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A programming workshop has been developed for biochemists and molecular biologists to introduce them to the power and flexibility of solving problems with Python. The workshop is designed to move users beyond a "plug-and-play" approach that is based on spreadsheets and web applications in their teaching and research to writing scripts to parse large collections of data and to perform dynamic calculations. The live-coding workshop is designed to introduce specific coding skills, as well as provide insight into the broader array of open-access resources and libraries that are available for scientific computation.

Background and Objective: Approximately 16,000 new cases of lung cancer are diagnosed each year in Australia and Aotearoa New Zealand, and it is the leading cause of cancer death in the region. Unwarranted variation in lung cancer care and outcomes has been described for many years, although clinical quality indicators to facilitate benchmarking across Australasia have not been established. The purpose of this study was to establish clinical quality indicators applicable to lung and other thoracic cancers across Australia and Aotearoa New Zealand. Methods: Following a literature review, a modified three round eDelphi consensus process was completed between October 2022 and June 2023. Participants included clinicians from all relevant disciplines, patient advocates, researchers and other stakeholders, with representatives from all Australian states and territories and Aotearoa New Zealand. Consensus was set at a threshold of 70%, with the first two rounds conducted as online surveys, and the final round held as a hybrid in person and virtual consensus meeting. Results: The literature review identified 422 international thoracic oncology indicators, and a total of 71 indicators were evaluated over the course of the Delphi consensus. Ultimately, 27 clinical quality indicators reached consensus, covering the continuum of thoracic oncologic care from diagnosis to first line treatment. Indicators benchmarking supportive care were poorly represented. Attendant numeric quality standards were developed to facilitate benchmarking. Conclusion: Twenty‐seven clinical quality indicators relevant to thoracic oncology care in Australasia were developed. Real world implementation will now be explored utilizing a prospective dataset collected across Australia. A three‐round Delphi consensus process developed 27 contemporary clinical quality indicators, spanning the continuum of lung cancer care from diagnosis to treatment at the end of life. Systematic benchmarking utilizing these indicators will enable the identification of unwarranted variation and promote equitable access to best practice care. [ABSTRACT FROM AUTHOR]

Background and Objective: Unwarranted variations in lung cancer care have been well described in both Australia and Aotearoa New Zealand, with shortfalls in hospital‐based workforce and infrastructure previously demonstrated. A survey of lung cancer clinicians was performed to gain an updated understanding of current workforce and infrastructure. Methods: An online Qualtrics survey included questions on institutional demographics, estimated lung cancer case load, multidisciplinary team (MDT) characteristics including workforce and local infrastructure. We sought to obtain one response from every institution treating lung cancer in Australia and Aotearoa New Zealand. Results: Responses were received from 89 institutions, estimated to include 85% centres treating lung cancer in Australia and 100% of public hospitals in Aotearoa New Zealand. Lung cancer nurse specialist and Nuclear Medicine are poorly represented in multidisciplinary teams (MDTs) with just 34/88 (38%) institutions fulfilling recommended core workforce for MDT meetings. Case presentation is low with 32/88 (36%) regularly discussing all lung cancer patients at MDT. Metropolitan institutions appear to have a more comprehensive range of services on site, compared to non‐metropolitan institutions. Few (4/88) institutions have embedded smoking cessation services. Compared to the previous 2021 Landscape Survey, thoracic surgery representation and core MDT workforce have improved, with modest change in specialist nurse numbers. Conclusion: This wide‐reaching survey has identified persistent deficiencies and variations in lung cancer workforce and gaps in infrastructure. Multidisciplinary collaboration and care coordination are needed to ensure all patients can access timely and equitable lung cancer care. [ABSTRACT FROM AUTHOR]

Background: Gaps in the treatment of patients with acute asthma have been repeatedly described in Australia. We conducted a retrospective audit of acute asthma care at a Victorian tertiary institution. Aims: To describe acute asthma care at a large health network in metropolitan Melbourne, and evaluate the extent to which Emergency Department (ED) care was consistent with National Asthma Council guidelines. Methods: A retrospective audit was performed of medical records between July 2017 and June 2019. We included adult patients admitted to campuses within the Western Health network in Melbourne, Victoria, where the length of stay was at least 12 h, and the primary discharge diagnosis was asthma. Results: Four hundred and ninety‐three admissions were included in the analysis, representing 392 individual patients. Seventy‐one percent of patients were female and 27% were current smokers. Ninety‐six percent of patients had a prior asthma diagnosis, 63% had a previous hospital presentation and 75% were prescribed an inhaled preventer. In the ED, systemic corticosteroids and inhaled salbutamol were prescribed in 65% and 82% admissions respectively; adjunctive treatments included ipratropium (67% of admissions), magnesium sulfate (30%), adrenaline (11%) and non‐invasive ventilation (9%). Overall, ED care was guideline concordant in 59% of admissions. On the wards, treatments prescribed within 24 h of admission included corticosteroids (90% of admissions), salbutamol (84%), ipratropium (64%) and inhaled preventers (63%). The proportion of patients prescribed these treatments, as well as documented follow up (e.g. asthma action plans), varied significantly depending on the treating specialty. Conclusion: The emergency treatment of patients with acute asthma frequently deviated from guidelines and there was significant variation in inpatient treatment. Quality improvement initiatives that incorporate structural changes are required to improve asthma care. [ABSTRACT FROM AUTHOR]

The field of computational molecular sciences (CMSs) has made innumerable contributions to the understanding of the molecular phenomena that underlie and control chemical processes, which is manifested in a large number of community software projects and codes. The CMS community is now poised to take the next transformative steps of better training in modern software design and engineering methods and tools, increasing interoperability through more systematic adoption of agreed upon standards and accepted best-practices, overcoming unnecessary redundancy in software effort along with greater reproducibility, and increasing the deployment of new software onto hardware platforms from in-house clusters to mid-range computing systems through to modern supercomputers. This in turn will have future impact on the software that will be created to address grand challenge science that we illustrate here: the formulation of diverse catalysts, descriptions of long-range charge and excitation transfer, and development of structural ensembles for intrinsically disordered proteins. [ABSTRACT FROM AUTHOR]

RNA-based therapeutics hold a great promise in treating a variety of diseases. However, double-stranded RNAs (dsRNAs) are inherently unstable, highly charged, and stiff macromolecules that require a delivery vehicle. Cationic ligand functionalized gold nanoparticles (AuNPs) are able to compact nucleic acids and assist in RNA delivery. Here, we use large-scale all-atom molecular dynamics simulations to show that correlations between ligand length, metal core size, and ligand excess free volume control the ability of nanoparticles to bend dsRNA far below its persistence length. The analysis of ammonium binding sites showed that longer ligands that bind deep within the major groove did not cause bending. By limiting ligand length and, thus, excess free volume, we have designed nanoparticles with controlled internal binding to RNA's major groove. NPs that are able to induce RNA bending cause a periodic variation in RNA's major groove width. Density functional theory studies on smaller models support large-scale simulations. Our results are expected to have significant implications in packaging of nucleic acids for their applications in nanotechnology and gene delivery. [ABSTRACT FROM AUTHOR]

The Molecular Sciences Software Institute (MolSSI) is a research and education center that supports software development in the computational molecular sciences (CMS). One of MolSSI's core objectives is to provide education and training for the next generation of computational researchers. MolSSI Education targets various career stages and skill levels through its live workshops, online resources, and software fellowship program. MolSSI Education focuses its efforts on four areas: programming and software development, high-performance computing, artificial intelligence, faculty and curriculum development, and the software fellowship program. This article delineates educational efforts at the MolSSI, overall goals, and resources that can be useful to researchers in the CMS. [ABSTRACT FROM AUTHOR]

The Molecular Sciences Software Institute (MolSSI) is an National Science Foundation (NSF) funded institute that focuses on improving software, education, and training in the computational molecular sciences. Through a collaboration with the Molecular Education and Research Consortium in Undergraduate computational chemistRY (MERCURY), the MolSSI has developed resources for undergraduate and other early career students to lay an educational foundation for the next generation of computational molecular scientists. The resources focus on introducing best practices in software engineering to students from the very start to make their software more useable, maintainable, and reproducible. [ABSTRACT FROM AUTHOR]

The interactions of nanoparticles (NPs) with single stranded nucleic acids (NAs) have important implications in gene delivery, and nanotechnological and biomedical applications. Here, the complexation of cationic ligand functionalized gold nanoparticles with single stranded deoxyribose nucleic acid (DNA) and ribonucleic acid (RNA) are examined using all atom molecular dynamics simulations. The results indicated that complexation depends mostly on charge of nanoparticle, and, to lesser extent, sequence and type of nucleic acid. For cationic nanoparticles, electrostatic interactions between charged ligands and the nucleic acid backbone dominate binding regardless of nanoparticle charge. Highly charged nanoparticles bind more tightly and cause compaction of the single-stranded NAs through disruption of intrastrand π-π stacking and hydrogen bonding. However, poly-purine strands (polyA-DNA, polyA-RNA) show less change in structure than polypyrimidine strands (polyT-DNA, polyU-RNA). Overall, the results show that control over ssNA structure may be achieved with cationic NPs with a charge of more than 30, but the extent of the structural changes depends on sequence [ABSTRACT FROM AUTHOR]

The regulation of thrombin activity offers an opportunity to regulate blood clotting because of the central role played by this molecule in the coagulation cascade. Thrombin-binding DNA aptamers have been used to inhibit thrombin activity. In the past, to address the low efficacy reported for these aptamers during clinical trials, multiple aptamers have been linked using DNA nanostructures. Here, we modify that strategy by linking multiple copies of various thrombin-binding aptamers using DNA weave tiles. The resulting constructs have very high anticoagulant activity in functional assays owing to their improved cooperative binding affinity to thrombin due to optimized spacing, orientation, and the high local concentration of aptamers. We also report the results of molecular dynamics simulations to gain insight into the solution conformations of the tiles. Moreover, by using DNA strand displacement, we were able to turn the coagulation cascade off and on as desired, thereby enabling significantly better control over blood coagulation. [ABSTRACT FROM AUTHOR]

The unique molecular recognition properties of DNA molecule, which store genetic information in cells, are responsible for the rise of DNA nanotechnology. In this article, we review the recent advances in atomistic and coarse-grained force fields along with simulations of DNA-based materials, as applied to DNA–nanoparticle assemblies for controlled material morphology, DNA–surface interactions for biosensor development and DNA origami. Evidently, currently available atomistic and coarse-grained representations of DNA are now at the stage of successfully reproducing and explaining experimentally observed phenomena. However, there is a clear need for the development of atomistic force fields which are robust at long timescales and in the improvement of the coarse-grained models. [ABSTRACT FROM AUTHOR]

Background: We investigated the detection of chlamydia at different stages of the menstrual cycle. Methods: Electronic medical records for women attending Melbourne Sexual Health Centre between March 2011 and 31st December 2012, who were tested for chlamydia by nucleic acid amplification of high vaginal, cervical, or urinary samples, and who recorded a date of last normal menstrual period (LNMP) between 0–28 days were included in the analysis. Logistic regression was used to calculate adjusted odds ratio (aOR) and 95% confidence intervals (CI) for the association of chlamydia with menstrual cycle adjusted by demographics and behavioural variables. Chlamydia and beta globin load were determined on those with stored samples. Results: Of the 10,017 consultations that included a test for chlamydia and a valid LNMP, there were 417 in which chlamydia was detected. The proportion of samples with chlamydia was greater in the luteal phase (4.8%, 184/3831) than in the follicular phase (3.4%, 233/6816) both in the crude (OR 1.29 95%CI 1.1–1.6, p = 0.01) and adjusted odds ratio (aOR) 1.4 (95%CI 1.1–1.8, p = 0.004). Among women using hormonal contraception, there was no significant association with the luteal phase of the menstrual cycle (aOR 1.3, 95%CI 0.9, 1.8, p = 0.18). Among women not using hormonal contraception, there was a significant association with the luteal phase (aOR 1.6, (95% CI 1.1–2.3, p = 0.007). The chlamydia load was not significantly different in the 329 positive stored samples in weeks 3 and 4 vs weeks 1 and 2 for any site (P>0.12). Conclusions: The higher detection of chlamydia detection in the luteal phase of the menstrual cycle in only those not taking hormonal contraception suggest that hormonal factors influence chlamydia detection. The absence of a significantly highly chlamydia load in women during the luteal phase raises questions about the mechanism. [ABSTRACT FROM AUTHOR]

Xenobiotics such as phenobarbital, 2,3,7,8-tetrachlorodibenzo-p-dioxin, and Aroclor 1254 significantly suppress the activity of a key gluconeogenic and glyceroneogenic enzyme, phosphoenolpyruvate carboxykinase (PEPCK), suggesting that xenobiotics disrupt hepatic glucose and fat metabolism. The effects of polybrominated diphenyl ethers (PBDE), a family of synthetic flame-retardant chemicals, on PEPCK activity is unknown. This study investigated the effect of DE-71, a commercial PBDE mixture, on PEPCK enzyme kinetics. Forty-eight 1-mo-old male Wistar rats were gavaged daily with either corn oil or corn oil containing 14 mg/kg DE-71 for 3, 14, or 28 d (n = 8/group). At each time point, fasting plasma glucose, insulin, and C-peptide were measured and hepatic PEPCK activity, lipid content, and three cytochrome P-450 enzymes (CYP1A, -2B, and -3A) were assayed. PBDE treatment for 28 d significantly decreased PEPCK Vmax (μmol/min/g liver weight) by 43% and increased liver lipid by 20%, compared to control. CYP1A, -2B, and -3A Vmax values were enhanced by 5-, 6-, and 39-fold, respectively, at both 14 and 28 d in treated rats compared to control. There was a significant inverse and temporal correlation between CYP3A and PEPCK Vmax for the treatment group. Fasting plasma glucose, insulin, and C-peptide levels were not markedly affected by treatment, but the glucose:insulin ratio was significantly higher in treated compared to control rats. Data suggest that in vivo PBDE treatment compromises liver glucose and lipid metabolism, and may influence whole-body insulin sensitivity. [ABSTRACT FROM AUTHOR]

Background: Poor differentiation predicts adverse outcomes in cutaneous squamous cell carcinoma (CSCC), but there is no standardized, reliable grading system., Objective: To explore which histologic features have the greatest impact on CSCC differentiation interrater agreement., Materials and Methods: In a prior study, 40 raters graded differentiation for 45 squamous cell carcinomas, and percent interrater agreements were calculated. Cases graded as well/moderately differentiated with 100% agreement (10), those graded as poorly differentiated with ≥80% agreement (5), and those that received a variety of grades with ≤60% agreement (7) were pulled for the current study. Three raters graded individual histologic features for each case, and percent interrater agreements were calculated using both the well/moderately/poorly differentiated grading system and a dichotomized system., Results: The percent interrater agreements were 34.8% for mitoses, 53% for pleomorphism, 59.1% for keratinization, 66.7% for cellular cohesion/intercellular bridges, and 78.8% for tumor edges. Percent agreements improved with dichotomous grading; the largest improvement was seen within the group of cases that had been graded as well/moderately differentiated with 100% agreement in the prior study., Conclusion: Future squamous cell carcinoma differentiation grading systems would benefit from eliminating mitotic rate, clearly defining how to grade other features, and dichotomous grading., (Copyright © 2024 by the American Society for Dermatologic Surgery, Inc. Published by Wolters Kluwer Health, Inc. All rights reserved.)

The development of nucleic acid (NA) based nanotechnology applications rely on the efficient packaging of DNA and RNA. However, the atomic details of NA-nanoparticle binding remains to be comprehensively characterized. Here, we examined how nanoparticle and solvent properties affect NA compaction. Our large-scale, all-atom simulations of ligand-functionalized gold nanoparticle (NP) binding to double stranded NAs as a function of NP charge and solution salt concentration reveal different responses of RNA and DNA to cationic NPs. We demonstrate that the ability of a nanoparticle to bend DNA is directly correlated with the NPs charge and ligand corona shape, where more than 50% charge neutralization and spherical shape of the NP ligand corona ensured the DNA compaction. However, NP with 100% charge neutralization is needed to bend DNA almost as efficiently as the histone octamer. For RNA in 0.1 M NaCl, even the most highly charged nanoparticles are not capable of causing bending due to charged ligand end groups binding internally to the major groove of RNA. We show that RNA compaction can only be achieved through a combination of highly charged nanoparticles with low salt concentration. Upon interactions with highly charged NPs, DNA bends through periodic variation in groove widths and depths, whereas RNA bends through expansion of the major groove.

The preparation of electrospun polymer microfibers with nitric oxide (NO)-release capabilities is described. Polymer solutions containing disodium 1-[2-(carboxylato)pyrrolidin-1-yl]diazen-1-ium-1,2-diolate (PROLI/NO), a low-molecular-weight NO donor, were electrospun to generate fibers ranging from 100-3000 nm in diameter capable of releasing NO upon immersion in aqueous solutions under physiological conditions (pH 7.4, 37 °C), with kinetics depending on polymer composition and fiber diameter. The NO release half-life for PROLI/NO-doped electrospun fibers was 2-200 times longer than that of PROLI/NO alone. The influence of polymer concentration, applied voltage, capillary diameter, solution conductivity, flow rate, and additives on fiber properties are reported and discussed with respect to potential applications.