Article
Biochemical Research Methods
Yu Zhang, Yichao Cai, Xavier Roca, Chee Keong Kwoh, Melissa Jane Fullwood
Summary: The study developed machine learning models using ChIA-PET data, demonstrating the importance of chromatin loop anchors in predicting transcript and exon usage.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biotechnology & Applied Microbiology
Zihao Zhang, Haian Zhong, Shudai Lin, Li Liang, Shaopan Ye, Zhenqiang Xu, Congliang Ji, Zhe Zhang, Dexiang Zhang, Xiquan Zhang
Summary: The study found significant associations between multiple SNPs in the genomic regions of the AMY1A gene and traits such as feed intake efficiency, growth traits, and carcass characteristics in chickens. Haplotypes based on specific SNPs in AMY1A were also found to be significantly associated with important traits like daily gain and abdominal fat. This research provides substantial evidence for the potential impact of AMY1A polymorphisms on chicken breeding programs.
Article
Biochemical Research Methods
Abhijit Chakraborty, Ferhat Ay, Ramana Davuluri
Summary: This study introduces a novel method called ExTraMapper, which accurately maps fine-scale orthology relationships at the exon and transcript levels using sequence conservation between exons of different organisms. By analyzing data from human and mouse, the method identifies a greater number of exon and transcript mappings, improving the correlation of transcript-specific expression levels.
Article
Biochemical Research Methods
Tobias Tekath, Martin Dugas
Summary: DTUrtle is a software package for analyzing bulk and single-cell RNA-seq datasets, allowing for transcript-level differential analysis with various result aggregation, visualization options, and a novel detection probability score. Successfully applied to human and mouse data, potential applications include identifying cell-type specific transcript isoforms.
Article
Biotechnology & Applied Microbiology
Jiazhong Guo, Rui Jiang, Ayi Mao, George E. Liu, Siyuan Zhan, Li Li, Tao Zhong, Linjie Wang, Jiaxue Cao, Yu Chen, Guojun Zhang, Hongping Zhang
Summary: The study identified two major genetic loci on chromosome 1 affecting the polled phenotype in goats. A diagnostic PCR method was also provided for accurately classifying horned, polled, and PIS-affected goats.
Article
Multidisciplinary Sciences
Yonathan Tilahun, Jessica Quijada Pinango, Felicia Johnson, Charles Lett, Kayla Smith, Terry Gipson, Malcolm McCallum, Peter Hoyt, Andrew Tritt, Archana Yadav, Mostafa Elshahed, Zaisen Wang
Summary: This study investigates the changes in hematological parameters and microbiome composition in Alpine goats parasitized by the barber pole worm. The results show that the blood samples of infected goats exhibit specific transcripts and an increase in microflora abundance and diversity as the goats age.
SCIENTIFIC REPORTS
(2022)
Article
Agriculture, Dairy & Animal Science
Ales Knoll, Michaela Nesvadbova, Tomas Urban
Summary: NREP gene plays a critical role in muscle transformation in pigs, with higher expression levels in Czech Large White pigs compared to wild boars and positive associations with meat-related traits, suggesting its potential as a marker for selection in improving pork production.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2022)
Article
Cell & Tissue Engineering
Anne Z. Eriksen, Rasmus Moller, Bar Makovoz, Skyler A. Uhl, Benjamin R. tenOever, Timothy A. Blenkinsop
Summary: The SARS-CoV-2 pandemic has caused unprecedented global disruption and significant loss of life. The eye may serve as a portal for viral entry, with potential implications for direct infection by SARS-CoV-2.
Article
Biochemical Research Methods
Alma Andersson, Joakim Lundeberg
Summary: In this study, a novel method was proposed to analyze spatial transcriptomics data, which simulated the diffusion of individual transcripts to extract genes with spatial patterns, generating satisfactory results on synthetic and real data. Compared to existing methods, this approach seemed to be less influenced by gene expression levels and showed better time performance when run with multiple cores.
Article
Genetics & Heredity
Chun Huang, Fei Ge, Wenwen Ren, Yongfeng Zhang, Xiaoyun Wu, Qiang Zhang, Xiaoming Ma, Pengjia Bao, Xian Guo, Min Chu, Ping Yan, Chunnian Liang
Summary: This study investigated the relationship between CNV of the HPGDS gene and growth traits in Ashidan yaks. Significant correlations were found between HPGDS-CNV and body weight as well as body length at different ages, indicating its potential as a candidate gene for marker-assisted selection (MAS) in yaks.
Article
Genetics & Heredity
Chun Huang, Fei Ge, Wenwen Ren, Yongfeng Zhang, Xiaoyun Wu, Qiang Zhang, Xiaoming Ma, Pengjia Bao, Xian Guo, Min Chu, Ping Yan, Chunnian Liang
Summary: In this study, significant correlations were observed between HPGDS-CNV and growth traits of Ashidan yaks. Individuals with gain copy number type performed better in body weight and body length compared to those with normal or loss copy number type, suggesting HPGDS gene CNV as a potential candidate for marker-assisted selection (MAS) in yaks.
Article
Genetics & Heredity
Chun Huang, Fei Ge, Wenwen Ren, Yongfeng Zhang, Xiaoyun Wu, Qiang Zhang, Xiaoming Ma, Pengjia Bao, Xian Guo, Min Chu, Ping Yan, Chunnian Liang
Summary: The study found that CNV of the HPGDS gene is correlated with growth traits in Ashidan yaks, with individuals having a gain copy number type performing better in body weight and body length. This suggests that the CNV of the HPGDS gene may be a candidate gene for marker-assisted selection of yaks.
Article
Plant Sciences
Jiangyan Xiong, Danyi Chen, Tingting Su, Qiufang Shen, Dezhi Wu, Guoping Zhang
Summary: This study investigated the SnRK family in barley, identifying 46 members classified into 3 sub-families. Through phylogenetic and conserved motif analyses, insights into the gene structures and evolutionary features of HvSnRKs were obtained. The researchers also found that HvSnRKs play a crucial role in responding to abiotic stress in barley.
Article
Genetics & Heredity
Chun Huang, Fei Ge, Wenwen Ren, Yongfeng Zhang, Xiaoyun Wu, Qiang Zhang, Xiaoming Ma, Pengjia Bao, Xian Guo, Min Chu, Ping Yan, Chunnian Liang
Summary: This study identified significant correlations between CNV of the HPGDS gene and growth traits in Ashidan yaks, with individuals having gain copy number type outperforming in body weight and body length. The findings suggest that the CNV of the HPGDS gene may be a potential candidate for marker-assisted selection in yaks.
Article
Plant Sciences
Juyun Zheng, Zeliang Zhang, Zhaolong Gong, Yajun Liang, Zhiwei Sang, Yanchao Xu, Xueyuan Li, Junduo Wang
Summary: This study analyzed the population structure and genetic diversity of 149 cotton plant materials, and identified SNP markers associated with salt tolerance traits using genome-wide association analysis. The findings provide insights into the genetic mechanisms underlying salt tolerance in cotton and can be used for the selection and breeding of salt-tolerant cotton varieties.
Article
Cell Biology
Maria Emilia Taskinen, Elisa Narva, James R. W. Conway, Laura Soto Hinojosa, Sergio Lilla, Anja Mai, Nicola De Franceschi, Laura L. Elo, Robert Grosse, Sara Zanivan, Jim C. Norman, Johanna Ivaska
JOURNAL OF CELL BIOLOGY
(2020)
Article
Cell Biology
James Ronald William Conway, Elisa Narva, Maria Emilia Taskinen, Johanna Ivaska
Article
Neurosciences
Jacopo Troisi, Reija Autio, Thanos Beopoulos, Carmela Bravaccio, Federica Carraturo, Giulio Corrivetti, Stephen Cunningham, Samantha Devane, Daniele Fallin, Serguei Fetissov, Manuel Gea, Antonio Giorgi, Francois Iris, Lokesh Joshi, Sarah Kadzielski, Aletta Kraneveld, Himanshu Kumar, Christine Ladd-Acosta, Geraldine Leader, Arlene Mannion, Elise Maximin, Alessandra Mezzelani, Luciano Milanesi, Laurent Naudon, Lucia N. Peralta Marzal, Paula Perez Pardo, Naika Z. Prince, Sylvie Rabot, Guus Roeselers, Christophe Roos, Lea Roussin, Giovanni Scala, Francesco Paolo Tuccinardi, Alessio Fasano
Article
Endocrinology & Metabolism
Leena Hakola, Iris Erlund, David Cuthbertson, Maija E. Miettinen, Reija Autio, Anita M. Nucci, Taina Harkonen, Jarno Honkanen, Outi Vaarala, Heikki Hyoty, Mikael Knip, Jeffrey P. Krischer, Sari Niinisto, Suvi M. Virtanen
Summary: Certain serum fatty acids are directly associated with the risk of islet autoimmunity in high-risk children, suggesting a potential role in the development of type 1 diabetes that warrants further investigation.
PEDIATRIC DIABETES
(2021)
Article
Cell Biology
Kai Liu, Lingjia Kong, Daniel B. Graham, Kimberly L. Carey, Ramnik J. Xavier
Summary: Phosphoinositides play a crucial role in regulating host innate defense response to intracellular bacterial replication. SAC1, a phosphoinositide phosphatase, is identified as an essential regulator of xenophagy. Loss of SAC1 leads to increased bacterial replication by impairing fusion between autophagosomes and lysosomes.
Article
Multidisciplinary Sciences
Elisa Narva, Maria E. Taskinen, Sergio Lilla, Aleksi Isomursu, Mika Pietila, Jere Weltner, Jorma Isola, Harri Sihto, Heikki Joensuu, Sara Zanivan, Jim Norman, Johanna Ivaska
Summary: MASTL plays an important role in stem cells and breast cancer progression, with its effects mediated through pathways such as TGFBR2 to regulate stemness factors.
Article
Health Care Sciences & Services
Helena Leppanen, Olli Kampman, Reija Autio, Tino Karolaakso, Turkka Nappila, Paivi Rissanen, Sami Pirkola
Summary: The study showed that in Finland, individuals with lower socioeconomic status were less likely to receive rehabilitative psychotherapy. Education level was found to be the most significant factor associated with the use of psychotherapy among CMD patients.
BMC HEALTH SERVICES RESEARCH
(2022)
Article
Engineering, Biomedical
Sini Riivari, Elisa Narva, Ilkka Kangasniemi, Jaana Willberg, Timo Narhi
Summary: This study compared the adhesion of epithelial cells and the expression of adhesion proteins on sol-gel prepared TiO2-coated and non-coated zirconia and titanium alloy surfaces. The results showed that coated zirconia and titanium discs had higher cell attachment and adhesion protein expression compared to non-coated discs. This suggests that the TiO2-coating has the potential to enhance mucosal attachment on implant surfaces.
JOURNAL OF BIOMEDICAL MATERIALS RESEARCH PART B-APPLIED BIOMATERIALS
(2022)
Article
Psychiatry
Tino Karolaakso, Reija Autio, Petra Suontausta, Helena Leppanen, Paivi Rissanen, Turkka Nappila, Martti T. Tuomisto, Sami Pirkola
Summary: The purpose of this study was to examine the association between Finnish municipalities' mental health service provision and the risk of mood disorder disability pensions. The findings showed that higher service richness and diversity were associated with a lower risk of disability pensions. These results suggest that the organization and structure of mental health services play a role in psychiatric disability pensioning and that richness and diversity can serve as quality indicators for regional mental health services.
SOCIAL PSYCHIATRY AND PSYCHIATRIC EPIDEMIOLOGY
(2023)
Article
Psychology, Clinical
Helena Leppanen, Olli Kampman, Reija Autio, Tino Karolaakso, Paivi Rissanen, Turkka Nappila, Sami Pirkola
Summary: Low socioeconomic status is a risk factor for work disability due to common mental disorders, which may be due to inequal use of services. This study examines differences in psychotherapy attendance based on socioeconomic and sociodemographic factors and explores the association between psychotherapy duration and return to work among individuals with temporary work disability.
PSYCHOTHERAPY RESEARCH
(2023)
Article
Public, Environmental & Occupational Health
Noora Seilo, Susanna Paldanius, Reija Autio, Kristina Kunttu, Minna Kaila
Summary: This study examined factors associated with university entrants' attendance at health checks. The results showed that male gender and low engagement with studies were strongly associated with non-attendance. On the other hand, having a low state of mind was negatively associated with non-attendance, indicating that it increased health check attendance. The study suggests that providing health checks in student health care can be an effective way of reaching students with health concerns.
ENVIRONMENTAL HEALTH AND PREVENTIVE MEDICINE
(2022)
Article
Humanities, Multidisciplinary
Paivi Rissanen, Reija Autio, Turkka Nappila, Sari Frojd, Sami Pirkola
Summary: The study found that being a lower-grade employee significantly promoted return to work for women, while being a manual worker did the same for men. In addition, psychotherapy and vocational rehabilitation were associated with an increased probability of return to work.
HUMANITIES & SOCIAL SCIENCES COMMUNICATIONS
(2021)
Article
Cell Biology
Kimberly L. Carey, Geraldine L. C. Paulus, Lingfei Wang, Dale R. Balce, Jessica W. Luo, Phil Bergman, Ianina C. Ferder, Lingjia Kong, Nicole Renaud, Shantanu Singh, Maria Kost-Alimova, Beat Nyfeler, Kara G. Lassen, Herbert W. Virgin, Ramnik J. Xavier
Article
Multidisciplinary Sciences
Mohd Moin Khan, Ubaid Ullah, Meraj H. Khan, Lingjia Kong, Robert Moulder, Tommi Valikangas, Santosh Dilip Bhosale, Elina Komsi, Omid Rasool, Zhi Chen, Laura L. Elo, Jukka Westermarck, Riitta Lahesmaa
Article
Health Care Sciences & Services
Susanna Paldanius, Noora Seilo, Kristina Kunttu, Reija Autio, Minna Kaila
JMIR RESEARCH PROTOCOLS
(2020)
