Publications by authors named "Jonathan Goodman"

Previous research in the evolutionary and psychological sciences has suggested that markers or tags of ethnic or group membership may help to solve cooperation and coordination problems. Cheating remains, however, a problem for these views, insofar as it is possible to fake the tag. While evolutionary psychologists have suggested that humans evolved the propensity to overcome this free rider problem, it is unclear how this module might manifest at the group level.

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C-H borylation is a high-value transformation in the synthesis of lead candidates for the pharmaceutical industry because a wide array of downstream coupling reactions is available. However, predicting its regioselectivity, especially in drug-like molecules that may contain multiple heterocycles, is not a trivial task. Using a data set of borylation reactions from Reaxys, we explored how a language model originally trained on USPTO_500_MT, a broad-scope set of patent data, can be used to predict the C-H borylation reaction product in different modes: product generation and site reactivity classification.

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In the pursuit of improved compound identification and database search tasks, this study explores heteronuclear single quantum coherence (HSQC) spectra simulation and matching methodologies. HSQC spectra serve as unique molecular fingerprints, enabling a valuable balance of data collection time and information richness. We conducted a comprehensive evaluation of the following four HSQC simulation techniques: ACD/Labs (ACD), MestReNova (MNova), Gaussian NMR calculations (DFT), and a graph-based neural network (ML).

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The epigenetic modification 5-methylcytosine plays a vital role in development, cell specific gene expression and disease states. The selective chemical modification of the 5-methylcytosine methyl group is challenging. Currently, no such chemistry exists.

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Owing to its high natural abundance compared to the commonly used transition (precious) metals, as well as its high Lewis acidity and ability to change oxidation state, aluminium has recently been explored as the basis for a range of single-site catalysts. This paper aims to establish the ground rules for the development of a new type of cationic alkene oligomerisation catalyst containing two Al(III) ions, with the potential to act co-operatively in stereoselective assembly. Five new dimers of the type [RAl(2-py')] (R=Me, Bu; py'=substituted pyridyl group) with different substituents on the Al atoms and pyridyl rings have been synthesised.

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The selectivity in a group of oxazaborolidinium ion-catalysed reactions between aldehyde and diazo compounds cannot be explained using transition state theory. VRAI-selectivity, developed to predict the outcome of dynamically controlled reactions, can account for both the chemo- and the stereo-selectivity in these reactions, which are controlled by reaction dynamics. Subtle modifications to the substrate or catalyst substituents alter the potential energy surface, leading to changes in predominant reaction pathways and altering the barriers to the major product when reaction dynamics are considered.

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Machine Learning (ML) is increasingly applied to fill data gaps in assessments to quantify impacts associated with chemical emissions and chemicals in products. However, the systematic application of ML-based approaches to fill chemical data gaps is still limited, and their potential for addressing a wide range of chemicals is unknown. We prioritized chemical-related parameters for chemical toxicity characterization to inform ML model development based on two criteria: (1) each parameter's relevance to robustly characterize chemical toxicity described by the uncertainty in characterization results attributable to each parameter and (2) the potential for ML-based approaches to predict parameter values for a wide range of chemicals described by the availability of chemicals with measured parameter data.

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Introduction: tDCS is a non-invasive neuromodulation technique that has been widely studied both as a therapy for neuropsychiatric diseases and for cognitive enhancement. However, recent meta-analyses have reported significant inconsistencies amongst tDCS studies. Enhancing empirical understanding of current flow in the brain may help elucidate some of these inconsistencies.

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Mimicry is an essential strategy for exploiting competitors in competitive co-evolutionary relationships. Protection against mimicry may, furthermore, be a driving force in human linguistic diversity: the potential harm caused by failing to detect mimicked group-identity signals may select for high sensitivity to mimicry of honest group members. Here we describe the results of five agent-based models that simulate multi-generational interactions between two groups of individuals: original members of a group with an honest identity signal, and members of an outsider group who mimic that signal, aiming to pass as members of the in-group.

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CONFPASS (ormer rioritizations and nalyi for DFT re-optimizations) has been developed to extract dihedral angle descriptors from conformational searching outputs, perform clustering, and return a priority list for density functional theory (DFT) re-optimizations. Evaluations were conducted with DFT data of the conformers for 150 structurally diverse molecules, most of which are flexible. CONFPASS gives a confidence estimate that the global minimum structure has been found, and based on our dataset, we can have 90% confidence after optimizing half of the FF structures.

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A rise in antisocial behaviour indicates covid-19 lockdowns disrupted our cultural evolution, says .

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The epigenetic modification 5-methylcytosine plays a vital role in development, cell specific gene expression and disease states. The selective chemical modification of the 5-methylcytosine methyl group is challenging. Currently, no such chemistry exists.

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Vibrational circular dichroism (VCD) spectroscopy can generate the data required for the assignment of absolute configuration, but the spectra are hard to interpret. We have recorded VCD data for thirty pairs of small organic compounds and we use this database to validate a method for the automated analysis of VCD spectra and the assignment of absolute configuration: the Cai•factor (Configuration: absolute information). The analysis of the data demonstrates that the procedure is a reliable and time-efficient method for determination of absolute configuration, which gives both the assignment and a measure of confidence in the outcome, even when the spectra are imperfect.

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Computational reaction prediction has become a ubiquitous task in chemistry due to the potential value accurate predictions can bring to chemists. Boronic acids are widely used in industry; however, understanding how to avoid the protodeboronation side reaction remains a challenge. We have developed an algorithm for prediction of the rate of protodeboronation of boronic acids.

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Background: The TYRX (Medtronic) absorbable antibacterial envelope has been shown to stabilize implantable cardiac devices and reduce infection. A third-generation envelope was developed to reduce surface roughness with a redesigned multifilament mesh and enhanced form factor but identical polymer coating and antibiotic concentrations as the currently available second-generation envelope.

Objective: The purpose of this study was to compare drug elution, bacterial challenge efficacy, stabilization, and absorption of second- vs third-generation envelopes.

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The use of machine learning techniques in computational chemistry has gained significant momentum since large molecular databases are now readily available. Predictions of molecular properties using machine learning have advantages over the traditional quantum mechanics calculations because they can be cheaper computationally without losing the accuracy. We present a new extrapolatable and explainable molecular representation based on bonds, angles and dihedrals that can be used to train machine learning models.

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Whenever a new molecule is made, a chemist will justify the proposed structure by analysing the NMR spectra. The widely-used DP4 algorithm will choose the best match from a series of possibilities, but draws no conclusions from a single candidate structure. Here we present the DP5 probability, a step-change in the quantification of molecular uncertainty: given one structure and one C NMR spectra, DP5 gives the probability of the structure being correct.

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-Triflylphosphoramides (NTPA), have become increasingly popular catalysts in the development of enantioselective transformations as they are stronger Brønsted acids than the corresponding phosphoric acids (PA). Their highly acidic, asymmetric active site can activate difficult, unreactive substrates. In this review, we present an account of asymmetric transformations using this type of catalyst that have been reported in the past ten years and we classify these reactions using the enantio-determining step as the key criterion.

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We propose a general barrier theory as an evolutionary framework for understanding coevolutionary effects of conflicts of interest in natural and human systems. It is generalized from the barrier theory of cancer, which describes how cancer develops through the evasion of mechanisms, that block unregulated cellular reproduction and survival. Barriers are naturally evolved or artificially implemented mechanisms for blocking exploitation; restraints are mechanisms that impede but do not block exploitation.

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Contagion culture.

New Sci

September 2021

The new social norm of isolating when ill with covid-19 should apply to other infectious diseases such as flu, says .

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Deep learning neural networks, constructed for the prediction of chemical binding at 79 pharmacologically important human biological targets, show extremely high performance on test data (accuracy 92.2 ± 4.2%, MCC 0.

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