410 Works

Molecular detection and identification of relapsing fever Borrelia in ticks and wild small mammals in China

Xiao-Ai Zhang, Feng Tian, Yue Li, Xiao-Long Zhang, Bao-Gui Jiang, Bao-Cheng Liu, Jing-Tao Zhang, Shen Tian, Heng Ding, Shuang Li, Hao Li, Li-Qun Fang & Wei Liu
We identified relapsing fever (RF) Borrelia in 1.45% (145/10426) of the ticks and 1.40% (40/2850) of the wild mammals in a field investigation in China. Three RF Borrelia species, including human-pathogenic Borrelia miyamotoi, Borrelia persica and unclassified Babesia sp. were determined. Main species determined from ticks was B. miyamotoi (44.14%), followed by the unclassified Borrelia sp. (42.76%), and Borrelia theileri (13.10%). In wild mammals, main species found was B. persica (57.50%), followed by the unclassified...

Additional file 2 of SWI/SNF complex gene variations are associated with a higher tumor mutational burden and a better response to immune checkpoint inhibitor treatment: a pan-cancer analysis of next-generation sequencing data corresponding to 4591 cases

Yue Li, Xinhua Yang, Weijie Zhu, Yuxia Xu, Jiangjun Ma, Caiyun He & Fang Wang
Additional file 2: Fig. S2 The progression-free survival (PFS) of patients receiving immune checkpoint inhibitor (ICI) treatment based on cancer types. The survival analysis was performed for individual cancer types that contained at least 10 cases in the SWI/SNF-mutant or SWI/SNF-non-mutant groups. The PFS of the SWI/SNF-mutant group was significantly superior to that of the SWI/SNF-non-mutant group in colorectal cancer (a) and gastric cancer (b), the same tendency was significant numerically by not statistically in...

SWI/SNF complex gene variations are associated with a higher tumor mutational burden and a better response to immune checkpoint inhibitor treatment: a pan-cancer analysis of next-generation sequencing data corresponding to 4591 cases

Yue Li, Xinhua Yang, Weijie Zhu, Yuxia Xu, Jiangjun Ma, Caiyun He & Fang Wang
Abstract Background Genes related to the SWItch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex are frequently mutated across cancers. SWI/SNF-mutant tumors are vulnerable to synthetic lethal inhibitors. However, the landscape of SWI/SNF mutations and their associations with tumor mutational burden (TMB), microsatellite instability (MSI) status, and response to immune checkpoint inhibitors (ICIs) have not been elucidated in large real-world Chinese patient cohorts. Methods The mutational rates and variation types of six SWI/SNF complex genes (ARID1A, ARID1B, ARID2,...

Targeted OUM1/PTPRZ1 silencing and synergetic CDT/enhanced chemical therapy toward uveal melanoma based on a dual-modal imaging-guided manganese metal–organic framework nanoparticles

Yue Li, Fang Li, Hui Pan, Xiaolin Huang, Jie Yu, Xueru Liu, Qinghao Zhang, Caiwen Xiao, He Zhang & Leilei Zhang
Abstract Metastasis and chemical resistance are the most serious problems in the treatment of highly aggressive uveal melanoma (UM). The newly identified lncRNA OUM1 is overexpressed in UM, functions as a catalyst and regulates protein tyrosine phosphatase (PTP) activity by binding to PTP receptor type Z1 (PTPRZ1), which plays an important role in cell proliferation, metastasis and chemotherapy resistance in the UM microenvironment. Hence, siRNAs that selectively knocking down the lncRNA OUM1 (siOUM1) and its...

A multi-country study on the impact of sex and age on oral features of COVID-19 infection in adolescents and young adults

Heba Jafar Sabbagh, Wafaa Abdelaziz, Maryam Quritum, Rana Abdullah Alamoudi, Nada Abu Bakr AlKhateeb, Joud Abourdan, Nafeesa Qureshi, Shabnum Qureshi, Ahmed H. N. Hamoud, Nada Mahmoud, Ruba Odeh, Nuraldeen Maher Al-Khanati, Rawiah Jaber, Abdulrahman Loaie Balkhoyor, Mohammed Shabi, Morenike Oluwatoyin Folayan, Omolola Alade, Noha Gomaa, Raqiya Alnahdi, Nawal A. Mahmoud, Hanane El Wazziki, Manal Alnaas, Bahia Samodien, Rawa A. Mahmoud, Nour Abu Assab … & Maha El Tantawi
Abstract Background Oral diseases are features of COVID-19 infection. There is, however, little known about oral diseases associated with COVID-19 in adolescents and young adults (AYA). Therefore, the aim of this study was to assess oral lesions’ association with COVID-19 infection in AYA; and to identify if sex and age will modify these associations. Methodology Data was collected for this cross-sectional study between August 2020 and January 2021 from 11-to-23 years old participants in 43-countries...

Data from: Selection bias in mutation accumulation

Lindi Wahl & Deepa Agashe
Mutation accumulation (MA) experiments, in which de novo mutations are sampled and subsequently characterized, are an essential tool in understanding the processes underlying evolution. In microbial populations, MA protocols typically involve a period of population growth between severe bottlenecks, such that a single individual can form a visible colony. While it has long been appreciated that the action of positive selection during this growth phase cannot be eliminated, it is typically assumed to be negligible....

sj-docx-1-cjk-10.1177_20543581221129442 – Supplemental material for The Living Kidney Donor Safety Study: Protocol of a Prospective Cohort Study

Amit X. Garg, Jennifer B. Arnold, Meaghan Cuerden, Christine Dipchand, Liane S. Feldman, John S. Gill, Martin Karpinski, Scott Klarenbach, Greg A. Knoll, Charmaine Lok, Matthew Miller, Mauricio Monroy-Cuadros, Christopher Nguan, G. V. Ramesh Prasad, Jessica M. Sontrop, Leroy Storsley & Neil Boudville
Supplemental material, sj-docx-1-cjk-10.1177_20543581221129442 for The Living Kidney Donor Safety Study: Protocol of a Prospective Cohort Study by Amit X. Garg, Jennifer B. Arnold, Meaghan Cuerden, Christine Dipchand, Liane S. Feldman, John S. Gill, Martin Karpinski, Scott Klarenbach, Greg A. Knoll, Charmaine Lok, Matthew Miller, Mauricio Monroy-Cuadros, Christopher Nguan, G. V. Ramesh Prasad, Jessica M. Sontrop, Leroy Storsley and Neil Boudville in Canadian Journal of Kidney Health and Disease

Additional file 1 of Comparative transcriptomic analysis provides insights into the molecular basis underlying pre-harvest sprouting in rice

Dong Liu, Mingyang Zeng, Yan Wu, Yanli Du, Jianming Liu, Shaoqiang Luo & Yongjun Zeng
Additional file 1: Fig. S1. Heatmap showing the results of pairwise correlation analyses between different samples.

Additional file 2 of Comparative transcriptomic analysis provides insights into the molecular basis underlying pre-harvest sprouting in rice

Dong Liu, Mingyang Zeng, Yan Wu, Yanli Du, Jianming Liu, Shaoqiang Luo & Yongjun Zeng
Additional file 2: Table S1. The list of annotated DEGs identified in JXZ-T vs. JXZ-C.

Additional file 6 of Comparative transcriptomic analysis provides insights into the molecular basis underlying pre-harvest sprouting in rice

Dong Liu, Mingyang Zeng, Yan Wu, Yanli Du, Jianming Liu, Shaoqiang Luo & Yongjun Zeng
Additional file 6: Table S5. The results of KEGG enrichment of DEGs in JXZ-T vs. JXZ-C.

Additional file 8 of Comparative transcriptomic analysis provides insights into the molecular basis underlying pre-harvest sprouting in rice

Dong Liu, Mingyang Zeng, Yan Wu, Yanli Du, Jianming Liu, Shaoqiang Luo & Yongjun Zeng
Additional file 8: Table S7. Summary of GO results of the DEGs in JXZ-T vs. JXZ-C.

Additional file 11 of Comparative transcriptomic analysis provides insights into the molecular basis underlying pre-harvest sprouting in rice

Dong Liu, Mingyang Zeng, Yan Wu, Yanli Du, Jianming Liu, Shaoqiang Luo & Yongjun Zeng
Additional file 11: Table S10. The list of representative DEGs related to carbon metabolism (associated with energy production).

Additional file 13 of Comparative transcriptomic analysis provides insights into the molecular basis underlying pre-harvest sprouting in rice

Dong Liu, Mingyang Zeng, Yan Wu, Yanli Du, Jianming Liu, Shaoqiang Luo & Yongjun Zeng
Additional file 13: Table S12. The list of representative DEGs related to phenylpropanoid biosynthesis.

Additional file 1 of Effective hospital readmission prediction models using machine-learned features

Sacha Davis, Jin Zhang, Ilbin Lee, Mostafa Rezaei, Russell Greiner, Finlay A. McAlister & Raj Padwal
Supplementary Material 1

Effective hospital readmission prediction models using machine-learned features

Sacha Davis, Jin Zhang, Ilbin Lee, Mostafa Rezaei, Russell Greiner, Finlay A. McAlister & Raj Padwal
Abstract Background: Hospital readmissions are one of the costliest challenges facing healthcare systems, but conventional models fail to predict readmissions well. Many existing models use exclusively manually-engineered features, which are labor intensive and dataset-specific. Our objective was to develop and evaluate models to predict hospital readmissions using derived features that are automatically generated from longitudinal data using machine learning techniques. Methods: We studied patients discharged from acute care facilities in 2015 and 2016 in Alberta,...

sj-pdf-1-cjk-10.1177_20543581221131201 – Supplemental material for Enhance Access to Kidney Transplantation and Living Kidney Donation (EnAKT LKD): Statistical Analysis Plan of a Registry-Based, Cluster-Randomized Clinical Trial

Stephanie N. Dixon, Kyla L. Naylor, Seychelle Yohanna, Susan McKenzie, Dmitri Belenko, Peter G Blake, Candice Coghlan, Rebecca Cooper, Lori Elliott, Leah Getchell, Vincent Ki, Istvan Mucsi, Gihad Nesrallah, Rachel E. Patzer, Justin Presseau, Marian Reich, Jessica M. Sontrop, Darin Treleaven, Amy D. Waterman, Jeffrey Zaltzman & Amit X. Garg
Supplemental material, sj-pdf-1-cjk-10.1177_20543581221131201 for Enhance Access to Kidney Transplantation and Living Kidney Donation (EnAKT LKD): Statistical Analysis Plan of a Registry-Based, Cluster-Randomized Clinical Trial by Stephanie N. Dixon, Kyla L. Naylor, Seychelle Yohanna, Susan McKenzie, Dmitri Belenko, Peter G Blake, Candice Coghlan, Rebecca Cooper, Lori Elliott, Leah Getchell, Vincent Ki, Istvan Mucsi, Gihad Nesrallah, Rachel E. Patzer, Justin Presseau, Marian Reich, Jessica M. Sontrop, Darin Treleaven, Amy D. Waterman, Jeffrey Zaltzman and Amit X. Garg...

Data from: Fine-scale genetic analysis of species-specific female preference in Drosophila simulans

Meghan Laturney & Amanda J. Moehring
Behavioral differences are thought to be the first components to contribute to species isolation, yet the precise genetic basis of behavioral isolation remains poorly understood. Here, we used a combination of behavior assays and genetic mapping to provide the first refined map locating candidate genes for interspecific female preference isolating Drosophila simulans from D. melanogaster. First, we tested whether two genes identified as affecting D. melanogaster female intraspecific mate choice also affect interspecific mate choice;...

Data from: Population genetic structure of the western cherry fruit fly Rhagoletis indifferens (Diptera: Tephritidae) in British Columbia, Canada

Sheri A. Maxwell, Howard M. A. Thistlewood & Nusha Keyghobadi
1. Population connectivity and movement are key ecological parameters influencing the impact of pests, and are important considerations in control strategies. For many insects, these parameters are difficult to assess directly, although they may be assessed indirectly using population genetic data. 2. We used microsatellite markers to examine population genetic structure of the western cherry fruit fly, the main pest of cherry crops in western North America, in British Columbia, Canada, and make inferences about...

Data from: Genes underlying altruism

Graham J. Thompson, Peter L. Hurd & Bernard J. Crespi
William D. Hamilton postulated the existence of 'genes underlying altruism', under the rubric of inclusive fitness theory, a half-century ago. Such genes are now poised for discovery. In this article we develop a set of intuitive criteria for the recognition and analysis of genes for altruism, and describe the first candidates for altruism genes from social insects and humans. We also provide evidence from a human population for genetically-based tradeoffs, underlain by oxytocin-system polymorphisms, between...

Data from: Assortative mating but no evidence of genetic divergence in a species characterized by a trophic polymorphism

S.F. Colborne, Shawn R. Garner, Fred J. Longstaffe, Bryan D. Neff & S. F. Colborne
Disruptive selection is a process that can result in multiple subgroups within a population, which is referred to as diversification. Foraging-related diversification has been described in many taxa, but many questions remain about the contribution of such diversification to reproductive isolation and potentially sympatric speciation. Here, we use stable isotope analysis of diet and morphological analysis of body shape to examine phenotypic divergence between littoral and pelagic foraging ecomorphs in a population of pumpkinseed sunfish...

Data from: Adaptation of a polyphagous herbivore to a novel host plant extensively shapes the transcriptome of herbivore and host

Nicky Wybouw, Vladimir Zhurov, Catherine Martel, Kristie A. Bruinsma, Frederik Hendrickx, Vojislava Grbić & Thomas Van Leeuwen
Generalist arthropod herbivores rapidly adapt to a broad range of host plants. However, the extent of transcriptional reprogramming in the herbivore and its hosts associated with adaptation remains poorly understood. Using the spider mite Tetranychus urticae and tomato as models with available genomic resources, we investigated the reciprocal genomewide transcriptional changes in both spider mite and tomato as a consequence of mite's adaptation to tomato. We transferred a genetically diverse mite population from bean to...

Data from: Effects of a 60 Hz magnetic field exposure up to 3000 µT on human brain activation as measured by functional magnetic resonance imaging

Alexandre Legros, Julien Modolo, Samantha Brown, John Robertson, Alex W. Thomas & John Roberston
Several aspects of the human nervous system and associated motor and cognitive processes have been reported to be modulated by extremely low-frequency (ELF, < 300 Hz) time-varying Magnetic Fields (MF). Due do their worldwide prevalence; power-line frequencies (60 Hz in North America) are of particular interest. Despite intense research efforts over the last few decades, the potential effects of 60 Hz MF still need to be elucidated, and the underlying mechanisms to be understood. In...

Data from: A cross-seasonal perspective on local adaptation: metabolic plasticity mediates responses to winter in a thermal-generalist moth

Caroline M. Williams, Wesley D. Chick & Brent J. Sinclair
The physiological and ecological impact of the thermal environment across life-stages can result in trade-offs that determine fitness and population dynamics. Understanding mechanisms and consequences of local adaptation for any organism that overwinters requires taking a cross-seasonal perspective. We used a trait-based approach to distinguish variation among ecotypes in ecological and physiological responses to overwintering conditions. We used fall webworms (Hyphantria cunea; Lepidoptera: Arctiidae) from Ottawa, Ontario and Columbus Ohio, representing the centre and periphery...

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