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From ultrasoft pseudopotentials to the projector augmented-wave method
The formal relationship between ultrasoft (US) Vanderbilt-type pseudopotentials and Bl\"ochl's projector augmented wave (PAW) method is derived. It is shown that the total energ...
Fitting Linear Mixed-Effects Models Using<b>lme4</b>
Maximum likelihood or restricted maximum likelihood (REML) estimates of the parameters in linear mixed-effects models can be determined using the lmer function in the lme4 packa...
ImageNet classification with deep convolutional neural networks
We trained a large, deep convolutional neural network to classify the 1.2 million high-resolution images in the ImageNet LSVRC-2010 contest into the 1000 different classes. On t...
The Measurement of Observer Agreement for Categorical Data
This paper presents a general statistical methodology for the analysis of multivariate categorical data arising from observer reliability studies. The procedure essentially invo...
Case Study Research: Design and Methods
"This new edition Case Study Research has been carefully revised, updated, and expanded while retaining virtually all of the features and coverage of the second edition. Robert ...
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and s...
MizAR 60 for Mizar 50
As a present to Mizar on its 50th anniversary, we develop an AI/TP system that automatically proves about 60% of the Mizar theorems in the hammer setting. We also automatically ...
Special points for Brillouin-zone integrations
A method is given for generating sets of special points in the Brillouin zone which provides an efficient means of integrating periodic functions of the wave vector. The integra...
Electric Field Effect in Atomically Thin Carbon Films
We describe monocrystalline graphitic films, which are a few atoms thick but are nonetheless stable under ambient conditions, metallic, and of remarkably high quality. The films...
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individu...
The Sequence Alignment/Map format and SAMtools
Abstract Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads ...