Recommended reporting standards for test accuracy studies of infectious diseases of finfish, amphibians, molluscs and crustaceans: the STRADAS-aquatic checklist

Complete and transparent reporting of key elements of diagnostic accuracy studies for infectious diseases in cultured and wild aquatic animals benefits end-users of these tests, enabling the rational design of surveillance programs, the assessment of test results from clinical cases and comparisons of diagnostic test performance. Based on deficiencies in the Standards for Reporting of Diagnostic Accuracy (STARD) guidelines identified in a prior finfish study (Gardner et al. 2014), we adapted the Standards for Reporting of Animal Diagnostic Accuracy Studies—paratuberculosis (STRADAS-paraTB) checklist of 25 reporting items to increase their relevance to finfish, amphibians, molluscs, and crustaceans and provided examples and explanations for each item. The checklist, known as STRADAS-aquatic, was developed and refined by an expert group of 14 transdisciplinary scientists with experience in test evaluation studies using field and experimental samples, in operation of reference laboratories for aquatic animal pathogens, and in development of international aquatic animal health policy. The main changes to the STRADAS-paraTB checklist were to nomenclature related to the species, the addition of guidelines for experimental challenge studies, and the designation of some items as relevant only to experimental studies and ante-mortem tests. We believe that adoption of these guidelines will improve reporting of primary studies of test accuracy for aquatic animal diseases and facilitate assessment of their fitness-for-purpose. Given the importance of diagnostic tests to underpin the Sanitary and Phytosanitary agreement of the World Trade Organization, the principles outlined in this paper should be applied to other World Organisation for Animal Health (OIE)-relevant species.

The accuracy of protein structure alignment servers

Background: Protein structural alignment is one of the most fundamental and crucial areas of research in the domain of computational structural biology. Comparison of a protein structure with known structures helps to classify it as a new or belonging to a known group of proteins. This, in turn, is useful to determine the function of protein, its evolutionary relationship with other protein molecules and grasping principles underlying protein architecture and folding. Results: A large number of protein structure alignment methods are available. Each protein structure alignment tool has its own strengths andweaknesses that need to be highlighted.We compared and presented results of six most popular and publically available servers for protein structure comparison. These web-based servers were compared with the respect to functionality (features provided by these servers) and accuracy (how well the structural comparison is performed). The CATH was used as a reference. The results showed that overall CE was top performer. DALI and PhyreStorm showed similar results whereas PDBeFold showed the lowest performance. In case of few secondary structural elements, CE, DALI and PhyreStorm gave 100% success rate. Conclusion: Overall none of the structural alignment servers showed 100% success rate. Studies of overall performance, effect of mainly alpha and effect of mainly beta showed consistent performance. CE, DALI, FatCat and PhyreStorm showed more than 90% success rate.

Evaluation of the GPS Accuracy of Tablets

Augmented Reality (AR) applications often require knowledge of the user’s position in some global coordinate system in order to draw the augmented content to its correct position on the screen. The most common method for coarse positioning is the Global Positioning System (GPS). One of the advantages of GPS is that GPS receivers can be found in almost every modern mobile device. This research was conducted in order to determine the accuracies of different GPS receivers. The tests included seven consumer-grade tablets, three external GPS modules and one professional-grade GPS receiver. All of the devices were tested with both static and mobile measurements. It was concluded that even the cheaper external GPS receivers were notably more accurate than the GPS receivers of the tested tablets. The absolute accuracy of the tablets is difficult to determine from the test results, since the results vary by a large margin between different measurements. The accuracy of the tested tablets in static measurements were between 0.30 meters and 13.75 meters.

An extension of STARD statements for reporting diagnostic accuracy studies on liver fibrosis tests: the Liver-FibroSTARD standards

International audience

Transfer function-noise modeling and spatial interpolation to evaluate the risk of extreme (shallow) water-table levels in the Brazilian Cerrados

Water regimes in the Brazilian Cerrados are sensitive to climatological disturbances and human intervention. The risk that critical water-table levels are exceeded over long periods of time can be estimated by applying stochastic methods in modeling the dynamic relationship between water levels and driving forces such as precipitation and evapotranspiration. In this study, a transfer function-noise model, the so called PIRFICT-model, is applied to estimate the dynamic relationship between water-table depth and precipitation surplus/deficit in a watershed with a groundwater monitoring scheme in the Brazilian Cerrados. Critical limits were defined for a period in the Cerrados agricultural calendar, the end of the rainy season, when extremely shallow levels (< 0.5-m depth) can pose a risk to plant health and machinery before harvesting. By simulating time-series models, the risk of exceeding critical thresholds during a continuous period of time (e.g. 10 days) is described by probability levels. These simulated probabilities were interpolated spatially using universal kriging, incorporating information related to the drainage basin from a digital elevation model. The resulting map reduced model uncertainty. Three areas were defined as presenting potential risk at the end of the rainy season. These areas deserve attention with respect to water-management and land-use planning.

Lineup identification accuracy: the effects of alcohol, target presence, confidence ratings, and response time

Despite the intoxication of many eyewitnesses at crime scenes, only four published studies to date have investigated the effects of alcohol intoxication on eyewitness identification performance. While one found intoxication significantly increased false identification rates from target absent showups, three found no such effect using the more traditional lineup procedure. The present study sought to further explore the effects of alcohol intoxication on identification performance and examine whether accurate decisions from intoxicated witnesses could be postdicted by confidence and response times. One hundred and twenty participants engaged in a study examining the effects of intoxication (control, placebo, and mild intoxication) and target presence on identification performance. Participants viewed a simultaneous lineup one week after watching a mock crime video of a man attempting to steal cars. Ethanol intoxication (0.6 ml/kg) was found to make no significant difference to identification accuracy and such identifications from intoxicated individuals were made no less confidently or slowly than those from sober witnesses. These results are discussed with respect to the previous research examining intoxicated witness identification accuracy and the misconceptions the criminal justice system holds about the accuracy of such witnesses.

SCOR WG 142: Quality Control Procedures for Oxygen and Other Biogeochemical Sensors on Floats and Gliders. Recommendation for oxygen measurements from Argo floats, implementation of in-air-measurement routine to assure highest long-term accuracy

Recommendation for Oxygen Measurements from Argo Floats: Implementation of In-Air-Measurement Routine to Assure Highest Long-term Accuracy As Argo has entered its second decade and chemical/biological sensor technology is improving constantly, the marine biogeochemistry community is starting to embrace the successful Argo float program. An augmentation of the global float observatory, however, has to follow rather stringent constraints regarding sensor characteristics as well as data processing and quality control routines. Owing to the fairly advanced state of oxygen sensor technology and the high scientific value of oceanic oxygen measurements (Gruber et al., 2010), an expansion of the Argo core mission to routine oxygen measurements is perhaps the most mature and promising candidate (Freeland et al., 2010). In this context, SCOR Working Group 142 “Quality Control Procedures for Oxygen and Other Biogeochemical Sensors on Floats and Gliders” (www.scor-int.org/SCOR_WGs_WG142.htm) set out in 2014 to assess the current status of biogeochemical sensor technology with particular emphasis on float-readiness, develop pre- and post-deployment quality control metrics and procedures for oxygen sensors, and to disseminate procedures widely to ensure rapid adoption in the community.

EXPLICIT WRITTEN CORRECTIVE FEEDBACK AND LANGUAGE APTITUDE IN SLA: IMPLICATIONS FOR IMPROVEMENT OF LINGUISTIC ACCURACY

Most second language researchers agree that there is a role for corrective feedback in second language writing classes. However, many unanswered questions remain concerning which linguistic features to target and the type and amount of feedback to offer. This study examined two new pieces of writing by 151 learners of English as a Second Language (ESL), in order to investigate the effect of direct and metalinguistic written feedback on errors with the simple past tense, the present perfect tense, dropped pronouns, and pronominal duplication. This inquiry also considered the extent to which learner differences in language-analytic ability (LAA), as measured by the LLAMA F, mediated the effects of these two types of explicit written corrective feedback. Learners in the feedback groups were provided with corrective feedback on two essays, after which learners in all three groups completed two additional writing tasks to determine whether or not the provision of corrective feedback led to greater gains in accuracy compared to no feedback. Both treatment groups, direct and metalinguistic, performed better than the comparison group on new pieces of writing immediately following the treatment sessions, yet direct feedback was more durable than metalinguistic feedback for one structure, the simple past tense. Participants with greater LAA proved more likely to achieve gains in the direct feedback group than in the metalinguistic group, whereas learners with lower LAA benefited more from metalinguistic feedback. Overall, the findings of the present study confirm the results of prior studies that have found a positive role for written corrective feedback in instructed second language acquisition.

The use of mo and cu monochromatic radiations for quantitative phase analysis: study of the accuracy

Cement hydration is a very complex process in which crystalline phases are dissolving in water and after supersaturation hydrated crystalline and amorphous phases precipitate. Great efforts are being made to develop analytical tools to accurately quantify these processes and X-ray Powder Diffraction (XRPD) combined with Rietveld methodology is a suitable tool to quantify these complex mixtures and their time evolutions. However, some problems/drawbacks should be overcome to fully apply it to cement pastes characterization in order to get accurate phase analyses. In order to tackle this issue, a comparison of the Rietveld quantitative phase analyses (RQPA) obtained using Cu-Kα1, Mo-Kα1, and synchrotron strictly monochromatic radiations of three set of mixtures with increasing amounts of a given phase (spiking-method) is presented. The main aim is to test a simple hypothesis: high energy Mo-radiation, combined with high resolution laboratory X-ray powder diffraction optics, could yield more accurate RQPA, for challenging samples, than well-established Cu-radiation procedure(s). Firstly, a series of crystalline inorganic phase mixtures with increasing amounts of an analyte was studied in order to determine if Mo-Kα1 methodology is as robust as the well-established Cu-Kα1 one. Secondly, a series of crystalline organic phase mixtures with increasing amounts of an organic compound was analyzed. This type of mixture can result in transparency problems in reflection and inhomogeneous loading in narrow capillaries for transmission studies. Finally, a third series with variable amorphous content was studied. Limit of detection in Cu-patterns, ~0.2 wt%, are slightly lower than those derived from Mo-patterns, ~0.3 wt%, for similar recording times and limit of quantification for a well crystallized inorganic phase using laboratory powder diffraction was established ~0.10 wt%. From the obtained results it is inferred that RQPA from Mo-Kα1 radiation have slightly better accuracies than those obtained from Cu-Kα1. The results obtained in the previous comparison have been taken into account to obtain accurate RQPA, including the amorphous component with internal standard methodology, of hydrating cement pastes. The final goal of this second study was understanding the early-stage hydration mechanisms of a variety of cementing systems (Ordinary Portland Cement or Belite Alite Ye’elimite cement) as a function of water content, superplasticizer additives and type and content of sulfate source. In order to do so, X-ray powder diffraction data were taken in-situ with the humidity chamber coupled to the Mo-Kα1 powder diffractometer. Some results of this ongoing investigation will be reported and discussed.

Head repositioning accuracy in patients with neck pain and asymptomatic subjects: concurrent validity, influence of motion speed, motion direction and target distance

Background: Cervicocephalic kinesthetic deficiencies have been demonstrated in patients with chronic neck pain (NP). On the other hand, authors emphasized the use of different motion speeds for assessing functional impairment of the cervical spine. Purpose: The objectives of this study were (1) to investigate the head repositioning accuracy in NP patients and control subjects and (2) to assess the influence of target distance, motion speed, motion direction and pain. Materials and methods: Seventy-one subjects (36 healthy subjects and 35 NP patients; age 30–55 years) performed the head repositioning test (HRT) at two different speeds for horizontal and vertical movements and at two different distances. For each condition, six consecutive trials were sampled. Results: The study showed the validity and reproducibility of the HRT, confirming a dysfunctional threshold of 4.5°. Normative values of head repositioning error up to 3.6° and 7.1° were identified for healthy and NP subjects, respectively. A distance of 180 cm from the target and a natural motion speed increased HRT accuracy. Repositioning after extension movement showed a significantly larger error in both groups. Intensity, duration of pain as well as pain level did not significantly alter head repositioning error. Conclusions: The assessment of proprioceptive performance in healthy and NP subjects allowed the validation of the HRT. The HRT is a simple, not expensive and fast test, easily implementable in daily practice to assess and monitor treatment and evolution of proprioceptive cervical deficits.

Comparing simulation output accuracy of discrete event and agent based models: a quantitative approach

In our research we investigate the output accuracy of discrete event simulation models and agent based simulation models when studying human centric complex systems. In this paper we focus on human reactive behaviour as it is possible in both modelling approaches to implement human reactive behaviour in the model by using standard methods. As a case study we have chosen the retail sector, and here in particular the operations of the fitting room in the women wear department of a large UK department store. In our case study we looked at ways of determining the efficiency of implementing new management policies for the fitting room operation through modelling the reactive behaviour of staff and customers of the department. First, we have carried out a validation experiment in which we compared the results from our models to the performance of the real system. This experiment also allowed us to establish differences in output accuracy between the two modelling methods. In a second step a multi-scenario experiment was carried out to study the behaviour of the models when they are used for the purpose of operational improvement. Overall we have found that for our case study example both, discrete event simulation and agent based simulation have the same potential to support the investigation into the efficiency of implementing new management policies.

Investigating output accuracy for a discrete event simulation model and an agent based simulation model

In this paper, we investigate output accuracy for a Discrete Event Simulation (DES) model and Agent Based Simulation (ABS) model. The purpose of this investigation is to find out which of these simulation techniques is the best one for modelling human reactive behaviour in the retail sector. In order to study the output accuracy in both models, we have carried out a validation experiment in which we compared the results from our simulation models to the performance of a real system. Our experiment was carried out using a large UK department store as a case study. We had to determine an efficient implementation of management policy in the store’s fitting room using DES and ABS. Overall, we have found that both simulation models were a good representation of the real system when modelling human reactive behaviour.

Accuracy of ASGE criteria for the prediction of choledocholithiasis

Background/aims: Few studies have validated the performance of guidelines for the prediction of choledocholithiasis (CL). Our objective was to prospectively assess the accuracy of the American Society for Gastrointestinal Endoscopy (ASGE) guidelines for the identification of CL. Methods: A two-year prospective evaluation of patients with suspected CL was performed. We evaluated the ASGE guidelines and its component variables in predicting CL. Results: A total of 256 patients with suspected CL were analyzed. Of the 208 patients with high-probability criteria for CL, 124 (59.6%) were found to have a stone/sludge at endoscopic retrograde cholangiopancreatography (ERCP). Among 48 patients with intermediate-probability criteria, 21 (43.8%) had a stone/sludge. The performance of ASGE high- and intermediate-probability criteria in our population had an accuracy of 59.0% (85.5% sensitivity, 24.3% specificity) and 41.0% (14.4% sensitivity, 75.6% specificity), respectively. The mean ERCP delay time was 6.1 days in the CL group and 6.4 days in the group without CL, p = 0.638. The presence of a common bile duct (CBD) > 6 mm (OR 2.21; 95% CI, 1.20-4.10), ascending cholangitis (OR 2.37; 95% CI, 1.01-5.55) and a CBD stone visualized on transabdominal US (OR 3.33; 95% CI, 1.48-7.52) were stronger predictors of CL. The occurrence of biliary pancreatitis was a strong protective factor for the presence of a retained CBD stone (OR 0.30; 95% CI, 0.17-0.55). Conclusions: Irrespective of a patient's ASGE probability for CL, the application of current guidelines in our population led to unnecessary performance of ERCPs in nearly half of cases.

Forecasting errors, directional accuracy and profitability of currency trading: The case of EUR/USD exchange rate

We provide a comprehensive study of out-of-sample forecasts for the EUR/USD exchange rate based on multivariate macroeconomic models and forecast combinations. We use profit maximization measures based on directional accuracy and trading strategies in addition to standard loss minimization measures. When comparing predictive accuracy and profit measures, data snooping bias free tests are used. The results indicate that forecast combinations, in particular those based on principal components of forecasts, help to improve over benchmark trading strategies, although the excess return per unit of deviation is limited.

Double Hybrid Functionals and the Π-System Bond Length Alternation Challenge: Rivaling Accuracy of Post-HF Methods

Predicting accurate bond length alternations (BLAs) in long conjugated oligomers has been a significant challenge for electronic-structure methods for many decades, made particularly important by the close relationships between BLA and the rich optoelectronic properties of π-delocalized systems. Here, we test the accuracy of recently developed, and increasingly popular, double hybrid (DH) functionals, positioned at the top of Jacobs Ladder of DFT methods of increasing sophistication, computational cost, and accuracy, due to incorporation of MP2 correlation energy. Our test systems comprise oligomeric series of polyacetylene, polymethineimine, and polysilaacetylene up to six units long. MP2 calculations reveal a pronounced shift in BLAs between the 6-31G(d) basis set used in many studies of BLA to date and the larger cc-pVTZ basis set, but only modest shifts between cc-pVTZ and aug-cc-pVQZ results. We hence perform new reference CCSD(T)/cc-pVTZ calculations for all three series of oligomers against which we assess the performance of several families of DH functionals based on BLYP, PBE, and TPSS, along with lower-rung relatives including global- and range-separated hybrids. Our results show that DH functionals systematically improve the accuracy of BLAs relative to single hybrid functionals. xDH-PBE0 (N4 scaling using SOS-MP2) emerges as a DH functional rivaling the BLA accuracy of SCS-MP2 (N5 scaling), which was found to offer the best compromise between computational cost and accuracy the last time the BLA accuracy of DFT- and wave function-based methods was systematically investigated. Interestingly, xDH-PBE0 (XYG3), which differs to other DHs in that its MP2 term uses PBE0 (B3LYP) orbitals that are not self-consistent with the DH functional, is an outlier of trends of decreasing average BLA errors with increasing fractions of MP2 correlation and HF exchange.