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Analyzing bivariate cross-trait genetic architecture in GWAS summary statistics with the BIGA cloud computing platform. 利用 BIGA 云计算平台分析 GWAS 摘要统计中的双变量跨性状遗传结构。
Pub Date : 2024-03-16 DOI: 10.1101/2023.04.28.538585
Yujue Li, Fei Xue, Bingxuan Li, Yilin Yang, Zirui Fan, Juan Shu, Xiaochen Yang, Xiyao Wang, Jinjie Lin, Carlos Copana, Bingxin Zhao

As large-scale biobanks provide increasing access to deep phenotyping and genomic data, genome-wide association studies (GWAS) are rapidly uncovering the genetic architecture behind various complex traits and diseases. GWAS publications typically make their summary-level data (GWAS summary statistics) publicly available, enabling further exploration of genetic overlaps between phenotypes gathered from different studies and cohorts. However, systematically analyzing high-dimensional GWAS summary statistics for thousands of phenotypes can be both logistically challenging and computationally demanding. In this paper, we introduce BIGA (https://bigagwas.org/), a website that aims to offer unified data analysis pipelines and processed data resources for cross-trait genetic architecture analyses using GWAS summary statistics. We have developed a framework to implement statistical genetics tools on a cloud computing platform, combined with extensive curated GWAS data resources. Through BIGA, users can upload data, submit jobs, and share results, providing the research community with a convenient tool for consolidating GWAS data and generating new insights.

随着大规模生物库提供越来越多的深度表型和基因组数据,全基因组关联研究(GWAS)正在迅速揭示各种复杂性状和疾病背后的遗传结构。全基因组关联研究出版物通常会公开其摘要级数据(全基因组关联研究摘要统计),以便进一步探索从不同研究和队列中收集的表型之间的遗传重叠。然而,系统分析数千种表型的高维 GWAS 摘要统计在逻辑上具有挑战性,在计算上要求也很高。在本文中,我们介绍了 BIGA ( https://bigagwas.org/ ),该网站旨在提供统一的数据分析管道和处理过的数据资源,用于使用 GWAS 摘要统计进行跨性状遗传结构分析。我们开发了一个在云计算平台上实现统计遗传学工具的框架,并结合了广泛的 GWAS 数据资源。通过 BIGA,用户可以上传数据、提交作业和分享结果,为研究界提供了一个整合 GWAS 数据和产生新见解的便捷工具。
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引用次数: 0
Early adversity and emotional awareness: A partial confirmation and extension of their relationship. 早期逆境与情感意识:对两者关系的部分确认和扩展。
Pub Date : 2024-01-01 Epub Date: 2023-06-05 DOI: 10.1080/26904586.2023.2216695
Ryan Smith, Anke Versluis, Anne E Chuning, John J B Allen, Karen L Weihs, Jos F Brosschot, Bart Verkuil, Abhishek Allam, Richard D Lane

Early adversity has been consistently linked to mental health outcomes, but the underlying pathways remain unclear. One previous study found an association between early adversity and trait emotional awareness (EA), which has itself been linked to health outcomes, but links to mental health were not explicitly examined. The aim of the current study was to test the hypothesis that the association between early adversity and health can be partially accounted for by differences in EA within a large student sample (n = 196). Participants completed measures of early adversity, EA, and current emotional functioning (i.e., depression, anxiety, somatization, positive/negative affect). Bayesian analyses found the most evidence for models with an interaction between sex and early adversity in predicting emotional functioning - revealing the expected negative relationship between early adversity and EA in females, but a positive relationship in males. Early adversity, but not EA, was associated with depression, anxiety, and implicit negative affect. Only explicit positive affect was associated with both early adversity and EA, and EA partially mediated the negative association between early adversity and positive affect. These results provide limited support for EA as a mediating pathway for the effects of early adversity on mental health.

早期逆境一直与心理健康结果有关,但其背后的途径仍不清楚。之前的一项研究发现,早期逆境与特质情绪意识(EA)之间存在关联,而特质情绪意识本身也与健康结果有关,但与心理健康的关联并未得到明确研究。本研究的目的是在一个大型学生样本(n = 196)中检验这样一个假设,即早期逆境与健康之间的关联可以通过情绪意识的差异得到部分解释。参与者完成了早期逆境、EA 和当前情绪功能(即抑郁、焦虑、躯体化、积极/消极情绪)的测量。贝叶斯分析发现,在预测情绪功能方面,性别与早期逆境相互作用的模型证据最多--女性的早期逆境与情绪功能之间存在预期的负相关,而男性的早期逆境与情绪功能之间存在正相关。早期逆境(而非 EA)与抑郁、焦虑和内隐消极情绪有关。只有明确的积极情绪与早期逆境和情感体验相关,而情感体验部分地调解了早期逆境与积极情绪之间的负相关。这些结果为EA作为早期逆境对心理健康影响的中介途径提供了有限的支持。
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引用次数: 0
Comparison of Outcomes of Early Versus Late Tracheostomy in the Treatment of Mechanically Ventilated Critically ill Patients. 早期与晚期气管切开术治疗机械通气危重患者的疗效比较。
Pub Date : 2023-12-01 Epub Date: 2023-07-16 DOI: 10.1007/s12070-023-04025-4
Nitika Gupta, Aditiya Saraf, Aadil Bashir, Dikshit Shivgotra, Parmod Kalsotra

Comparative evaluation of early and late tracheostomy outcomes in mechanically ventilated patients. The present retrospective study was conducted in Government medical college Jammu from April 2021 to November 2022 on 111 tracheotomised patient in intensive care unit. All tracheostomies with in 10 days of intubation were grouped as early tracheostomy (ET) group and all those done after 10 days were grouped as LATE TRACHEOSTOMY (LT) group. APACHE II score at the time of intensive care unit admission of all included tracheotomised patients was noted. Data regarding mortality, duration of mechanical ventilation and length of stay in intensive care unit (ICU) was studied. Mean age of presentation was 41.5 ± 15.7 yrs, with male preponderance. Out of 111 patients, 57 patients underwent early tracheostomy and 54 underwent late TRACHEOSTOMY. In APACHE II, < 25 category-short term mortality was 4 in ET and 5 in LT; long term mortality in ET was 4 and 10 in LT; average days of mechanical ventilation were 11.2 in ET and 3 in LT; average stay in ICU was 18 days in ET and 61 days in LT. in APACHE II > 25-short term mortality was 4 in ET and 5 in LT; long term mortality in ET was 3 and 9 in LT. Average days of mechanical ventilation were 10.8 in ET and 57 in LT; average stay in ICU was 24 days in ET and 79 days in LT. Early tracheostomy is superior to late Tracheostomy in terms of mortality, number of days of mechanical ventilation and the duration of intensive care unit stay.

机械通气患者气管造口术早期与晚期预后的比较评价。本回顾性研究于2021年4月至2022年11月在查谟政府医学院对重症监护室的111名气管切开患者进行了研究。将插管10 d内的气管造口术分为早期气管造口术(ET)组,10 d后的气管造口术分为晚期气管造口术(LT)组。记录所有气管切开患者在重症监护病房入院时的APACHE II评分。研究了死亡率、机械通气时间和重症监护病房(ICU)住院时间的数据。平均发病年龄41.5±15.7岁,男性居多。在111例患者中,57例患者接受了早期气管切开术,54例患者接受了晚期气管切开术。在APACHE II中,短期死亡率为25,ET为4,LT为5;ET组的长期死亡率分别为3和9。ET组的平均机械通气天数为10.8天,LT组为57天;ET组平均住院时间为24天,lt组平均住院时间为79天。在死亡率、机械通气天数和重症监护病房住院时间方面,早期气管切开术优于晚期气管切开术。
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引用次数: 0
A Case Report of Chondromyxoid Fibroma of the Nasal Cavity. 鼻腔软骨粘液样纤维瘤1例报告。
Pub Date : 2023-12-01 Epub Date: 2023-06-28 DOI: 10.1007/s12070-023-03981-1
Jasmeet Kaur, Ankita Aggarwal, Vishav Yadav, Sanjeev Bhagat, Dinesh Sharma

The chondromyxoid fibroma is a benign osseocartilaginous tumor histopathologically characterized by chondroid, fibrous, and myxoid tissues (Nazeer et al. in Skeltal Radiol 25:779-78, 1996). Its occurrence is quite rare, accounting for less than 0.5% of all bone tumors, with 1-5% of cases reported in the head and neck region. We report an unusual case of 25 years old male who presented with progressive swelling over dorsum of nose with bilateral nasal obstruction over 1 year. The histopathological examination was suggestive of chondromyxoid fibroma. The tumor was completely excised via open approach. We report this case owing to the rarity of the disease, sometimes masquerading as invasive/malignant pathology.

软骨粘液样纤维瘤是一种以软骨样、纤维样和粘液样组织为特征的良性骨软骨瘤(Nazeer et al. in Skeltal Radiol 25:779- 78,1996)。它的发生是相当罕见的,占所有骨肿瘤的不到0.5%,1-5%的病例报告在头颈部。我们报告一个不寻常的情况下,25岁的男性谁提出了进行性肿胀在鼻背和双侧鼻塞超过1年。组织病理学检查提示为软骨粘液样纤维瘤。经开放入路完全切除肿瘤。我们报告这个病例是因为罕见的疾病,有时伪装成侵袭性/恶性病理。
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引用次数: 0
Effects of COVID-19 Infection and Vaccines on Patients with Epilepsy: Real-Life Experiences. COVID-19 感染和疫苗对癫痫患者的影响:真实体验。
IF 1 Pub Date : 2023-11-18 eCollection Date: 2023-01-01 DOI: 10.29399/npa.28314
Özge Öcek, Pınar Ortan

Introduction: The current study evaluates the effects of COVID-19 infection and the safety of vaccines in patients with epilepsy (PWEs).

Method: The study was conducted with PWEs who were vaccinated against COVID-19. The sample was separated into two groups as those with drug-resistant epilepsy (DRE) and those with non-resistant epilepsy, and their seizure frequencies, seizure types, development of status epilepticus, changes in doses and/or types of drugs, electroencephalographs (EEGs) before and after COVID-19 infection, and vaccination with mRNA or inactivated vaccines were monitored and compared. Changes in seizure patterns were also inquired about following the administration of vaccines other than COVID-19.

Results: Included in the study were 307 PWEs with a mean age of 42.62±14.74, among whom COVID-19 PCR positivity was detected in 97(31.6%). Those who experienced no increase in seizure frequency while infected with COVID-19 were significantly under monotherapy (p=0.031). The mean seizure frequency was 2.70±5.19 per year before vaccination, but increased to 3.20±5.82 after. A significant relationship was identified between abnormal EEG and increased seizure frequency across the entire sample and the mRNA group (p=0.011, p=0.004). The frequency of seizures increased significantly in the DRE patients after receiving the mRNA vaccine (p=0.023). Overall, increased seizure frequencies were observed in 29.9% of the sample during COVID-19 infection, with increases of 16.4% in those who received the mRNA vaccine, 8.6% after inactivated vaccines and 25% after non-COVID-19 vaccines.

Conclusion: COVID-19 infection was found to be associated with a higher increased seizure frequency risk than being vaccinated, and COVID-19 vaccines do not differ from other vaccines in terms of the risk to PWEs.

简介:本研究评估了COVID-19感染癫痫患者的影响和疫苗的安全性:本研究评估了癫痫患者(PWEs)感染 COVID-19 的影响以及疫苗的安全性:研究对象是接种了COVID-19疫苗的癫痫患者。将样本分为两组,即耐药性癫痫(DRE)患者和非耐药性癫痫患者,监测并比较他们在感染 COVID-19 和接种 mRNA 或灭活疫苗前后的癫痫发作频率、发作类型、癫痫状态的发展、药物剂量和/或类型的变化、脑电图(EEG)。此外,还询问了接种 COVID-19 以外的疫苗后癫痫发作模式的变化:研究共纳入 307 名平均年龄为(42.62±14.74)岁的残疾人,其中 97 人(31.6%)检测出 COVID-19 PCR 阳性。感染 COVID-19 后癫痫发作频率没有增加的患者明显接受了单一疗法(P=0.031)。接种疫苗前,平均癫痫发作频率为每年 2.70±5.19,但接种疫苗后增至每年 3.20±5.82。在整个样本和 mRNA 组中,异常脑电图与癫痫发作频率增加之间存在明显关系(p=0.011,p=0.004)。接种 mRNA 疫苗后,DRE 患者的癫痫发作频率明显增加(p=0.023)。总体而言,29.9%的样本在感染COVID-19期间癫痫发作频率增加,其中接种mRNA疫苗的患者癫痫发作频率增加16.4%,接种灭活疫苗的患者癫痫发作频率增加8.6%,接种非COVID-19疫苗的患者癫痫发作频率增加25%:结论:与接种疫苗相比,COVID-19 感染与癫痫发作频率增加的风险更相关,COVID-19 疫苗与其他疫苗对公共卫生专家的风险没有区别。
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引用次数: 0
Sunless and Indoor Tanning Among U.S. Non-Hispanic White Women Ages 18-49 Years. 美国 18-49 岁非西班牙裔白人女性中的日光浴和室内日光浴。
IF 0.4 Pub Date : 2023-05-01 DOI: 10.1097/jdn.0000000000000736
Andrew B Seidenberg, Anne K Julian, Anne M Hartman, Dawn M Holman

The use of indoor UV tanning devices (also known as "indoor tanning") has declined in recent years. Less is known about use of dihydroxyacetone-containing products used for tanning (also known as "sunless tanning"). We analyzed data from the 2015 National Health Interview Survey. Analysis was limited to non-Hispanic White women ages 18-49 years. We estimated the proportion of women reporting spray tanning, self-applied lotion tanning, and indoor tanning and used weighted multivariable logistic regression models to examine the relationships between socio-demographic characteristics, skin cancer risk factors, and other cancer risk factors with sunless and indoor tanning. Overall, 17.7% of women reported sunless tanning. Lotion tanning was more common (15.3%) than spray tanning (6.8%), while 12.0% of women engaged in indoor tanning. Among sunless tanners, 23.7% also engaged in indoor tanning. Younger age, ever having a skin exam, skin reactions to the sun, binge drinking, and being at a healthy weight were associated with sunless tanning. While sunless tanning may be less harmful for skin cancer risk than indoor tanning, the frequency with which the two behaviors co-occur suggests that efforts to address societal pressures for women to alter their skin color may have important public health benefits.

近年来,室内紫外线美黑设备(又称 "室内美黑")的使用有所减少。人们对用于日光浴的含二羟基丙酮产品(又称 "日光浴")的使用情况知之甚少。我们分析了 2015 年全国健康访谈调查的数据。分析对象仅限于 18-49 岁的非西班牙裔白人女性。我们估算了报告喷雾美黑、自行涂抹乳液美黑和室内美黑的女性比例,并使用加权多变量逻辑回归模型研究了社会人口特征、皮肤癌风险因素和其他癌症风险因素与日光浴和室内美黑之间的关系。总体而言,有 17.7% 的妇女报告了日光浴。乳液晒黑(15.3%)比喷雾晒黑(6.8%)更常见,而从事室内晒黑的妇女占 12.0%。在不晒太阳的人中,23.7%的人也在室内晒黑。年龄较小、曾经做过皮肤检查、皮肤对阳光的反应、酗酒和体重健康与日光浴有关。虽然日光浴对皮肤癌风险的危害可能小于室内日光浴,但这两种行为同时出现的频率表明,努力消除女性改变肤色的社会压力可能会对公共健康产生重要的益处。
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引用次数: 0
Impact of Platelet Reactivity on Ischemic and Bleeding Events After Percutaneous Coronary Intervention - A Long-Term Perspective. 血小板反应性对经皮冠状动脉介入治疗后缺血和出血事件的影响--长期展望。
IF 3.1 Pub Date : 2022-08-25 Epub Date: 2022-05-31 DOI: 10.1253/circj.CJ-22-0297
Yohei Numasawa
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引用次数: 0
The Time Course of Language Production as Revealed by Pattern Classification of MEG Sensor Data. 通过脑电传感器数据的模式分类揭示语言产生的时间过程。
Pub Date : 2022-07-20 Epub Date: 2022-06-09 DOI: 10.1523/JNEUROSCI.1923-21.2022
Francesca Carota, Jan-Mathijs Schoffelen, Robert Oostenveld, Peter Indefrey

Language production involves a complex set of computations, from conceptualization to articulation, which are thought to engage cascading neural events in the language network. However, recent neuromagnetic evidence suggests simultaneous meaning-to-speech mapping in picture naming tasks, as indexed by early parallel activation of frontotemporal regions to lexical semantic, phonological, and articulatory information. Here we investigate the time course of word production, asking to what extent such "earliness" is a distinctive property of the associated spatiotemporal dynamics. Using MEG, we recorded the neural signals of 34 human subjects (26 males) overtly naming 134 images from four semantic object categories (animals, foods, tools, clothes). Within each category, we covaried word length, as quantified by the number of syllables contained in a word, and phonological neighborhood density to target lexical and post-lexical phonological/phonetic processes. Multivariate pattern analyses searchlights in sensor space distinguished the stimulus-locked spatiotemporal responses to object categories early on, from 150 to 250 ms after picture onset, whereas word length was decoded in left frontotemporal sensors at 250-350 ms, followed by the latency of phonological neighborhood density (350-450 ms). Our results suggest a progression of neural activity from posterior to anterior language regions for the semantic and phonological/phonetic computations preparing overt speech, thus supporting serial cascading models of word production.SIGNIFICANCE STATEMENT Current psycholinguistic models make divergent predictions on how a preverbal message is mapped onto articulatory output during the language planning. Serial models predict a cascading sequence of hierarchically organized neural computations from conceptualization to articulation. In contrast, parallel models posit early simultaneous activation of multiple conceptual, phonological, and articulatory information in the language system. Here we asked whether such earliness is a distinctive property of the neural dynamics of word production. The combination of the millisecond precision of MEG with multivariate pattern analyses revealed subsequent onset times for the neural events supporting semantic and phonological/phonetic operations, progressing from posterior occipitotemporal to frontal sensor areas. The findings bring new insights for refining current theories of language production.

语言的产生涉及一系列复杂的计算,从概念化到发音,这些计算被认为涉及语言网络中的级联神经事件。然而,最近的神经磁性证据表明,在图片命名任务中,意义到语音的映射是同步进行的,这体现在前颞叶区域对词汇语义、语音和发音信息的早期平行激活。在这里,我们研究了单词产生的时间过程,询问这种 "早期性 "在多大程度上是相关时空动态的一个独特属性。我们使用 MEG 记录了 34 名人类受试者(26 名男性)公开命名四个语义对象类别(动物、食物、工具、衣服)中 134 幅图像时的神经信号。在每个类别中,我们将单词长度(以单词所含音节数量化)和语音邻域密度进行协方差分析,以确定词汇和词汇后语音/发音过程。传感器空间的多变量模式分析探照灯区分了物体类别的刺激锁定时空反应,早期为图像开始后的 150 至 250 毫秒,而单词长度在左额叶颞传感器中的解码时间为 250 至 350 毫秒,其次是语音邻域密度的潜伏期(350 至 450 毫秒)。我们的研究结果表明,在准备公开言语的语义和语音/音素计算过程中,神经活动会从后部语言区域逐渐过渡到前部语言区域,从而支持单词生成的序列级联模型。串行模型预测了从概念化到发音的神经计算的层叠序列。相比之下,平行模型则认为语言系统中的多种概念、语音和发音信息会在早期同时激活。在这里,我们要问的是,这种早期性是否是造词神经动力学的一个独特属性。通过将 MEG 的毫秒精度与多元模式分析相结合,我们发现了支持语义和语音/发音操作的神经事件的后续启动时间,这些神经事件从后枕颞部逐渐发展到额部传感器区域。这些发现为完善当前的语言生成理论带来了新的启示。
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引用次数: 0
Generating Bioactive Natural Product-inspired Molecules with Machine Intelligence. 利用机器智能生成受天然产物启发的生物活性分子。
IF 1.2 Pub Date : 2022-05-25 DOI: 10.2533/chimia.2022.396
Petra Schneider, Karl-Heinz Altmann, Gisbert Schneider

The computer-assisted design of new chemical entities has made a leap forward with the development of machine learning models for automated molecule generation. The overarching goal of this conceptual approach is to augment the creativity of medicinal chemists with a machine intelligence. In this Perspective we highlight prospective applications of "de novo" drug design and target prediction, aiming to generate natural product-inspired bioactive compounds from scratch. A virtual chemist transforms pharmacologically active natural products into new, easily synthesizable small molecules with desired properties and activity. Computational activity prediction and automated compound generation offer the possibility to systematically transfer the wealth of pharmaceutically active natural products to synthetic small molecule drug discovery. We present selected prospective examples and dare a forecast into the future of natural product-inspired drug discovery.

随着用于自动分子生成的机器学习模型的发展,新的化学实体的计算机辅助设计取得了飞跃。这种概念性方法的首要目标是用机器智能来增强药物化学家的创造力。在这方面,我们强调了“从头开始”药物设计和靶标预测的前景应用,旨在从零开始产生天然产物启发的生物活性化合物。虚拟化学家将具有药理活性的天然产物转化为具有所需性质和活性的易于合成的新小分子。计算活动预测和自动化合物生成提供了系统地将具有药用活性的天然产物财富转移到合成小分子药物发现的可能性。我们提出了一些有前景的例子,并对未来天然产物启发的药物发现进行了预测。
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引用次数: 0
Spotlight on Tepotinib and Capmatinib for Non-Small Cell Lung Cancer with MET Exon 14 Skipping Mutation. 聚焦特泊替尼和卡马替尼治疗MET 14外显子跳越突变的非小细胞肺癌。
IF 5.1 Pub Date : 2022-05-13 eCollection Date: 2022-01-01 DOI: 10.2147/LCTT.S360574
Danielle Brazel, Shannon Zhang, Misako Nagasaka

Mesenchymal-epithelial transition (MET) receptor tyrosine kinase is overexpressed, amplified, or mutated in 1-20% of NSCLC. MET dysregulation is associated with a poor prognosis. Recently, development of targeted therapies against MET exon 14 mutations has demonstrated efficacy and tolerability in early trials. Here we focus on tepotinib and capmatinib in regards to molecular characteristics, early preclinical and clinical data, and the emerging role in future studies and clinical practice.

间质-上皮转化(MET)受体酪氨酸激酶在 1-20% 的 NSCLC 中过度表达、扩增或突变。MET 失调与预后不良有关。最近,针对 MET 14 号外显子突变的靶向疗法在早期试验中显示出了疗效和耐受性。在此,我们将重点介绍特泊替尼(tepotinib)和卡马替尼(capmatinib)的分子特征、早期临床前和临床数据以及在未来研究和临床实践中的新作用。
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引用次数: 0
期刊
Journal of The American Dietetic Association
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