Three-nucleotide periodicity of nucleotide diversity in a population enables the identification of open reading frames.

Accurate prediction of open reading frames (ORFs) is important for studying and using genome sequences. Ribosomes move along mRNA strands with a step of three nucleotides and datasets carrying this information can be used to predict ORFs. The ribosome-protected footprints (RPFs) feature a significant 3-nt periodicity on mRNAs and are powerful in predicting translating ORFs, including small ORFs (sORFs), but the application of RPFs is limited because they are too short to be accurately mapped in complex genomes. In this study, we found a significant 3-nt periodicity in the datasets of populational genomic variants in coding sequences, in which the nucleotide diversity increases every three nucleotides. We suggest that this feature can be used to predict ORFs and develop the Python package 'OrfPP', which recovers ~83% of the annotated ORFs in the tested genomes on average, independent of the population sizes and the complexity of the genomes. The novel ORFs, including sORFs, identified from single-nucleotide polymorphisms are supported by protein mass spectrometry evidence comparable to that of the annotated ORFs. The application of OrfPP to tetraploid cotton and hexaploid wheat genomes successfully identified 76.17% and 87.43% of the annotated ORFs in the genomes, respectively, as well as 4704 sORFs, including 1182 upstream and 2110 downstream ORFs in cotton and 5025 sORFs, including 232 upstream and 234 downstream ORFs in wheat. Overall, we propose an alternative and supplementary approach for ORF prediction that can extend the studies of sORFs to more complex genomes.

A survey of social network status and its related factors for older adults with type 2 diabetes in Beijing, China.

AIM: To understand the social network status of older adults with type 2 diabetes mellitus (T2DM) in Beijing, China and explore its related factors. DESIGN: A cross-sectional survey using a sample of convenience was conducted. METHODS: From April to September 2019, Lubben Social Network Scale-6 (LSNS-6) was used to evaluate the social network of 300 older adults with T2DM from the outpatient and inpatient departments of three hospitals and five communities in Beijing. Self-designed demographics and clinical sheets, Summary of Diabetes Self-Care Activities Scale, Social Support Rating Scale and Geriatric Depression Scale-15 were used to investigate the related factors of their social networks. The Equator Research Checklist used in this study is STROBE checklist. RESULTS: The score of LSNS-6 of the older adults was 16.75 ± 7.02 (scale: 0 ~ 30), the score of family network dimension was 8.32 ± 3.63 (scale: 0 ~ 15), and friends network dimension was 8.43 ± 4.74 (scale: 0 ~ 15). Additionally, 22.67% of the older adults had social isolation. Social support, medical payment, self-assessed health status, residential arrangement and smoking status were associated with the social network level of the older adults with T2DM (p < .05).

A new strain of Volutella citrinella with nematode predation and nematicidal activity, isolated from the cysts of potato cyst nematodes in China.

BACKGROUND: Plant parasitic nematodes (PPNs) are responsible for causing many plant diseases and are extremely difficult to control at present. Currently, due to the negative effects of chemical agents on the environment and human health, the development of new biological pesticides has become an important part of plant nematode control. Nematophagous fungi refers to a class of fungi that kill plant nematodes. Notably, a large number of nematophagous fungi resources remain to be studied. The objective of our study was to use in vitro screening to identify nematophagous fungi and select strains that were highly active against nematodes, providing a primary research for the development and utilization of new nematophagous fungi. RESULTS: A new nematophagous fungal strain (GUCC2219) was isolated from cysts of possibly Globodera spp. and Heterodera spp., identified as Volutella citrinella. The hyphae of V. citrinella produced ring structures of variable size and exhibited predatory and nematicidal activity. The hyphal predation rates (in vitro) against three species of nematodes, Aphelenchoides besseyi, Bursaphelenchus xylophilus, and Ditylenchus destructor, averaged 59.45, 33.35, and 50.95%, respectively, while the fermentation broth produced by the fungus exhibited mortality rates of 100, 100, and 55.63%, respectively, after 72 h. CONCLUSION: V. citrinella is a new strain with nematophagous properties, which are a novel discovery. At the same time, this is the first report of nematicidal and nematode predation activity in the genus Volutella.

Recurrence Rates After Microvascular Decompression in Patients With Primary Trigeminal Neuralgia and Its Influencing Factors: A Systematic Review and Meta-Analysis Based on 8,172 Surgery Patients.

Background: Primary trigeminal neuralgia (PTN) is known to reoccur following microvascular decompression (MVD) surgery. However, the rates and contributing factors related to PTN recurrence remain controversial. The purpose of this study was to explore the postoperative recurrence rates and related influencing factors of patients with PTN after MVD. Additionally, recurrence rates after different treatments were compared to provide guidelines for clinicians. Methods: We conducted systematic reviews and meta-analyses in accordance with the preferred reporting items of the PRISMA guidelines. We searched nine databases, namely, the PubMed, EMBASE, Cochrane Library, Web of Science, CINAHL, CBM, CNKI, VIP, and Wanfang databases, from establishment to July 13, 2020, selecting for studies about the long-term postoperative efficacy of MVD in the treatment of PTN. Factors associated with higher recurrence rates after MVD and long-term postoperative results of other treatments underwent formal meta-analysis, where odds ratios (ORs) with the corresponding 95% confidence intervals (CIs) were calculated. The dose-response model was used to inspect the associations between several factors and higher recurrence rates. Results: Seventy-four studies (8,172 patients, 32 case series studies, and 42 non-randomized controlled trials) were analyzed in our research. Overall, 956 out of 8,172 patients relapsed, and the pooled recurrence rate was 0.096 (0.080-0.113). Influencing factors of relatively higher recurrence rates included atypical trigeminal neuralgia symptoms, lack of nerve groove, non-arterial compression, patients who were 50-60 years old, and longer disease duration. Dose-response analysis showed that the recurrence rate had a significant trend with the published year and the follow-up time. Simultaneously, the recurrence rate of MVD treatment was much lower than that of conventional drug treatment, gamma knife surgery, percutaneous balloon compression, and radiofrequency thermocoagulation. When the surgical technique was improved or combined with partial sensory rhizotomy (PSR), the postoperative recurrence rates were significantly reduced. Conclusions: Even for PTN patients who have a successful operation, ~10% of them will still relapse. This research identifies several factors that can affect the recurrence rate. Compared with other operations, MVD has a relatively lower recurrence rate. Our analysis suggests that improved surgical techniques and combining PSR and MVD will yield better results. Systematic Review Registration: https://www.crd.york.ac.uk/PROSPERO/, identifier: CRD42020159276.

Association of pre-existing comorbidities with mortality and disease severity among 167,500 individuals with COVID-19 in Canada: A population-based cohort study.

BACKGROUND: The novel coronavirus disease 2019 (COVID-19) has infected 1.9% of the world population by May 2, 2021. Since most previous studies that examined risk factors for mortality and severity were based on hospitalized individuals, population-based cohort studies are called for to provide evidence that can be extrapolated to the general population. Therefore, we aimed to examine the associations of comorbidities with mortality and disease severity in individuals with COVID-19 diagnosed in 2020 in Ontario, Canada. METHODS AND FINDINGS: We conducted a retrospective cohort study of all individuals with COVID-19 in Ontario, Canada diagnosed between January 15 and December 31, 2020. Cases were linked to health administrative databases maintained in the ICES which covers all residents in Ontario. The primary outcome is all-cause 30-day mortality after the first COVID-19 diagnosis, and the secondary outcome is a composite severity index containing death and hospitalization. To examine the risk factors for the outcomes, we employed Cox proportional hazards regression models and logistic regression models to adjust for demographic, socio-economic variables and comorbidities. Results were also stratified by age groups. A total of 167,500 individuals were diagnosed of COVID-19 in 2020 and included in the study. About half (43.8%, n = 73,378) had at least one comorbidity. The median follow-up period were 30 days. The most common comorbidities were hypertension (24%, n = 40,154), asthma (16%, n = 26,814), and diabetes (14.7%, n = 24,662). Individuals with comorbidity had higher risk of mortality compared to those without (HR = 2.80, 95%CI 2.35-3.34; p<0.001), and the risk substantially was elevated from 2.14 (95%CI 1.76-2.60) to 4.81 (95%CI 3.95-5.85) times as the number of comorbidities increased from one to five or more. Significant predictors for mortality included comorbidities such as solid organ transplant (HR = 3.06, 95%CI 2.03-4.63; p<0.001), dementia (HR = 1.46, 95%CI 1.35-1.58; p<0.001), chronic kidney disease (HR = 1.45, 95%CI 1.34-1.57; p<0.001), severe mental illness (HR = 1.42, 95%CI%, 1.12-1.80; p<0.001), cardiovascular disease (CVD) (HR = 1.22, 95%CI, 1.15-1.30), diabetes (HR = 1.19, 95%, 1.12-1.26; p<0.001), chronic obstructive pulmonary disease (COPD) (HR = 1.19, 95%CI 1.12-1.26; p<0.001), cancer (HR = 1.17, 95%CI, 1.09-1.27; p<0.001), hypertension (HR = 1.16, 95%CI, 1.07-1.26; p<0.001). Compared to their effect in older age groups, comorbidities were associated with higher risk of mortality and severity in individuals under 50 years old. Individuals with five or more comorbidities in the below 50 years age group had 395.44 (95%CI, 57.93-2699.44, p<0.001) times higher risk of mortality compared to those without. Limitations include that data were collected during 2020 when the new variants of concern were not predominant, and that the ICES databases do not contain detailed individual-level socioeconomic and racial variables. CONCLUSION: We found that solid organ transplant, dementia, chronic kidney disease, severe mental illness, CVD, hypertension, COPD, cancer, diabetes, rheumatoid arthritis, HIV, and asthma were associated with mortality or severity. Our study highlights that the number of comorbidities was a strong risk factor for deaths and severe outcomes among younger individuals with COVID-19. Our findings suggest that in addition of prioritizing by age, vaccination priority groups should also include younger population with multiple comorbidities.

Systematic review of effectiveness and cost-effectiveness of lifestyle interventions to improve clinical diabetes outcome measures in women with a history of GDM.

OBJECTIVE: Lifestyle interventions have been shown to be both effective and cost-effective in reducing diabetes and metabolic risk in high-risk populations. We systematically reviewed the effectiveness and cost-effectiveness of lifestyle interventions on anthropometric, glycemic and cardiovascular outcomes in women with previous gestational diabetes mellitus (GDM). METHOD: Relevant randomized control trials (RCT) were identified by searching multiple electronic databases through 20th June 2018. Data were pooled using random-effects models. The review protocol was registered on the PROSPERO international prospective register of systematic reviews (PROSPERO 2016: CRD42018108870). RESULTS: Twenty-one studies met the inclusion criteria and 16 studies with outcome data were analyzed in the meta-analysis. No RCT studies included cost-effectiveness data on lifestyle interventions. The pooled estimate for postpartum weight showed a significant mean reduction in the intervention arm (-1.8 kg [95% CI: -2.9, -0.6; p = 0.002; I2 = 92.2%; p < 0.05]). Further, the effect of lifestyle intervention on weight change was significantly greater in studies of longer duration. Most of the other endpoints had modest improvements but only anthropometric endpoints were statistically significant. However, there was high heterogeneity between the studies. CONCLUSIONS: Lifestyle interventions showed statistically and clinically significant improvements in anthropometric outcomes. However, more research is needed to explore lifestyle effects on glycemic and cardiovascular risk factors and to establish cost-effectiveness. Methodologically sound, large scale studies on diverse ethnicities and with longer follow-up would establish the real effect of lifestyle interventions to reduce diabetes risk in women with previous GDM.

A Study on the Association Between Polymorphisms in the Cytochrome P450 Family 17 Subfamily A Member 1 Gene Region and Type 2 Diabetes Mellitus in Han Chinese.

BACKGROUND: Cytochrome P450 family 17 subfamily A member 1 (CYP17A1) gene encodes a key enzyme in the synthesis and metabolism of steroid hormones and has been associated with various factors, such as hypertension, insulin resistance, and polycystic ovary syndrome. However, whether the gene was associated with type 2 diabetes mellitus (T2DM) has not been reported yet. Therefore, we sought to investigate whether CYP17A1 was associated with T2DM and related traits among Han Chinese. METHODS: Three tagging single nucleotide polymorphisms (rs1004467, rs17115149, and rs12413409), in the CYP17A1 gene region were selected and genotyped in a case-control study that included 440 diabetes and 1,320 control subjects. Effects of genetic loci were studied using univariate unconditional logistic regression and multivariate logistic regression analysis adjusted for age, sex, family history, body mass index, smoking, and drinking. Bioinformatics analysis was also conducted using the GEO DataSets and PROMO database to gain hints of possible mechanism. RESULTS: Rs17115149 and rs12413409 polymorphisms were significantly associated with the risk of T2DM, even after adjusting for age, sex, family history, body mass index, smoking, and drinking. In stratified analyses, rs1004467 and rs12413409 showed significant association with T2DM in the older age group (≥65 years) and, in the case of rs12413409, the risk of T2DM was significant in men but not in women. Rs17115149 had significant association with T2DM in the hypertension subgroup, and rs12413409 in the non-hypertension subgroup. Moreover, rs12413409 showed significant association with plasma glucose levels in the recessive model (P = 0.020) among subjects not taking hypoglycemic measures. Bioinformatics analysis revealed significantly higher CYP17A1 gene expression in T2DM patients compared to healthy controls. Finally, the mutant T allele of the rs17115149 polymorphism allowed binding to the RBP-Jkappa transcription factor. CONCLUSION: This is the first report to identify that variants rs1004467, rs17115149, and rs12413409 of CYP17A1, are related to plasma glucose levels and T2DM among Han Chinese. Our results suggest that CYP17A1 might constitute a risk gene for progression to T2DM.

Association study of genetic variants at newly identified lipid gene TRIB1 with coronary heart disease in Chinese Han population.

BACKGROUND: Recent genome-wide association studies (GWAS) have identified the variants near TRIB1 gene affecting blood lipid levels. However, the association between the reported variants and risk of coronary heart disease (CHD) was not confirmed. METHODS: We conducted two independent case-control studies. The first study consisted of 300 CHD patients and 300 controls and the second study had 1,332 CHD patients and 2,811 controls. The genotypes of two variants rs3201475 and rs17321515 in TRIB1 were determined by TaqMan assay. The dual-luciferase reporter assay was performed for evaluating the function of the SNP rs3201475. RESULTS: The statistical analysis indicated that single nucleotide polymorphism (SNP) rs17321515 was replicated to be associated with triglyceride (TG) level, which was also significantly associated with CHD risk when using the stratified analysis after adjusting for conventional risk factors. Compared with GG genotype, AA carriers of SNP rs17321515 had higher risk in males (odds ratio (OR)=1.28, 95%CI=1.01-1.61; P=0.03) and smokers (OR=1.41, 95%CI=1.09-1.88; P=0.01). We did not find significantly association between genotypes of rs3201475 and CHD risk. In addition, no significant difference was found in the luciferase activity assay of SNP rs3201475. CONCLUSIONS: Our findings indicated that SNP rs17321515 is significantly associated with plasma TG level and the increasing risk of CHD among males and smokers in Chinese, whereas there is no positive association between SNP rs3201475 and CHD risk. Smoking could modify the effects of TRIB1 on CHD risk.