Overlapping memory replay during sleep builds cognitive schemata

Sleep enhances integration across multiple stimuli, abstraction of general rules, insight into hidden solutions and false memory formation. Newly learned information is better assimilated if compatible with an existing cognitive framework or schema. This article proposes a mechanism by which the reactivation of newly learned memories during sleep could actively underpin both schema formation and the addition of new knowledge to existing schemata. Under this model, the overlapping replay of related memories selectively strengthens shared elements. Repeated reactivation of memories in different combinations progressively builds schematic representations of the relationships between stimuli. We argue that this selective strengthening forms the basis of cognitive abstraction, and explain how it facilitates insight and false memory formation

Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening

Computational techniques such as structure-based virtual screening require carefully prepared 3D models of potential small-molecule ligands. Though powerful, existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. Freely available alternatives, though often effective, do not fully account for all possible ionization, tautomeric, and ring-conformational variants. We here present Gypsum-DL, a free, robust open-source program that addresses these challenges. As input, Gypsum-DL accepts virtual compound libraries in SMILES or flat SDF formats. For each molecule in the virtual library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, Gypsum-DL produces an SDF file containing each molecular form, with 3D coordinates assigned. To demonstrate its utility, we processed 1558 molecules taken from the NCI Diversity Set VI and 56,608 molecules taken from a Distributed Drug Discovery (D3) combinatorial virtual library. We also used 4463 high-quality protein-ligand complexes from the PDBBind database to show that Gypsum-DL processing can improve virtual-screening pose prediction. Gypsum-DL is available free of charge under the terms of the Apache License, Version 2.0

Schema-conformant memories are preferentially consolidated during REM sleep

Memory consolidation is most commonly described by the standard model, which proposes an initial binding role for the hippocampus which diminishes over time as intracortical connections are strengthened. Recent evidence suggests that slow wave sleep (SWS) plays an essential role in this process. Existing animal and human studies have suggested that memories which fit tightly into an existing knowledge framework or schema might use an alternative consolidation route in which the medial prefrontal cortex takes on the binding role. In this study we sought to investigate the role of sleep in this process using a novel melodic memory task. Participants were asked to remember 32 melodies, half of which conformed to a tonal schema present in all enculturated listeners, and half of which did not fit with this schema. After a 24-h consolidation interval, participants were asked to remember a further 32 melodies, before being given a recognition test in which melodies from both sessions were presented alongside some previously unheard foils. Participants remembered schema-conformant melodies better than non-conformant ones. This was much more strongly the case for consolidated melodies, suggesting that consolidation over a 24-h period preferentially consolidated schema-conformant items. Overnight sleep was monitored between the sessions, and the extent of the consolidation benefit for schema-conformant items was associated with both the amount of REM sleep obtained and EEG theta power in frontal and central regions during REM sleep. Overall our data suggest that REM sleep plays a crucial role in the rapid consolidation of schema-conformant items. This finding is consistent with previous results from animal studies and the SLIMM model of Van Kesteren, Ruiter, Fernández, and Henson (2012), and suggest that REM sleep, rather than SWS, may be involved in an alternative pathway of consolidation for schema-conformant memories. Copyright © 2015. Published by Elsevier Inc

Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design.

The relaxed complex scheme, a virtual-screening methodology that accounts for protein receptor flexibility, was used to identify a low-micromolar, non-bisphosphonate inhibitor of farnesyl diphosphate synthase. Serendipitously, we also found that several predicted farnesyl diphosphate synthase inhibitors were low-micromolar inhibitors of undecaprenyl diphosphate synthase. These results are of interest because farnesyl diphosphate synthase inhibitors are being pursued as both anti-infective and anticancer agents, and undecaprenyl diphosphate synthase inhibitors are antibacterial drug leads

AutoClickChem: Click Chemistry in Silico

Academic researchers and many in industry often lack the financial resources available to scientists working in “big pharma.” High costs include those associated with high-throughput screening and chemical synthesis. In order to address these challenges, many researchers have in part turned to alternate methodologies. Virtual screening, for example, often substitutes for high-throughput screening, and click chemistry ensures that chemical synthesis is fast, cheap, and comparatively easy. Though both in silico screening and click chemistry seek to make drug discovery more feasible, it is not yet routine to couple these two methodologies. We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. AutoClickChem can be used to produce large combinatorial libraries of compound models for use in virtual screens. As the compounds of these libraries are constructed according to the reactions of click chemistry, they can be easily synthesized for subsequent testing in biochemical assays. Additionally, in silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization. AutoClickChem is based on the pymolecule toolbox, a framework that may facilitate the development of future python-based programs that require the manipulation of molecular models. Both the pymolecule toolbox and AutoClickChem are released under the GNU General Public License version 3 and are available for download from http://autoclickchem.ucsd.edu

Towards the development of novel Trypanosoma brucei RNA editing ligase 1 inhibitors

Abstract Background Trypanosoma brucei (T. brucei) is an infectious agent for which drug development has been largely neglected. We here use a recently developed computer program called AutoGrow to add interacting molecular fragments to S5, a known inhibitor of the validated T. brucei drug target RNA editing ligase 1, in order to improve its predicted binding affinity. Results The proposed binding modes of the resulting compounds mimic that of ATP, the native substrate, and provide insights into novel protein-ligand interactions that may be exploited in future drug-discovery projects. Conclusions We are hopeful that these new predicted inhibitors will aid medicinal chemists in developing novel therapeutics to fight human African trypanosomiasis

Opportunities and challenges of the digital lifespan:views of service providers and citizens in the UK

<p>Information about UK citizens’ use of digital technologies is often expressed in statistics – x% lack Internet access; y% get online to engage in online banking, update social media sites, or participate in online auctions. There are many social implications to digital technology use, however – individuals may communicate online as a major way to stay in touch with friends and family, and as Internet access rises and government and public sector budgets shrink, online services become an increasingly attractive way for government and public sector service providers to communicate with citizens. This paper presents selected results of an exploratory study designed to investigate the digital personhood of UK citizens through interviews with participants at three life transitions: leaving secondary school, becoming a parent, and retiring from work. Digital personhood in this paper implies identity information online, and some interaction with others around that information. We then report on our presentation of a selection of these results to thirteen stakeholders who represented UK government departments, public sector organisations, and industry. We found that citizen and stakeholder concerns were quite different, especially at the new parent life transition, and that stakeholders tended to <i>underestimate</i> the willingness and ability of citizens to become involved online with the government and public sector, and <i>overestimate</i> citizens’ vulnerability online. Future research should investigate practical strategies for increasing communication between stakeholders and citizens, and also how to encourage stakeholders to work together to benefit their common clientele – the citizens.</p

Trust, Identity, Privacy, and Security Considerations For Designing a Peer Data Sharing Platform Between People Living With HIV

Resulting from treatment advances, the Human Immunodeficiency Virus(HIV) is now a long-term condition, and digital solutions are being developed to support people living with HIV in self-management. Sharing their health data with their peers may support self-management, but the trust, identity, privacy and security (TIPS) considerations of people living with HIV remain underexplored. Working with a peer researcher who is expert in the lived experience of HIV, we interviewed 26 people living with HIV in the United Kingdom (UK) to investigate how to design a peer data sharing platform. We also conducted rating activities with participants to capture their atitudes towards sharing personal data. Our mixed methods study showed that participants were highly sophisticated in their understanding of trust and in their requirements for robust privacy and security. Tey indicated willingness to share digital identity atributes, including gender, age, medical history, health and well-being data, but not details that could reveal their personal identity. Participants called for TIPS measures to foster and to sustain responsible data sharing within their community. Tese findings can inform the development of trustworthy and secure digital platforms that enable people living with HIV to share data with their peers and provide insights for researchers who wish to facilitate data sharing in other communities with stigmatised health conditions

Photocurrents from photosystem II in a metal oxide hybrid system: electron transfer pathways

We have investigated the nature of the photocurrent generated by Photosystem II (PSII), the water oxidizing enzyme, isolated from Thermosynechococcus elongatus, when immobilized on nanostructured titanium dioxide on an indium tin oxide electrode (TiO2/ITO). We investigated the properties of the photocurrent from PSII when immobilized as a monolayer versus multilayers, in the presence and absence of an inhibitor that binds to the site of the exchangeable quinone (QB) and in the presence and absence of exogenous mobile electron carriers (mediators). The findings indicate that electron transfer occurs from the first quinone (QA) directly to the electrode surface but that the electron transfer through the nanostructured metal oxide is the rate-limiting step. Redox mediators enhance the photocurrent by taking electrons from the nanostructured semiconductor surface to the ITO electrode surface not from PSII. This is demonstrated by photocurrent enhancement using a mediator incapable of accepting electrons from PSII. This model for electron transfer also explains anomalies reported in the literature using similar and related systems. The slow rate of the electron transfer step in the TiO2 is due to the energy level of electron injection into the semiconducting material being below the conduction band. This limits the usefulness of the present hybrid electrode. Strategies to overcome this kinetic limitation are discussed

In situ observation of picosecond polaron self-localisation in α-Fe2O3 photoelectrochemical cells

Hematite (α-Fe2O3) is the most studied artificial oxygen-evolving photo-anode and yet its efficiency limitations and their origin remain unknown. A sub-picosecond reorganisation of the hematite structure has been proposed as the mechanism which dictates carrier lifetimes, energetics and the ultimate conversion yields. However, the importance of this reorganisation for actual device performance is unclear. Here we report an in situ observation of charge carrier self-localisation in a hematite device, and demonstrate that this process affects recombination losses in photoelectrochemical cells. We apply an ultrafast, device-based optical-control method to resolve the subpicosecond formation of small polarons and estimate their reorganisation energy to be ~0.5 eV. Coherent oscillations in the photocurrent signals indicate that polaron formation may be coupled to specific phonon modes (<100 cm-1). Our results bring together spectroscopic and device characterisation approaches to reveal new photophysics of broadly-studied hematite devices