Ancestral sequence reconstructions evaluated by extant sequence cross-validation

Ancestral sequence reconstruction (ASR) has become widely used to analyze the properties of ancient biomolecules and to elucidate the mechanisms of molecular evolution. By recapitulating the structural, mechanistic, and functional changes of proteins during their evolution, ASR has been able to address many fundamental and challenging evolutionary questions where more traditional methods have failed. Despite the tangible successes of ASR, the accuracy of its reconstructions is currently unknown, because it is generally impossible to compare resurrected proteins to the true ancient ancestors that are now extinct. Which evolutionary models are the best for ASR? How accurate are the resulting inferences? Here we answer these questions by applying cross-validation (CV) to sets of aligned extant sequences. To assess the adequacy of a chosen evolutionary model for predicting extant sequence data, our column-wise CV method iteratively cross-validates each column in an alignment. Unlike other phylogenetic model selection criteria, this method does not require bias correction and does not make restrictive assumptions commonly violated by phylogenetic data. We find that column-wise CV generally provides a more conservative criterion than the AIC by preferring less complex models. To validate ASR methods, we also apply cross-validation to each sequence in an alignment by reconstructing the extant sequences using ASR methodology, a method we term extant sequence reconstruction (ESR). We can thus quantify the accuracy of ASR methodology by comparing ESR reconstructions to the corresponding true sequences. We find that a common measure of the quality of a reconstructed sequence, the average probability of the sequence, is indeed a good estimate of the fraction of the sequence that is correct when the evolutionary model is accurate or overparameterized. However, the average probability is a poor measure for comparing reconstructions, because more accurate phylogenetic models typically result in reconstructions with lower average probabilities. In contrast, the entropy of the reconstructed distribution is a reliable indicator of the quality of a reconstruction, as the entropy provides an accurate estimate of the log-probability of the true sequence. Both column-wise CV and ESR are useful methods to validate evolutionary models used for ASR and can be applied in practice to any phylogenetic analysis of real biological sequences.

Extremizing and Antiextremizing in Bayesian Ensembles of Binary-Event Forecasts

Many organizations combine forecasts of probabilities of binary events to support critical business decisions, such as the approval of credit or the recommendation of a drug. To aggregate individual probabilities, we offer a new method based on Bayesian principles that can help identify why and when combined probabilities need to be extremized. Extremizing is typically viewed as shifting the average probability farther from one half; we emphasize that it is more suitable to define extremizing as shifting it farther from the base rate. We introduce the notion of antiextremizing, cases in which it might be beneficial to make average probabilities less extreme. Analytically, we find that our Bayesian ensembles often extremize the average forecast but sometimes antiextremize instead. On several publicly available data sets, we demonstrate that our Bayesian ensemble performs well and antiextremizes anywhere from 18% to 73% of the cases. Antiextremizing is required more often when there is bracketing with respect to the base rate among the probabilities being aggregated than with no bracketing.

Spatio-Temporal Analysis of Dust Storm Activity in Chryse Planitia Using MGS-MOC Observations from Mars Years 24–28

Dust storms, observed in all seasons, are among the most momentous of Mars’ atmospheric activities. The Entry–Descent–Landing (EDL) activity of a Martian landing mission is influenced by local atmospheric conditions, especially the probability of dust storm activity. Chryse Planitia, featuring many of the largest and most prominent outflow channels and possible mud volcanoes, is an important target site for current and future Mars landing missions. It is of great significance to understand that a Mars landing probe may encounter a dust storm situation during EDL season in the Chryse Planitia. In this study, based on four Martian years, Mars Orbiter Camera (MOC) Mars Daily Global Maps (MDGMs), 1172 dust storms were identified within Chryse’s 1600 km-radius ring. Secondly, the daily mean dust storm probability was calculated, binned by 1° of solar longitude in the Chryse landing area. The two active periods of dust storm activity are Ls = 177–239° and Ls = 288–4°, with an average daily mean dust storm probability of 9.5% and 4.1%. Dust storm activity frequency is closely interrelated with the seasonal ebb and flow of the north polar ice cap; consequently, most dust storms occur in either the cap’s growth or recession phase. We divided the Chryse landing area into square grids of 0.5° and computed the average probability of dust storm occurrence in each grid, which ranged from 0.19% to 2.42%, with an average of 1.22%. The dust storm activity probability in space was also inhomogeneous—low in the west and south but high in the east and north—which was mainly affected by the origin and the path of dust storm sequences. Based on empirical orthogonal function (EOF) analysis of storms in the Chryse area, 40.5% are cap-edge storms in the northern hemisphere. Finally, we concluded that the preferred time of a Mars landing mission is Ls = 18–65° in the Chryse Planitia, and three preferred landing areas were selected with low dust storm probability.

Proposal for a destructive controlled phase gate using linear optics

Knill, Laflamme, and Milburn showed that linear optics techniques could be used to implement a nonlinear sign gate. They also showed that two of their nonlinear sign gates could be combined to implement a controlled-phase gate, which has a number of practical applications. Here we describe an alternative implementation of a controlled-phase gate for a single-rail target qubit that only requires the use of a single nonlinear sign gate. This gives a much higher average probability of success when the required ancilla photons are generated using heralding techniques. This implementation of a controlled-phase gate destroys the control qubit, which is acceptable in a number of applications where the control qubit would have been destroyed in any event, such as in a postselection process.

Optimal Planning of the Mobile Cargo Ropeway Repair Strategy

The focus of this research is to increase the reliability of mobile cargo ropeways formed by autonomous self-propelled transport units. The article deals with the development of a method for forming an effective technical and economic strategy for the restoration during planned repairs of those structural elements of transport units that can lead to critical failures of the ropeway. The method involves predicting the kinetics of the probability of failure-free operation of the ropeway during the entire life of its operation on the basis of predicting the failure-free operation of key elements of the transport units, the failure of which leads to an emergency disruption of the ropeway. In the process of integrating the system of Chapman-Kolmogorov differential equations, its periodic reformation is performed at the time of planned repairs, which allows us to take into account the need for a discrete change in the probability of failure-free operation of the restored structural elements. As a criterion for the optimality of the repairs strategy, the condition for obtaining the minimum total cost of repairs is used, while ensuring the average probability of failure-free operation. The formation of such an optimal strategy includes planning the schedules, number, time points, volume and cost of restoration work. The effectiveness of the repair strategy is determined by the total number of planned repairs and the minimum permissible probability of critical failure of structural elements. Conditions have been established under which further improvement of the level of ropeway reliability becomes an economically unprofitable task.

Investigating the Meteorological Drought Using CZI in Nineveh Governorate, Iraq.

This paper deals with the study of drought in the Nineveh region usingthe Chinese Z index (CZI) for a time scale (1 month). Historical data wereused from 1981 to 2018 for Mosul, Sinjar, and Tal Afar stations. Thereturn period and probability event for the moderate drought werecalculated for each month separately. The results indicated that allstations experienced the highest drought intensity in March comparedwith the other months. The average probability of moderate droughtranged between 0-0.31 for all months, and the maximum severity of thedrought was found in December from 2004 to 2008 for all stations. Inaddition, the results showed that the region's climate during the studyperiod was within the mild drought and humidity (closest to normal).This paper is the first study using the Chinese Z-index (CZI) in the studyarea and the Iraq region

Probability of Default Bank Umum di Indonesia: Alternatif dalam Implementasi Sisitem Premi Deferensial

The Indonesian Deposit Insurance Corporation (LPS) initially imposed the flat rate premium system, the same premium rate for all banks, which is 0.2% of the total third party funds (DPK) of commercial banks. However; when there is a change in the value of deposits guaranteed, LPS needs to change from the flat rate premium system to the Differential Premium System. This study uses Probability of Default (PoD), derived from the Merton Model (1974), for each individual Commercial Bank in Indonesia in implementing the Differential Premium System as the mandate of Article 15 paragraph (1) of the Law. Thus, each individual bank will pay a premium in accordance with the probability of default to LPS. This study finds that the average of probability of default of all commercial banks in the period 2002-2014 reaches 57.12%. Bank that has the smallest average Probability of Default (PoD) is Bank 151Â with a PoD of 14.10% and an AA category rating. The second position is Bank 427 with a PoD of 18.20% and a rating of A. While the third position is Bank 14 with a PoD of 18.70% also with a rating of A. This study finds that the Differential Premium System in Indonesia can be implemented, given that LPS revenue will not be reduced much or at least close to the flat rate premium system, when LPS imposes the Differential Premium System.

Destructive Controlled-Phase Gate using Linear Optics

Knill, Laflamme, and Milburn showed that linear optics techniques could be used to implement a nonlinear sign gate. They also showed that two of their nonlinear sign gates could be combined to implement a controlled-phase gate, which has a number of practical applications. Here we describe an alternative implementation of a controlled-phase gate that only requires the use of a single nonlinear sign gate. This gives a much higher average probability of success when the required ancilla photons are generated using heralding techniques. This implementation of a controlled-phase gate destroys the control qubit, which is acceptable in a number of applications where the control qubit would have been destroyed in any event, such as in a postselection process.

Urbanizing the floodplain: Global changes of imperviousness in flood-prone areas

Cities have historically developed close to rivers and coasts, increasing human exposure to flooding. That exposure is exacerbated by changes in climate and population, and by urban encroachment on floodplains. Although the mechanisms of how urbanization affects flooding are relatively well understood, there have been limited efforts to assess the magnitude of floodplain encroachment globally and how it has changed in both space and time. Highly resolved global datasets of both flood risk and changes in urban area from 1985-2015 are now available, enabling the reconstruction of the history of floodplain encroachment at high spatial resolutions. Here we show that the urbanized area in floodplains that have an average probability of flooding of 1/100 years, has almost doubled since 1985. Further, the rate of urban expansion into these floodplains increased by a factor of 1.5 after the year 2000. We also find that urbanization rates were highest in the most hazardous areas of floodplains, with population growth in these urban floodplains suggesting an accompanying increase in population density. These results reveal the scope, trajectory and extent of global floodplain encroachment. With tangible implications for flood risk management, these data can be directly used with integrated models to assess adaptation pathways for urban flooding.

An Analysis on the Effectiveness of Nitrogen Oxide Reduction from Applying Titanium Dioxide on Urban Roads Using a Statistical Method

The purpose of this study was to analyze the effect of titanium dioxide (TiO2) on reducing nitrogen oxide (NOx) concentrations using the statistical method of the Anderson-Darling test. To compare and analyze this effect, a spray-type form of TiO2 was applied to the asphalt pavement surface on urban roads. Data acquisition for NOx concentration was collected from a test section with TiO2 applied and a reference section without TiO2 applied. The probabilities of occurrence of the NOx concentration in the test and reference section were estimated and compared using the Anderson-Darling test. In sum, most of the NOx concentrations were probabilistically lower in the test section. The average probability of the NOx concentration in the test section in the ‘low’ range was 46.2% higher than in the reference section. In the ‘high’ and ‘moderate’ ranges, the average probability of the NOx concentration compared to that of the reference section was lower by 28.1% and 18.8%, respectively. These results revealed that the photochemical reaction from the TiO2 material applied on asphalt pavement was effective in reducing NOx.