Accelerating the Evolution of Nonhuman Primate Neuroimaging

Nonhuman primate neuroimaging is on the cusp of a transformation, much in the same way its human counterpart was in 2010, when the Human Connectome Project was launched to accelerate progress. Inspired by an open data-sharing initiative, the global community recently met and, in this article, breaks through obstacles to define its ambitions

Hydrological modelling for reservoir operation: application of SWAT Model for Kalu Ganga Catchment, Sri Lanka

Kalu Ganga, a major tributary of Amban Ganga, is one of the perennial rivers of Sri Lanka. Also, Amban Ganga is a major tributary of Mahaweli Ganga. The Kalu Ganga starts from Knuckles mountains, and about 90% of the catchment is covered with forests. The Government of Sri Lanka constructed Kalu Ganga and Moragahakanda Reservoirs in 2014 to increase the water availability in Mahaweli Basin to improve the agricultural and drinking water benefits in several provinces. This study used the Soil Water Assessment Tool (SWAT) to simulate the hydrology of the Kalu Ganga catchment and estimate the daily streamflow series of the Kalu Ganga. The long-term mean annual flow of the Kalu Ganga at the dam site would be 196 MCM (equivalent to 6.24 m3/s) with a standard deviation of 57.5 MCM and coefficient of variation of 0.29. The mean annual catchment rainfall is 2763 mm, streamflow is 59%, and evapotranspiration is 33% of the rainfall. The Kalu Ganga catchment hydrology is dominated by the wet season rainfall, which governs the Kalu Ganga flow, where 89% of the annual flow volume is produced. Further, 67% of the flow volume is produced from November to January. The model results show that 89% of the annual average of streamflow is generated as baseflow, a feature of a perennial river. The high baseflow fraction is hydrologically favourable for the water availability of the catchment as this shows the utilizable quantity of water is high

QM/MM Simulations on NVIDIA and AMD GPUs

We have ported and optimized the GPU accelerated QUICK and AMBER based ab initio QM/MM implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra operations. General performance improvements to the QUICK GPU code are also presented. Benchmarks carried out on NVIDIA V100 and AMD MI100 cards display similar performance on both hardware for standalone HF/DFT calculations with QUICK and QM/MM molecular dynamics simulations with QUICK/AMBER. Furthermore, with respect to the QUICK/AMBER release version 21, significant speedups are observed for QM/MM molecular dynamics simulations. This significantly increases the range of scientific problems that can be addressed with open-source QM/MM software on state-of-the-art computer hardware

Geometry Optimization: A Comparison of Different Open-Source Geometry Optimizers

Based on a series of energy minimizations with starting structures obtained from the Baker test set of 30 organic molecules, a comparison is made between various open-source geometry optimization codes that are interfaced with the open-source QUantum Interaction Computational Kernel (QUICK) program for gradient and energy calculations. The findings demonstrate how the choice of the coordinate system influences the optimization process to reach an equilibrium structure. With fewer steps, internal coordinates outperform Cartesian coordinates, while the choice of the initial Hessian and Hessian update method in quasi-Newton approaches made by different optimization algorithms also contributes to the rate of convergence. Furthermore, an available open-source machine learning method based on Gaussian process regression (GPR) was evaluated for energy minimizations over surrogate potential energy surfaces with both Cartesian and internal coordinates with internal coordinates outperforming Cartesian. Overall, geomeTRIC and DL-FIND with their default optimization method as well as with the GPR-based model using Hartree–Fock theory with the 6-31G** basis set needed a comparable number of geometry optimization steps to the approach of Baker using a unit matrix as the initial Hessian to reach the optimized geometry. On the other hand, the Berny and Sella offerings in ASE outperformed the other algorithms. Based on this, we recommend using the file-based approaches, ASE/Berny and ASE/Sella, for large-scale optimization efforts, while if using a single executable is preferable, we now distribute QUICK integrated with DL-FIND

Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units

We have ported and optimized the graphics processing unit (GPU)-accelerated QUICK and AMBER-based ab initio quantum mechanics/molecular mechanics (QM/MM) implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra operations. General performance improvements to the QUICK GPU code are also presented. Benchmarks carried out on NVIDIA V100 and AMD MI100 cards display similar performance on both hardware for standalone HF/DFT calculations with QUICK and QM/MM molecular dynamics simulations with QUICK/AMBER. Furthermore, with respect to the QUICK/AMBER release version 21, significant speedups are observed for QM/MM molecular dynamics simulations. This significantly increases the range of scientific problems that can be addressed with open-source QM/MM software on state-of-the-art computer hardware

Gastric emptying and antral motility parameters in children with functional dyspepsia: association with symptom severity

Functional dyspepsia (FD) is an important gastrointestinal problem with obscure etiology. Abnormal gastric motility is suggested as a possible pathophysiological mechanism for symptoms. The main objective of this study was to assess gastric motility in Sri Lankan children with FD. Forty-one children (19 [46.3%] males, age 4-14 years, mean 7.5 years, SD 2.6 years) referred to the Gastroenterology Research Laboratory, Faculty of Medicine, University of Kelaniya, from January 2007 to December 2011, were screened. Those fulfilling Rome III criteria for FD were recruited. None had clinical or laboratory evidence of organic disorders. Twenty healthy children were recruited as controls (eight [40%] males, age 4-14 years, mean 8.4 years, SD 3.0 years). Liquid gastric emptying rate (GE) and antral motility parameters were assessed using an ultrasound-based method. Average GE (45.6% vs 66.2% in controls), amplitude of antral contractions (58.2% vs 89.0%) and antral motility index (5.1 vs 8.3) were lower and fasting antral area (1.5 cm(2) vs 0.6 cm(2)) was higher in patients with FD (P  < 0.01). Frequency of antral contractions (8.8 vs 9.3) did not show a significant difference (P = 0.07). Scores obtained for severity of abdominal pain negatively correlated with GE (r = -0.35, P = 0.025). Children with FD, exposed to stressful events had higher fasting antral area (1.9 cm(2)) than those not exposed to stress (1.0 cm(2)) (P = 0.02). GE and antral motility parameters were significantly impaired in children with FD compared with controls. GE negatively correlated with severity of symptoms. This study points to disturbances in gastric motility as an etiological factor for F

Geometry Optimization: A Comparison of Different Open-Source Geometry Optimizers

Based on a series of energy minimizations with starting structures obtained from the Baker test set of 30 organic molecules, a comparison is made between various open-source geometry optimization codes that are interfaced with the open-source QUantum Interaction Computational Kernel (QUICK) program for gradient and energy calculations. The findings demonstrate how the choice of the coordinate system influences the optimization process to reach an equilibrium structure. With fewer steps, internal coordinates outperform Cartesian coordinates, while the choice of the initial Hessian and Hessian update method in quasi-Newton approaches made by different optimization algorithms also contributes to the rate of convergence. Furthermore, an available open-source machine learning method based on Gaussian process regression (GPR) was evaluated for energy minimizations over surrogate potential energy surfaces with both Cartesian and internal coordinates with internal coordinates outperforming Cartesian. Overall, geomeTRIC and DL-FIND with their default optimization method as well as with the GPR-based model using Hartree–Fock theory with the 6-31G** basis set needed a comparable number of geometry optimization steps to the approach of Baker using a unit matrix as the initial Hessian to reach the optimized geometry. On the other hand, the Berny and Sella offerings in ASE outperformed the other algorithms. Based on this, we recommend using the file-based approaches, ASE/Berny and ASE/Sella, for large-scale optimization efforts, while if using a single executable is preferable, we now distribute QUICK integrated with DL-FIND

Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units

We have ported and optimized the graphics processing unit (GPU)-accelerated QUICK and AMBER-based ab initio quantum mechanics/molecular mechanics (QM/MM) implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra operations. General performance improvements to the QUICK GPU code are also presented. Benchmarks carried out on NVIDIA V100 and AMD MI100 cards display similar performance on both hardware for standalone HF/DFT calculations with QUICK and QM/MM molecular dynamics simulations with QUICK/AMBER. Furthermore, with respect to the QUICK/AMBER release version 21, significant speedups are observed for QM/MM molecular dynamics simulations. This significantly increases the range of scientific problems that can be addressed with open-source QM/MM software on state-of-the-art computer hardware

Association between functional gastrointestinal diseases and exposure to abuse in teenagers

Abdominal pain-predominant functional gastrointestinal diseases (AP-FGD) are common in children and commonly attributed to exposure to child abuse. However, this relationship has not been studied in teenagers, and the main objective of the current study was to assess it. Teenagers were recruited from four randomly selected schools in Western province of Sri Lanka. Data were collected using a validated self-administered questionnaire. AP-FGD were diagnosed using Rome III criteria. A total of 1850 teenagers aged 13-18 years were included. Three hundred and five (16.5%) had AP-FGD. AP-FGD were significantly higher in those exposed to sexual (34.0%), emotional (25.0%) and physical (20.2%) abuse, than in those not abused (13.0%, p < 0.001). Those with AP-FGD exposed to abuse had a higher severity score for bowel symptoms (30.8% vs. 24.7% in not abused, p < 0.05). This study highlights the importance of identifying exposure to abuse in management of teenagers with AP-FG