QCManyBody: A flexible implementation of the many-body expansion.

While the many-body expansion (MBE) and counterpoise treatments are commonly used to mitigate the high scaling of accurate ab initio methods, researchers may need to piece together tools and scripts if their primary chosen software does not support targeted features. To further modular software in quantum chemistry, the arbitrary-order, multiple-model-chemistry, counterpoise-enabled MBE implementation from Psi4 has been extracted into an independent, lightweight, and open-source Python module, QCManyBody, with new schema underpinning, application programming interface, and software integrations. The package caters to direct users by facilitating single-point and geometry optimization MBE calculations backed by popular quantum chemistry codes through the QCEngine runner and by defining a schema for requesting and reporting many-body computations.

Nutmeg and SPICE: Models and Data for Biomolecular Machine Learning.

We describe version 2 of the SPICE data set, a collection of quantum chemistry calculations for training machine learning potentials. It expands on the original data set by adding much more sampling of chemical space and more data on noncovalent interactions. We train a set of potential energy functions called Nutmeg on it.

Digital dashboards for direct oral anticoagulant surveillance, intervention and operational efficiency: uptake, obstacles, and opportunities.

Direct oral anticoagulants (DOAC) are the most widely prescribed oral anticoagulants in the United States. Despite advantages over warfarin, system-level improvements are needed to optimize outcomes. While Veterans Health Administration and others have described successful DOAC management dashboard implementation, the extent of use nationally is unknown.

Digital dashboards for oral anticoagulation management: a literature scoping review.

This scoping review summarizes the extent and characteristics of the published literature describing digital population management dashboards implemented to improve the quality of anticoagulant management. A standardized search protocol was executed to identify relevant manuscripts published between January 1, 2015 and May 31, 2022. The resulting records were systematically evaluated by multiple blinded reviewers and the findings from selected papers were evaluated and summarized.

SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials.

Machine learning potentials are an important tool for molecular simulation, but their development is held back by a shortage of high quality datasets to train them on. We describe the SPICE dataset, a new quantum chemistry dataset for training potentials relevant to simulating drug-like small molecules interacting with proteins. It contains over 1.

Identification of the first glyphosate-resistant capeweed (Arctotheca calendula) population.

Background: Glyphosate is routinely used in Australia to control the Arctotheca species Arctotheca calendula (L.) Levyns (referred hereinafter as capeweed). This study identifies the first global case of field-evolved glyphosate-resistant capeweed, collected from the grainbelt of Western Australia.

Psi4 1.4: Open-source software for high-throughput quantum chemistry.

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python.

A position statement on screening and management of prediabetes in adults in primary care in Australia.

Prediabetes has a high prevalence, with early detection essential to facilitate optimal management to prevent the development of conditions such as type 2 diabetes and cardiovascular disease. Prediabetes can include impaired fasting glucose, impaired glucose tolerance and elevated HbA1c. This position statement outlines the approaches to screening and management of prediabetes in primary care.

New Basis Set Exchange: An Open, Up-to-Date Resource for the Molecular Sciences Community.

The Basis Set Exchange (BSE) has been a prominent fixture in the quantum chemistry community. First publicly available in 2007, it is recognized by both users and basis set creators as the de facto source for information related to basis sets. This popular resource has been rewritten, utilizing modern software design and best practices.

Home gardens as a predictor of enhanced dietary diversity and food security in rural Myanmar.

Background: Home gardens have been found to improve food security and dietary diversity in a wide range of settings. However, there is a need to place home gardens within the larger food and nutrition system landscapes that shape the construction of household diets. Myanmar offers a unique opportunity to study these research questions, given the decades of political isolation, high levels of food insecurity and poor nutrition levels.

Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science.

The field of computational molecular sciences (CMSs) has made innumerable contributions to the understanding of the molecular phenomena that underlie and control chemical processes, which is manifested in a large number of community software projects and codes. The CMS community is now poised to take the next transformative steps of better training in modern software design and engineering methods and tools, increasing interoperability through more systematic adoption of agreed upon standards and accepted best-practices, overcoming unnecessary redundancy in software effort along with greater reproducibility, and increasing the deployment of new software onto hardware platforms from in-house clusters to mid-range computing systems through to modern supercomputers. This in turn will have future impact on the software that will be created to address grand challenge science that we illustrate here: the formulation of diverse catalysts, descriptions of long-range charge and excitation transfer, and development of structural ensembles for intrinsically disordered proteins.

Electronically Excited States in Solution via a Smooth Dielectric Model Combined with Equation-of-Motion Coupled Cluster Theory.

We present a method for computing excitation energies for molecules in solvent, based on the combination of a minimal parameter implicit solvent model and the equation-of-motion coupled-cluster singles and doubles method (EOM-CCSD). In this method, the solvent medium is represented by a smoothly varying dielectric function, constructed directly from the quantum mechanical electronic density using only two tunable parameters. The solvent-solute electrostatic interactions are computed by numerical solution of the nonhomogeneous Poisson equation and incorporated at the Hartree-Fock stage of the EOM-CCSD calculation by modification of the electrostatic potential.

Factors Affecting Measurement of Salivary Cortisol and Secretory Immunoglobulin A in Field Studies of Athletes.

Aims: Biological and lifestyle factors, such as daily rhythm, caffeine ingestion, recent infection, and antibiotic intake, have been shown to influence measurements of salivary cortisol (SC) and secretory immunoglobulin A (sIgA). Current methodology in unsynchronized, field-based biomarker studies does not take these effects into account. Moreover, very little is known about the combined effects of biological and lifestyle factors on SC and sIgA.

Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability.

Psi4 is an ab initio electronic structure program providing methods such as Hartree-Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex tasks, such as geometry optimization using complete-basis-set extrapolation or focal-point methods.

A mixed-method evaluation of peer-education workshops for school-aged children to teach about antibiotics, microbes and hygiene.

Background: Delivering health topics in schools through peer education is known to be beneficial for all students involved. In this study, we have evaluated a peer-education workshop that aims to educate primary and secondary school students on hygiene, the spread of infection and antibiotics.

Methods: Four schools in south-west England, in a range of localities, took part in peer-education workshops, with students completing before, after and knowledge-retention questionnaires.

Canine reproductive ultrasound examination for predicting future sperm quality.

The reproductive potential of male animals is commonly evaluated using a breeding soundness examination incorporating B-mode ultrasound examination of the testes and recently Doppler ultrasound examination of the testicular arteries. These techniques may detect testicular normality or pathology, and while some measured parameters are associated with semen quality at the time of ultrasound examination, few studies have investigated the relationship with future semen quality. We hypothesized that B-mode and Doppler ultrasound measurements would correlate with future semen quality.

Horizontal vectorization of electron repulsion integrals.

We present an efficient implementation of the Obara-Saika algorithm for the computation of electron repulsion integrals that utilizes vector intrinsics to calculate several primitive integrals concurrently in a SIMD vector. Initial benchmarks display a 2-4 times speedup with AVX instructions over comparable scalar code, depending on the basis set. Speedup over scalar code is found to be sensitive to the level of contraction of the basis set, and is best for (lAlB|lClD) quartets when lD  = 0 or lB=lD=0, which makes such a vectorization scheme particularly suitable for density fitting.

Comparison of Allograft and Bovine Xenograft in Calcaneal Lengthening Osteotomy for Flatfoot Deformity in Cerebral Palsy.

Background: The Evan's calcaneal lengthening osteotomy is a treatment method for spastic flatfoot deformity in patients with cerebral palsy that fail nonoperative measures. Autograft and allograft have been reported as potential graft choices. Bovine xenograft has been introduced as an alternative, but limited human data exists supporting its efficacy.

Ensembl regulation resources.

New experimental techniques in epigenomics allow researchers to assay a diversity of highly dynamic features such as histone marks, DNA modifications or chromatin structure. The study of their fluctuations should provide insights into gene expression regulation, cell differentiation and disease. The Ensembl project collects and maintains the Ensembl regulation data resources on epigenetic marks, transcription factor binding and DNA methylation for human and mouse, as well as microarray probe mappings and annotations for a variety of chordate genomes.

Effects from spin-orbit coupling on electron-nucleus hyperfine coupling calculated at the restricted active space level for Kramers doublets.

Calculations of electron-nucleus hyperfine coupling were implemented at the restricted active space state interaction (RASSI) level to treat spin-orbit (SO) coupling, based on scalar relativistic restricted active space wave functions. The current implementation is suitable for light atomic systems, for light ligand atoms in heavy metal complexes, and for spin-orbit coupling-induced hyperfine coupling of heavy atoms if the unpaired electrons are described by orbitals with high angular momentum. Spin polarization is reasonably well treated by allowing one hole and one electron in a window of active orbitals ('ras1', 'ras3') surrounding the principal active space ('ras2').

Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table.

In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm.

Single-ion 4f element magnetism: an ab-initio look at Ln(COT)2(-).

The electron densities associated with the Ln 4f shell, and spin and orbital magnetizations ('magnetic moment densities'), are investigated for the Ln(COT)2(-) series. The densities are obtained from ab-initio calculations including spin-orbit coupling. For Ln = Ce, Pr the magnetizations are also derived from crystal field models and shown to agree with the ab-initio results.