Relationship between rice farming and polygenic scores potentially linked to agriculture in China.
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ABSTRACT:
SUBMITTER: Zhu C
PROVIDER: S-EPMC8371358 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundCognitive impairment is a clinically important feature of schizophrenia. Polygenic risk score (PRS) methods have demonstrated genetic overlap between schizophrenia, bipolar disorder (BD), major depressive disorder (MDD), educational attainment (EA), and IQ, but very few studies have examined associations between these PRS and cognitive phenotypes within schizophrenia cases.MethodsWe combined genetic and cognitive data in 3034 schizophrenia cases from 11 samples using the general intelligence factor g as the primary measure of cognition. We used linear regression to examine the association between cognition and PRS for EA, IQ, schizophrenia, BD, and MDD. The results were then meta-analyzed across all samples. A genome-wide association studies (GWAS) of cognition was conducted in schizophrenia cases.ResultsPRS for both population IQ (P = 4.39 × 10-28) and EA (P = 1.27 × 10-26) were positively correlated with cognition in those with schizophrenia. In contrast, there was no association between cognition in schizophrenia cases and PRS for schizophrenia (P = .39), BD (P = .51), or MDD (P = .49). No individual variant approached genome-wide significance in the GWAS.ConclusionsCognition in schizophrenia cases is more strongly associated with PRS that index cognitive traits in the general population than PRS for neuropsychiatric disorders. This suggests the mechanisms of cognitive variation within schizophrenia are at least partly independent from those that predispose to schizophrenia diagnosis itself. Our findings indicate that this cognitive variation arises at least in part due to genetic factors shared with cognitive performance in populations and is not solely due to illness or treatment-related factors, although our findings are consistent with important contributions from these factors.
| S-EPMC7442352 | biostudies-literature
Project description:Recent large-scale, genome-wide association studies (GWAS) have identified hundreds of genetic loci associated with general intelligence. The cumulative influence of these loci on brain structure is unknown. We examined if cortical morphology mediates the relationship between GWAS-derived polygenic scores for intelligence (PSi) and g-factor. Using the effect sizes from one of the largest GWAS meta-analysis on general intelligence to date, PSi were calculated among 10 P value thresholds. PSi were assessed for the association with g-factor performance, cortical thickness (CT), and surface area (SA) in two large imaging-genetics samples (IMAGEN N = 1651; IntegraMooDS N = 742). PSi explained up to 5.1% of the variance of g-factor in IMAGEN (F1,1640 = 12.2-94.3; P < 0.005), and up to 3.0% in IntegraMooDS (F1,725 = 10.0-21.0; P < 0.005). The association between polygenic scores and g-factor was partially mediated by SA and CT in prefrontal, anterior cingulate, insula, and medial temporal cortices in both samples (PFWER-corrected < 0.005). The variance explained by mediation was up to 0.75% in IMAGEN and 0.77% in IntegraMooDS. Our results provide evidence that cumulative genetic load influences g-factor via cortical structure. The consistency of our results across samples suggests that cortex morphology could be a novel potential biomarker for neurocognitive dysfunction that is among the most intractable psychiatric symptoms.
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Project description:Patient experience is an important dimension of health care quality and is assessed using the standard Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) survey for inpatients. The HCAHPS scores may vary based on survey response rate and hospital size. The objective of this study was to describe the association between survey response rate and HCAHPS scores and examine whether the relationship varies based on hospital size. Medicare's Hospital Compare publicly reported HCAHPS data were used. Pearson correlation, controlling for number of staffed beds, and linear regression models were used for the analysis. Hospitals were grouped into quartiles based on number of staffed beds to delineate the effect of increasing hospital size on the relationship between survey response rate and HCAHPS scores. A significant association between HCAHPS survey response rate and all examined HCAHPS domain scores was observed. The effect size across HCAHPS domains varied based on hospital size. The relationship between HCAHPS score and survey response rate differed significantly between hospitals in the smallest and largest size quartiles for discharge information, nurse communication, and hospital quietness. While a causal relationship cannot be inferred from this study, the response rate could be a direct and/or indirect driver of HCAHPS scores. Future research should be aimed to further explore the basis of this relationship and to determine how it may inform the interpretation of HCAHPS results.
| S-EPMC7786668 | biostudies-literature
Project description:The sustainable development of agriculture is one of the key issues of ensuring food security and mitigating climate change. Since innovative large-scale agriculture is gaining popularity in cities in China, where the agricultural landscape is dominated by conventional smallholder farming, it is necessary to investigate the difference in carbon emissions between conventional smallholder operation and innovative largescale agriculture. This study evaluated the carbon footprint (CF) of conventional and innovative urban agriculture in Beijing using the cradle-to-consumption Life Cycle Assessment (LCA). Two modes of greenhouse vegetable and fruit production were analyzed and compared respectively: conventional smallholder operated vegetable farms that sell in local markets versus largescale home-delivery agriculture (HDA) that deliver vegetables to consumers' home directly, conventional smallholder operated fruit farms that sell in farm shops versus largescale pick-your-own (PYO) initiatives. Results showed that HDA and PYO can reduce CF per area in on-farm cultivation compared to smallholder operation, while may bring an increase in CF per product weight unit and the gap was wider if the supply chain was considered. This is mainly because innovative large-scale farming consumes fewer agricultural inputs (e.g., fertilizer, pesticides) and obtains lower yields than conventional smallholder operations. Plastic materials with high carbon emission, fossil energy dependence and transportation efficiency are CF hotspots of both modes and therefore can be prioritized and targeted for carbon reduction adjustment. The results of this work further advance understanding of how innovative largescale agriculture and conventional smallholder operation compare and which particular inputs and activities should be prioritized to effectively reduce the CF in China during agricultural transformation.
| S-EPMC8253110 | biostudies-literature
Project description:Schizophrenia is a multifactorial disease associated with widespread cognitive impairment. Although cognitive deficits are one of the factors most strongly associated with functional impairment in schizophrenia (SZ), current treatment strategies hardly tackle these impairments. To develop more efficient treatment strategies in patients, a better understanding of their pathogenesis is needed. Recent progress in genetics, driven by large genome-wide association studies (GWAS) and the use of polygenic risk scores (PRS), has provided new insights about the genetic architecture of complex human traits, including cognition and SZ. Here, we review the recent findings examining the genetic links between SZ and cognitive functions in population-based samples as well as in participants with SZ. The performed meta-analysis showed a negative correlation between the polygenetic risk score of schizophrenia and global cognition (p < 0.001) when the samples rely on general and healthy participants, while no significant correlation was detected when the three studies devoted to schizophrenia patients were meta-analysed (p > 0.05). Our review and meta-analysis therefore argues against universal pleiotropy for schizophrenia alleles and cognition, since cognition in SZ patients would be underpinned by the same genetic factors than in the general population, and substantially independent of common variant liability to the disorder.
| S-EPMC7074036 | biostudies-literature
Project description:Information on the effects of changing agricultural management on crop and livestock performance is critical for developing evidence-based policies, investments, and programs. Evidence for Resilient Agriculture (ERA) v1.0.1 presents a dataset that harmonizes and aggregates 112,859 observations from 2,011 agricultural studies taken place in Africa between 1934 and 2018. The dataset includes information on the effect of 364 combinations of management practices and technologies on 87 environmental, social, and economic indicators of outcomes. Observations are geolocated and temporally tagged and thus can be linked to other datasets such as historical weather, soil properties, and road networks. ERA offers a new resource for understanding the impacts of changing farming practices under diverse environmental contexts, providing data to support strategic interventions aimed to enhance productivity, resilience, and sustainability of African agriculture.
| S-EPMC11372062 | biostudies-literature
Project description:Data recently published in PNAS mapped out regional differences in the tightness of social norms across China [R. Y. J. Chua, K. G. Huang, M. Jin, Proc. Natl. Acad. Sci. U.S.A. 116, 6720-6725 (2019)]. Norms were tighter in developed, urbanized areas and weaker in rural areas. We tested whether historical paddy rice farming has left a legacy on social norms in modern China. Premodern rice farming could plausibly create strong social norms because paddy rice relied on irrigation networks. Rice farmers coordinated their water use and kept track of each person's labor contributions. Rice villages also established strong norms of reciprocity to cope with labor demands that were twice as high as dryland crops like wheat. In line with this theory, China's historically rice-farming areas had tighter social norms than wheat-farming areas, even beyond differences in development and urbanization. Rice-wheat differences were just as large among people in 10 neighboring provinces (n = 3,835) along the rice-wheat border. These neighboring provinces differ sharply in rice and wheat, but little in latitude, temperature, and other potential confounding variables. Outside of China, rice farming predicted norm tightness in 32 countries around the world. Finally, people in rice-farming areas scored lower on innovative thinking, which tends to be lower in societies with tight norms. This natural test case within China might explain why East Asia-historically reliant on rice farming-has tighter social norms than the wheat-farming West.
| S-EPMC7443949 | biostudies-literature
Project description:BackgroundPolygenic risk scores (PRS) serve as valuable tools for connecting initial genetic discoveries with clinical applications in disease risk estimation. However, limited studies have explored the association between PRS and gestational diabetes mellitus (GDM), particularly in predicting GDM risk among Chinese populations.AimTo evaluate the relationship between PRS and GDM and explore the predictive capability of PRS for GDM risk in a Chinese population.MethodsA prospective cohort study was conducted, which included 283 GDM and 2,258 non-GDM cases based on demographic information on pregnancies. GDM was diagnosed using the oral glucose tolerance test (OGTT) at 24-28 weeks. The strength of the association between PRS and GDM odds was assessed employing odds ratios (ORs) with 95% confidence intervals (CIs) derived from logistic regression. Receiver operating characteristic curves, net reclassification improvement (NRI), and integrated discrimination improvement (IDI) were employed to evaluate the improvement in prediction achieved by the new model.ResultsWomen who developed GDM exhibited significantly higher PRS compared to control individuals (OR = 2.01, 95% CI = 1.33-3.07). The PRS value remained positively associated with fasting plasma glucose (FPG), 1-hour post-glucose load (1-h OGTT), and 2-hour post-glucose load (2-h OGTT) (all p < 0.05). The incorporation of PRS led to a statistically significant improvement in the area under the curve (0.71, 95% CI: 0.66-0.75, p = 0.024) and improved discrimination and classification (IDI: 0.007, 95% CI: 0.003-0.012, p < 0.001; NRI: 0.258, 95% CI: 0.135-0.382, p < 0.001).ConclusionsThis study highlights the increased odds of GDM associated with higher PRS values and modest improvements in predictive capability for GDM.
| S-EPMC11333217 | biostudies-literature
Project description:Polygenic risk scores (PRS) are proposed for use in clinical and research settings for risk stratification. However, there are limited investigations on how different PRS diverge from each other in risk prediction of individuals. We compared two recently published PRS for each of three conditions, breast cancer, hypertension and dementia, to assess the stability of using these algorithms for risk prediction in a single large population. We used imputed genotyping data from the UK Biobank prospective cohort, limited to the White British subset. We found that: (1) 20% or more of SNPs in the first PRS were not represented in the more recent PRS for all three diseases, by the same SNP or a surrogate with R2 > 0.8 by linkage disequilibrium (LD). (2) Although the difference in the area under the receiver operating characteristic curve (AUC) obtained using the two PRS is hardly appreciable for all three diseases, there were large differences in individual risk prediction between the two PRS. For instance, for each disease, of those classified in the top 5% of risk by the first PRS, over 60% were not so classified by the second PRS. We found substantial discordance between different PRS for the same disease, indicating that individuals could receive different medical advice depending on which PRS is used to assess their genetic susceptibility. It is desirable to resolve this uncertainty before using PRS for risk stratification in clinical settings.
| S-EPMC9329440 | biostudies-literature
Project description:BackgroundPolygenic risk scores (PRS) are valuable to translate the results of genome-wide association studies (GWAS) into clinical practice. To date, most GWAS have been based on individuals of European-ancestry leading to poor performance in populations of non-European ancestry.ResultsWe introduce the polygenic transcriptome risk score (PTRS), which is based on predicted transcript levels (rather than SNPs), and explore the portability of PTRS across populations using UK Biobank data.ConclusionsWe show that PTRS has a significantly higher portability (Wilcoxon p=0.013) in the African-descent samples where the loss of performance is most acute with better performance than PRS when used in combination.
| S-EPMC8759285 | biostudies-literature