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.

Prevention of respiratory virus transmission by resident memory CD8+ T cells.

An ideal vaccine both attenuates virus growth and disease in infected individuals and reduces the spread of infections in the population, thereby generating herd immunity. Although this strategy has proved successful by generating humoral immunity to measles, yellow fever and polio, many respiratory viruses evolve to evade pre-existing antibodies1. One approach for improving the breadth of antiviral immunity against escape variants is through the generation of memory T cells in the respiratory tract, which are positioned to respond rapidly to respiratory virus infections2-6. However, it is unknown whether memory T cells alone can effectively surveil the respiratory tract to the extent that they eliminate or greatly reduce viral transmission following exposure of an individual to infection. Here we use a mouse model of natural parainfluenza virus transmission to quantify the extent to which memory CD8+ T cells resident in the respiratory tract can provide herd immunity by reducing both the susceptibility of acquiring infection and the extent of transmission, even in the absence of virus-specific antibodies. We demonstrate that protection by resident memory CD8+ T cells requires the antiviral cytokine interferon-γ (IFNγ) and leads to altered transcriptional programming of epithelial cells within the respiratory tract. These results suggest that tissue-resident CD8+ T cells in the respiratory tract can have important roles in protecting the host against viral disease and limiting viral spread throughout the population.

Outcomes After Hybrid Palliation for Infants With Critical Left Heart Obstruction.

BACKGROUND: Hybrid palliation (bilateral pulmonary artery banding with or without ductal stenting) is an initial management strategy for infants with critical left heart obstruction and serves as palliation until subsequent operations are pursued. OBJECTIVES: This study sought to determine patient characteristics and factors associated with subsequent outcomes for infants who underwent hybrid palliation. METHODS: From 2005 to 2019, 214 of 1,236 prospectively enrolled infants within the Congenital Heart Surgeons' Society's critical left heart obstruction cohort underwent hybrid palliation across 24 institutions. Multivariable hazard modeling with competing risk methodology was performed to determine risk and factors associated with outcomes of biventricular repair, Fontan procedure, transplantation, or death. RESULTS: Preoperative comorbidities (eg, prematurity, low birth weight, genetic syndrome) were identified in 70% of infants (150 of 214). Median follow-up was 7 years, ranging up to 17 years. Overall 12-year survival was 55%. At 5 years after hybrid palliation, 9% had biventricular repair, 36% had Fontan procedure, 12% had transplantation, 35% died without surgical endpoints, and 8% were alive without an endpoint. Factors associated with transplantation were absence of ductal stent, older age, absent interatrial communication, smaller aortic root size, larger tricuspid valve area z-score, and larger left ventricular volume. Factors associated with death were low birth weight, concomitant genetic syndrome, cardiopulmonary bypass use during hybrid palliation, moderate to severe tricuspid valve regurgitation, and smaller ascending aortic size. CONCLUSIONS: Mortality remains high after hybrid palliation for infants with critical left heart obstruction. Nonetheless, hybrid palliation may facilitate biventricular repair for some infants and for others may serve as stabilization for intended functional univentricular palliation or primary transplantation.

Rituximab Chimeric Anti-CD20 Monoclonal Antibody Therapy for Relapsed Indolent Lymphoma: Half of Patients Respond to a Four-Dose Treatment Program.

PURPOSE: The CD20 antigen is expressed on more than 90% of B-cell lymphomas. It is appealing for targeted therapy, because it does not shed or modulate. A chimeric monoclonal antibody more effectively mediates host effector functions and is itself less immunogenic than are murine antibodies. PATIENTS AND METHODS: This was a multiinstitutional trial of the chimeric anti-CD20 antibody, IDEC-C2B8. Patients with relapsed low grade or follicular lymphoma received an outpatient treatment course of IDEC-C2B8 375 mg/m2 intravenously weekly for four doses. RESULTS: From 31 centers, 166 patients were entered. Of this intent-to-treat group, 48% responded. With a median follow-up duration of 11.8 months, the projected median time to progression for responders is 13.0 months. Serum antibody levels were sustained longer after the fourth infusion than after the first, and were higher in responders and in patients with lower tumor burden. The majority of adverse events occurred during the first infusion and were grade 1 or 2; fever and chills were the most common events. Only 12% of patients had grade 3 and 3% grade 4 toxicities. A human antichimeric antibody was detected in only one patient. CONCLUSION: The response rate of 48% with IDEC-C2B8 is comparable to results with single-agent cytotoxic chemotherapy. Toxicity was mild. Attention needs to be paid to the rate of antibody infusion, with titration according to toxicity. Further investigation of this agent is warranted, including its use in conjunction with standard chemotherapy.

A survey of hospice day services in the United Kingdom & Republic of Ireland : how did hospices offer social support to palliative care patients, pre-pandemic?

INTRODUCTION: Social support is described by patients and other stakeholders to be a valuable component of palliative day care. Less is known about the range of hospice services that have been used in practice that facilitate social support. An online survey aimed to gain an overview of all hospice day services that facilitated social support for adults outside of their own homes. METHODS: An online survey was distributed via email to people involved in managing hospice day services. Questions were asked on hospice characteristics, including staff and volunteer roles. Respondents were asked to identify services they felt offered social support to patients. Data collection took place between August 2017 and May 2018. RESULTS: Responses were received from 103 hospices in the UK and ROI (response rate 49.5%). Results provide an overview of hospice day and outpatient services that offer social support to patients. These are: multi-component interventions, activity groups, formal support groups, befriending, and informal social activities. Multi-component interventions, such as palliative day care, were the most commonly reported. Their stated aims tend to focus on clinical aspects, but many survey respondents considered these multicomponent interventions to be the 'most social' service at their hospice. The survey also identified a huge variety of activity groups, as well as formal therapeutic support groups. Informal 'social-only' activities were present, but less common. Over a third of all the services were described as 'drop in'. Most responding hospices did not routinely use patient reported outcome measures in their 'most social' services. CONCLUSIONS: The survey documents hospice activity in facilitating social support to be diverse and evolving. At the time of data collection, many hospices offered multiple different services by which a patient might obtain social support outside of their own home and in the presence of other patients.

Practising pharmacists want more nutrition education.

BACKGROUND AND PURPOSE: Although pharmacists are first and foremost medication specialists and suppliers, in Australia they are also ideally positioned within the healthcare setting to encourage and support positive lifestyle choices in the community. Little has been done to assess their nutrition knowledge in over 20 years. We aimed to explore pharmacists' nutrition knowledge and associated practice and to subsequently develop and evaluate a short course to fill identified gaps. EDUCATIONAL ACTIVITY AND SETTING: The General Nutrition Knowledge Questionnaire was revised for testing nutrition knowledge in the pharmacy setting. Once validated, the questionnaire was distributed to pharmacists using social/professional media advertising. A short course was then developed, and its effectiveness assessed on final-year pharmacy students. FINDINGS: Pharmacists' (N = 258) mean score was 89.9 out of 121 (SD = 10.6) with significant variation. Nutrition education provision in practice was provided inconsistently and was associated with how strongly participants rated their own knowledge. Most pharmacists (95.7%) agreed they are well-placed to assist in disease burden reduction through nutrition education; however, most (98.4%) felt their knowledge needed improvement. The short course was well received by participants, deemed to be appropriate in context, and resulted in a median improvement in matched scores of 14.7% (P < .001) with no significant decline in knowledge when reassessed three weeks later (P = .383). SUMMARY: Pharmacists' nutrition knowledge and practice was variable. Further education can improve knowledge without significant time outlay and is likely to improve associated counselling practices.

Implementation of apertures in a proton pencil-beam dose algorithm.

The use of field-specific apertures, routine in scattered or uniform-scanned proton fields, are still a necessity in pencil-beam scanned (PBS) fields to sharpen the penumbral edge at low energies and in high fraction dose application beyond that achievable with small spot size. We describe a model implemented in our clinical pencil-beam algorithm that models the insertion of a shaped aperture, including shapes adapted per energy layer such as may be achieved with a multi-leaf collimator. The model decomposes the spot transport into discrete steps. The first step transport a uniform intensity field of high-resolution sub-pencil-beams at the layer energy through the medium. This transport only considers primary scattering in both the patient and an optional range-shifter. The second step models the aperture areas and edge penumbral transition as a modulation of the uniform intensity. The third step convolves individual steps over the uniform-transported field including the aperture-modified intensities. We also introduce an efficient model based on a Clarkson sector integration for nuclear scattered halo protons. This avoids the explicit modeling of long range halo protons to the detriment of computational efficiency in calculation and optimization. We demonstrate that the aperture effect is primarily due to in-patient and shifter scattering with a small contribution from the apparent beam source position. The model provides insight into the primary physics contributions to the penumbra and the nuclear halo. The model allowed us to fully deploy our PBS capacity at our two-gantry center without which PBS treatments would have been inferior compared to scattered fields with apertures. Finally, Monte Carlo calculations have (nearly) replaced phenomenological pencil-beam models for collimated fields. Phenomenological models do, however, allow exposition of underlying clinical phenomena and closer connection to representative clinical observables.

The management and outcome of large volume liposarcomas encasing the sciatic nerve.

This paper outlines the oncological outcomes of patients with large volume liposarcomas of the posterior thigh who underwent nerve-preserving surgery utilising epineural dissection. Thirty-seven consecutive patients (group I) with a mean age of 66.2 (31-96) were surgically treated with a planned marginal resection and epineurectomy for liposarcoma with known sciatic nerve involvement between March 1997 and January 2015. The mean follow-up was 79 months (15-192). All patients underwent multidisciplinary team (MDT) pre-operative assessment and staging, with follow-up in Sarcoma Clinic. Pre-operative function was assessed by applying the Toronto extremity salvage score (TESS). Oncological and functional outcomes were recorded. In grades 1, 2, and 3, 24, 6, and 7 liposarcomas, respectively, were included with mean volume 1859 cm3. Sciatic nerve involvement extended for 13-30 cm; in one case, the nerve was abutting the tumour throughout its length. Soft tissue reconstructive surgery was required in three cases. The remainder underwent direct primary closure. Seventeen patients underwent post-operative adjuvant radiotherapy 46-60 Gy and three received chemotherapy. There was local recurrence of disease in three patients. One patient had post-radiation wound breakdown treated non-operatively. Three patients died of an unrelated cause. When compared to a cohort of 37 patients without sciatic nerve involvement (group II), there were no significant differences in local and systemic recurrence rate or post-operative survival. In conclusion, sciatic nerve-preserving surgery is both possible and safe when using a planned epineural dissection in large volume tumours encasing the sciatic nerve.

Tubulointerstitial nephritis and uveitis in Northern Ireland.

OBJECTIVES: This paper looks at patients with a diagnosis of tubulointerstitial nephritis and uveitis (TINU) presenting to the Northern Ireland regional adult and paediatric uveitis service in the Belfast Health and Social Care Trust. The demographic distribution, treatment required and the visual and renal outcomes of these patients are documented. METHODS: Data were collected retrospectively on 24 patients with TINU using the Northern Ireland Electronic Care Record, central pathology records alongside the adult and paediatric uveitis databases from 2011 to 2021. Patients were categorised into two groups using the Mandeville classification system. Standard Uveitis Nomenclature (SUN) was used to classify the uveitis. RESULTS: The population prevalence is at least 12.6 cases per million based on a population of 1.9 million. Nineteen of 24 cases were definite TINU and five of 24 probable. Seventeen out of 24 had biopsy-positive TIN, all of which met all of the Mandeville clinical diagnostic features required for a definite diagnosis. All but one presented with acute bilateral anterior uveitis. The paediatric cases ranged from age 12 to 18 at age of onset with a mean age of 14. Of the 18 adult onset cases, the age ranged from 20 to 76 years. The mean age of onset for the adult cases was 53 years. Of these patients 71% were female; 42% required second-line immunosuppression for ocular disease. Visual acuity was maintained. Follow-up time ranged from 3 months to 16 years. No patient developed long-term renal impairment. CONCLUSIONS: TINU is a cause of uveitis in both the paediatric and adult populations. In Northern Ireland average age with TINU was older than much of the published literature. Long-term immunosuppression for uveitis may be required as ongoing ocular, rather than renal inflammation seemed to require treatment.

Registries, Databases and Repositories for Developing Artificial Intelligence in Cancer Care.

Modern artificial intelligence techniques have solved some previously intractable problems and produced impressive results in selected medical domains. One of their drawbacks is that they often need very large amounts of data. Pre-existing datasets in the form of national cancer registries, image/genetic depositories and clinical datasets already exist and have been used for research. In theory, the combination of healthcare Big Data with modern, data-hungry artificial intelligence techniques should offer significant opportunities for artificial intelligence development, but this has not yet happened. Here we discuss some of the structural reasons for this, barriers preventing artificial intelligence from making full use of existing datasets, and make suggestions as to enable progress. To do this, we use the framework of the 6Vs of Big Data and the FAIR criteria for data sharing and availability (Findability, Accessibility, Interoperability, and Reuse). We share our experience in navigating these barriers through The Brain Tumour Data Accelerator, a Brain Tumour Charity-supported initiative to integrate fragmented patient data into an enriched dataset. We conclude with some comments as to the limits of such approaches.

Safe and Ethical Artificial Intelligence in Radiotherapy - Lessons Learned From the Aviation Industry.

Ethical artificial intelligence (AI) frameworks can be the catalyst in improving the safety and wellbeing of people when developing AI systems. In 2020 Rolls-Royce released its ethical and trustworthiness toolkit, The Aletheia FrameworkTM, which helps guide organisations as they consider the ethics around the use of AI. It covers three facets: social impact, accuracy and trust, and governance - which apply across all uses of AI. By adopting AI ethics and trust frameworks, oncologists can ensure the ratio between the benefit and harms of AI can be maximised. With AI transforming every sector, collaboration across industries to share ideas and learn from each other - even unlikely partnerships between engineering and oncology - could help optimise that transition.

Review of Conventional and High Dose Rate Brain Radiation (FLASH): Neurobehavioural, Neurocognitive and Assessment Issues in Rodent Models.

Ionising radiation causes secondary tumours and/or enduring cognitive deficits, especially in children. Proton radiotherapy reduces exposure of the developing brain in children but may still cause some lasting effects. Recent observations show that ultra-high dose rate radiation treatment (≥40 Gy/s), called the FLASH effect, is equally effective at tumour control but less damaging to surrounding tissue compared with conventional dose rate protons (0.03-3 Gy/s). Most studies on the FLASH effect in brain and other tissues with different radiation modalities (electron and photon radiation), show FLASH benefits in these preclinical rodent models, but the data are limited, especially for proton FLASH, including for dose, dose rate and neurochemical and neurobehavioural outcomes. Tests of neurocognitive outcomes have been limited despite clinical evidence that this is the area of greatest concern. The FLASH effect in the context of proton exposure is promising, but a more systematic and comprehensive approach to outcomes is needed.

Head and neck sarcoma: three-year data from a tertiary referral centre.

INTRODUCTION: Sarcomas of the head and neck are neoplasms arising from the embryonic mesenchyme. They are rare and heterogeneous in nature and are associated with significant morbidity and mortality. This study evaluates patients referred to the Oxford Sarcoma Service, a tertiary referral centre. METHODS: Patients discussed over a three-year period were included. Medical records were analysed using the electronic patient record database. Data were acquired on a range of domains, including: demographics, histopathology, treatment modality, recurrence, mortality, survival, etc. RESULTS: Thirty-two eligible patients, 21 male and 11 female, were identified with a mean age of 58 years; 26 out of 32 patients had high-grade sarcomas. The commonest histological subtype was chondrosarcoma (8/32). Twenty-two underwent planned multidisciplinary team surgical resection after biopsy and staging: negative margins were noted in 9, with close and involved margins in 5 and 8, respectively. Local recurrence was noted in 13 and 6 had metastatic disease out of the 32 eligible patients. Mortality was noted in 10 out of 32 patients. Mean survival was 69.5 months. Five-year overall survival was 64%. Surgery demonstrated statistically significant improvement in survival (p=0.0095). There were no significant differences in survival, recurrence or marginal status between methods of adjuvant or neoadjuvant therapy. CONCLUSION: Outcomes of head and neck sarcomas are inferior compared with other types of sarcoma. The nature of the complex surrounding anatomy presents unique challenges in surgical management. This in turn affects rates of local recurrence and prognosis. Therefore, it is critical that they are managed in tertiary, specialist centres with a multidisciplinary approach.

MRI versus CT: a retrospective investigation of the feasibility and agreeability in post-operative evaluation of screw position after posterior lumbar interbody fusion.

PURPOSE: Many patients receive magnetic resonance (MR) and computed tomography (CT) scans post-operatively to review screw placement. Traditionally, CT is diagnostic but as metal artefact reduction sequences are advancing in MR, the necessity for both MR and CT scans is questionable. The objective is to establish the statistical agreeability of MR and CT for evaluation of adequate screw placement in posterior lumbar interbody fusion. METHODS: This opportunistic retrospective study of 58 patients investigated 297 images of 296 implanted screws. Post-operative MR and CT images were scrutinised for depiction of lumbar pedicle screw position using a 5-point scale. Kappa value for statistical agreeability tested MR against CT. RESULTS: The 297 images of screws resulted in strong to near-perfect agreement between MR and CT (n = 297 k = 0.8042 p < 0.025). MRI resulted in high sensitivity (88.7%) and positive predictive value (78.3%). MRI demonstrated very high specificity (96.2%) and negative predictive value (98.2%). MR depicted screws (mean 12.6 mm diameter, mean 65.3 mm length) with 50% error in diameter and 30% in length from susceptibility artefact compared to manufacturer dimensions (6.5-7.5 mm diameter, 40-50 mm length). Adequate screw placement was high despite this (85.8%). On MR, the cortex border visibility was 60.7% and the spinal canal visibility was 74.6%. CONCLUSION: There is strong to near-perfect agreement between MR and CT for evaluating adequate screw position in PLIF surgery. MR alone is useful for analyzing screw placement and should be considered first-line imaging in uncomplicated cases with CT analysis reserved for cases of uncertainty. LEVEL OF EVIDENCE: Level III retrospective cohort study.

MR Imaging Characteristics of Intraocular Perfluoro-n-Octane.

We describe the unique MR imaging characteristics of intraocular perfluoro-n-octane, a liquid used for intraoperative and postoperative tamponade in the context of complex retinal detachment repair, and contrast it with other intraocular pathologies. Because trace amounts of perfluoro-n-octane may be left in the globe postoperatively, it may be confused for other abnormalities, such as foreign bodies or tumors.