A global dataset of publicly available dengue case count data

OpenDengue is a global database of dengue case data collated from public sources and standardised and formatted to facilitate easy reanalysis. Dataset version 1.2 of this database contains information on over 56 million dengue cases from 102 countries between 1924 and 2023, making it the largest and most comprehensive dengue case database currently available. Over 95% of records are at the weekly or monthly temporal resolution and subnational data is available for 40 countries. To build OpenDengue we systematically searched databases, ministry of health websites, peer reviewed literature and Pro-MED mail reports and extracted denominator-based case count data. We undertake standardisation and error checking protocols to ensure consistency and resolve discrepancies. We meticulously documented the extraction process to ensure records are attributable and reproducible. The OpenDengue database remains under development with plans for further disaggregation and user contributions are encouraged. This new dataset can be used to better understand the long-term drivers of dengue transmission, improve estimates of disease burden, targeting and evaluation of interventions and improving future projections.

Ameliorating effect of 2'-Fucosyllactose and 6'-Sialyllactose on lipopolysaccharide-induced intestinal inflammation

Human milk oligosaccharides (HMO) affect gut microbiota during neonatal development, particularly with respect to the immune system. Bovine milk-based infant formulas have low oligosaccharide contents. Thus, efforts to fortify infant formulas with HMO are being undertaken. Two major HMO, 2'-fucosyllactose (2'-FL) and 6'-sialyllactose (6'-SL), exert anti-inflammatory effects; however, the associations between anti-inflammatory effects induced by 2'-FL and 6'-SL co-treatment and gut microbiota composition and metabolite modulation remain unclear. Therefore, in this study, we evaluated the effects of a mixture of these HMO. To determine the optimal HMO ratio for anti-inflammatory effects and elucidate its mode of action, LPS-induced inflammatory HT-29 epithelial cells and intestinal inflamed suckling mice were treated with various mixtures of 2'-FL and 6'-SL. 2'-FL:6'-SL ratio of 5:1 was identified as the most effective pre-treatment HMO mixture in vitro; thus, this ratio was selected and used for low, middle, and high-dose treatments for subsequent in vivo studies. In vivo, high-dose HMO treatment restored LPS-induced inflammation symptoms, such as body weight loss, colon length reduction, histological structural damage, and intestinal gene expression related to inflammatory responses. High-dose HMO was the only treatment that modulated the major phyla Bacteroidetes and Firmicutes and the genera Ihubacter, Mageeibacillus, and Saccharofermentans. These changes in microbial composition were correlated with intestinal inflammation-related gene expression and short-chain fatty acid production. To our knowledge, our study is the first to report the effects of Ihubacter, Mageeibacillus, and Saccharofermentans on short chain fatty acid levels, which can subsequently affect inflammatory cytokine and tight junction protein levels. Conclusively, the HMO mixture exerted anti-inflammatory effects through changes in microbiota and metabolite production. These findings suggested that supplementation of infant formula with HMO may benefit formula-fed infants by forming unique microbiota contributing to neonatal development.

Single-Component Multilayered Self-Assembling Protein Nanoparticles Displaying Extracellular Domains of Matrix Protein 2 as a Pan-influenza A Vaccine

The development of a cross-protective pan-influenza A vaccine remains a significant challenge. In this study, we designed and evaluated single-component self-assembling protein nanoparticles (SApNPs) presenting the conserved extracellular domain of matrix protein 2 (M2e) as vaccine candidates against influenza A viruses. The SApNP-based vaccine strategy was first validated for human M2e (hM2e) and then applied to tandem repeats of M2e from human, avian, and swine hosts (M2ex3). Vaccination with M2ex3 displayed on SApNPs demonstrated higher survival rates and less weight loss compared to the soluble M2ex3 antigen against the lethal challenges of H1N1 and H3N2 in mice. M2ex3 I3-01v9a SApNPs formulated with a squalene-based adjuvant were retained in the lymph node follicles over 8 weeks and induced long-lived germinal center reactions. Notably, a single low dose of M2ex3 I3-01v9a SApNP formulated with a potent adjuvant, either a Toll-like receptor 9 (TLR9) agonist or a stimulator of interferon genes (STING) agonist, conferred 90% protection against a lethal H1N1 challenge in mice. With the ability to induce robust and durable M2e-specific functional antibody and T cell responses, the M2ex3-presenting I3-01v9a SApNP provides a promising pan-influenza A vaccine candidate.

Discriminatory Ability and Clinical Utility of the AJCC7 and AJCC8 Staging Systems for Breast Cancer in a Middle-Income Setting

(1) Background: Differences in access to biomarker testing and cancer treatment in resource-limited settings may affect the clinical utility of the AJCC8 staging system compared to the anatomical AJCC7 system. (2) Methods: A total of 4151 Malaysian women who were newly diagnosed with breast cancer from 2010 to 2020 were followed-up until December 2021. All patients were staged using the AJCC7 and AJCC8 systems. Overall survival (OS) and relative survival (RS) were determined. Concordance-index was used to compare the discriminatory ability between the two systems. (3) Results: Migration from the AJCC7 to AJCC8 staging system resulted in the downstaging of 1494 (36.0%) patients and the upstaging of 289 (7.0%) patients. Approximately 5% of patients could not be staged using the AJCC8 classification. Five-year OS varied between 97% (Stage IA) and 66% (Stage IIIC) for AJCC7, and 96% (Stage IA) and 60% (Stage IIIC) for AJCC8. Concordance-indexes for predicting OS using the AJCC7 and AJCC8 models were 0.720 (0.694-0.747) and 0.745 (0.716-0.774), and for predicting RS they were 0.692 (0.658-0.728) and 0.710 (0.674-0.748), respectively. (4) Conclusions: Given the comparable discriminatory ability between the two staging systems in predicting the stage-specific survival of women with breast cancer in the current study, the continued use of the AJCC7 staging system in resource-limited settings seems pragmatic and justifiable.

Impact of COVID-19 pandemic on pancreatic cancer disparities and outcomes in Florida

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Background: Pancreatic cancer (PDAC) is the third-leading cause of cancer death in the United States. Florida had a high infection rate with several peaks throughout 2020 and 2021. The first aim of this study is to evaluate the impact of the COVID-19 pandemic on survival time, rate of surgical resection, and time to treatment of newly diagnosed pancreatic cancer in Florida. The second aim was to assess whether disparities with respect to race, age, income, and gender were exacerbated in newly diagnosed pancreatic cancer via stratified analysis of pandemic groups. Methods: This retrospective study included patients identified by OneFlorida+ Clinical Research Network, a statewide data trust, who were newly diagnosed with pancreatic adenocarcinoma via ICD 10 coding from January 1st, 2017 to October 31st, 2020. Patients were compared between 3 cohorts based on date of pancreatic cancer diagnosis: pre-pandemic (01/01/2017- 09/30/2019), transition (10/01/2019-02/28/2020), and pandemic (03/1/2020-10/31/2020). Patients with a diagnosis of neuroendocrine carcinoma were excluded. Results: 934 unique patients were identified for analysis, of whom 81.3% were in the pre-pandemic cohort, 8.2% in the transition cohort, and 10.5% in the pandemic cohort. The racial distribution was 19.4% African American, 70.2% Caucasian, 0.7% Asian, 8.2% of Other races, and 1.3% reported unknown race or refused to answer. The median age was 67 years (range, 27–89 years). Gender was even. The median income was $52,915 (range, $23,704–$124,821). The differences in overall survival were not significant for age and gender across the 3 groups. Patients with income <$53,000 had significantly lower survival time across all groups. African Americans had significantly lower survival time in the pre-pandemic and transition cohort (p< .005), but Caucasians had the lowest survival time for the pandemic group (p <.005). 60.2% of early-stage patients did not have surgery and the group distribution was 64.2% pre-pandemic, 48.5% transition, and 44.4% pandemic (p< 0.027). Time to treatment was not significant across all groups and demographics. Conclusions: This study found a decrease in diagnosis, survival rate for some groups, and surgical resection rates during the COVID-19 pandemic in Florida. Resource planning should target these disparities in income and race.[Table: see text]

Protocol for the Brain Health Support Program Study of the Canadian Therapeutic Platform Trial for Multidomain Interventions to Prevent Dementia (CAN-THUMBS UP): A Prospective 12-Month Intervention Study

BACKGROUND/OBJECTIVES

CAN-THUMBS UP is designed as a comprehensive and innovative fully remote program to 1) develop an interactive and compelling online Brain Health Support Program intervention, with potential to positively influence dementia literacy, self-efficacy and lifestyle risk factors; 2) enroll and retain a community-dwelling Platform Trial Cohort of individuals at risk of dementia who will participate in the intervention; 3) support an open platform trial to test a variety of multidomain interventions that might further benefit individuals at risk of dementia. This manuscript presents the Brain Health Support Program Study protocol.

DESIGN/SETTING

Twelve-month prospective multi-center longitudinal study to evaluate a fully remote web-based educational intervention. Participants will subsequently be part of a Platform Trial Cohort and may be eligible to participate in further dementia prevention clinical trials.

PARTICIPANTS

Three hundred fifty older adults who are cognitively unimpaired or have mild cognitive impairment, with at least 1 well established dementia risk factor.

INTERVENTION

Participants engage in the Brain Health Support Program intervention for 45-weeks and complete pre/post intervention measures. This intervention is designed to convey best available evidence for dementia prevention, consists of 181 chapters within 8 modules that are progressively delivered, and is available online in English and French. The program has been developed as a collaborative effort by investigators with recognized expertise in the program's content areas, along with input from older-adult citizen advisors.

MEASUREMENTS

This study utilizes adapted remote assessments with accessible technologies (e.g. videoconferencing, cognitive testing via computer and mobile phone, wearable devices to track physical activity and sleep, self-administered saliva sample collection). The primary outcome is change in dementia literacy, as measured by the Alzheimer's Disease Knowledge Scale. Secondary outcomes include change in self-efficacy; engagement using the online program; user satisfaction ratings; and evaluation of usability and acceptance. Exploratory outcomes include changes in attitudes toward dementia, modifiable risk factors, performance on the Neuropsychological Test Battery, performance on self-administered online cognitive assessments, and levels of physical activity and sleep; success of the national recruitment plan; and the distribution of age adjusted polygenic hazard scores.

CONCLUSIONS

This fully remote study provides an accessible approach to research with all study activities being completed in the participants' home environment. This approach may reduce barriers to participation, provide an easier and less demanding participant experience, and reach a broader geography with recruitment from all regions of Canada. CAN-THUMBS UP represents a Canadian contribution to the global World-Wide FINGERS program (alz.org/wwfingers).

Accumulation of marine litter in cold-water coral habitats: A comparative study of two Irish Special Areas of Conservation, NE Atlantic

Cold-water corals (CWCs) have come under threat from anthropogenic activities such as fishing despite their ecological significance as biodiversity hotspots and as such are being protected in Europe under the EU Habitats Directive with some designated as Special Areas of Conservation (SACs). This study maps the distribution and sources of marine litter in CWC habitats in two SACs on the Irish margin. Data were collected with remotely operated vehicle in the SACs. The density, abundance and composition of litter were assessed, with differences observed between the two sites. The regional morphology influences the distribution of litter in the SACs, with CWC reefs and rock exposures trapping more marine litter. Fishing gear (80.7%) and plastics (55.1%) were commonly found. The observed fisheries-derived litter in the SACs exceed global averages of 10-20% fishing gear, suggesting the SACs appear to offer limited protection to the coral habitats with respect to marine litter.

Results of the phase IIa RADICAL trial of the FGFR inhibitor AZD4547 in endocrine resistant breast cancer

We conducted a phase IIa, multi-centre, open label, single arm study (RADICAL; NCT01791985) of AZD4547 (a potent and selective inhibitor of Fibroblast Growth Factor Receptor (FGFR)-1, 2 and 3 receptor tyrosine kinases) administered with anastrozole or letrozole in estrogen receptor positive metastatic breast cancer patients who had become resistant to aromatase inhibitors. After a safety run-in study to assess safety and tolerability, we recruited 52 patients. The primary endpoint was change in tumour size at 12 weeks, and secondary endpoints were to assess response at 6 weeks, 20 weeks and every 8 weeks thereafter and tolerability of the combined treatment. Two partial responses (PR) and 19 stable disease (SD) patients were observed at the 12-week time point. At 28 weeks, according to centrally reviewed Response Evaluation Criteria in Solid Tumours (RECIST) criteria, five PR and 8 SD patients were observed in 50 assessable cases. Overall, objective response rate (5 PR) was of 10%, meeting the pre-specified endpoint. Fourteen patients discontinued due to adverse events. Eleven patients had retinal pigment epithelial detachments which was asymptomatic and reversible in all but one patient. Exploratory ribonucleic acid sequencing (RNA-Seq) analysis was done on patients' samples: 6 differentially-expressed-genes could distinguish those who benefited from the addition of AZD4547.

A health survey of the reef forming scleractinian cold-water corals Lophelia pertusa and Madrepora oculata in a remote submarine canyon on the European continental margin, NE Atlantic

Monitoring of cold-water corals (CWCs) for pathogens and diseases is limited due to the environment, protected nature of the corals and their habitat and as well as the challenging and sampling effort required. It is recognised that environmental factors such as temperature and pH can expedite the ability of pathogens to cause diseases in cold-water corals therefore the characterisation of pathogen diversity, prevalence and associated pathologies is essential. The present study combined histology and polymerase chain reaction (PCR) diagnostic techniques to screen for two significant pathogen groups (bacteria of the genus Vibrio and the protozoan Haplosporidia) in the dominant NE Atlantic deep-water framework corals Lophelia pertusa (13 colonies) and Madrepora oculata (2 colonies) at three sampling locations (canyon head, south branch and the flank) in the Porcupine Bank Canyon (PBC), NE Atlantic. One M. oculata colony and four L. pertusa colonies were collected from both the canyon flank and the south branch whilst five L. pertusa colonies were collected from the canyon head. No pathogens were detected in the M. oculata samples. Neither histology nor PCR detected Vibrio spp. in L. pertusa, although Illumina technology used in this study to profile the CWCs microbiome, detected V. shilonii (0.03%) in a single L. pertusa individual, from the canyon head, that had also been screened in this study. A macroborer was observed at a prevalence of 0.07% at the canyon head only. Rickettsiales-like organisms (RLOs) were visualised with an overall prevalence of 40% and with a low intensity of 1 to 4 (RLO) colonies per individual polyp by histology. L. pertusa from the PBC canyon head had an RLO prevalence of 13.3% with the highest detection of 26.7% recorded in the south branch corals. Similarly, unidentified cells observed in L. pertusa from the south branch (20%) were more common than those observed in L. pertusa from the canyon head (6.7%). No RLOs or unidentified cells were observed in corals from the flank. Mean particulate organic matter concentration is highest in the south branch (2,612 μg l^-1) followed by the canyon head (1,065 μg l^-1) and lowest at the canyon flank (494 μg l^-1). Although the route of pathogen entry and the impact of RLO infection on L. pertusa is unclear, particulate availability and the feeding strategies employed by the scleractinian corals may be influencing their exposure to pathogens. The absence of a pathogen in M. oculata may be attributed to the smaller number of colonies screened or the narrower diet in M. oculata compared to the unrestricted diet exhibited in L. pertusa, if ingestion is a route of entry for pathogen groups. The findings of this study also shed some light on how environmental conditions experienced by deep sea organisms and their life strategies may be limiting pathogen diversity and prevalence.

Co-Variation of Serum Osteoprotegerin and Pigment-Epithelial Derived Factor as Biomarker of Pancreatic Cancer

Pancreatic cancer is one the most lethal cancers. Currently, there are reliable predictive markers to assess cancer development. Widely used CA19-9 molecular marker has been less effective in the diagnosis of early stages of cancer.

OBJECTIVE

To study if the soluble Osteoprotegerin (OPG) and pigment-epithelial derived factor (PEDF) levels in serum will be an indicator of cancer progression.

METHODS

Soluble OPG and PEDF were measured from human pancreatic cancer patients by ELISA.

RESULTS

We show that while OPG has been less predictive features, PEDF is more sensitive than CA19-9 in cancer detection. More importantly, PEDF and CA19-9 as combined markers showed higher sensitivity in stratifying early stages of pancreatic cancer.

CONCLUSION

Results from the pilot studies suggest that PEDF is useful biomarker for pancreatic cancer.

Impact of shelter-in-place orders on TB case notifications and mortality in the Philippines during the COVID-19 pandemic

Background

Policies implemented to slow transmission of COVID-19 are expected to have disrupted delivery of routine health services, including tuberculosis (TB) care.

Methods

We analyzed daily counts of drug-susceptible (DS)-TB case notifications from all health facilities affiliated with the Philippines National TB Program (NTP) before and after implementation of community quarantine (January 1-December 31, 2020). Using an interrupted time series design, we assessed the immediate and sustained effects of community quarantine on TB case reporting. Using 2019 WHO estimates of national TB incidence, treatment, and mortality rates for the Philippines, we modeled excess mortality from TB, assuming a national decline in TB case reporting were extended for 12 months, followed by a return to pre-community quarantine trends.

Results

The analysis included 192,918 DS-TB case notifications from 2,986 facilities located in 113 provinces and highly urbanized cities across 17 regions and covered 49 observations days before and 174 days after community quarantine implementation. We found an significant drop and steeper decline in daily TB case notifications after the implementation of community quarantine, resulting in 44.6% (95% CI 38.3–50.1) fewer daily TB case notifications 60 days after implementation of community quarantine. During 2020, DS-TB case notifications never returned to pre-quarantine levels. Assuming a 12-month disruption of TB case reporting, we estimate there will be 56.3% increase in TB-related deaths in the Philippines.

Conclusion

Modified delivery of TB prevention and care should be prioritized alongside efforts to combat COVID-19.

1126 Improving Hand Trauma Clerking Using an Electronic Proforma: A Full Cycle Clinical Audit

Aim

The BSSH standards of care in hand trauma emphasise the importance of accurate and comprehensive documentation. This quality improvement project aimed to evaluate whether an electronic proforma could improve documentation rates in hand trauma.

Method

This prospective, closed-loop audit involved two cycles of seven consecutive days. Outcomes were evaluated against BSSH standards of care using 15 data points. Pre-audit, a bespoke proforma was piloted in the hand trauma clinic and revised following feedback.

In the first cycle (‘Loop 1’), documentation in the hand trauma clinic was compared with that of the acute take, where clinicians were still using free text. The second cycle (‘Loop 2’) compared documentation pre- and post-introduction of the proforma within the acute take setting. Categorical data were interrogated using the χ2 test with significance set at p &lt; 0.05.

Results

122 patients were included in the Loop 1 dataset. Free text clerking quality varied between clinician groups (e.g., surgical trainees significantly outperformed advanced nurse practitioners in 5/15 data points); however, some data points were universally poorly documented. 99 patients were included in the Loop 2 dataset. There was excellent uptake of the proforma in both acute take (95%) and hand trauma clinic (100%) settings. Statistically significant improvements were seen in 11/15 data points following the introduction of the proforma.

Conclusions

This project demonstrates that the introduction of a hand trauma clerking proforma led to significant improvements in documentation quality. The proforma has now been developed into a Trust-wide ClinDoc which brings additional benefits in terms of research, audit and service evaluation.

Rare incidence of cholecystocolonic fistula and robotic-assisted surgical management

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This case report aims to highlight intraoperative management of the fistula and review the existing literature.

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Cholecystocolonic fistulas are one of the rare complications associated with gallstone disease.

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Close evaluation of patient imaging studies and clinical presentation is of utmost importance.

We present a patient who was found to have a cholecystocolonic fistula during robotic cholecystectomy. The patient initially presented with Non-ST-elevation myocardial infarction (NSTEMI) and biliary obstruction. A delayed cholecystectomy was performed robotically after managing his Coronary Artery Disease (CAD) and relief of his biliary obstruction with endoscopic retrograde cholangiopancreatography (ERCP). Intraoperatively, a cholecystocolonic fistula, was found. This case report aims to highlight intraoperative management of the fistula and review the existing literature.

A generative co-design framework for healthcare innovation: development and application of an end-user engagement framework

Background Continual improvements to health systems, products, and services are necessary for improvements in health. However, many of these improvements are not incorporated into everyday practice. When designing new health systems, products, and services, involving members of the healthcare community and the public with personal healthcare experience can help to make sure that improvements will be useful and relevant to others like them. Methods Together with healthcare workers and family members with healthcare experience, we developed and applied a step-by-step guide to involving those with personal experience in the design of health system improvements. Results Our guide has three phases- 'Pre-Design', 'Co-Design', and 'Post-Design'. This paper describes each of these phases and illustrates how we applied them to our own project, which is to use virtual healthcare methods to improve care for children with chronic healthcare conditions and their families. In our own work, we found that healthcare workers and family members with personal healthcare experiences were able to use their knowledge and creativity to help us imagine how to improve care for children with chronic healthcare conditions and their families. We have created action items from these family member- and healthcare worker-identified needs, which we will use to shape our virtual healthcare system. Conclusions This paper may be useful for those seeking to involve members of the healthcare community and the public in the creation of better healthcare systems, products, and services. Background Challenges with the adoption, scale, and spread of health innovations represent significant gaps in the evidence-to-practice cycle. In the health innovation design process, a lack of attention paid to the needs of end-users, and subsequent tailoring of innovations to meet these needs, is a possible reason for this deficit. In the creative field of health innovation, which includes the design of healthcare products, systems (governance and organization mechanisms), and services (delivery mechanisms), a framework for both soliciting the needs of end-users and translating these needs into the design of health innovations is needed. Methods To address this gap, our team developed and applied a seven-step methodological framework, called A Generative Co-Design Framework for Healthcare Innovation. This framework was developed by an interdisciplinary team that included patient partners. Results This manuscript contributes a framework and applied exemplar for those seeking to engage end-users in the creative process of healthcare innovation. Through the stages of 'Pre-Design', 'Co-Design', and 'Post-Design', we were able to harness the creative insights of end-users, drawing on their experiences to shape a future state of care. Using an expository example of our own work, the DigiComp Kids project, we illustrate the application of each stage of the Framework. Conclusions A Generative Co-Design Framework for Healthcare Innovation provides healthcare innovators, applied health science researchers, clinicians, and quality improvement specialists with a guide to eliciting and incorporating the viewpoints of end-users while distilling practical considerations for healthcare innovation and design.

Multimodality treatment of intracranial arteriovenous malformations in South Island, New Zealand

Treatment of intracranial arteriovenous malformations is complex and multidisciplinary. This article presents the treatment model utilized in Christchurch, New Zealand which provides cerebrovascular surgery and interventional neuroradiology to the entire south island (approximate population of 1.1 million). A total of 40 patients treated over a 10 year period (2004-2014) are analysed here. Nine patients were managed surgically and complete resection was achieved in 100% of cases. Permanent mortality was 0% and permanent morbidity was 22% however median mRS improved from 3.0 preoperatively to 1.0 at follow up. Embolisation was utilized in 31 patients (mean age 40), of which 45% presented with haemorrhage, 39% with seizures, 10% with a headache only, and 6% with a deficit. None were found incidentally. The Spetzler-Martin grade 1 cases accounted for 10% of the cohort, 23% were grade II, 42% grade III, 23% grade IV and 3% grade V. A single aneurysm was present in 42% of cases, and multiple in 13%. The nidus was obliterated in 9.6% of cases with a morbidity rate of 6.5% and mortality rate of 3%. Modified Rankin scale improved marginally from 0.9 at diagnosis to 0.88 at final follow up (mean 22 months). There were no cases of recanalization. The total nidus obliteration rate using our algorithm of surgery alone for small accessible lesions, then staged embolization for larger lesions with adjuvant radiosurgery reserved for cases with residual nidus, was 50%.

Ultrasound-based liver elastography in the assessment of fibrosis

Ultrasound-based elastography has rapidly replaced the need for liver biopsy in most patients with chronic liver disease in recent years. The technique is now widely supported by many manufacturers. This review will introduce various current ultrasound-based elastography techniques, review the physics and scanning techniques, discuss potential cofounding factors as well as summarising the evidence for its use in staging liver fibrosis using shear-wave elastography among different disease aetiologies. Future challenges and directions will be also be discussed.

Safety assessment of the biotechnologically produced human-identical milk oligosaccharide 3-Fucosyllactose (3-FL)

3-Fucosyllactose (3-FL), a highly abundant complex carbohydrate in human breast milk, functions as a prebiotic promoting early microbial colonization of the gut, increasing pathogen resistance and modulating immune responses. To investigate potential health benefits, 3-FL was produced by fermentation using a genetically modified E. coli K12 strain. The safety assessment of 3-FL included acute oral toxicity, in vitro and in vivo assessment of genetic toxicity, and a subchronic rodent feeding study. 3-FL was not acutely toxic at 5000 mg/kg bw, and there was no evidence of genetic toxicity in the bacterial reverse mutation test and chromosomal aberration assay. There was a repeatable statistically-significant trend in the 4-h S9-activated test conditions in the in vitro micronucleus assay; the confirmatory in vivo mouse micronucleus study was negative at all doses. Dietary subchronic exposure of rats to 3-FL (5% and 10%) did not produce any statistical or biologically-relevant differences in growth, food intake or efficiency, clinical observations, or clinical or anatomic pathology changes at average daily intakes of 5.98 and 7.27 g/kg bw/day for males and females, respectively. The weight of evidence from these studies support the safe use of 3-FL produced using biotechnology as a nutritional ingredient in foods.

Pan-Genomic and Polymorphic Driven Prediction of Antibiotic Resistance in Elizabethkingia

The Elizabethkingia are a genetically diverse genus of emerging pathogens that exhibit multidrug resistance to a range of common antibiotics. Two representative species, Elizabethkingia bruuniana and E. meningoseptica, were phenotypically tested to determine minimum inhibitory concentrations (MICs) for five antibiotics. Ultra-long read sequencing with Oxford Nanopore Technologies (ONT) and subsequent de novo assembly produced complete, gapless circular genomes for each strain. Alignment based annotation with Prokka identified 5,480 features in E. bruuniana and 5,203 features in E. meningoseptica, where none of these identified genes or gene combinations corresponded to observed phenotypic resistance values. Pan-genomic analysis, performed with an additional 19 Elizabethkingia strains, identified a core-genome size of 2,658,537 bp, 32 uniquely identifiable intrinsic chromosomal antibiotic resistance core-genes and 77 antibiotic resistance pan-genes. Using core-SNPs and pan-genes in combination with six machine learning (ML) algorithms, binary classification of clindamycin and vancomycin resistance achieved f1 scores of 0.94 and 0.84, respectively. Performance on the more challenging multiclass problem for fusidic acid, rifampin and ciprofloxacin resulted in f1 scores of 0.70, 0.75, and 0.54, respectively. By producing two sets of quality biological predictors, pan-genome genes and core-genome SNPs, from long-read sequence data and applying an ensemble of ML techniques, our results demonstrated that accurate phenotypic inference, at multiple AMR resolutions, can be achieved.

Nanopore ultra-long read sequencing technology for antimicrobial resistance detection in Mannheimia haemolytica

Disruptive innovations in long-range, cost-effective direct template nucleic acid sequencing are transforming clinical and diagnostic medicine. A multidrug resistant strain and a pan-susceptible strain of Mannheimia haemolytica, isolated from pneumonic bovine lung samples, were sequenced at 146× and 111× coverage, respectively with Oxford Nanopore Technologies MinION. De novo assembly produced a complete genome for the non-resistant strain and a nearly complete assembly for the drug resistant strain. Functional annotation using RAST (Rapid Annotations using Subsystems Technology), CARD (Comprehensive Antibiotic Resistance Database) and ResFinder databases identified genes conferring resistance to different classes of antibiotics including β-lactams, tetracyclines, lincosamides, phenicols, aminoglycosides, sulfonamides and macrolides. Resistance phenotypes of the M. haemolytica strains were determined by minimum inhibitory concentration (MIC) of the antibiotics. Sequencing with a highly portable MinION device corresponded to MIC assays with most of the antimicrobial resistant determinants being identified with as few as 5437 reads, except for the genes responsible for resistance to Fluoroquinolones. The resulting quality assemblies and AMR gene annotation highlight the efficiency of ultra-long read, whole-genome sequencing (WGS) as a valuable tool in diagnostic veterinary medicine.

Dose intensity of nab-paclitaxel and gemcitabine chemotherapy in metastatic pancreatic cancer

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Background: Combination chemotherapy with nab-paclitaxel/gemcitabine is a standard of care option in metastatic pancreatic cancer management with increasing use due to an improvement in median overall survival of 1.8 months compared to gemcitabine alone. It is also used in practice in the second and third-line settings for patients that have progressed on fluorouracil based regimens. As the utility of this combination chemotherapy has grown, dose intensity (DI) in relation to survival outcome is an important measure for real world application. Methods: Fifty-six patients that were 18 years or older with metastatic pancreatic cancer treated with nab-paclitaxel/gemcitabine as first-line therapy from January 1, 2013 to December 31, 2014 at Moffitt Cancer Center were identified through medical records. The subjects were retrospectively reviewed, and demographic, treatment outcomes (survival and progression), and DI were collected. Overall survival was calculated with Kaplan Meier survival curves. Multi-Cox regression models estimated multivariable-adjusted hazard ratio with 95% confidence intervals. Results: There was no significant relationship between receiving a DI > 85% regimen in relation to independent variables of age > 65, sex, primary site, and known distant metastasis; however DI > 85% was significant for patients that received additional chemotherapy following nab-paclitaxel/gemcitabine (p = 0.044). The DI > 85% group compared to the < 85% group had a hazard ratio (HR) for all-cause mortality of 0.285 (0.106-0.764, p = 0.013). Six and 12-month survival were higher in the DI > 85% group (p = 0.009, p = 0.02 respectively). Conclusions: DI > 85% for nab-paclitaxel/gemcitabine compared to DI < 85% may have a lower all-cause mortality and higher 6 and 12-month survival.

Video-tube thoracostomy in trauma resuscitation: A pilot study

BACKGROUND

Complications related to incorrect positioning of tube thoracostomy (TT) have been reported to be as high as 30%. The aim of this study was to assess the feasibility of flexible videoscope guided placement of a pre-loaded chest tube, permitting direct intrapleural visualization and placement (Video-Tube Thoracostomy [V-TT]).

METHODS

A prospective, single centre, phase 1 pilot study with a parallel control group was undertaken. The population studied were adult thoracic trauma patients requiring emergency TT who were haemodynamically stable. The intervention performed was VTT. Patients in the control group underwent conventional TT. The primary outcome was tube position as defined by a consultant radiologist's interpretation of chest x-ray (CXR) or CT. The trial was registered with ANZCTR.org.au (ACTRN: 12,615,000,870,550).

RESULTS

There were 37 patients enrolled in the study - 12 patients allocated to the VTT intervention group and 25 patients allocated to conventional TT. Mean age of participants was 48 years (SD 15) in intervention group and 46 years (SD 15) years in the control group. In the VTT group all patients were male; the indications were pneumothorax (83%), haemothorax (8%) and haemopneumothorax (8%). The median injury severity score was 23 (16-28). There were 1 positional and 1 insertional complications. In the control group 72% of patients were male, the indications were pneumothorax (56%), haemothorax (4%) and haemopneumothorax (40%). The median injury severity score was 24 (14-36). There were 8 (32%) positional complications and no insertional complications.

CONCLUSION

V-TT was demonstrated to be a feasible alternative to conventional thoracostomy and merits further investigation.

Respiratory syncytial virus (RSV) infection in children with medical complexity

Children with medical complexity (CMC) are vulnerable to respiratory illness hospitalization (RIH) and respiratory syncytial virus (RSV)-related hospitalization (RSVH) due to multisystem disorders and compromised airways. It is unknown whether RSV prophylaxis is effective, or if RSVH is associated with significant morbidities in CMC. The study objectives were to (1) determine the incidence of RSV-related infection in prophylaxed CMC during the first 3 years of life and (2) assess the burden of illness following RSVH. A single tertiary center, retrospective study, was conducted of CMC who received palivizumab during the 2012-2016 RSV seasons. Fifty-four subjects were enrolled; most received one (38.9%, n = 21) or two (57.4%, n = 31) seasons of prophylaxis (mean = 4.2 [SD = 1.24], palivizumab doses per season). The cohort comprised children with multiple medical conditions (n = 22, 40.8%), tracheostomy (n = 18, 33.3%), and invasive (n = 10, 18.5%) or non-invasive (n = 4, 7.4%) ventilation. Of the CMC, 24 were hospitalized 47 times for a viral-related respiratory illness. RSV incidence in the first 3 years of life was 7.4%. Viral-related RIH and RSVH rates were 44.4% (n = 24/54) and 1.9% (n = 1/54), respectively. Of the four RSV-positive children, one was ventilated for 9 days, two acquired nosocomial RSV that was managed on the ward, and one was discharged home under close complex care supervision. All four RSV-positive cases required additional oxygen during their illness. CMC experience a high viral-related RIH rate and palivizumab likely minimizes RSV-related events and associated morbidities. The efficacy of palivizumab in CMC, especially in those ≤ 3 years, should be prospectively evaluated.

Permafrost thaw and climate warming may decrease the CO2, carbon, and metal concentration in peat soil waters of the Western Siberia Lowland

Soil pore waters are a vital component of the ecosystem as they are efficient tracers of mineral weathering, plant litter leaching, and nutrient uptake by vegetation. In the permafrost environment, maximal hydraulic connectivity and element transport from soils to rivers and lakes occurs via supra-permafrost flow (i.e. water, gases, suspended matter, and solutes migration over the permafrost table). To assess possible consequences of permafrost thaw and climate warming on carbon and Green House gases (GHG) dynamics we used a "substituting space for time" approach in the largest frozen peatland of the world. We sampled stagnant supra-permafrost (active layer) waters in peat columns of western Siberia Lowland (WSL) across substantial gradients of climate (-4.0 to -9.1°C mean annual temperature, 360 to 600mm annual precipitation), active layer thickness (ALT) (>300 to 40cm), and permafrost coverage (sporadic, discontinuous and continuous). We analyzed CO₂, CH₄, dissolved carbon, and major and trace elements (TE) in 93 soil pit samples corresponding to several typical micro landscapes constituting the WSL territory (peat mounds, hollows, and permafrost subsidences and depressions). We expected a decrease in intensity of DOC and TE mobilization from soil and vegetation litter to the supra-permafrost water with increasing permafrost coverage, decreasing annual temperature and ALT along a latitudinal transect from 62.3°N to 67.4°N. However, a number of solutes (DOC, CO₂, alkaline earth metals, Si, trivalent and tetravalent hydrolysates, and micronutrients (Mn, Co, Ni, Cu, V, Mo) exhibited a northward increasing trend with highest concentrations within the continuous permafrost zone. Within the "substituting space for time" climate change scenario and northward shift of the permafrost boundary, our results suggest that CO₂, DOC, and many major and trace elements will decrease their concentration in soil supra-permafrost waters at the boundary between thaw and frozen layers. As a result, export of DOC and elements from peat soil to lakes and rivers of the WSL (and further to the Arctic Ocean) may decrease.

Inhalational versus Propofol-Based Total Intravenous Anaesthesia: Practice Patterns and Perspectives among Australasian Anaesthetists

Increasing evidence suggests that total intravenous anaesthesia (TIVA) may be the preferred anaesthetic for cancer resection surgery. To assist the preparation of a randomised controlled trial (RCT) examining Volatile (versus TIVA) Anaesthesia and Perioperative Outcomes Related to Cancer (VAPOR-C) we developed an 18-question electronic survey to investigate practice patterns and perspectives (emphasising indications, barriers, and impact on cancer outcomes) of TIVA versus inhalational general anaesthesia in Australasia. The survey was emailed to 1,000 (of 5,300 active Fellows) randomly selected Australian and New Zealand College of Anaesthetists (ANZCA) Fellows. The response rate was 27.5% (n=275). Of the respondents, 18% use TIVA for the majority of cases. In contrast, 46% use TIVA 20% of the time or less. Respondents described indications for TIVA as high risk of nausea, neurosurgery, and susceptibility to malignant hyperthermia. Lack of equipment, lack of education and cost were not considered barriers to TIVA use, and a significant proportion (41%) of respondents would use TIVA more often if setup were easier. Of the respondents, 43% thought that TIVA was associated with less cancer recurrence than inhalational anaesthesia, while 46% thought that there was no difference. Yet, only 29% of respondents reported that they use TIVA often or very often for cancer surgery. In Australasia, there is generally a low frequency of TIVA use despite a perception of benefit when compared with inhalational anaesthesia. Anaesthetists are willing to use TIVA for indications where sufficient evidence supports a meaningful level of improvement in clinical outcome. The survey explores attitudes towards use of TIVA for cancer surgery and demonstrates equipoise in anaesthetists’ opinions regarding this indication. The inconsistent use of TIVA in Australasia, minimal barriers to its use, and the equipoise in anaesthetists’ opinions regarding the effect of TIVA versus inhalational anaesthesia on cancer outcomes support the need for a large prospective RCT.

Novel targeted treatment options for advanced cholangiocarcinoma

INTRODUCTION

Surgical resection remains the mainstay of potentially curative treatment in the early stages of cholangiocarcinoma, whereas for the advanced stage, systemic chemotherapeutics and experimental targeted therapies are the primary treatment options. The molecular heterogeneity of the tumor is based on location, liver dysfunction, and relative rarity of the disease and confers challenges for clinical trial enrollment. The advancements in the understanding of molecular pathogenesis of cholangiocarcinoma have led to the development of targeted therapies that are currently being evaluated in the clinical trials.

AREAS COVERED

This review summarizes the current understanding and future directions of targeted therapeutic options in the management of advanced cholangiocarcinoma.

EXPERT OPINION

Advanced cholangiocarcinoma has a dismal prognosis; improved understanding of the molecular pathogenesis and advancements in development of targeted therapy offers hope that we may improve outcomes in this rare, but highly lethal cancer. Among the newly discovered molecular alterations, targeting FGFR2 fusions, IDH1/2 mutations and HER2 receptors hold great promise for improving the future management of cholangiocarcinoma. Immunotherapy in combination with targeted agents and chemotherapy may improve outcomes. In addition, drugs targeting the MEK, EGFR, KRAS, BRAF, and ROS1 pathways and neo-angiogenesis may also provide new horizons in the management of cholangiocarcinoma.

Abstract PD2-04: Enhanced pre-operative axillary staging using intradermal microbubbles and contrast-enhanced ultrasound (CEUS) to identify and biopsy sentinel lymph nodes (SLN) in breast cancer is a reproducible technique and may characterise a group of patients who can completely avoid axillary surgery

Purpose

In patients with breast cancer, avoiding overtreatment of the axilla without compromising oncological outcomes is an important clinical goal. Previous work has suggested that patients with a normal grey-scale ultrasound and benign radiological core biopsy of SLN identified with CEUS are unlikely to have high volume axillary metastases. We therefore assessed the reproducibility of this biopsy technique in multiple centres and in 2 centres, measured the volume of axillary metastases at the end of primary surgical treatment in patients with a false negative SLN core biopsy.

Materials and Methods

Between 2010 and 2016 data were collected on patients with early breast cancer; 1361 from Maidstone Breast Clinic (1) (prospective, sequential), 376 from Tunbridge Wells Breast Clinic (2) (retrospective, sequential), 122 from Leeds Breast Clinic (3) (retrospective, selected) and 48 from Imperial College Healthcare (4) (prospective, selected). Patients at Centres 1 and 2 had a normal grey-scale axillary ultrasound. Patients had a CEUS SLN core biopsy procedure prior to axillary surgery (sentinel lymph node excision (SLNE)/axillary lymph node dissection (ALND)).

Results

SLN were successfully core biopsied (nodal tissue retrieved) in 80% (Centre 1), 79.5% (Centre 2), 77.5% (Centre 3) and 88% (Centre 4). Patients with invasive breast cancer and a successful SLN core biopsy went on to have primary surgical treatment, 816 (Centre 1), 215 (Centre 2), 80 (Centre 3) and 38 (Centre 4). As a test to identify all SLN metastases, the sensitivities were 47.5% (95% CI 39.9-55.1), 52.5% (95% CI 39.1-65.7), 46.4% (95% CI 27.5-66.1) and 45.5% (95% CI 16.7-76.6) respectively. Specificities; 99.7% (95% CI 98.9-100), 98.1 (95% CI 94.5-99.6), 100% (95% CI 93.2-100%) and 96.3% (95% CI 81-99.9) respectively. Negative predictive values; 87.3% (95% CI 84.6-89.6), 84.5% (95% CI 78.4-89.5), 86.9% (95% CI 82.4-90.3) and 86.2% (95% CI 78.4-91.5) respectively. At Centres 1 and 2, 13/637 (2%) and 6/183 (3%) respectively of patients with a benign microbubble/ CEUS SLN core biopsy had 2 or more LN macrometastases found at SLNE/ ALND.

Conclusion

The identification and biopsy of SLN using CEUS is a reproducible technique. Despite the low sensitivity, the negative predictive value is high and in a large cohort of patients from centres 1 and 2, only a small proportion of patients had 2 or more 2 lymph node macro metastases that were both occult on grey-scale ultrasound and missed by SLN core biopsy. In the era of axillary conservation, these results indicate that some patients may be suitable for complete radiological staging of the axilla and thus safely avoid axillary surgery.

Citation Format: Cox KL, Sharma N, Taylor-Phillips S, Weeks J, Mills P, Lim A, Haigh I, Sever A, Wallis M, DeSilva T, Hashem M. Enhanced pre-operative axillary staging using intradermal microbubbles and contrast-enhanced ultrasound (CEUS) to identify and biopsy sentinel lymph nodes (SLN) in breast cancer is a reproducible technique and may characterise a group of patients who can completely avoid axillary surgery [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD2-04.

Relationship between tumor-infiltrating lymphocytes (TIL) and absolute lymphocyte count (ALC) or lymphocyte to neutrophil ratio (LTN) in cholangiocarcinoma (CCA)

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Background: Tumor microenvironment is potentially a powerful predictive and prognostic marker of immunotherapy. The presence of CD8 TIL has been suggested as a predictive and prognostic marker of PD-1 inhibitor therapy in several malignancies. However, evaluation of TIL is not always feasible especially during or after immunotherapy. Therefore, easily accessible markers are needed for immune monitoring. In CCA, ALC and LTN in peripheral blood have been reported as prognostic factors. We evaluate the relationship between ALC or LTN and CD8 TILs in CCA. Methods: Formalin-fixed paraffin-embedded tumor samples from 41 patients with resected and histologically verified CCA between 1990 and 2015 were identified and immunohistochemically (IHC) stained with anti-CD8. Absolute lymphocyte and neutrophil count of the patients was obtained within 1 week before surgery. The association between ALC, LTN and CD8+ TIL status was investigated using unpaired Student t test and Spearman rank correlation. Results: The median age was 64 (41-85) with 53% male. 22%, 41% and 37% were stage I, II, and III respectively. In CD8 TIL positive, the average ALC was 1764 and in CD8 TIL negative, the average ALC was 2072. There was no significant difference between the two groups (p = 0.38). No difference of LTN was observed between CD8 TIL positive and negative tumors (0.39 vs 0.38, p = 0.69). The correlation between density of CD8 TILs and ALC or LTN was evaluated. No correlation was observed between CD8 TIL density and ALC (R = 0.02, P = 0.3) or LTN (R = 0.02, P = 0.8). Conclusions: ALC or LTN in peripheral blood may not predict CD8 TIL status in patients with CCA.