Data-driven and hybrid coastal morphological prediction methods for mesoscale forecasting

It is now common for coastal planning to anticipate changes anywhere from 70 to 100 years into the future. The process models developed and used for scheme design or for large-scale oceanography are currently inadequate for this task. This has prompted the development of a plethora of alternative methods. Some, such as reduced complexity or hybrid models simplify the governing equations retaining processes that are considered to govern observed morphological behaviour. The computational cost of these models is low and they have proven effective in exploring morphodynamic trends and improving our understanding of mesoscale behaviour. One drawback is that there is no generally agreed set of principles on which to make the simplifying assumptions and predictions can vary considerably between models. An alternative approach is data-driven techniques that are based entirely on analysis and extrapolation of observations. Here, we discuss the application of some of the better known and emerging methods in this category to argue that with the increasing availability of observations from coastal monitoring programmes and the development of more sophisticated statistical analysis techniques data-driven models provide a valuable addition to the armoury of methods available for mesoscale prediction. The continuation of established monitoring programmes is paramount, and those that provide contemporaneous records of the driving forces and the shoreline response are the most valuable in this regard. In the second part of the paper we discuss some recent research that combining some of the hybrid techniques with data analysis methods in order to synthesise a more consistent means of predicting mesoscale coastal morphological evolution. While encouraging in certain applications a universally applicable approach has yet to be found. The route to linking different model types is highlighted as a major challenge and requires further research to establish its viability. We argue that key elements of a successful solution will need to account for dependencies between driving parameters, (such as wave height and tide level), and be able to predict step changes in the configuration of coastal systems

Evaluation of pedometry as a patient-centered outcome in patients undergoing hematopoietic cell transplant (HCT): A comparison of pedometry and patient-reports of symptoms, health, and quality of life.

Aims We evaluated pedometry as a novel patient-centered outcome because it enables passive continuous assessment of activity and may provide information about the consequences of symptomatic toxicity complementary to self-report. Methods Adult patients undergoing hematopoietic cell transplant (HCT) wore pedometers and completed PRO assessments during transplant hospitalization (4 weeks) and 4 weeks post-discharge. Patient reports of symptomatic treatment toxicities (single items from PROCTCAE, http://healthcaredelivery.cancer.gov/pro-ctcae) and symptoms, physical health, mental health, and quality of life (PROMIS Global-10, http://nih.promis.org), assessed weekly with 7-day recall on Likert scales, were compared individually with pedometry data, summarized as average daily steps per week, using linear mixed models. Results Thirty-two patients [mean age 55 (SD = 14), 63 % male, 84 % white, 56 % autologous, 43 % allogeneic] completed a mean 4.6 (SD = 1.5, range 1–8) evaluable assessments. Regression model coefficients (β) indicated within-person decrements in average daily steps were associated with increases in pain (β = -852; 852 fewer steps per unit increase in pain score, p<0.001), fatigue (β = -886, p<0.001), vomiting (β = -518, p<0.01), shaking/chills (β = -587, p<0.01), diarrhea (β = -719, p<0.001), shortness of breath (β = -1018, p<0.05), reduction in carrying out social activities (β = 705, p<0.01) or physical activities (β = 618, p<0.01), and global physical health (β = 101, p<0.001), but not global mental health or quality of life. Conclusions In this small sample of HCT recipients, more severe symptoms, impaired physical health, and restrictions in the performance of usual daily activities were associated with statistically significant decrements in objectively measured daily steps. Pedometry may be a valuable outcome measure and validation anchor in clinical research

Sequence-based prediction for vaccine strain selection and identification of antigenic variability in foot-and-mouth disease virus

Identifying when past exposure to an infectious disease will protect against newly emerging strains is central to understanding the spread and the severity of epidemics, but the prediction of viral cross-protection remains an important unsolved problem. For foot-and-mouth disease virus (FMDV) research in particular, improved methods for predicting this cross-protection are critical for predicting the severity of outbreaks within endemic settings where multiple serotypes and subtypes commonly co-circulate, as well as for deciding whether appropriate vaccine(s) exist and how much they could mitigate the effects of any outbreak. To identify antigenic relationships and their predictors, we used linear mixed effects models to account for variation in pairwise cross-neutralization titres using only viral sequences and structural data. We identified those substitutions in surface-exposed structural proteins that are correlates of loss of cross-reactivity. These allowed prediction of both the best vaccine match for any single virus and the breadth of coverage of new vaccine candidates from their capsid sequences as effectively as or better than serology. Sub-sequences chosen by the model-building process all contained sites that are known epitopes on other serotypes. Furthermore, for the SAT1 serotype, for which epitopes have never previously been identified, we provide strong evidence - by controlling for phylogenetic structure - for the presence of three epitopes across a panel of viruses and quantify the relative significance of some individual residues in determining cross-neutralization. Identifying and quantifying the importance of sites that predict viral strain cross-reactivity not just for single viruses but across entire serotypes can help in the design of vaccines with better targeting and broader coverage. These techniques can be generalized to any infectious agents where cross-reactivity assays have been carried out. As the parameterization uses pre-existing datasets, this approach quickly and cheaply increases both our understanding of antigenic relationships and our power to control disease

Evaluation of different recall periods for the US National Cancer Institute’s Patient-Reported Outcomes version of the Common Terminology Criteria for Adverse Events (PRO-CTCAE)

Aims—The U.S. National Cancer Institute recently developed the Patient-Reported Outcomes version of the Common Terminology Criteria for Adverse Events (PRO-CTCAE). PRO-CTCAE is a library of questions for clinical trial participants to self-report symptomatic adverse events (e.g., nausea). The objective of this study is to inform evidence-based selection of a recall period when PRO-CTCAE is included in a trial. We evaluated differences between 1-week, 2-week, 3-week, and 4-week recall periods, using daily reporting as the reference. Methods—English-speaking patients with cancer receiving chemotherapy and/or radiotherapy were enrolled at four U.S. cancer centers and affiliated community clinics. Participants completed 27 PRO-CTCAE items electronically daily for 28 days, and then weekly over 4 weeks, using 1-week, 2-week, 3-week, and 4-week recall periods. For each recall period, mean differences, effect sizes, and intraclass correlation coefficients were calculated to evaluate agreement between the maximum of daily ratings and the corresponding ratings obtained using longer recall periods (e.g., maximum of daily scores over 7 days vs. 1-week recall). Analyses were repeated using the average of daily scores within each recall period rather than the maximum of daily scores. Results—127 subjects completed questionnaires (57% male; median age 57). The median of the 27 mean differences in scores on the PRO-CTCAE 5-point response scale comparing the maximum daily versus the longer recall period (and corresponding effect size), was −0.20 (−0.20) for 1-week recall; −0.36 (−0.31) for 2-week recall; −0.45 (−0.39) for 3-week recall; and −0.47 (−0.40) for 4-week recall. The median intraclass correlation across 27 items between the maximum of daily ratings and the corresponding longer recall ratings for 1-week recall was 0.70 (range: 0.54–0.82); 2-week recall: 0.74 (range: 0.58–0.83); 3-week recall: 0.72 (range: 0.61–0.84); and 4-week recall: 0.72 (range: 0.64–0.86). Similar results were observed for all analyses using the average of daily scores rather than the maximum of daily scores. Conclusions—1-week recall corresponds best to daily reporting. Although intraclass correlations remain stable over time, there are small but progressively larger differences between daily and longer recall periods at 2, 3, and 4 weeks, respectively. The preferred recall period for the PRO-CTCAE is the past 7 days, although investigators may opt for recall periods of 2, 3, or 4 weeks with an understanding that there may be some information loss

The emergence of a stable neuronal ensemble from a wider pool of activated neurons in the dorsal medial prefrontal cortex during appetitive learning in mice

Animals selectively respond to environmental cues associated with food reward to optimize nutrient intake. Such appetitive CS-US associations are thought to be encoded in select, stable neuronal populations or neuronal ensembles, which undergo physiological modifications during appetitive conditioning. These ensembles in the medial prefrontal cortex (mPFC) control well-established, cue-evoked food seeking, but the mechanisms involved in the genesis of these ensembles are unclear. Here, we utilized male Fos-GFP mice that express the green fluorescent protein (GFP) in recently behaviorally-activated neurons, to reveal how dorsal mPFC neurons are recruited and modified to encode CS-US memory representations using an appetitive conditioning task. In the initial conditioning session, animals did not exhibit discriminated, cue-selective food seeking, but did so in later sessions indicating that a CS-US association was established. Using microprism-based in vivo 2-Photon imaging, we revealed that only a minority of neurons activated during the initial session was consistently activated throughout subsequent conditioning sessions and during cue-evoked memory recall. Notably, using ex vivo electrophysiology we found that neurons activated following the initial session exhibited transient hyper-excitability. Chemogenetically enhancing the excitability of these neurons throughout subsequent conditioning sessions interfered with the development of reliable cue-selective food seeking, indicated by persistent, non-discriminated performance. We demonstrate how appetitive learning consistently activates a subset of neurons to form a stable neuronal ensemble during the formation of a CS-US association. This ensemble may arise from a pool of hyper-excitable neurons activated during the initial conditioning session

TOM40 Mediates Mitochondrial Dysfunction Induced by α-Synuclein Accumulation in Parkinson's Disease.

Alpha-synuclein (α-Syn) accumulation/aggregation and mitochondrial dysfunction play prominent roles in the pathology of Parkinson's disease. We have previously shown that postmortem human dopaminergic neurons from PD brains accumulate high levels of mitochondrial DNA (mtDNA) deletions. We now addressed the question, whether alterations in a component of the mitochondrial import machinery -TOM40- might contribute to the mitochondrial dysfunction and damage in PD. For this purpose, we studied levels of TOM40, mtDNA deletions, oxidative damage, energy production, and complexes of the respiratory chain in brain homogenates as well as in single neurons, using laser-capture-microdissection in transgenic mice overexpressing human wildtype α-Syn. Additionally, we used lentivirus-mediated stereotactic delivery of a component of this import machinery into mouse brain as a novel therapeutic strategy. We report here that TOM40 is significantly reduced in the brain of PD patients and in α-Syn transgenic mice. TOM40 deficits were associated with increased mtDNA deletions and oxidative DNA damage, and with decreased energy production and altered levels of complex I proteins in α-Syn transgenic mice. Lentiviral-mediated overexpression of Tom40 in α-Syn-transgenic mice brains ameliorated energy deficits as well as oxidative burden. Our results suggest that alterations in the mitochondrial protein transport machinery might contribute to mitochondrial impairment in α-Synucleinopathies

Clustering cliques for graph-based summarization of the biomedical research literature

BACKGROUND: Graph-based notions are increasingly used in biomedical data mining and knowledge discovery tasks. In this paper, we present a clique-clustering method to automatically summarize graphs of semantic predications produced from PubMed citations (titles and abstracts). RESULTS: SemRep is used to extract semantic predications from the citations returned by a PubMed search. Cliques were identified from frequently occurring predications with highly connected arguments filtered by degree centrality. Themes contained in the summary were identified with a hierarchical clustering algorithm based on common arguments shared among cliques. The validity of the clusters in the summaries produced was compared to the Silhouette-generated baseline for cohesion, separation and overall validity. The theme labels were also compared to a reference standard produced with major MeSH headings. CONCLUSIONS: For 11 topics in the testing data set, the overall validity of clusters from the system summary was 10% better than the baseline (43% versus 33%). While compared to the reference standard from MeSH headings, the results for recall, precision and F-score were 0.64, 0.65, and 0.65 respectively

Perspectives of Portuguese People with Physical Disabilities Regarding Their Sexual Health: A Focus Group Study

The World Health Organization has considered sexual health as a major dimension of global health and a sexual right. However, the sexual health of people with physical disabilities is still poorly addressed by health and social care professionals, and it is very stigmatized by society. This study aimed to assess the perspectives of Portuguese people living with physical disabilities regarding issues affecting their sexual health. Nine women and 17 men with different physical disabilities participated in the study. Participants were recruited from a professional rehabilitation facility located in the North of Portugal and were assigned to four groups in one-hour sessions. Three main categories emerged from the content analysis: (1) meanings and beliefs regarding sexuality; (2) experiences of sexuality; (3) necessary changes. Despite the positive social changes towards sexuality, participants expressed that their sexual rights are still unfulfilled, as they live in a context that perpetuates their dependency. They pointed out low self-esteem, prejudice and social isolation, poor architectural accessibility and scarcity of financial support as some of the barriers to their lives and their sexual health. Finally, participants identified the main needs regarding their sexual health, such as: access to specialized information; training for health professionals. This study gives voice to people with physical disabilities and sheds light into both individual and contextual factors affecting their sexual health. Of utmost importance, this study draws attention to the need for reinforcing sexuality of people with disabilities in the social agenda and brings implications for future research and practice.This study was supported by a Grant attributed to the first author by the Portuguese Foundation for Science and Technology (SFRH/BD/112168/2015)info:eu-repo/semantics/publishedVersio

Feasibility of Frequent Patient-Reported Outcome Surveillance in Patients Undergoing Hematopoietic Cell Transplantation

Patient-reported outcomes (PROs), including symptoms and health-related quality of life (HRQOL), provide a patient-centered description of hematopoietic cell transplantation (HCT)-related toxicity. These data characterize the patient experience after HCT and may have prognostic usefulness for long-term outcomes after HCT. We conducted a study of 32 patients after HCT (10 autologous HCT recipients, 11 full-intensity conditioning allogeneic HCT recipients, and 11 reduced-intensity conditioning allogeneic HCT recipients) to determine the feasibility of weekly electronic PRO collection from HCT until day (D) + 100. We used questions from the PRO version of the Common Terminology Criteria for Adverse Events to capture symptoms, and the Patient-Reported Outcomes Measurement Information System Global Health scale to measure physical and mental HRQOL. The vast majority (94%) of patients used the electronic PRO system, with only 6% opting for paper-and-pencil only. The median weekly percentage of participants who completed the surveys was 100% in all cohorts through hospital discharge, and remained 100% for the autologous HCT and reduced-intensity allogeneic HCT cohorts through D+100. Patients were satisfied with the electronic system, giving high marks for readability, comfort, and questionnaire length. Symptom severity varied by absolute level and type of symptom across the 3 cohorts, with the full-intensity allogeneic HCT cohort exhibiting the greatest median overall symptom severity, peaking at D+7. Median physical health HRQOL scores decreased with time in the 3 cohorts, and HRQOL was generally correlated with overall symptom severity. Our results demonstrate the feasibility of frequent electronic PROs in the early post-HCT period. Future studies in larger populations to explore predictive models using frequent PRO data for outcomes, including long-term HRQOL and survival, are warranted

Performance Measures Based on How Adults With Cancer Feel and Function: Stakeholder Recommendations and Feasibility Testing in Six Cancer Centers

PURPOSE Patient-reported outcome measures (PROMs) that assess how patients feel and function have potential for evaluating quality of care. Stakeholder recommendations for PRO-based performance measures (PMs) were elicited, and feasibility testing was conducted at six cancer centers. METHODS Interviews were conducted with 124 stakeholders to determine priority symptoms and risk adjustment variables for PRO-PMs and perceived acceptability. Stakeholders included patients and advocates, caregivers, clinicians, administrators, and thought leaders. Feasibility testing was conducted in six cancer centers. Patients completed PROMs at home 5-15 days into a chemotherapy cycle. Feasibility was operationalized as $75$ 75% patient acceptability. RESULTS Stakeholder priority PRO-PMs for systemic therapy were GI symptoms (diarrhea, constipation, nausea, vomiting), depression/anxiety, pain, insomnia, fatigue, dyspnea, physical function, and neuropathy. Recommended risk adjusters included demographics, insurance type, cancer type, comorbidities, emetic risk, and difficulty paying bills. In feasibility testing, 653 patients enrolled (approximately 110 per site), and 607 (93%) completed PROMs, which indicated high feasibility for home collection. The majority of patients (470 of 607; 77%) completed PROMs without a reminder call, and 137 (23%) of 607 completed them after a reminder call. Most patients (72%) completed PROMs through web, 17% paper, or 2% interactive voice response (automated call that verbally asked patient questions). For acceptability, . 95% of patients found PROM items to be easy to understand and complete. CONCLUSION Clinicians, patients, and other stakeholders agree that PMs that are based on how patients feel and function would be an important addition to quality measurement. This study also shows that PRO-PMs can be feasibly captured at home during systemic therapy and are acceptable to patients. PRO-PMs may add value to the portfolio of PMs as oncology transitions from fee-for-service payment models to performance-based care that emphasizes outcome measures