BioNetGen 2.2: Advances in Rule-Based Modeling

BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model specification and simulation. Here, we report on these additions, discussing how they facilitate the construction, simulation, and analysis of larger and more complex models than previously possible.Comment: 3 pages, 1 figure, 1 supplementary text file. Supplementary text includes a brief discussion of the RK-PLA along with a performance analysis, two tables listing all new actions/arguments added in BioNetGen 2.2, and the "BioNetGen Quick Reference Guide". Accepted for publication in Bioinformatic

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

STUDY ON ANTIMICROBIAL RESISTANCE PATTERN IN A TERTIARY CARE HOSPITAL – AN OBSERVATIONAL RETROSPECTIVE STUDY

Objective: The aim of the study was to monitor the magnitude and trends in antimicrobial resistance through surveillance programs and bacteriological diagnostic methods. Methods: The study research has performed a retrospective observational study for period of 6 months (Dec 2019–June 2020) to determine the antimicrobial susceptibility pattern on cultures of various specimens at Vivekanandha Medical Care Hospital. The resultant data were computed in Microsoft Excel. Analyses were expressed as the total number, frequencies, and percentage. Results: A total of 110 culture and sensitivity reports were collected from microbiology departments. Among the culture report, 84% accounted for gram-negative and 16% for Gram-positive organisms. Out of eight specimens, 15 different bacteria were identified and the most common bacteria were Klebsiella pneumonia (25%), E. coli (14%), Staphylococcus aureus (13%), and Pseudomonas aeruginosa (12%). Conclusion: The interferences from the present study can help in bridging the gap in future educations, training, and adequate decision-making

First report of asthma prevalence in Afghanistan using international standardized methods Premier rapport sur l�asthme en Afghanistan utilisant des méthodes internationales normalisées

No data on the prevalence of asthma in Afghanistan have been published before. In a school-based survey in 2010�2011 the wheezing section of the International Study of Asthma and Allergies in Childhood (ISAAC) questionnaire was completed by a random sample of 1500 children aged 6�7 years and 1500 adolescents aged 13�14 years old. The prevalence of physician-diagnosed asthma was 12.5 in 6�7-year-olds and 17.3 in 13�14-year-olds (P = 0.002). The prevalence of wheeze in the last 12 months was similar in children and adolescents (19.2 and 21.7 respectively). The prevalence of ever wheezing, night attacks, speech-limiting wheeze and exercise-induced wheeze was 23.1, 4.8, 12.2 and 9.6 respectively in children and 30.5, 4.4, 13.0 and 13.6 respectively in adolescents. These rates are higher than those in neighbouring countries. This first epidemiological survey of asthma in Afghanistan shows that asthma and wheezing are common in Kabul students. © 2015, World Health Organization. All Rights Reserved

Synthesis of Schiff Bases via Environmentally Benign and Energy-Efficient Greener Methodologies

Non classical methods (water based reaction, microwave and grindstone chemistry) were used for the preparation of Schiff bases from 3-chloro-4-fluoro aniline and several benzaldehydes. The key raw materials were allowed to react in water, under microwave irradiation and grindstone. These methodologies constitute an energy-efficient and environmentally benign greener chemistry version of the classical condensation reactions for Schiff bases formation

Primary immunodeficiency disorders in Iran: Update and new insights from the third report of the national registry

Background: Primary immunodeficiency disorders (PID) are a group of heterogeneous disorders mainly characterized by severe and recurrent infections and increased susceptibility to malignancies, lymphoproliferative and autoimmune conditions. National registries of PID disorders provide epidemiological data and increase the awareness of medical personnel as well as health care providers. Methods: This study presents the demographic data and clinical manifestations of Iranian PID patients who were diagnosed from March 2006 till the March of 2013 and were registered in Iranian PID Registry (IPIDR) after its second report of 2006. Results: A total number of 731 new PID patients (455 male and 276 female) from 14 medical centers were enrolled in the current study. Predominantly antibody deficiencies were the most common subcategory of PID (32.3 %) and were followed by combined immunodeficiencies (22.3 %), congenital defects of phagocyte number, function, or both (17.4 %), well-defined syndromes with immunodeficiency (17.2 %), autoinflammatory disorders (5.2 %), diseases of immune dysregulation (2.6 %), defects in innate immunity (1.6 %), and complement deficiencies (1.4 %). Severe combined immunodeficiency was the most common disorder (21.1 %). Other prevalent disorders were common variable immunodeficiency (14.9 %), hyper IgE syndrome (7.7 %), and selective IgA deficiency (7.5 %). Conclusions: Registration of Iranian PID patients increased the awareness of medical community of Iran and developed diagnostic and therapeutic techniques across more parts of the country. Further efforts must be taken by increasing the coverage of IPIDR via electronically registration and gradual referral system in order to provide better estimation of PID in Iran and reduce the number of undiagnosed cases. © 2014 Springer Science+Business Media

Humans and fire: changing relations in early agricultural and built environments in the Zagros, Iran, Iraq

Fire-centred studies have recently been highlighted as powerful avenues for investigation of energy flows and relations between humans, materials, environments and other species. The aim in this paper is to evaluate this potential first by reviewing the diverse theories and methods that can be applied to investigate the ecological and social significance of anthropogenic fire, and second by applying these to new and existing data sets in archaeology. This paper examines how fire-centred approaches can inform on one of the most significant step-changes in human lifeways and inter-relations with environment and other species – the transition from mobile hunting-gathering to more sedentary agriculture in a key heartland of change, the Zagros region of Iraq and Iran, c. 12,000–8,000 BP. In the review and case studies multiple links are investigated between human fire use and environment, ecology, energy use, technology, the built environment, health, social roles and relations, cultural practices and catastrophic event

Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density

MicroRNAs (miRNAs) are post-transcriptional regulators that bind to their target mRNAs through base complementarity. Predicting miRNA targets is a challenging task and various studies showed that existing algorithms suffer from high number of false predictions and low to moderate overlap in their predictions. Until recently, very few algorithms considered the dynamic nature of the interactions, including the effect of less specific interactions, the miRNA expression level, and the effect of combinatorial miRNA binding. Addressing these issues can result in a more accurate miRNA:mRNA modeling with many applications, including efficient miRNA-related SNP evaluation. We present a novel thermodynamic model based on the Fermi-Dirac equation that incorporates miRNA expression in the prediction of target occupancy and we show that it improves the performance of two popular single miRNA target finders. Modeling combinatorial miRNA targeting is a natural extension of this model. Two other algorithms show improved prediction efficiency when combinatorial binding models were considered. ComiR (Combinatorial miRNA targeting), a novel algorithm we developed, incorporates the improved predictions of the four target finders into a single probabilistic score using ensemble learning. Combining target scores of multiple miRNAs using ComiR improves predictions over the naïve method for target combination. ComiR scoring scheme can be used for identification of SNPs affecting miRNA binding. As proof of principle, ComiR identified rs17737058 as disruptive to the miR-488-5p:NCOA1 interaction, which we confirmed in vitro. We also found rs17737058 to be significantly associated with decreased bone mineral density (BMD) in two independent cohorts indicating that the miR-488-5p/NCOA1 regulatory axis is likely critical in maintaining BMD in women. With increasing availability of comprehensive high-throughput datasets from patients ComiR is expected to become an essential tool for miRNA-related studies. © 2012 Coronnello et al