A systematic analysis of genetic interactions and their underlying biology in childhood cancer.

Childhood cancer is a major cause of child death in developed countries. Genetic interactions between mutated genes play an important role in cancer development. They can be detected by searching for pairs of mutated genes that co-occur more (or less) often than expected. Co-occurrence suggests a cooperative role in cancer development, while mutual exclusivity points to synthetic lethality, a phenomenon of interest in cancer treatment research. Little is known about genetic interactions in childhood cancer. We apply a statistical pipeline to detect genetic interactions in a combined dataset comprising over 2,500 tumors from 23 cancer types. The resulting genetic interaction map of childhood cancers comprises 15 co-occurring and 27 mutually exclusive candidates. The biological explanation of most candidates points to either tumor subtype, pathway epistasis or cooperation while synthetic lethality plays a much smaller role. Thus, other explanations beyond synthetic lethality should be considered when interpreting genetic interaction test results.

Increased incidence of rhino-orbital mucormycosis in an educational therapeutic hospital during the COVID-19 pandemic in western Iran: An observational study.

BACKGROUND: COVID-19 patients, especially the patients requiring hospitalisation, have a high risk of several complications such as opportunistic bacterial and fungal infections. Mucormycosis is a rare and opportunistic fungal infection that mainly affects diabetic and immunocompromised patients. An increase has been observed in the number of rhino-orbital mucormycosis in patients with COVID-19 admitted to Imam Khomeini Hospital, Kermanshah, Iran, since October 2020. This is a report of the frequency, risk factors, clinical manifestations, treatment and prognosis of COVID-19 associated with mucormycosis infection. METHODS: The medical records of COVID-19 patients with rhino-orbital mucormycosis who were diagnosed in an educational therapeutic hospital in Kermanshah, west of Iran were surveyed. Several parameters were analysed including demographic, clinical, therapeutic and laboratory characteristics. RESULTS: Twelve patients with COVID-19-associated rhino-orbital mucormycosis were identified from 12 October to 18 November 2020. All cases reported as proven mucormycosis had a history of hospitalisation due to COVID-19. Comorbidities mainly included diabetes mellitus (83.33%) and hypertension (58.33%). Seventy-five per cent of patients received corticosteroids for COVID- 19 treatment. The sites of involvement were rhino-sino-orbital (83%) and rhino-sino (17%). Amphotericin B/liposomal amphotericin B alone or in combination with surgical debridement or orbital exenteration was used as the first-line therapy. The overall mortality rate was 66.7% (8/12). CONCLUSIONS: We found a high incidence of mucormycosis among COVID-19 patients. Diabetes mellitus and corticosteroid use were the dominant predisposing factor of mucormycosis. Mucormycosis is a life-threatening and opportunistic infection; therefore, physicians should know the signs and symptoms of the disease so that a timely diagnosis and therapy can be performed.

A framework for exhaustive modelling of genetic interaction patterns using Petri nets.

MOTIVATION: Genetic interaction (GI) patterns are characterized by the phenotypes of interacting single and double mutated gene pairs. Uncovering the regulatory mechanisms of GIs would provide a better understanding of their role in biological processes, diseases and drug response. Computational analyses can provide insights into the underpinning mechanisms of GIs. RESULTS: In this study, we present a framework for exhaustive modelling of GI patterns using Petri nets (PN). Four-node models were defined and generated on three levels with restrictions, to enable an exhaustive approach. Simulations suggest ∼5 million models of GIs. Generalizing these we propose putative mechanisms for the GI patterns, inversion and suppression. We demonstrate that exhaustive PN modelling enables reasoning about mechanisms of GIs when only the phenotypes of gene pairs are known. The framework can be applied to other GI or genetic regulatory datasets. AVAILABILITY AND IMPLEMENTATION: The framework is available at http://www.ibi.vu.nl/programs/ExhMod. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The ability of transcription factors to differentially regulate gene expression is a crucial component of the mechanism underlying inversion, a frequently observed genetic interaction pattern.

Genetic interactions, a phenomenon whereby combinations of mutations lead to unexpected effects, reflect how cellular processes are wired and play an important role in complex genetic diseases. Understanding the molecular basis of genetic interactions is crucial for deciphering pathway organization as well as understanding the relationship between genetic variation and disease. Several hypothetical molecular mechanisms have been linked to different genetic interaction types. However, differences in genetic interaction patterns and their underlying mechanisms have not yet been compared systematically between different functional gene classes. Here, differences in the occurrence and types of genetic interactions are compared for two classes, gene-specific transcription factors (GSTFs) and signaling genes (kinases and phosphatases). Genome-wide gene expression data for 63 single and double deletion mutants in baker's yeast reveals that the two most common genetic interaction patterns are buffering and inversion. Buffering is typically associated with redundancy and is well understood. In inversion, genes show opposite behavior in the double mutant compared to the corresponding single mutants. The underlying mechanism is poorly understood. Although both classes show buffering and inversion patterns, the prevalence of inversion is much stronger in GSTFs. To decipher potential mechanisms, a Petri Net modeling approach was employed, where genes are represented as nodes and relationships between genes as edges. This allowed over 9 million possible three and four node models to be exhaustively enumerated. The models show that a quantitative difference in interaction strength is a strict requirement for obtaining inversion. In addition, this difference is frequently accompanied with a second gene that shows buffering. Taken together, these results provide a mechanistic explanation for inversion. Furthermore, the ability of transcription factors to differentially regulate expression of their targets provides a likely explanation why inversion is more prevalent for GSTFs compared to kinases and phosphatases.

Growth condition dependency is the major cause of non-responsiveness upon genetic perturbation.

Investigating the role and interplay between individual proteins in biological processes is often performed by assessing the functional consequences of gene inactivation or removal. Depending on the sensitivity of the assay used for determining phenotype, between 66% (growth) and 53% (gene expression) of Saccharomyces cerevisiae gene deletion strains show no defect when analyzed under a single condition. Although it is well known that this non-responsive behavior is caused by different types of redundancy mechanisms or by growth condition/cell type dependency, it is not known what the relative contribution of these different causes is. Understanding the underlying causes of and their relative contribution to non-responsive behavior upon genetic perturbation is extremely important for designing efficient strategies aimed at elucidating gene function and unraveling complex cellular systems. Here, we provide a systematic classification of the underlying causes of and their relative contribution to non-responsive behavior upon gene deletion. The overall contribution of redundancy to non-responsive behavior is estimated at 29%, of which approximately 17% is due to homology-based redundancy and 12% is due to pathway-based redundancy. The major determinant of non-responsiveness is condition dependency (71%). For approximately 14% of protein complexes, just-in-time assembly can be put forward as a potential mechanistic explanation for how proteins can be regulated in a condition dependent manner. Taken together, the results underscore the large contribution of growth condition requirement to non-responsive behavior, which needs to be taken into account for strategies aimed at determining gene function. The classification provided here, can also be further harnessed in systematic analyses of complex cellular systems.

Pain management in trauma: A review study.

BACKGROUND: Pain in trauma has a role similar to the double-edged sword. On the one hand, pain is a good indicator to determine the severity and type of injury. On the other hand, pain can induce sever complications and it may lead to further deterioration of the patient. Therefore, knowing how to manage pain in trauma patients is an important part of systemic approach in trauma. The aim of this manuscript is to provide information about pain management in trauma in the Emergency Room settings. METHODS: In this review we searched among electronic and manual documents covering a 15-yr period between 2000 and 2016. Our electronic search included Pub Med, Google scholar, Web of Science, and Cochrane databases. We looked for articles in English and in peer-reviewed journals using the following keywords: acute pain management, trauma, emergency room and injury. RESULTS: More than 3200 documents were identified. After screening based on the study inclusion criteria, 560 studies that had direct linkage to the study aim were considered for evaluation based World Health Organization (WHO) pain ladder chart. CONCLUSIONS: To provide adequate pain management in trauma patients require: adequate assessment of age-specific pharmacologic pain management; identification of adequate analgesic to relieve moderate to severe pain; cognizance of serious adverse effects of pain medications and weighting medications against their benefits, and regularly reassessing patients and reevaluating their pain management regimen. Patient-centered trauma care will also require having knowledge of barriers to pain management and discussing them with the patient and his/her family to identify solutions.

A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions.

BACKGROUND: Genetic interactions, or non-additive effects between genes, play a crucial role in many cellular processes and disease. Which mechanisms underlie these genetic interactions has hardly been characterized. Understanding the molecular basis of genetic interactions is crucial in deciphering pathway organization and understanding the relationship between genotype, phenotype and disease. RESULTS: To investigate the nature of genetic interactions between gene-specific transcription factors (GSTFs) in Saccharomyces cerevisiae, we systematically analyzed 72 GSTF pairs by gene expression profiling double and single deletion mutants. These pairs were selected through previously published growth-based genetic interactions as well as through similarity in DNA binding properties. The result is a high-resolution atlas of gene expression-based genetic interactions that provides systems-level insight into GSTF epistasis. The atlas confirms known genetic interactions and exposes new ones. Importantly, the data can be used to investigate mechanisms that underlie individual genetic interactions. Two molecular mechanisms are proposed, "buffering by induced dependency" and "alleviation by derepression". CONCLUSIONS: These mechanisms indicate how negative genetic interactions can occur between seemingly unrelated parallel pathways and how positive genetic interactions can indirectly expose parallel rather than same-pathway relationships. The focus on GSTFs is important for understanding the transcription regulatory network of yeast as it uncovers details behind many redundancy relationships, some of which are completely new. In addition, the study provides general insight into the complex nature of epistasis and proposes mechanistic models for genetic interactions, the majority of which do not fall into easily recognizable within- or between-pathway relationships.

A case-control study of psychosocial risk and protective factors of self-immolation in Iran.

Self-immolation is the third leading cause of years of life lost (YLL) among women in Iran. The aim of this study is to investigate self-immolation-related risk and protective factors in the western region of Iran, a province with the highest prevalent of self-immolation in the country. Using a case-control design, we compared 151 cases of self-immolation attempters who were admitted to a burn center in Kermanshah with 302-matched control group from the same community/locality between March 21st, 2009, and March 20th, 2012. We conducted descriptive, bivariate, and multivariate analysis to examine the associations of self-immolation with demographic and familial risk factors, adverse life events, mental disorders, as well as potential protective factors. According to our findings, the highest percentage of self-immolation was in the 16-25 year-old age group (60%) and in females (76%). Of the potential risk factors in the study, major depression, adjustment disorders, individual history of suicide attempts and opium dependence, were statistically significant predictors of self-immolation. Suggestions for translating the local picture of self-immolation portrayed by our findings, into meaningful prevention strategies that have a good fit with the social and interpersonal context within which self-immolation takes place are discussed.

Effect of intrathecal midazolam in the severity of pain in cesarean section: a randomized controlled trail.

BACKGROUND: The benzodiazepines are used primarily for anxiolysis, amnesia and sedation. However, recent investigations have shown that some forms of this group of drugs have also direct effect on pain. This study aims to determine the effect of midazolam in reducing the severity of pain in women scheduled for elective cesarean section. METHODS: In a prospective, double blind randomized controlled trial, two groups parallel study, was conducted in Imam Reza/Moatazedi Hospital, an affiliate of Kermanshah University of Medical Sciences. Parturient women who met study inclusion criteria were consecutively assigned into either experimental (n=62) or control groups (n=62). Women in the experimental group received bupivacaine (10 mg) plus intrathecal midazolam (2 mg/ml) (BM) and those in the control group received bupivacaine plus normal saline (BNS). The outcome pain severity was measured by Verbal Numerical Rating Scale. RESULTS: In comparison with the BNS group, mothers in the BM group reported a significant relief in pain (15 min and 120 min) after the surgery. There were no significant differences between the groups regarding the intensity of pain 5, 30, 60 and 240 min after the surgery. The average time until the first dose of additional analgesic, per mother's request was 142.18±55.19 min in the BNS vs 178.06±77.33 min in the BM group. CONCLUSION: Combination of bupivacaine plus intrathecal midazolam was an effective anesthetic technique to provide improvement in pain. The onset of sedation was faster in the BM group compared with the BNS group. The duration of effective analgesia, and the time for regression of sensory analgesia was the same in both groups in our study. However, incidence of nausea and vomiting was higher in the experimental group.

Traumatic injuries in pregnant women: a case of motor vehicle accident for "Ground Round" discussion.

UNLABELLED: The main objective for introducing this case study is to create a platform from which the importance of road traffic related injuries and traumas can be emphasized and discussed within and across various fields of investigation. The long term goal is to entice public campaign around unmet needs for higher road safety measures to reduce primary, secondary, and tertiary risks of injuries and traumas. CASE: a 28-year-old pregnant woman with a 16-week gestational age fetus was involved in a road car crash resulting in multiple traumas. Evaluation and treatment was initiated in the local Urgent Care Unit and continued in the emergency department and operation room. Patient underwent the following procedures: laparotomy, diverting colostomy, terminating pregnancy, right calcaneal traction and long leg splint, as well as multiple irrigation-debridements. Finally, the wound was left open and the patient was admitted to Intensive Care Unit. We hope that the introduction of this case for a "Ground Round" discussion will stir up a comprehensive discussion regarding the injury and trauma related preventive measures as well as treatment approaches in cases involving pregnant women in car accidents, and will bring about a holistic overview of this issue by the experts in various fields.