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The purpose of this review is to evaluate various challenges and opportunities as well as propose solutions for the development and implementation of a prospective COVID-19 patient registry within a regional context in the Philippines. To comprehensively study the course of COVID-19 in the Philippine population, it is essential to develop a comprehensive dataset that includes relevant treatment and diagnostic information. While individual patient reports related to the disease are available at various institutions in the Philippines, there is a need for a more extensive and representative database to facilitate robust analysis. The primary clinical objective of establishing a COVID-19 patient registry was to enhance the accuracy of disease diagnosis. In this review, we present a comprehensive explanation of the systematic rationale, design, and execution of a COVID-19 patient registry in the Western Visayas region of the Philippines. Based on this review, several factors exist that hinder the implementation of a COVID-19 patient registry in this regional setting in the Philippines, including lack of funding, facilities, infrastructure, manpower, and expertise, and unwillingness of some hospitals to pursue research. We also discussed herewith the proposed program implementation for the establishment of such a registry in a regional setting in the Philippines.

The production of biodiesel generates glycerol as a by-product that needs valorization. Glycerol, when converted to polyglycerol, is a potential polyol for bio-based thermoplastic polyurethane (TPU) production. In this study, a novel polyglycerol polyester polyol (PPP) was developed from refined glycerol and coconut oil-based polyester polyol. Glycerol was first converted to glycerol acetate and then polymerized with coconut oil-based polyester polyol (CPP) as secondary polyol and phthalic anhydride. The resulting PPP polymerized at 220 °C and OH:COOH molar ratio of 2.5 exhibited an OH number of

Lackawanna, a US county seat in Northeastern Pennsylvania has an estimated population of 216,000 in 2020. Over the years, it has been reported that several bodies of water found within the county have been contaminated with various metals. However, a comprehensive examination of the presence of these metals has not been conducted. The goal of this brief report was to perform a preliminary quantitative determination of the concentration of various metals found in Lackawanna County water sources. The sources analyzed included Lake Scranton, the Lackawanna River, the Griffin Reservoir, and Keyser Creek. Samples were taken from each source and analyses of copper, lead, zinc, iron, manganese, and cadmium using atomic absorption spectroscopy were performed. A copper concentration of 0.100 ppm was found in the Griffin Reservoir, and 0.380 ppm of iron was found in the Lackawanna River. The concentration of copper and iron in the Griffin Reservoir and Lackawanna River, respectively, were determined to be within safe levels according to guidelines set by the US Environmental Protection Agency.

Abstract Artificial intelligence and radiomics have the potential to revolutionise cancer prognostication and personalised treatment. Manual outlining of the tumour volume for extraction of radiomics features (RF) is a subjective process. This study investigates robustness of RF to inter-observer variation (IOV) in contouring in lung cancer. We utilised two public imaging datasets: ‘NSCLC-Radiomics’ and ‘NSCLC-Radiomics-Interobserver1’ (‘Interobserver’). For ‘NSCLC-Radiomics’, we created an additional set of manual contours for 92 patients, and for ‘Interobserver’, there were five manual and five semi-automated contours available for 20 patients. Dice coefficients (DC) were calculated for contours. 1113 RF were extracted including shape, first order and texture features. Intraclass correlation coefficient (ICC) was computed to assess robustness of RF to IOV. Cox regression analysis for overall survival (OS) was performed with a previously published radiomics signature. The median DC ranged from 0.81 (‘NSCLC-Radiomics’) to 0.85 (‘Interobserver’—semi-automated). The median ICC for the ‘NSCLC-Radiomics’, ‘Interobserver’ (manual) and ‘Interobserver’ (semi-automated) were 0.90, 0.88 and 0.93 respectively. The ICC varied by feature type and was lower for first order and gray level co-occurrence matrix (GLCM) features. Shape features had a lower median ICC in the ‘NSCLC-Radiomics’ dataset compared to the ‘Interobserver’ dataset. Survival analysis showed similar separation of curves for three of four RF apart from ‘original_shape_Compactness2’, a feature with low ICC (0.61). The majority of RF are robust to IOV, with first order, GLCM and shape features being the least robust. Semi-automated contouring improves feature stability. Decreased robustness of a feature is significant as it may impact upon the features’ prognostic capability.

Background: Emerging data suggest that dose-sparing several key cardiac regions is prognostically beneficial in lung cancer radiotherapy. The cardiac substructures are challenging to contour due to their complex geometry, poor soft tissue definition on computed tomography (CT) and cardiorespiratory motion artefact. A neural network was previously trained to generate the cardiac substructures using three-dimensional radiotherapy planning CT scans (3D-CT). In this study, the performance of that tool on the average intensity projection from four-dimensional (4D) CT scans (4D-AVE), now commonly used in lung radiotherapy, was evaluated. Materials and Methods: The 4D-AVE of n=20 patients completing radiotherapy for lung cancer 2015–2020 underwent manual and automated cardiac substructure segmentation. Manual and automated substructures were compared geometrically and dosimetrically. Two senior clinicians also qualitatively assessed the auto-segmentation tool’s output. Results: Geometric comparison of the automated and manual segmentations exhibited high levels of similarity across parameters, including volume difference (11.8% overall) and Dice similarity coefficient (0.85 overall), and were consistent with 3D-CT performance. Differences in mean (median 0.2 Gy, range −1.6–0.3 Gy) and maximum (median 0.4 Gy, range −2.2–0.9 Gy) doses to substructures were generally small. Nearly all structures (99.5 %) were deemed to be appropriate for clinical use without further editing. Conclusions: Cardiac substructure auto-segmentation using a deep learning-based tool trained on a 3D-CT dataset was feasible on the 4D-AVE scan, meaning this tool is suitable for use on 4D-CT radiotherapy planning scans. Application of this tool would increase the practicality of routine clinical cardiac substructure delineation, and enable further cardiac radiation effects research.

Background ImmunoPET is a multicentre, single arm, phase 0–1 study that aims to establish if 89Zr-durvalumab PET/CT can be used to interrogate the expression of PD-L1 in larger, multicentre clinical trials.Methods The phase 0 study recruited 5 PD-L1+ patients with metastatic non-small cell lung cancer (NSCLC). Patients received 60MBq/70 kg 89Zr-durva up to a maximum of 74 MBq, with scan acquisition at days 0, 1, 3 or 5±1 day. Data on (1) Percentage of injected 89Zr-durva dose found in organs of interest (2) Absorbed organ doses (µSv/MBq of administered 89Zr-durva) and (3) whole-body dose expressed as mSv/100MBq of administered dose was collected to characterise biodistribution.The phase 1 study will recruit 20 patients undergoing concurrent chemoradiotherapy for stage III NSCLC. Patients will have 89Zr-durva and FDG-PET/CT before, during and after chemoradiation. In order to establish the feasibility of 89Zr-durva PET/CT for larger multicentre trials, we will collect both imaging and toxicity data. Feasibility will be deemed to have been met if more than 80% of patients are able complete all trial requirements with no significant toxicity.Ethics and dissemination This phase 0 study has ethics approval (HREC/65450/PMCC 20/100) and is registered on the Australian Clinical Trials Network (ACTRN12621000171819). The protocol, technical and clinical data will be disseminated by conference presentations and publications. Any modifications to the protocol will be formally documented by administrative letters and must be submitted to the approving HREC for review and approval.Trial registration number Australian Clinical Trials Network ACTRN12621000171819.

Abstract Background The enhanced knowledge of cancer biology has led to considerable advancement in systemic therapy for advanced breast cancer. Recently, studies showed that cyclin-dependent kinase (CDK) 4/6 inhibitor, when added to endocrine therapy, had improved the outcomes of patients with advanced ER-positive HER2-negative breast cancer. However, the disease often progresses following a period of treatment response. In a subset of patients, disease progression may occur at limited sites, i.e., oligoprogressive disease (OPD). In the past few years, stereotactic radiotherapy (SRT) has emerged as a safe and effective treatment for advanced cancer when delivered to limited metastatic sites. Hence, it is worth investigating the role of SRT in the setting of oligoprogressive breast cancer. Method AVATAR is a multicentre phase II registry trial of SRT with endocrine therapy and CDK 4/6 inhibitor for the management of advanced ER-positive HER2-negative breast cancer. The study aims to enrol 32 patients with OPD limited to 5 lesions. The primary endpoint of the study is time to change systemic therapy measured from the commencement of SRT to change in systemic therapy. Secondary objectives include overall survival, progression free survival and treatment related toxicity. The exploratory objective is to describe the time to change in systemic therapy by the site (bone only vs. non-bone lesions) and number (1 vs. > 1) of OPD. Discussion This study aims to explore the effect of SRT in maximising the benefit of systemic therapy in patients with oligoprogressive ER-positive HER2-negative breast cancer. This approach might help reduce the burden of disease and improve the life quality in these patients. Trial registration ACTRN, ACTRN12620001212943 . Date of registration 16 November 2020- Retrospectively registered.

BackgroundBiology-guided radiotherapy (BgRT) uses real-time functional imaging to guide radiation therapy treatment. Positron emission tomography (PET) tracers targeting prostate-specific membrane antigen (PSMA) are superior for prostate cancer detection than conventional imaging. This study aims at describing nodal and distant metastasis distribution from prostate cancer and at determining the proportion of metastatic lesions suitable for BgRT.MethodsA single-institution patient subset from the ProPSMA trial (ID ACTRN12617000005358) was analysed. Gross tumour volumes (GTV) were delineated on the CT component of a PSMA PET/CT scan. To determine the suitability of BgRT tracking zones, the normalized SUV (nSUV) was calculated as the ratio of SUVmax inside the GTV to the SUVmean of adjacent three-dimensional shells of thickness 5 mm/10 mm/20 mm as a measure of signal to background contrast. Targets were suitable for BgRT if (1) nSUV was larger than an nSUV threshold and (2) non-tumour tissue inside adjacent shell was free of PET-avid uptake.ResultsOf this cohort of 84 patients, 24 had at least one pelvic node or metastatic site disease, 1 to 13 lesions per patient, with a total of 98 lesions (60 pelvic nodes/38 extra-pelvic nodal diseases and haematogenous metastases). Target volumes ranged from 0.08 to 9.6 cm3 while SUVmax ranged from 2.1 to 55.0. nSUV ranged from 1.9 to 15.7/2.4 to 25.7/2.5 to 34.5 for the 5 mm/10 mm/20 mm shell expansion. Furthermore, 74%/68%/34% of the lesions had nSUV ≥ 3 and were free of PSMA PET uptake inside the GTV outer shell margin expansion of 5 mm/10 mm/20 mm. Adjacent avid organs were another lesion, bladder, bowel, ureter, prostate, and liver.ConclusionsThe majority of PSMA PET/CT-defined radiotherapy targets would be suitable for BgRT by using a 10-mm tracking zone in prostate cancer. A subset of lesions had adjacent non-tumour uptake, mainly due to the proximity of ureter or bladder, and may require exclusion from emission tracking during BgRT.

Lung cancer is the leading cause of cancer mortality worldwide and most patients are unsuitable for ‘gold standard’ treatment, which is concurrent chemoradiotherapy. CONCORDE is a platform study seeking to establish the toxicity profiles of multiple novel radiosensitisers targeting DNA repair proteins in patients treated with sequential chemoradiotherapy. Time-to-event continual reassessment will facilitate efficient dose-finding.

Abstract Background The last two decades have seen revolutionary developments in both radiotherapy technology and postgraduate medical training. Trainees are expected to attain competencies using a mix of experiential learning, formal postgraduate teaching, self-directed learning and peer education. Radiation (Clinical) Oncology is a recognised ‘craft specialty’ where the apprenticeship model of training is applicable. This scoping review examines the evidence in relation to how medical trainees learn radiotherapy. Methods A systematic search of MEDINE and EMBASE was undertaken to identify studies of trainee and/or trainer experience of radiotherapy learning published 1999–2018. Results pertaining to Medical Oncology, workforce trends, undergraduate radiotherapy exposure, academic training, global health, non-medical staff, health service infrastructure and recruitment to training programmes were not included. Results A total of 146 publications were included in the synthesis. Five themes were apparent through careful iterative analysis representing broadly inter-related issues. Most articles studied radiotherapy training from the perspective of the trainee doctor. Most literature reports results of observational, local or national surveys with a tightly defined scope. Considerable variation exists within hospitals, within countries, over time and between different curricular areas. Conclusions Medical education has not kept pace with changes in the field of radiotherapy and large differences are demonstrated in experience between trainees in different hospitals, countries and training stages. Interpersonal relationships, departmental organisation, and national curricula impact on training quality. Qualitative and quantitative research examining modern radiotherapy learning has been uncommon and uncoordinated, until recently. To date no single study has been designed to comprehensively assess a department’s training scheme.

Objective To gather preliminary qualitative data that will assist in the codesign and development of a new informational and supportive website to assist informal cancer carers in Australia.Design and setting Utilising a previously tested codesign process, informal carers’ experiences and perspectives, including those of healthcare professionals’, were examined via focus groups and/or interviews. Data were analysed via thematic analysis.Participants Rural (n=9) and urban (n=11) carers’, and healthcare professionals’ (n=8) perspectives were collected. Carers participated in a focus group (n=9) or telephone interview (n=11). Healthcare professionals completed an interview (n=6) or online survey (n=2).Results Rural and urban carers typically felt ill prepared for their multitudinal caregiving responsibilities. Supporting patient-to-healthcare professional liaisons could especially challenge. Carers’ biopsychosocial and fiscal strains were affected by patients’ hardships and available informal supports. Rural carers described greater social support than urban carers. Both rural and urban carers also described discontentment related to a carer neglecting healthcare system. Both carers and healthcare professionals endorsed the need for a user-friendly, carer-specific website encompassing practical information and resources, peer-driven advice and evidence-based illness information, tailored to the Australian context.Conclusions Carers and healthcare professionals recognise the pressing need for an Australian, cancer carer-specific online resource. Findings will inform the next phase, where a resource will be designed, developed and tested.

Excessive use of animal manure as fertilizers can lead to pollution through the introduction of nitrogen, phosphorus, and other mineral compounds to the environment. Wet chemical analytical methods are traditionally used to determine the precise chemical composition of manure to manage the application of animal waste to the soil. However, such methods require significant resources to carry out the processes. Affordable, rapid, and accurate methods of analyses of various chemical components present in animal manure, therefore, are valuable in managing soil and mitigating water pollution. In this study, a stacked regression ensemble approach using near-infrared spectroscopy was developed to simultaneously determine the amount of dry matter, total ammonium nitrogen, total nitrogen, phosphorus pentoxide, calcium oxide, magnesium oxide, and potassium oxide contents in both cattle and poultry manure collected from livestock production areas in France and Reunion Island. The performance of the stacked regression, an ensemble learning algorithm that is formed by collating the well-performing models for prediction was then compared with that of various other machine learning techniques, including support vector regression (linear, polynomial, and radial), least absolute shrinkage and selection operator, ridge regression, elastic net, partial least squares, random forests, recursive partitioning and regression trees, and boosted trees. Results show that stack regression performed optimally well in predicting the seven abovementioned chemical constituents in the testing set and may provide an alternative to the traditional partial least squares method for a more accurate and simultaneous method in determining the chemical properties of animal manure.

The endoplasmic reticulum (ER) is composed of sheets and tubules. Here we report that the COPII coat subunit, SEC24C, works with the long form of the tubular ER-phagy receptor, RTN3, to target dominant-interfering mutant proinsulin Akita puncta to lysosomes. When the delivery of Akita puncta to lysosomes was disrupted, large puncta accumulated in the ER. Unexpectedly, photobleach analysis indicated that Akita puncta behaved as condensates and not aggregates, as previously suggested. Akita puncta enlarged when either RTN3 or SEC24C were depleted, or when ER sheets were proliferated by either knocking out Lunapark or overexpressing CLIMP63. Other ER-phagy substrates that are segregated into tubules behaved like Akita, while a substrate (type I procollagen) that is degraded by the ER-phagy sheets receptor, FAM134B, did not. Conversely, when ER tubules were augmented in Lunapark knock-out cells by overexpressing reticulons, ER-phagy increased and the number of large Akita puncta was reduced. Our findings imply that segregating cargoes into tubules has two beneficial roles. First, it localizes mutant misfolded proteins, the receptor, and SEC24C to the same ER domain. Second, physically restraining condensates within tubules, before they undergo ER-phagy, prevents them from enlarging and impacting cell health.

Inbreeding depression has been observed in many different species, but in humans a systematic analysis has been difficult so far. Here, analysing more than 1.3 million individuals, the authors show that a genomic inbreeding coefficient (FROH) is associated with disadvantageous outcomes in 32 out of 100 traits tested.

Objectives: To study the link between frailty and cellular senescence, the authors examined the association of leukocyte telomere length (LTL) with a recently introduced measure of subclinical frailty that is based entirely on laboratory test biomarkers (FI-LAB). Methods: This study was conducted on a random sample of 1,890 Americans aged ≥60 years. Multiple linear regression was used to examine the relationship between FI-LAB and LTL. Secondary analyses were performed to identify the individual biomarkers driving the association between FI-LAB and LTL. Results: A statistically significant association was found between FI-LAB and LTL after adjusting for multiple covariates, indicating that higher FI-LAB scores are associated with shorter telomeres. Secondary analyses revealed that this association is driven largely by a small number of FI-LAB biomarkers independently linked with telomere shortening. Conclusion: The study results established a link between subclinical frailty (FI-LAB) and cellular ageing, which may help elucidate the pathophysiological mechanisms that give rise to frailty.

Purpose: Thoracic reirradiation for non-small cell lung cancer with curative intent is potentially associated with severe toxicity. There are limited prospective data on the best method to deliver this treatment. We sought to develop expert consensus guidance on the safe practice of treating non-small cell lung cancer with radiation therapy in the setting of prior thoracic irradiation. Methods and Materials: Twenty-one thoracic radiation oncologists were invited to participate in an international Delphi consensus process. Guideline statements were developed and refined during 4 rounds on the definition of reirradiation, selection of appropriate patients, pretreatment assessments, planning of radiation therapy, and cumulative dose constraints. Consensus was achieved once ≥75% of respondents agreed with a statement. Statements that did not reach consensus in the initial survey rounds were revised based on respondents’ comments and re-presented in subsequent rounds. Results: Fifteen radiation oncologists participated in the 4 surveys between September 2019 and March 2020. The first 3 rounds had a 100% response rate, and the final round was completed by 93% of participants. Thirty-three out of 77 statements across all rounds achieved consensus. Key recommendations are as follows: (1) appropriate patients should have a good performance status and can have locally relapsed disease or second primary cancers, and there are no absolute lung function values that preclude reirradiation; (2) a full diagnostic workup should be performed in patients with suspected local recurrence and; (3) any reirradiation should be delivered using optimal image guidance and highly conformal techniques. In addition, consensus cumulative dose for the organs at risk in the thorax are described. Conclusions: These consensus statements provide practical guidance on appropriate patient selection for reirradiation, appropriate radiation therapy techniques, and cumulative dose constraints.

Genetically encoded probes with red-shifted absorption and fluorescence are highly desirable for imaging applications because they can report from deeper tissue layers with lower background and because they provide additional colors for multicolor imaging. Unfortunately, red and especially far-red fluorescent proteins have very low quantum yields, which undermines their other advantages. Elucidating the mechanism of nonradiative relaxation in red fluorescent proteins (RFPs) could help developing ones with higher quantum yields. Here we consider two possible mechanisms of fast nonradiative relaxation of electronic excitation in RFPs. The first, known as the energy gap law, predicts a steep exponential drop of fluorescence quantum yield with a systematic red shift of fluorescence frequency. In this case the relaxation of excitation occurs in the chromophore without any significant changes of its geometry. The second mechanism is related to a twisted intramolecular charge transfer in the excited state, followed by an ultrafast internal conversion. The chromophore twisting can strongly depend on the local electric field because the field can affect the activation energy. We present a spectroscopic method of evaluating local electric fields experienced by the chromophore in the protein environment. The method is based on linear and two-photon absorption spectroscopy, as well as on quantum-mechanically calculated parameters of the isolated chromophore. Using this method, which is substantiated by our molecular dynamics simulations, we obtain the components of electric field in the chromophore plane for seven different RFPs with the same chromophore structure. We find that in five of these RFPs, the nonradiative relaxation rate increases with the strength of the field along the chromophore axis directed from the center of imidazolinone ring to the center of phenolate ring. Furthermore, this rate depends on the corresponding electrostatic energy change (calculated from the known fields and charge displacements), in quantitative agreement with the Marcus theory of charge transfer. This result supports the dominant role of the twisted intramolecular charge transfer mechanism over the energy gap law for most of the studied RFPs. It provides important guidelines of how to shift the absorption wavelength of an RFP to the red, while keeping its brightness reasonably high.

Current first-line systemic treatment in most patients with metastatic hormone receptor-positive, HER-2 negative breast cancer is an aromatase inhibitor in combination with a cyclin dependant kinase (CDK) 4/6 inhibitor. Frequently, these patients require palliative radiotherapy (RT) for symptomatic disease management. There is a paucity of data on the safety of combining a CDK 4/6 inhibitor with palliative RT, with conflicting case reports in the literature. We report on 5 cases at our institution where enhanced radiotherapy toxicity was observed when palliative doses of RT was delivered during or prior to treatment with a CDK 4/6 inhibitor. After review of pre-clinical and mechanistic data, we hypothesise that the effects of CDK4/6 inhibition on normal tissue and the tumour microenvironment may impede tissue recovery and exacerbate acute radiation and radiation recall toxicities. Further studies are required to clarify the potential toxicities of this combination. Clinicians should consider the potential risks when combining CDK 4/6 inhibitors with palliative RT and individualise patient management accordingly.

Chemometric techniques such as partial least-squares (PLS) regression have been applied with huge success to a wide array of chemical problems including multicomponent analysis of analytes in complex mixtures. Despite this, there are few examples of laboratory pedagogical exercises that involve students in the acquisition of chemical data from infrared spectroscopic-based instrumentation, followed by quantitative chemometric analysis using PLS. In this article, we present a computational activity that introduces undergraduate students in an instrumental analysis laboratory setting to data acquisition using attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy followed by data analysis using PLS. The first part of the activity involved students creating mixture designs of binary terpene components consisting of p-cymene and limonene. These mixtures were then analyzed using an ATR-FTIR spectrometer, where students became familiarized with the instrument and were shown how to characterize and differentiate the aforementioned terpenes using their generated FTIR spectra. The second part of the activity involved preprocessing the acquired FTIR spectral data from the first part followed by the simultaneous quantitative determination of the prepared terpenes using PLS. On the basis of student surveys, it can be concluded that this convenient and inexpensive activity was ultimately successful in introducing students to the use of chemometrics for quantitative analysis of terpenes using an ATR-FTIR. This easy-to-do two-week activity can be used as a standalone for instrumental analysis laboratory classes and can even be integrated in advanced courses in applied spectroscopy and chemometrics.

Introduction: Innovative motor therapies have attempted to reduce upper extremity impairment after stroke but have not made substantial improvement as over 50% of people post-stroke continue to have sensorimotor deficits affecting their self-care and participation in daily activities. Intervention studies have focused on the role of increased dosing, however recent studies have indicated that timing of rehabilitation interventions may be as important as dosing and importantly, that dosing and timing interact in mediating effectiveness. This study is designed to empirically test dosing and timing.Methods and Analysis: In this single-blinded, interventional study, subjects will be stratified on two dimensions, impairment level (Fugl-Meyer Upper Extremity Assessment (FM) and presence or absence of Motor Evoked Potentials (MEPs) as follows; (1) Severe, FM score 10–19, MEP+, (2) Severe, FM score 10–19, MEP–, (3) Moderate, FM score 20–49, MEP+, (4) Moderate, FM score 20–49, MEP–. Subjects not eligible for TMS will be assigned to either group 2 (if severe) or group 3 (if moderate). Stratified block randomization will then be used to achieve a balanced assignment. Early Robotic/VR Therapy (EVR) experimental group will receive in-patient usual care therapy plus an extra 10 h of intensive upper extremity therapy focusing on the hand using robotically facilitated rehabilitation interventions presented in virtual environments and initiated 5–30 days post-stroke. Delayed Robotic/VR Therapy (DVR) experimental group will receive the same intervention but initiated 30–60 days post-stroke. Dose-matched usual care group (DMUC) will receive an extra 10 h of usual care initiated 5–30 days post-stroke. Usual Care Group (UC) will receive the usual amount of physical/occupational therapy.Outcomes: There are clinical, neurophysiological, and kinematic/kinetic measures, plus measures of daily arm use and quality of life. Primary outcome is the Action Research Arm Test (ARAT) measured at 4 months post-stroke.Discussion: Outcome measures will be assessed to determine whether there is an early time period in which rehabilitation will be most effective, and whether there is a difference in the recapture of premorbid patterns of movement vs. the development of an efficient, but compensatory movement strategy.Ethical Considerations: The IRBs of New Jersey Institute of Technology, Rutgers University, Northeastern University, and Kessler Foundation reviewed and approved all study protocols. Study was registered in https://ClinicalTrials.gov (NCT03569059) prior to recruitment. Dissemination will include submission to peer-reviewed journals and professional presentations.

Using mRNA sequencing and de novo transcriptome assembly, we identified, cloned, and characterized 9 previously undiscovered fluorescent protein (FP) homologs from Aequorea victoria and a related Aequorea species, with most sequences highly divergent from A. victoria green fluorescent protein (avGFP). Among these FPs are the brightest green fluorescent protein (GFP) homolog yet characterized and a reversibly photochromic FP that responds to UV and blue light. Beyond green emitters, Aequorea species express purple- and blue-pigmented chromoproteins (CPs) with absorbances ranging from green to far-red, including 2 that are photoconvertible. X-ray crystallography revealed that Aequorea CPs contain a chemically novel chromophore with an unexpected crosslink to the main polypeptide chain. Because of the unique attributes of several of these newly discovered FPs, we expect that Aequorea will, once again, give rise to an entirely new generation of useful probes for bioimaging and biosensing.

Introduction Radiotherapy technology and postgraduate medical training have both evolved significantly over the last 20 years. Clinical Oncology is a recognised craft specialty where the apprenticeship model of clinical training is applicable. The challenges of learning radiotherapy in the modern radiotherapy department workplace have not been comprehensively described and no optimal method has been identified.Methods and analysis Five Clinical Oncology trainers and five Clinical Oncology trainees at a regional cancer centre will be invited to undertake a semistructured interview regarding their personal accounts of learning radiotherapy. Both trainees and consultants will be treated as equal co-investors in the process of radiotherapy learning, with the common shared aim of passing radiotherapy skills from trainers to trainees. Interviews will last up to 40 min. After transcription, an interpretative phenomenological analysis will be performed. All trainees and trainers at the same centre (n=34) will then be invited to complete the same purpose-built questionnaire. Four trainers and three trainees have piloted the questionnaire, and input was sought from the national leads of the biennial UK Clinical Oncology training survey. Significance testing will be performed on predefined questions and thematic analysis on white space questions.Ethics and dissemination Medical education research is evolving in Clinical Oncology and Radiation Oncology but there are few studies comprehensively assessing this from the viewpoint of trainees and trainers. Pending the success of the proposed study, the approach detailed represents a novel method that could be used to identify the strengths and weaknesses of radiotherapy training in other centres and settings. Ethical and governance approvals have been granted by the University Research Ethics Committee and the Integrated Research Application System, respectively. This study has been funded by Friends of the Cancer Centre.

Abstract A novel treatment planning framework, the Relative Biological Effective Dose (RBED), for high Z nanoparticle (NP)-enhanced photon radiotherapy is developed and tested in silico for the medical exemplar of neoadjuvant (preoperative) breast cancer MV photon radiotherapy. Two different treatment scenarios, conventional and high Z NP enhanced, were explored with a custom Geant4 application that was developed to emulate the administration of a single 2 Gy fraction as part of a 50 Gy radiotherapy treatment plan. It was illustrated that there was less than a 1% difference in the dose deposition throughout the standard and high Z NP-doped adult female phantom. Application of the RBED framework found that the extent of possible biological response with high Z NP doping was great than expected via the dose deposition alone. It is anticipated that this framework will assist the scientific community in future high Z NP-enhanced in-silico, pre-clinical and clinical trials.

Honey exhibits antibacterial and antioxidant activities that are ascribed to its diverse secondary metabolites. In the Philippines, the antibacterial and antioxidant activities, as well as the bioactive metabolite contents of the honey, have not been thoroughly described. In this report, we investigated the in vitro antibacterial and antioxidant activities of honey from Apis mellifera and Tetragonula biroi, identified the compound responsible for the antibacterial activity, and compared the observed bioactivities and metabolite profiles to that of Manuka honey, which is recognized for its antibacterial and antioxidant properties. The secondary metabolite contents of honey were extracted using a nonionic polymeric resin followed by antibacterial and antioxidant assays, and then spectroscopic analyses of the phenolic and flavonoid contents. Results showed that honey extracts produced by T. biroi exhibits antibiotic activity against Staphylococcal pathogens as well as high antioxidant activity, which are correlated to its high flavonoid and phenolic content as compared to honey produced by A. mellifera. The bioassay-guided fractionation paired with Liquid Chromatography Mass Spectrometry (LCMS) and tandem MS analyses found the presence of the flavonoid isorhamnetin (3-methylquercetin) in T. biroi honey extract, which was demonstrated as one of the compounds with inhibitory activity against multidrug-resistant Staphylococcus aureus ATCC BAA-44. Our findings suggest that Philippine honey produced by T. biroi is a potential nutraceutical that possesses antibiotic and antioxidant activities.

Radical radiotherapy (RT) is a potentially curative treatment in non-small cell lung cancer (NSCLC) and is delivered in conventional 2-Gy fractions, hypofractionated and ablative stereotactic courses. No reliable, predictive biomarkers for the clinical events of local control, appearance of distant metastases and development of toxicity have been introduced in routine clinical practice. Such a test would enable the Radiotherapist to tailor the clinical management of individual patients, considering their pre-treatment characteristics, in order reduce the risk of recurrence or toxicity e.g., dose modification, accelerated fractionation, hypofractionation, or concurrent systemic therapy. The aim of this review was to map the published literature relating to investigations of the potential predictive value of patient or treatment characteristics in radical RT for NSCLC. These investigations should remain a research focus for disease control given the upward trends in lung cancer incidence, and for the avoidance of toxicity, given the survivorship afforded to the cohort of patients that do well with radical RT, or with the increasing range of systemic agents following metastatic relapse. The conclusion of the presented analysis is that there are no published, effective and validated predictive tools for estimation of risk of local/distant recurrence or toxicity after radical RT for NSCLC. The authors have identified an important space for future research in the field of lung cancer radiotherapy.

This supplement is intended to focus on the use of machine learning techniques to generate meaningful information on biological data. This supplement under Bioinformatics and Biology Insights aims to provide scientists and researchers working in this rapid and evolving field with online, open-access articles authored by leading international experts in this field. Advances in the field of biology have generated massive opportunities to allow the implementation of modern computational and statistical techniques. Machine learning methods in particular, a subfield of computer science, have evolved as an indispensable tool applied to a wide spectrum of bioinformatics applications. Thus, it is broadly used to investigate the underlying mechanisms leading to a specific disease, as well as the biomarker discovery process. With a growth in this specific area of science comes the need to access up-to-date, high-quality scholarly articles that will leverage the knowledge of scientists and researchers in the various applications of machine learning techniques in mining biological data.

Introduction The majority of stage III patients with non-small cell lung cancer (NSCLC) are unsuitable for concurrent chemoradiotherapy, the non-surgical gold standard of care. As the alternative treatment options of sequential chemoradiotherapy and radiotherapy alone are associated with high local failure rates, various intensification strategies have been employed. There is evidence to suggest that altered fractionation using hyperfractionation, acceleration, dose escalation, and individualisation may be of benefit. The MAASTRO group have pioneered the concept of ‘isotoxic’ radiotherapy allowing for individualised dose escalation using hyperfractionated accelerated radiotherapy based on predefined normal tissue constraints. This study aims to evaluate whether delivering isotoxic radiotherapy using intensity modulated radiotherapy (IMRT) is achievable.Methods and analysis Isotoxic IMRT is a multicentre feasibility study. From June 2014, a total of 35 patients from 7 UK centres, with a proven histological or cytological diagnosis of inoperable NSCLC, unsuitable for concurrent chemoradiotherapy will be recruited. A minimum of 2 cycles of induction chemotherapy is mandated before starting isotoxic radiotherapy. The dose of radiation will be increased until one or more of the organs at risk tolerance or the maximum dose of 79.2 Gy is reached. The primary end point is feasibility, with accrual rates, local control and overall survival our secondary end points. Patients will be followed up for 5 years.Ethics and dissemination The study has received ethical approval (REC reference: 13/NW/0480) from the National Research Ethics Service (NRES) Committee North West—Greater Manchester South. The trial is conducted in accordance with the Declaration of Helsinki and Good Clinical Practice (GCP). The trial results will be published in a peer-reviewed journal and presented internationally.Trial registration number NCT01836692; Pre-results.

Although a considerable proportion of serum lipids loci identified in European ancestry individuals (EA) replicate in African Americans (AA), interethnic differences in the distribution of serum lipids suggest that some genetic determinants differ by ethnicity. We conducted a comprehensive evaluation of five lipid candidate genes to identify variants with ethnicity-specific effects. We sequenced ABCA1, LCAT, LPL, PON1, and SERPINE1 in 48 AA individuals with extreme serum lipid concentrations (high HDLC/low TG or low HDLC/high TG). Identified variants were genotyped in the full population-based sample of AA (n = 1694) and tested for an association with serum lipids. rs328 (LPL) and correlated variants were associated with higher HDLC and lower TG. Interestingly, a stronger effect was observed on a "European" vs. "African" genetic background at this locus. To investigate this effect, we evaluated the region among West Africans (WA). For TG, the effect size among WA was the same in AA with only African local ancestry (2-3% lower TG), while the larger association among AA with local European ancestry matched previous reports in EA (10%). For HDLC, there was no association with rs328 in AA with only African local ancestry or in WA, while the association among AA with European local ancestry was much greater than what has been observed for EA (15 vs. ∼ 5 mg/dl), suggesting an interaction with an environmental or genetic factor that differs by ethnicity. Beyond this ancestry effect, the importance of African ancestry-focused, sequence-based work was also highlighted by serum lipid associations of variants that were in higher frequency (or present only) among those of African ancestry. By beginning our study with the sequence variation present in AA individuals, investigating local ancestry effects, and seeking replication in WA, we were able to comprehensively evaluate the role of a set of candidate genes in serum lipids in AA.

Posterior cruciate ligament (PCL) reconstructions are challenging surgeries. Recent advances have included double-bundle PCL, arthroscopic inlay, and all-inside techniques. This technical note presents an anatomic, single-bundle, all-inside PCL reconstruction with an anterior tibialis allograft GraftLink construct. The surgery was performed with FlipCutter guide pins and ACL TightRope RT. The case involved a 22-year-old woman with an isolated grade 3 PCL tear that had failed nonoperative treatment. The technique described is minimally invasive.

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.