Deep learning for augmented process monitoring of scalable perovskite thin-film fabrication.

Reproducible large-area fabrication is one of the remaining challenges for the commercialization of perovskite photovoltaics. Imaging methods augmented with deep learning (DL) enable in-line detection of spatial or temporal inconsistencies and predict the impact of observed changes on device performance. In this work, we showcase three use cases of how DL augments complex experimental data analysis of the large-area perovskite thin film formation, even on moderate-sized datasets.

Streaming Large-Scale Microscopy Data to a Supercomputing Facility.

Data management is a critical component of modern experimental workflows. As data generation rates increase, transferring data from acquisition servers to processing servers via conventional file-based methods is becoming increasingly impractical. The 4D Camera at the National Center for Electron Microscopy generates data at a nominal rate of 480 Gbit s-1 (87,000 frames s-1), producing a 700 GB dataset in 15 s.

Quantum-parallel vectorized data encodings and computations on trapped-ion and transmon QPUs.

Compact data representations in quantum systems are crucial for the development of quantum algorithms for data analysis. In this study, we present two innovative data encoding techniques, known as QCrank and QBArt, which exhibit significant quantum parallelism via uniformly controlled rotation gates. The QCrank method encodes a series of real-valued data as rotations on data qubits, resulting in increased storage capacity.

Segmentation of 71 Anatomical Structures Necessary for the Evaluation of Guideline-Conforming Clinical Target Volumes in Head and Neck Cancers.

The delineation of the clinical target volumes (CTVs) for radiation therapy is time-consuming, requires intensive training and shows high inter-observer variability. Supervised deep-learning methods depend heavily on consistent training data; thus, State-of-the-Art research focuses on making CTV labels more homogeneous and strictly bounding them to current standards. International consensus expert guidelines standardize CTV delineation by conditioning the extension of the clinical target volume on the surrounding anatomical structures.

A bacterial sensor taxonomy across earth ecosystems for machine learning applications.

Microbial communities have evolved to colonize all ecosystems of the planet, from the deep sea to the human gut. Microbes survive by sensing, responding, and adapting to immediate environmental cues. This process is driven by signal transduction proteins such as histidine kinases, which use their sensing domains to bind or otherwise detect environmental cues and "transduce" signals to adjust internal processes.

Interpreting macromolecular diffraction through simulation.

This chapter discusses the use of diffraction simulators to improve experimental outcomes in macromolecular crystallography, in particular for future experiments aimed at diffuse scattering. Consequential decisions for upcoming data collection include the selection of either a synchrotron or free electron laser X-ray source, rotation geometry or serial crystallography, and fiber-coupled area detector technology vs. pixel-array detectors.

XFEL Microcrystallography of Self-Assembling Silver -Alkanethiolates.

New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.

Remembering the Work of Phillip L. Geissler: A Coda to His Scientific Trajectory.

Phillip L. Geissler made important contributions to the statistical mechanics of biological polymers, heterogeneous materials, and chemical dynamics in aqueous environments. He devised analytical and computational methods that revealed the underlying organization of complex systems at the frontiers of biology, chemistry, and materials science.

A detailed study of ion transport through the SARS-CoV-2 E protein ion channel.

The envelope (E) protein encoded in the genome of an RNA virus is crucial for the replication, budding and pathophysiology of the virus. In the light of the ongoing pandemic, we explored similarities/differences between SARS-CoV-1 and SARS-CoV-2 E protein ion channels in terms of their selectivity. Further, we also examined the impact of variation of the bath concentration and introduction of potential and concentration gradients across the channel on the binding ratios of sodium and chloride ions for the SARS-CoV-2 E protein.

An end-to-end computer vision methodology for quantitative metallography.

Metallography is crucial for a proper assessment of material properties. It mainly involves investigating the spatial distribution of grains and the occurrence and characteristics of inclusions or precipitates. This work presents a holistic few-shot artificial intelligence model for Quantitative Metallography, including Anomaly Detection, that automatically quantifies the degree of the anomaly of impurities in alloys.

Chemical crystallography by serial femtosecond X-ray diffraction.

Inorganic-organic hybrid materials represent a large share of newly reported structures, owing to their simple synthetic routes and customizable properties. This proliferation has led to a characterization bottleneck: many hybrid materials are obligate microcrystals with low symmetry and severe radiation sensitivity, interfering with the standard techniques of single-crystal X-ray diffraction and electron microdiffraction. Here we demonstrate small-molecule serial femtosecond X-ray crystallography (smSFX) for the determination of material crystal structures from microcrystals.

Meniscus Injury and its Surgical Treatment Does not Increase Initial Whole Knee Joint Friction.

While it is generally accepted that traumatic meniscus pathologies lead to degenerative articular cartilage changes in the mid-to long-term and consecutively to post-traumatic osteoarthritis (PTOA), very little is known about how such injuries initiate tribological changes within the knee and their possible impact on PTOA acceleration. Therefore, the aim of this study was to investigate the influence of three different medial meniscus states (intact, posterior root tear, total meniscectomy) on the initial whole knee joint friction. Six ovine knee joints were tested in a passive pendulum friction testing device under an axial load of 250 N and an initial deflection of 12°, representing swing phase conditions, and under an axial load of 1000 N and an initial deflection of 5°, simulating stance phase conditions.

Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I.

Photosystem I (PS I) has a symmetric structure with two highly similar branches of pigments at the center that are involved in electron transfer, but shows very different efficiency along the two branches. We have determined the structure of cyanobacterial PS I at room temperature (RT) using femtosecond X-ray pulses from an X-ray free electron laser (XFEL) that shows a clear expansion of the entire protein complex in the direction of the membrane plane, when compared to previous cryogenic structures. This trend was observed by complementary datasets taken at multiple XFEL beamlines.

X-ray linear dichroic ptychography.

Biominerals such as seashells, coral skeletons, bone, and tooth enamel are optically anisotropic crystalline materials with unique nanoscale and microscale organization that translates into exceptional macroscopic mechanical properties, providing inspiration for engineering new and superior biomimetic structures. Using coral skeleton as a model, here, we experimentally demonstrate X-ray linear dichroic ptychography and map the -axis orientations of the aragonite (CaCO) crystals. Linear dichroic phase imaging at the oxygen K-edge energy shows strong polarization-dependent contrast and reveals the presence of both narrow (<35°) and wide (>35°) -axis angular spread in the coral samples.

An ultrahigh-resolution soft x-ray microscope for quantitative analysis of chemically heterogeneous nanomaterials.

The analysis of chemical states and morphology in nanomaterials is central to many areas of science. We address this need with an ultrahigh-resolution scanning transmission soft x-ray microscope. Our instrument provides multiple analysis tools in a compact assembly and can achieve few-nanometer spatial resolution and high chemical sensitivity via x-ray ptychography and conventional scanning microscopy.

Investigating ion transport inside the pentameric ion channel encoded in COVID-19 E protein.

Ion flow inside an ion channel can be described through continuum based Born-Poisson-Nernst-Planck (BPNP) equations in conjunction with the Lennard-Jones potential. Keeping in mind the ongoing pandemic, in this study, an attempt has been made to understand the selectivity and the current voltage relation of the COVID-19 E protein pentameric ion channel. Two ionic species, namely Na^{+} and Cl^{-}, have been considered here.

Simulation study of a coincidence detection system for non-invasive determination of arterial blood time-activity curve measurements.

Background: Arterial sampling in PET studies for the purposes of kinetic modeling remains an invasive, time-intensive, and expensive procedure. Alternatives to derive the blood time-activity curve (BTAC) non-invasively are either reliant on large vessels in the field of view or are laborious to implement and analyze as well as being prone to many processing errors. An alternative method is proposed in this work by the simulation of a non-invasive coincidence detection unit.

Adapted Feeding Utensils for People With Parkinson's-Related or Essential Tremor.

Objective: Our objective was to evaluate the effectiveness of four adapted feeding utensils with participants with essential tremor (ET) or tremor related to Parkinson's disease (PD).

Method: Participants performed a simulated feeding task under five conditions: (1) standard spoon (control condition), (2) weighted spoon with standard handle, (3) weighted spoon with built-up handle, (4) swivel spoon, and (5) Liftware Steady™ spoon, a product using active tremor cancellation technology. Participants rated each adapted utensil in comparison with the standard spoon regarding performance, ease of use, speed, neatness, and aesthetics.

MAGI: A Method for Metabolite Annotation and Gene Integration.

Metabolomics is a widely used technology for obtaining direct measures of metabolic activities from diverse biological systems. However, ambiguous metabolite identifications are a common challenge and biochemical interpretation is often limited by incomplete and inaccurate genome-based predictions of enzyme activities (that is, gene annotations). Metabolite Annotation and Gene Integration (MAGI) generates a metabolite-gene association score using a biochemical reaction network.

Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes.

Background: As microbiome research becomes increasingly prevalent in the fields of human health, agriculture and biotechnology, there exists a need for a resource to better link organisms and environmental chemistries. Exometabolomics experiments now provide assertions of the metabolites present within specific environments and how the production and depletion of metabolites is linked to specific microbes. This information could be broadly useful, from comparing metabolites across environments, to predicting competition and exchange of metabolites between microbes, and to designing stable microbial consortia.

Exhaustive search for epistatic effects on the human methylome.

Studies assessing the existence and magnitude of epistatic effects on complex human traits provide inconclusive results. The study of such effects is complicated by considerable increase in computational burden, model complexity, and model uncertainty, which in concert decrease model stability. An additional source introducing significant uncertainty with regard to the detection of robust epistasis is the biological distance between the genetic variation and the trait under study.