Universal access: user needs for immersive captioning.

This article focuses on building a prototyping for immersive captioning following a user-centric approach. This methodology is characterised by following a bottom-up approach, where usability and user needs are at the heart of the development. Recent research on user requirements for captioning in immersive environments has shown that there is both a need for improvement and a wealth of research opportunities. The final aim is to identify how to display captions for an optimal viewing experience. This work began four years ago with some partial findings. We build from the lessons learnt, focussing on the user-centric design requirements cornerstone: prototyping. Our prototype framework integrates methods used in existing solutions aiming at instant contrast-and-compare functionalities. The first part of the article presents the state of the art for user requirements identifying the reasons behind the development of the prototyping framework. The second part of the article describes the two-stage framework development. The initial framework concept answered to the challenges resulting from the previous research. As soon as the first framework was developed, it became obvious that a second improved solution was required, almost as a showcase on how ideas can quickly be implemented for user testing, and for users to elicit requirements and creative solutions. The article finishes with a list of functionalities, resulting in new caption modes, and the opportunity of becoming a comprehensive immersive captions testbed, where tools such as eye-tracking, or physiological testing devices could be testing captions across any device with a web browser.

Temozolomide with irinotecan versus temozolomide, irinotecan plus bevacizumab for recurrent medulloblastoma of childhood: Report of a COG randomized Phase II screening trial.

BACKGROUND: Approximately 30% of children with medulloblastoma (MB) experience recurrence, which is usually incurable. This study compared the overall survival (OS) of patients receiving temozolomide (TMZ) and irinotecan with that of patients receiving TMZ, irinotecan, and bevacizumab for recurrent MB/central nervous system (CNS) primitive neuroectodermal tumor (PNET). METHODS: Patients with relapsed/refractory MB or CNS PNET were randomly assigned to receive TMZ (150 mg/m2 /day PO on days 1-5) and irinotecan (50 mg/m2 /day IV on days 1-5) with or without bevacizumab (10 mg/kg IV on days 1 and 15). RESULTS: One hundred five patients were eligible and treated on study. Median OS was 13 months in the standard arm and 19 months with the addition of bevacizumab; median event-free survival (EFS) was 6 months in the standard arm and 9 months with the addition of bevacizumab. The hazard ratio for death from the stratified relative-risk regression model is 0.63. Overall, 23 patients completed 12 courses of planned protocol therapy, 23% (12/52) in the experimental arm with bevacizumab versus 21% (11/53) in the standard arm. Toxicity profiles were comparable in both treatment arms. The estimate of the incidence of feasibility events associated with the bevacizumab arm is three of 52 (5.8%) (95% CI 1.2-16%). Events included myelosuppression, electrolyte abnormalities, diarrhea, and elevated transaminases. One intracranial hemorrhage event was observed in each arm. CONCLUSION: The addition of bevacizumab to TMZ/irinotecan significantly reduced the risk of death in children with recurrent MB. The combination was relatively well tolerated in this heavily pretreated cohort. The three-drug regimen demonstrated a sufficient risk reduction to warrant further investigation.

COVID-19, nationalism, and the politics of crisis: A scholarly exchange.

In this article, several scholars of nationalism discuss the potential for the COVID-19 pandemic to impact the development of nationalism and world politics. To structure the discussion, the contributors respond to three questions: (1) how should we understand the relationship between nationalism and COVID-19; (2) will COVID-19 fuel ethnic and nationalist conflict; and (3) will COVID-19 reinforce or erode the nation-state in the long run? The contributors formulated their responses to these questions near to the outset of the pandemic, amid intense uncertainty. This made it acutely difficult, if not impossible, to make predictions. Nevertheless, it was felt that a historically and theoretically informed discussion would shed light on the types of political processes that could be triggered by the COVID-19 pandemic. In doing so, the aim is to help orient researchers and policy-makers as they grapple with what has rapidly become the most urgent issue of our times.

Advances in quadrupole and time-of-flight mass spectrometry for peptide MRM based translational research analysis.

The application of unit resolution tandem quadrupole and high-resolution orthogonal acceleration ToF mass spectrometers for the quantitation and translational analysis of proteolytic peptides is described. The MS platforms were contrasted in terms of sensitivity and linear response. Moreover, the selectivity of the platforms was investigated and the effect on quantitative precision studied. Chromatographic LC conditions, including gradient length and configuration, were investigated with respect to speed/throughput, while minimizing isobaric interferences, thereby providing information with regard to practical sample cohort size limitations of LC-MS for large cohort experiments. In addition to these fundamental analytical performance metrics, precision and linear dynamic ranges were also studied. An LC-MS configuration that encompasses the best combination of throughput and analytical accuracy for translational studies was chosen, despite the MS platforms giving similar quantitative performance, and instances were identified where alternative combinations were found to be beneficial. This configuration was utilized to demonstrate that proteolytically digested nondepleted samples from heart failure patients could be classified with good discriminative power using a subset of proteins previously suggested as candidate biomarkers for cardiovascular diseases.

Progress and clinical potential of antibody-targeted therapy for arthritic damage.

INTRODUCTION: The advent of biologic drugs like infliximab, Etanercept, rituximab and tocilizumab has greatly improved the treatment of rheumatoid arthritis, however, increased risk of infection and high cost still remain unmet needs. A new generation of targeted therapeutics is being developed to target payload drug specifically to arthritic tissue; to concentrate the drug in the disease area and limit the off target systemic exposure. This might also reduce total effective dose. AREAS COVERED: This article summarizes the properties and progress of targeted therapies that have been published on PubMed, and addresses their clinical potential. Expert commentary: Incredible progress with targeted therapies has already been made in the short time since the principle was first proven in animal models in 2007 when targeting payload drug to overexpressed oncofetal domain of fibronectin in inflamed arthritic joints.

The Use of an Indwelling Catheter Protocol to Reduce Rates of Postoperative Urinary Tract Infections.

BACKGROUND: Catheter-associated urinary tract infections (CAUTI) have been associated with increases in morbidity and mortality as well as increased costs of hospitalization. At our institution, we implemented a protocol for indwelling catheter use, maintenance, and removal based on Center for Medicare and Medicaid Services (CMS) guidelines, in efforts to reduce CAUTI rates. METHODS: A hospital committee of quality stewards focused on several measures which included staff education, modification of existing systems to ensure compliance, and auditing of patient care areas for catheter utilization before implementation of the protocol. Pre- and postintervention postoperative cohorts were then identified through American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) for prevalence of CAUTI. Data were collected through chart review and postdischarge patient interviews. RESULTS: A total of 3873 patients were identified between September 2007 and December 2010. Thirty-six patients (2.6%) were diagnosed with a CAUTI in the preintervention group (N = 1404) compared to 38 (1.5%) patients who were diagnosed with a CAUTI in the postintervention group (N = 2469). There was a 1.1% decrease in CAUTI rate after protocol implementation (P < .028). This reduction in rates resulted in annual estimated savings of $81,840 to $320,540 annually. CONCLUSION: A simple, multifaceted approach consisting of staff education and changing existing processes to reflect best care practices has the potential to significantly reduce the incidence of postoperative CAUTI.

Additional precursor purification in isobaric mass tagging experiments by traveling wave ion mobility separation (TWIMS).

Despite the increasing popularity of data-independent acquisition workflows, data-dependent acquisition (DDA) is still the prevalent method of LC-MS-based proteomics. DDA is the basis of isobaric mass tagging technique, a powerful MS2 quantification strategy that allows coanalysis of up to 10 proteomics samples. A well-documented limitation of DDA, however, is precursor coselection, whereby a target peptide is coisolated with other ions for fragmentation. Here, we investigated if additional peptide purification by traveling wave ion mobility separation (TWIMS) can reduce precursor contamination using a mixture of Saccharomyces cerevisiae and HeLa proteomes. In accordance with previous reports on FAIMS-Orbitrap instruments, we find that TWIMS provides a remarkable improvement (on average 2.85 times) in the signal-to-noise ratio for sequence ions. We also report that TWIMS reduces reporter ions contamination by around one-third (to 14-15% contamination) and even further (to 6-9%) when combined with a narrowed quadrupole isolation window. We discuss challenges associated with applying TWIMS purification to isobaric mass tagging experiments, including correlation between ion m/z and drift time, which means that coselected peptides are expected to have similar mobility. We also demonstrate that labeling results in peptides having more uniform m/z and drift time distributions than observed for unlabeled peptides. Data are available via ProteomeXchange with identifier PXD001047.

Educational impact of an assessment of medical students' collaboration in health care teams.

CONTEXT: This paper explores how structured feedback and other features of workplace-based assessment (WBA) impact on medical students' learning in the context of an evaluation of a workplace-based performance assessment: the teamwork mini-clinical evaluation exercise (T-MEX). The T-MEX enables observation-based measurement of and feedback on the behaviours required to collaborate effectively as a junior doctor within the health care team. The instrument is based on the mini-clinical evaluation exercise (mini-CEX) format and focuses on clinical encounters such as consultations with medical and allied health professionals, discharge plan preparation, handovers and team meetings. METHODS: The assessment was implemented during a 6-week period in 2010 with 25 medical students during their final clinical rotation. Content analysis was conducted on the written feedback provided by 23 assessors and the written reflections and action plans proposed by the 25 student participants (in 88 T-MEX forms). Semi-structured interviews with seven assessors and three focus groups with 14 student participants were conducted and the educational impact was explored through thematic analysis. RESULTS: The study enabled the identification of features of WBA that promote the development of collaborative competencies. The focus of the assessment on clinical encounters and behaviours important for collaboration provided opportunities for students to engage with the health care team and highlighted the role of teamwork in these encounters. The focus on specific behaviours and a stage-appropriate response scale helped students identify learning goals and facilitated the provision of focused feedback. Incorporating these features within an established format helped students and supervisors to engage with the instrument. Extending the format to include structured reflection enabled students to self-evaluate and develop plans for improvement. CONCLUSIONS: The findings illuminate the mechanisms by which WBA facilitates learning. The educational features highlighted include effectively structured feedback processes, support for situated learning, a positive backwash (facilitation of learning through preparation for the assessment), and facilitation of informed self-assessment.

Mass spectrometry-based proteomic analysis of the matrix microenvironment in pluripotent stem cell culture.

The cellular microenvironment comprises soluble factors, support cells, and components of the extracellular matrix (ECM) that combine to regulate cellular behavior. Pluripotent stem cells utilize interactions between support cells and soluble factors in the microenvironment to assist in the maintenance of self-renewal and the process of differentiation. However, the ECM also plays a significant role in shaping the behavior of human pluripotent stem cells, including embryonic stem cells (hESCs) and induced pluripotent stem cells. Moreover, it has recently been observed that deposited factors in a hESC-conditioned matrix have the potential to contribute to the reprogramming of metastatic melanoma cells. Therefore, the ECM component of the pluripotent stem cell microenvironment necessitates further analysis. In this study we first compared the self-renewal and differentiation properties of hESCs grown on Matrigel™ pre-conditioned by hESCs to those on unconditioned Matrigel™. We determined that culture on conditioned Matrigel™ prevents differentiation when supportive growth factors are removed from the culture medium. To investigate and identify factors potentially responsible for this beneficial effect, we performed a defined SILAC MS-based proteomics screen of hESC-conditioned Matrigel™. From this proteomics screen, we identified over 80 extracellular proteins in matrix conditioned by hESCs and induced pluripotent stem cells. These included matrix-associated factors that participate in key stem cell pluripotency regulatory pathways, such as Nodal/Activin and canonical Wnt signaling. This work represents the first investigation of stem-cell-derived matrices from human pluripotent stem cells using a defined SILAC MS-based proteomics approach.

3D measuring tool for estimating femoroacetabular impingement.

Osteoarthritis of the hip is commonly caused by the repetitive contact between abnormal skeletal prominences between the anterosuperior femoral head-neck junction and the rim of the acetabular socket. Current methods for estimating femoroacetabular impingement by analyzing the sphericity of the femoral head require manual measurements which are both inaccurate and open to interpretation. In this research we provide a prototype software tool for improving this estimation.

A directed particle system for optimised visualization of blood flow in complex networks.

This paper introduces a novel technique for the visualization of blood (or other fluid) flowing through a complex 3D network of vessels. The Directed Particle System (DPS) approach is loosely based on the computer graphics concept of flocking agents. It has been developed and optimised to provide effective real time visualization and qualitative simulation of fluid flow. There are many potential applications of DPS, and one example - a decision support tool for coronary collateralization - is discussed.

Phase II Randomized Trial of Lenalidomide in Children With Pilocytic Astrocytomas and Optic Pathway Gliomas: A Report From the Children's Oncology Group.

PURPOSE: Children with low-grade glioma often require long-term therapy and suffer from treatment morbidity. Although targeted agents are promising, tumor targets often encompass normal developmental pathways and long-term effects of inhibition are unknown. Lenalidomide is an immunomodulatory agent with wide-ranging properties. Phase I studies indicated greater tolerability of lenalidomide in children compared with adults and a potential dose-response effect. PATIENTS AND METHODS: We performed a phase II trial of lenalidomide in children with pilocytic astrocytomas and optic pathway gliomas who failed initial therapy. Primary objectives included determination of objective response rate of children randomly assigned to regimen A, low-dose (20 mg/m2/dose), or regimen B, high-dose (115 mg/m2/dose) lenalidomide, and assessment for early progression. Secondary objectives included estimation of event-free survival, overall survival, incidence of toxic events, and assessment of plasma lenalidomide concentrations. Lenalidomide was administered once daily × 21 days of each 28-day cycle for each regimen. RESULTS: Seventy-four eligible patients were enrolled (n = 37, each arm). The predefined activity level of interest was achieved for both arms. Four objective responses were observed in each arm, and the number of early progressors was low. Eighteen patients completed 26 cycles of therapy (regimen A, n = 12; regimen B, n = 6). The median number of cycles was 14 (range, 2-26) for regimen A and 11 for regimen B (range, 1-26). Of 74 eligible patients who received study drug, 30 required dose reduction for toxicity (regimen A, n = 6; regimen B, n = 24) and 16 discontinued because of toxicity (regimen A, n = 2; regimen B, n = 14). CONCLUSION: Lenalidomide demonstrates a sufficient level of activity in children with low-grade glioma to warrant further exploration. Low-dose (20 mg/m2/dose administered once daily × 21 days of each 28-day cycle) lenalidomide appears to have better tolerability with comparable activity.

Comparison of one- and two-dimensional liquid chromatography approaches in the label-free quantitative analysis of Methylocella silvestris.

The proteome of the bacterium Methylocella silvestris has been characterized using reversed phase ultra high pressure liquid chromatography (UPLC) and two-dimensional reversed phase (high pH)-reversed phase (low pH) UPLC prior to mass spectrometric analysis. Variations in protein expression levels were identified with the aid of label-free quantification in a study of soluble protein extracts from the organism grown using methane, succinate, or propane as a substrate. The number of first dimensional fractionation steps has been varied for 2D analyses, and the impact on data throughput and quality has been demonstrated. Comparisons have been made regarding required experimental considerations including total loading of biological samples required, instrument time, and resulting data file sizes. The data obtained have been evaluated with respect to number of protein identifications, confidence of assignments, sequence coverage, relative levels of proteins, and dynamic range. Good qualitative and quantitative agreement was observed between the different approaches, and the potential benefits and limitations of the reversed phase-reversed phase UPLC technique in label-free analysis are discussed. A preliminary screen of the protein regulation data has also been performed, providing evidence for a possible propane assimilation route.

Development of a novel recombinant biotherapeutic with applications in targeted therapy of human arthritis.

OBJECTIVE: To isolate recombinant antibodies with specificity for human arthritic synovium and to develop targeting reagents with joint-specific delivery capacity for therapeutic and/or diagnostic applications. METHODS: In vivo single-chain Fv (scFv) antibody phage display screening using a human synovial xenograft model was used to isolate antibodies specific to the microvasculature of human arthritic synovium. Single-chain Fv antibody tissue-specific reactivity was assessed by immunostaining of synovial tissues from normal controls and from patients with rheumatoid arthritis and osteoarthritis, normal human tissue arrays, and tissues from other patients with inflammatory diseases displaying neovasculogenesis. In vivo scFv antibody tissue-specific targeting capacity was examined in the human synovial xenograft model using both (125)I-labeled and biotinylated antibody. RESULTS: We isolated a novel recombinant human antibody, scFv A7, with specificity for the microvasculature of human arthritic synovium. We showed that in vivo, this antibody could efficiently target human synovial microvasculature in SCID mice transplanted with human arthritic synovial xenografts. Our results demonstrated that scFv A7 antibody had no reactivity with the microvasculature or with other cellular components found in a comprehensive range of normal human tissues including normal human synovium. Further, we showed that the reactivity of the scFv A7 antibody was not a common feature of neovasculogenesis associated with chronic inflammatory conditions. CONCLUSION: Here we report for the first time the identification of an scFv antibody, A7, that specifically recognizes an epitope expressed in the microvasculature of human arthritic synovium and that has the potential to be developed as a joint-specific pharmaceutical.

Using ion purity scores for enhancing quantitative accuracy and precision in complex proteomics samples.

To accurately determine the quantitative change of peptides and proteins in complex proteomics samples requires knowledge of how well each ion has been measured. The precision of each ions' calculated area is predicated on how uniquely it occupies its own space in m/z and elution time. Given an initial assumption that prior to the addition of the "heavy" label, all other ion detections are unique, which is arguably untrue, an initial attempt at quantifying the pervasiveness of ion interference events in a representative binary SILAC experiment was made by comparing the centered m/z and retention time of the ion detections from the "light" variant to its "heavy" companion. Ion interference rates were determined for LC-MS data acquired at mass resolving powers of 20 and 40 K with and without ion mobility separation activated. An ion interference event was recorded, if present in the companion dataset was an ion within ± its Δ mass at half-height, ±15 s of its apex retention time and if utilized by ±1 drift bin. Data are presented illustrating a definitive decrease in the frequency of ion interference events with each additional increase in selectivity of the analytical workflow. Regardless of whether the quantitative experiment is a composite of labeled samples or label free, how well each ion is measured can be determined given knowledge of the instruments mass resolving power across the entire m/z scale and the ion detection algorithm reporting both the centered m/z and Δ mass at half-height for each detected ion. Given these measurements, an effective resolution can be calculated and compared with the expected instrument performance value providing a purity score for the calculated ions' area based on mass resolution. Similarly, chromatographic and drift purity scores can be calculated. In these instances, the error associated to an ions' calculated peak area is estimated by examining the variation in each measured width to that of their respective experimental median. Detail will be disclosed as to how a final ion purity score was established, providing a first measure of how accurately each ions' area was determined as well as how precise the calculated quantitative change between labeled or unlabelled pairs were determined. Presented is how common ion interference events are in quantitative proteomics LC-MS experiments and how ion purity filters can be utilized to overcome and address them, providing ultimately more accurate and precise quantification results across a wider dynamic range.

Does a summative portfolio foster the development of capabilities such as reflective practice and understanding ethics? An evaluation from two medical schools.

Portfolios need to be evaluated to determine whether they encourage students to develop in capabilities such as reflective practice and ethical judgment. The aims of this study were (i) to determine whether preparing a portfolio helps promote students' development in a range of capabilities including understanding ethical and legal principles, reflective practice and effective communication, and (ii) to determine to what extent the format of the portfolio affected the outcome by comparing the experiences of students at two different medical schools. A questionnaire was designed to evaluate undergraduate medical students' experiences of completing a portfolio at two medical schools. A total of 526 (45% response rate) students answered the on-line questionnaire. Students from both medical schools gave the highest ranking for the portfolio as a trigger for reflective practice. 63% of students agreed their portfolio helped them develop reflective practice skills (p < 0.001), whereas only 22% disagreed. 48% of students agreed portfolios helped them understand ethical and legal principles whereas 29% disagreed (p < 0.001). In contrast, only 34% of students thought the portfolio helped them to develop effective communication. Students perceive portfolio preparation as an effective learning tool for the development of capabilities such as understanding ethical and legal principles and reflective practice, whereas other capabilities such as effective communication require complementary techniques and other modes of assessment.

A Phase 2 Trial of Response-Based Radiation Therapy for Localized Central Nervous System Germ Cell Tumors: Patterns of Failure and Radiation Dosimetry for Nongerminomatous Germ Cell Tumors.

PURPOSE: Children's Oncology Group study ACNS1123 tested the efficacy of reduced dose and field of radiation therapy (RT) for patients with localized nongerminomatous germ cell tumors (NGGCT) who achieved a complete (CR) or partial response (PR) to chemotherapy. Here, we evaluate the quality of RT and patterns of failure for patients eligible for reduced RT in this phase 2 trial. METHODS AND MATERIALS: Patients with localized NGGCT with CR/PR after induction chemotherapy received reduced RT to 30.6 Gy whole ventricular irradiation and 54 Gy tumor-bed total dose. An atlas was provided to assist with complex RT volumes. Early interventional review was performed for the initial RT plan. Complete RT plans for all patients and images of relapsed patients were centrally reviewed at completion of therapy. RESULTS: Between May 2012 and September 2016, 107 eligible patients were enrolled and 66 achieved a CR/PR after induction chemotherapy (± second-look surgery) and were eligible for reduced RT. Median follow-up was 4.4 years. Median age was 11.0 years (3.7-21.6), and 75% were male. Progression-free survival and overall survival at 4 years were 87.9% ± 4.0% and 92.4% ± 3.3% for 66 evaluable patients, respectively. Eight patients relapsed: 6 with isolated spinal relapse and 2 with disease in the brain and spine. After central review, 62 (94%) patients had RT targets contoured and dose delivered per protocol. None of the patients with deviations (n = 4) have progressed. CONCLUSIONS: Patterns of failure suggest the spine is at risk for recurrence for patients with localized NGGCT who receive reduced RT after a CR/PR to induction chemotherapy. Although survival data are encouraging, the pattern of failure has influenced the next prospective trial design. RT compliance was excellent despite complexity of radiation volumes, suggesting that providing visual guidance in the form of an online atlas contributes to higher quality RT plans.

Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy.

The SARS-CoV-2 pandemic has differentially impacted populations across race and ethnicity. A multi-omic approach represents a powerful tool to examine risk across multi-ancestry genomes. We leverage a pandemic tracking strategy in which we sequence viral and host genomes and transcriptomes from nasopharyngeal swabs of 1049 individuals (736 SARS-CoV-2 positive and 313 SARS-CoV-2 negative) and integrate them with digital phenotypes from electronic health records from a diverse catchment area in Northern California. Genome-wide association disaggregated by admixture mapping reveals novel COVID-19-severity-associated regions containing previously reported markers of neurologic, pulmonary and viral disease susceptibility. Phylodynamic tracking of consensus viral genomes reveals no association with disease severity or inferred ancestry. Summary data from multiomic investigation reveals metagenomic and HLA associations with severe COVID-19. The wealth of data available from residual nasopharyngeal swabs in combination with clinical data abstracted automatically at scale highlights a powerful strategy for pandemic tracking, and reveals distinct epidemiologic, genetic, and biological associations for those at the highest risk.

Proteomic analysis of extracellular matrices used in stem cell culture.

Numerous matrices for the growth of human embryonic stem cells (hESC) in vitro have been described. However, their exact composition is typically unknown. Information on the components of these matrices will aid in the development of a fully defined growth surface for hESCs. These matrices typically consist of mixture of proteins present in a wide range of abundance making their characterization challenging. In this study, we performed the proteomic analysis of five previously uncharacterized matrices: CellStart, Human Basement Membrane Extract (Human BME), StemXVivo, Bridge Human Extracellular Matrix (BridgeECM), and mouse embryonic fibroblast conditioned matrix (MEF-CMTX). Based on a proteomics protocol optimized using lysates from HeLa cells, we undertook the analysis of the five complex extracellular matrix (ECM) samples using a combination of strong anion and cation exchange chromatography and SDS-PAGE. For each of these matrices, we identify numerous proteins, indicating their complex nature. We also compared these results with a similar proteomics analysis of the growth matrix, Matrigel™. From these analyses, we observed that fibronectin is a primary component of nearly all hESC supportive matrices. This observation led to the investigation of the suitability of fibronectin as a defined ECM for the growth of hESCs. We found that fibronectin promotes the maintenance of pluripotent H9 and CA1 hESCs in an undifferentiated state using mTeSR1 medium. This finding validates the utility of characterizing matrices used for hESC growth in revealing ECM components required for culturing hESCs in a universally applicable defined system.