The complex polyploid genome architecture of sugarcane

Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

Sub-1.4 cm3 capsule for detecting labile inflammatory biomarkers in situ

Transient molecules in the gastrointestinal tract such as nitric oxide and hydrogen sulfide are key signals and mediators of inflammation. Owing to their highly reactive nature and extremely short lifetime in the body, these molecules are difficult to detect. Here we develop a miniaturized device that integrates genetically engineered probiotic biosensors with a custom-designed photodetector and readout chip to track these molecules in the gastrointestinal tract. Leveraging the molecular specificity of living sensors1, we genetically encoded bacteria to respond to inflammation-associated molecules by producing luminescence. Low-power electronic readout circuits2 integrated into the device convert the light emitted by the encapsulated bacteria to a wireless signal. We demonstrate in vivo biosensor monitoring in the gastrointestinal tract of small and large animal models and the integration of all components into a sub-1.4 cm3 form factor that is compatible with ingestion and capable of supporting wireless communication. With this device, diseases such as inflammatory bowel disease could be diagnosed earlier than is currently possible, and disease progression could be more accurately tracked. The wireless detection of short-lived, disease-associated molecules with our device could also support timely communication between patients and caregivers, as well as remote personalized care.

Emissions and energy impacts of the Inflation Reduction Act

Economy-wide emissions drop 43 to 48% below 2005 levels by 2035 with accelerated clean energy deployment.

Pan-sarbecovirus prophylaxis with human anti-ACE2 monoclonal antibodies

Human monoclonal antibodies (mAbs) that target the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein have been isolated from convalescent individuals and developed into therapeutics for SARS-CoV-2 infection. However, therapeutic mAbs for SARS-CoV-2 have been rendered obsolete by the emergence of mAb-resistant virus variants. Here we report the generation of a set of six human mAbs that bind the human angiotensin-converting enzyme-2 (hACE2) receptor, rather than the SARS-CoV-2 spike protein. We show that these antibodies block infection by all hACE2 binding sarbecoviruses tested, including SARS-CoV-2 ancestral, Delta and Omicron variants at concentrations of ~7-100 ng ml-1. These antibodies target an hACE2 epitope that binds to the SARS-CoV-2 spike, but they do not inhibit hACE2 enzymatic activity nor do they induce cell-surface depletion of hACE2. They have favourable pharmacology, protect hACE2 knock-in mice against SARS-CoV-2 infection and should present a high genetic barrier to the acquisition of resistance. These antibodies should be useful prophylactic and treatment agents against any current or future SARS-CoV-2 variants and might be useful to treat infection with any hACE2-binding sarbecoviruses that emerge in the future.

Current intraoperative storage and handling practices of autologous bypass conduit: A survey of the royal australasian college of surgeons

During bypass surgery for peripheral arterial occlusive disease and ischaemic heart disease, autologous graft conduit including great saphenous veins and radial arteries are frequently stored in solution. Endothelial damage adversely affects the performance and patency of autologous bypass grafts, and intraoperative graft storage solutions have been shown to influence this process. The distribution of storage solutions currently used amongst Cardiothoracic and Vascular Surgeons from Australia and New Zealand is not well defined in the literature. The aim of this study was to determine current practices regarding autologous graft storage and handling amongst this cohort of surgeons, and discuss their potential relevance in the context of early graft failure. From this survey, the most frequently used storage solutions were heparinized saline for great saphenous veins, and pH-buffered solutions for radial arteries. Duration of storage was 30–45 min for almost half of respondents, although responses to this question were limited. Further research is required to investigate whether ischaemic endothelial injury generates a prothrombotic state, whether different storage media can alter this state, and whether this is directly associated with clinical outcomes of interest such as early graft failure.

Challenges and opportunities of remote public involvement and community engagement during a pandemic: refining the MapMe childhood healthy weight intervention

AIMS

Including parents and other stakeholders in the development of interventions to address the sensitive public health issues such as childhood obesity, through public involvement is critical. However, the Covid-19 pandemic has created a challenge for public involvement and engagement activities (PICE). The aim of this paper is to describe the process and challenges of setting up, maintaining, evaluating, and recording impact of three public and stakeholder groups via remote methods in the context of the MapMe2 study during the Covid-19 pandemic. Parental reaction to result letters received as part of the National Child Measurement Programme (NCMP) informing parents of their child's overweight status is often one of hostility or disbelief. As a result, parents often do not act on these letters to address child overweight. The MapMe2 study is working in collaboration with the NCMP and local authorities, building on previous work (MapMe) and aims to support parents of primary school-aged children to recognise and maintain a healthy weight in their child. The existing MapMe Intervention includes an enhanced NCMP child weight result letter, supplemented with Body Image Scales (BIS), and an intervention website with material to support healthy eating, physical activity, and signposting supporting information. The intervention was to be refined and the evaluation informed with PICE input.

METHODS

Covid-19 restrictions meant that planned face-to-face PICE methods had to be altered with all recruitment, all correspondence, and activities taking place remotely. A Parent Involvement Panel (PIP), a child panel, and an expert panel were established. Several adaptations were made to accommodate a new way of involving the public in research.

RESULTS/CONCLUSIONS

Working remotely created many challenges and was a learning experience for all involved. However, an active group was successfully established. Using continuous assessment and evaluation methods, we were able to demonstrate successful involvement and engagement in the refinement of the MapMe2 study. Through the sharing of PICE methods practice, this paper adds to the literature, the value of partnership working.

Insights into complex nanopillar-bacteria interactions: Roles of nanotopography and bacterial surface proteins

Nanopillared surfaces have emerged as a promising strategy to combat bacterial infections on medical devices. However, the mechanisms that underpin nanopillar-induced rupture of the bacterial cell membrane remain speculative. In this study, we have tested three medically relevant poly(ethylene terephthalate) (PET) nanopillared-surfaces with well-defined nanotopographies against both Gram-negative and Gram-positive bacteria. Focused ion beam scanning electron microscopy (FIB-SEM) and contact mechanics analysis were utilised to understand the nanobiophysical response of the bacterial cell envelope to a single nanopillar. Given their importance to bacterial adhesion, the contribution of bacterial surface proteins to nanotopography-mediated cell envelope damage was also investigated. We found that, whilst cell envelope deformation was affected by the nanopillar tip diameter, the nanopillar density affected bacterial metabolic activities. Moreover, three different types of bacterial cell envelope deformation were observed upon contact of bacteria with the nanopillared surfaces. These were attributed to bacterial responses to cell wall stresses resulting from the high intrinsic pressure caused by the engagement of nanopillars by bacterial surface proteins. Such influences of bacterial surface proteins on the antibacterial action of nanopillars have not been previously reported. Our findings will be valuable to the improved design and fabrication of effective antibacterial surfaces.

Comparison of peak wall stress and peak wall rupture index in ruptured and asymptomatic intact abdominal aortic aneurysms

BACKGROUND

Previous studies have suggested that finite element analysis (FEA) can estimate the rupture risk of an abdominal aortic aneurysm (AAA); however, the value of biomechanical estimates over measurement of AAA diameter alone remains unclear. This study aimed to compare peak wall stress (PWS) and peak wall rupture index (PWRI) in participants with ruptured and asymptomatic intact AAAs.

METHODS

The reproducibility of semiautomated methods for estimating aortic PWS and PWRI from CT images was assessed. PWS and PWRI were estimated in people with ruptured AAAs and those with asymptomatic intact AAAs matched by orthogonal diameter on a 1 : 2 basis. Spearman's correlation coefficient was used to assess the association between PWS or PWRI and AAA diameter. Independent associations between PWS or PWRI and AAA rupture were identified by means of logistic regression analyses.

RESULTS

Twenty individuals were included in the analysis of reproducibility. The main analysis included 50 patients with an intact AAA and 25 with a ruptured AAA. Median orthogonal diameter was similar in ruptured and intact AAAs (82·3 (i.q.r. 73·5-92·0) versus 81·0 (73·2-92·4) mm respectively; P = 0·906). Median PWS values were 286·8 (220·2-329·6) and 245·8 (215·2-302·3) kPa respectively (P = 0·192). There was no significant difference in PWRI between the two groups (P = 0·982). PWS and PWRI correlated positively with orthogonal diameter (both P < 0·001). Participants with high PWS, but not PWRI, were more likely to have a ruptured AAA after adjusting for potential confounders (odds ratio 5·84, 95 per cent c.i. 1·22 to 27·95; P = 0·027). This association was not maintained in all sensitivity analyses.

CONCLUSION

High aortic PWS had an inconsistent association with greater odds of aneurysm rupture in patients with a large AAA.

293 Enhancing Your Recovery: A Mobile Application for Patients Undergoing Vascular Surgery

Aim:

With increasing demands on the healthcare system, a central (and currently essential) push for remote consultations, and an increasing number of co morbidities in the surgical population, the aim was to create an application that placed the focus on pre-hospital optimisation, education and autonomy – addressing these sector trends to enhance outcomes for patients and ease the burden on healthcare settings.

Method

After obtaining baseline data, I worked alongside students from the Queensland University of Technology to produce an application suitable for both iOS and android platforms.

Results

The application has four facets which mirror a patient’s journey from their initial outpatient appointment through to recovery. The application is easy to use, free to download and readily accessible. On opening the application, the user can select their planned operation and navigate along a personalised decision tree.

Conclusions

The application has been designed to educate and empower a patient to become an active participant in their care, leading to long-term changes in healthcare. Assessment is ongoing but early indications suggest that this will be a valuable tool in optimising outcomes for patients undergoing vascular surgery – leading to fewer post-operative complications and earlier restoration of functional status.

Residual lymph node tumour burden following removal of a single axillary sentinel lymph with macrometastatic disease in women with screen-detected invasive breast cancer

Background

Women with screen-detected invasive breast cancer who have macrometastatic disease on axillary sentinel lymph node biopsy (SLNB) are usually offered either surgical axillary node clearance (ANC) or axillary radiotherapy. These treatments can lead to significant complications for patients. The aim of this study was to identify a group of patients who may not require completion ANC.

Methods

Data from the NHS Breast Screening Programme between 1 April 2012 and 31 March 2017 were interrogated to identify women with invasive breast carcinoma and a single sentinel lymph node (SLN) with macrometastatic disease who subsequently proceeded to completion ANC. Univariable and multivariable analyses were performed to identify patients with a single positive SLN who had no further lymph node metastasis on ANC.

Results

Of the 2401 women included in the cohort, the presence of non-sentinel node disease was significantly affected by: the number of nodes obtained at SLNB (odds ratio (OR) 0.49 for retrieval of more than 1 node), invasive size of tumour (OR 1.63 for size greater than 20 mm), surgical treatment (OR 1.34 for mastectomy), human epidermal growth factor receptor (HER) 2 status (OR 0.71 for HER2 positivity), and patient age (OR 1.10 for age less than 50 years; OR 1.46 for age greater than 70 years). Patients aged less than 70 years, with tumour size smaller than 2 cm, more than one node retrieved on SLNB, and who had breast-conserving surgery had a lower chance of positive non-sentinel nodes on completion ANC compared with other patients.

Conclusion

This study, of a purely screen-detected breast cancer cohort, identified a subset of patients who may be spared completion ANC in the event of a single axillary SLN with macrometastasis.

Antibacterial effects of nanopillar surfaces are mediated by cell impedance, penetration and induction of oxidative stress

Some insects, such as dragonflies, have evolved nanoprotrusions on their wings that rupture bacteria on contact. This has inspired the design of antibacterial implant surfaces with insect-wing mimetic nanopillars made of synthetic materials. Here, we characterise the physiological and morphological effects of mimetic titanium nanopillars on bacteria. The nanopillars induce deformation and penetration of the Gram-positive and Gram-negative bacterial cell envelope, but do not rupture or lyse bacteria. They can also inhibit bacterial cell division, and trigger production of reactive oxygen species and increased abundance of oxidative stress proteins. Our results indicate that nanopillars' antibacterial activities may be mediated by oxidative stress, and do not necessarily require bacterial lysis.

Evaluation of VIDAS Listeria monocytogenes II (LMO2) Immunoassay Method for the Detection of Listeria monocytogenes in Foods: Collaborative Study

A multilaboratory study was conducted to compare the VIDAS®Listeria monocytogenes II (LMO2) immunoassay and the standard cultural methods for the detection of Listeria monocytogenes in foods. Five food types—vanilla ice cream, brie cheese, cooked roast beef, frozen green beans, and frozen tilapia fish—at 3 levels were analyzed by each method. A total of 26 laboratories representing government and industry participated. In this study, 1404 test portions were analyzed of which 1152 were used in the statistical analysis. There were 448 positive by the VIDAS LMO2 assay and 457 positive by the standard culture methods. A χ2 analysis of each of the 5 food types, at the 3 inoculation levels tested, was performed. The resulting χ2 value, 0.36, indicates that overall, there are no statistical differences between the VIDAS LMO2 assay and the standard methods at the 5% level of significance.

Evaluation of the VIDAS® Listeria (LIS) Immunoassay for the Detection of Listeria in Foods Using Demi-Fraser and Fraser Enrichment Broths, as Modification of AOAC Official Method 999.06 (AOAC Official Method 2004.06)

A multilaboratory study was conducted to compare the VIDAS® LIS immunoassay with the standard cultural methods for the detection of Listeria in foods using an enrichment modification of AOAC Official Method 999.06. The modified enrichment protocol was implemented to harmonize the VIDAS LIS assay with the VIDAS LMO2 assay. Five food types—brie cheese, vanilla ice cream, frozen green beans, frozen raw tilapia fish, and cooked roast beef—at 3 inoculation levels, were analyzed by each method. A total of 15 laboratories representing government and industry participated. In this study, 1206 test portions were tested, of which 1170 were used in the statistical analysis. There were 433 positive by the VIDAS LIS assay and 396 positive by the standard culture methods. A Chi-square analysis of each of the 5 food types, at the 3 inoculation levels tested, was performed. The resulting average Chi square analysis, 0.42, indicated that, overall, there are no statistical differences between the VIDAS LIS assay and the standard methods at the 5% level of significance.

Evaluation of the BAX® System for Detection of Listeria monocytogenes in Foods: Collaborative Study

A multilaboratory study was conducted to compare the automated BAX® system and the standard cultural methods for detection of Listeria monocytogenes in foods. Six food types (frankfurters, soft cheese, smoked salmon, raw, ground beef, fresh radishes, and frozen peas) were analyzed by each method. For each food type, 3 inoculation levels were tested: high (average of 2 CFU/g), low (average of 0.2 CFU/g) and uninoculated controls. A total of 25 laboratories representing government and industry participated. Of the 2335 samples analyzed, 1109 were positive by the BAX system and 1115 were positive by the standard method. A Chi square analysis of each of the 6 food types, at the 3 inoculation levels tested, was performed. For all foods, except radishes, the BAX system performed as well as or better than the standard reference methods based on the Chi square results.

Evaluation of the BAX® System for Detection of Salmonella in Selected Foods: Collaborative Study

A multilaboratory study was conducted to compare the automated BAX® System to the standard cultural methods for detection of Salmonella in selected foods. Five food types—frankfurters, raw ground beef, mozzarella cheese, raw frozen tilapia fish, and orange juice—at 3 inoculation levels, were analyzed by each method. A sixth food type, raw ground chicken, was tested using 3 naturally contaminated lots. A total of 16 laboratories representing government and industry participated. In this study, 1386 samples were analyzed, of which 1188 were paired samples and 198 were unpaired samples. Of the 1188 paired samples, 461 were positive by both methods and 404 were negative by both methods. Thirty-seven samples were positive by the BAX System but negative by the standard reference method, and 11 samples were positive by standard cultural method and negative by the BAX System. Of the 198 unpaired samples, 106 were positive by the BAX System and 60 were positive by the standard cultural method. A Chi square analysis of each of the 6 food types, at the 3 inoculation levels tested, was performed. For all foods, the BAX System demonstrated results comparable to those of the standard reference methods based on the Chi square results.

Long-term survival of pig-to-rhesus macaque renal xenografts is dependent on CD4 T cell depletion

The shortage of available organs remains the greatest barrier to expanding access to transplant. Despite advances in genetic editing and immunosuppression, survival in experimental models of kidney xenotransplant has generally been limited to <100 days. We found that pretransplant selection of recipients with low titers of anti-pig antibodies significantly improved survival in a pig-to-rhesus macaque kidney transplant model (6 days vs median survival time 235 days). Immunosuppression included transient pan-T cell depletion and an anti-CD154-based maintenance regimen. Selective depletion of CD4⁺ T cells but not CD8⁺ T cells resulted in long-term survival (median survival time >400 days vs 6 days). These studies suggested that CD4⁺ T cells may have a more prominent role in xenograft rejection compared with CD8⁺ T cells. Although animals that received selective depletion of CD8⁺ T cells showed signs of early cellular rejection (marked CD4⁺ infiltrates), animals receiving selective CD4⁺ depletion exhibited normal biopsy results until late, when signs of chronic antibody rejection were present. In vitro study results suggested that rhesus CD4⁺ T cells required the presence of SLA class II to mount an effective proliferative response. The combination of low pretransplant anti-pig antibody and CD4 depletion resulted in consistent, long-term xenograft survival.

An analysis of 11.3 million screening tests examining the association between needle biopsy rates and cancer detection rates in the English NHS Breast Cancer Screening Programme

AIM

To examine the association between recall, needle biopsy, and cancer detection rates to inform the setting of target ranges to optimise the benefit to harm ratio of breast screening programmes.

MATERIALS AND METHODS

Annual screening programme information from 2009/10 to 2015/16 for the 80 screening units of the English National Health Service Breast Screening Programme (totalling 11.3 million screening tests) was obtained from annual (KC62) returns. Linear regression models were used to examine the association between needle biopsy rates and recall rates and non-linear regression models to examine the association between cancer detection rates and needle biopsy rates.

RESULTS

The models show and quantify the diminishing returns for prevalent screens with increasing biopsy rates. A biopsy rate increase from 10 to 20 per 1,000 increases the cancer detection rate by 2.13 per 1,000 with four extra biopsies per extra cancer detected. Increasing the biopsy rate from 40 to 50 per 1,000, increases the cancer detection rate by only 0.25 per 1,000, with 40 extra biopsies per extra cancer detected. Although diminishing returns are also seen at incident screens, screening is generally more efficient.

CONCLUSIONS

Increasing needle biopsy rates leads to rapidly diminishing returns in cancer detection and a marked increase in non-malignant/benign needle biopsies. Much of the harms associated with screening in terms of false-positive recall rates and non-cancer biopsies occur at prevalent screens with much lower rates at incident screens. Needle biopsy rate targets should be considered together with recall rate targets to maximise benefit and minimise harm.

Incidental diagnosis of tuberous sclerosis complex by exome sequencing in three families with subclinical findings

Tuberous sclerosis complex (TSC) is an autosomal-dominant neurocutaneous disorder characterized by lesions and benign tumors in multiple organ systems including the brain, skin, heart, eyes, kidneys, and lungs. The phenotype is highly variable, although penetrance is reportedly complete. We report the molecular diagnosis of TSC in individuals exhibiting extreme intra-familial variability, including the incidental diagnosis of asymptomatic family members. Exome sequencing was performed in three families, with probands referred for epilepsy, autism, and absent speech (Family 1); epileptic spasms (Family 2); and connective tissue disorders (Family 3.) Pathogenic variants in TSC1 or TSC2 were identified in nine individuals, including relatives with limited or no medical concerns at the time of testing. Of the nine individuals reported here, six had post-diagnosis examinations and three met clinical diagnostic criteria for TSC. One did not meet clinical criteria for a possible or definite diagnosis of TSC, and two had only a possible clinical diagnosis following post-diagnosis workup. These individuals as well as their mothers demonstrated limited features that would not raise concern for TSC in the absence of molecular results. In addition, three individuals exhibited epilepsy with normal brain MRIs, and two without seizures or intellectual disability had MRI findings fulfilling major criteria for TSC highlighting the difficulty providers face when relying on clinical criteria to guide genetic testing. Given the importance of a timely TSC diagnosis for clinical management, such cases demonstrate a potential benefit for clinical criteria to include seizures and an unbiased molecular approach to genetic testing.

Role of performance metrics in breast screening imaging - where are we and where should we be?

The NHS Breast Screening Programme (NHSBSP) was started in 1988 and is a large, organised cancer screening programme. It is delivered by 80 services across England and screens over 2 million women each year. As a screening programme, it must balance the detection of cancers against possible harm to women who do not have cancer. The NHSBSP was therefore designed with detailed information gathering and performance metrics right from the start. In this review paper, we examine how performance metrics in screening mammography have improved the national screening programme and the further developments and challenges that are expected in the years to come.

Risk of major amputation in patients with intermittent claudication undergoing early revascularization

BACKGROUND

Revascularization is being used increasingly for the treatment of intermittent claudication and yet few studies have reported the long-term outcomes of this strategy. The aim of this study was to compare the long-term outcome of patients with intermittent claudication who underwent revascularization compared with a group initially treated without revascularization.

METHODS

Patients with symptoms of intermittent claudication and a diagnosis of peripheral arterial disease were recruited from outpatient clinics at three hospitals in Queensland, Australia. Based on variation in the practices of different vascular specialists, patients were either treated by early revascularization or received initial conservative treatment. Patients were followed in outpatient clinics using linked hospital admission record data. The primary outcome was the requirement for major amputation. Kaplan-Meier curves, Cox regression and competing risks analyses were used to compare major amputation rates.

RESULTS

Some 456 patients were recruited; 178 (39·0 per cent) underwent early revascularization and 278 (61·0 per cent) had initial conservative treatment. Patients were followed for a mean(s.d.) of 5·00(3·37) years. The estimated 5-year major amputation rate was 6·2 and 0·7 per cent in patients undergoing early revascularization and initial conservative treatment respectively (P = 0·003). Early revascularization was associated with an increased requirement for major amputation in models adjusted for other risk factors (relative risk 5·40 to 4·22 in different models).

CONCLUSION

Patients presenting with intermittent claudication who underwent early revascularization appeared to be at higher risk of amputation than those who had initial conservative treatment.

Likely Transiting Exocomets Detected By Kepler

We present the first good evidence for exocomet transits of a host star in continuum light in data from the Kepler mission. The Kepler star in question, KIC 3542116, is of spectral type F2V and is quite bright at Kp = 10. The transits have a distinct asymmetric shape with a steeper ingress and slower egress that can be ascribed to objects with a trailing dust tail passing over the stellar disk. There are three deeper transits with depths of ≃ 0.1% that last for about a day, and three that are several times more shallow and of shorter duration. The transits were found via an exhaustive visual search of the entire Kepler photometric data set, which we describe in some detail. We review the methods we use to validate the Kepler data showing the comet transits, and rule out instrumental artefacts as sources of the signals. We fit the transits with a simple dust-tail model, and find that a transverse comet speed of ∼35-50 km s-1 and a minimum amount of dust present in the tail of ∼ 1016 g are required to explain the larger transits. For a dust replenishment time of ∼10 days, and a comet lifetime of only ∼300 days, this implies a total cometary mass of ≳ 3 × 1017 g, or about the mass of Halley's comet. We also discuss the number of comets and orbital geometry that would be necessary to explain the six transits detected over the four years of Kepler prime-field observations. Finally, we also report the discovery of a single comet-shaped transit in KIC 11084727 with very similar transit and host-star properties.

Pediatric cancer pathology review from a single institution: Neuropathology expert opinion is essential for accurate diagnosis of pediatric brain tumors

BACKGROUND AND OBJECTIVES

Second pathology review has been reported to improve accuracy in oncologic diagnoses, including pediatric malignancies. We assessed the impact of second review on the diagnosis of pediatric malignancies at a tertiary care referral center in Beirut, Lebanon.

METHODS

Pathology reports of patients treated at the Children's Cancer Institute in Lebanon were retrospectively reviewed for the period 2008-2016 and compared with same samples' diagnoses at St. Jude Children's Research Hospital. Diagnostic disagreements were divided into major, minor, and none based on their effect on diagnosis and/or patient management.

RESULTS

Second review was requested for 171 cases, accounting for 19% of all cases during that period. Second opinion was mostly requested for brain tumors (62% of all brain tumor cases) and neuroblastoma for NMYC testing (65% of all neuroblastoma), while hematologic malignancies had the fewest referrals (3% of all hematologic cases). Major disagreements in second review occurred in 20 cases (12% of total), and minor disagreements in 21 cases (12% of total). The largest proportion of major disagreements (71%) occurred in pediatric brain tumors, and novel molecular tests contributed to the diagnosis in 55% of these cases.

CONCLUSIONS

The availability of a specialized pediatric neuropathologist and a basic panel of relevant molecular testing are essential for appropriate diagnosis of pediatric brain tumors. Centers that do not have the available infrastructure in place can benefit greatly from second review referrals for this challenging subset of tumors.

Association between metformin prescription and growth rates of abdominal aortic aneurysms

Background

It has been suggested that diabetes medications, such as metformin, may have effects that inhibit abdominal aortic aneurysm (AAA) growth. The aim of this study was to examine the association of diabetes treatments with AAA growth in three patient cohorts.

Methods

AAA growth was studied using ultrasound surveillance in cohort 1, repeated CT in cohort 2 and more detailed repeat CT in cohort 3. Growth was estimated by the mean annual increase in maximum AAA diameter.

Results

A total of 1697 patients with an AAA were studied, of whom 118, 39 and 16 patients were prescribed metformin for the treatment of diabetes in cohorts 1, 2 and 3 respectively. Prescription of metformin was associated with a reduced likelihood of median or greater AAA growth in all three cohorts (cohort 1: adjusted odds ratio (OR) 0·59, 95 per cent c.i. 0·39 to 0·87, P = 0·008; cohort 2: adjusted OR 0·38, 0·18 to 0·80, P = 0·011; cohort 3: adjusted OR 0·13, 0·03 to 0·61, P = 0·010). No other diabetes treatment was significantly associated with AAA growth in any cohort.

Conclusion

These findings suggest a potential role for metformin in limiting AAA growth.

Population based MRI and DTI templates of the adult ferret brain and tools for voxelwise analysis

Non-invasive imaging has the potential to play a crucial role in the characterization and translation of experimental animal models to investigate human brain development and disorders, especially when employed to study animal models that more accurately represent features of human neuroanatomy. The purpose of this study was to build and make available MRI and DTI templates and analysis tools for the ferret brain as the ferret is a well-suited species for pre-clinical MRI studies with folded cortical surface, relatively high white matter volume and body dimensions that allow imaging with pre-clinical MRI scanners. Four ferret brain templates were built in this study – in-vivo MRI and DTI and ex-vivo MRI and DTI – using brain images across many ferrets and region of interest (ROI) masks corresponding to established ferret neuroanatomy were generated by semi-automatic and manual segmentation. The templates and ROI masks were used to create a web-based ferret brain viewing software for browsing the MRI and DTI volumes with annotations based on the ROI masks. A second objective of this study was to provide a careful description of the imaging methods used for acquisition, processing, registration and template building and to demonstrate several voxelwise analysis methods including Jacobian analysis of morphometry differences between the female and male brain and bias-free identification of DTI abnormalities in an injured ferret brain. The templates, tools and methodological optimization presented in this study are intended to advance non-invasive imaging approaches for human-similar animal species that will enable the use of pre-clinical MRI studies for understanding and treating brain disorders.

A pilot study to assess the role of the Internet to provide structured training in obstetrics and gynaecology

Recent recommendations in the Calman Report on medical training address perceived deficiencies in the current system in the UK. These recommendations include shorter and more structured training for junior doctors. Structured training will require the provision of specific educational and assessment materials. The current expansion of the Internet may provide a timely opportunity to help with these educational challenges. Our pilot study will investigate the potential role of the Internet in the delivery of structured training materials. We will also be evaluating a number of educational strategies supported by the Internet, particularly computer based simulation, for teaching the management of two sample obstetric emergencies: post partum haemorrhage and pre-eclampsia.

EkoSonic Thrombolysis as a Therapeutic Adjunct in Venous Occlusive Disease

The use of ultrasound waves in conjunction with local thrombolysis may accelerate clot resolution and serve as an important therapeutic adjunct in the treatment of venous occlusive disease. Our goal was to provide a larger sample population over a 5-year period to evaluate our experience with the EkoSonic endovascular system (EKOS, EKOS Corporation, Bothell, WA). We suspected that ultrasound-accelerated thrombolysis (UAT) using EKOS would provide excellent thrombolysis and midterm patency rates with minimal thrombolytic complications. A retrospective study was conducted to provide a case series with UAT using EKOS. Data were collected over a 5-year period. Primary end points included degree of thrombolysis. Secondarily, we analyzed thrombolytic usage, complication rates, and midterm patency, over a 1-year period. A total of 48 limbs were treated with UAT. Forty cases were diagnosed as acute, whereas the remaining 8 were chronic. Complete thrombolysis was successful in 38/48 (79%) of patients, and partial thrombolysis was accomplished in 10/48 (21%) of patients. Overall mean infusion time was 22.4 hours ±3.6. There were a total of three complications (6%), all of which were minor bleeding. One-year patency was shown to be 87% with no signs of valvular reflux. UAT using EKOS demonstrated effective rates of thrombolysis with very few complications. In addition, our 1-year patency rates were comparable to published data using conventional catheter-directed thrombolysis. UAT provides lytic therapy by utilizing the benefits of ultrasonic waves to help augment the fibrinolytic process. Our institution currently favors the use of EKOS as the treatment of choice in patients that are appropriate thrombolytic candidates.

The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle

The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. Here we select Spirodela polyrhiza for whole-genome sequencing. We show that Spirodela has a genome with no signs of recent retrotranspositions but signatures of two ancient whole-genome duplications, possibly 95 million years ago (mya), older than those in Arabidopsis and rice. Its genome has only 19,623 predicted protein-coding genes, which is 28% less than the dicotyledonous Arabidopsis thaliana and 50% less than monocotyledonous rice. We propose that at least in part, the neotenous reduction of these aquatic plants is based on readjusted copy numbers of promoters and repressors of the juvenile-to-adult transition. The Spirodela genome, along with its unique biology and physiology, will stimulate new insights into environmental adaptation, ecology, evolution and plant development, and will be instrumental for future bioenergy applications.

Spirodela, or duckweed, is a basal monocotyledonous plant with both pharmaceutical and commercial value. Here, the authors sequence the genome of Spirodela polyrhiza, suggesting its genome has evolved by neotenous reduction and clonal propagation, and provide a platform for future comparative genomic studies in angiosperms.

Ohmage

Participatory sensing (PS) is a distributed data collection and analysis approach where individuals, acting alone or in groups, use their personal mobile devices to systematically explore interesting aspects of their lives and communities [Burke et al. 2006]. These mobile devices can be used to capture diverse spatiotemporal data through both intermittent self-report and continuous recording from on-board sensors and applications.

Ohmage (http://ohmage.org) is a modular and extensible open-source, mobile to Web PS platform that records, stores, analyzes, and visualizes data from both prompted self-report and continuous data streams. These data streams are authorable and can dynamically be deployed in diverse settings. Feedback from hundreds of behavioral and technology researchers, focus group participants, and end users has been integrated into ohmage through an iterative participatory design process. Ohmage has been used as an enabling platform in more than 20 independent projects in many disciplines. We summarize the PS requirements, challenges and key design objectives learned through our design process, and ohmage system architecture to achieve those objectives. The flexibility, modularity, and extensibility of ohmage in supporting diverse deployment settings are presented through three distinct case studies in education, health, and clinical research.

Genomic landscape of paediatric adrenocortical tumours

Pediatric adrenocortical carcinoma is a rare malignancy with poor prognosis. Here we analyze 37 adrenocortical tumors (ACTs) by whole genome, whole exome and/or transcriptome sequencing. Most cases (91%) show loss of heterozygosity (LOH) of chromosome 11p, with uniform selection against the maternal chromosome. IGF2 on chromosome 11p is overexpressed in 100% of the tumors. TP53 mutations and chromosome 17 LOH with selection against wild-type TP53 are observed in 28 ACTs (76%). Chromosomes 11p and 17 undergo copy-neutral LOH early during tumorigenesis, suggesting tumor-driver events. Additional genetic alterations include recurrent somatic mutations in ATRX and CTNNB1 and integration of human herpesvirus-6 in chromosome 11p. A dismal outcome is predicted by concomitant TP53 and ATRX mutations and associated genomic abnormalities, including massive structural variations and frequent background mutations. Collectively, these findings demonstrate the nature, timing and potential prognostic significance of key genetic alterations in pediatric ACT and outline a hypothetical model of pediatric adrenocortical tumorigenesis.