A neural algorithm for computing bipartite matchings.

Finding optimal bipartite matchings-e.g., matching medical students to hospitals for residency, items to buyers in an auction, or papers to reviewers for peer review-is a fundamental combinatorial optimization problem.

In vivo optogenetic manipulations of endogenous proteins reveal spatiotemporal roles of microtubule and kinesin in dendrite patterning.

During animal development, the spatiotemporal properties of molecular events largely determine the biological outcomes. Conventional gene analysis methods lack the spatiotemporal resolution for precise dissection of developmental mechanisms. Although optogenetic tools exist for manipulating designer proteins in cultured cells, few have been successfully applied to endogenous proteins in live animals.

Visualizing and Measuring Dendrite Arborization in Drosophila Somatosensory Neurons.

Dendrites of neurons receive synaptic or sensory inputs and are important sites of neuronal computation. The morphological features of dendrites not only are hallmarks of the neuronal type but also largely determine a neuron's function. Thus, dendrite morphogenesis has been a subject of intensive study in neuroscience.

Light-induced trapping of endogenous proteins reveals spatiotemporal roles of microtubule and kinesin-1 in dendrite patterning of sensory neurons.

Animal development involves numerous molecular events, whose spatiotemporal properties largely determine the biological outcomes. Conventional methods for studying gene function lack the necessary spatiotemporal resolution for precise dissection of developmental mechanisms. Optogenetic approaches are powerful alternatives, but most existing tools rely on exogenous designer proteins that produce narrow outputs and cannot be applied to diverse or endogenous proteins.

CRYSTAL23: A Program for Computational Solid State Physics and Chemistry.

The Crystal program for quantum-mechanical simulations of materials has been bridging the realm of molecular quantum chemistry to the realm of solid state physics for many years, since its first public version released back in 1988. This peculiarity stems from the use of atom-centered basis functions within a linear combination of atomic orbitals (LCAO) approach and from the corresponding efficiency in the evaluation of the exact Fock exchange series. In particular, this has led to the implementation of a rich variety of hybrid density functional approximations since 1998.

Barely sufficient practices in scientific computing.

The importance of software to modern research is well understood, as is the way in which software developed for research can support or undermine important research principles of findability, accessibility, interoperability, and reusability (FAIR). We propose a minimal subset of common software engineering principles that enable FAIRness of computational research and can be used as a baseline for software engineering in any research discipline.

Cells with loss-of-heterozygosity after exposure to ionizing radiation in Drosophila are culled by p53-dependent and p53-independent mechanisms.

Loss of Heterozygosity (LOH) typically refers to a phenomenon in which diploid cells that are heterozygous for a mutant allele lose their wild type allele through mutations. LOH is implicated in oncogenesis when it affects the remaining wild type copy of a tumor suppressor. Drosophila has been a useful model to identify genes that regulate the incidence of LOH, but most of these studies use adult phenotypic markers such as multiple wing hair (mwh).

Cost-effective composite methods for large-scale solid-state calculations.

Following the development in recent years of progressively more accurate approximations to the exchange-correlation functional, the use of density functional theory (DFT) methods to examine increasingly large and complex systems has grown, in particular for solids and other condensed matter systems. However the cost of these calculations is high, often requiring the use of specialist HPC facilities. As such, for the purpose of large-scale high-throughput screening of material properties, a hierarchy of simplified DFT methods has been proposed that allows rapid electronic structure calculation of large systems, and we have recently extended this scheme to the solid state (sol-3c).

The CRYSTAL code, 1976-2020 and beyond, a long story.

CRYSTAL is a periodic ab initio code that uses a Gaussian-type basis set to express crystalline orbitals (i.e., Bloch functions).

QuEST and High Performance Simulation of Quantum Computers.

We introduce QuEST, the Quantum Exact Simulation Toolkit, and compare it to ProjectQ, qHipster and a recent distributed implementation of Quantum++. QuEST is the first open source, hybrid multithreaded and distributed, GPU accelerated simulator of universal quantum circuits. Embodied as a C library, it is designed so that a user's code can be deployed seamlessly to any platform from a laptop to a supercomputer.

Fast spatially-resolved T measurements with constant-gradient CPMG.

Speed of acquisition is paramount for the application of magnetic resonance to flow experiments through porous rocks. One popular method for imaging core floods is the spatially resolved T experiment which can separate fluids either by their viscosity contrast or by doping one fluid with a relaxation agent. Existing techniques for spatial-T may suffer from long acquisition times and eddy currents due to the pulsing of magnetic field gradients.

Large-Scale Condensed Matter DFT Simulations: Performance and Capabilities of the CRYSTAL Code.

Nowadays, the efficient exploitation of high-performance computing resources is crucial to extend the applicability of first-principles theoretical methods to the description of large, progressively more realistic molecular and condensed matter systems. This can be achieved only by devising effective parallelization strategies for the most time-consuming steps of a calculation, which requires some effort given the usual complexity of quantum-mechanical algorithms, particularly so if parallelization is to be extended to all properties and not just to the basic functionalities of the code. In this Article, the performance and capabilities of the massively parallel version of the Crystal17 package for first-principles calculations on solids are discussed.

Fast imaging of laboratory core floods using 3D compressed sensing RARE MRI.

Three-dimensional (3D) imaging of the fluid distributions within the rock is essential to enable the unambiguous interpretation of core flooding data. Magnetic resonance imaging (MRI) has been widely used to image fluid saturation in rock cores; however, conventional acquisition strategies are typically too slow to capture the dynamic nature of the displacement processes that are of interest. Using Compressed Sensing (CS), it is possible to reconstruct a near-perfect image from significantly fewer measurements than was previously thought necessary, and this can result in a significant reduction in the image acquisition times.

Communication: Three-fold covariance imaging of laser-induced Coulomb explosions.

We apply a three-fold covariance imaging method to analyse previously acquired data [C. S. Slater et al.

The retinoid X receptor agonist bexarotene relieves positive symptoms of schizophrenia: a 6-week, randomized, double-blind, placebo-controlled multicenter trial.

Objective: The limitations of antipsychotic therapy in schizophrenia and schizoaffective disorder led to the investigation of the putative utility of pharmacologic augmentation strategies. The antitumor agent bexarotene via nuclear retinoid X receptor (RXR) activation might modulate numerous metabolic pathways involved in the pathogenesis of schizophrenia and schizoaffective disorder. This trial aimed to investigate efficacy and safety of add-on bexarotene to ongoing antipsychotic treatment of patients with schizophrenia or schizoaffective disorder.

A new massively parallel version of CRYSTAL for large systems on high performance computing architectures.

Fully ab initio treatment of complex solid systems needs computational software which is able to efficiently take advantage of the growing power of high performance computing (HPC) architectures. Recent improvements in CRYSTAL, a periodic ab initio code that uses a Gaussian basis set, allows treatment of very large unit cells for crystalline systems on HPC architectures with high parallel efficiency in terms of running time and memory requirements. The latter is a crucial point, due to the trend toward architectures relying on a very high number of cores with associated relatively low memory availability.

Unhealthy parenting and potential mediators as contributing factors to future intimate violence: a review of the literature.

Efforts to understand and prevent intimate violence have often focused on the intergenerational transmission of intimate violence. Although witnessing and/or experiencing abuse in the family of origin is well supported in the literature as a key component of the intergenerational transmission of intimate violence, there has been less attention to other family-of-origin factors that contribute to or mediate and/or moderate future intimate violence. Particularly, a focus on the effect of parenting on future intimate violence is needed beyond the effect of modeling abusive behavior.

On the performance of molecular dynamics applications on current high-end systems.

The effective exploitation of current high performance computing (HPC) platforms in molecular simulation relies on the ability of the present generation of parallel molecular dynamics code to make effective utilisation of these platforms and their components, including CPUs and memory. In this paper, we investigate the efficiency and scaling of a series of popular molecular dynamics codes on the UK's national HPC resources, an IBM p690+ cluster and an SGI Altix 3700. Focusing primarily on the AMBER, DL_POLY and NAMD simulation codes, we demonstrate the major performance and scalability advantages that arise through a distributed, rather than a replicated data approach.

Synchronous phase detection for optical fiber interferometric sensors.

A system has been developed to accurately detect phase signals produced in optical interferometric sensors. The system employs optical heterodyning and synchronously detects optical phase by feeding back an error signal to a phase modulator in the reference leg of the interferometer. This system is seen to have properties similar to a phase-locked loop.

Acoustic desensitization of single-mode fibers utilizing nickel coatings.

The pressure sensitivity of the phase of light propagating in a single-mode fiber coated with a thin nickel jacket is determined both analytically and experimentally. The measured acoustic response of the fiber is found to be 1 order of magnitude lower than that of the bare fiber, in agreement with analytical predictions. The technique thus appears to be a promising way for desensitizing optical-fiber leads for use with fiber-optic sensors.