Joint profiling of DNA methylation and chromatin architecture in single cells.

We report a molecular assay, Methyl-HiC, that can simultaneously capture the chromosome conformation and DNA methylome in a cell. Methyl-HiC reveals coordinated DNA methylation status between distal genomic segments that are in spatial proximity in the nucleus, and delineates heterogeneity of both the chromatin architecture and DNA methylome in a mixed population. It enables simultaneous characterization of cell-type-specific chromatin organization and epigenome in complex tissues

Generic nano-imprint process for fabrication of nanowire arrays

A generic process has been developed to grow nearly defect free arrays of (heterostructured) InP and GaP nanowires. Soft nanoimprint lithography has been used to pattern gold particle arrays on full 2 inch substrates. After lift-off organic residues remain on the surface, which induce the growth of additional undesired nanowires. We show that cleaning of the samples before growth with piranha solution in combination with a thermal anneal at 550 C for InP and 700 C for GaP results in uniform nanowire arrays with 1% variation in nanowire length, and without undesired extra nanowires. Our chemical cleaning procedure is applicable to other lithographic techniques such as e-beam lithography, and therefore represents a generic process.Comment: 12 pages, 4 figures, 2 table

TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations

TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy–cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe–Salpeter methods, second-order Møller–Plesset theory, and explicitly correlated coupled-cluster methods. TURBOMOLE is based on Gaussian basis sets and has been pivotal for the development of many fast and low-scaling algorithms in the past three decades, such as integral-direct methods, fast multipole methods, the resolution-of-the-identity approximation, imaginary frequency integration, Laplace transform, and pair natural orbital methods. This review focuses on recent additions to TURBOMOLE’s functionality, including excited-state methods, RPA and Green’s function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems. A variety of illustrative applications along with accuracy and timing data are discussed. Moreover, available interfaces to users as well as other software are summarized. TURBOMOLE’s current licensing, distribution, and support model are discussed, and an overview of TURBOMOLE’s development workflow is provided. Challenges such as communication and outreach, software infrastructure, and funding are highlighted

TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations

TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy–cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe–Salpeter methods, second-order Møller–Plesset theory, and explicitly correlated coupled-cluster methods. TURBOMOLE is based on Gaussian basis sets and has been pivotal for the development of many fast and low-scaling algorithms in the past three decades, such as integral-direct methods, fast multipole methods, the resolution-of-the-identity approximation, imaginary frequency integration, Laplace transform, and pair natural orbital methods. This review focuses on recent additions to TURBOMOLE’s functionality, including excited-state methods, RPA and Green’s function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems. A variety of illustrative applications along with accuracy and timing data are discussed. Moreover, available interfaces to users as well as other software are summarized. TURBOMOLE’s current licensing, distribution, and support model are discussed, and an overview of TURBOMOLE’s development workflow is provided. Challenges such as communication and outreach, software infrastructure, and funding are highlighted

An excess of niche differences maximizes ecosystem functioning

Ecologists have long argued that higher functioning in diverse communities arises from the niche differences stabilizing species coexistence and from the fitness differences driving competitive dominance. However, rigorous tests are lacking. We couple field-parameterized models of competition between 10 annual plant species with a biodiversity-functioning experiment under two contrasting environmental conditions, to study how coexistence determinants link to biodiversity effects (selection and complementarity). We find that complementarity effects positively correlate with niche differences and selection effects differences correlate with fitness differences. However, niche differences also contribute to selection effects and fitness differences to complementarity effects. Despite this complexity, communities with an excess of niche differences (where niche differences exceeded those needed for coexistence) produce more biomass and have faster decomposition rates under drought, but do not take up nutrients more rapidly. We provide empirical evidence that the mechanisms determining coexistence correlate with those maximizing ecosystem functioning. It is unclear how biodiversity-ecosystem functioning and species coexistence mechanisms are linked. Here, Godoy and colleagues combine field-parameterised competition models with a BEF experiment to show that mechanisms leading to more stable species coexistence lead to greater productivity, but not necessarily to enhanced functions other than primary production

Environmental pleiotropy and demographic history direct adaptation under antibiotic selection

Evolutionary rescue following environmental change requires mutations permitting population growth in the new environment. If change is severe enough to prevent most of the population reproducing, rescue becomes reliant on mutations already present. If change is sustained, the fitness effects in both environments, and how they are associated-termed 'environmental pleiotropy'-may determine which alleles are ultimately favoured. A population's demographic history-its size over time-influences the variation present. Although demographic history is known to affect the probability of evolutionary rescue, how it interacts with environmental pleiotropy during severe and sustained environmental change remains unexplored. Here, we demonstrate how these factors interact during antibiotic resistance evolution, a key example of evolutionary rescue fuelled by pre-existing mutations with pleiotropic fitness effects. We combine published data with novel simulations to characterise environmental pleiotropy and its effects on resistance evolution under different demographic histories. Comparisons among resistance alleles typically revealed no correlation for fitness-i.e., neutral pleiotropy-above and below the sensitive strain's minimum inhibitory concentration. Resistance allele frequency following experimental evolution showed opposing correlations with their fitness effects in the presence and absence of antibiotic. Simulations demonstrated that effects of environmental pleiotropy on allele frequencies depended on demographic history. At the population level, the major influence of environmental pleiotropy was on mean fitness, rather than the probability of evolutionary rescue or diversity. Our work suggests that determining both environmental pleiotropy and demographic history is critical for predicting resistance evolution, and we discuss the practicalities of this during in vivo evolution

Removing situation descriptions from situational judgment test items: Does the impact differ for video-based versus text-based formats?

Recent research has shown that many text-based situational judgment test (SJT) items can be solved even when the situational descriptions in the item stems are not presented to test takers. This finding challenges the traditional view of SJTs as low-fidelity simulations that rely on 'situational' (context-dependent) judgment. However, media richness theory and construal level theory suggest that situation descriptions presented in a richer and more concrete format (video format) will reduce uncertainty about inherent requirements and facilitate the perception that the situation is taking place in the here and now. Therefore, we hypothesized that situational judgment would be more important in video situation descriptions than in text situation descriptions. We adapted a leadership SJT to realize a 3 (situation description in the item stem: video vs. text vs. none) x 2 (response format: video response options vs. text response options) between-subjects design (N = 279). Participants were randomly assigned to one of the six conditions. The removal of video-based situation descriptions in item stems led to an equivalent decrease in SJT scores as the removal of text-based situation descriptions in item stems (video-based version: Cohen's d = 0.535 vs. text-based version: Cohen's d = 0.531). SJT scores were also contingent on the presentation format of both situation descriptions and response options: The highest scores were observed when situation descriptions and response options were presented in the same format. Implications for SJT theory and research are discussed. Practitioner points The presentation format did not moderate the effect of omitting situation descriptions in SJTs - that is, the context dependency of SJT performance did not increase when the SJT was administered in a video-based rather than a text-based format. The elimination of situation descriptions in item stems had a medium effect on overall test scores: SJT scores were significant lower without situation descriptions in comparison to SJT scores with situation descriptions (video-based version: Cohen's d = 0.535 vs. text-based version: Cohen's d = 0.531). It is important to match the stimulus and response formats in SJTs

Effect of response format on cognitive reflection: Validating a two- and four-option multiple choice question version of the Cognitive Reflection Test

The Cognitive Reflection Test, measuring intuition inhibition and cognitive reflection, has become extremely popular since it reliably predicts reasoning performance, decision-making and beliefs. Across studies, the response format of CRT items sometimes differs, assuming construct equivalence of the tests with open-ended vs. multiple choice items (the equivalence hypothesis). Evidence and theoretical reasons, however, suggest that the cognitive processes measured by these response formats and their associated performances might differ (the non-equivalence hypothesis). We tested the two hypotheses experimentally by assessing the performance in tests with different response formats and by comparing their predictive and construct validity. In a between-subjects experiment (n = 452), participants answered an open-ended, a two- or a four-option response format of stem-equivalent CRT items and completed tasks on belief bias, denominator neglect and paranormal beliefs (benchmark indicators of predictive validity) as well as actively open-minded thinking and numeracy (benchmark indicators of construct validity). We found no significant differences between the three response formats in the number of correct responses, the number of intuitive responses (with the exception of the two-option version being higher than the other tests) and in the correlational patterns with the indicators of predictive and construct validity. All three test versions were similarly reliable but the multiple-choice formats were completed more quickly. We speculate that the specific nature of the CRT items helps to build construct equivalence among the different response formats. We recommend using the validated multiple-choice version of the CRT presented here, particularly the four-option CRT, for practical and methodological reasons

Software for the frontiers of quantum chemistry:An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design