Imputation in missing not at random SNPs data using EM algorithm

    The relation between single nucleotide polymorphisms (SNPs) and some diseases has been concerned by many researchers. Also the missing SNPs are quite common in genetic association studies. Hence, this article investigates the relation between existing SNPs in DNMT1 of human chromosome 19 with colorectal cancer. This article aims is to presents an imputation method for missing SNPs not at random. In this case-control study, 100 patients suffering from colorectal cancer consulting with the Research Institute for Gastroenterology and Liver Disease of Shahid Beheshti University of Medical Sciences were considered as the case group and 100 other patients consulting with the same research institute were considered as the control group and the genetic test was applied in order to identify the genotype of the 6 SNPs of the DNMT1 of chromosom 19 for all the patients under investigation. The obtained data were analyzed using logistic regression, then a fraction of the data was eliminated both at random and not at random and the imputation was done through the EM algorithm and the logistic regression coefficients variation before and after the imputation was compared. The results of this study implied that in both methods, at random and not at random missing SNPs, the estimation of the logistic regression coefficients after the imputation through EM algorithm has a greater correspondence to the results obtained from the complete data in comparison with the method of eliminating the missing values.

Global age-sex-specific fertility, mortality, healthy life expectancy (HALE), and population estimates in 204 countries and territories, 1950-2019 : a comprehensive demographic analysis for the Global Burden of Disease Study 2019

Background: Accurate and up-to-date assessment of demographic metrics is crucial for understanding a wide range of social, economic, and public health issues that affect populations worldwide. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 produced updated and comprehensive demographic assessments of the key indicators of fertility, mortality, migration, and population for 204 countries and territories and selected subnational locations from 1950 to 2019. Methods: 8078 country-years of vital registration and sample registration data, 938 surveys, 349 censuses, and 238 other sources were identified and used to estimate age-specific fertility. Spatiotemporal Gaussian process regression (ST-GPR) was used to generate age-specific fertility rates for 5-year age groups between ages 15 and 49 years. With extensions to age groups 10–14 and 50–54 years, the total fertility rate (TFR) was then aggregated using the estimated age-specific fertility between ages 10 and 54 years. 7417 sources were used for under-5 mortality estimation and 7355 for adult mortality. ST-GPR was used to synthesise data sources after correction for known biases. Adult mortality was measured as the probability of death between ages 15 and 60 years based on vital registration, sample registration, and sibling histories, and was also estimated using ST-GPR. HIV-free life tables were then estimated using estimates of under-5 and adult mortality rates using a relational model life table system created for GBD, which closely tracks observed age-specific mortality rates from complete vital registration when available. Independent estimates of HIV-specific mortality generated by an epidemiological analysis of HIV prevalence surveys and antenatal clinic serosurveillance and other sources were incorporated into the estimates in countries with large epidemics. Annual and single-year age estimates of net migration and population for each country and territory were generated using a Bayesian hierarchical cohort component model that analysed estimated age-specific fertility and mortality rates along with 1250 censuses and 747 population registry years. We classified location-years into seven categories on the basis of the natural rate of increase in population (calculated by subtracting the crude death rate from the crude birth rate) and the net migration rate. We computed healthy life expectancy (HALE) using years lived with disability (YLDs) per capita, life tables, and standard demographic methods. Uncertainty was propagated throughout the demographic estimation process, including fertility, mortality, and population, with 1000 draw-level estimates produced for each metric. Findings: The global TFR decreased from 2·72 (95% uncertainty interval [UI] 2·66–2·79) in 2000 to 2·31 (2·17–2·46) in 2019. Global annual livebirths increased from 134·5 million (131·5–137·8) in 2000 to a peak of 139·6 million (133·0–146·9) in 2016. Global livebirths then declined to 135·3 million (127·2–144·1) in 2019. Of the 204 countries and territories included in this study, in 2019, 102 had a TFR lower than 2·1, which is considered a good approximation of replacement-level fertility. All countries in sub-Saharan Africa had TFRs above replacement level in 2019 and accounted for 27·1% (95% UI 26·4–27·8) of global livebirths. Global life expectancy at birth increased from 67·2 years (95% UI 66·8–67·6) in 2000 to 73·5 years (72·8–74·3) in 2019. The total number of deaths increased from 50·7 million (49·5–51·9) in 2000 to 56·5 million (53·7–59·2) in 2019. Under-5 deaths declined from 9·6 million (9·1–10·3) in 2000 to 5·0 million (4·3–6·0) in 2019. Global population increased by 25·7%, from 6·2 billion (6·0–6·3) in 2000 to 7·7 billion (7·5–8·0) in 2019. In 2019, 34 countries had negative natural rates of increase; in 17 of these, the population declined because immigration was not sufficient to counteract the negative rate of decline. Globally, HALE increased from 58·6 years (56·1–60·8) in 2000 to 63·5 years (60·8–66·1) in 2019. HALE increased in 202 of 204 countries and territories between 2000 and 2019

Global burden of 369 diseases and injuries in 204 countries and territories, 1990–2019: a systematic analysis for the Global Burden of Disease Study 2019

Background: In an era of shifting global agendas and expanded emphasis on non-communicable diseases and injuries along with communicable diseases, sound evidence on trends by cause at the national level is essential. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) provides a systematic scientific assessment of published, publicly available, and contributed data on incidence, prevalence, and mortality for a mutually exclusive and collectively exhaustive list of diseases and injuries. Methods: GBD estimates incidence, prevalence, mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life-years (DALYs) due to 369 diseases and injuries, for two sexes, and for 204 countries and territories. Input data were extracted from censuses, household surveys, civil registration and vital statistics, disease registries, health service use, air pollution monitors, satellite imaging, disease notifications, and other sources. Cause-specific death rates and cause fractions were calculated using the Cause of Death Ensemble model and spatiotemporal Gaussian process regression. Cause-specific deaths were adjusted to match the total all-cause deaths calculated as part of the GBD population, fertility, and mortality estimates. Deaths were multiplied by standard life expectancy at each age to calculate YLLs. A Bayesian meta-regression modelling tool, DisMod-MR 2.1, was used to ensure consistency between incidence, prevalence, remission, excess mortality, and cause-specific mortality for most causes. Prevalence estimates were multiplied by disability weights for mutually exclusive sequelae of diseases and injuries to calculate YLDs. We considered results in the context of the Socio-demographic Index (SDI), a composite indicator of income per capita, years of schooling, and fertility rate in females younger than 25 years. Uncertainty intervals (UIs) were generated for every metric using the 25th and 975th ordered 1000 draw values of the posterior distribution. Findings: Global health has steadily improved over the past 30 years as measured by age-standardised DALY rates. After taking into account population growth and ageing, the absolute number of DALYs has remained stable. Since 2010, the pace of decline in global age-standardised DALY rates has accelerated in age groups younger than 50 years compared with the 1990–2010 time period, with the greatest annualised rate of decline occurring in the 0–9-year age group. Six infectious diseases were among the top ten causes of DALYs in children younger than 10 years in 2019: lower respiratory infections (ranked second), diarrhoeal diseases (third), malaria (fifth), meningitis (sixth), whooping cough (ninth), and sexually transmitted infections (which, in this age group, is fully accounted for by congenital syphilis; ranked tenth). In adolescents aged 10–24 years, three injury causes were among the top causes of DALYs: road injuries (ranked first), self-harm (third), and interpersonal violence (fifth). Five of the causes that were in the top ten for ages 10–24 years were also in the top ten in the 25–49-year age group: road injuries (ranked first), HIV/AIDS (second), low back pain (fourth), headache disorders (fifth), and depressive disorders (sixth). In 2019, ischaemic heart disease and stroke were the top-ranked causes of DALYs in both the 50–74-year and 75-years-and-older age groups. Since 1990, there has been a marked shift towards a greater proportion of burden due to YLDs from non-communicable diseases and injuries. In 2019, there were 11 countries where non-communicable disease and injury YLDs constituted more than half of all disease burden. Decreases in age-standardised DALY rates have accelerated over the past decade in countries at the lower end of the SDI range, while improvements have started to stagnate or even reverse in countries with higher SDI. Interpretation: As disability becomes an increasingly large component of disease burden and a larger component of health expenditure, greater research and developm nt investment is needed to identify new, more effective intervention strategies. With a rapidly ageing global population, the demands on health services to deal with disabling outcomes, which increase with age, will require policy makers to anticipate these changes. The mix of universal and more geographically specific influences on health reinforces the need for regular reporting on population health in detail and by underlying cause to help decision makers to identify success stories of disease control to emulate, as well as opportunities to improve. Funding: Bill & Melinda Gates Foundation. © 2020 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 licens

The effect of tactile stimulation on consciousness and vital signs of traumatic brain injury patients hospitalized in intensive care units in social health care system and medical science university centers in Qazvin,Iran

Background: hospitalization in intensive care units (ICUs) result in tactile deprivation and receiving excessive tactile stimulation, which may cause physiologic imbalance in the patients. Patients and method: the current clinical trial was conducted on 60 patients with severe brain trauma admitted to ICUs in Qazvin, Iran, in 2016. The subjects were selected by the convenience sampling method and assigned into 2 groups of intervention and control. Hands, wrists, and palms were touched for 3 minutes twice a day, morning and evening, and the level of consciousness and vital signs of the patients were recorded immediately from the day 1 to 5 of admission. Data were analyzed using SPSS version 21 by the paired and independent t tests. Results: according to the results of the current study, tactile stimulation increased the level of consciousness (P=0.001), decreased systolic blood pressure level (P=0.0001), diastolic blood pressure (P 0.05). Conclusion: considering the positive effect of tactile stimulation on the increase of consciousness and decrease of heartbeat rate and blood pressure in patients with brain trauma, it is recommended to employ tactile stimulation methods on patients admitted to ICUs. Keywords: tactile stimulation, vital signs, level of consciousness, brain trauma, tactile deprivatio

Effect of warm footbath with vibration on arteriovenous fistula puncture-related pain in hemodialysis patients

Background: Pain and stress of hemodialysis are experienced by more than 50% of patients who are suffering from renal disease; hence decreasing a part of these adverse effects can be effective on individual’s long term coping with hemodialysis. The current study was done to determine the effect of warm footbath with vibration on arteriovenous fistula puncture-related pain in hemodialysis patients.Methods: This clinical trial was conducted on 31 hemodialysis patients in 2014. The patients were selected by simple random sampling method and placed in one group. First, the pain intensity of all patients was measured in the six frequent hemodialysis sessions without any intervention (control method). After two weeks, the intervention of warm footbath with vibration was done on all patients and the pain intensity was measured for six frequent hemodialysis sessions (intervention method). The patients were received 40±2 °C footbath with vibration by foot massage spa machine for ten minutes; then, fistula needles were placed and the pain intensity was assessed by using a numerical rating scale. Data were analyzed by ANOVA and T test.Results: The study group had contained 20 males (64.5%), 11 females (35.5%), with an average age of 44.16±14.85 and a range of 18 to 65 years old, which shows that the pain intensity of the warm footbath with vibration method was lower than the control method (P< 0.05).Conclusions: Warm footbath with vibration can be used as an effective palliative method to reduce pain of hemodialysis patients

The Oral Diadochokinesis in Normal-Hearing and Hearing-Impaired Adolescents

Background and Aim: Hearing loss results in impairment of muscles coordination and survival essential that are engaged in motor speech timing tasks. It will negatively affect the acquisition of speech sounds. The purpose of this study was to compare the oral diadochokinesis in normal-hearing and hearing - impaired adolescents. Materials and Methods: This research was conducted on sixty-one adolescents aged 15-18 years old. Forty-six had moderately severe, severe, or profound hearing loss and fifteen were normal. The time spent to perform each oral diadochokinesis tasks was measured by speech analyzer of Dr. speech software, version four. Results: Results indicated that hearing – impaired performed significantly slower on all speech timing tasks than their normal hearing peers except those with moderately severe hearing-impaired group. There were significant differences between profound hearing-impaired group and both other groups. Conclusion: The results of this study point out the motor speech problems in hearing impairment. The differences, in general, indicate that speech-timing coordination deficits are compromise with hearing loss degree

Efficacy of Compound Therapy by Ginseng and Ciprofloxacin on Bacterial Prostatitis

Objective: Genitourinary tract infections play a significant role in male infertility. Infections of reproductive sex glands, such as the prostate, impair function and indirectly affect male fertility. The general aim of this study is to investigate the protective effect of Korean red ginseng (KRG) on prostatitis in male rats treated with ciprofloxacin (CIPX). Materials and Methods: In this experimental study, we randomly divided 72 two male Wistar rats into 9 groups. The groups were treated as follows for 10 days: i. Control (no medication), ii. Sham [(normal saline injection into the vas deferens and oral administration of phosphate-buffered saline (PBS)], iii. Ginseng, iv. CPIX, v. CIPX+ginseng, vi. Uropathogenic Escherichia coli (E. coli) (UPEC), vii. UPEC+ginseng, viii. UPEC+CIPX, and ix. UPEC+ginseng+CIPX. The rats were killed 14 days after the last injection and the prostate glands were removed. After sample preparation, routine histology was performed using hematoxylin and eosin staining. The terminal deoxynucleotidyl transferase mediated dUTP-biotin nick end labeling (TUNEL) method was used to determine the presence of apoptotic cells. Results: The severity score for acinar changes and inflammatory cell infiltration in the UPEC+CIPX group did not significantly different from the UPEC group. However this score significantly decreased in the UPEC+CIPX+ginseng group compared to the UPEC group. Apoptotic index of all ginseng treated groups significantly decreased compared to the UPEC and CPIX groups. Conclusion: These results suggested that ginseng might be an effective adjunct in CIPX treatment of prostatitis. The combined use ginseng and CIPX was more effective than ginseng or CIPX alone

Blockade of fast A-type and TEA-sensitive potassium channels provide an antiparkinsonian effect in a 6-OHDA animal model

inhibitors in treatment of parkinson’s disease (PD). Methods: This prospective comparative study was conducted in the Qazvin University of Medical Sciences, Iran, from April 2015 to January 2016. Male rats (n=37) received intraperitoneal doses of TEA (2 and 5 mg/kg) or 4-AP (0.5 and 1 mg/kg) twice-daily, before a stereotactic injection of 6-hydroxydopamine Disclosure. This work was funded by grants-in aid from Iran National Science Foundation and Qazvin University of Medical Sciences, Qazvin, Iran. Neurosciences 2017; Vol. 22 (1) ( 6-OHDA) for the following 7 days. The 6-OHDA was injected into right medial forebrain bundle (MFB) of the rat brains. Development and severity of PD were assessed using the apomorphine-induced rotational test, the elevated body swing test and rotarod tests. Concentration of malondialdehyde (MDA), a marker of oxidative stress, was measured in rat sera. Results: Tetraethylammonium and 4-AP significantly reduced the number of apomorphine-induced rotations and improved motor learning in the rotarod test at both doses. Administration of 4-AP and TEA together was more effective than single administration of either agent. Malondialdehyde measurement showed that pretreatment with TEA could not prevent 6-OHDA-induced oxidative stress. Conclusion: Our results showed that pretreatment with TEA and 4-AP has a neuroprotective effect against 6-OHDA in dopaminergic neurons in the substantia nigra

Mapping routine measles vaccination in low- and middle-income countries

The safe, highly effective measles vaccine has been recommended globally since 1974, yet in 2017 there were more than 17 million cases of measles and 83,400 deaths in children under 5 years old, and more than 99% of both occurred in low- and middle-income countries (LMICs)1–4. Globally comparable, annual, local estimates of routine first-dose measles-containing vaccine (MCV1) coverage are critical for understanding geographically precise immunity patterns, progress towards the targets of the Global Vaccine Action Plan (GVAP), and high-risk areas amid disruptions to vaccination programmes caused by coronavirus disease 2019 (COVID-19)5–8. Here we generated annual estimates of routine childhood MCV1 coverage at 5 × 5-km2 pixel and second administrative levels from 2000 to 2019 in 101 LMICs, quantified geographical inequality and assessed vaccination status by geographical remoteness. After widespread MCV1 gains from 2000 to 2010, coverage regressed in more than half of the districts between 2010 and 2019, leaving many LMICs far from the GVAP goal of 80% coverage in all districts by 2019. MCV1 coverage was lower in rural than in urban locations, although a larger proportion of unvaccinated children overall lived in urban locations; strategies to provide essential vaccination services should address both geographical contexts. These results provide a tool for decision-makers to strengthen routine MCV1 immunization programmes and provide equitable disease protection for all children