Reliability and validity in comparative studies of software prediction models

Empirical studies on software prediction models do not converge with respect to the question "which prediction model is best?" The reason for this lack of convergence is poorly understood. In this simulation study, we have examined a frequently used research procedure comprising three main ingredients: a single data sample, an accuracy indicator, and cross validation. Typically, these empirical studies compare a machine learning model with a regression model. In our study, we use simulation and compare a machine learning and a regression model. The results suggest that it is the research procedure itself that is unreliable. This lack of reliability may strongly contribute to the lack of convergence. Our findings thus cast some doubt on the conclusions of any study of competing software prediction models that used this research procedure as a basis of model comparison. Thus, we need to develop more reliable research procedures before we can have confidence in the conclusions of comparative studies of software prediction models

Telomere anchoring at the nuclear periphery requires the budding yeast Sad1-UNC-84 domain protein Mps3

Positioning of telomeres at the nuclear periphery can have dramatic effects on gene expression by establishment of heritable, transcriptionally repressive subdomains. However, little is known about the integral membrane proteins that mediate telomere tethering at the nuclear envelope. Here, we find a previously unrecognized function for the Saccharomyces cerevisiae Sad1-UNC-84 domain protein Mps3 in regulating telomere positioning in mitotic cells. Our data demonstrate that the nucleoplasmic N-terminal acidic domain of Mps3 is not essential for viability. However, this acidic domain is necessary and sufficient for telomere tethering during S phase and the silencing of reporter constructs integrated at telomeres. We show that this is caused by the role of the Mps3 acidic domain in binding and localization of the silent information regulator protein Sir4 to the nuclear periphery. Thus, Mps3 functions as an integral membrane anchor for telomeres and is a novel nuclear receptor for the Sir4 pathway of telomere tethering and gene inactivation

Species-level divergences in multiple functional traits between the two endemic subspecies of Blue Chaffinches Fringilla teydea in Canary Islands

Background: One of the biggest challenges in avian taxonomy is the delimitation of allopatric species because their reproductive incompatibility cannot be directly studied in the wild. Instead, reproductive incompatibility has to be inferred from multiple, divergent character sets that indicate a low likelihood of allopatric populations amalgamating upon secondary contact. A set of quantitative criteria for species delimitation has been developed for avian taxonomy. Results: Here, we report a broad multi-trait comparison of the two insular subspecies of the Blue Chaffinch Fringilla teydea, endemic to the pine forests of Tenerife (ssp. teydea) and Gran Canaria (ssp. polatzeki) in the Canary Islands. We found that the two taxa were reciprocally monophyletic in their whole mitogenomes and two Z chromosome introns. The genetic distance in mitogenomes indicates around 1 Mya of allopatric evolution. There were diagnostic differences in body morphometrics, song and plumage reflectance spectra, whose combined divergence score (=11) exceeds the threshold level (=7) set for species delimitation by Tobias et al. (Ibis 152:724–746, 2010). Moreover, we found a marked divergence in sperm lengths with little range overlap. Relatively long sperm with low intra- and intermale CV compared to other passerines suggest a mating system with high levels of sperm competition (extrapair paternity) in these taxa. Conclusion: The large and diagnostic divergences in multiple functional traits qualify for species rank, i.e., Tenerife Blue Chaffinch (Fringilla teydea) and Gran Canaria Blue Chaffinch (Fringilla polatzeki). We encourage a wider use of sperm traits in avian taxonomy because sperm divergences might signal reproductive incompatibility at the postcopulatory prezygotic stage, especially in species with sperm competition

Total colonic aganglionosis : multicentre study of surgical treatment and patient-reported outcomes up to adulthood

Background: Surgery for total colonic aganglionosis (TCA) is designed to preserve continence and achieve satisfactory quality of life. This study evaluated a comprehensive group of clinical and social outcomes. Methods: An international multicentre study from eight Nordic hospitals involving examination of case records and a patient-reported questionnaire survey of all patients born with TCA between 1987 and 2006 was undertaken. Results: Of a total of 116 patients, five (4 center dot 3 per cent) had died and 102 were traced. Over a median follow-up of 12 (range 0 center dot 3-33) years, bowel continuity was established in 75 (73 center dot 5 per cent) at a median age of 11 (0 center dot 5-156) months. Mucosectomy with a short muscular cuff and straight ileoanal anastomosis (SIAA) (29 patients) or with aJpouch (JIAA) (26) were the most common reconstructions (55 of 72, 76 per cent). Major early postoperative complications requiring surgical intervention were observed in four (6 per cent) of the 72 patients. In 57 children aged over 4 years, long-term functional bowel symptoms after reconstruction included difficulties in holding back defaecation in 22 (39 per cent), more than one faecal accident per week in nine (16 per cent), increased frequency of defaecation in 51 (89 per cent), and social restrictions due to bowel symptoms in 35 (61 per cent). Enterocolitis occurred in 35 (47 per cent) of 72 patients. Supplementary enteral and/or parenteral nutrition was required by 51 (55 per cent) of 93 patients at any time during follow-up. Of 56 responders aged 2-20 years, true low BMI for age was found in 20 (36 per cent) and 13 (23 per cent) were short for age. Conclusion: Reconstruction for TCA was associated with persistent bowel symptoms, and enterocolitis remained common. Multidisciplinary follow-up, including continuity of care in adulthood, might improve care standards in patients with TCA.Peer reviewe

Ensemble prediction for nowcasting with a convection-permitting model—I: description of the system and the impact of radar-derived surface precipitation rates

A key strategy to improve the skill of quantitative predictions of precipitation, as well as hazardous weather such as severe thunderstorms and flash floods is to exploit the use of observations of convective activity (e.g. from radar). In this paper, a convection-permitting ensemble prediction system (EPS) aimed at addressing the problems of forecasting localized weather events with relatively short predictability time scale and based on a 1.5 km grid-length version of the Met Office Unified Model is presented. Particular attention is given to the impact of using predicted observations of radar-derived precipitation intensity in the ensemble transform Kalman filter (ETKF) used within the EPS. Our initial results based on the use of a 24-member ensemble of forecasts for two summer case studies show that the convective-scale EPS produces fairly reliable forecasts of temperature, horizontal winds and relative humidity at 1 h lead time, as evident from the inspection of rank histograms. On the other hand, the rank histograms seem also to show that the EPS generates too much spread for forecasts of (i) surface pressure and (ii) surface precipitation intensity. These may indicate that for (i) the value of surface pressure observation error standard deviation used to generate surface pressure rank histograms is too large and for (ii) may be the result of non-Gaussian precipitation observation errors. However, further investigations are needed to better understand these findings. Finally, the inclusion of predicted observations of precipitation from radar in the 24-member EPS considered in this paper does not seem to improve the 1-h lead time forecast skill

The Effect of Intensive Implementation Support on Fidelity for Four Evidence‑Based Psychosis Treatments: A Cluster Randomized Trial

Abstract Purpose: Service providers need effective strategies to implement evidence-based practices (EBPs) with high fidelity. This study aimed to evaluate an intensive implementation support strategy to increase fidelity to EBP standards in treatment of patients with psychosis. Methods: The study used a cluster randomized design with pairwise assignment of practices within each of 39 Norwegian mental health clinics. Each site chose two of four practices for implementation: physical health care, antipsychotic medication management, family psychoeducation, illness management and recovery. One practice was assigned to the experimental condition (toolkits, clinical training, implementation facilitation, data-based feedback) and the other to the control condition (manual only). The outcome measure was fidelity to the EBP, measured at baseline and after 6, 12, and 18 months, analyzed using linear mixed models and effect sizes. Results: The increase in fidelity scores (within a range 1-5) from baseline to 18 months was significantly greater for experimental sites than for control sites for the combined four practices, with mean difference in change of 0.86 with 95% CI (0.21; 1.50), p = 0.009). Effect sizes for increase in group difference of mean fidelity scores were 2.24 for illness management and recovery, 0.68 for physical health care, 0.71 for antipsychotic medication management, and 0.27 for family psychoeducation. Most improvements occurred during the first 12 months. Conclusions: Intensive implementation strategies (toolkits, clinical training, implementation facilitation, data-based feedback) over 12 months can facilitate the implementation of EBPs for psychosis treatment. The approach may be more effective for some practices than for others. Keywords: Evidence-based practice; Fidelity scale; Implementation support; Mental health services; Psychoses. © 2021. The Author(s).publishedVersio

Simulations of the 2004 North American Monsoon: NAMAP2

The second phase of the North American Monsoon Experiment (NAME) Model Assessment Project (NAMAP2) was carried out to provide a coordinated set of simulations from global and regional models of the 2004 warm season across the North American monsoon domain. This project follows an earlier assessment, called NAMAP, that preceded the 2004 field season of the North American Monsoon Experiment. Six global and four regional models are all forced with prescribed, time-varying ocean surface temperatures. Metrics for model simulation of warm season precipitation processes developed in NAMAP are examined that pertain to the seasonal progression and diurnal cycle of precipitation, monsoon onset, surface turbulent fluxes, and simulation of the low-level jet circulation over the Gulf of California. Assessment of the metrics is shown to be limited by continuing uncertainties in spatially averaged observations, demonstrating that modeling and observational analysis capabilities need to be developed concurrently. Simulations of the core subregion (CORE) of monsoonal precipitation in global models have improved since NAMAP, despite the lack of a proper low-level jet circulation in these simulations. Some regional models run at higher resolution still exhibit the tendency observed in NAMAP to overestimate precipitation in the CORE subregion; this is shown to involve both convective and resolved components of the total precipitation. The variability of precipitation in the Arizona/New Mexico (AZNM) subregion is simulated much better by the regional models compared with the global models, illustrating the importance of transient circulation anomalies (prescribed as lateral boundary conditions) for simulating precipitation in the northern part of the monsoon domain. This suggests that seasonal predictability derivable from lower boundary conditions may be limited in the AZNM subregion.open131

Increasing source to image distance for AP pelvis imaging – impact on radiation dose and image quality

Aim: A quantative primary study to determine whether increasing source to image distance (SID), with and without the use of automatic exposure control (AEC) for antero-posterior (AP) pelvis imaging, reduces dose whilst still producing an image of diagnostic quality. Methods: Using a computed radiography (CR) system, an anthropomorphic pelvic phantom was positioned for an AP examination using the table bucky. SID was initially set at 110 cm, with tube potential set at a constant 75 kVp, with two outer chambers selected and a fine focal spot of 0.6 mm. SID was then varied from 90 cm to 140 cm with two exposures made at each 5 cm interval, one using the AEC and another with a constant 16 mAs derived from the initial exposure. Effective dose (E) and entrance surface dose (ESD) were calculated for each acquisition. Seven experienced observers blindly graded image quality using a 5-point Likert scale and 2 Alternative Forced Choice software. Signal-to-Noise Ratio (SNR) was calculated for comparison. For each acquisition, femoral head diameter was also measured for magnification indication. Results: Results demonstrated that when increasing SID from 110 cm to 140 cm, both E and ESD reduced by 3.7% and 17.3% respectively when using AEC and 50.13% and 41.79% respectively, when the constant mAs was used. No significant statistical (T-test) difference (p ¼ 0.967) between image quality was detected when increasing SID, with an intra-observer correlation of 0.77 (95% confidence level). SNR reduced slightly for both AEC (38%) and no AEC (36%) with increasing SID. Conclusion: For CR, increasing SID significantly reduces both E and ESD for AP pelvis imaging without adversely affecting image quality