scholarly journals INFERENCE FROM LARGE SETS OF RADIOCARBON DATES: SOFTWARE AND METHODS

Radiocarbon ◽  
2020 ◽  
pp. 1-17 ◽  
Author(s):  
Enrico R Crema ◽  
Andrew Bevan
Keyword(s):  
Open Source Software ◽  
Population Change ◽  
Computational Techniques ◽  
Radiocarbon Dates ◽  
Large Sets ◽  
Simulation Based ◽  
Main Paper ◽  
Open Source Software Package ◽  
Supplementary Material ◽  
Reproducible Analysis

ABSTRACT The last decade has seen the development of a range of new statistical and computational techniques for analysing large collections of radiocarbon (14C) dates, often but not exclusively to make inferences about human population change in the past. Here we introduce rcarbon, an open-source software package for the R statistical computing language which implements many of these techniques and looks to foster transparent future study of their strengths and weaknesses. In this paper, we review the key assumptions, limitations and potentials behind statistical analyses of summed probability distribution of 14C dates, including Monte-Carlo simulation-based tests, permutation tests, and spatial analyses. Supplementary material provides a fully reproducible analysis with further details not covered in the main paper.

scholarly journals QuCumber: wavefunction reconstruction with neural networks

2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Matthew J. S. Beach ◽  
Isaac De Vlugt ◽  
Anna Golubeva ◽  
Patrick Huembeli ◽  
Bohdan Kulchytskyy ◽  
...  
Keyword(s):  
Open Source Software ◽  
Software Package ◽  
Original Data ◽  
Quantum States ◽  
Computational Techniques ◽  
Boltzmann Machine ◽  
New Era ◽  
Open Source Software Package ◽  
Quantum Technology ◽  
Projective Measurements

As we enter a new era of quantum technology, it is increasingly important to develop methods to aid in the accurate preparation of quantum states for a variety of materials, matter, and devices. Computational techniques can be used to reconstruct a state from data, however the growing number of qubits demands ongoing algorithmic advances in order to keep pace with experiments. In this paper, we present an open-source software package called QuCumber that uses machine learning to reconstruct a quantum state consistent with a set of projective measurements. QuCumber uses a restricted Boltzmann machine to efficiently represent the quantum wavefunction for a large number of qubits. New measurements can be generated from the machine to obtain physical observables not easily accessible from the original data.

OnPoint: A package for online experiments in motor control and motor learning

2020 ◽  
Author(s):  
Jonathan Sanching Tsay ◽  
Alan S. Lee ◽  
Guy Avraham ◽  
Darius E. Parvin ◽  
Jeremy Ho ◽  
...  
Keyword(s):  
Motor Control ◽  
Motor Learning ◽  
Open Source Software ◽  
Research Progress ◽  
Global Pandemic ◽  
Large N ◽  
Open Source Software Package ◽  
Potential Applications ◽  
Temporal And Spatial ◽  
The One

Motor learning experiments are typically run in-person, exploiting finely calibrated setups (digitizing tablets, robotic manipulandum, full VR displays) that provide high temporal and spatial resolution. However, these experiments come at a cost, not limited to the one-time expense of purchasing equipment but also the substantial time devoted to recruiting participants and administering the experiment. Moreover, exceptional circumstances that limit in-person testing, such as a global pandemic, may halt research progress. These limitations of in-person motor learning research have motivated the design of OnPoint, an open-source software package for motor control and motor learning researchers. As with all online studies, OnPoint offers an opportunity to conduct large-N motor learning studies, with potential applications to do faster pilot testing, replicate previous findings, and conduct longitudinal studies (GitHub repository: https://github.com/alan-s-lee/OnPoint).

scholarly journals PRISMS-Fatigue computational framework for fatigue analysis in polycrystalline metals and alloys

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Mohammadreza Yaghoobi ◽  
Krzysztof S. Stopka ◽  
Aaditya Lakshmanan ◽  
Veera Sundararaghavan ◽  
John E. Allison ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Large Scale ◽  
Metals And Alloys ◽  
Analysis Tool ◽  
Computational Framework ◽  
Crystal Plasticity Finite Element ◽  
Polycrystalline Metals ◽  
Simulation Based ◽  
Open Source Framework

AbstractThe PRISMS-Fatigue open-source framework for simulation-based analysis of microstructural influences on fatigue resistance for polycrystalline metals and alloys is presented here. The framework uses the crystal plasticity finite element method as its microstructure analysis tool and provides a highly efficient, scalable, flexible, and easy-to-use ICME community platform. The PRISMS-Fatigue framework is linked to different open-source software to instantiate microstructures, compute the material response, and assess fatigue indicator parameters. The performance of PRISMS-Fatigue is benchmarked against a similar framework implemented using ABAQUS. Results indicate that the multilevel parallelism scheme of PRISMS-Fatigue is more efficient and scalable than ABAQUS for large-scale fatigue simulations. The performance and flexibility of this framework is demonstrated with various examples that assess the driving force for fatigue crack formation of microstructures with different crystallographic textures, grain morphologies, and grain numbers, and under different multiaxial strain states, strain magnitudes, and boundary conditions.

Population Fluctuation and the Adoption of Food Production in Prehistoric Korea: Using Radiocarbon Dates as a Proxy for Population Change

Radiocarbon ◽  
2017 ◽  
Vol 59 (6) ◽  
pp. 1761-1770 ◽  
Author(s):  
Yongje Oh ◽  
Matthew Conte ◽  
Seungho Kang ◽  
Jangsuk Kim ◽  
Jaehoon Hwang
Keyword(s):  
Probability Distribution ◽  
Population Growth ◽  
Food Production ◽  
Population Change ◽  
Population Pressure ◽  
Population Fluctuation ◽  
Intensive Agriculture ◽  
Rice Farming ◽  
Radiocarbon Dates ◽  
Transition To Agriculture

AbstractPopulation growth has been evoked both as a causal factor and consequence of the transition to agriculture. The use of radiocarbon (14C) dates as proxies for population allows for reevaluations of population as a variable in the transition to agriculture. In Korea, numerous rescue excavations during recent decades have offered a wealth of14C data for this application. A summed probability distribution (SPD) of14C dates is investigated to reconstruct population trends preceding and following adoptions of food production in prehistoric Korea. Important cultivars were introduced to Korea in two episodes: millets during the Chulmun Period (ca. 6000–1500 BCE) and rice during the Mumun Period (ca. 1500–300 BCE). The SPD suggests that while millet production had little impact on Chulmun populations, a prominent surge in population appears to have followed the introduction of rice. The case in prehistoric Korea demonstrates that the adoption of food production does not lead inevitably towards sustained population growth. Furthermore, the data suggest that the transition towards intensive agriculture need not occur under conditions of population pressure resulting from population growth. Rather, intensive rice farming in prehistoric Korea began during a period of population stagnation.

scholarly journals Integration of enabling methods for the automated flow preparation of piperazine-2-carboxamide

2014 ◽  
Vol 10 ◽  
pp. 641-652 ◽  
Author(s):  
Richard J Ingham ◽  
Claudio Battilocchio ◽  
Joel M Hawkins ◽  
Steven V Ley
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Software Package ◽  
Flow Chemistry ◽  
Raspberry Pi ◽  
Step Flow ◽  
Simultaneous Control ◽  
Open Source Software Package

Here we describe the use of a new open-source software package and a Raspberry Pi® computer for the simultaneous control of multiple flow chemistry devices and its application to a machine-assisted, multi-step flow preparation of pyrazine-2-carboxamide – a component of Rifater®, used in the treatment of tuberculosis – and its reduced derivative piperazine-2-carboxamide.

scholarly journals ogttMetrics: Data structures and algorithms for oral glucose tolerance tests

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 684
Author(s):  
Benjamin J. Stubbs ◽  
Keith Frankston ◽  
Marcel Ramos ◽  
Nancy Laranjo ◽  
Frank M. Sacks ◽  
...  
Keyword(s):  
Glucose Tolerance ◽  
Open Source Software ◽  
Oral Glucose ◽  
Oral Glucose Tolerance ◽  
Estimation Of Parameters ◽  
Large Clinical Trial ◽  
Oral Glucose Tolerance Tests ◽  
Open Source Software Package ◽  
Glucose Tolerance Tests ◽  
Data Structures And Algorithms

We describe an open source software package, ogttMetrics, to compute diverse measures of glucose metabolism derived from oral glucose tolerance tests (OGTTs). Tools are provided to organize, visualize and compare OGTT data from large cohorts. Numerical difficulties in estimation of parameters of the Bergman minimal model are described, and in one large clinical trial, the simpler closed form index of Matsuda is observed to lead to similar rankings of individuals with respect to insulin sensitivity, and similar inferences concerning effects of modifications to carbohydrate content and glycemic index of experimental diets.

scholarly journals DP4-AI Automated NMR Data Analysis: Straight from Spectrometer to Structure

2020 ◽  
Author(s):  
Alexander Howarth ◽  
Kristaps Ermanis ◽  
Jonathan Goodman
Keyword(s):  
1H Nmr ◽  
Open Source Software ◽  
Processing Speed ◽  
Structure Elucidation ◽  
Structural Information ◽  
Fold Increase ◽  
Structural Uncertainty ◽  
Large Sets ◽  
Nmr Data ◽  
Objective Model

<div> <p>A robust system for automatic processing and assignment of raw 13C and 1H NMR data DP4-AI has been developed and integrated into our computational organic molecule structure elucidation workflow. Starting from a molecular structure with undefined stereochemistry or other structural uncertainty, this system allows for completely automated structure elucidation. Methods for NMR peak picking using objective model selection and algorithms for matching the calculated 13C and 1H NMR shifts to peaks in noisy experimental NMR data were developed. DP4-AI achieved a 60-fold increase in processing speed, and near-elimination of the need for scientist time, when rigorously evaluated used a challenging test set of molecules. DP4-AI represents a leap forward in NMR structure elucidation and a step-change in the functionality of DP4. It enables high-throughput analyses of databases and large sets of molecules, which were previously impossible, and paves the way for the discovery of new structural information through machine learning. This new functionality has been coupled with an intuitive GUI and is available as open-source software at https://github.com/KristapsE/DP4-AI.</p> </div> <br>

scholarly journals An open and reproducible analysis of a controversial criminal law decision: Mission IMM-possible?

2020 ◽  
Author(s):  
Jason Chin
Keyword(s):  
Open Source Software ◽  
Research Process ◽  
High Court ◽  
The Public ◽  
Judicial Decisions ◽  
Research Fields ◽  
Law And Policy ◽  
Criminological Research ◽  
Reproducible Analysis ◽  
High Court Of Australia

Reproducibility and open access are central to the research process, enabling researchers to verify and build upon each other’s work, and allowing the public to rely on that work. These ideals are perhaps even more important in legal and criminological research, fields that actively seek to inform law and policy. This article has two goals. First, it seeks to advance legal and criminological research methods by serving as an example of a reproducible and open analysis of a controversial criminal evidence decision. Towards that end, this study relies on open source software, and includes an app (https://openlaw.shinyapps.io/imm-app/) allowing readers to access and read through the judicial decisions being analysed. The second goal is to examine the effect of the 2016 High Court of Australia decision, IMM v The Queen, which appeared to limit safeguards against evidence known to contribute to wrongful convictions in Australia and abroad.

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