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Plant Phenomics (Washington, D.C.) 2024Grape cluster architecture and compactness are complex traits influencing disease susceptibility, fruit quality, and yield. Evaluation methods for these traits include...
Grape cluster architecture and compactness are complex traits influencing disease susceptibility, fruit quality, and yield. Evaluation methods for these traits include visual scoring, manual methodologies, and computer vision, with the latter being the most scalable approach. Most of the existing computer vision approaches for processing cluster images often rely on conventional segmentation or machine learning with extensive training and limited generalization. The Segment Anything Model (SAM), a novel foundation model trained on a massive image dataset, enables automated object segmentation without additional training. This study demonstrates out-of-the-box SAM's high accuracy in identifying individual berries in 2-dimensional (2D) cluster images. Using this model, we managed to segment approximately 3,500 cluster images, generating over 150,000 berry masks, each linked with spatial coordinates within their clusters. The correlation between human-identified berries and SAM predictions was very strong (Pearson's = 0.96). Although the visible berry count in images typically underestimates the actual cluster berry count due to visibility issues, we demonstrated that this discrepancy could be adjusted using a linear regression model (adjusted = 0.87). We emphasized the critical importance of the angle at which the cluster is imaged, noting its substantial effect on berry counts and architecture. We proposed different approaches in which berry location information facilitated the calculation of complex features related to cluster architecture and compactness. Finally, we discussed SAM's potential integration into currently available pipelines for image generation and processing in vineyard conditions.
PubMed: 38939746
DOI: 10.34133/plantphenomics.0202 -
Frontiers in Public Health 2024Ticks and pathogens they carry seriously impact human and animal health, with some diseases like Lyme and Alpha-gal syndrome posing risks. Searching for health...
INTRODUCTION
Ticks and pathogens they carry seriously impact human and animal health, with some diseases like Lyme and Alpha-gal syndrome posing risks. Searching for health information online can change people's health and preventive behaviors, allowing them to face the tick risks. This study aimed to predict the potential risks of tickborne diseases by examining individuals' online search behavior.
METHODS
By scrutinizing the search trends across various geographical areas and timeframes within the United States, we determined outdoor activities associated with potential risks of tick-related diseases. Google Trends was used as the data collection and analysis tool due to its accessibility to big data on people's online searching behaviors. We interact with vast amounts of population search data and provide inferences between population behavior and health-related phenomena. Data were collected in the United States from April 2022 to March 2023, with some terms about outdoor activities and tick risks.
RESULTS AND DISCUSSION
Results highlighted the public's risk susceptibility and severity when participating in activities. Our results found that searches for terms related to tick risk were associated with the five-year average Lyme Disease incidence rates by state, reflecting the predictability of online health searching for tickborne disease risks. Geographically, the results revealed that the states with the highest relative search volumes for tick-related terms were predominantly located in the Eastern region. Periodically, terms can be found to have higher search records during summer. In addition, the results showed that terms related to outdoor activities, such as "corn maze," "hunting," "u-pick," and "park," have moderate associations with tick-related terms. This study provided recommendations for effective communication strategies to encourage the public's adoption of health-promoting behaviors. Displaying warnings in the online search results of individuals who are at high risk for tick exposure or collaborating with outdoor activity locations to disseminate physical preventive messages may help mitigate the risks associated with tickborne diseases.
Topics: Humans; Tick-Borne Diseases; United States; Animals; Search Engine; Internet; Lyme Disease; Ticks; Information Seeking Behavior
PubMed: 38939559
DOI: 10.3389/fpubh.2024.1410713 -
JACC. Advances Jun 2024Abdominal aortic aneurysm (AAA) is an important cause of cardiovascular mortality.
BACKGROUND
Abdominal aortic aneurysm (AAA) is an important cause of cardiovascular mortality.
OBJECTIVES
The authors aimed to explore the associations between sleep patterns and genetic susceptibility to AAA.
METHODS
We included 344,855 UK Biobank study participants free of AAA at baseline. A sleep pattern was defined by chronotype, sleep duration, insomnia, snoring, and daytime sleepiness, and an overall sleep score was constructed with a range from 0 to 5, where a high score denotes a healthy sleep pattern. Polygenic risk score based on 22 single nucleotide polymorphisms was categorized into tertiles and used to evaluate the genetic risk for AAA. Cox proportional hazards regression models were used to assess the association between sleep, genetic factors, and the incidence of AAA.
RESULTS
During a median of 12.59 years of follow-up, 1,622 incident AAA cases were identified. The HR per 1-point increase in the sleep score was 0.91 (95% CI: 0.86-0.96) for AAA. Unhealthy sleep patterns, defined as a sleep score ranging from 0 to 3, were found to be associated with a higher risk of AAA for the intermediate (HR: 1.18, 95% CI: 1.06-1.31) and poor sleep patterns (HR: 1.40, 95% CI: 1.13-1.73), respectively, compared to the healthy pattern. Participants with poor sleep patterns and high genetic risks had a 2.5-fold higher risk of AAA than those with healthy sleep patterns and low genetic risk.
CONCLUSIONS
In this large prospective study, healthy sleep patterns were associated with a lower risk of AAA among participants with low, intermediate, or high genetic risk.
PubMed: 38938869
DOI: 10.1016/j.jacadv.2024.100967 -
Frontiers in Immunology 2024The comorbidity rate of inflammatory bowel disease (IBD) and rheumatoid arthritis (RA) is high; nevertheless, the reasons behind this high rate remain unclear. Their...
BACKGROUND
The comorbidity rate of inflammatory bowel disease (IBD) and rheumatoid arthritis (RA) is high; nevertheless, the reasons behind this high rate remain unclear. Their similar genetic makeup probably contributes to this comorbidity.
METHODS
Based on data obtained from the genome-wide association study of IBD and RA, we first assessed an overall genetic association by performing the linkage disequilibrium score regression (LDSC) analysis. Further, a local correlation analysis was performed by estimating the heritability in summary statistics. Next, the causality between the two diseases was analyzed by two-sample Mendelian randomization (MR). A genetic overlap was analyzed by the conditional/conjoint false discovery rate (cond/conjFDR) method.LDSC with specific expression of gene analysis was performed to identify related tissues between the two diseases. Finally, GWAS multi-trait analysis (MTAG) was also carried out.
RESULTS
IBD and RA are correlated at the genomic level, both overall and locally. The MR results suggested that IBD induced RA. We identified 20 shared loci between IBD and RA on the basis of a conjFDR of <0.01. Additionally, we identified two tissues, namely spleen and small intestine terminal ileum, which were commonly associated with both IBD and RA.
CONCLUSION
Herein, we proved the presence of a polygenic overlap between the genetic makeup of IBD and RA and provided new insights into the genetic architecture and mechanisms underlying the high comorbidity between these two diseases.
Topics: Arthritis, Rheumatoid; Humans; Genome-Wide Association Study; Inflammatory Bowel Diseases; Genetic Predisposition to Disease; Linkage Disequilibrium; Polymorphism, Single Nucleotide; Mendelian Randomization Analysis; Comorbidity
PubMed: 38938570
DOI: 10.3389/fimmu.2024.1359857 -
Frontiers in Endocrinology 2024Insulin resistance (IR) and beta cell dysfunction are the major drivers of type 2 diabetes (T2D). Genome-Wide Association Studies (GWAS) on IR have been predominantly...
Insulin resistance (IR) and beta cell dysfunction are the major drivers of type 2 diabetes (T2D). Genome-Wide Association Studies (GWAS) on IR have been predominantly conducted in European populations, while Middle Eastern populations remain largely underrepresented. We conducted a GWAS on the indices of IR (HOMA2-IR) and beta cell function (HOMA2-%B) in 6,217 non-diabetic individuals from the Qatar Biobank (QBB; Discovery cohort; n = 2170, Replication cohort; n = 4047) with and without body mass index (BMI) adjustment. We also developed polygenic scores (PGS) for HOMA2-IR and compared their performance with a previously derived PGS for HOMA-IR (PGS003470). We replicated 11 loci that have been previously associated with HOMA-IR and 24 loci that have been associated with HOMA-%B, at nominal statistical significance. We also identified a novel locus associated with beta cell function near gene, tagged by rs61552983 ( = 4.38 × 10). Moreover, our best performing PGS (Q-PGS4; Adj R = 0.233 ± 0.014; = 1.55 x 10) performed better than PGS003470 (Adj R = 0.194 ± 0.014; = 5.45 x 10) in predicting HOMA2-IR in our dataset. This is the first GWAS on HOMA2 and the first GWAS conducted in the Middle East focusing on IR and beta cell function. Herein, we report a novel locus in that is implicated in beta cell dysfunction. Inclusion of under-represented populations in GWAS has potentials to provide important insights into the genetic architecture of IR and beta cell function.
Topics: Humans; Insulin Resistance; Genome-Wide Association Study; Female; Male; Middle Aged; Multifactorial Inheritance; Diabetes Mellitus, Type 2; Adult; Qatar; Polymorphism, Single Nucleotide; Insulin-Secreting Cells; Aged; Body Mass Index; Cohort Studies; Genetic Predisposition to Disease
PubMed: 38938516
DOI: 10.3389/fendo.2024.1384103 -
Journal of Preventive Medicine and... Jun 2024Comorbidities increase susceptibility to severe coronavirus disease 2019 (COVID-19) infections, but limited information has been published regarding HIV and COVID-19...
OBJECTIVES
Comorbidities increase susceptibility to severe coronavirus disease 2019 (COVID-19) infections, but limited information has been published regarding HIV and COVID-19 co-infections. This study explored the relationships among socioeconomic characteristics, sexual behaviors, and COVID-19 infection rates among Korean men who have sex with men (MSMs) who are also living with HIV.
METHODS
Data were collected through a web survey aimed at members of the largest gay portal site in Korea, supported by the National Research Foundation of Korea (n=1,005). The primary independent variables included COVID-19-related vaccinations and sexual behaviors. The dependent variable was the incidence of COVID-19 infection among respondents during the pandemic. For statistical analysis, hierarchical multiple logistic regression was performed, controlling for potential confounding variables.
RESULTS
Model I indicated that older MSM were less likely to contract COVID-19 (adjusted odds ratio [aOR], 0.975; 95% CI, 0.962-0.989). Model II demonstrated that HIV-positive MSM were nearly twice as likely to be infected with COVID-19 compared to their HIV-negative counterparts (aOR, 1.974; 95% CI, 1.144-3.408). Furthermore, even after accounting for COVID-19 vaccination status in model III, HIV-positive MSM continued to show a higher risk of infection (aOR, 1.934; 95% CI, 1.118-3.346).
CONCLUSIONS
The findings of this study indicate that HIV-positive MSM are at an increased risk of contracting COVID-19, even when their vaccination status is considered. Therefore, it is essential to prioritize the prevention of COVID-19 infections in HIV-positive individuals by administering appropriate antiretroviral therapy and ensuring adherence to public health guidelines.
PubMed: 38938044
DOI: 10.3961/jpmph.24.196 -
BMC Psychiatry Jun 2024Observational studies have indicated a correlation between immunological inflammation and the risk of autism spectrum disorder (ASD). However, the causal relationship... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Observational studies have indicated a correlation between immunological inflammation and the risk of autism spectrum disorder (ASD). However, the causal relationship between immunological inflammation and ASD remains uncertain.
METHODS
Immunity-wide data sources were retrieved from the GWAS catalog. Genetic summary data on ASD were retrieved from two independent GWAS. We performed two independent bi-directional, two-sample Mendelian randomization (MR) analyses and a meta-analysis based on the two independent MR estimates to assess the causal relationship between ASD and immune cell signatures.
RESULTS
We have discovered 26 potential correlations between genetic predisposition in the immunophenotypes and ASD. The meta-analysis of the two inverse variance weighted (IVW)-produced estimates provided further evidence supporting the potential causal relationship between immunophenotypes and ASD. Based on the findings of the reverse MR analysis, it was determined that there are two potential negative causal relationships between ASD and immunophenotypes. However, the meta-analysis of the two IVW-derived MR estimates indicated that immunophenotypes were not significantly influenced by ASD (OR = 0.87, 95% CI = 0.73 -1.03, P = 0.09; OR = 0.91, 95% CI = 0.81-1.01, P = 0.08).
CONCLUSIONS
This study expanded immune cell subtypes that were potentially causally associated with ASD risk as well as identified ASD-specific immune cell subtypes. The discovery has the potential to lead to earlier detection and more effective treatment techniques.
Topics: Humans; Mendelian Randomization Analysis; Autism Spectrum Disorder; Genetic Predisposition to Disease; Genome-Wide Association Study; Immunophenotyping; Inflammation
PubMed: 38937836
DOI: 10.1186/s12888-024-05927-5 -
Immunity & Ageing : I & A Jun 2024Although it is well known that the older people have been the most susceptible to COVID-19, there are conflicting data on the susceptibility of centenarians. Two...
BACKGROUND
Although it is well known that the older people have been the most susceptible to COVID-19, there are conflicting data on the susceptibility of centenarians. Two epidemiological study have shown that older centenarians (> 101 years old at the time of the 2020 pandemic peak) are more resilient than the remaining centenarians, suggesting that this resilience might be linked to the 1918 Spanish Flu pandemic. To gain insight into this matter, specifically whether the resilience of older centenarians to SARS-CoV-2 infection is linked to the Spanish Flu they had been affected by, we conducted a retrospective serological study. This study examined serum samples from 33 centenarians, encompassing semi- (aged > 104 < 110 years, N = 7) and supercentenarians (aged > 109 years, N = 4), born between 1905 and 1922, against both SARS-CoV-2 and 1918 H1N1 pseudotype virus.
RESULTS
Anamnestic and laboratory data suggest that SARS-CoV-2 infection occurred in 8 centenarians. The infection appeared to have been asymptomatic or mild, and hospitalization was not required, despite 3 out of 8 being between 109 and 110 years old. The levels of anti-spike antibodies in centenarians infected and/or vaccinated were higher, although not significantly, than those produced by a random sample of seventy-year-old individuals used as controls. All centenarians had antibody levels against the 1918 H1N1 virus significantly higher (almost 50 times) than those observed in the quoted group of seventy-year-old subjects, confirming the key role in maintaining immunological memory from a priming that occurred over 100 years ago. Centenarians whose blood was collected prior to the pandemic outbreak demonstrated neutralising antibodies against the 1918 H1N1 virus, but all these subjects tested negative for SARS-CoV-2.
CONCLUSION
This retrospective study shows that older centenarians are quite resilient to COVID-19, as they are capable of producing good levels of neutralising antibodies and experiencing mild or asymptomatic disease. This could be attributed to the 1918 Spanish flu pandemic through mechanisms other than the presence of cross-reactive antibodies between the 1918 H1N1 virus and SARS-CoV-2. Another possibility is that the association is purely temporal, solely correlated with the advanced age of resilient centenarians compared to those born after 1918, since older centenarians are known to have better control of immune-inflammatory responses.
PubMed: 38937774
DOI: 10.1186/s12979-024-00450-3 -
Lipids in Health and Disease Jun 2024Digestive system cancers represent a significant global health challenge and are attributed to a combination of demographic and lifestyle changes. Lipidomics has emerged...
BACKGROUND
Digestive system cancers represent a significant global health challenge and are attributed to a combination of demographic and lifestyle changes. Lipidomics has emerged as a pivotal area in cancer research, suggesting that alterations in lipid metabolism are closely linked to cancer development. However, the causal relationship between specific lipid profiles and digestive system cancer risk remains unclear.
METHODS
Using a two-sample Mendelian randomization (MR) approach, we elucidated the causal relationships between lipidomic profiles and the risk of five types of digestive system cancer: stomach, liver, esophageal, pancreatic, and colorectal cancers. The aim of this study was to investigate the effect impact of developing lipid profiles on the risk of digestive system cancers utilizing data from public databases such as the GWAS Catalog and the UK Biobank. The inverse‒variance weighted (IVW) method and other strict MR methods were used to evaluate the potential causal links. In addition, we performed sensitivity analyses and reverse MR analyses to ensure the robustness of the results.
RESULTS
Significant causal relationships were identified between certain lipidomic traits and the risk of developing digestive system cancers. Elevated sphingomyelin (d40:1) levels were associated with a reduced risk of developing gastric cancer (odds ratio (OR) = 0.68, P < 0.001), while elevated levels of phosphatidylcholine (16:1_20:4) increased the risk of developing esophageal cancer (OR = 1.31, P = 0.02). Conversely, phosphatidylcholine (18:2_0:0) had a protective effect against colorectal cancer (OR = 0.86, P = 0.036). The bidirectional analysis did not suggest reverse causality between cancer risk and lipid levels. Strict MR methods demonstrated the robustness of the above causal relationships.
CONCLUSION
Our findings underscore the significant causal relationships between specific lipidomic traits and the risk of developing various digestive system cancers, highlighting the potential of lipid profiles in informing cancer prevention and treatment strategies. These results reinforce the value of MR in unraveling complex lipid-cancer interactions, offering new avenues for research and clinical application.
Topics: Humans; Mendelian Randomization Analysis; Digestive System Neoplasms; Genome-Wide Association Study; Lipid Metabolism; Lipids; Risk Factors; Lipidomics; Genetic Predisposition to Disease; Sphingomyelins; Esophageal Neoplasms
PubMed: 38937739
DOI: 10.1186/s12944-024-02191-0 -
Molecular Medicine (Cambridge, Mass.) Jun 2024Ubiquitin-specific protease 38 (USP38), belonging to the USP family, is recognized for its role in controlling protein degradation and diverse biological processes....
BACKGROUND
Ubiquitin-specific protease 38 (USP38), belonging to the USP family, is recognized for its role in controlling protein degradation and diverse biological processes. Ventricular arrhythmias (VAs) following heart failure (HF) are closely linked to ventricular electrical remodeling, yet the specific mechanisms underlying VAs in HF remain inadequately explored. In this study, we examined the impact of USP38 on VAs in pressure overload-induced HF.
METHODS
Cardiac-specific USP38 knockout mice, cardiac-specific USP38 transgenic mice and their matched control littermates developed HF induced by aortic banding (AB) surgery. After subjecting the mice to AB surgery for a duration of four weeks, comprehensive investigations were conducted, including pathological analysis and electrophysiological assessments, along with molecular analyses.
RESULTS
We observed increased USP38 expression in the left ventricle of mice with HF. Electrocardiogram showed that the USP38 knockout shortened the QRS interval and QTc, while USP38 overexpression prolonged these parameters. USP38 knockout decreased the susceptibility of VAs by shortening action potential duration (APD) and prolonging effective refractory period (ERP). In addition, USP38 knockout increased ion channel and Cx43 expression in ventricle. On the contrary, the increased susceptibility of VAs and the decreased expression of ventricular ion channels and Cx43 were observed with USP38 overexpression. In both in vivo and in vitro experiments, USP38 knockout inhibited TBK1/AKT/CAMKII signaling, whereas USP38 overexpression activated this pathway.
CONCLUSION
Our data indicates that USP38 increases susceptibility to VAs after HF through TBK1/AKT/CAMKII signaling pathway, Consequently, USP38 may emerge as a promising therapeutic target for managing VAs following HF.
Topics: Animals; Mice; Mice, Knockout; Ventricular Remodeling; Heart Failure; Ubiquitin-Specific Proteases; Disease Models, Animal; Male; Arrhythmias, Cardiac; Heart Ventricles; Mice, Transgenic; Signal Transduction; Electrocardiography
PubMed: 38937697
DOI: 10.1186/s10020-024-00846-3