Towards nationally curated data archives for clinical radiology image analysis at scale: Learnings from national data collection in response to a pandemic.

The prevalence of the coronavirus SARS-CoV-2 disease has resulted in the unprecedented collection of health data to support research. Historically, coordinating the collation of such datasets on a national scale has been challenging to execute for several reasons, including issues with data privacy, the lack of data reporting standards, interoperable technologies, and distribution methods. The coronavirus SARS-CoV-2 disease pandemic has highlighted the importance of collaboration between government bodies, healthcare institutions, academic researchers and commercial companies in overcoming these issues during times of urgency. The National COVID-19 Chest Imaging Database, led by NHSX, British Society of Thoracic Imaging, Royal Surrey NHS Foundation Trust and Faculty, is an example of such a national initiative. Here, we summarise the experiences and challenges of setting up the National COVID-19 Chest Imaging Database, and the implications for future ambitions of national data curation in medical imaging to advance the safe adoption of artificial intelligence in healthcare.

An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis.

BACKGROUND: The National COVID-19 Chest Imaging Database (NCCID) is a centralized database containing mainly chest X-rays and computed tomography scans from patients across the UK. The objective of the initiative is to support a better understanding of the coronavirus SARS-CoV-2 disease (COVID-19) and the development of machine learning technologies that will improve care for patients hospitalized with a severe COVID-19 infection. This article introduces the training dataset, including a snapshot analysis covering the completeness of clinical data, and availability of image data for the various use-cases (diagnosis, prognosis, longitudinal risk). An additional cohort analysis measures how well the NCCID represents the wider COVID-19-affected UK population in terms of geographic, demographic, and temporal coverage. FINDINGS: The NCCID offers high-quality DICOM images acquired across a variety of imaging machinery; multiple time points including historical images are available for a subset of patients. This volume and variety make the database well suited to development of diagnostic/prognostic models for COVID-associated respiratory conditions. Historical images and clinical data may aid long-term risk stratification, particularly as availability of comorbidity data increases through linkage to other resources. The cohort analysis revealed good alignment to general UK COVID-19 statistics for some categories, e.g., sex, whilst identifying areas for improvements to data collection methods, particularly geographic coverage. CONCLUSION: The NCCID is a growing resource that provides researchers with a large, high-quality database that can be leveraged both to support the response to the COVID-19 pandemic and as a test bed for building clinically viable medical imaging models.

Automated audiovisual behavior recognition in wild primates.

Large video datasets of wild animal behavior are crucial to produce longitudinal research and accelerate conservation efforts; however, large-scale behavior analyses continue to be severely constrained by time and resources. We present a deep convolutional neural network approach and fully automated pipeline to detect and track two audiovisually distinctive actions in wild chimpanzees: buttress drumming and nut cracking. Using camera trap and direct video recordings, we train action recognition models using audio and visual signatures of both behaviors, attaining high average precision (buttress drumming: 0.87 and nut cracking: 0.85), and demonstrate the potential for behavioral analysis using the automatically parsed video. Our approach produces the first automated audiovisual action recognition of wild primate behavior, setting a milestone for exploiting large datasets in ethology and conservation.

Chimpanzee face recognition from videos in the wild using deep learning.

Video recording is now ubiquitous in the study of animal behavior, but its analysis on a large scale is prohibited by the time and resources needed to manually process large volumes of data. We present a deep convolutional neural network (CNN) approach that provides a fully automated pipeline for face detection, tracking, and recognition of wild chimpanzees from long-term video records. In a 14-year dataset yielding 10 million face images from 23 individuals over 50 hours of footage, we obtained an overall accuracy of 92.5% for identity recognition and 96.2% for sex recognition. Using the identified faces, we generated co-occurrence matrices to trace changes in the social network structure of an aging population. The tools we developed enable easy processing and annotation of video datasets, including those from other species. Such automated analysis unveils the future potential of large-scale longitudinal video archives to address fundamental questions in behavior and conservation.

Origin of Many-Body Vibrational Frequency Shifts in Water Clusters.

We have demonstrated the application of many-body expansions to calculations of the anharmonic, local-mode, OH-stretching vibrational frequencies of water clusters. We focused on five low-lying isomers of the water hexamer and the DD*(20,1) isomer of (H2O)21. Our approach provides accurate OH-stretching vibrational frequencies when treating one- and two-body interactions with the CCSD(T)-F12 level of theory and the three- and four-body interactions with the DF-MP2-F12 level. Additionally, we have investigated the physical origin of the large contribution that two- and three-body interactions make to the shifts of vibrational frequencies using symmetry-adapted perturbation theory (SAPT). We conclude that while two-body vibrational frequency shifts can be correlated linearly with electrostatic energies, all strongly shifted three-body interactions can be correlated to the induction energy with a single regression coefficient of approximately 70 cm-1 (kcal·mol-1)-1.

Cumulative culture in nonhumans: overlooked findings from Japanese monkeys?

Cumulative culture, generally known as the increasing complexity or efficiency of cultural behaviors additively transmitted over successive generations, has been emphasized as a hallmark of human evolution. Recently, reviews of candidates for cumulative culture in nonhuman species have claimed that only humans have cumulative culture. Here, we aim to scrutinize this claim, using current criteria for cumulative culture to re-evaluate overlooked qualitative but longitudinal data from a nonhuman primate, the Japanese monkey (Macaca fuscata). We review over 60 years of Japanese ethnography of Koshima monkeys, which indicate that food-washing behaviors (e.g., of sweet potato tubers and wheat grains) seem to have increased in complexity and efficiency over time. Our reassessment of the Koshima ethnography is preliminary and nonquantitative, but it raises the possibility that cumulative culture, at least in a simple form, occurs spontaneously and adaptively in other primates and nonhumans in nature.

Development of radiodetection systems towards miniaturised quality control of PET and SPECT radiopharmaceuticals.

The ability to detect radiation in microfluidic devices is important for the on-chip analysis of radiopharmaceuticals, but previously reported systems have largely suffered from various limitations including cost, complexity of fabrication, and insufficient sensitivity and/or speed. Here, we present the use of sensitive, low cost, small-sized, commercially available silicon photomultipliers (SiPMs) for the detection of radioactivity inside microfluidic channels fabricated from a range of conventional microfluidic chip substrates. We demonstrate the effects of chip material and thickness on the detection of the positron-emitting isotope, [(18)F]fluoride, and find that, while the SiPMs are light sensors, they are able to detect radiation even through opaque chip materials via direct positron and gamma (γ) ray interaction. Finally, we employed the SiPM platform for analysis of the PET (positron emission tomography) radiotracers 2-[(18)F]fluoro-2-deoxy-d-glucose ([(18)F]FDG) and [(68)Ga]gallium-citrate, and highlight the ability to detect the γ ray emitting SPECT (single photon emission computed tomography) radiotracer, [(99m)Tc]pertechnetate.

Sorption of H2 to open metal sites in a metal-organic framework: a symmetry-adapted perturbation theory analysis.

Metal-organic frameworks (MOFs) show considerable promise as materials for gas storage and separation. Many MOF structures have open metal sites, which allow for coordination of gas molecules to the metal centers. In this work, we use coupled-cluster and symmetry-adapted perturbation theory to probe the interaction between hydrogen gas and unsaturated metal sites in mimic structures based on the MOF HKUST-1. The interactions are of a mixed electrostatic/dispersive nature, with the relative magnitudes of these components dependent on the metal center. The strongest binding was found for magnesium- and zinc-containing MOFs, with an overall interaction energy of -4.5 kcal mol(-1).

Vibrational spectroscopy of the water-nitrate complex in the O-H stretching region.

The vibrational spectroscopy of the nitrate-water isotopologues is studied in the O-H and O-D stretching regions using temperature-dependent infrared multiple photon dissociation spectroscopy combined with calculations of the anharmonic spectra. At a temperature of 15 K a series of discrete peaks is observed in the IRMPD spectra of NO3(-)·H2O, NO3(-)·HDO, and NO3(-)·D2O. This structure is considerably more complex than predicted by harmonic calculations. A signal is only observed in the hydrogen-bonded O-H (O-D) stretching region, characteristic of a double hydrogen-bond donor binding motif. With increasing temperature, the peaks broaden, leading to a quasi-continuous absorption from 3150 to 3600 cm(-1) (2300-2700 cm(-1)) for NO3(-)·H2O (NO3(-)·D2O) and, above 100 K, an additional band in the free O-H (O-D) stretching region, suggesting the population of complexes containing only a single hydrogen bond at higher internal energies. Vibrational configuration interaction calculations confirm that much of the structure observed in the IRMPD spectra derives from progressions in the water rocking mode resulting from strong cubic coupling between the O-H (O-D) stretch and water rock degrees of freedom. The spectra of both NO3(-)·H2O and NO3(-)·D2O display a strong peak that does not derive from the water rock progression but results instead from a Fermi resonance between the O-H (O-D) stretch and H-O-H (D-O-D) bend overtone. Additional insight into the nature of the O-H (O-D) stretch and water rocking coupling in these complexes is provided by an effective Hamiltonian that allows for the cubic coupling between the O-H stretch and water rock degrees of freedom.

Understanding the sensor response of metal-decorated carbon nanotubes.

We have explored the room temperature response of metal nanoparticle decorated single-walled carbon nanotubes (NP-SWNTs) using a combination of electrical transport, optical spectroscopy, and electronic structure calculations. We have found that upon the electrochemical growth of Au NPs on SWNTs, there is a transfer of electron density from the SWNT to the NP species, and that adsorption of CO molecules on the NP surface is accompanied by transfer of electronic density back into the SWNT. Moreover, the electronic structure calculations indicate dramatic variations in the charge density at the NP-SWNT interface, which supports our previous observation that interfacial potential barriers dominate the electrical behavior of NP-SWNT systems.

How the shape of an H-bonded network controls proton-coupled water activation in HONO formation.

Many chemical reactions in atmospheric aerosols and bulk aqueous environments are influenced by the surrounding solvation shell, but the precise molecular interactions underlying such effects have rarely been elucidated. We exploited recent advances in isomer-specific cluster vibrational spectroscopy to explore the fundamental relation between the hydrogen (H)-bonding arrangement of a set of ion-solvating water molecules and the chemical activity of this ensemble. We find that the extent to which the nitrosonium ion (NO+)and water form nitrous acid (HONO) and a hydrated proton cluster in the critical trihydrate depends sensitively on the geometrical arrangement of the water molecules in the network. Theoretical analysis of these data details the role of the water network in promoting charge delocalization.

Molecular dynamics simulations of bromine clathrate hydrates.

A polarizable force field that explicitly includes contributions from exchange repulsion, dispersion, charge penetration, and multipole electrostatics was developed to describe the interaction between bromine and water. This force field was combined with a polarizable force field for water and used in molecular dynamics simulations to calculate the relative energetics of three bromine clathrate hydrates. The simulations predict the tetragonal structure (Allen, K. W.; Jeffrey, G. A. J. Chem. Phys. 1963, 38, 2304) to be the most stable, with the CS-I and CS-II cubic structures being less stable. Although the CS-II species is not the most stable energetically, we argue that it could be formed under conditions of low bromine concentration, in agreement with recent measurements (Goldschleger, I. U.; Kerenskaya, G.; Janda, K. C.; Apkarian, V. A. J. Phys. Chem. A 2008, 112, 787) that provide evidence for three different bromine hydrate crystal types.

Entropy-driven population distributions in a prototypical molecule with two flexible side chains: O-(2-acetamidoethyl)-N-acetyltyramine.

Resonant two-photon ionization (R2PI), resonant ion-dip infrared (RIDIR), and UV-UV hole-burning spectroscopies have been employed to obtain conformation-specific infrared and ultraviolet spectra under supersonic expansion conditions for O-(2-acetamidoethyl)-N-acetyltyramine (OANAT), a doubly substituted aromatic in which amide-containing alkyl and alkoxy side chains are located in para positions on a phenyl ring. For comparison, three single-chain analogs were also studied: (i) N-phenethyl-acetamide (NPEA), (ii) N-(p-methoxyphenethyl-acetamide) (NMPEA), and (iii) N-(2-phenoxyethyl)-acetamide (NPOEA). Six conformations of OANAT have been resolved, with S(0)-S(1) origins ranging from 34,536 to 35,711 cm(-1), denoted A-F, respectively. RIDIR spectra show that conformers A-C each possess an intense, broadened amide NH stretch fundamental shifted below 3400 cm(-1), indicative of the presence of an interchain H bond, while conformers D-F have both amide NH stretch fundamentals in the 3480-3495 cm(-1) region, consistent with independent-chain structures with two free NH groups. NPEA has a single conformer with S(0)-S(1) origin at 37,618 cm(-1). NMPEA has three conformers, two that dominate the R2P1 spectrum, with origin transitions between 35,580 and 35,632 cm(-1). Four conformations, one dominate and three minor, of NPOEA have been resolved with origins between 35,654 and 36,423 cm(-1). To aid the making of conformational assignments, the geometries of low-lying structures of all four molecules have been optimized and the associated harmonic vibrational frequencies calculated using density functional theory (DFT) and RIMP2 methods. The S(0)-S(1) adiabatic excitation energies have been calculated using the RICC2 method and vertical excitation energies using single-point time-dependent DFT. The sensitivity of the S(0)-S(1) energy separation in OANAT and NPOEA primarily arises from different orientations of the chain attached to the phenoxy group. Using the results of the single-chain analogs, tentative assignments have been made for the observed conformers of OANAT. The RIMP2 calculations predict that interchain H-bonded conformers of OANAT are 25-30 kJ/mol more stable than the extended-chain structures. However, the free energies of the interchain H-bonded and extended structures calculated at the preexpansion temperature (450 K) differ by less than 10 kJ/mol, and the number of extended structures far outweighs the number of H-bonded conformers. This entropy-driven effect explains the presence of the independent-chain conformers in the expansion, and cautions future studies that rely solely on relative energies of conformers in considering possible assignments.

Theoretical investigation of the electronically excited states of chlorine hydrate.

As a step toward a first principles characterization of the optical properties of chlorine hydrate, we have calculated the electronic absorption spectrum of a chlorine molecule trapped in dodecahedral (H2O)20 and hexakaidodecahedral (H2O)24 cages. For comparison, spectra were also calculated for an isolated Cl2 molecule as well as for selected Cl2(H2O)n, n < or =8, clusters cut out of the Cl2(H2O)20 cluster, allowing us to follow the evolution of the low-lying excited states with increasing number of surrounding water molecules. Although encapsulation of a chlorine molecule within the water cages has relatively little effect on its low-lying valence transitions, it does result in a large number of solvent-to-solute charge-transfer transitions at energies starting near 48,000 cm(-1).

Hydrogen bonded OH-stretching vibration in the water dimer.

We have calculated the frequencies and intensities of the hydrogen-bonded OH-stretching transitions in the water dimer complex. The potential-energy curve and dipole-moment function are calculated ab initio at the coupled cluster with singles, doubles, and perturbative triples level of theory with correlation-consistent Dunning basis sets. The vibrational frequencies and wavefunctions are found from a numerical solution to a one-dimensional Schrödinger equation. The corresponding transition intensities are found from numerical integration of these vibrational wavefunctions with the ab initio calculated dipole moment function. We investigate the effect of counterpoise correcting both the potential-energy surface and dipole-moment function. We find that the effect of using a numeric potential is significant for higher overtones and that inclusion of a counterpoise correction for basis set superposition error is important.

The lowest 2A' excited state of the water-hydroxyl complex.

Vertical and adiabatic excitation energies of the lowest (2)A(') excited state in the water-hydroxyl complex have been determined using coupled cluster, multireference configuration interaction, multireference perturbation theory, and density-functional methods. A significant redshift of about 0.4 eV in the vertical excitation energy of the complex compared to that of the hydroxyl radical monomer is found with the coupled cluster calculations validating previous results. Electronic excitation leads to a structure with near-equal sharing of the hydroxyl hydrogen by both oxygen atoms and a concomitantly large redshift of the adiabatic excitation energy of approximately 1 eV relative to the vertical excitation energy. The combination of redshifts ensures that the electronic transition in the complex lies well outside the equivalent excitation in the hydroxyl radical monomer. The complex is approximately five times more strongly bound in the excited state than in the ground state.

The OH-stretching and OOH-bending overtone spectrum of HOONO.

We have simulated the HOONO vibrational overtone spectrum with use of a local mode Hamiltonian that includes the OH-stretching, OOH-bending, and NOOH-torsional modes and coupling between all three modes. The local mode parameters and the dipole moment function are calculated with coupled-cluster ab initio theory and an augmented Dunning-type triple-zeta basis set. We investigate the accuracy of the local mode parameters obtained from two different potential-energy fitting routines, as well as the sensitivity of these parameters to the basis set employed. We compare our simulated spectra to previously published action spectra in the first and second OH-stretching overtone regions. In addition we have recorded the spectrum in the OH-stretch and OOH-bend combination region around 7700 cm-1 and we also compare to this. Our simulated spectrum is in qualitative agreement with experiment in the first and second OH-stretching overtone and in the stretch-bend regions.

Effect of OH internal torsion on the OH-stretching spectrum of cis,cis-HOONO.

We show that a simple two-dimensional vibrational model can explain most of the features observed in the first and second OH-stretching overtone region of the room temperature cis,cis-HOONO spectrum. The model uses ab initio calculated parameters and includes the OH-stretching mode coupled to the internal torsion of the OH group.

Infrared identification of matrix isolated H2O.O2.

Theoretical studies of the H2O.O2 complex have been carried out over the past decade, but the complex has not previously been experimentally identified. We have assigned IR vibrations from an H2O.O2 complex in an inert rare gas matrix. This identification is based upon theoretical calculations and concentration dependent behavior of absorption bands observed upon co-deposition of H2O and O2 in argon matrixes at 11.5 +/- 0.5 K. To aid assignment, we have used a harmonically coupled anharmonic oscillator local mode model with an ab initio calculated dipole moment function to calculate the OH-stretching and HOH-bending frequencies and intensities in the complex. The high abundance of H2O and O2 makes the H2O.O2 complex likely to be significant in atmospheric and astrophysical chemistry.