Establishing breath as a biomarker platform-take home messages from the Breath Biopsy Conference 2023.

The annual Breath Biopsy Conference hosted by Owlstone Medical gathers together the leading experts, early career researchers, and physicians working with breath as a biomarker platform for clinical purposes. The current topics in breath research are discussed and presented, and an overarching topical theme is identified and discussed as part of an expert panel to close the conference. The profiling of normal breath composition and the establishment of standards for analyzing breath compared to background signal were two important topics that were major focuses of this conference, as well as important innovative progress that has been made since last year, including the development of a non-invasive breath test for lung cancer and liver disease. This meeting report offers an overview of the key take-home messages from the various presentations, posters, and discussions from the conference.

Transcriptionally active chromatin loops contain both 'active' and 'inactive' histone modifications that exhibit exclusivity at the level of nucleosome clusters.

Chromatin state is thought to impart regulatory function to the underlying DNA sequence. This can be established through histone modifications and chromatin organisation, but exactly how these factors relate to one another to regulate gene expression is unclear. In this study, we have used super-resolution microscopy to image the Y loops of Drosophila melanogaster primary spermatocytes, which are enormous transcriptionally active chromatin fibres, each representing single transcription units that are individually resolvable in the nuclear interior. We previously found that the Y loops consist of regular clusters of nucleosomes, with an estimated median of 54 nucleosomes per cluster with wide variation.In this study, we report that the histone modifications H3K4me3, H3K27me3, and H3K36me3 are also clustered along the Y loops, with H3K4me3 more associated with diffuse chromatin compared to H3K27me3. These histone modifications form domains that can be stretches of Y loop chromatin micrometres long, or can be in short alternating domains. The different histone modifications are associated with different sizes of chromatin clusters and unique morphologies. Strikingly, a single chromatin cluster almost always only contains only one type of the histone modifications that were labelled, suggesting exclusivity, and therefore regulation at the level of individual chromatin clusters. The active mark H3K36me3 is more associated with actively elongating RNA polymerase II than H3K27me3, with polymerase often appearing on what are assumed to be looping regions on the periphery of chromatin clusters.These results provide a foundation for understanding the relationship between chromatin state, chromatin organisation, and transcription regulation - with potential implications for pause-release dynamics, splicing complex organisation and chromatin dynamics during polymerase progression along a gene.

Prediction of Effectiveness and Toxicities of Immune Checkpoint Inhibitors Using Real-World Patient Data.

PURPOSE: Although immune checkpoint inhibitors (ICIs) have improved outcomes in certain patients with cancer, they can also cause life-threatening immunotoxicities. Predicting immunotoxicity risks alongside response could provide a personalized risk-benefit profile, inform therapeutic decision making, and improve clinical trial cohort selection. We aimed to build a machine learning (ML) framework using routine electronic health record (EHR) data to predict hepatitis, colitis, pneumonitis, and 1-year overall survival. METHODS: Real-world EHR data of more than 2,200 patients treated with ICI through December 31, 2018, were used to develop predictive models. Using a prediction time point of ICI initiation, a 1-year prediction time window was applied to create binary labels for the four outcomes for each patient. Feature engineering involved aggregating laboratory measurements over appropriate time windows (60-365 days). Patients were randomly partitioned into training (80%) and test (20%) sets. Random forest classifiers were developed using a rigorous model development framework. RESULTS: The patient cohort had a median age of 63 years and was 61.8% male. Patients predominantly had melanoma (37.8%), lung cancer (27.3%), or genitourinary cancer (16.4%). They were treated with PD-1 (60.4%), PD-L1 (9.0%), and CTLA-4 (19.7%) ICIs. Our models demonstrate reasonably strong performance, with AUCs of 0.739, 0.729, 0.755, and 0.752 for the pneumonitis, hepatitis, colitis, and 1-year overall survival models, respectively. Each model relies on an outcome-specific feature set, though some features are shared among models. CONCLUSION: To our knowledge, this is the first ML solution that assesses individual ICI risk-benefit profiles based predominantly on routine structured EHR data. As such, use of our ML solution will not require additional data collection or documentation in the clinic.

Pediatric Animal Model of Extracorporeal Cardiopulmonary Resuscitation after Prolonged Circulatory Arrest.

Congenital heart disease (CHD) is the most prevalent congenital malformation, with about one million births impacted worldwide per year. Comprehensive investigation of this disease requires appropriate and validated animal models. Piglets are commonly used for translational research due to their analogous anatomy and physiology. This work aimed to describe and validate a neonatal piglet model of cardiopulmonary bypass (CPB) with circulatory and cardiac arrest (CA) as a tool for studying severe brain damage and other complications of cardiac surgery. In addition to including a list of materials, this work provides a roadmap for other investigators to plan and execute this protocol. After experienced practitioners performed several trials, the representative results of the model demonstrated a 92% success rate, with failures attributed to small piglet size and variant vessel anatomy. Furthermore, the model allowed practitioners to select from a wide variety of experimental conditions, including varying times in CA, temperature alterations, and pharmacologic interventions. In summary, this method uses materials readily available in most hospital settings, is reliable and reproducible, and can be widely employed to enhance translational research in children undergoing heart surgery.

Pulmonary valve replacement for treatment of severe pulmonary regurgitation in patients with previous tetralogy of Fallot repair surgery.

Tetralogy of Fallot was classically described as the combination of pulmonary stenosis, right ventricle hypertrophy, perimembranous ventricular septal defect and an aortic root that overrides the ventricular septal defect. Full surgical repair, which is usually indicated in toddlers, comprises closure of the ventricular septal defect and alleviation of the pulmonary stenosis. Because there is a wide anatomical spectrum, the cause and severity of the pulmonary stenosis are variable. However, when the pulmonary valve is stenotic and not well-developed, it has to be removed, and one has to accept severe pulmonary regurgitation as a sequela. In the ensuing years, when signs of damage to the right ventricle are proven, pulmonary valve replacement is indicated. We present the case of a 16-year-old patient with tetralogy of Fallot that was corrected during the first year of life. Follow-up demonstrated progressive exercise intolerance and moderate-to-severe right ventricle dilatation. Thus, surgical pulmonary valve replacement was indicated. The surgical approach was through a full median redo sternotomy. Central cardiopulmonary bypass was established with bicaval drainage. The operation was performed under assisted non-clamped circulatory support. The calcified previous pericardial patch was removed, and a 25-mm bioprosthetic valve was implanted in the pulmonary annulus. A new pericardial heterologous patch was used for the transannular pulmonary plasty.

The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy.

While the biochemistry of gene transcription has been well studied, our understanding of how this process is organised in 3D within the intact nucleus is less well understood. Here we investigate the structure of actively transcribed chromatin and the architecture of its interaction with active RNA polymerase. For this analysis, we have used super-resolution microscopy to image the Drosophila melanogaster Y loops which represent huge, several megabases long, single transcription units. The Y loops provide a particularly amenable model system for transcriptionally active chromatin. We find that, although these transcribed loops are decondensed they are not organised as extended 10nm fibres, but rather they largely consist of chains of nucleosome clusters. The average width of each cluster is around 50nm. We find that foci of active RNA polymerase are generally located off the main fibre axis on the periphery of the nucleosome clusters. Foci of RNA polymerase and nascent transcripts are distributed around the Y loops rather than being clustered in individual transcription factories. However, as the RNA polymerase foci are considerably less prevalent than the nucleosome clusters, the organisation of this active chromatin into chains of nucleosome clusters is unlikely to be determined by the activity of the polymerases transcribing the Y loops. These results provide a foundation for understanding the topological relationship between chromatin and the process of gene transcription.

Zooming into the COVID Era Together.

The pre-clinical medical school curriculum provides students with extraordinary experiences in preparation to become physicians. However, it was not originally designed to be delivered remotely. The COVID-19 pandemic promptly threw the medical education process into unforeseen circumstances. A model of student-faculty collaboration created to address new challenges and implement practical solutions rapidly is presented. This model was used effectively to respond to pre-clinical educational interruptions that were imposed by the COVID-19 pandemic and maintain high-quality training. Our experience provides valuable insights and lessons learned that can be applied to the ongoing pandemic response and to future educational challenges.

Neuraxial anesthesia for post-operative pain control after hip surgery in children with cerebral palsy and pre-existing intrathecal baclofen pumps.

PURPOSE: The purpose of this study is to describe the efficacy and adverse events of neuraxial anesthesia for post-operative pain control in non-ambulatory children with cerebral palsy with pre-existing intrathecal baclofen (ITB) pumps undergoing hip reconstructive or palliative surgery. METHODS: Twelve children (mean age 11.25 years) were included in the study with the following neuraxial anesthesia methods: indwelling epidural catheter (8 patients), neuraxial opioids administered through the side port of the ITB pump (3 patients), and single injection spinal anesthetic (1 patient). Observational pain scores and opioid requirements were quantified for all patients. RESULTS: There were no ITB pump or surgical complications at a mean follow-up of 2.2 years. The average length of stay was 6 days. Patients had good post-operative pain control with a mean observational pain score of 0.7 and mean morphine equivalent use of 0.26mg/kg/day. Four patients required anti-emetics to control nausea and three patients had urinary retention requiring repeat catheterization, but all medical complications resolved prior to discharge. CONCLUSION: Neuraxial anesthesia can effectively control post-operative pain in children with a pre-existing ITB pump. Utilizing the side port of the ITB pump for administration of neuraxial opioids is an option when epidural or spinal anesthesia is not possible.

Impact of Health Literacy on Satisfaction Following Male Prosthetic Surgery.

OBJECTIVE: To determine whether a patient's health literacy impacts patient satisfaction following inflatable penile prosthesis (IPP) or artificial urinary sphincter (AUS) placement. MATERIALS AND METHODS: A retrospective study of patients who underwent IPP or AUS between January 1, 2016 and July 31, 2020 was performed. A telephone questionnaire assessed overall satisfaction and if patients would undergo surgery again. Health literacy was measured using the Brief Health Literacy Screen (BHLS). Multivariate ordinal logistic regression was used to assess the association between health literacy and patient satisfaction. RESULTS: At a median follow up of 2.4 years, 113 (70%) of the 162 IPP patients were either satisfied or very satisfied with their procedure and 120 (74%) patients would undergo surgery again. Of the 76 AUS patients, 65 (86%) were either satisfied or very satisfied with their procedure and 65 (86%) patients would undergo surgery again. After adjustment for potential confounders, increasing BHLS score was significantly associated with satisfaction for both IPP (OR 1.31, 95% CI 1.11-1.54; P = .001) and AUS surgery (OR 1.25, 95% CI 1.02-1.56; P = .034), as well as with likelihood of undergoing IPP surgery again (OR 1.53, 95% CI 1.25-1.87; P <.001). BHLS was not associated, however, with likelihood of undergoing AUS surgery again (P = .403). CONCLUSION: Men with lower health literacy are less likely to be satisfied following prosthetic surgery. The BHLS is an important tool that can be used to identify patients who may benefit from increased preoperative counseling to improve patient expectations and quality of life following prosthetic surgery.

Emergency dental care triage during the COVID-19 pandemic.

Introduction Due to the COVID-19 pandemic, from 23 March 2020, routine dental treatment was stopped by the Chief Dental Officer, with the emphasis towards urgent dental care only.Aim To evaluate the activities of the emergency service at a secondary care Urgent Dental Care (UDC) hub during the COVID-19 pandemic.Materials and methods The total number of patients seen from 30 March to 20 June 2020 was recorded. The effectiveness of telephone triage and the appropriateness of patients invited for a clinical assessment were evaluated over a two-week period.Results The number of calls into the UDC hub were highest during the first few weeks, with up to 249 per day. The most commonly provided emergency treatments included extractions and pulp extirpations.Discussion As other UDC hubs opened, the number of calls reduced, with patients being directed to a UDC nearer to where they lived.Conclusions The dental profession had to make some significant changes in the way they worked due to the risk of COVID-19 transmission and due to the effects of the lockdown. This review highlights the effectiveness of telephone triage as well as its drawbacks.

Transparent teamwork: The practice of supervision and delegation within the multi-tiered nursing team.

Supervision and delegation are important leadership skills that nurses require when practising within the multi-tiered nursing team. In response to increasing demands globally on healthcare systems, Nursing Assistants are becoming more prevalent members of the nursing workforce in the acute care setting. An exploratory descriptive research design was used to examine supervision and delegation of Nursing Assistants in an acute hospital setting in Victoria, Australia. It was found that supervision and delegation in the context of a multi-tier nursing team required a complex assessment and decision-making process which was influenced by multiple factors. This research promotes developing transparent nursing practices and mutual understanding in the multi-tier nursing team to facilitate effective supervision and delegation based on informed decision-making and culture of openness and trust. Pre-registration education and continuing education and support for nurses are important to build transparent supervision and delegation practices and teamwork, empowering the nursing team to practice to their full scope of practice to provide high-quality patient care.

A systematic review and quality appraisal of bereavement care practice guidelines.

Bereavement care practice guidelines assist in delivering high-quality bereavement care. However, the quality of published guidelines is unknown. A systematic review was conducted to identify and evaluate the quality of the process used to develop bereavement care practice guidelines using the Appraisal of Guidelines for Research and Evaluation (AGREE II) instrument. A keyword search was conducted in MEDLINE-Complete, CINAHL-Complete, Health-Source (Nursing/Academic Edition), Psychology and Behavioral Sciences Collection, and an internet search engine in October 2017. Sixteen guidelines with differing scope and purpose but similar core values were identified from the grey literature and then appraised at high quality (n = 1), moderate quality (n = 4), or low quality (n = 11). The domains "clarity of presentation" and "scope and purpose" achieved the highest scores (mean ± SD 71.0 ± 27.6% and 64.4 ± 37.5%, respectively), while "editorial independence" showed the lowest mean score (9.2 ± 13.3%). While few of the bereavement care practice guidelines met the AGREE II quality standards related to their development process, neither the quality of the content of each guideline nor the in-context application was assessed by the AGREE II instrument. Ongoing development of practice guidelines may benefit from consideration and application of the framework outlined in the AGREE II or similar appraisal instrument.

Lactobacillus acidophilus DDS-1 Modulates Intestinal-Specific Microbiota, Short-Chain Fatty Acid and Immunological Profiles in Aging Mice.

Distribution of the microbiota varies according to the location in the gastrointestinal (GI) tract. Thus, dysbiosis during aging may not be limited to faecal microbiota and extend to the other parts of the GI tract, especially the cecum and colon. Lactobacillus acidophilus DDS-1, a probiotic strain, has been shown to modulate faecal microbiota and its associated metabolic phenotype in aging mice. In the present study, we investigated the effect of L. acidophilus DDS-1 supplementation on caecal- and mucosal-associated microbiota, short-chain fatty acids (SCFAs) and immunological profiles in young and aging C57BL/6J mice. Besides differences in the young and aging control groups, we observed microbial shifts in caecal and mucosal samples, leading to an alteration in SCFA levels and immune response. DDS-1 treatment increased the abundances of beneficial bacteria such as Akkermansia spp. and Lactobacillus spp. more effectively in caecal samples than in mucosal samples. DDS-1 also enhanced the levels of butyrate, while downregulating the production of inflammatory cytokines (IL-6, IL-1ß, IL-1α, MCP-1, MIP-1α, MIP-1ß, IL-12 and IFN-γ) in serum and colonic explants. Our findings suggest distinct patterns of intestinal microbiota, improvements in SCFA and immunological profiles with DDS-1 supplementation in aging mice.

Predispositional genome sequencing in healthy adults: design, participant characteristics, and early outcomes of the PeopleSeq Consortium.

BACKGROUND: Increasing numbers of healthy individuals are undergoing predispositional personal genome sequencing. Here we describe the design and early outcomes of the PeopleSeq Consortium, a multi-cohort collaboration of predispositional genome sequencing projects, which is examining the medical, behavioral, and economic outcomes of returning genomic sequencing information to healthy individuals. METHODS: Apparently healthy adults who participated in four of the sequencing projects in the Consortium were included. Web-based surveys were administered before and after genomic results disclosure, or in some cases only after results disclosure. Surveys inquired about sociodemographic characteristics, motivations and concerns, behavioral and medical responses to sequencing results, and perceived utility. RESULTS: Among 1395 eligible individuals, 658 enrolled in the Consortium when contacted and 543 have completed a survey after receiving their genomic results thus far (mean age 53.0 years, 61.4% male, 91.7% white, 95.5% college graduates). Most participants (98.1%) were motivated to undergo sequencing because of curiosity about their genetic make-up. The most commonly reported concerns prior to pursuing sequencing included how well the results would predict future risk (59.2%) and the complexity of genetic variant interpretation (56.8%), while 47.8% of participants were concerned about the privacy of their genetic information. Half of participants reported discussing their genomic results with a healthcare provider during a median of 8.0 months after receiving the results; 13.5% reported making an additional appointment with a healthcare provider specifically because of their results. Few participants (< 10%) reported making changes to their diet, exercise habits, or insurance coverage because of their results. Many participants (39.5%) reported learning something new to improve their health that they did not know before. Reporting regret or harm from the decision to undergo sequencing was rare (< 3.0%). CONCLUSIONS: Healthy individuals who underwent predispositional sequencing expressed some concern around privacy prior to pursuing sequencing, but were enthusiastic about their experience and not distressed by their results. While reporting value in their health-related results, few participants reported making medical or lifestyle changes.

A human origin strain Lactobacillus acidophilus DDS-1 exhibits superior in vitro probiotic efficacy in comparison to plant or dairy origin probiotics.

Background: The health benefits of probiotics are well established and known to be strain-specific. However, the role of probiotics obtained from different origins and their efficacy largely remains unexplored. The aim of this study is to investigate the in vitro efficacy of probiotics from different origins. Methods: Probiotic strains utilized in this study include Lactobacillus acidophilus DDS-1 (human origin), Bifidobacterium animalis ssp. lactis UABla-12 (human origin), L. plantarum UALp-05 (plant origin) and Streptococcus thermophilus UASt-09 (dairy origin). Screening assays such as in vitro digestion simulation, adhesion, cell viability and cytokine release were used to evaluate the probiotic potential. Results: All strains showed good resistance in the digestion simulation process, especially DDS-1 and UALp-05, which survived up to a range of 107 to 108 CFU/mL from an initial concentration of 109 CFU/mL. Two human colonic mucus-secreting cells, HT-29 and LS174T, were used to assess the adhesion capacity, cytotoxicity/viability, and cytokine quantification. All strains exhibited good adhesion capacity. No significant cellular cytotoxicity or loss in cell viability was observed. DDS-1 and UALp-05 significantly upregulated anti-inflammatory IL-10 and downregulated pro-inflammatory TNF-α cytokine production. All the strains were able to downregulate IL-8 cytokine levels. Conclusion: Of the 4 strains tested, DDS-1 demonstrated superior survival rates, good adhesion capacity and strong immunomodulatory effect under different experimental conditions.

Gut Microbial Changes, Interactions, and Their Implications on Human Lifecycle: An Ageing Perspective.

Gut microbiota is established during birth and evolves with age, mostly maintaining the commensal relationship with the host. A growing body of clinical evidence suggests an intricate relationship between the gut microbiota and the immune system. With ageing, the gut microbiota develops significant imbalances in the major phyla such as the anaerobic Firmicutes and Bacteroidetes as well as a diverse range of facultative organisms, resulting in impaired immune responses. Antimicrobial therapy is commonly used for the treatment of infections; however, this may also result in the loss of normal gut flora. Advanced age, antibiotic use, underlying diseases, infections, hormonal differences, circadian rhythm, and malnutrition, either alone or in combination, contribute to the problem. This nonbeneficial gastrointestinal modulation may be reversed by judicious and controlled use of antibiotics and the appropriate use of prebiotics and probiotics. In certain persistent, recurrent settings, the option of faecal microbiota transplantation can be explored. The aim of the current review is to focus on the establishment and alteration of gut microbiota, with ageing. The review also discusses the potential role of gut microbiota in regulating the immune system, together with its function in healthy and diseased state.

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

The advent of next-generation sequencing has dramatically decreased the cost for whole-genome sequencing and increased the viability for its application in research and clinical care. The Personal Genome Project (PGP) provides unrestricted access to genomes of individuals and their associated phenotypes. This resource enabled the Critical Assessment of Genome Interpretation (CAGI) to create a community challenge to assess the bioinformatics community's ability to predict traits from whole genomes. In the CAGI PGP challenge, researchers were asked to predict whether an individual had a particular trait or profile based on their whole genome. Several approaches were used to assess submissions, including ROC AUC (area under receiver operating characteristic curve), probability rankings, the number of correct predictions, and statistical significance simulations. Overall, we found that prediction of individual traits is difficult, relying on a strong knowledge of trait frequency within the general population, whereas matching genomes to trait profiles relies heavily upon a small number of common traits including ancestry, blood type, and eye color. When a rare genetic disorder is present, profiles can be matched when one or more pathogenic variants are identified. Prediction accuracy has improved substantially over the last 6 years due to improved methodology and a better understanding of features.

An unbiased index to quantify participant's phenotypic contribution to an open-access cohort.

The Personal Genome Project (PGP) is an effort to enroll many participants to create an open-access repository of genome, health and trait data for research. However, PGP participants are not enrolled for studying any specific traits and participants choose the phenotypes to disclose. To measure the extent and willingness and to encourage and guide participants to contribute phenotypes, we developed an algorithm to score and rank the phenotypes and participants of the PGP. The scoring algorithm calculates the participation index (P-index) for every participant, where 0 indicates no reported phenotypes and 100 indicate complete phenotype reporting. We calculated the P-index for all 5,015 participants in the PGP and they ranged from 0 to 96.7. We found that participants mainly have either high scores (P-index > 90, 29.5%) or low scores (P-index < 10, 57.8%). While, there are significantly more males than female participants (1,793 versus 1,271), females tend to have on average higher P-indexes (P = 0.015). We also reported the P-indexes of participants based on demographics and states like Missouri and Massachusetts have better P-indexes than states like Utah and Minnesota. The P-index can therefore be used as an unbiased way to measure and rank participant's phenotypic contribution towards the PGP.

The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes.

BACKGROUND: Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. However, most of these were sequenced without experimental haplotype data and are therefore missing an important aspect of genome biology. In addition, much of the genomic data is not available to the public and lacks phenotypic information. FINDINGS: As part of the Personal Genome Project, blood samples from 184 participants were collected and processed using Complete Genomics' Long Fragment Read technology. Here, we present the experimental whole genome haplotyping and sequencing of these samples to an average read coverage depth of 100X. This is approximately three-fold higher than the read coverage applied to most whole human genome assemblies and ensures the highest quality results. Currently, 114 genomes from this dataset are freely available in the GigaDB repository and are associated with rich phenotypic data; the remaining 70 should be added in the near future as they are approved through the PGP data release process. For reproducibility analyses, 20 genomes were sequenced at least twice using independent LFR barcoded libraries. Seven genomes were also sequenced using Complete Genomics' standard non-barcoded library process. In addition, we report 2.6 million high-quality, rare variants not previously identified in the Single Nucleotide Polymorphisms database or the 1000 Genomes Project Phase 3 data. CONCLUSIONS: These genomes represent a unique source of haplotype and phenotype data for the scientific community and should help to expand our understanding of human genome evolution and function.