| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Elsik, Christine G., et al.
(författare)
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The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
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Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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| 3. |
- Sodergren, Erica, et al.
(författare)
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The genome of the sea urchin Strongylocentrotus purpuratus.
- 2006
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 314:5801, s. 941-52
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Tidskriftsartikel (refereegranskat)abstract
- We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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| 4. |
- Bränn, Emma, et al.
(författare)
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Bidirectional association between autoimmune disease and perinatal depression : a nationwide study with sibling comparison
- 2024
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Ingår i: Molecular Psychiatry. - : Springer Nature. - 1359-4184 .- 1476-5578. ; 29:3, s. 602-610
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Tidskriftsartikel (refereegranskat)abstract
- Although major depression, characterized by a pro-inflammatory profile, genetically overlap with autoimmune disease (AD) and the perinatal period involve immune system adaptations and AD symptom alterations, the bidirectional link between perinatal depression (PND) and AD is largely unexplored. Hence, the objective of this study was to investigate the bidirectional association between PND and AD. Using nationwide Swedish population and health registers, we conducted a nested case-control study and a matched cohort study. From 1,347,901 pregnancies during 2001-2013, we included 55,299 incident PND, their unaffected full sisters, and 10 unaffected matched women per PND case. We identified 41 subtypes of AD diagnoses recorded in the registers and compared PND with unaffected population-matched women and full sisters, using multivariable regressions. Women with an AD had a 30% higher risk of subsequent PND (95% CI 1.2-1.5) and women exposed to PND had a 30% higher risk of a subsequent AD (95% CI 1.3-1.4). Comparable associations were found when comparing exposed women with their unaffected sisters (nested case-control OR: 1.3, 95% CI 1.2-1.5, matched cohort HR: 1.3, 95% CI 1.1-1.6), and when studying antepartum and postpartum depression. The bidirectional association was more pronounced among women without psychiatric comorbidities (nested case-control OR: 1.5, 95% CI 1.4-1.6, matched cohort HR: 1.4, 95% CI 1.4-1.5) and strongest for multiple sclerosis (nested case-control OR: 2.0, 95% CI 1.6-2.3, matched cohort HR: 1.8, 95% CI 1.0-3.1). These findings demonstrate a bidirectional association between AD and PND independent of psychiatric comorbidities, suggesting possibly shared biological mechanisms. If future translational science confirms the underlying mechanisms, healthcare providers need to be aware of the increased risk of PND among women with ADs and vice versa.
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| 5. |
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| 6. |
- Chen, Yufeng
(författare)
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An epidemiological study on nasopharyngeal carcinoma
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Nasopharyngeal carcinoma (NPC) is a malignancy known for its unique geographic and ethnic distribution characterized by particularly high incidence in southern China, Southeast Asia, and North and East Africa, but being rare in the rest of the world. Its etiology has remained enigmatic and the accumulated evidence suggests that genetic predisposition, environmental factors, and infection with Epstein-Barr virus (EBV) are involved. Nevertheless, the association between environmental exposures and NPC carcinogenesis remains largely elusive to date, and how environmental risk factors interact with EBV in the development of NPC has been rarely studied. In addition, oral microbiome is emerging as a vital factor contributing to carcinogenic processes, but its role in NPC is largely unknown. The overall aim of this thesis is to provide more solid evidence and precise insights into the etiology of NPC, with focus on the associations of NPC with environmental, viral, and other microbial factors. To address these knowledge gaps, we carried out a large-scale population-based case-control study entitled NPC Genes, Environment, and EBV (NPCGEE) in southern China from 2010 to 2014. In short, 2,554 histopathologically confirmed, incident NPC cases, and 2,648 controls frequency matched to cases on age, sex and geographic area from general population were recruited. In Study I, we investigated the magnitude and pattern of associations between NPC and various residential exposures. Based on the NPCGEE study questionnaire data of a lifelong residential history, we found poor residential conditions including living in inferior housing types, using less clean fuels for cooking, house with poor ventilation, using untreated water sources, exposure to smoke when cooking, burning incense, and residential proximity to a factory area, were associated with a higher risk of NPC, and the associations were notably stronger for exposures at young ages. In Study II, we examined the relationship of NPC risk with occupational exposures based also on the NPCGEE study. With the analysis of the complete occupational history data, we found significantly elevated risk of NPC associated with exposures to broad categories of occupational pollutants, including dusts, chemical vapors, exhausts/smokes, and acids/alkalis. These associations were primarily explained by 14 subtypes of occupational agents within the above-mentioned broad categories. Moreover, the strengths of the associations were generally stronger with increasing duration of exposure. In Study III, we assessed whether there is an association between environmental factors and EBV reactivation, a critical step in the NPC carcinogenesis, in the healthy population controls of the NPCGEE study. Overall, we found no associations between EBV reactivation and extensive environmental factors, including alcohol or tea drinking, a history of chronic ear/nose/throat diseases, use of medications or herbs, consumption of salted fish or other preserved foods, oral hygiene, sibship structure, and various residential and occupational exposures. Cigarette smoking is the only factor associated with EBV reactivation. In Study IV, we investigated the relationship between oral fungal microbiome and NPC status using Internal Transcribed Spacer (ITS)-2 sequencing in a subset of NPCGEE study samples (538 NPC patients, 537 controls). We found a significantly reduced fungal community richness and diversity in NPC patients compared with those in controls, and the global fungal community compositions significantly differed between cases and controls. Furthermore, a number of differentially abundant oral fungal organisms in NPC cases and healthy controls were identified. In conclusion, findings from this thesis work support that individuals exposed to both residential and occupational risk factors are at increased risk of NPC. Most environmental factors, except for cigarette smoking, are not likely to induce EBV reactivation; other mechanisms such as host genetic and viral variations in the EBV reactivation deserve to be further studied. Dysbiotic oral mycobiome characterized by reduced community richness and diversity, as well as an increased abundance in pathogenic fungi and a decrease in commensal fungi may contribute to the development of NPC.
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| 7. |
- Chen, Yufeng, et al.
(författare)
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Incidence Trajectories of Psychiatric Disorders After Assault, Injury, and Bereavement
- 2024
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Ingår i: JAMA psychiatry. - : American Medical Association (AMA). - 2168-6238 .- 2168-622X. ; 81:4, s. 374-385
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Tidskriftsartikel (refereegranskat)abstract
- IMPORTANCE: Traumatic events have been associated with elevated risks of psychiatric disorders, while the contributions of familial factors to these associations remain less clear.OBJECTIVE: To determine the contribution of familial factors to long-term incidence trajectories of psychiatric disorders following potentially traumatic events.DESIGN, SETTING, AND PARTICIPANTS: This cohort study evaluated 3 separate cohorts of individuals residing in Sweden who were free of previous diagnosed psychiatric disorders when first exposed to assault (n = 49 957), injury (n = 555 314), or bereavement (n = 321 263) from January 1987 to December 2013, together with their unexposed full siblings, and 10 age-, sex-, and birthplace-matched unexposed individuals (per exposed individual). Cohorts were created from the Swedish Total Population Register linked to health and population registers. Data were analyzed from March 2022 to April 2023.EXPOSURES: Potentially traumatic events, including various types of assault, injuries, and bereavement (death of a child or of a spouse or partner), were ascertained from the Swedish national registers.MAIN OUTCOMES AND MEASURES: Incident psychiatric disorders were ascertained from the Swedish Patient Register. Flexible parametric and Cox models were used to estimate associations of potentially traumatic events with incident psychiatric disorders after multivariable adjustment.RESULTS: The median (IQR) age at exposure to assault, injury, and bereavement was 22 (18-31), 19 (8-40), and 60 (51-68) years, respectively. During a median (IQR) follow-up of 4.9 (2.2-8.2), 9.1 (4.1-15.6), and 8.1 (3.4-14.8) years, the incidence rates of any psychiatric disorder were 38.1, 13.9, and 9.0 per 1000 person-years for the exposed groups of the 3 cohorts, respectively. Elevated risk of any psychiatric disorder was observed during the first year after exposure to any assault (hazard ratio [HR], 4.55; 95% CI, 4.34-4.77), injury (HR, 3.31; 95% CI,3.23-3.38), or bereavement (HR, 2.81; 95% CI, 2.72-2.91) and thereafter (assault HR, 2.50; 95% CI, 2.43-2.56; injury HR, 1.69; 95% CI, 1.68-1.70; bereavement HR, 1.42; 95% CI, 1.40-1.44). Comparable associations were obtained in sibling comparison (first year: assault HR, 3.70; 95% CI, 3.37-4.05; injury HR, 2.98; 95% CI, 2.85-3.12; bereavement HR, 2.72; 95% CI, 2.54-2.91; thereafter: assault HR, 1.93; 95% CI, 1.84-2.02; injury HR, 1.51; 95% CI, 1.48-1.53; bereavement HR, 1.35; 95% CI, 1.31-1.38). The risk elevation varied somewhat by type of traumatic events and psychiatric disorders, with the greatest HR noted for posttraumatic stress disorder after sexual assault (sibling comparison HR, 4.52; 95% CI, 3.56-5.73 during entire follow-up period).CONCLUSIONS AND RELEVANCE: In this study, the long-term risk elevation of psychiatric disorders after potentially traumatic events was largely independent of familial factors. The risk elevation observed immediately after these events motivates early clinical surveillance and mental health services for these vulnerable populations.
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| 8. |
- Chen, Yufeng
(författare)
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Loss Filtering Factor for Crowd Counting
- 2024
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Ingår i: PATTERN RECOGNITION AND COMPUTER VISION, PRCV 2023, PT III. - : Springer Nature. - 9789819984343 - 9789819984350 ; , s. 3-15
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Konferensbidrag (refereegranskat)abstract
- In crowd counting datasets, each person is annotated by a point, typically representing the center of the head. However, due to the dense crowd, variety of scenarios, significant obscuration and low resolution, label noise in the dataset is inevitable and such label noise has a negative impact on the performance of the model. To alleviate the negative effects of label noise, in this paper we propose the Loss Filtering Factor, which can filter out the losses assumed to be caused by label noise during the training process. By doing so, the model can prioritize non-noise data and focus on it during training and predicting. Extensive experimental evaluations have demonstrated that the proposed Loss Filtering Factor consistently improves the performance of all models across all datasets used in the experiments. On average, it leads to a 5.48% improvement in MAE and 6.43% in MSE. Moreover, the proposed approach is universal and it can be easily implemented into any neural network model architecture to improve performance.
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| 9. |
- Chen, Yufeng, et al.
(författare)
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Oral fungal profiling and risk of nasopharyngeal carcinoma : a population-based case-control study
- 2023
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Ingår i: EBioMedicine. - 2352-3964. ; 96
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Dysbiosis of the oral mycobiome has been linked to some diseases, including cancers. However, the role of oral fungal communities in nasopharyngeal carcinoma (NPC) carcinogenesis has not previously been investigated.METHODS: We characterized the oral salivary fungal mycobiome in 476 untreated incident NPC patients and 537 population-based controls using fungal internal transcribed spacer (ITS)-2 sequencing. The relationship between oral fungal mycobiome and the risk of NPC was assessed through bioinformatic and biostatistical analyses.FINDINGS: We found that lower fungal alpha diversity was associated with an increased odds of NPC [lower vs. higher: observed features (adjusted odds ratio [OR] = 5.81, 95% confidence interval [CI] = 3.60-9.38); Simpson diversity (1.53, 1.03-2.29); Shannon diversity (2.03, 1.35-3.04)]. We also observed a significant difference in global fungal community patterns between cases and controls based on Bray-Curtis dissimilarity (P < 0.001). Carriage of oral fungal species, specifically, Saccharomyces cerevisiae, Candida tropicalis, Lodderomyces elongisporus, Candida albicans, and Fusarium poae, was associated with significantly higher odds of NPC, with ORs ranging from 1.56 to 4.66. Individuals with both low fungal and low bacterial alpha diversity had a profoundly elevated risk of NPC.INTERPRETATION: Our results suggest that dysbiosis in the oral mycobiome, characterized by a loss of fungal community diversity and overgrowth of several fungal organisms, is associated with a substantially increased risk of NPC.FUNDING: This work was funded by the US National Institutes of Health, the Swedish Research Council, the High-level Talents Research Start-up Project of Fujian Medical University, and the China Scholarship Council.
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| 10. |
- Jiao, Xiang, et al.
(författare)
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Comparative analysis of nonlinear growth curve models for Arabidopsis thaliana rosette leaves
- 2018
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Ingår i: Acta Physiologiae Plantarum. - : Springer. - 0137-5881 .- 1861-1664. ; 40:6
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Tidskriftsartikel (refereegranskat)abstract
- As a model organism, modeling and analysis of the phenotype of Arabidopsis thaliana (A. thaliana) leaves for a given genotype can help us better understand leaf growth regulation. A. thaliana leaves growth trajectories are to be nonlinear and the leaves contribute most to the above-ground biomass. Therefore, analysis of their change regulation and development of nonlinear growth models can better understand the phenotypic characteristics of leaves (e.g., leaf size) at different growth stages. In this study, every individual leaf size of A. thaliana rosette leaves was measured during their whole life cycle using non-destructive imaging measurement. And three growth models (Gompertz model, logistic model and Von Bertalanffy model) were analyzed to quantify the rosette leaves growth process of A. thaliana. Both graphical (plots of standardized residuals) and numerical measures (AIC, R2 and RMSE) were used to evaluate the fitted models. The results showed that the logistic model fitted better in describing the growth of A. thaliana leaves compared to Gompertz model and Von Bertalanffy model, as it gave higher R2 and lower AIC and RMSE for the leaves of A. thaliana at different growth stages (i.e., early leaf, mid-term leaf and late leaf).
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