Ab initio molecular dynamics calculations of ion hydration free energies

We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li+, Cl-, and Ag+ ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (Delta G(hyd)) within a few kcal/mol, or better than 4%, of Tissandier 's [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li+/Cl- and Ag+/Cl- AIMD Delta G(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag++Ni+-> Ag+Ni2+ in water. The predictions for this reaction suggest that existing estimates of Delta G(hyd) for unstable radiolysis intermediates such as Ni+ may need to be extensively revised.Comment: 18 pages, 8 figures. This version is essentially the one published in J. Chem. Phy

Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning

Classical intermolecular potentials typically require an extensive parametrization procedure for any new compound considered. To do away with prior parametrization, we propose a combination of physics-based potentials with machine learning (ML), coined IPML, which is transferable across small neutral organic and biologically-relevant molecules. ML models provide on-the-fly predictions for environment-dependent local atomic properties: electrostatic multipole coefficients (significant error reduction compared to previously reported), the population and decay rate of valence atomic densities, and polarizabilities across conformations and chemical compositions of H, C, N, and O atoms. These parameters enable accurate calculations of intermolecular contributions---electrostatics, charge penetration, repulsion, induction/polarization, and many-body dispersion. Unlike other potentials, this model is transferable in its ability to handle new molecules and conformations without explicit prior parametrization: All local atomic properties are predicted from ML, leaving only eight global parameters---optimized once and for all across compounds. We validate IPML on various gas-phase dimers at and away from equilibrium separation, where we obtain mean absolute errors between 0.4 and 0.7 kcal/mol for several chemically and conformationally diverse datasets representative of non-covalent interactions in biologically-relevant molecules. We further focus on hydrogen-bonded complexes---essential but challenging due to their directional nature---where datasets of DNA base pairs and amino acids yield an extremely encouraging 1.4 kcal/mol error. Finally, and as a first look, we consider IPML in denser systems: water clusters, supramolecular host-guest complexes, and the benzene crystal.Comment: 15 pages, 9 figure

Constant Size Molecular Descriptors For Use With Machine Learning

A set of molecular descriptors whose length is independent of molecular size is developed for machine learning models that target thermodynamic and electronic properties of molecules. These features are evaluated by monitoring performance of kernel ridge regression models on well-studied data sets of small organic molecules. The features include connectivity counts, which require only the bonding pattern of the molecule, and encoded distances, which summarize distances between both bonded and non-bonded atoms and so require the full molecular geometry. In addition to having constant size, these features summarize information regarding the local environment of atoms and bonds, such that models can take advantage of similarities resulting from the presence of similar chemical fragments across molecules. Combining these two types of features leads to models whose performance is comparable to or better than the current state of the art. The features introduced here have the advantage of leading to models that may be trained on smaller molecules and then used successfully on larger molecules.Comment: 18 pages, 5 figure

The Privatization Origins of Political Corporations: Evidence from the Pinochet Regime

We show that the sale of state owned firms in dictatorships can help political corporations to emerge and persist over time. Using new data, we characterize Pinochet’s privatizations in Chile and find that some firms were sold underpriced to politically connected buyers. These newly private firms benefited financially from the Pinochet regime. Once democracy arrived, they formed connections with the new government, financed political campaigns, and were more likely to appear in the Panama Papers. These findings reveal how dictatorships can influence young democracies using privatization reforms

Ontologies, Mental Disorders and Prototypes

As it emerged from philosophical analyses and cognitive research, most concepts exhibit typicality effects, and resist to the efforts of defining them in terms of necessary and sufficient conditions. This holds also in the case of many medical concepts. This is a problem for the design of computer science ontologies, since knowledge representation formalisms commonly adopted in this field do not allow for the representation of concepts in terms of typical traits. However, the need of representing concepts in terms of typical traits concerns almost every domain of real world knowledge, including medical domains. In particular, in this article we take into account the domain of mental disorders, starting from the DSM-5 descriptions of some specific mental disorders. On this respect, we favor a hybrid approach to the representation of psychiatric concepts, in which ontology oriented formalisms are combined to a geometric representation of knowledge based on conceptual spaces

Skirting the Issue: What Does Believing in Repression Mean?

We show that, in contrast to Brewin, Li, Ntarantana, Unsowrth, and McNeilis (2019), large proportions of laypersons believe in the scientifically controversial phenomenon of unconscious repressed memories. We provide new survey data showing that when participants are asked specific questions about what they mean when they report that traumatic memories can be repressed, most provide answers strongly consistent with unconscious repression. Our findings continue to show that researchers, legal professionals, and clinicians should be wary of invoking unconscious repression in their work. (PsycInfo Database Record (c) 2020 APA, all rights reserved).</p

Extramedullary disease in multiple myeloma: a systematic literature review

Extramedullary involvement (or extramedullary disease, EMD) represents an aggressive form of multiple myeloma (MM), characterized by the ability of a clone and/or subclone to thrive and grow independent of the bone marrow microenvironment. Several different definitions of EMD have been used in the published literature. We advocate that true EMD is restricted to soft-tissue plasmacytomas that arise due to hematogenous spread and have no contact with bony structures. Typical sites of EMD vary according to the phase of MM. At diagnosis, EMD is typically found in skin and soft tissues; at relapse, typical sites involved include liver, kidneys, lymph nodes, central nervous system (CNS), breast, pleura, and pericardium. The reported incidence of EMD varies considerably, and differences in diagnostic approach between studies are likely to contribute to this variability. In patients with newly diagnosed MM, the reported incidence ranges from 0.5% to 4.8%, while in relapsed/refractory MM the reported incidence is 3.4 to 14%. Available data demonstrate that the prognosis is poor, and considerably worse than for MM without soft-tissue plasmacytomas. Among patients with plasmacytomas, those with EMD have poorer outcomes than those with paraskeletal involvement. CNS involvement is rare, but prognosis is even more dismal than for EMD in other locations, particularly if there is leptomeningeal involvement. Available data on treatment outcomes for EMD are derived almost entirely from retrospective studies. Some agents and combinations have shown a degree of efficacy but, as would be expected, this is less than in MM patients with no extramedullary involvement. The paucity of prospective studies makes it difficult to justify strong recommendations for any treatment approach. Prospective data from patients with clearly defined EMD are important for the optimal evaluation of treatment outcomes

Extramedullary disease in multiple myeloma: a systematic literature review

Extramedullary involvement (or extramedullary disease, EMD) represents an aggressive form of multiple myeloma (MM), characterized by the ability of a clone and/or subclone to thrive and grow independent of the bone marrow microenvironment. Several different definitions of EMD have been used in the published literature. We advocate that true EMD is restricted to soft-tissue plasmacytomas that arise due to hematogenous spread and have no contact with bony structures. Typical sites of EMD vary according to the phase of MM. At diagnosis, EMD is typically found in skin and soft tissues; at relapse, typical sites involved include liver, kidneys, lymph nodes, central nervous system (CNS), breast, pleura, and pericardium. The reported incidence of EMD varies considerably, and differences in diagnostic approach between studies are likely to contribute to this variability. In patients with newly diagnosed MM, the reported incidence ranges from 0.5% to 4.8%, while in relapsed/refractory MM the reported incidence is 3.4 to 14%. Available data demonstrate that the prognosis is poor, and considerably worse than for MM without soft-tissue plasmacytomas. Among patients with plasmacytomas, those with EMD have poorer outcomes than those with paraskeletal involvement. CNS involvement is rare, but prognosis is even more dismal than for EMD in other locations, particularly if there is leptomeningeal involvement. Available data on treatment outcomes for EMD are derived almost entirely from retrospective studies. Some agents and combinations have shown a degree of efficacy but, as would be expected, this is less than in MM patients with no extramedullary involvement. The paucity of prospective studies makes it difficult to justify strong recommendations for any treatment approach. Prospective data from patients with clearly defined EMD are important for the optimal evaluation of treatment outcomes

Who Believes in the Giant Skeleton Myth? An Examination of Individual Difference Correlates

This study examined individual difference correlates of belief in a narrative about the discovery of giant skeletal remains that contravenes mainstream scientific explanations. A total of 364 participants from Central Europe completed a survey that asked them to rate their agreement with a short excerpt describing the giant skeleton myth. Participants also completed measures of the Big Five personality factors, New Age orientation, anti-scientific attitudes, superstitious beliefs, and religiosity. Results showed that women, as compared with men, and respondents with lower educational qualifications were significantly more likely to believe in the giant skeleton myth, although effect sizes were small. Correlational analysis showed that stronger belief in the giant skeleton myth was significantly associated with greater anti-scientific attitudes, stronger New Age orientation, greater religiosity, stronger superstitious beliefs, lower Openness to Experience scores, and higher Neuroticism scores. However, a multiple regression showed that the only significant predictors of belief in myth were Openness, New Age orientation, and anti-scientific attitudes. These results are discussed in relation to the potential negative consequences of belief in myths

Emergence of qualia from brain activity or from an interaction of proto-consciousness with the brain: which one is the weirder? Available evidence and a research agenda

This contribution to the science of consciousness aims at comparing how two different theories can explain the emergence of different qualia experiences, meta-awareness, meta-cognition, the placebo effect, out-of-body experiences, cognitive therapy and meditation-induced brain changes, etc. The first theory postulates that qualia experiences derive from specific neural patterns, the second one, that qualia experiences derive from the interaction of a proto-consciousness with the brain\u2019s neural activity. From this comparison it will be possible to judge which one seems to better explain the different qualia experiences and to offer a more promising research agenda