UVFP recordings had higher intensity than controls, when UVFP patients tend to have weaker voices, revealing a dataset-specific bias which we mitigate in an additional analysis.

Conclusion: We demonstrate that recording biases in audio duration and intensity created dataset-specific differences between patients and controls, which models used to improve classification. Furthermore, clinician's ratings provide further evidence that patients were over-projecting their voices and being recorded at a higher amplitude signal than controls. Interestingly, after matching audio duration and removing variables associated with intensity in order to mitigate the biases, the models were able to achieve a similar high performance. We provide a set of recommendations to avoid bias when building and evaluating machine learning models for screening in laryngology.

引言:从语音记录中检测语音障碍可以在昂贵的临床就诊和更具侵入性的喉镜检查之前进行频繁、远程和低成本的筛查。我们的目标是使用机器学习从语音记录中检测单侧声带麻痹(UVFP),确定哪些声学变量对预测很重要,以增加信任,并确定模型性能相对于临床医生的性能。方法:纳入经内镜检查确诊为UVFP的患者(N=77)和年龄和性别匹配的正常声音对照组(N=77。语音样本是通过阅读彩虹通道和保持元音“a”的发音来获得的。使用了四个不同复杂度的机器学习模型。SHAP用于识别重要特征。结果:根据记录,自举ROC AUC得分的最高中位数为0.87,超过了临床医生的表现(范围:0.74-0.81)。与直觉相反,许多UVFP记录的强度高于对照组。我们使用临床医生的评分来提供证据,证明声音较弱的UVFP患者过度突出了他们的声音,并且被录音的麦克风增益比对照组更高,这使得模型能够利用这种录音特性来改进分类。有趣的是,当去除与强度变量相关的所有变量以减轻偏差时,模型仍然能够实现类似的高性能。结论:使用迄今为止研究UVFP的最大数据集,我们只需几秒钟的语音记录就实现了高性能,超过了专业临床医生的性能。我们发现,当个体声音柔和时,声音生物标志物研究中可能会出现偏差。我们提供了一组建议,以避免在建立和评估用于咽喉科筛查的机器学习模型时存在偏见。因此,可解释的机器学习提供了一种机制来检测UVFP,揭示声学变量如何表征特定的病理生理学,并揭示偏见。
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引用次数: 0
WITHDRAWN: Evaluation of Fourier Transform Infrared spectroscopy (IR Biotyper) as a complement to Whole genome sequencing (WGS) to characterise Enterobacter cloacae , Citrobacter freundii and Klebsiella pneumoniae isolates recovered from hospital sinks. 撤销:评估傅立叶变换红外光谱法(IR Biotyper)作为全基因组测序(WGS)的补充方法,以确定从医院水槽中分离的泄殖腔肠杆菌、弗氏柠檬杆菌和肺炎克雷伯菌的特征。
Pub Date : 2024-03-08 DOI: 10.1101/2023.04.24.23289028
P Aranega-Bou, C Cornbill, G Rodger, M Bird, G Moore, A Roohi, K L Hopkins, S Hopkins, P Ribeca, N Stoesser, S I Lipworth

The authors have withdrawn their manuscript due to becoming aware of methodology issues related to the curation of the training set used to determine cut-off values for Biotyper cluster assignation and lack of replicate measurements on different days for the isolates analysed. It is therefore unclear whether the conclusions of the manuscript are founded and no further work is possible to correct these issues as the instrument is no longer available to the authors. If you have any questions, please contact the corresponding author.

由于意识到用于确定 Biotyper 集群分配临界值的训练集的整理方法存在问题,以及缺乏对所分析分离物在不同日期的重复测量,作者已撤回其手稿。因此,目前尚不清楚手稿中的结论是否有依据,而且由于作者已无法获得该仪器,因此无法进一步开展工作来纠正这些问题。如有任何疑问,请联系通讯作者。
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引用次数: 0
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medRxiv : the preprint server for health sciences
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