Genotype-Corrector: improved genotype calls for genetic mapping in F2 and RIL populations

F2 and recombinant inbred lines (RILs) populations are very commonly used in plant genetic mapping studies. Although genome-wide genetic markers like single nucleotide polymorphisms (SNPs) can be readily identified by a wide array of methods, accurate genotype calling remains challenging, especially for heterozygous loci and missing data due to low sequencing coverage per individual. Therefore, we developed Genotype-Corrector, a program that corrects genotype calls and imputes missing data to improve the accuracy of genetic mapping. Genotype-Corrector can be applied in a wide variety of genetic mapping studies that are based on low coverage whole genome sequencing (WGS) or Genotyping-by-Sequencing (GBS) related techniques. Our results show that Genotype-Corrector achieves high accuracy when applied to both synthetic and real genotype data. Compared with using raw or only imputed genotype calls, the linkage groups built by corrected genotype data show much less noise and significant distortions can be corrected. Additionally, Genotype-Corrector compares favorably to the popular imputation software LinkImpute and Beagle in both F2 and RIL populations

Role of Positive Selection in Functional Divergence of Mammalian Neuronal Apoptosis Inhibitor Proteins during Evolution

Neuronal apoptosis inhibitor proteins (NAIPs) are members of Nod-like receptor (NLR) protein family. Recent research demostrated that some NAIP genes were strongly associated with both innate immunity and many inflammatory diseases in humans. However, no similar phenomena have been reported in other mammals. Furthermore, some NAIP genes have undergone pseudogenization or have been lost during the evolution of some higher mammals. We therefore aimed to determine if functional divergence had occurred, and if natural selection had played an important role in the evolution of these genes. The results showed that NAIP genes have undergone pseudogenization and functional divergence, driven by positive selection. Positive selection has also influenced NAIP protein structure, resulting in further functional divergence

Etiologic Diagnosis of Lower Respiratory Tract Bacterial Infections Using Sputum Samples and Quantitative Loop-Mediated Isothermal Amplification

Etiologic diagnoses of lower respiratory tract infections (LRTI) have been relying primarily on bacterial cultures that often fail to return useful results in time. Although DNA-based assays are more sensitive than bacterial cultures in detecting pathogens, the molecular results are often inconsistent and challenged by doubts on false positives, such as those due to system- and environment-derived contaminations. Here we report a nationwide cohort study on 2986 suspected LRTI patients across P. R. China. We compared the performance of a DNA-based assay qLAMP (quantitative Loop-mediated isothermal AMPlification) with that of standard bacterial cultures in detecting a panel of eight common respiratory bacterial pathogens from sputum samples. Our qLAMP assay detects the panel of pathogens in 1047(69.28%) patients from 1533 qualified patients at the end. We found that the bacterial titer quantified based on qLAMP is a predictor of probability that the bacterium in the sample can be detected in culture assay. The relatedness of the two assays fits a logistic regression curve. We used a piecewise linear function to define breakpoints where latent pathogen abruptly change its competitive relationship with others in the panel. These breakpoints, where pathogens start to propagate abnormally, are used as cutoffs to eliminate the influence of contaminations from normal flora. With help of the cutoffs derived from statistical analysis, we are able to identify causative pathogens in 750 (48.92%) patients from qualified patients. In conclusion, qLAMP is a reliable method in quantifying bacterial titer. Despite the fact that there are always latent bacteria contaminated in sputum samples, we can identify causative pathogens based on cutoffs derived from statistical analysis of competitive relationship

Altered Serum Tumor Necrosis Factor and Interleukin-1β in First-Episode Drug-Naive and Chronic Schizophrenia

Objective: Abnormality of the immune system might play a significant role in the pathogenesis of schizophrenia. We want to identity whether the serum TNF-α and IL-1β levels were changed in FEDN patients and CP and to investigate the relationship between both cytokines and psychopathological symptoms.Methods: We recruited 69 FEDN patients, 87 CP and 61 healthy controls. Schizophrenia symptomatology was evaluated with the Positive and Negative Syndrome Scale (PANSS), the Scale for the Assessment of Negative Symptoms (SANS) and Clinical Global Impression Scale (CGI). Serum TNF-α and IL-1β levels were examined using sandwich enzyme-linked immunosorbent assay (ELISA).Results: TNF-α and IL-1β levels in CP were significantly higher compared to healthy controls, but TNF-α and IL-1β levels in FEDN patients were significantly lower than in both CP and healthy controls. A moderate correlation between serum TNF-α or IL-1β levels and PANSS negative subscore was found in CP. But there was no correlation between altered cytokines and clinical symptoms in FEDN patients.Conclusions: Increased TNF-α and IL-1β levels in chronic patients may be associated with the progression, psychotropic drugs or other factors occur during chronic stage. Immune modulating treatments may become a new strategy of therapy for this subgroup of patients

A Longitudinal Study of Stress in New Nurses in their First Year of Employment

Objective. This study aimed to analyze changes in occupational stress in new nurses during the first year of employment. Methods. A prospective longitudinal study was conducted from 2020 to 2021 using one questionnaire four times on 127 newly employed nurses in a tertiary general teaching hospital in the province of Fujian. Results. The results showed that new nurses had moderate to high levels of stress in all four stages, with the highest stress level at 4 and 8 months of employment and the lowest stress level at 12 months; the differences in stress scores at different time points were statistically significant (p<0.05). The trends in each stressor dimension varied across different periods. The highest scores were for pressure caused by “time allocation and workload,” which peaked in month 8. The same trend was observed for stress from “patient care” and “work environment and equipment.” “Management and interpersonal relationships” scored the highest overall stress score at the start of employment before declining. The lowest stress score was from “work environment and equipment” at the start of employment, and the lowest was from “management and interpersonal relationships” from month 4 onward. Conclusion. New nurses had higher overall occupational stress during their first year of employment under different stressors. Therefore, nursing managers should actively focus on stress factors of new nurses and provide targeted interventions to help them during their training period

Genotype-Corrector: improved genotype calls for genetic mapping in F2 and RIL populations

F2 and recombinant inbred lines (RILs) populations are very commonly used in plant genetic mapping studies. Although genome-wide genetic markers like single nucleotide polymorphisms (SNPs) can be readily identified by a wide array of methods, accurate genotype calling remains challenging, especially for heterozygous loci and missing data due to low sequencing coverage per individual. Therefore, we developed Genotype-Corrector, a program that corrects genotype calls and imputes missing data to improve the accuracy of genetic mapping. Genotype-Corrector can be applied in a wide variety of genetic mapping studies that are based on low coverage whole genome sequencing (WGS) or Genotyping-by-Sequencing (GBS) related techniques. Our results show that Genotype-Corrector achieves high accuracy when applied to both synthetic and real genotype data. Compared with using raw or only imputed genotype calls, the linkage groups built by corrected genotype data show much less noise and significant distortions can be corrected. Additionally, Genotype-Corrector compares favorably to the popular imputation software LinkImpute and Beagle in both F2 and RIL populations

The complete chloroplast genome of the Chinese banyan tree Ficus microcarpa

Banyan tree or Ficus microcarpa is a large perennial plant with extraordinary aerial roots from the Moraceae family. In this study, the complete chloroplast genome sequence of F. microcarpa was assembled using PacBio data. The chloroplast genome size is 141,611 bp, consisting of a large single-copy (LSC) region and a small single-copy (SSC) region of 101,835 bp and 9,676 bp, respectively, which are separated by a pair of 15,050 bp inverted repeat (IR) regions. The genome includes 74 protein-coding genes, 43 tRNA genes, and 8 rRNA genes. A phylogenetic tree reconstructed by 25 complete chloroplast genomes reveals that F. microcarpa is mostly related to Ficus racemosa

Live it up without drinking up! ladies night out! 2012.

This paper presents the “Ladies Night Out! 2012” (LNO) project, a responsible drinking health campaign undertaken by four final year undergraduates from the Nanyang Technological University Wee Kim Wee School of Communication and Information. This campaign is primarily targeted to reach female youths in Singapore, aged 18-25 years old. LNO aims to build a larger community of responsible and aware drinkers. This report covers LNO campaign plans and key strategies used. Post-campaign evaluation provides an insight to the effectiveness of the campaign, and the campaign’s future directions are explored.Bachelor of Communication Studie

Prevalence and risk factors for hypokalemia in patients scheduled for laparoscopic colorectal resection and its association with post-operative recovery

Abstract Background Perioperative serum potassium levels are closely associated with postoperative clinical outcomes after gastrointestinal surgery. The aim of our retrospective study was to identify the prevalence and risk factors for preoperative hypokalemia (before pneumoperitoneum) and to evaluate the influence of preoperative hypokalemia on the recovery of postoperative gastrointestinal function. Methods In this retrospective study, patients scheduled for laparoscopic colorectal resection from November 11 2014 to October 20 2016, were considered for inclusion. A blood potassium level between 3.5 and 5.5 mmol/L was defined as normal, with levels between 3.0 to 3.5 mmol/L, 2.5 to 3.0 mmol/L and < 2.5 mmol/L considered as slight, moderate, and severe level of hypokalemia. The factors including age, gender, ASA grade, BMI, hypertension, diabetes, anti-hypertension drugs, lactose oral soluble, oral cathartics, oral cathartics, cathartic enemas, and blood potassium level before gastrointestinal preparation which might be associated with blood potassium level before pneumoperitoneum were analysed. The time to postoperative first flatus (FFL) and first feces (FFE) was compared between patients with and without hypokalemia. Results The final analysis was based on the data of 108 patients. Hypokalemia was identified in 70.37% patients, with the following distribution of blood potassium levels before pneumoperitoneum: slight, 49 (45.37%) patients; moderate, 23 (21.30%); and severe, 4 (3.70%) patients. Hypokalemia was significantly associated with hypertension and the use of ≥2 types of oral cathartics for preoperative gastrointestinal preparation. With treatment, potassium levels recovered to normal levels in all patients within 48 h postoperatively. Hypokalemia was associated with a longer postoperative time to first feces, compared to patients with a normal potassium level before pneumoperitoneum. Conclusions Our findings underlie the importance of early monitoring and management of serum potassium levels in these patients