Encoder-decoder convolutional neural network for simple CT segmentation of COVID-19 infected lungs.

This work presents the application of an Encoder-Decoder convolutional neural network (ED-CNN) model to automatically segment COVID-19 computerised tomography (CT) data. By doing so we are producing an alternative model to current literature, which is easy to follow and reproduce, making it more accessible for real-world applications as little training would be required to use this. Our simple approach achieves results comparable to those of previously published studies, which use more complex deep-learning networks.

Application of the C3-Methyltransferase StspM1 for the Synthesis of the Natural Pyrroloindole Motif.

Even though pyrroloindoles are widely present in natural products with different kinds of biological activities, their selective synthesis remains challenging with existing tools in organic chemistry, and there is furthermore a demand for stereoselective and mild methods to access this structural motif. Nature uses C3-methyltransferases to form the pyrroloindole framework, starting from the amino acid tryptophan. In the present study, the SAM-dependent methyltransferase StspM1 from sp.

Evaluation of the dataset quality in gamma passing rate predictions using machine learning methods.

Objective: Gamma passing rate (GPR) predictions using machine learning methods have been explored for treatment verification of radiotherapy plans. However, these methods presented datasets with unbalanced number of plans having different treatment conditions (heterogeneous datasets), such as anatomical sites or dose per fractions, leading to lower model interpretability and prediction performance.

Methods: We investigated the impact of the dataset composition on GPR binary classification (pass/fail) using random forest (RF), XG-boost, and neural network (NN) models.

Machine learning-based predictions of gamma passing rates for virtual specific-plan verification based on modulation maps, monitor unit profiles, and composite dose images.

Machine learning (ML) methods have been implemented in radiotherapy to aid virtual specific-plan verification protocols, predicting gamma passing rates (GPR) based on calculated modulation complexity metrics because of their direct relation to dose deliverability. Nevertheless, these metrics might not comprehensively represent the modulation complexity, and automatically extracted features from alternative predictors associated with modulation complexity are needed. For this reason, three convolutional neural networks (CNN) based models were trained to predict GPR values (regression and classification), using respectively three predictors: (1) the modulation maps (MM) from the multi-leaf collimator, (2) the relative monitor units per control point profile (MUcp), and (3) the composite dose image (CDI) used for portal dosimetry, from 1024 anonymized prostate plans.

, a Chelator for Ga Positron Emission Tomography: Hydroxide Coordination Increases Biological Stability of [Ga][Ga(BnDT3A)(OH)].

The chelator was used to produce a novel Ga complex for positron emission tomography (PET). Unusually, this system is stabilized by a coordinated hydroxide in aqueous solutions above pH 5, which confers sufficient stability for it to be used for PET. complexes Ga in a hexadentate manner, forming a complex with log ([Ga()]) = 18.

Smolyak Algorithm Adapted to a System-Bath Separation: Application to an Encapsulated Molecule with Large-Amplitude Motions.

A Smolyak algorithm adapted to system-bath separation is proposed for rigorous quantum simulations. This technique combines a sparse grid method with the system-bath concept in a specific configuration without limitations on the form of the Hamiltonian, thus achieving a highly efficient convergence of the excitation transitions for the "system" part. Our approach provides a general way to overcome the perennial convergence problem for the standard Smolyak algorithm and enables the simulation of floppy molecules with more than a hundred degrees of freedom.

Ocean Acidification Amplifies the Olfactory Response to 2-Phenylethylamine: Altered Cue Reception as a Mechanistic Pathway?

With carbon dioxide (CO) levels rising dramatically, climate change threatens marine environments. Due to increasing CO concentrations in the ocean, pH levels are expected to drop by 0.4 units by the end of the century.

Promiscuous Esterases Counterintuitively Are Less Flexible than Specific Ones.

Understanding mechanisms of promiscuity is increasingly important from a fundamental and application point of view. As to enzyme structural dynamics, more promiscuous enzymes generally have been recognized to also be more flexible. However, examples for the opposite received much less attention.

Effect of treatment planning system parameters on beam modulation complexity for treatment plans with single-layer multi-leaf collimator and dual-layer stacked multi-leaf collimator.

Objective: High levels of beam modulation complexity (MC) and monitor units (MU) can compromise the plan deliverability of intensity-modulated radiotherapy treatments. Our study evaluates the effect of three treatment planning system (TPS) parameters on MC and MU using different multi-leaf collimator (MLC) architectures.

Methods: 192 volumetric modulated arc therapy plans were calculated using one virtual prostate phantom considering three main settings: (1) three TPS-parameters (Convergence; Aperture Shape Controller, ASC; and Dose Calculation Resolution, DCR) selected from Eclipse v15.

Finite element assessment of a disc-replacement implant for treating scoliotic deformity.

Background: Bracing and spinal fusion surgery have long been the primary methods for idiopathic scoliosis correction; however, there exist multiple limitations with both techniques. Growth modulation techniques have recently been attempted, but are typically performed across multiple vertebral elements. The aim of this study was to quantify the corrective abilities of a dual-angled, wedge shaped, rigid disc implant designed to correct spinal deformity.

Discovery of new acetylcholinesterase inhibitors for Alzheimer's disease: virtual screening and characterisation.

For more than two decades, the development of potent acetylcholinesterase (AChE) inhibitors has been an ongoing task to treat dementia associated with Alzheimer's disease and improve the pharmacokinetic properties of existing drugs. In the present study, we used three docking-based virtual screening approaches to screen both ZINC15 and MolPort databases for synthetic analogs of physostigmine and donepezil, two highly potent AChE inhibitors. We characterised the inhibitory concentration of 11 compounds, ranging from 14 to 985 μM.

The first microsolvation step for furans: New experiments and benchmarking strategies.

The site-specific first microsolvation step of furan and some of its derivatives with methanol is explored to benchmark the ability of quantum-chemical methods to describe the structure, energetics, and vibrational spectrum at low temperature. Infrared and microwave spectra in supersonic jet expansions are used to quantify the docking preference and some relevant quantum states of the model complexes. Microwave spectroscopy strictly rules out in-plane docking of methanol as opposed to the top coordination of the aromatic ring.

Biomechanical analysis of sagittal correction parameters for surgical instrumentation with pedicle subtraction osteotomy in adult spinal deformity.

Background: High complication rate has been documented in spinal instrumentation with pedicle subtraction osteotomy. The objective was to analyze the biomechanics of spinal instrumentation with pedicle subtraction osteotomy as functions of three instrumentation parameters.

Methods: Patient-specific biomechanical computer models of 3 adult patients who were instrumented with pedicle subtraction osteotomy were used to simulate the actual instrumentations and alternative instrumentations derived by varying instrumentation parameters: pedicle subtraction osteotomy wedge angle and rod contouring angle, location of the osteotomy, and number of rods (2 vs.

Toward the design of efficient transglycosidases: the case of the GH1 of Thermus thermophilus.

Using the information available in the sequences of well-characterized transglycosidases found in plants, mutations were introduced in the glycoside hydrolase of the bacterium Thermus thermophilus, with the aim of turning it into an efficient transglycosidase. All mutants happen to have fair catalytic efficiencies, being at worst 25 times less efficient than the wild type. Noteworthy, W120F, one of our high transglycosylation yield (≈ 50%) mutants, is only two times less efficient than the wild type.

Intramolecular stretching vibrational states and frequency shifts of (H) confined inside the large cage of clathrate hydrate from an eight-dimensional quantum treatment using small basis sets.

We report the results of calculations pertaining to the HH intramolecular stretching fundamentals of (p-H) encapsulated in the large cage of structure II clathrate hydrate. The eight-dimensional (8D) quantum treatment assumes rotationless (j = 0) H moieties and a rigid clathrate structure but is otherwise fully coupled. The (H)-clathrate interaction is constructed in a pairwise-additive fashion, by combining the ab initio H-HO pair potential for flexible H and rigid HO [D.

Short- and Medium-Term Exposure to Ocean Acidification Reduces Olfactory Sensitivity in Gilthead Seabream.

The effects of ocean acidification on fish are only partially understood. Studies on olfaction are mostly limited to behavioral alterations of coral reef fish; studies on temperate species and/or with economic importance are scarce. The current study evaluated the effects of short- and medium-term exposure to ocean acidification on the olfactory system of gilthead seabream (), and attempted to explain observed differences in sensitivity by changes in the protonation state of amino acid odorants.

H, HD, and D in the small cage of structure II clathrate hydrate: Vibrational frequency shifts from fully coupled quantum six-dimensional calculations of the vibration-translation-rotation eigenstates.

We report the first fully coupled quantum six-dimensional (6D) bound-state calculations of the vibration-translation-rotation eigenstates of a flexible H, HD, and D molecule confined inside the small cage of the structure II clathrate hydrate embedded in larger hydrate domains with up to 76 HO molecules, treated as rigid. Our calculations use a pairwise-additive 6D intermolecular potential energy surface for H in the hydrate domain, based on an ab initio 6D H-HO pair potential for flexible H and rigid HO. They extend to the first excited (v = 1) vibrational state of H, along with two isotopologues, providing a direct computation of vibrational frequency shifts.

The inhibitory subunit of cardiac troponin (cTnI) is modified by arginine methylation in the human heart.

Background: The inhibitory subunit of cardiac troponin (cTnI) is a gold standard cardiac biomarker and also an essential protein in cardiomyocyte excitation-contraction coupling. The interactions of cTnI with other proteins are fine-tuned by post-translational modification of cTnI. Mutations in cTnI can lead to hypertrophic cardiomyopathy.

Does cage quantum delocalisation influence the translation-rotational bound states of molecular hydrogen in clathrate hydrate?

In this study, we examine the effect of a flexible description of the clathrate hydrate framework on the translation-rotation (TR) eigenstates of guest molecules such as molecular hydrogen. Traditionally, the water cage structure is assumed to be rigid, thus ignoring the quantum nature of hydrogen nuclei in the water framework. However, it has been shown that protons in a water molecule possess a marked delocalised character in many situations, ranging from water clusters to proton transfer in the bulk.

Assessing the impacts of imperfect detection on estimates of diversity and community structure through multispecies occupancy modeling.

Detecting all species in a given survey is challenging, regardless of sampling effort. This issue, more commonly known as imperfect detection, can have negative impacts on data quality and interpretation, most notably leading to false absences for rare or difficult-to-detect species. It is important that this issue be addressed, as estimates of species richness are critical to many areas of ecological research and management.

The effect of the condensed-phase environment on the vibrational frequency shift of a hydrogen molecule inside clathrate hydrates.

We report a theoretical study of the frequency shift (redshift) of the stretching fundamental transition of an H molecule confined inside the small dodecahedral cage of the structure II clathrate hydrate and its dependence on the condensed-phase environment. In order to determine how much the hydrate water molecules beyond the confining small cage contribute to the vibrational frequency shift, quantum five-dimensional (5D) calculations of the coupled translation-rotation eigenstates are performed for H in the v=0 and v=1 vibrational states inside spherical clathrate hydrate domains of increasing radius and a growing number of water molecules, ranging from 20 for the isolated small cage to over 1900. In these calculations, both H and the water domains are treated as rigid.

Influence of Solvent Representation on Nuclear Shielding Calculations of Protonation States of Small Biological Molecules.

In this study, we assess the influence of solvation on the accuracy and reliability of isotropic nuclear magnetic shielding calculations for amino acids in comparison to experimental data. We focus particularly on the performance of solvation methods for different protonation states, as biological molecules occur almost exclusively in aqueous solution and are subject to protonation with pH. We identify significant shortcomings of current implicit solvent models and present a hybrid solvation approach that improves agreement with experimental data by taking into account the presence of direct interactions between amino acid protonation state and water molecules.