Autoencoder-based detection of the residues involved in G protein-coupled receptor signaling

Regulator binding and mutations alter protein dynamics. The transmission of the signal of these alterations to distant sites through protein motion results in changes in protein expression and cell function. The detection of residues involved in signal transmission contributes to an elucidation of the mechanisms underlying processes as vast as cellular function and disease pathogenesis. We developed an autoencoder (AE) based method that detects residues essential for signaling by comparing the fluctuation data, particularly the time fluctuation of the side-chain distances between residues, during molecular dynamics simulations between the ligand-bound and -unbound forms or wild-type and mutant forms of proteins. Here, the AE-based method was applied to the G protein-coupled receptor (GPCR) system, particularly a class A-type GPCR, CXCR4, to detect the essential residues involved in signaling. Among the residues involved in the signaling of the homolog CXCR2, which were extracted from the literature based on the complex structures of the ligand and G protein, our method could detect more than half of the essential residues involved in G protein signaling, including those spanning the fifth and sixth transmembrane helices in the intracellular region, despite the lack of information regarding the interaction with G protein in our CXCR4 models.

ANALYSIS OF WIND DRIVEN CURRENT IN ISHIKARI BAY AND NEARSHORE CURRENT AT ISHIKARI-HAMA BEACH, JAPAN

In August 2016, four swimmers were carried away by the waves and drowned at Ishikari-hama beach in Hokkaido. In recent years, several other similar accidents occurred around the Ishikari coast. Therefore, in this paper, we tried to comprehend the features of the current dynamics in Ishikari Bay and Ishikari-hama beach. As research contents, we grasped the accident that occurred in the past years around the Ishikari coast. In this case, we used the on-line database of the newspaper article. As the result, we comprehended the feature of the accident in Ishikari Bay. Secondary, we made a field survey at Ishikari-hama beach. Thirdly, we confirmed the fluctuation of the current in Ishikari Bay due to short time fluctuation of the wind direction. Finally, we simulated the rip current and the wind driven current in Ishikari Bay.

Temperature and humidity monitoring to identify ideal periods for liquefaction on Earth and Mars – data from the High Andes

During an almost two week-long field campaign in the Atacama Desert high altitude region of Ojos del Salado volcano, temperature (T) and relative humidity (RH) values were monitored on the surface and <1–5 cm sized rocks, focusing on the night-time values. The aim was to identify and evaluate potential temporal characteristics of daily T and RH changes, searching for ideal periods for deliquescence that has recently been proposed for Mars. Although the atmospheric pressure on Mars is much lower than on Earth, and the atmosphere is drier in general, the huge daily temperature fluctuation there could produce elevated humidity values at night-time; this aspect has thus been analysed on Earth at a desert location, where because of the high elevation night-time cooling is very strong, just like on Mars. Different nearby surface locations showed the same temporal T/RH characteristics, but evident variations were observed between different days. Strong fluctuations could be observed on 10–20 minute long temporal scales, that might influence the deliquescence process, and should be accounted for in future missions aiming to analyse this process on Mars. Night-time periods were favourable for deliquescence. Among the modelled Mars-relevant salts [CaCl2, Ca(ClO4)2, Mg(ClO4)2, NaCl] the longest durations of possible deliquescence were for CaCl2, Ca(ClO4)2 and Mg(ClO4)2, ~7–12 hours for one day. The duration for deliquescence showed some increase along with the rising elevation, due to the decreasing night-time temperature. Thus despite the low humidity on Mars, the cold nights may cause elevated RH towards deliquescence. The Atacama Desert locations analysed are a useful analogue of the deliquescence process on Mars. Fluctuation in RH was observed in night-time, suggesting that similar variability might be present on Mars, and that should be considered in the future, including in evaluating how fast the microscopic liquid formation progresses. Night-time slope winds expected on Mars might have a strong impact on the local T/RH conditions. A more detailed analysis in the future should focus on identifying and separating regions with and without much of the expected night-time fluctuation

Hydrogeology of the Karst Area of the Grassano and Telese Springs

This work deals with the hydraulic phenomenon of the ascendant groundwater flow affecting the karst area of the Grassano and Telese springs (Campania, Southern Italy). It has been investigated through piezometric measurements, discharge and chemical-physical monitoring of springs and measurements of the radon 222Rn activity. The presence of ascendant flows is supported by numerous and different types of evidences in the area: location and topographical position of the springs; amazing density of sinkholes connected to geomorphic processes that develop below the topographic surface and involve the rising of CO2 and H2S rich waters; constancy of the temperature and the electrical conductivity of the spring waters over the time; fluctuation of the radon activity during the hydrological year; increasing of the hydraulic head with depth; presence of artesian conditions in the alluvial plain. Numerical simulations of the groundwater flow also support the general phenomenon of the ascendant flow in the discharge area and represent a useful background to interpret hydrological phenomena in the study area. The results of the simulations are suitable with all the hydrogeological processes observed in the area of the Grassano and Telese springs; this last is thought to belong to the regional groundwater flow system of the Matese massif and represents its discharge zone.

The kinematics of cyclic human movement

Models describing cyclic movement can roughly be divided into the categories theory or data driven. Theory driven models include anatomical and physiological aspects. They are principally suitable for answering questions about the reasons for movement characteristics. But, they are complicated and substantial simplifications do not allow generally valid results. Data driven models allow answering specific questions but lack the understanding of the general movement characteristic. With this paper we try a compromise not having to rely on anatomy, neurology and muscle function. We hypothesize a general kinematic description of cyclic human motion is possible without having to specify the movement generating processes, and still getting the kinematic right. The model proposed consisting of a superposition of six contributions – subject’s attractor, morphing, short time fluctuation, transient effect, control mechanism and sensor noise -, with characterizing numbers and random contributions. We test the model with data form treadmill running and stationary biking. Applying the model in form of a simulation results in good agreement between measured data and simulation values.

Influence of Evacuation Walkway Design Parameters on Passenger Evacuation Time along Elevated Rail Transit Lines Using a Multi-Agent Simulation

Passenger evacuation on elevated railway lines has always been an important issue for elevated rail transit safety management, because it is challenging to evacuate passengers efficiently in the event of man-made calamities and natural disasters. Therefore, an evacuation walkway has been designed as a primary solution to assist passenger evacuation during an emergency on elevated rail transit lines. However, investigations on how evacuation walkway designs influence passenger evacuation time are still limited. This study established two evacuation scenarios of interval evacuation on elevated rail transit lines and put forward a new evacuation time measurement method, based on the concept of ‘evacuation time for passengers leaving the evacuation walkway risk zone’. Then, the evacuation time for 90 combinations of entrance widths and walkway widths was simulated by a multi-agent evacuation simulator, Pathfinder, considering 1032 passengers being evacuated both unidirectionally and bidirectionally. The results show that the entrance width and walkway width have a combined effect on passenger evacuation time. An increase in the walkway width from 0.7 m to 1.5 m may potentially reduce the evacuation time by 54.5% in unidirectional evacuation, and 35.2% in bidirectional evacuation. An increase in the entrance width results in a noticeable evacuation time fluctuation when the walkway width is 0.7 and 0.8 m for both evacuation scenarios, while in a bidirectional evacuation, a noticeable fluctuation also can be observed when the walkway width is within the range of 1.4–1.5 m. According to the study, a potentially good design parameter combination for a newly built evacuation walkway is 1.3 m and 1.4 m for the walkway width and entrance width, respectively. The findings from this study may provide a useful reference in the optimization of the design of evacuation facilities and improvement of passenger evacuation safety in rail transit systems.