129 Works

Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges

Beatriz Portinha, Amaury Avril, Christian Bernasconi, Heikki Heläntera, Josie Monaghan, Bernhard Seifert, Vítor C. Sousa, Jonna Kulmuni & Pierre Nouhaud
The application of demographic history modelling and inference to the study of divergence between species has become a cornerstone of speciation genomics. Speciation histories are usually reconstructed by analysing single populations from each species, assuming that the inferred population history represents the actual speciation history. However, this assumption may not be met when species diverge with gene flow, e.g., when secondary contact may be confined to specific geographic regions. Here, we tested whether divergence histories...

Natal dispersal does not entail survival costs but is linked to breeding dispersal in a migratory shorebird, the southern dunlin Calidris alpina schinzii

Veli-Matti Pakanen, Veli-Matti Pakanen, Kari Koivula, Blandine Doligez, Lars-Åke Flodin, Angela Pauliny, Nelli Rönkä & Donald Blomqvist
The costs and benefits of dispersal are often assessed by comparing fitness between dispersing and non-dispersing individuals. Importantly, individuals that disperse between their natal and first breeding site may subsequently be more likely to disperse between breeding sites compared to those that remained philopatric to their natal site. Such within-individual consistency in dispersal behaviour can bias local survival estimation, and thus the survival comparison between dispersing and non-dispersing individuals, if breeding dispersal leads to permanent...

Additional file 6 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 6. Figure S3: Prognostic values of postsurgical ctDNA detection at 3 months and 6 months. A-B) The recurrence-free survival analysis (top panel) and multi-variant Cox regression (bottom panel) of postsurgical ctDNA detection at 3 months (A) and 6 months (B). For the analysis at 6 months after surgeries, only patients with plasma samples available at this scheduled point and followed-up for more than 6 months were included. Abbreviations: RFS – recurrence-free survival, LNM...

Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Abstract Background Circulating tumor DNA (ctDNA) has been proven as a marker for detecting minimal residual diseases following systemic therapies in mid-to-late-stage non-small-cell lung cancers (NSCLCs) by multiple studies. However, fewer studies cast light on ctDNA-based MRD monitoring in early-to-mid-stage NSCLCs that received surgical resection as the standard of care. Methods We prospectively recruited 128 patients with stage I–III NSCLCs who received curative surgical resections in our Lung Cancer Tempo-spatial Heterogeneity prospective cohort. Plasma samples...

Additional file 12 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 12. Supplementary discussion.

Additional file 2 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 2. Table S2: Adjuvant treatment information.

Additional file 4 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 4. Figure S1: Availability of plasma samples. The availability of plasma samples for analysis at each schedule collection time point. Blue and red blocks denote samples collected before and after disease recurrence, respectively. Abbreviations: LUAD – lung adenocarcinoma, LUSC - lung squamous-cell carcinoma, RFS – recurrence-free survival, AT – adjuvant therapy, RT – radiotherapy, LNM – lymph node metastasis.

Additional file 2 of Randomized controlled trials in de-implementation research: a systematic scoping review

Aleksi J. Raudasoja, Petra Falkenbach, Robin W. M. Vernooij, Jussi M. J. Mustonen, Arnav Agarwal, Yoshitaka Aoki, Marco H. Blanker, Rufus Cartwright, Herney A. Garcia-Perdomo, Tuomas P. Kilpeläinen, Olli Lainiala, Tiina Lamberg, Olli P. O. Nevalainen, Eero Raittio, Patrick O. Richard, Philippe D. Violette, Jorma Komulainen, Raija Sipilä & Kari A. O. Tikkinen
Additional file 2. Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) Checklist.

A novel neo-sex chromosome in Sylvietta brachyura (Macrosphenidae) adds to the extraordinary avian sex chromosome diversity among Sylvioidea songbirds

Hanna Sigeman
We report the discovery of a novel neo-sex chromosome in an African warbler, Sylvietta brachyura (northern crombec; Macrosphenidae). This species is part of the Sylvioidea superfamily, where four separate autosome–sex chromosome translocation events have previously been discovered via comparative genomics of 11 of the 22 families in this clade. Our discovery here resulted from analyses of genomic data of single-species representatives from three additional Sylvioidea families (Macrosphenidae, Pycnonotidae, and Leiothrichidae). In all three species, we...

Altered dynamic functional connectivity in rectal cancer patients with and without chemotherapy: a resting-state fMRI study

Qin Zhang, Wenwen Zhang, Pengfei Zhang, Ziyang Zhao, Lin Yang, Fang Zheng, Lingyu Zhang, Gang Huang, Jing Zhang, Weihao Zheng, Rong Ma, Zhijun Yao & Bin Hu
Purpose: Understanding the mechanism of brain functional alterations in rectal cancer (RC) patients is of great significance to improve the prognosis and quality of life of patients. Additionally, the influence of chemotherapy on brain function in RC patients is still unclear. In this study, we aimed to investigate the alterations of brain functional network dynamics in RC patients and explore the effects of chemotherapy on temporal dynamics of dynamic functional connectivity (DFC). Methods: The group...

Additional file 2 of Use of antibiotics and risk of type 2 diabetes, overweight and obesity: the Cardiovascular Risk in Young Finns Study and the national FINRISK study

Joel Nuotio, Teemu Niiranen, Tomi T. Laitinen, Jessica Miller, Matthew A. Sabin, Aki S. Havulinna, Jorma S. A. Viikari, Tapani Rönnemaa, Nina Hutri-Kähönen, Tomi P. Laitinen, Päivi Tossavainen, Veikko Salomaa, Olli T. Raitakari, David P. Burgner & Markus Juonala
Additional file 2.

Additional file 2 of Use of antibiotics and risk of type 2 diabetes, overweight and obesity: the Cardiovascular Risk in Young Finns Study and the national FINRISK study

Joel Nuotio, Teemu Niiranen, Tomi T. Laitinen, Jessica Miller, Matthew A. Sabin, Aki S. Havulinna, Jorma S. A. Viikari, Tapani Rönnemaa, Nina Hutri-Kähönen, Tomi P. Laitinen, Päivi Tossavainen, Veikko Salomaa, Olli T. Raitakari, David P. Burgner & Markus Juonala
Additional file 2.

Additional file 3 of Use of antibiotics and risk of type 2 diabetes, overweight and obesity: the Cardiovascular Risk in Young Finns Study and the national FINRISK study

Joel Nuotio, Teemu Niiranen, Tomi T. Laitinen, Jessica Miller, Matthew A. Sabin, Aki S. Havulinna, Jorma S. A. Viikari, Tapani Rönnemaa, Nina Hutri-Kähönen, Tomi P. Laitinen, Päivi Tossavainen, Veikko Salomaa, Olli T. Raitakari, David P. Burgner & Markus Juonala
Additional file 3.

Additional file 3 of Use of antibiotics and risk of type 2 diabetes, overweight and obesity: the Cardiovascular Risk in Young Finns Study and the national FINRISK study

Joel Nuotio, Teemu Niiranen, Tomi T. Laitinen, Jessica Miller, Matthew A. Sabin, Aki S. Havulinna, Jorma S. A. Viikari, Tapani Rönnemaa, Nina Hutri-Kähönen, Tomi P. Laitinen, Päivi Tossavainen, Veikko Salomaa, Olli T. Raitakari, David P. Burgner & Markus Juonala
Additional file 3.

Antioxidant supplements relieve insulin resistance but do not improve lipid metabolism in women with polycystic ovary syndrome: a meta-analysis of randomized clinical trials

Ruye Wang, Chenyun Miao, Yun Chen, Ying Zhao, Liuqing Yang, Wei Cheng & Qin Zhang
Objective: The effect of antioxidant supplements on glucose metabolism and lipid profiles in polycystic ovary syndrome (PCOS) remains controversial. This systematic review and meta-analysis aimed to evaluate whether antioxidant supplements improve glucose metabolism and lipid profiles in women with PCOS to provide optimal nutritional supplement advice in clinical practice. Methods: The search was conducted across multiple medical databases from inception to January 1, 2022 and performed following the Preferred Reporting Items for Systematic Reviews and...

Additional file 2 of MED12 mutation as a potential predictive biomarker for immune checkpoint inhibitors in pan-cancer

Yong Zhou, Yuan Tan, Qin Zhang, Qianqian Duan & Jun Chen
Additional file 2: Fig. S2. The pan-cancer landscape of MED12 mutations across human tumors. The proportion of MED12 mutated tumors identified for each cancer type with alteration frequency in TCGA pan-cancer cohorts.

Additional file 5 of MED12 mutation as a potential predictive biomarker for immune checkpoint inhibitors in pan-cancer

Yong Zhou, Yuan Tan, Qin Zhang, Qianqian Duan & Jun Chen
Additional file 5: Table S1. Detailed clinical information of the five WES cohorts and the MSKCC cohort.

MED12 mutation as a potential predictive biomarker for immune checkpoint inhibitors in pan-cancer

Yong Zhou, Yuan Tan, Qin Zhang, Qianqian Duan & Jun Chen
Abstract Immune checkpoint inhibitors (ICIs) therapy elicits admirable anti-tumor responses across many types of cancer. Growing evidence point to a link to Mediator complex subunit 12 (MED12) and DNA damage repair (DDR) and TGF-β signing, while the clinical data on the association of MED12 and ICIs response are lacking. In this study, clinical and whole-exome sequencing (WES) data from published studies were merged as a WES cohort to explore the association between MED12 mutation (MED12-Mut)...

Supplemental Material - The Association of Metformin, Other Antidiabetic Medications, and Statins With the Prognosis of Colon Cancer in Patients With Type 2 Diabetes: A Retrospective Cohort Study

Sami Erkinantti, Ari Hautakoski, Reijo Sund, Martti Arffman, Elina Urpilainen, Ulla Puistola, Arja Jukkola, Karihtala Peeter & Esa Läärä
Supplemental Material for The Association of Metformin, Other Antidiabetic Medications, and Statins With the Prognosis of Colon Cancer in Patients With Type 2 Diabetes: A Retrospective Cohort Study by Sami Erkinantti, Ari Hautakoski, Reijo Sund, Martti Arffman, Elina Urpilainen, Ulla Puistola, Arja Jukkola, Peeter Karihtala, and Esa Läärä in Cancer Control

The Association of Metformin, Other Antidiabetic Medications, and Statins With the Prognosis of Colon Cancer in Patients With Type 2 Diabetes: A Retrospective Cohort Study

Sami Erkinantti, Ari Hautakoski, Reijo Sund, Martti Arffman, Elina Urpilainen, Ulla Puistola, Arja Jukkola, Karihtala Peeter & Esa Läärä
BackgroundUse of metformin and statins have been associated with improved prognosis of colon cancer (CC) in patients with type 2 diabetes (T2D). We examined the survival from CC in relation to the use of metformin, other oral antidiabetic medications (ADM), insulin, and statins in T2D patients.Materials and MethodsA cohort (n = 2252) of persons with pre-existing T2D diagnosed with incident CC between 1998 and 2011 was identified from several Finnish registers. Cox models were fitted...

Additional file 1 of Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing

Dan Wang, Kerui Xie, Yanyan Wang, Jiaqing Hu, Wenqiang Li, Aiguo Yang, Qin Zhang, Chao Ning & Xinzhong Fan
Additional file 1: Figure S1. Venn diagram illustrating the number of the variants called by BaseVar, GATK and Bcftools. Figure S2. CLR and Pi analyses in the Angora rabbit population. Figure S3. Q-Q plots for the Angora rabbits. Figure S4. Manhattan plots for the Angora rabbits.

Additional file 1 of Economic evaluation of infliximab, synthetic triple therapy and methotrexate in the treatment of newly diagnosed juvenile idiopathic arthritis

Maarit Tarkiainen, Pirjo Tynjälä, Paula Vähäsalo, Kristiina Aalto, Liisa Kröger, Katariina Rebane, Pekka Lahdenne & Janne Martikainen
Additional file 1. Resource use during the first year treatment of Juvenile Idiopathic Arthritis.

Satellite-based agricultural water consumption assessment in the ungauged and transboundary Helmand Basin between Iran and Afghanistan

Mahdi Akbari & Ali Torabi Haghighi
Hamun Lake, the greatest (>8500 km2) freshwater in the Iran plateau, has almost entirely dried over the last 20 years. The flow of the Hirmand (or Helmand) River, the most important feeding river, has decreased from 4.0 to 1.9 km3 in the border of Iran-Afghanistan. In this river basin, the annual water consumption for irrigation is over 90% of the total consumed water. This study aims to calculate the increase in agricultural water consumption in...

Additional file 1 of Factors associated with body size perception among adolescent goal-oriented sports participants and non-participants: a cross-sectional Finnish study

Leevi Mäkituomas, Laura Heikkilä, Marjukka Nurkkala, Raija Korpelainen, Lauri Alanko, Olli J. Heinonen, Sami Kokko, Urho Kujala, Jari Parkkari, Kai Savonen, Maarit Valtonen, Tommi Vasankari, Jari Villberg & Marja Vanhala
Additional file 1: Supplementary Table 1. Motives to exercise by competitive goals in sports. Supplementary Table 2. Motives to exercise by body size perception.

Maternally-transferred thyroid hormones and life-history variation in birds

Bin-Yan Hsu Hsu, Veli-Matti Pakanen, Winnie Boner, Blandine Doligez, Tapio Eeva, Ton Groothuis, Erkki Korpimäki, Toni Laaksonen, Asmoro Lelono, Pat Monaghan, Tom Sarraude, Robert Thomson, Jere Tolvanen, Barbara Tschirren, Rodrigo Vásquez & Suvi Ruuskanen
1. In vertebrates, thyroid hormones (THs) play an important role in the regulation of growth, development, metabolism, photoperiodic responses and migration. Maternally transferred THs are important for normal early-phase embryonic development when embryos are not able to produce endogenous THs. Previous studies have shown that variation in maternal THs within the physiological range can influence offspring phenotype. 2. Given the essential functions of maternal THs in development and metabolism, THs may be a mediator of...

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