Kookaburra Optimization Algorithm: A New Bio-Inspired Metaheuristic Algorithm for Solving Optimization Problems

In this paper, a new bio-inspired metaheuristic algorithm named the Kookaburra Optimization Algorithm (KOA) is introduced, which imitates the natural behavior of kookaburras in nature. The fundamental inspiration of KOA is the strategy of kookaburras when hunting and killing prey. The KOA theory is stated, and its mathematical modeling is presented in the following two phases: (i) exploration based on the simulation of prey hunting and (ii) exploitation based on the simulation of kookaburras' behavior in ensuring that their prey is killed. The performance of KOA has been evaluated on 29 standard benchmark functions from the CEC 2017 test suite for the different problem dimensions of 10, 30, 50, and 100. The optimization results show that the proposed KOA approach, by establishing a balance between exploration and exploitation, has good efficiency in managing the effective search process and providing suitable solutions for optimization problems. The results obtained using KOA have been compared with the performance of 12 well-known metaheuristic algorithms. The analysis of the simulation results shows that KOA, by providing better results in most of the benchmark functions, has provided superior performance in competition with the compared algorithms. In addition, the implementation of KOA on 22 constrained optimization problems from the CEC 2011 test suite, as well as 4 engineering design problems, shows that the proposed approach has acceptable and superior performance compared to competitor algorithms in handling real-world applications.

Impact of SARS-CoV-2 Infection on the Association Between Laboratory Tests and Severe Outcomes Among Hospitalized Children

Background

To assist clinicians with identifying children at risk of severe outcomes, we assessed the association between laboratory findings and severe outcomes among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected children and determined if SARS-CoV-2 test result status modified the associations.

Methods

We conducted a cross-sectional analysis of participants tested for SARS-CoV-2 infection in 41 pediatric emergency departments in 10 countries. Participants were hospitalized, had laboratory testing performed, and completed 14-day follow-up. The primary objective was to assess the associations between laboratory findings and severe outcomes. The secondary objective was to determine if the SARS-CoV-2 test result modified the associations.

Results

We included 1817 participants; 522 (28.7%) SARS-CoV-2 test-positive and 1295 (71.3%) test-negative. Seventy-five (14.4%) test-positive and 174 (13.4%) test-negative children experienced severe outcomes. In regression analysis, we found that among SARS-CoV-2-positive children, procalcitonin ≥0.5 ng/mL (adjusted odds ratio [aOR], 9.14; 95% CI, 2.90-28.80), ferritin >500 ng/mL (aOR, 7.95; 95% CI, 1.89-33.44), D-dimer ≥1500 ng/mL (aOR, 4.57; 95% CI, 1.12-18.68), serum glucose ≥120 mg/dL (aOR, 2.01; 95% CI, 1.06-3.81), lymphocyte count <1.0 × 109/L (aOR, 3.21; 95% CI, 1.34-7.69), and platelet count <150 × 109/L (aOR, 2.82; 95% CI, 1.31-6.07) were associated with severe outcomes. Evaluation of the interaction term revealed that a positive SARS-CoV-2 result increased the associations with severe outcomes for elevated procalcitonin, C-reactive protein (CRP), D-dimer, and for reduced lymphocyte and platelet counts.

Conclusions

Specific laboratory parameters are associated with severe outcomes in SARS-CoV-2-infected children, and elevated serum procalcitonin, CRP, and D-dimer and low absolute lymphocyte and platelet counts were more strongly associated with severe outcomes in children testing positive compared with those testing negative.

XA4C: eXplainable representation learning via Autoencoders revealing Critical genes

Machine Learning models have been frequently used in transcriptome analyses. Particularly, Representation Learning (RL), e.g., autoencoders, are effective in learning critical representations in noisy data. However, learned representations, e.g., the "latent variables" in an autoencoder, are difficult to interpret, not to mention prioritizing essential genes for functional follow-up. In contrast, in traditional analyses, one may identify important genes such as Differentially Expressed (DiffEx), Differentially Co-Expressed (DiffCoEx), and Hub genes. Intuitively, the complex gene-gene interactions may be beyond the capture of marginal effects (DiffEx) or correlations (DiffCoEx and Hub), indicating the need of powerful RL models. However, the lack of interpretability and individual target genes is an obstacle for RL's broad use in practice. To facilitate interpretable analysis and gene-identification using RL, we propose "Critical genes", defined as genes that contribute highly to learned representations (e.g., latent variables in an autoencoder). As a proof-of-concept, supported by eXplainable Artificial Intelligence (XAI), we implemented eXplainable Autoencoder for Critical genes (XA4C) that quantifies each gene's contribution to latent variables, based on which Critical genes are prioritized. Applying XA4C to gene expression data in six cancers showed that Critical genes capture essential pathways underlying cancers. Remarkably, Critical genes has little overlap with Hub or DiffEx genes, however, has a higher enrichment in a comprehensive disease gene database (DisGeNET) and a cancer-specific database (COSMIC), evidencing its potential to disclose massive unknown biology. As an example, we discovered five Critical genes sitting in the center of Lysine degradation (hsa00310) pathway, displaying distinct interaction patterns in tumor and normal tissues. In conclusion, XA4C facilitates explainable analysis using RL and Critical genes discovered by explainable RL empowers the study of complex interactions.

OOBO: A New Metaheuristic Algorithm for Solving Optimization Problems

This study proposes the One-to-One-Based Optimizer (OOBO), a new optimization technique for solving optimization problems in various scientific areas. The key idea in designing the suggested OOBO is to effectively use the knowledge of all members in the process of updating the algorithm population while preventing the algorithm from relying on specific members of the population. We use a one-to-one correspondence between the two sets of population members and the members selected as guides to increase the involvement of all population members in the update process. Each population member is chosen just once as a guide and is only utilized to update another member of the population in this one-to-one interaction. The proposed OOBO's performance in optimization is evaluated with fifty-two objective functions, encompassing unimodal, high-dimensional multimodal, and fixed-dimensional multimodal types, and the CEC 2017 test suite. The optimization results highlight the remarkable capacity of OOBO to strike a balance between exploration and exploitation within the problem-solving space during the search process. The quality of the optimization results achieved using the proposed OOBO is evaluated by comparing them to eight well-known algorithms. The simulation findings show that OOBO outperforms the other algorithms in addressing optimization problems and can give more acceptable quasi-optimal solutions. Also, the implementation of OOBO in six engineering problems shows the effectiveness of the proposed approach in solving real-world optimization applications.

Frequency of cardiac arrhythmias in horses during straight and untethered swimming

BACKGROUND

Cardiac arrhythmias have not been previously reported in horses while swimming.

OBJECTIVES

To describe the type and frequency of encountered arrhythmias during repetitive swimming cycles.

STUDY DESIGN

Descriptive observational study.

METHODS

Sixteen horses swam five pool lengths (75 m), each separated by an active recovery walk. Continuous electrocardiograms (ECGs) were recorded (n = 80) and analysed during the pre-swim, swim and active-recovery periods. Arrhythmias were categorised as sinus arrhythmia (SA), sinus block, sinus pause (compensatory and non-compensatory), second degree atrioventricular block (2AVB) for physiological arrhythmias, supraventricular premature depolarisation (SVPD) and ventricular premature depolarisation (VPD) for non-physiological arrhythmias. A linear mixed-effects model was used to examine the effects of repetitive swim lengths on arrhythmias and swimming parameters. Data were reported as median [interquartile range].

RESULTS

Fifteen horses (94%) experienced at least one arrhythmia; however, the frequency remained low and 2AVB were only observed during the pre-swim period. The swimming heart rate (HR) was 162 bpm [141;173]. Sinus blocks, sinus pauses, SA, SVPD and VPD were all recorded at least once during swimming. Except for one VPD couplet, all premature depolarisations were isolated. During active-recovery, the HR was 105 bpm [103;106], with SA observed in 13 horses (81%), isolated SVPD in six horses (38%), sinus pause in one horse (6%) but no VPD present.

MAIN LIMITATIONS

Limited number of horses precluding population prevalence assessment.

CONCLUSION AND CLINICAL IMPORTANCE

High-quality underwater ECGs were acquired in swimming horses for the first time. The frequency of arrhythmias remained low and rare pathological arrhythmias were observed during repetitive swimming and active-recovery cycles. Swimming with active-recovery periods is not a high-risk cardio-arrhythmic exercise.

Estimation of natural methane emissions from the largest oil sand deposits on earth

Worldwide methane emission by various industrial sources is one of the important human concerns due to its serious climate and air-quality implications. This study investigates less-considered diffusive natural methane emissions from the world's largest oil sand deposits. An analytical model, considering the first-order methane degradation, in combination with Monte Carlo simulations, is used to quantitatively characterize diffusive methane emissions from Alberta's oil sands formations. The results show that the average diffusive methane emissions from Alberta's oil sands formations is 1.56 × 10-4 kg/m2/year at the 90th percentile of cumulative probability. The results also indicate an annual diffusive methane emissions rate of 0.857 ± 0.013 Million tons of CO2e/year (MtCO2e/year) from Alberta's oil sands formations. This finding suggests that natural diffusive leakages from the oil sands contribute an additional 1.659 ± 0.025 and 5.194 ± 0.079% to recent Canada's 2019 and Alberta's 2020 methane emission estimates from the upstream oil and gas sector, respectively. The developed model combined with Monte Carlo simulations can be used as a tool for assessing methane emissions and current inventories.

Engaging families and parent advocates in research on substance use and drug policy reform: Guiding principles from a Canadian community-academic partnership

Canada is in the midst of a public health emergency in drug poisoning (overdose) deaths. In this context parents, and especially mothers, of those who have died from drug poisoning have mobilised to advocate for urgent responses and drug policy reforms. To document this emerging women-led advocacy, we initiated a community-academic research partnership with three parent groups representing families in Canada bereaved by drug-related deaths. In this commentary, we describe four guiding principles we developed during the course of this project, to ensure an ethical and equitable approach to conducting our research partnership. In particular, we emphasise how we navigated parents' roles as vocal advocates for addressing drug stigma and expanding harm reduction while actively working to avoid eclipsing the need to centre the perspectives of people who use drugs. Meaningful and collaborative partnerships between academics and community groups may facilitate greater understandings of how families and communities can be allied in drug policy reforms urgently needed to prevent drug poisoning deaths.

SARS-CoV-2 virus-like-particles via liposomal reconstitution of spike glycoproteins

The SARS-CoV-2 virus, implicated in the COVID-19 pandemic, recognizes and binds host cells using its spike glycoprotein through an angiotensin converting enzyme 2 (ACE-2) receptor-mediated pathway. Recent research suggests that spatial distributions of the spike protein may influence viral interactions with target cells and immune systems. The goal of this study has been to develop a liposome-based virus-like particle (VLP) by reconstituting the SARS-CoV-2 spike glycoprotein within a synthetic nanoparticle membrane, aiming to eventually establish tunability in spike protein presentation on the nanoparticle surface. Here we report on first steps to this goal, wherein liposomal SARS-CoV-2 VLPs were successfully produced via detergent mediated spike protein reconstitution. The resultant VLPs are shown to successfully co-localize in vitro with the ACE-2 receptor on lung epithelial cell surfaces, followed by internalization into these cells. These VLPs are the first step toward the overall goal of this research which is to form an understanding of the relationship between spike protein surface density and cell-level immune response, eventually toward creating better vaccines and anti-viral therapeutics.

Alberta Childhood Cancer Survivorship Research Program

Adverse outcomes after childhood cancer have been assessed in a range of settings, but most existing studies are historical and ascertain outcomes only after 5-year survival. Here, we describe the Alberta Childhood Cancer Survivorship Research Program and its foundational retrospective, population-based cohort of Albertan residents diagnosed with a first primary neoplasm between the ages of 0 and 17 years from 1 January 2001 to 31 December 2018. The cohort was established in collaboration with the Alberta Cancer Registry and Cancer in Young People in Canada program and has been linked to existing administrative health databases and patient-reported outcome questionnaires. The cohort comprised 2580 survivors of childhood cancer, 1379 (53.4%) of whom were 5-year survivors. Approximately 48% of the cohort was female, 47% of the cohort was diagnosed between 0 and 4 years of age, and the most frequent diagnoses were leukemias (25.4%), central nervous system tumors (24.0%), and lymphomas (14.9%). Detailed treatment information was available for 1741 survivors (67.5%), with manual abstraction ongoing for those with missing data. By the study exit date, the median time since diagnosis was 5.5 years overall and 10.4 years for 5-year survivors. During the follow-up time, 82 subsequent primary cancers were diagnosed, 20,355 inpatient and 555,425 ambulatory/outpatient events occurred, 606,773 claims were reported, and 437 survivors died. The results from this research program seek to inform and improve clinical care and reduce cancer-related sequelae via tertiary prevention strategies.

Clinical Use of Blood Flow Analysis through 4D-Flow Imaging in Aortic Valve Disease

Bicuspid aortic valve (BAV), which affects 1% of the general population, results from the abnormal fusion of the cusps of the aortic valve. BAV can lead to the dilatation of the aorta, aortic coarctation, development of aortic stenosis (AS), and aortic regurgitation. Surgical intervention is usually recommended for patients with BAV and bicuspid aortopathy. This review aims to examine 4D-flow imaging as a tool in cardiac magnetic resonance imaging for assessing abnormal blood flow and its clinical application in BAV and AS. We present a historical clinical approach summarizing evidence of abnormal blood flow in aortic valve disease. We highlight how abnormal flow patterns can contribute to the development of aortic dilatation and novel flow-based biomarkers that can be used for a better understanding of the disease progression.

Bifunctional Gas Diffusion Electrode Enables In Situ Separation and Conversion of CO2 to Ethylene from Dilute Stream

The requirement of concentrated carbon dioxide (CO₂ ) feedstock significantly limits the economic feasibility of electrochemical CO₂ reduction (eCO₂ R) which often involves multiple intermediate processes, including CO₂ capture, energy-intensive regeneration, compression, and transportation. Herein, a bifunctional gas diffusion electrode (BGDE) for separation and eCO₂ R from a low-concentration CO₂ stream is reported. The BGDE is demonstrated for the selective production of ethylene (C₂ H₄ ) by combining high-density-polyethylene-derived porous carbon (HPC) as a physisorbent with polycrystalline copper as a conversion catalyst. The BGDE shows substantial tolerance to 10 vol% CO₂ exhibiting a Faradaic efficiency of ≈45% toward C₂ H₄ at a current density of 80 mA cm^-2 , outperforming previous reports that utilized such partial pressure (P_CO2 = 0.1 atm and above) and unaltered polycrystalline copper. Molecular dynamics simulation and mixed gas permeability assessment reveal that such selective performance is ensured by high CO₂ uptake of the microporous HPC as well as continuous desorption owing to the molecular diffusion and concentration gradient created by the binary flow of CO₂ and nitrogen (CO₂ |N₂ ) within the sorbent boundary. Based on detailed techno-economic analysis, it is concluded that this in situ process can be economically compelling by precluding the C₂ H₄ production cost associated with the energy-intensive intermediate steps of the conventional decoupled process.

Lessons learned from implementing the Non-Communicable Diseases Kit in a humanitarian emergency: an operational evaluation in Sudan

Non-communicable diseases (NCDs) are a major global health concern, and their management is particularly challenging in humanitarian contexts where healthcare resources are limited. The WHO Non-Communicable Diseases Kit (WHO-NCDK) is a health system intervention targeted at the primary healthcare (PHC) level and designed to provide essential medicines and equipment for NCDs management in emergency settings, meeting the needs of 10 000 people for 3 months. This operational evaluation aimed to assess the effectiveness and utility of the WHO-NCDK in two PHC facilities in Sudan and identify key contextual factors that may influence its implementation and impact. Using a cross-sectional mixed-methods observational approach that combined quantitative and qualitative data, the evaluation found that the kit played a critical role in maintaining continuity of care when other supply chain solutions were disrupted. However, contextual factors such as local communities' unfamiliarity with healthcare facilities, the national integration of NCDs into PHC, and the existence of monitoring and evaluation systems were identified as important considerations for enhancing the WHO-NCDK's utility and usefulness. The evaluation suggests that the WHO-NCDK can be an effective intervention in emergency settings, provided that contextual factors such as local needs, facility capacity and healthcare worker capacity are considered before kit deployments.

Altered longitudinal structural connectome in paediatric mild traumatic brain injury: an Advancing Concussion Assessment in Paediatrics study

Advanced diffusion-weighted imaging techniques have increased understanding of the neuropathology of paediatric mild traumatic brain injury (i.e. concussion). Most studies have examined discrete white-matter pathways, which may not capture the characteristically subtle, diffuse and heterogenous effects of paediatric concussion on brain microstructure. This study compared the structural connectome of children with concussion to those with mild orthopaedic injury to determine whether network metrics and their trajectories across time post-injury differentiate paediatric concussion from mild traumatic injury more generally. Data were drawn from of a large study of outcomes in paediatric concussion. Children aged 8-16.99 years were recruited from five paediatric emergency departments within 48 h of sustaining a concussion (n = 360; 56% male) or mild orthopaedic injury (n = 196; 62% male). A reliable change score was used to classify children with concussion into two groups: concussion with or without persistent symptoms. Children completed 3 T MRI at post-acute (2-33 days) and/or chronic (3 or 6 months, via random assignment) post-injury follow-ups. Diffusion-weighted images were used to calculate the diffusion tensor, conduct deterministic whole-brain fibre tractography and compute connectivity matrices in native (diffusion) space for 90 supratentorial regions. Weighted adjacency matrices were constructed using average fractional anisotropy and used to calculate global and local (regional) graph theory metrics. Linear mixed effects modelling was performed to compare groups, correcting for multiple comparisons. Groups did not differ in global network metrics. However, the clustering coefficient, betweenness centrality and efficiency of the insula, cingulate, parietal, occipital and subcortical regions differed among groups, with differences moderated by time (days) post-injury, biological sex and age at time of injury. Post-acute differences were minimal, whereas more robust alterations emerged at 3 and especially 6 months in children with concussion with persistent symptoms, albeit differently by sex and age. In the largest neuroimaging study to date, post-acute regional network metrics distinguished concussion from mild orthopaedic injury and predicted symptom recovery 1-month post-injury. Regional network parameters alterations were more robust and widespread at chronic timepoints than post-acutely after concussion. Results suggest that increased regional and local subnetwork segregation (modularity) and inefficiency occurs across time after concussion, emerging after post-concussive symptom resolve in most children. These differences persist up to 6 months after concussion, especially in children who showed persistent symptoms. While prognostic, the small to modest effect size of group differences and the moderating effects of sex likely would preclude effective clinical application in individual patients.

Mothers of disabled infants had higher cortisol levels in a free-ranging group of Japanese macaques (Macaca fuscata)

Glucocorticoids (GCs) are hormones released in response to stressors and can provide insight into an organism's physiological well-being. Experiencing chronic challenges to homeostasis is associated with significant deviations from baseline fecal GCs (fGCs) in many species, providing a noninvasive biomarker for assessing stress. In the group of free-ranging Japanese macaques (Macaca fuscata) at the Awajishima Monkey Center in Japan, ~17% have congenital limb malformations. We collected 646 fecal samples from 27 females over three consecutive birth seasons (May-August) and analyzed them using enzyme immunoassay to extract fGCs. We explored the relationship between fGC levels and individual (physical impairment and reproductive status), social (dominance rank and availability of kin for social support), and ecological variables (exposure to potential predators, rainfall, and wild fruit availability). A disabled infant was associated significantly with higher fGC in the mother; however, physical impairment in adult females was not significantly related to fGC levels. Females with higher dominance rank had significantly lower fGC levels than lower ranking females. Other factors did not relate significantly to fGC. These results suggest that providing care that meets the support needs of disabled infants poses a physiological challenge for mothers and suggests that physically impaired adults are able to effectively compensate for their disabilities with behavioral plasticity. Once an individual with congenital limb malformations survives infancy through their mother's care, physical impairment does not appear to influence fGC values, while social variables like dominance rank significantly influenced cortisol values in free-ranging female Japanese macaques.

Protective equipment in youth ice hockey: are mouthguards and helmet age relevant to concussion risk?

OBJECTIVES

To compare the incidence rates and odds of concussion between youth ice hockey players based on mouthguard use and helmet age.

MATERIALS AND METHODS

Within a 5-year longitudinal cohort (2013/2014 to 2017/2018) of male and female ice hockey players (ages 11-18; n=3330 players) in Alberta (Canada), we analysed the relationship of equipment and concussion in both a prospective cohort and nested case (concussion) control (acute musculoskeletal injury) approach. The prospective cohort included baseline assessments documenting reported mouthguard use (yes/sometimes, no use), helmet age (newer/<2 years old, older/≥2 years old) and important covariables (weight, level of play, position of play, concussion history, body checking policy), with weekly player participation throughout the season. The nested case-control component used injury reports to document equipment (mouthguard use, helmet age) and other information (eg, mechanism and type of injury) for the injury event. Multivariable mixed effects negative binomial regression (prospective cohort, incidence rate ratios (IRRs)) and multivariable mixed effects logistic regression (nested case-control, odds ratios (OR)) examined the association between equipment and concussion.

RESULTS

Players who reported wearing a mouthguard had a 28% lower concussion rate (IRR=0.72, 95% CI 0.56 to 0.93) and 57% lower odds of concussion (OR=0.43, 95% CI 0.27 to 0.70) compared with non-wearers. There were no associations in the concussion rate (IRR=0.94, 95% CI 0.75 to 1.15) and odds (OR=1.16, 95% CI 0.73 to 1.86) between newer and older helmets.

CONCLUSIONS

Wearing a mouthguard was associated with a lower concussion rate and odds. Policy mandating use should be considered in youth ice hockey. More research is needed to identify other helmet characteristics (eg, quality, fit) that could lower concussion risk.

Coinfection with Strongyloides and SARS-CoV-2: A Systematic Review

BACKGROUND

Treatments for COVID-19, including steroids, might exacerbate Strongyloides disease in patients with coinfection. We aimed to systematically review clinical and laboratory features of SARS-CoV-2 and Strongyloides coinfection, investigate possible interventions, assess outcomes, and identify research gaps requiring further attention.

METHODS

We searched two electronic databases, LitCOVID and WHO, up to August 2022, including SARS-CoV-2 and Strongyloides coinfection studies. We adapted the World Health Organization-Uppsala Monitoring Centre (WHO-UMC) system for standardized case causality assessment to evaluate if using corticosteroids or other immunosuppressive drugs in COVID-19 patients determined acute manifestations of strongyloidiasis.

RESULTS

We included 16 studies reporting 25 cases of Strongyloides and SARS-CoV-2 coinfection: 4 with hyperinfection syndrome; 2 with disseminated strongyloidiasis; 3 with cutaneous reactivation of strongyloidiasis; 3 with isolated digestive symptoms; and 2 with solely eosinophilia, without clinical manifestations. Eleven patients were asymptomatic regarding strongyloidiasis. Eosinopenia or normal eosinophil count was reported in 58.3% of patients with Strongyloides reactivation. Steroids were given to 18/21 (85.7%) cases. A total of 4 patients (19.1%) received tocilizumab and/or Anakirna in addition to steroids. Moreover, 2 patients (9.5%) did not receive any COVID-19 treatment. The causal relationship between Strongyloides reactivation and COVID-19 treatments was considered certain (4% of cases), probable (20% of patients), and possible (20% of patients). For 8% of cases, it was considered unlikely that COVID-19 treatment was associated with strongyloidiasis reactivations; the relationship between the Strongyloides infection and administration of COVID-19 treatment was unassessable/unclassifiable in 48% of cases. Of 13 assessable cases, 11 (84.6%) were considered to be causally associated with Strongyloides, ranging from certain to possible.

CONCLUSIONS

Further research is needed to assess the frequency and risk of Strongyloides reactivation in SARS-CoV-2 infection. Our limited data using causality assessment supports recommendations that clinicians should screen and treat for Strongyloides infection in patients with coinfection who receive immunosuppressive COVID-19 therapies. In addition, the male gender and older age (over 50 years) may be predisposing factors for Strongyloides reactivation. Standardized guidelines should be developed for reporting future research.

The global epidemiology of SLE: narrowing the knowledge gaps

SLE is a global health concern that unevenly affects certain ethnic/racial groups. Individuals of Asian, Black, Hispanic and Indigenous ethnicity/race are amongst those who experience increased prevalence, incidence, morbidity and mortality. Population-based surveillance studies from many regions are few and often still in nascent stages. Many of these areas are challenged by restricted access to diagnostics and therapeutics. Without accurately capturing the worldwide burden and distribution of SLE, appropriately dedicating resources to improve global SLE outcomes may be challenging. This review discusses recent SLE epidemiological studies, highlighting the challenges and emerging opportunities in low- and middle-income countries. We suggest means of closing these gaps to better address the global health need in SLE.

Gut microbiota biofilms: From regulatory mechanisms to therapeutic targets

Gut microbiota contain communities of viruses, bacteria, fungi, and Eukarya, and live as biofilms. In health, these biofilms adhere to the intestinal mucus surface without contacting the epithelium. Disruptions to the equilibrium between these biofilms and the host may create invasive pathobionts from these commensal communities and contribute to disease pathogenesis. Environmental factors appear to dominate over genetics in determining the shifts in microbiota populations and function, including when comparing microbiota between low-income and industrialized countries. The observations discussed herein carry enormous potential for the development of novel therapies targeting phenotype in microbiota dysbiosis.

Gravity Drainage of Bitumen Induced by Solvent Leaching

Steam-based thermal recovery processes are energy-intensive and pose environmental concerns due to their high greenhouse gas emissions. The application of solvents has shown promise in reducing the environmental impact of these processes. In this work, the solvent chamber theory is used to study the gravity drainage of bitumen. The results reveal that the drainage rate can be scaled using the thermophysical properties of solvents. The drainage rate is shown to be directly related to the density difference between bitumen and solvent and inversely proportional to the mixture viscosity. A universal scaling relation between the Sherwood number, as a measure of the mass transfer, and Rayleigh number, as a measure of the natural convection, in the form of Sh = βRa is presented using the experimental data of various solvents. This linear relationship is consistent with the theoretical studies of buoyancy-driven convection. Moreover, the scaling prefactor β is found to decrease with increasing natural log of the mobility ratio (α), which results in a lower rate of convective mass transfer. Furthermore, a new critical Rayleigh number equation based on the power-law mixing rule (PLMR) is derived, and the results are compared with the available theories in the literature based on the exponential mixing rule (EMR). The findings provide insights into understanding the convective dissolution with large viscosity contrast. Furthermore, the developed scaling relation provides a useful tool to predict the convective mixing of different bitumen/solvent systems. The results find application in the design of the solvent-based bitumen recovery processes.

Stabilized COre gene and Pathway Election uncovers pan-cancer shared pathways and a cancer-specific driver

Approaches systematically characterizing interactions via transcriptomic data usually follow two systems: (i) coexpression network analyses focusing on correlations between genes and (ii) linear regressions (usually regularized) to select multiple genes jointly. Both suffer from the problem of stability: A slight change of parameterization or dataset could lead to marked alterations of outcomes. Here, we propose Stabilized COre gene and Pathway Election (SCOPE), a tool integrating bootstrapped least absolute shrinkage and selection operator and coexpression analysis, leading to robust outcomes insensitive to variations in data. By applying SCOPE to six cancer expression datasets (BRCA, COAD, KIRC, LUAD, PRAD, and THCA) in The Cancer Genome Atlas, we identified core genes capturing interaction effects in crucial pan-cancer pathways related to genome instability and DNA damage response. Moreover, we highlighted the pivotal role of CD63 as an oncogenic driver and a potential therapeutic target in kidney cancer. SCOPE enables stabilized investigations toward complex interactions using transcriptome data.

Development of reference intervals for pupillometry in healthy dogs

BACKGROUND

Pupillometry, the measurement of pupil size and reactivity to a stimulus, has various uses in both human and veterinary medicine. These reflect autonomic tone, with the potential to assess nociception and emotion. Infrared pupillometry reduces inaccuracies that may occur when the pupillary light reflex is determined subjectively by the examiner. To our knowledge, there are no published studies outlining normal reference intervals for automated pupillometry in dogs.

OBJECTIVE

The objective of this study was to develop de novo automated pupillometry reference intervals from 126 healthy canine eyes.

METHODS

The pupillary light reflex (PLR) was measured with a handheld pupillometer (NeurOptics™ PLR-200™ Pupillometer). Parameters recorded included maximum pupil diameter (MAX), minimum pupil diameter (MIN), percent constriction (CON), latency (LAT), average constriction velocity (ACV), maximum constriction velocity (MCV), average dilation velocity (ADV) and time to 75% pupil diameter recovery (T75). One measurement was obtained for each eye.

RESULTS

The following reference intervals were developed: MAX (6.05-11.30 mm), MIN (3.76-9.44 mm), CON (-37.89 to -9.64 %), LAT (0.11-0.30 s), ACV (-6.39 to -2.63 mm/ s), MCV (-8.45 to -3.75 mm/s), ADV (-0.21-1.77 mm/s), and T75 (0.49-3.20 s).

CLINICAL SIGNIFICANCE

The reference intervals developed in this study are an essential first step to facilitate future research exploring pupillometry as a pain assessment method in dogs.

Enteric Pathogen Testing Importance for Children with Acute Gastroenteritis: a Modified Delphi Study

The application of clinical diagnostics for gastroenteritis in children has implications for a broad collection of stakeholders, impacting clinical care, communicable disease control, and laboratory utilization. To support diagnostic stewardship as gastroenteritis testing options continue to advance, it is critical to understand which enteropathogens constitute priorities for testing across stakeholder groups. Using a modified Delphi technique, we elicited opinions of subject matter experts to determine clinical and public health testing priorities. There was a high level of overall agreement (≥80%) among stakeholders (final round n = 15) that testing was important for Campylobacter, Escherichia coli O157 and other Shiga toxin-producing E. coli, Salmonella, Shigella, Vibrio, Yersinia, norovirus, and rotavirus. Immunocompromised children were identified as a special population that warranted the additional testing of three to four bacterial and parasitic targets. To support these clinical and public health testing priorities, diagnostic stewardship strategies can be employed, such as educating clinicians, developing new decision support tools, and using multiplex testing in concert with selective result reporting and annotation. IMPORTANCE Children with diarrhea and vomiting who seek care can be infected with a wide variety of infectious agents. This study reports findings from a survey of clinical, public health, and laboratory subject matter experts on the infectious agents that are most important to test for. The majority agreed on the importance of testing children likely infected with several bacterial agents, as well as two common viruses. Although confirming a child is positive for a viral agent is unlikely to change clinical care, participants noted the importance of monitoring these viruses for public health purposes. To avoid over-testing children, however, these results should be used to support diagnostic stewardship strategies and design new decision support tools.

Synthesis and properties of multi-functionalized graphene quantum dots with tunable photoluminescence and hydrophobicity from asphaltene and its oxidized and reduced derivatives

Graphene quantum dots (GQDs) with tunable photoluminescence (PL) and hydrophobicity were synthesized from an abundant natural carbon source containing nitrogen, sulfur, and oxygen heteroatoms. Asphaltene and its oxidized and reduced derivatives were used as precursors to produce GQDs in organic solvents (i.e., methanol, toluene, and chloroform) using a facile ultrasonication technique. Asphaltene surface chemistry was tuned by sequential oxidation and reduction to investigate the surface effects on GQD properties. Spectroscopic characterizations confirmed the presence of N, S, and O heteroatoms and different electron-donating and electron-withdrawing groups. Microscopic characterizations revealed that these crystalline carbon nanomaterials have mono-layered or multi-layered structures with lateral sizes in the range of ∼5-15 nm. The asphaltene-derived GQDs exhibit tunable PL with emission colors ranging from blue to orange, depending on the carbon precursor and the organic solvent. Solvent exchange studies also revealed that asphaltene and its derivatives contain hydrophilic and hydrophobic fractions, resulting in varied hydrophobicity of the synthesized GQDs. Adding to the appeal of the present work, PL quenching of GQD-silica hybrid materials upon exposure to nitro-aromatics confirms that these GQDs can be incorporated to different host materials for advanced sensing or optoelectronic applications.

Comparison of four different hematocrit assays and the effect of albumin on their measurements

Clinical decisions are influenced by hematocrit values. Centrifugation (reference standard), conductivity, optical and impedance methods are often used interchangeably to measure hematocrit. The effects of albumin, which are known to affect conductivity methods, have not been evaluated for limits of agreement (LOA) between hematocrit assays in small animals. Canine venous blood was collected from 74 clinical cases and measured by centrifugation (n = 72), conductivity (n = 73), impedance (n = 24) and optical (n = 50) methods. Bland-Altman analysis determined bias (± SD) and 95% LOA between methods. There was a statistically significant difference between centrifugation hematocrit values and values obtained via conductivity (p &lt; 0.0001), optical (p &lt; 0.0001), and impedance (p = 0.0082) methods. The conductivity method underestimated hematocrit by 2.1 ± 2.9% (95% LOA −3.54 to 7.88), the optical method by 3.1 ± 3.6% (95% LOA −4.0 to 10.2), and the impedance method by 2.3 ± 3.7% (95% LOA −5 to 9.6) when compared to centrifuged hematocrit values. The hematocrit difference between conductivity and centrifugation methods was statistically different for low (4%, 0–5%), within reference limits (3%, −5 to 8%), and high (2%, −2 to 5%) albumin values, respectively (p = 0.02), with post-hoc analysis demonstrating that the difference occurred between the low and high albumin groups. This study confirms that albumin values outside reference limits can affect the conductivity method and that hematocrit values obtained via conductivity, optical and impedance methods underestimate values obtained via centrifugation. Therefore, the hematocrit methods cannot be used interchangeably. The wide limits of agreement also demonstrates that care must be taken when making clinical decisions with different hematocrit methodologies.

Devonian to Carboniferous continental-scale carbonate turnover in Western Laurentia (North America): upwelling or climate cooling?

The Devonian to Carboniferous (DC) transition coincided with a green-to-ice house climatic shift, anoxia, disappearance of lower latitude carbonate banks, and turnover from warm-to-cool water carbonate factories. In western Laurentia, the switch to carbonate factories dominated by cool-water biota was contemporaneous with a tectonically driven palaeogeographic change. To investigate this depositional shift and infer the relative impact of climate vs tectonics, a continental-scale sedimentological and geochemical study was conducted on twelve stratigraphic sections of DC strata from western Canada to southern Nevada (USA). The spatial-temporal distribution of microfacies records the turnover from [i] a Famennian lime mud-rich, shallow warm-water carbonate ramp with low sedimentation rates, mesotrophic conditions and tabular geometry to [ii] Tournaisian to Viséan lime mud-depleted and grainstone dominated cool-water carbonate ramp with anomalous high sedimentation rates, oligotrophic conditions and a pronounced slope. Positive excursions of δ ¹⁸O_carb (+ 2‰ V-PDB) and δ ¹³C_carb (+ 4‰ V-PDB) of Lower Mississippian carbonates likely correspond to the first cooling peak of the Carboniferous-Permian icehouse climate, following carbon withdrawal during black shale deposition during the late Famennian and early Tournaisian. However, late Tournaisian return of photozoan elements and their persistence throughout the Viséan suggests that warmer surface water existed, revealing a decoupling of the lower latitude ocean and the atmosphere. Shoaling of the thermocline was likely a result of cold-water upwelling along an open coast, as the Antler orogen no longer provided an oceanic obstruction to the west. This study shows that carbonate platforms are more susceptible to regional changes than global shifts.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10347-022-00653-4.