Magnetic Resonance Fingerprinting Using a Residual Convolutional Neural Network

Conventional dictionary matching based MR Fingerprinting (MRF) reconstruction approaches suffer from time-consuming operations that map temporal MRF signals to quantitative tissue parameters. In this paper, we design a 1-D residual convolutional neural network to perform the signature-to-parameter mapping in order to improve inference speed and accuracy. In particular, a 1-D convolutional neural network with shortcuts, a.k.a skip connections, for residual learning is developed using a TensorFlow platform. To avoid the requirement for a large amount of MRF data, the designed network is trained on synthesized MRF data simulated with the Bloch equations and fast imaging with steady state precession (FISP) sequences. The proposed approach was validated on both synthetic data and phantom data generated from a healthy subject. The reconstruction performance demonstrates a significantly improved speed - only 1.6s for reconstructing a pair of T1/T2 maps of size 128 × 128 - 50× faster than the original dictionary matching based method. The better performance was also confirmed by improved signal to noise ratio (SNR) and reduced root mean square error (RMSE). Furthermore, it is more compact to store a network instead of a large dictionary

The effect of a domestic violence interclerkship on the knowledge, attitudes, and skills of third-year medical students

PURPOSE: To determine whether participation in an intensive domestic violence interclerkship (DVI) improved the knowledge, attitudes, and skills of two successive cohorts of students at the University of Massachusetts Medical School. METHOD: The authors measured the knowledge, attitudes, and skills pertaining to domestic violence of third-year students in the classes of 1997 and 1998 using a validated written examination administered before, immediately after, and six months after participation in a 3.5-day or two-day DVI, respectively; they compared the scores using paired t-tests. Nine months after the DVI, the students\u27 domestic violence screening skills were measured by a performance-based assessment (OSCE); using unpaired t-tests, the authors compared the OSCE scores with those of a previous third-year class that had not participated in a DVI. Immediately after the OSCE, the students reported their levels of confidence in domestic violence screening and their satisfaction with the domestic violence curriculum; using chi-square analysis, those self-reports were compared with those of the class with no DVI. RESULTS: The students who participated in the DVIs immediately and significantly improved their knowledge, attitudes, and skills (p \u3c .001), and fully or partially sustained those improvements six months later (p \u3c .001). Nine months after the DVI, the students performed domestic violence screening more effectively (p \u3c .001), expressed greater comfort with domestic violence screening (p \u3c .001), and felt better-prepared by the curriculum to address domestic violence issues (p \u3c .001) than did the students with no DVI. CONCLUSION: Participation in a short, focused DVI curriculum produced sustainable improvements in knowledge, attitudes, and skills that were successfully applied by third-year medical students to effective domestic violence screening. Interclerkships are an effective way to fit into the clinical curriculum those subjects that transcend the traditional biomedical domain and intersect all areas of medical practice

Hidrogenionic potential (pH) of the attractant, trap density and control threshold for Ceratitis capitata (Diptera: tephritidae) on Hamlin oranges in São Paulo central region, Brazil

This study evaluated the effect of initial pH values of 4.5, 6.5 and 8.5 of the attractant (protein bait) Milhocina® and borax (sodium borate) in the feld, on the capture of fruit flies in McPhail traps, using 1, 2, 4 and 8 traps per hectare, in order to estimate control thresholds in a Hamlin orange grove in the central region of the state of São Paulo. The most abundant fruit fly species was Ceratitis capitata, comprising almost 99% of the fruit flies captured, of which 80% were females. The largest captures of C. capitata were found in traps baited with Milhocina® and borax at pH 8.5. Captures per trap for the four densities were similar, indicating that the population can be estimated with one trap per hectare in areas with high populations. It was found positive relationships between captures of C. capitata and the number of Hamlin oranges damaged, 2 and 3 weeks after capture. It was obtained equations that correlate captures and damage levels which can be used to estimate control thresholds. The average loss caused in Hamlin orange fruits by C. capitata was 2.5 tons per hectare or 7.5% of production.Esta pesquisa teve como objetivos: avaliar o efeito do pH inicial, 4.5; 6.5 e 8.5, do atrativo proteico Milhocina® e bórax (tetraborato de sódio) na captura de moscas-das-frutas em armadilhas McPhail; estudar densidades de armadilhas, 1; 2; 4 e 8 por hectare, para estimar níveis de controle em laranja cv. Hamlin, na região central de São Paulo. A espécie predominante, com 99% das moscas-das-frutas capturadas, foi Ceratitis capitata, sendo 80% de fêmeas. As maiores capturas de C. capitata ocorreram nas armadilhas com Milhocina® e bórax em pH 8.5. As capturas, nas 4 densidades, foram semelhantes, indicando que a população pode ser estimada com uma armadilha por hectare em áreas de altas populações. Houve relações positivas entre capturas de C. capitata e o número de frutos danificados, 2 e 3 semanas após a captura. Assim, foram obtidas equações que relacionam a captura e o dano, possibilitando estimar níveis de controle desse inseto. As perdas médias causadas por C. capitata em laranja cv. Hamlin chegaram a 2,5 toneladas de frutos por hectare ou 7,5% da produção.info:eu-repo/semantics/publishedVersio

Electronic Health Record Portal Messages and Interactive Voice Response Calls to Improve Rates of Early Season Influenza Vaccination: Randomized Controlled Trial

BACKGROUND: Patient reminders for influenza vaccination, delivered via an electronic health record patient portal and interactive voice response calls, offer an innovative approach to engaging patients and improving patient care. OBJECTIVE: The goal of this study was to test the effectiveness of portal and interactive voice response outreach in improving rates of influenza vaccination by targeting patients in early September, shortly after vaccinations became available. METHODS: Using electronic health record portal messages and interactive voice response calls promoting influenza vaccination, outreach was conducted in September 2015. Participants included adult patients within a large multispecialty group practice in central Massachusetts. Our main outcome was electronic health record-documented early influenza vaccination during the 2015-2016 influenza season, measured in November 2015. We randomly assigned all active portal users to 1 of 2 groups: (1) receiving a portal message promoting influenza vaccinations, listing upcoming clinics, and offering online scheduling of vaccination appointments (n=19,506) or (2) receiving usual care (n=19,505). We randomly assigned all portal nonusers to 1 of 2 groups: (1) receiving interactive voice response call (n=15,000) or (2) receiving usual care (n=43,596). The intervention also solicited patient self-reports on influenza vaccinations completed outside the clinic. Self-reported influenza vaccination data were uploaded into the electronic health records to increase the accuracy of existing provider-directed electronic health record clinical decision support (vaccination alerts) but were excluded from main analyses. RESULTS: Among portal users, 28.4% (5549/19,506) of those randomized to receive messages and 27.1% (5294/19,505) of the usual care group had influenza vaccinations documented by November 2015 (P=.004). In multivariate analysis of portal users, message recipients were slightly more likely to have documented vaccinations when compared to the usual care group (OR 1.07, 95% CI 1.02-1.12). Among portal nonusers, 8.4% (1262/15,000) of those randomized to receive calls and 8.2% (3586/43,596) of usual care had documented vaccinations (P=.47), and multivariate analysis showed nonsignificant differences. Over half of portal messages sent were opened (10,112/19,479; 51.9%), and over half of interactive voice response calls placed (7599/14,984; 50.7%) reached their intended target, thus we attained similar levels of exposure to the messaging for both interventions. Among portal message recipients, 25.4% of message openers (2570/10,112) responded to a subsequent question on receipt of influenza vaccination; among interactive voice response recipients, 72.5% of those reached (5513/7599) responded to a similar question. CONCLUSIONS: Portal message outreach to a general primary care population achieved a small but statistically significant improvement in rates of influenza vaccination (OR 1.07, 95% CI 1.02-1.12). Interactive voice response calls did not significantly improve vaccination rates among portal nonusers (OR 1.03, 95% CI 0.96-1.10). Rates of patient engagement with both modalities were favorable. TRIAL REGISTRATION: ClinicalTrials.gov NCT02266277; https://clinicaltrials.gov/ct2/show/NCT02266277. Lloyd Fisher, Peggy Preusse, Devi Sundaresan, Lawrence Garber, Kathleen M Mazor, Sarah L Cutrona. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 25.09.2020

Estimating the sustainability of towed fishing-gear impacts on seabed habitats: a simple quantitative risk assessment method applicable to data-limited fisheries

1. Impacts of bottom fishing, particularly trawling and dredging, on seabed (benthic) habitats are commonly perceived to pose serious environmental risks. Quantitative ecological risk assessment can be used to evaluate actual risks and to help guide the choice of management measures needed to meet sustainability objectives. 2. We develop and apply a quantitative method for assessing the risks to benthic habitats by towed bottom-fishing gears. The method is based on a simple equation for relative benthic status (RBS), derived by solving the logistic population growth equation for the equilibrium state. Estimating RBS requires only maps of fishing intensity and habitat type — and parameters for impact and recovery rates, which may be taken from meta-analyses of multiple experimental studies of towed-gear impacts. The aggregate status of habitats in an assessed region is indicated by the distribution of RBS values for the region. The application of RBS is illustrated for a tropical shrimp-trawl fishery. 3. The status of trawled habitats and their RBS value depend on impact rate (depletion per trawl), recovery rate and exposure to trawling. In the shrimp-trawl fishery region, gravel habitat was most sensitive, and though less exposed than sand or muddy-sand, was most affected overall (regional RBS=91% relative to un-trawled RBS=100%). Muddy-sand was less sensitive, and though relatively most exposed, was less affected overall (RBS=95%). Sand was most heavily trawled but least sensitive and least affected overall (RBS=98%). Region-wide, >94% of habitat area had >80% RBS because most trawling and impacts were confined to small areas. RBS was also applied to the region's benthic invertebrate communities with similar results. 4. Conclusions. Unlike qualitative or categorical trait-based risk assessments, the RBS method provides a quantitative estimate of status relative to an unimpacted baseline, with minimal requirements for input data. It could be applied to bottom-contact fisheries worldwide, including situations where detailed data on characteristics of seabed habitats, or the abundance of seabed fauna are not available. The approach supports assessment against sustainability criteria and evaluation of alternative management strategies (e.g. closed areas, effort management, gear modifications)

Can we identify non-stationary dynamics of trial-to-trial variability?"

Identifying sources of the apparent variability in non-stationary scenarios is a fundamental problem in many biological data analysis settings. For instance, neurophysiological responses to the same task often vary from each repetition of the same experiment (trial) to the next. The origin and functional role of this observed variability is one of the fundamental questions in neuroscience. The nature of such trial-to-trial dynamics however remains largely elusive to current data analysis approaches. A range of strategies have been proposed in modalities such as electro-encephalography but gaining a fundamental insight into latent sources of trial-to-trial variability in neural recordings is still a major challenge. In this paper, we present a proof-of-concept study to the analysis of trial-to-trial variability dynamics founded on non-autonomous dynamical systems. At this initial stage, we evaluate the capacity of a simple statistic based on the behaviour of trajectories in classification settings, the trajectory coherence, in order to identify trial-to-trial dynamics. First, we derive the conditions leading to observable changes in datasets generated by a compact dynamical system (the Duffing equation). This canonical system plays the role of a ubiquitous model of non-stationary supervised classification problems. Second, we estimate the coherence of class-trajectories in empirically reconstructed space of system states. We show how this analysis can discern variations attributable to non-autonomous deterministic processes from stochastic fluctuations. The analyses are benchmarked using simulated and two different real datasets which have been shown to exhibit attractor dynamics. As an illustrative example, we focused on the analysis of the rat's frontal cortex ensemble dynamics during a decision-making task. Results suggest that, in line with recent hypotheses, rather than internal noise, it is the deterministic trend which most likely underlies the observed trial-to-trial variability. Thus, the empirical tool developed within this study potentially allows us to infer the source of variability in in-vivo neural recordings

Stochastic Growth Equations and Reparametrization Invariance

It is shown that, by imposing reparametrization invariance, one may derive a variety of stochastic equations describing the dynamics of surface growth and identify the physical processes responsible for the various terms. This approach provides a particularly transparent way to obtain continuum growth equations for interfaces. It is straightforward to derive equations which describe the coarse grained evolution of discrete lattice models and analyze their small gradient expansion. In this way, the authors identify the basic mechanisms which lead to the most commonly used growth equations. The advantages of this formulation of growth processes is that it allows one to go beyond the frequently used no-overhang approximation. The reparametrization invariant form also displays explicitly the conservation laws for the specific process and all the symmetries with respect to space-time transformations which are usually lost in the small gradient expansion. Finally, it is observed, that the knowledge of the full equation of motion, beyond the lowest order gradient expansion, might be relevant in problems where the usual perturbative renormalization methods fail.Comment: 42 pages, Revtex, no figures. To appear in Rev. of Mod. Phy

Direct Recruitment of Polycomb Repressive Complex 1 to Chromatin by Core Binding Transcription Factors

Polycomb repressive complexes (PRCs) play key roles in developmental epigenetic regulation. Yet the mechanisms that target PRCs to specific loci in mammalian cells remain incompletely understood. In this study we show that Bmi1, a core component of Polycomb Repressive Complex 1 (PRC1), binds directly to the Runx1/CBFβ transcription factor complex. Genome-wide studies in megakaryocytic cells demonstrate significant chromatin occupancy overlap between the PRC1 core component Ring1b and Runx1/CBFβ and functional regulation of a considerable fraction of commonly bound genes. Bmi1/Ring1b and Runx1/CBFβ deficiencies generate partial phenocopies of one another in vivo. We also show that Ring1b occupies key Runx1 binding sites in primary murine thymocytes and that this occurs via PRC2-independent mechanisms. Genetic depletion of Runx1 results in reduced Ring1b binding at these sites in vivo. These findings provide evidence for site-specific PRC1 chromatin recruitment by core binding transcription factors in mammalian cells.Stem Cell and Regenerative Biolog

Complaints handling in hospitals: an empirical study of discrepancies between patients' expectations and their experiences

<p>Abstract</p> <p>Background</p> <p>Many patients are dissatisfied with the way in which their complaints about health care are dealt with. This study tested the assumption that this dissatisfaction consists – in part at least – of unmet expectations.</p> <p>Methods</p> <p>Subjects were 279 patients who lodged a complaint with the complaints committees of 74 hospitals in the Netherlands. They completed two questionnaires; one on their expectations at the start of the complaints handling process, and one on their experiences after the complaints procedure (pre-post design; response 50%). Dependent variables are patients' satisfaction and their feeling that justice was done; independent variables are the association between patients' expectations and their experiences.</p> <p>Results</p> <p>Only 31% of the patients felt they had received justice from the complaints process.</p> <p>Two thirds of the patients were satisfied with the conduct of the complaints committee, but fewer were satisfied with the conduct of the hospital or the medical professional (29% and 18%). Large discrepancies between expectations and experiences were found in the case of doctors not admitting errors when errors had been made, and of hospital managements not providing information on corrective measures that were taken. Discrepancies collectively explained 51% of patients' dissatisfaction with the committee and one third of patients' dissatisfaction with the hospital and the professional. The feeling that justice was done was influenced by the decision on the complaint (well-founded or not), but also by the satisfaction with the conduct of the committee, the hospital management and the professional involved.</p> <p>Conclusion</p> <p>It is disappointing to observe that less than one third of the patients felt that justice had been done through the complaints handling process. This study shows that the feeling that justice had been done is not only influenced by the judgement of the complaints committee, but also by the response of the professional. Furthermore, hospitals and professionals should communicate on how they are going to prevent a recurrence of the events that led to the complaint.</p

Processing DNA molecules as text

Polymerase Chain Reaction (PCR) is the DNA-equivalent of Gutenberg’s movable type printing, both allowing large-scale replication of a piece of text. De novo DNA synthesis is the DNA-equivalent of mechanical typesetting, both ease the setting of text for replication. What is the DNA-equivalent of the word processor? Biology labs engage daily in DNA processing—the creation of variations and combinations of existing DNA—using a plethora of manual labor-intensive methods such as site-directed mutagenesis, error-prone PCR, assembly PCR, overlap extension PCR, cleavage and ligation, homologous recombination, and others. So far no universal method for DNA processing has been proposed and, consequently, no engineering discipline that could eliminate this manual labor has emerged. Here we present a novel operation on DNA molecules, called Y, which joins two DNA fragments into one, and show that it provides a foundation for DNA processing as it can implement all basic text processing operations on DNA molecules including insert, delete, replace, cut and paste and copy and paste. In addition, complicated DNA processing tasks such as the creation of libraries of DNA variants, chimeras and extensions can be accomplished with DNA processing plans consisting of multiple Y operations, which can be executed automatically under computer control. The resulting DNA processing system, which incorporates our earlier work on recursive DNA composition and error correction, is the first demonstration of a unified approach to DNA synthesis, editing, and library construction