Organizing gene literature retrieval, profiling, and visualization training workshops for early career researchers

Developing the skills needed to effectively search and extract information from biomedical literature is essential for early-career researchers. It is, for instance, on this basis that the novelty of experimental results, and therefore publishing opportunities, can be evaluated. Given the unprecedented volume of publications in the field of biomedical research, new systematic approaches need to be devised and adopted for the retrieval and curation of literature relevant to a specific theme. Here we describe a hands-on training curriculum aimed at retrieval, profiling, and visualization of literature associated with a given topic. This curriculum was implemented in a workshop in January 2021. We provide supporting material and step-by-step implementation guidelines with the ISG15 gene literature serving as an illustrative use case. Through participation in such a workshop, trainees can learn: 1) to build and troubleshoot PubMed queries in order to retrieve the literature associated with a gene of interest; 2) to identify key concepts relevant to given themes (such as cell types, diseases, and biological processes); 3) to measure the prevalence of these concepts in the gene literature; 4) to extract key information from relevant articles, and 5) to develop a background section or summary on the basis of this information. Finally, trainees can learn to consolidate the structured information captured through this process for presentation via an interactive web application

An approximation algorithm for the solution of the nonlinear Lane-Emden type equations arising in astrophysics using Hermite functions collocation method

In this paper we propose a collocation method for solving some well-known classes of Lane-Emden type equations which are nonlinear ordinary differential equations on the semi-infinite domain. They are categorized as singular initial value problems. The proposed approach is based on a Hermite function collocation (HFC) method. To illustrate the reliability of the method, some special cases of the equations are solved as test examples. The new method reduces the solution of a problem to the solution of a system of algebraic equations. Hermite functions have prefect properties that make them useful to achieve this goal. We compare the present work with some well-known results and show that the new method is efficient and applicable.Comment: 34 pages, 13 figures, Published in "Computer Physics Communications

Monitoring of drinking water quality using automated ATP quantification

A microfluidic based system was developed for automated online method for the rapid detection and monitoring of drinking water contamination utilising microbial Adrenosine-5′-Triphosphate (ATP) as a bacterial indicator. The system comprises a polymethyl methacrylate based microfluidic cartridge inserted into an enclosure incorporating the functions of fluid storage and delivery, lysis steps and real-time detection. Design, integration and operation of the resulting automated system are reported, including the lysis method, the design of the mixing circuit, the choices of flow rate, temperature and reagent amount. Calibration curves of both total and free ATP were demonstrated to be highly linear over a range from 2.5–5000 pg/mL with the limit of detection being lower than 2.5 pg/mL of total ATP. The system was trialled in a lab study with different types of water, with lysis efficiency being found to be strongly dependent upon water type. Further development is required before online implementation

Aging diminishes the resistance of AO rats to EAE: putative role of enhanced generation of GM-CSF Expressing CD4+T cells in aged rats

Background: Aging influences immune response and susceptibility to EAE in a strain specific manner. The study was designed to examine influence of aging on EAE induction in Albino Oxford (AO) rats. Results: Differently from 3-month-old (young) rats, which were resistant to EAE induction, the majority of aged (24-26-month-old) rats developed mild chronic form of EAE. On 16th day post-immunization, when in aged rats the neurological deficit reached plateau, more mononuclear cells, including CD4+ T lymphocytes was retrieved from spinal cord of aged than young rats. The frequencies of IL-17+ and GM-CSF+ cells within spinal cord infiltrating CD4+ lymphocytes were greater in aged rats. To their increased frequency contributed the expansion of GM-CSF + IL-17 + IFN-gamma+ cells, which are highly pathogenic in mice. The expression of the cytokines (IL-1 beta and IL-23/p19) driving GM-CSF + IL-17 + IFN-gamma + cell differentiation in mice was also augmented in aged rat spinal cord mononuclear cells. Additionally, in aged rat spinal cord the expansion of GM-CSF + IL-17-IFN-gamma- CD4+ T lymphocytes was found. Consistently, the expression of mRNAs for IL-3, the cytokine exhibiting the same expression pattern as GM-CSF, and IL-7, the cytokine driving differentiation of GM-CSF + IL-17-IFN-gamma- CD4 + lymphocytes in mice, was upregulated in aged rat spinal cord mononuclear cells, and the tissue, respectively. This was in accordance with the enhanced generation of the brain antigen-specific GM-CSF+ CD4+ lymphocytes in aged rat draining lymph nodes, as suggested by (i) the higher frequency of GM-CSF+ cells (reflecting the expansion of IL-17-IFN-gamma- cells) within their CD4+ lymphocytes and (ii) the upregulated GM-CSF and IL-3 mRNA expression in fresh CD4+ lymphocytes and MBP-stimulated draining lymph node cells and IL-7 mRNA in lymph node tissue from aged rats. In agreement with the upregulated GM-CSF expression in aged rats, strikingly more CD11b + CD45(int) (activated microglia) and CD45(hi) (mainly proinflammatory dendritic cells and macrophages) cells was retrieved from aged than young rat spinal cord. Besides, expression of mRNA for SOCS1, a negative regulator of proinflammatory cytokine expression in innate immunity cells, was downregulated in aged rat spinal cord mononuclear cells. Conclusions: The study revealed that aging may overcome genetic resistance to EAE, and indicated the cellular and molecular mechanisms contributing to this phenomenon in AO rats

Developing criteria for Cesarean Section using the RAND appropriateness method

<p>Abstract</p> <p>Background</p> <p>Cesarean section rates are increasing worldwide, and a rapid increase has been observed in Iran. Disagreement exists between clinicians about when to use cesarean section. We aimed to identify the appropriateness criteria for the use of cesarean section in Iran.</p> <p>Method</p> <p>A consensus development study using a modified version of the RAND Appropriateness Method (RAM). We generated scenarios from valid clinical guidelines and expert opinions. A panel of experts participated in consensus development: first round via mail (12 members), second round face-to-face (9 members). We followed the RAM recommendations for the development of the scenario lists, rating scales, and statistical analyses.</p> <p>Results</p> <p>294 scenarios relevant to cesarean section were identified. 191 scenarios were considered appropriate, of which 125 scenarios were agreed upon. The panel found cesarean inappropriate for 21% of scenarios, and 'equivocal' for 14% of scenarios.</p> <p>Conclusion</p> <p>RAM is useful for identifying stakeholder views in settings with limited resources. The participants' views on appropriateness of certain indications differed with available evidence. A large number of scenarios without agreement may partly explain why it has been difficult to curb the growth in cesarean section rate.</p

Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk

Lung-function impairment underlies chronic obstructive pulmonary disease (COPD) and predicts mortality. In the largest multi-ancestry genome-wide association meta-analysis of lung function to date, comprising 580,869 participants, we identified 1,020 independent association signals implicating 559 genes supported by ≥2 criteria from a systematic variant-to-gene mapping framework. These genes were enriched in 29 pathways. Individual variants showed heterogeneity across ancestries, age and smoking groups, and collectively as a genetic risk score showed strong association with COPD across ancestry groups. We undertook phenome-wide association studies for selected associated variants as well as trait and pathway-specific genetic risk scores to infer possible consequences of intervening in pathways underlying lung function. We highlight new putative causal variants, genes, proteins and pathways, including those targeted by existing drugs. These findings bring us closer to understanding the mechanisms underlying lung function and COPD, and should inform functional genomics experiments and potentially future COPD therapies

Report of experience in 190 patients with the use of closed suction drainage in arthroscopic knee procedures

The goal of this study is to report our experience with the use of suction drainage for various arthroscopic knee procedures. One hundred and ninety patients who underwent arthroscopic knee procedures participated in the study, and were divided into two groups (Group 1: Suction drainage, Group 2: No suction drainage). For every patient, the following parameters were recorded: age, gender, operative time, tourniquet or pump use, the amount of fluid collected in the hemovac drain, presence of meniscal tear, type of the operative procedure, date of the operation, and presence of effusion at the follow-up. Statistical analysis was performed to detect any significant statistical difference between the amount of fluid collected in the hemovac drain and the other mentioned parameters in Group 1; and these patients were divided into four subgroups to facilitate the statistical evaluation between the procedures and the amount of fluid collected in the hemovac drain. The partial meniscectomy subgroup had significantly lower amounts of collected fluid when compared to the subtotal meniscectomy subgroup. Drilling of the osteochondral faces led to significantly higher amounts of fluid when compared to non-drilling cases. Use of an infusion pump during surgery and shorter operation time led to lower amounts of fluid to be collected. No case in either main group suffered from effusion at the follow-up. Our investigation demonstrated that in different arthroscopic interventions, variable amounts of fluid can be collected in the hemovac drains. Subtotal meniscal resection, drilling of the osteochondral faces and longer duration of the operation increase the amount of fluid. In cases of partial meniscal resection and/or chondral debridement, limited synovial and plica resection, suction drainage is unnecessary

Carbon Footprint Of Post-Earthquake Bridge Repair

Previous performance-based earthquake engineering investigations on highway bridges focused on repair cost and repair time metrics. These are primarily related to economic life cycle-cost analysis decision-making strategies for evaluating the vulnerability of bridge infrastructure. However, equally important considerations for decision making are those associated with the complete life-cycle assessment of the same infrastructure. Quantifying the sustainability of bridge designs using carbon footprint as the performance metric is investigated in this paper. A set of multi-span reinforced concrete highway overpass bridges in California is used to illustrate the probabilistic carbon accounting methodology. The bridges were selected because repair cost and time data are already available, allowing comparison of the cost-based performance metrics with the derived sustainability metrics. The performance groups and material quantities that drive the major contributions to carbon footprint as compared to economic costs are presented