rworkflows: automating reproducible practices for the R community.

Despite calls to improve reproducibility in research, achieving this goal remains elusive even within computational fields. Currently, >50% of R packages are distributed exclusively through GitHub. While the trend towards sharing open-source software has been revolutionary, GitHub does not have any default built-in checks for minimal coding standards or software usability. This makes it difficult to assess the current quality R packages, or to consistently use them over time and across platforms. While GitHub-native solutions are technically possible, they require considerable time and expertise for each developer to write, implement, and maintain. To address this, we develop rworkflows; a suite of tools to make robust continuous integration and deployment ( https://github.com/neurogenomics/rworkflows ). rworkflows can be implemented by developers of all skill levels using a one-time R function call which has both sensible defaults and extensive options for customisation. Once implemented, any updates to the GitHub repository automatically trigger parallel workflows that install all software dependencies, run code checks, generate a dedicated documentation website, and deploy a publicly accessible containerised environment. By making the rworkflows suite free, automated, and simple to use, we aim to promote widespread adoption of reproducible practices across a continually growing R community.

Avoiding false discoveries in single-cell RNA-seq by revisiting the first Alzheimer's disease dataset.

Mathys et al. conducted the first single-nucleus RNA-seq (snRNA-seq) study of Alzheimer's disease (AD) (Mathys et al., 2019). With bulk RNA-seq, changes in gene expression across cell types can be lost, potentially masking the differentially expressed genes (DEGs) across different cell types. Through the use of single-cell techniques, the authors benefitted from increased resolution with the potential to uncover cell type-specific DEGs in AD for the first time. However, there were limitations in both their data processing and quality control and their differential expression analysis. Here, we correct these issues and use best-practice approaches to snRNA-seq differential expression, resulting in 549 times fewer DEGs at a false discovery rate of 0.05. Thus, this study highlights the impact of quality control and differential analysis methods on the discovery of disease-associated genes and aims to refocus the AD research field away from spuriously identified genes.

NOx Emissions Control Area (NECA) scenario for ports in the North Adriatic Sea.

In response to global warming, the International Maritime Organisation (IMO) set rules of 50% Greenhouse Gas (GHG) reduction by 2050, from 2008 levels. Signatory countries to the IMO's regulation require frequent assessment of the contribution of GHG emissions from shipping calling at their ports or trading in their territorial waters to ensure their compliance with the regulations. This demands a rapid and accurate method to assess shipping's contribution to GHG emissions. Current methodologies for estimating emissions from ships can be described on a scale between bottom-up and top-down methods. Top-down methods provide rapid estimates - primarily based on fuel sales reports - without considering individual vessel details. Therefore, they are less accurate and do not provide a breakdown of emissions by ship types or in specific regions. Bottom-up methodologies are detailed vessel-based estimates; however, they are data and time-demanding. The Ship Emissions Assessment method (SEA) (Topic et al., 2021) fills the gap between bottom-up and top-down methods by providing an innovative hybrid solution for rapid but accurate ship emission estimation. It uses publicly available, cost-effective data sets for emission estimates. The SEA method is capable of estimating ships' emissions in designated areas to understand regulations' effectiveness and provide emission quantification evidence. This research objective was to apply the SEA method to quantify CO2, SOX and NOX exhaust emissions from containerships for the three crucial containership ports: Trieste, Rijeka and Venice, in the North of the Adriatic Sea. The SEA methodology was applied to assess emissions and forecast efficiency in scenarios of different regulatory measures. A reduction in NOx emissions was estimated for the event of the implementation of NECA in all three ports. Results showed that 447.13 tonnes of NOx could be reduced each year in the North Adriatic Sea area around the ports of Rijeka, Trieste and Venice in the event that NECA regulations are stipulated.

FRDA: Fingerprint Region based Data Augmentation using explainable AI for FTIR based microplastics classification.

Marine microplastics (MPs) contamination has become an enormous hazard to aquatic creatures and human life. For MP identification, many Machine learning (ML) based approaches have been proposed using Attenuated Total Reflection Fourier Transform Infrared Spectroscopy (ATR-FTIR). One major challenge for training MP identification models now is the imbalanced and inadequate samples in MP datasets, especially when these conditions are combined with copolymers and mixtures. To improve the ML performance in identifying MPs, data augmentation method is an effective approach. This work utilizes Explainable Artificial Intelligence (XAI) and Gaussian Mixture Models (GMM) to reveal the influence of FTIR spectral regions in identifying each type of MPs. Based on the identified regions, this work proposes a Fingerprint Region based Data Augmentation (FRDA) method to generate new FTIR data to supplement MP datasets. The evaluation results show that FRDA outperforms the existing spectral data augmentation approaches.

EpiCompare: R package for the comparison and quality control of epigenomic peak files.

Summary: EpiCompare combines a variety of downstream analysis tools to compare, quality control and benchmark different epigenomic datasets. The package requires minimal input from users, can be run with just one line of code and provides all results of the analysis in a single interactive HTML report. EpiCompare thus enables downstream analysis of multiple epigenomic datasets in a simple, effective and user-friendly manner. Availability and implementation: EpiCompare is available on Bioconductor (≥ v3.15): https://bioconductor.org/packages/release/bioc/html/EpiCompare.html; all source code is publicly available via GitHub: https://github.com/neurogenomics/EpiCompare; documentation website https://neurogenomics.github.io/EpiCompare; and EpiCompare DockerHub repository: https://hub.docker.com/repository/docker/neurogenomicslab/epicompare.

Transcriptomic analyses reveal neuronal specificity of Leigh syndrome associated genes.

Leigh syndrome is a rare, inherited, complex neurometabolic disorder with genetic and clinical heterogeneity. Features present in affected patients range from classical stepwise developmental regression to ataxia, seizures, tremor, and occasionally psychiatric manifestations. Currently, more than 100 monogenic causes of Leigh syndrome have been identified, yet the pathophysiology remains unknown. Here, we sought to determine the cellular specificity within the brain of all genes currently associated with Leigh syndrome. Further, we aimed to investigate potential genetic commonalities between Leigh syndrome and other disorders with overlapping clinical features. Enrichment of our target genes within the brain was evaluated with co-expression (CoExp) network analyses constructed using existing UK Brain Expression Consortium data. To determine the cellular specificity of the Leigh associated genes, we employed expression weighted cell type enrichment (EWCE) analysis of single-cell RNA-Seq data. Finally, CoExp network modules demonstrating enrichment of Leigh syndrome associated genes were then utilised for synaptic gene ontology analysis and heritability analysis. CoExp network analyses revealed that Leigh syndrome associated genes exhibit the highest levels of expression in brain regions most affected on MRI in affected patients. EWCE revealed significant enrichment of target genes in hippocampal and somatosensory pyramidal neurons and interneurons of the brain. Analysis of CoExp modules enriched with our target genes revealed preferential association with pre-synaptic structures. Heritability studies suggested some common enrichment between Leigh syndrome and Parkinson disease and epilepsy. Our findings suggest a primary mitochondrial dysfunction as the underlying basis of Leigh syndrome, with associated genes primarily expressed in neuronal cells.

Prudence in end-of-life decision making: A virtue-based analysis of physician communication with patients and surrogates.

Despite significant improvements in end-of-life care over several decades, belated hospice referrals and hospital staffing patterns make challenging end-of-life conversations between strangers unsurprising, especially when the interaction is time-sensitive. Understanding how physicians perform under these circumstances is relevant to patient quality and medical education. This study is a secondary analysis of transcripts from a simulation that placed 88 intensivists, hospitalists, and ED physicians in the setting of responding to a nurse's call to evaluate a floor patient for impending respiratory collapse. A philosophical account of prudence guided the analytical approach and was operationalized through behavior-based and exemplar-based qualitative coding strategies. Exemplary performances and specific behaviors were then compared with preferred outcomes. Results indicate that exemplary performance correlated with a cluster of 3 behaviors that predicted the desired outcomes, but did not determine them: (1) directly affirming the likelihood that the patient will die in the near term; (2) explicitly soliciting the patient's preferences for care; and (3) asking what other family and friends should be involved. The current study implies that educational initiatives aimed at improving end-of-life conversations should expose clinicians both to technical competencies and to the virtues required to employ these competencies well.

Multidimensional Dynamics of the Proteome in the Neurodegenerative and Aging Mammalian Brain.

The amount of any given protein in the brain is determined by the rates of its synthesis and destruction, which are regulated by different cellular mechanisms. Here, we combine metabolic labeling in live mice with global proteomic profiling to simultaneously quantify both the flux and amount of proteins in mouse models of neurodegeneration. In multiple models, protein turnover increases were associated with increasing pathology. This method distinguishes changes in protein expression mediated by synthesis from those mediated by degradation. In the AppNL-F knockin mouse model of Alzheimer's disease, increased turnover resulted from imbalances in both synthesis and degradation, converging on proteins associated with synaptic vesicle recycling (Dnm1, Cltc, Rims1) and mitochondria (Fis1, Ndufv1). In contrast to disease models, aging in wild-type mice caused a widespread decrease in protein recycling associated with a decrease in autophagic flux. Overall, this simple multidimensional approach enables a comprehensive mapping of proteome dynamics and identifies affected proteins in mouse models of disease and other live animal test settings.

Discovery of inhibition of Burkholderia cenocepacia, Pseudomonas aeruginosa and Stenotrophomonas maltophilia by the Brown Rot Basidiomycete Fungus, Postia placenta.

Antimicrobial resistance (AMR) has now emerged as a major global public health problem. Certain bacterial pathogens, particularly Gram negative organisms associated with patients with cystic fibrosis (CF), have become resistant to several classes of antibiotics resulting in pan-resistance, which creates a clinical treatment dilemma. This study wished to explore the production of antibacterial extracellular metabolites from plant pathogenic fungi. Fungal Culture Extracts (FCEs) were prepared from 10 fungi (Armillaria gallica, Clitocybe nebularis, Fusarium coeruleum, Fusarium oxysporum, Fusarium poae, Hymenoscyphus fraxineus, Nectria fuckeliana, Phytophthora infestans, Phytophthora ramorum, Postia placenta), which were tested for activity against the CF pathogens, Pseudomonas aeruginosa (PA) (n=8), Burkholderia cenocepacia (n=2) and Stenotrophomonas maltophilia (n=2). In addition, FCE were assessed for their ability to alter antibiotic susceptibility in PA (n=8), with six antipseudomonal antibiotics (ceftazidime, ciprofloxacin, colistin, meropenem, piperacillin/tazobactam, tobramycin). None of the FCEs showed inhibitory activity to the 12 bacterial isolates tested, with the exception of the FCE from Postia placenta, which showed inhibition against all 12 bacteria. An antagonistic interaction was observed, where a statistically significant decrease in mean zone sizes was noted with Armillaria gallica (p=0.03) and Phytophthora infestans (p=0.03) FCEs and their interaction with the fluoroquinolone antibiotic, ciprofloxacin. Given the increase in clinical morbidity and mortality associated with chronic lung infections with Pseudomonas aeruginosa, Burkholderia cenocepacia and Stenotrophomonas maltophilia, coupled with the difficulty in treating such chronic infection due to overwhelming antimicrobial resistance, any novel substance showing inhibition of these organisms merits further investigation as a potential future antimicrobial agent, with potential clinical therapeutic application.

MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics.

MOTIVATION: Genome-wide association studies (GWAS) summary statistics have popularized and accelerated genetic research. However, a lack of standardization of the file formats used has proven problematic when running secondary analysis tools or performing meta-analysis studies. RESULTS: To address this issue, we have developed MungeSumstats, a Bioconductor R package for the standardization and quality control of GWAS summary statistics. MungeSumstats can handle the most common summary statistic formats, including variant call format (VCF) producing a reformatted, standardized, tabular summary statistic file, VCF or R native data object. AVAILABILITY AND IMPLEMENTATION: MungeSumstats is available on Bioconductor (v 3.13) and can also be found on Github at: https://neurogenomics.github.io/MungeSumstats. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Description of wylie-stanley agar for the recovery of mycobacterium abscessus.

Background: The microbiology of cystic fibrosis (CF) is complicated by the presence of several species, including Mycobacterium abscessus, which are highly resistant to antibiotics. Conventional selective bacteriological methods employ antibiotics which favor the growth of one bacterial component over others in a mixed population. For in vitro studies examining multiple species, for example, in dual biofilm models, it is difficult to successfully separate M. abscessus from nontuberculous mycobacterial (NTM) species. Therefore, it was the aim of this study to develop a selective agar medium that was able to isolate M. abscessus from a pool of other highly-resistant Gram-negative organisms, which would be useful to microbiologists performing co-culture experiments and which require re-isolation of the NTM organism. Methods: Wylie-Stanley agar (WSA) was developed consisting of glucose, 16 g/l; yeast extract, 30 g/l; peptone, 6.8 g/l; and agar, 20 g/l along with selective supplements including chloramphenicol, 50 mg/l; ceftazidime, 32 mg/l; colistin, 24 mg/l; trimethoprim, 21.3 mg/l; sulfamethoxazole, 106.7 mg/l; and novobiocin, 50 mg/l. This medium was (i) challenged with 10 non-NTM species (27 isolates) of common Gram-negative and Gram-positive organisms associated with CF and (ii) compared to Columbia Blood Agar and Middlebrook 7H10 Agar for the isolation of M. abscessus organisms from mixed cultures of NTM organisms and Pseudomonas aeruginosa and Stenotrophomonas maltophilia. Results: This medium was highly specific for the growth of M. abscessus organisms and grew all NTM organisms. WSA medium did not allow the growth of any of the non-NTM species. When mixed cultures of M. abscessus species and P. aeruginosa and S. maltophilia were inoculated onto WSA medium, only the NTM organism could be grown successfully, highlighting the specificity of this medium. In contrast, both Columbia Blood Agar and Middlebrook 7H10 Agar allowed the growth of both NTM and non-NTM organisms. Conclusion: While the specificity was high, the sensitivity of WSA was low, and therefore, we do not advocate employment of WSA medium for the primary isolation of M. abscessus organisms from CF sputum, rather for the purposes of separating M. abscessus populations of organisms from other highly-resistant organisms, including P. aeruginosa and S. maltophilia, which would be useful to microbiologists performing co-culture experiments and which require re-isolation of the pure M. abscessus organism.

Re-opening hairdressing salons, barber shops and gyms following COVID-19 lockdown: reducing risks from Legionella species through successful domestic steam disinfection of showerheads.

Given the importance of disinfecting showerheads from Legionella species and the lack of instructions as to how to successfully achieve this, the aim of this study was to examine the ability of domestic steam disinfection to successfully disinfect showerheads from Legionella species. Steam disinfection of Legionella pneumophila [n=3; L. pneumophila serogroup 2-15 (wildtype environmental water isolate); L. pneumophila serogroup 1 NCTC11192 (reference strain); L. pneumophila serogroup 1 (wildtype environmental water isolate)], L. erythra (wildtype environmental water isolate) and L. bozemanii CRM11368M (reference strain) were examined in this study. Steam disinfection employing a baby bottle steam disinfector device eradicated all Legionella organisms tested. Steam disinfection, when performed properly under the manufacturer's instructions, offers a relatively inexpensive, simple, versatile and widely available technology for the elimination of Legionella species from contaminated showerheads. We therefore advocate the employment of such devices to regularly disinfect showerheads and shower tubing in hairdressing salons, barber shops and gyms, as a critical control in the elimination of these organisms from these sources, thereby enhancing customer/client/staff safety.

Cultures of Practice: Specialty-Specific Differences in End-of-Life Conversations.

Importance: Goals of care discussions at the end of life give opportunity to affirm the autonomy and humanity of dying patients. Best practices exist for communication around goals of care, but there is no research on differences in approach taken by different specialties engaging these conversations. Objective: To describe the communication practices of internal medicine (IM), emergency medicine (EM), and critical care (CC) physicians in a high-fidelity simulation of a terminally ill patient with stable and defined end-of-life preferences. Design, Setting, and Participants: Mixed-methods secondary analysis of transcripts obtained from a multicenter study simulating high stakes, time-limited end-of-life decision making in a cohort of 88 volunteer physicians (27 IM, 22 EM, and 39 CC) who were called to evaluate a standardized patient in extremis. The patient had clear comfort-oriented goals of care that the physician needed to elicit and use to inform treatment decisions. Discussions were coded at the level of the sentence for semantic content. Exposures: Data were analyzed by physician specialty. Main Outcome Measure: Occurrence of content codes indicative of prudent (right outcome by the right means) goals of care conversations. Data were analyzed both for number of occurrences of the code in a simulated conversation and for presence or absence of the code within a conversation. Results: There was no difference between physician types in intubation rates or intensive care unit admissions. Codes for "comfort as a goal of care," "noncurative goals of care," and "oblique references to death" emerged as significantly different between physician types. Conclusions and Relevance: This experiment shows demonstrable differences in practice patterns between physician specialties when addressing end-of-life decision making. Some of the variation likely arose from differences in setting, but these data suggest that training in goals of care conversations may benefit if it is adapted to the distinct needs and culture of each specialty.

Re-purposing of domestic steam disinfectors within the hospital-at-home setting.

BACKGROUND: Vulnerable patients being cared for in hospital-at-home settings require safe disinfection of their medical devices, including nebulisers and other respiratory equipment. The scale of patients now being cared for in hospital-at-home settings as a result of COVID19 places huge pressure on hospital central sterile services departments (CSSDs) to provide consumable items to safely support such patients' care. This places new importance on the disinfection of mundane objects, including crockery, cutlery and frequently touched objects in the home environment. This study examined temperature performance of steam disinfectors and the consequences of potential operator misuse on the survival of 62 bacteria and yeast organisms. METHODS: Thermal performance of steam disinfectors was evaluated using calibrated thermocouple probes in multiple permutations of device usage with 62 test organisms. RESULTS: Thermocouple data demonstrated disinfection A0 values of 6000 (upper layer) and 60 (lower layer). Steam disinfection of baby bottles had a thermal lethality of at least A0 = 600. Variation in disinfector temperatures were noted, depending on the geometric location of thermocouples. Additional notable temperature reductions occurred with device underfilling with suboptimal water volumes. Steam disinfection eradicated all 62 non-spore-forming Gram-positive, Gram-negative and yeast organisms tested and eradicated all organisms in the inner teat space of contaminated babies' dummies, rendering safe steam disinfection of babies' dummies. CONCLUSION: Domestic steam disinfection offers an inexpensive, simple, versatile and widely available technology for the elimination of common non-spore-forming nosocomial pathogens and safe disinfection of medical devices, fomites and other mundane objects within the hospital-at-home scenario, thereby enhancing patient safety.

Key Physician Behaviors that Predict Prudent, Preference Concordant Decisions at the End of Life.

BACKGROUND: This study introduces an empirical approach for studying the role of prudence in physician treatment of end-of-life (EOL) decision making. METHODS: A mixed-methods analysis of transcripts from 88 simulated patient encounters in a multicenter study on EOL decision making. Physicians in internal medicine, emergency medicine, and critical care medicine were asked to evaluate a decompensating, end-stage cancer patient. Transcripts of the encounters were coded for actor, action, and content to capture the concept of Aristotelian prudence, and then quantitatively and qualitatively analyzed to identify actions associated with preference-concordant treatment. RESULTS: Focusing on codes that describe characteristics of physician-patient interaction, the code for physicians restating patient preferences was associated with avoiding intubation. Multiple codes were associated with secondary measures of preference-concordant treatment. CONCLUSIONS: Prudent actions can be identified empirically, and research focused on the virtue of prudence may provide a new avenue for assessment and training in EOL care.

Fibrocartilaginous Embolic Encephalopathy in a Pig.

A 1-year-old boar was investigated after presenting with acute onset collapse and obtundance. No significant gross lesions were observed at post-mortem examination. Histopathological investigation revealed a severe bilateral and multifocal necrotizing encephalopathy with an amorphous material, which obstructed neuroparenchymal vessels in the metencephalon and mesencephalon. Alcian blue staining identified the material as of cartilaginous origin and a diagnosis of cerebral fibrocartilaginous embolism was established. No gross evidence of vertebral disc disease was detected and the origin of the embolic material was not found. Although cerebral fibrocartilaginous embolism has been reported in a human, and rarely in animals, it has not been reported previously in the pig.

Steam disinfection of toothbrushes from patients with cystic fibrosis: Evidence-based recommendations.

BACKGROUND: Patients with cystic fibrosis have increased morbidity/mortality due to chronic respiratory infections, which primarily originate from the environment. Infection prevention and control emphasize the importance of cleaning and disinfection of respiratory devices, however, there is a paucity of guidance on toothbrush hygiene, which have been shown to be a source of cystic fibrosis (CF) pathogens. METHODS: This study examined steam disinfection of toothbrushes contaminated with clinically significant CF isolates (n = 80; Gram positive = 33; Gram negative = 32, and non-tuberculous mycobacteria = 6) and yeasts (n = 9), as well as oral streptococci (n = 26) and environmental Pseudomonas aeruginosa (n = 12). RESULTS: Steam disinfection eradicated all organisms tested, as well as all organisms in CF sputum applied to toothbrushes. CONCLUSIONS: Steam disinfection offers a relatively simple, cheap and available method of eliminating non-spore-forming CF pathogens on toothbrushes. Toothbrushes should be thoroughly rinsed after each use before steam disinfection, to remove plaque, epithelial cells, and residual toothpaste. Toothbrushes should be steam disinfected after each use employing a baby bottle steam disinfector, adhering to manufacturers' operating instructions and stored in the disinfector until next used within 12 to 24 hours. Toothbrushes should be replaced every 3 to 4 months, or sooner if the bristles look worn out, as well as every time a pulmonary exacerbation occurs or every time the patient is treated for a pulmonary/throat infection. Steam disinfection of toothbrushes is crucial when the patient is undergoing eradication regimes for P. aeruginosa and methicillin-resistant Staphylococcus aureus, so that the patient does not become reinfected from this source, thereby aiding eradication and enhancing patient safety.

Attributional life cycle assessment of biofuels for shipping: Addressing alternative geographical locations and cultivation systems.

The purpose of this study is to evaluate a life cycle assessment of straight vegetable oil (SVO) and biodiesel addressing alternative upstream pathways. The pathways are SVO and biodiesel produced in the United Kingdom (UK) using European rapeseed and also, SVO and biodiesel produced in the UK using soybean grain and soybean oil imported from Argentina. Four environmental impact categories have been assessed using the SimaPro (ReCiPe life-cycle impact assessment) method: this includes global warming potential (GWP); acidification; eutrophication and particulate matter. Rapeseed based biofuel had the lowest emission impact in terms of GHG emissions. Significant greenhouse gas (GHG) emissions can result from land use change due to the expansion and cultivation of soybean in Argentina. When land use change is not considered, the soy based biofuel system has the lowest GHG impact with more than 70% GHG emission reduction. The GHG emission at cultivation stage far outweighs the impacts of the other life-cycle stages irrespective of the feedstock used for the biofuel production systems. The use of fertilizers and associated soil emissions are the main contributors. The environmental impacts of biofuel can be reduced by avoiding land use change, improving soil management practices and yield, and also optimizing transportation routes. Effective implementation of options for biofuels production were explored to improve sustainability in shipping.

The impact of an alcohol consumption intervention in community sports clubs on safety and participation: an RCT.

OBJECTIVE: Sports clubs have been identified as settings where high levels of risky alcohol consumption occurs. Settings characterised by such behaviour are likely to negatively impact on levels of safety, participation and amenity. DESIGN: The study was part of a randomised control trial, designed to help community sports clubs responsibly manage the sale and consumption of alcohol; the primary outcome was reduction in alcohol consumption. This study examined the secondary effects of safety and participation. METHODS: A multilevel analysis examining the pathways between the alcohol intervention, risky alcohol consumption, and safety and participation was undertaken. RESULTS: It was identified that average overall risky consumption at the club level mediated the association between the intervention and increased participation; the intervention reduced overall hazardous consumption, which in turn increased participation at the club. CONCLUSION: Interventions that target responsible alcohol management can also increase club participation. Implications for public health: Given the number of individuals involved with sports clubs, responsibly managing alcohol will also ensure that sports clubs are health promoting settings that promote community participation and engagement.