pinecone/core-2020-05-10-deduplication huggingface dataset:
BAGEL: Brilliantly Advanced General Electronic-structure Library

On behalf of the development team, I review the capabilities of the BAGEL
program package in this article. BAGEL is a newly-developed full-fledged
program package for electronic-structure computation in quantum chemistry,
which is released under the GNU General Public License with many contributions
from the developers. The unique features include analytical CASPT2 nuclear
energy gradients and derivative couplings, relativistic multireference wave
functions based on the Dirac equation, and implementations of novel electronic
structure theories. All of the programs are efficiently parallelized using both
threads and MPI processes. We also discuss the code generator SMITH3, which has
been used to implement some of the programs in BAGEL. The developers'
contributions are listed at the end of the main text.Comment: Software Focus article, WIREs: Computational Molecular Scienc
Ab initio computations of molecular systems by the auxiliary-field
  quantum Monte Carlo method

The auxiliary-field quantum Monte Carlo (AFQMC) method provides a
computational framework for solving the time-independent Schroedinger equation
in atoms, molecules, solids, and a variety of model systems. AFQMC has recently
witnessed remarkable growth, especially as a tool for electronic structure
computations in real materials. The method has demonstrated excellent accuracy
across a variety of correlated electron systems. Taking the form of stochastic
evolution in a manifold of non-orthogonal Slater determinants, the method
resembles an ensemble of density-functional theory (DFT) calculations in the
presence of fluctuating external potentials. Its computational cost scales as a
low-power of system size, similar to the corresponding independent-electron
calculations. Highly efficient and intrinsically parallel, AFQMC is able to
take full advantage of contemporary high-performance computing platforms and
numerical libraries. In this review, we provide a self-contained introduction
to the exact and constrained variants of AFQMC, with emphasis on its
applications to the electronic structure in molecular systems. Representative
results are presented, and theoretical foundations and implementation details
of the method are discussed.Comment: 22 pages, 11 figure
First language attrition

Speakers who live in an L2 environment for an extended period of time often experience change in the way in which they use their L1, a process referred to as L1 attrition. This article provides an overview of language attrition phenomena at various linguistic levels. However, attrition cannot be trivially or linearly related to factors such as the frequency of use of the L1. It is argued here that attrition phenomena are not the outcome of a change to the underlying linguistic system nor of access problems due to an increase in activation thresholds, but of cross-linguistic influence in online speech production. © 2013 John Wiley & Sons, Ltd
Experimental and theoretical models of human cultural evolution.

The modern field of cultural evolution is now over 30 years old, and an extensive body of theory and data has been amassed. This article reviews models of cultural evolution, both experimental and theoretical, and surveys what they can tell us about cultural evolutionary processes. The models are grouped according to which of four broad questions they address: (1) How are cultural traits changed during transmission? (2) How and why do cultural traits accumulate over time? (3) What social learning biases do people use? and (4) What are the population-level consequences of different social learning biases? We conclude by highlighting gaps in the literature and promising future research directions, including the further integration of theoretical models and experimental data, the identification of the factors underlying cumulative cultural evolution, and the explanation of individual and cultural variation in social learning biases
Time perception: The bad news and the good

Time perception is fundamental and heavily researched, but the field faces a number of obstacles to theoretical progress. In this advanced review, we focus on three pieces of “bad news” for time perception research: temporal perception is highly labile across changes in experimental context and task; there are pronounced individual differences not just in overall performance but in the use of different timing strategies and the effect of key variables; and laboratory studies typically bear little relation to timing in the “real world”. We describe recent examples of these issues and in each case offer some “good news” by showing how new research is addressing these challenges to provide rich insights into the neural and information-processing bases of timing and time perception
Time perception: The bad news and the good

Time perception is fundamental and heavily researched, but the field faces
a number of obstacles to theoretical progress. In this advanced review, we
focus on three pieces of ‘bad news’ for time perception research: temporal
perception is highly labile across changes in experimental context and task; there
are pronounced individual differences not just in overall performance but in the
use of different timing strategies and the effect of key variables; and laboratory
studies typically bear little relation to timing in the ‘real world’. We describe recent
examples of these issues and in each case offer some ‘good news’ by showing how
new research is addressing these challenges to provide rich insights into the neural
and information-processing bases of timing and time perception.This is the final published version. It originally appeared at http://onlinelibrary.wiley.com/doi/10.1002/wcs.1298/abstract, published by Wiley
Interdisciplinarity as cognitive integration : auditory verbal hallucinations as a case study.

In this article, we advocate a bottom-up direction for the methodological modeling of interdisciplinary research based on concrete interactions among individuals within interdisciplinary projects. Drawing on our experience in Hearing the Voice (a cross-disciplinary project on auditory verbal hallucinations running at Durham University), we focus on the dynamic if also problematic integration of cognitive science (neuroscience, cognitive psychology, and of mind), phenomenology, and humanistic disciplines (literature, narratology, history, and theology). We propose a new model for disciplinary integration which brings to the fore an under-investigated dynamic of interdisciplinary projects, namely their being processes of distributed cognition and cognitive integration
Neuroethical issues in pharmacological cognitive enhancement

This is the published manuscript. It is available online from the Wiley in Wiley Interdisciplinary Reviews: Cognitive Science here: http://onlinelibrary.wiley.com/doi/10.1002/wcs.1306/abstract;jsessionid=05002026F7F8502EFC9A9553EC8CE45C.f03t02.Neuroethics is an emerging field that in general deals with the ethics of neuroscience and the neuroscience of ethics. In particular, it is concerned with the ethical issues in the translation of neuroscience to clinical practice and in the public domain. Numerous ethical issues arise when healthy individuals use pharmacological substances known as pharmacological cognitive enhancers (PCEs) for non-medical purposes in order to boost higher-order cognitive processes such as memory, attention, and executive functions. However, information regarding their actual use, benefits, and harms to healthy individuals is currently lacking. Neuroethical issues that arise from their use include the unknown side effects that are associated with these drugs, concerns about the modification of authenticity and personhood, and as a result of inequality of access to these drugs, the lack of distributive justice and competitive fairness that they may cause in society. Healthy individuals might be coerced by social institutions that force them to take these drugs to function better. These drugs might enable or hinder healthy individuals to gain better moral and self-understanding and autonomy. However, how these drugs might achieve this still remains speculative and unknown. Hence, before concrete policy decisions are made, the cognitive effects of these drugs should be determined. The initiation of accurate surveys to determine the actual usage of these drugs by healthy individuals from different sections of the society is proposed. In addition, robust empirical research need to be conducted to delineate not only whether or not these drugs modify complex higher-order cognitive processes but also how they might alter important human virtues such as empathy, moral reasoning, creativity, and motivation in healthy individuals
Food Sharing and Social Cognition

Many non-human animals share food with each other, with kin, mates, and other unrelated individuals. When individuals share food with others they lose a valuable resource. Thus, traditionally much research has investigated how this behavior can be an evolutionarily stable strategy. Only recently has food-sharing behavior been exploited to investigate non-human cognition. Certain evolutionarily stable strategies that have been proposed as accounts for food-sharing behaviors, such as reciprocity and interchange, may rely on complex cognitive abilities. In these cases, individuals may calculate the benefit they may receive from sharing with the recipient. In some species, sharing of food can facilitate the recipients' rate and extent of learning. This form of teaching may be cognitively complex if the donor takes into account the level of the recipient's abilities. In addition, an animal's food-sharing behavior, which in itself may be based on a simple cognitive mechanism, could be used as a tool to investigate the extent to which the individual may be capable of complex cognitive abilities, for example, mental-state attribution. These three areas of research, reciprocity, teaching, and mental-state attribution, illustrate how food-sharing behavior can be used as a valuable natural behavior to investigate cognition in non-human animals.This is the accepted manuscript. The final version is available from Wiley at http://onlinelibrary.wiley.com/doi/10.1002/wcs.1329/abstract
Linguistic capacity of non-human animals

This paper was funded by European Union's Seventh Framework Programme for research, technological development and demonstration. Grant Number: 283871Linguists interested in language evolution tend to focus on combinatorial features and rightly point out the lack of comparable evidence in animal communication. However, human language is based on various unique capacities, such as a motor capacity of sophisticated vocal control and a cognitive capacity of acting on others' psychological states. These features are only present in very rudimentary forms in non-human primates, suggesting they have evolved more recently in the human lineage. Here, the evidence from recent fieldwork for precursors of these abilities is reviewed, notably sequence-based semantic communication, vocal tract control, and audience awareness. Overall, there is evidence for both continuity and discontinuity when comparing modern primate and human communication, suggesting that the origin of language is the result of multiple gradual transitions from earlier forms of primate-like communication and social cognition, rather than a sudden and fundamental redesign in ancestral human communication and cognition.PostprintPeer reviewe
Neurodevelopmental disorders

Recent technological advances allow us to measure how the infant brain functions in ways that were not possible just a decade ago. Although methodological advances are exciting, we must also consider how theories guide research: what we look for and how we explain what we find. Indeed, the ways in which research findings are interpreted affects the design of policies, educational practices, and interventions. Thus, the theoretical approaches adopted by scientists have a real impact on the lives of children with neurodevelopmental disorders (NDDs) and their families, as well as on the wider community. Here, we introduce and compare two theoretical approaches that are used to understand NDDs: the neuropsychological account and neuroconstructivism. We show how the former, adult account, is inadequate for explaining NDDs and illustrate this using the examples of Williams syndrome and specific language impairment. Neuroconstructivism, by contrast, focuses on the developing organism and is helping to change the way in which NDDs are investigated. Whereas neuropsychological static approaches assume that one or more ‘modules’ (e.g., visuospatial ability in Williams syndrome) are impaired while the rest of the system is spared (e.g., language in Williams syndrome), neuroconstructivism proposes that basic‐level deficits have subtle cascading effects on numerous domains over development. Neuroconstructivism leads researchers to embrace complexity by establishing large research consortia to integrate findings at multiple levels (e.g., genetic, neural, cognitive, environmental) across developmental time
Echolocation in humans : an overview.

Bats and dolphins are known for their ability to use echolocation. They emit bursts of sounds and listen to the echoes that bounce back to detect the objects in their environment. What is not as well-known is that some blind people have learned to do the same thing, making mouth clicks, for example, and using the returning echoes from those clicks to sense obstacles and objects of interest in their surroundings. The current review explores some of the research that has examined human echolocation and the changes that have been observed in the brains of echolocation experts. We also discuss potential applications and assistive technology based on echolocation. Blind echolocation experts can sense small differences in the location of objects, differentiate between objects of various sizes and shapes, and even between objects made of different materials, just by listening to the reflected echoes from mouth clicks. It is clear that echolocation may enable some blind people to do things that are otherwise thought to be impossible without vision, potentially providing them with a high degree of independence in their daily lives and demonstrating that echolocation can serve as an effective mobility strategy in the blind. Neuroimaging has shown that the processing of echoes activates brain regions in blind echolocators that would normally support vision in the sighted brain, and that the patterns of these activations are modulated by the information carried by the echoes. This work is shedding new light on just how plastic the human brain is
Spatial cognition in mice and rats: similarities and differences in brain and behavior

The increasing use of mice models in cognitive tasks that were originally designed for rats raises crucial questions about cross-species comparison in the study of spatial cognition. The present review focuses on the major neuroethological differences existing between mice and rats, with particular attention given to the neurophysiological basis of space coding. While little difference is found in the basic properties of space representation in these two species, it appears that the stability of this representation changes more drastically over time in mice than in rats. We consider several hypotheses dealing with attentional, perceptual, and genetic aspects and offer some directions for future research that might help in deciphering hippocampal function in learning and memory processes. WIREs Cogn Sci 2016, 7:406-421. doi: 10.1002/wcs.141
Analyzing effective connectivity with fMRI

Functional neuroimaging techniques are used widely in cognitive neuroscience to investigate aspects of functional specialization and functional integration in the human brain. Functional integration can be characterized in two ways, functional connectivity and effective connectivity. While functional connectivity describes statistical dependencies between data, effective connectivity rests on a mechanistic model of the causal effects that generated the data. This review addresses the conceptual and methodological basis of established techniques for characterizing effective connectivity using functional magnetic resonance imaging (fMRI) data. In particular, we focus on dynamic causal modeling (DCM) of fMRI data and emphasize the importance of model selection procedures and nonlinear mechanisms for context-dependent changes in connection strengths
Imitation: what animal imitation tells us about animal cognition

Imitation of actions is widespread in the animal kingdom, but the mental capacities thereby implied vary greatly according to the adaptive function of copying. Behavioral synchrony in social species has many possible benefits, including minimizing predation risk and using food resources optimally, but can be understood by the simple cognitive mechanism of response facilitation by priming. Imitation can send a social message, either one of short-term meshing or group identity. Where the imitative match is opaque, as in neonatal imitation, the correspondence problem may imply an innate system of behavior matching; but in other cases, no more than priming may be involved, although there are persistent suggestions that great ape imitation implies empathic abilities. Imitation in the service of learning new skills by following another’s example can be divided into contextual imitation (when to employ a familiar action, and to what problem) and production imitation (learning of new skills by imitation). Cognitively, the former requires little more than response facilitation, whereas production imitation needs at least the ability to extract the statistical regularities of repeated action and to incorporate the result into hierarchical program-construction. Among our close relatives, only the great apes show much evidence of production imitation of actions, along with the ability to selectively imitate the most rational components of what they observe
Core pathways controlling shoot meristem maintenance

Essential to the function of shoot meristems in plants to act as sites of continuous organ and tissue formation is the ability of cells within the meristem to remain undifferentiated and proliferate indefinitely. These are characteristics of the stem cells within meristems that are critical for their growth properties. Stem cells are found in tight association with the stem cell niche—those cells that signal to maintain stem cells. Shoot meristems are unique among stem cell systems in that the stem cell niche is a constantly changing population of recent daughter stem cells. Recent progress from Arabidopsis and other systems have uncovered a large number of genes with defined roles in meristem structure and maintenance. This review will focus on well‐studied pathways that represent signaling between the stem cells and the niche, that prevent ectopic differentiation of stem cells, that regulate the chromatin status of stem cell factors, and that reveal intersection of hormone signaling and meristem maintenance.  WIREs Dev Biol  2013, 2:671–684. doi: 10.1002/wdev.110  For further resources related to this article, please visit the  WIREs website
Emergence of neuronal diversity from patterning of telencephalic progenitors

During central nervous system (CNS) development, hundreds of distinct neuronal subtypes are generated from a single layer of multipotent neuroepithelial progenitor cells. Within the rostral CNS, initial regionalization of the telencephalon marks the territories where the cerebral cortex and the basal ganglia originate. Subsequent refinement of the primary structures determines the formation of domains of differential gene expression, where distinct fate-restricted progenitors are located. To understand how diversification of neural progenitors and neurons is achieved in the telencephalon, it is important to address early and late patterning events in this context. In particular, important questions include: How does the telencephalon become specified and regionalized along the major spatial axes? Within each region, are the differences in neuronal subtypes established at the progenitor level or at the postmitotic stage? If distinct progenitors exist that are committed to subtype-specific neuronal lineages, how does the diversification emerge? What is the contribution of positional and temporal cues and how is this information integrated into the intrinsic programs of cell identity?This work was supported by Medical Research Council (MRC) grants G0700758 and MR/K018329/1 and	 Doctoral Training Award (LH); RA	 is supported by an	MRC postdoctoral fellowship.This is the accepted manuscript. The final version is available from Wiley at http://onlinelibrary.wiley.com/doi/10.1002/wdev.174/abstract
Wind turbine condition monitoring : technical and commercial challenges.

Deployment of larger scale wind turbine systems, particularly offshore, requires more organized operation and maintenance strategies to ensure systems are safe, profitable and cost-effective. Among existing maintenance strategies, reliability centred maintenance is regarded as best for offshore wind turbines, delivering corrective and proactive (i.e. preventive and predictive) maintenance techniques enabling wind turbines to achieve high availability and low cost of energy. Reliability centred maintenance analysis may demonstrate that an accurate and reliable condition monitoring system is one method to increase availability and decrease the cost of energy from wind. In recent years, efforts have been made to develop efficient and cost-effective condition monitoring techniques for wind turbines. A number of commercial wind turbine monitoring systems are available in the market, most based on existing techniques from other rotating machine industries. Other wind turbine condition monitoring reviews have been published but have not addressed the technical and commercial challenges, in particular, reliability and value for money. The purpose of this paper is to fill this gap and present the wind industry with a detailed analysis of the current practical challenges with existing wind turbine condition monitoring technology
Persistence of low wind speed conditions and implications for wind power variability

As the penetration of wind generation increases on power systems throughout the world, the effects of wind variability on power systems are of increasing concern. This study focuses on sustained occurrences of low wind speeds over durations ranging from 1 h to 20 days. Such events have major implications for the variability of energy yields from wind farms. This, in turn, influences the accuracy of wind resource assessment. The frequency analysis techniques commonly used to study wind variability cannot represent the autocorrelation properties of wind speeds and thus provide no information on the probabilities of occurrence of such sustained, low wind events. We present two complementary methods for assessing wind variability, runs analysis and intensity–duration–frequency analysis, both with emphasis on characterising the occurrence of continuous, extended periods (up to several days) of low wind speeds. Multi-annual time series of hourly wind speeds from meteorological stations in Ireland are analysed with both techniques. Sustained 20-day periods corresponding to extremely low levels of wind generation are found to have return periods of around 10 years in coastal areas. Persistent, widespread low wind speed conditions across the entire country are found to occur only rarely