BayMiR: inferring evidence for endogenous miRNA-induced gene repression from mRNA expression profiles

BACKGROUND: Popular miRNA target prediction techniques use sequence features to determine the functional miRNA target sites. These techniques commonly ignore the cellular conditions in which miRNAs interact with their targets in vivo. Gene expression data are rich resources that can complement sequence features to take into account the context dependency of miRNAs. RESULTS: We introduce BayMiR, a new computational method, that predicts the functionality of potential miRNA target sites using the activity level of the miRNAs inferred from genome-wide mRNA expression profiles. We also found that mRNA expression variation can be used as another predictor of functional miRNA targets. We benchmarked BayMiR, the expression variation, Cometa, and the TargetScan “context scores” on two tasks: predicting independently validated miRNA targets and predicting the decrease in mRNA abundance in miRNA overexpression assays. BayMiR performed better than all other methods in both benchmarks and, surprisingly, the variation index performed better than Cometa and some individual determinants of the TargetScan context scores. Furthermore, BayMiR predicted miRNA target sets are more consistently annotated with GO and KEGG terms than similar sized random subsets of genes with conserved miRNA seed regions. BayMiR gives higher scores to target sites residing near the poly(A) tail which strongly favors mRNA degradation using poly(A) shortening. Our work also suggests that modeling multiplicative interactions among miRNAs is important to predict endogenous mRNA targets. CONCLUSIONS: We develop a new computational method for predicting the target mRNAs of miRNAs. BayMiR applies a large number of mRNA expression profiles and successfully identifies the mRNA targets and miRNA activities without using miRNA expression data. The BayMiR package is publicly available and can be readily applied to any mRNA expression data sets

Biokemijske značajke hidatidne tekućine cista Echinococcus granulosus podrijetlom iz čovjeka i životinja u Iranu.

A comparative study on the biochemical parameters in hydatid cyst fluids of sheep, goat, camel, cattle and human cystic forms of Echinococcus granulosus has been made in Iran. Quantitative variations in the levels of glucose, calcium and creatinine in the cystic fluids of camels were found with hydatid fluids of sheep, goat, cattle and humans. These differences were statistically significant (P<0.05). Similarities in the biochemical composition in hydatid cyst fluids of sheep, goat, cattle and humans suggest the existence of sheep strains of E. granulosus and differences in the biochemical composition in hydatid cyst fluids of camel with other domestic animals and humans suggest the existence of camel strains of E. granulosus in Iran.Provedeno je komparativno istraživanje biokemijskih pokazatelja hidatidne tekućine iz cista Echinococcus granulosus u ovaca, koza, deva, goveda i čovjeka u Iranu. Dokazana su kvantitativna kolebanja u nalazima glukoze, kalcija i kreatinina u cističnoj tekućini kod deva u odnosu na ovce, koze, govedo i čovjeka. Razlike su bile statistički značajne (P<0,05). Sličnosti u biokemijskom sastavu hidatidne tekućine u ovaca, koza, goveda i čovjeka ukazuju na prisutnost cista E. granulosus podrijetlom iz ovce dok razlike u biokemijskom sastavu hidatidnih tekućina deve i ostalih domaćih životinja i čovjeka ukazuju na prisutnost cista E. granulosus podrijetlom iz deve

Proširenost i morfološke značajke cisti Cysticercus tenuicollis (cisticerci Taenia hydatigena) ovaca i koza u Iranu.

Prevalence and a comparative study on the larval rostellar hook morphology of Taenia hydatigena cysticerci from sheep and goats have been made in Iran. The 1336 sheep and 1674 goats slaughtered at the Kerman abattoir were investigated for infection with Cysticercus tenuicollis cyst. C. tenuicollis cysts were found in 172 sheep (12.87%) and 302 goats (18.04%) and this difference was significant (P<0.05). The predominant predilection site of cysticerci in sheep (84.85%) and goats (82.14%) was signifi cantly (P<0.05) the omentum. The morphological characters in small hooks (including length of hooks, length of handle and length of guard) were significantly different in cysticerci from sheep and goats (P<0.05). It is concluded that the cysticerci of sheep and goat origin probably represent two different strains and possibly follow the same pattern of speciation as reported in the related taeniid, Echinococcus granulosus.Istraživana je proširenost i morfologija larvalnih rostralnih kukica cisticerka Taenia hydatigena ovaca i koza u Iranu. Pregledano je 1336 ovaca i 1674 koze zaklane na klaonici u Kermanu na invaziju cistama Cysticercus tenuicollis. Ciste C. tenuicollis su nađene u 172 ovce (12,87%) i 302 koze (18,40%) a razlika je bila značajna (P<0,05). Omentum je bio najčešće predilekcijsko mjesto (P<0,05) i to kod ovaca 84,85%, a kod koza 82,14%. Morfološke značajke malih kukica (uključujući dužinu kukica, dužinu drška i dužinu šiljka) značajno su se razlikovale u ovaca i koza (P<0,05). Zaključak je da su cisticerci iz ovaca i koza vjerojatno dva različita soja, kako je opisano u srodne teniidne trakavice, Echinococcus granulosus

A sub-threshold differential cmos schmitt trigger with adjustable hysteresis based on body bias technique

This paper presents a sub-threshold differential CMOS Schmitt trigger with tunable hysteresis, which can be used to enhance the noise immunity of low-power electronic systems. By exploiting the body bias technique to the positive feedback transistors, the hysteresis of the proposed Schmitt trigger is generated, and it can be adjusted by the applied bias voltage to the bulk terminal of the utilized PMOS transistors. The principle of operation and the main formulas of the proposed circuit are discussed. The circuit is designed in a 0.18-μm standard CMOS process with a 0.6 V power supply. Post-layout simulation results show that the hysteresis width of the Schmitt trigger can be adjusted from 45.5 mV to 162 mV where the ratio of the hysteresis width variation to supply voltage is 19.4%. This circuit consumes 10.52 × 7.91 μm2 of silicon area, and its power consumption is only 1.38 μW, which makes it a suitable candidate for low-power applications such as portable electronic, biomedical, and bio-implantable systems

Sleep Pattern, Duration and Quality in Relation with Glycemic Control in People with Type 2 Diabetes Mellitus

Sleep disturbances have been shown to be associated with diabetes control, but the relation between planned wakings or napping with glycemic indices has not been evaluated yet. This study evaluated the relation between sleep quality, duration, and pattern, including daytime napping of people with diabetes and their glycemic control. A cross-sectional correlation research design was used for this study. We enrolled 118 people with type 2 diabetes receiving oral agents without major complications at the Shahid Bahonar Center, Kerman. The age, weight, height, serum HbA1c, as well as other glycemic indices and lipid profile were measured. BMI was also calculated. All participants were requested to fill in the Pittsburgh Sleep Quality Index (PSQI) questionnaire to evaluate their sleep quality. In addition, they were inquired about their sleep schedule during day and night. Pearson correlation and multiple regression analyses were conducted to examine the correlation between HbA1c and sleep pattern variables. The variables were also compared between participants with or without napping using t-test. All analyses were performed with the SPSS version 19 (SPSS, Chicago, IL, USA). The mean age was 58±11 years and mean HbA1c (%) was 7.8±11 (62±13 mmol/mol). Sleep duration and the number of sleep segments significantly predicted HbA1c (F (2,114)=5.232, P=0.007, R2=0.084). A one-hour increment in sleep duration was associated with a 0.174% (1.4 mmol/mol) decrement in HbA1c. PSQI score did not contribute to the regression model. Moreover, participants who napped (66%) had a lower HbA1c (7.6±1) compared to others (8.1±1.3) (P=0.04). We concluded that napping and segmented sleep are associated with a better glycemic control in type 2 diabetes and there is a linear correlation between sleep duration and better glycemic control

Assessment of Toxoplasma Seropositivity in Children Suffering from Anxiety Disorders.

peer reviewed[en] OBJECTIVE: This study aimed to assess the seroprevalence of Toxoplasma gondii in children with anxiety disorders. MATERIALS & METHODS: This cross-sectional study was conducted between Sep 2012 and May 2013 in Pediatrics Clinic of Baqiyatallah Hospital, Tehran, Iran. Children were assessed clinically. Diagnosis of patients with anxiety disorders was based on DSM-4 system, performed by child psychiatrist. Then their anti-Toxoplasma antibodies were measured. A questionnaire was verbally administered to all individuals' parents including demographic information and questions about life style, family history, medical history, economic situation, residence, nutritional patterns and contact with animals. RESULTS: Ninety-six male and female cases with a mean age of 8.56±2.5 and 8.42±1.9 yr underwent analysis. Anti- T. gondii IgG antibody was found in one case of each group. There was no significant difference between case and control groups for serum Toxoplasma IgG antibody (P=0.14). No case individuals had Anti- T. gondii IgM antibody, while it was found in one control individual. No significant difference was seen between case and control groups for Toxoplasma IgM antibody (P=0.27). CONCLUSION: Toxoplasmosis has no direct effect on the incidence of anxiety disorders. More studies are needed with a larger volume of individuals in future

Assessment of Toxoplasma Seropositivity in Children Suffering from Attention Deficit Hyperactivity Disorder

peer reviewedBackground: Toxoplasmosis, a protozoan infection caused by Toxoplasma gondii, is suggested to be a risk factor for many psychological disorders such as schizophrenia and depression. Attention deficit hyperactivity disorder (ADHD) is one of the most common psychiatric disorders among children. Previous studies have assessed the correlation between ADHD and infectious diseases like toxoplasmosis. So we aimed to investigate the possible correlation between Toxoplasma seropositivity and ADHD in children. Materials and Methods: In this cross-sectional study children with signs of ADHD were regarded as patients and underwent clinical assessments. Diagnosis of these patients was based on DSM-IV-TR system which was performed by a pediatric psychiatrist. Forty-eight Children without signs of ADHD or other psychic disorders were considered as control, and 48 patients were considered as case group. Parents were asked to answer a questionnaire including demographic, pregnancy and habitual questions. Blood samples were taken from all individuals and assessed for anti-Toxoplasma IgM and IgG antibodies. Results: Ninety-six male and female patients with a mean age of 8.12 years underwent analysis. Seropositivity rate for anti-T.gondii IgG antibody was 4.2% in the case and 2.1% in control individuals (P=0.92). Anti-T.gondii IgM antibodies were not found in control individuals while it was found in 2.1% of case individuals (P=0.74). There was no statistically significant association between seroprevalence of IgM (P=0.74) and IgG (P=0.92) antibodies and ADHD in study individuals. Conclusion: Our findings showed that the toxoplasmosis seropositivity has no significant difference between children with and without ADHD. Further studies are needed with a larger amount of individuals. [GMJ. 2016;5(4):188-93

Global, regional, and national comparative risk assessment of 84 behavioural, environmental and occupational, and metabolic risks or clusters of risks for 195 countries and territories, 1990–2017 : a systematic analysis for the Global Burden of Disease Study 2017

Background: The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 comparative risk assessment (CRA) is a comprehensive approach to risk factor quantification that offers a useful tool for synthesising evidence on risks and risk outcome associations. With each annual GBD study, we update the GBD CRA to incorporate improved methods, new risks and risk outcome pairs, and new data on risk exposure levels and risk outcome associations. Methods: We used the CRA framework developed for previous iterations of GBD to estimate levels and trends in exposure, attributable deaths, and attributable disability-adjusted life-years (DALYs), by age group, sex, year, and location for 84 behavioural, environmental and occupational, and metabolic risks or groups of risks from 1990 to 2017. This study included 476 risk outcome pairs that met the GBD study criteria for convincing or probable evidence of causation. We extracted relative risk and exposure estimates from 46 749 randomised controlled trials, cohort studies, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. Using the counterfactual scenario of theoretical minimum risk exposure level (TMREL), we estimated the portion of deaths and DALYs that could be attributed to a given risk. We explored the relationship between development and risk exposure by modelling the relationship between the Socio-demographic Index (SDI) and risk-weighted exposure prevalence and estimated expected levels of exposure and risk-attributable burden by SDI. Finally, we explored temporal changes in risk-attributable DALYs by decomposing those changes into six main component drivers of change as follows: (1) population growth; (2) changes in population age structures; (3) changes in exposure to environmental and occupational risks; (4) changes in exposure to behavioural risks; (5) changes in exposure to metabolic risks; and (6) changes due to all other factors, approximated as the risk-deleted death and DALY rates, where the risk-deleted rate is the rate that would be observed had we reduced the exposure levels to the TMREL for all risk factors included in GBD 2017. Findings: In 2017,34.1 million (95% uncertainty interval [UI] 33.3-35.0) deaths and 121 billion (144-1.28) DALYs were attributable to GBD risk factors. Globally, 61.0% (59.6-62.4) of deaths and 48.3% (46.3-50.2) of DALYs were attributed to the GBD 2017 risk factors. When ranked by risk-attributable DALYs, high systolic blood pressure (SBP) was the leading risk factor, accounting for 10.4 million (9.39-11.5) deaths and 218 million (198-237) DALYs, followed by smoking (7.10 million [6.83-7.37] deaths and 182 million [173-193] DALYs), high fasting plasma glucose (6.53 million [5.23-8.23] deaths and 171 million [144-201] DALYs), high body-mass index (BMI; 4.72 million [2.99-6.70] deaths and 148 million [98.6-202] DALYs), and short gestation for birthweight (1.43 million [1.36-1.51] deaths and 139 million [131-147] DALYs). In total, risk-attributable DALYs declined by 4.9% (3.3-6.5) between 2007 and 2017. In the absence of demographic changes (ie, population growth and ageing), changes in risk exposure and risk-deleted DALYs would have led to a 23.5% decline in DALYs during that period. Conversely, in the absence of changes in risk exposure and risk-deleted DALYs, demographic changes would have led to an 18.6% increase in DALYs during that period. The ratios of observed risk exposure levels to exposure levels expected based on SDI (O/E ratios) increased globally for unsafe drinking water and household air pollution between 1990 and 2017. This result suggests that development is occurring more rapidly than are changes in the underlying risk structure in a population. Conversely, nearly universal declines in O/E ratios for smoking and alcohol use indicate that, for a given SDI, exposure to these risks is declining. In 2017, the leading Level 4 risk factor for age-standardised DALY rates was high SBP in four super-regions: central Europe, eastern Europe, and central Asia; north Africa and Middle East; south Asia; and southeast Asia, east Asia, and Oceania. The leading risk factor in the high-income super-region was smoking, in Latin America and Caribbean was high BMI, and in sub-Saharan Africa was unsafe sex. O/E ratios for unsafe sex in sub-Saharan Africa were notably high, and those for alcohol use in north Africa and the Middle East were notably low. Interpretation: By quantifying levels and trends in exposures to risk factors and the resulting disease burden, this assessment offers insight into where past policy and programme efforts might have been successful and highlights current priorities for public health action. Decreases in behavioural, environmental, and occupational risks have largely offset the effects of population growth and ageing, in relation to trends in absolute burden. Conversely, the combination of increasing metabolic risks and population ageing will probably continue to drive the increasing trends in non-communicable diseases at the global level, which presents both a public health challenge and opportunity. We see considerable spatiotemporal heterogeneity in levels of risk exposure and risk-attributable burden. Although levels of development underlie some of this heterogeneity, O/E ratios show risks for which countries are overperforming or underperforming relative to their level of development. As such, these ratios provide a benchmarking tool to help to focus local decision making. Our findings reinforce the importance of both risk exposure monitoring and epidemiological research to assess causal connections between risks and health outcomes, and they highlight the usefulness of the GBD study in synthesising data to draw comprehensive and robust conclusions that help to inform good policy and strategic health planning

A global survey on changes in the supply, price, and use of illicit drugs and alcohol, and related complications during the 2020 COVID-19 pandemic

Background and Aims : COVID-19 has infected more than 77 million people worldwide and impacted the lives of many more, with a particularly devastating impact on vulnerable populations, including people with substance use disorders (SUDs). Quarantines, travel bans, regulatory changes, social distancing, and "lockdown" measures have affected drug and alcohol supply chains and subsequently their availability, price, and use patterns, with possible downstream effects on presentations of SUDs and demand for treatment. Given the lack of multicentric epidemiologic studies, we conducted a rapid global survey within the International Society of Addiction Medicine (ISAM) network in order to understand the status of substance-use patterns during the current pandemic. Design : Cross-sectional survey. Setting : Worldwide. Participants : Starting on April 4, 2020 during a 5-week period, the survey received 185 responses from 77 countries. Measurements : To assess addiction medicine professionals' perceived changes in drug and alcohol supply, price, use pattern, and related complications during the COVID-19 pandemic. Findings : Participants reported (among who answered "decreased" or "increased") a decrease in drug supply (69.0%) and at the same time an increase in price (95.3%) globally. With respect to changes in use patterns, an increase in alcohol (71.7%), cannabis (63.0%), prescription opioids (70.9%), and sedative/hypnotics (84.6%) use was reported, while the use of amphetamines (59.7%), cocaine (67.5%), and opiates (58.2%) was reported to decrease overall. Conclusions : The global report on changes in the availability, use patterns, and complications of alcohol and drugs during the COVID-19 pandemic should be considered in making new policies and in developing mitigating measures and guidelines during the current pandemic (and probable future ones) in order to minimize risks to people with SUD.Publisher PDFPeer reviewe

Solo Sonographically Guided PCNL under Spinal Anesthesia: Defining Predictors of Success

Aim. Sonography has been brought in percutaneous nephrolithotripsy (PCNL) as an adjunct to or substitute for X-ray to restrict radiation exposure. Tis study was designed to investigate the possible predictors for the success of the solo sonographically guided PCNL. Methods. 148 consecutive cases were prospectively enrolled. All steps of PCNL were performed solely with sonography guidance under spinal anesthesia. Residual stones were evaluated the day afer surgery using sonography and plain radiography. Results. Te mean age was 46 ± 15 years; 40% of kidneys had hydronephrosis. Te mean stone burden was 504 ± 350 mm2. Te mean duration of surgery was 43 ± 21 minutes. Te early stone-free rate was 92% in inferior or middle calyceal stones, 89.5% in single pelvic stones, 81.5% in partial staghorn stones, and 61.9% in staghorn stones. Te mean residual stone size was 13 ± 8 mm. Logistic regression showed that a lower age and a larger stone burden signifcantly predicted positive residual stones. Fifeen percent of patients presented with grade I or II and six percent showed grade III complication based on Clavien classifcation. Tere was no cases of organ injury or death. Conclusion. Solo ultrasonographically guided PCNL under spinal anesthesia is feasible with an acceptable stone-free rate and complication rate