Computing infrared spectra of proteins using the exciton model

The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are a vital complement to 2DIR experimental measurements, allowing the observed signals to be interpreted in terms of detailed structural and dynamical information. In this article, we have studied nine structurally and spectroscopically well-characterized proteins, representing a range of structural types. We have simulated the equilibrium conformational dynamics in an explicit point charge water model. Using the resulting trajectories based on MD simulations, we have computed the one and two dimensional infrared spectra in the Amide I region, using an exciton approach, in which a local mode basis of carbonyl stretches is considered. The role of solvent in shifting the Amide I band (by 30 to 50 cm−1) is clearly evident. Similarly, the conformational dynamics contribute to the broadening of peaks in the spectrum. The inhomogeneous broadening in both the 1D and 2D spectra reflects the significant conformational diversity observed in the simulations. Through the computed 2D cross-peak spectra, we show how different pulse schemes can provide additional information on the coupled vibrations

Capturing the temporal evolution of choice across prefrontal cortex

Activity in prefrontal cortex (PFC) has been richly described using economic models of choice. Yet such descriptions fail to capture the dynamics of decision formation. Describing dynamic neural processes has proven challenging due to the problem of indexing the internal state of PFC and its trial-by-trial variation. Using primate neurophysiology and human magnetoencephalography, we here recover a single-trial index of PFC internal states from multiple simultaneously recorded PFC subregions. This index can explain the origins of neural representations of economic variables in PFC. It describes the relationship between neural dynamics and behaviour in both human and monkey PFC, directly bridging between human neuroimaging data and underlying neuronal activity. Moreover, it reveals a functionally dissociable interaction between orbitofrontal cortex, anterior cingulate cortex and dorsolateral PFC in guiding cost-benefit decisions. We cast our observations in terms of a recurrent neural network model of choice, providing formal links to mechanistic dynamical accounts of decision-making

A circuit mechanism for irrationalities in decision-making and NMDA receptor hypofunction: behaviour, computational modelling, and pharmacology

Decision-making biases can be systematic features of normal behaviour, or deficits underlying neuropsychiatric symptoms. We used behavioural psychophysics, spiking-circuit modelling and pharmacological manipulations to explore decision-making biases in health and disease. Monkeys performed an evidence integration task in which they showed a pro-variance bias (PVB): a preference to choose options with more variable evidence. The PVB was also present in a spiking circuit model, revealing a neural mechanism for this behaviour. Because NMDA receptor (NMDA-R) hypofunction is a leading hypothesis for neuropathology in schizophrenia, we simulated behavioural effects of NMDA-R hypofunction onto either excitatory or inhibitory neurons in the model. These were tested experimentally using the NMDA-R antagonist ketamine, yielding changes in decision-making consistent with lowered cortical excitation/inhibition balance from NMDA-R hypofunction onto excitatory neurons. These results provide a circuit-level mechanism that bridges across explanatory scales, from the synaptic to the behavioural, in neuropsychiatric disorders where decision-making biases are prominent. Significance People can make apparently irrational decisions because of underlying features in their decision circuitry. Deficits in the same neural circuits may also underlie debilitating cognitive symptoms of neuropsychiatric patients. Here, we reveal a neural circuit mechanism explaining an irrationality frequently observed in healthy humans making binary choices – the pro-variance bias. Our circuit model could be perturbed by introducing deficits in either excitatory or inhibitory neuron function. These two perturbations made specific, dissociable predictions for the types of irrational decisionmaking behaviour produced. We used the NMDA-R antagonist ketamine, an experimental model for schizophrenia, to test if these predictions were relevant to neuropsychiatric pathophysiology. The results were consistent with impaired excitatory neuron function, providing important new insights into the pathophysiology of schizophrenia

A circuit mechanism for decision-making biases and NMDA receptor hypofunction

Decision-making biases can be features of normal behaviour, or deficits underlying neuropsychiatric symptoms. We used behavioural psychophysics, spiking-circuit modelling and pharmacological manipulations to explore decision-making biases during evidence integration. Monkeys showed a pro-variance bias (PVB): a preference to choose options with more variable evidence. The PVB was also present in a spiking circuit model, revealing a potential neural mechanism for this behaviour. To model possible effects of NMDA receptor (NMDA-R) antagonism on this behaviour, we simulated the effects of NMDA-R hypofunction onto either excitatory or inhibitory neurons in the model. These were then tested experimentally using the NMDA-R antagonist ketamine, a pharmacological model of schizophrenia. Ketamine yielded an increase in subjects' PVB, consistent with lowered cortical excitation/inhibition balance from NMDA-R hypofunction predominantly onto excitatory neurons. These results provide a circuit-level mechanism that bridges across explanatory scales, from the synaptic to the behavioural, in neuropsychiatric disorders where decision-making biases are prominent

The integrated dynamic land use and transport model MARS

Cities worldwide face problems like congestion or outward migration of businesses. The involved transport and land use interactions require innovative tools. The dynamic Land Use and Transport Interaction model MARS (Metropolitan Activity Relocation Simulator) is part of a structured decision making process. Cities are seen as self organizing systems. MARS uses Causal Loop Diagrams from Systems Dynamics to explain cause and effect relations. MARS has been benchmarked against other published models. A user friendly interface has been developed to support decision makers. Its usefulness was tested through workshops in Asia. This paper describes the basis, capabilities and uses of MARS

Altered distribution of mucosal NK cells during HIV infection.

The human gut mucosa is a major site of human immunodeficiency virus (HIV) infection and infection-associated pathogenesis. Increasing evidence shows that natural killer (NK) cells have an important role in control of HIV infection, but the mechanism(s) by which they mediate antiviral activity in the gut is unclear. Here, we show that two distinct subsets of NK cells exist in the gut, one localized to intraepithelial spaces (intraepithelial lymphocytes, IELs) and the other to the lamina propria (LP). The frequency of both subsets of NK cells was reduced in chronic infection, whereas IEL NK cells remained stable in spontaneous controllers with protective killer immunoglobulin-like receptor/human leukocyte antigen genotypes. Both IEL and LP NK cells were significantly expanded in immunological non-responsive patients, who incompletely recovered CD4+ T cells on highly active antiretroviral therapy (HAART). These data suggest that both IEL and LP NK cells may expand in the gut in an effort to compensate for compromised CD4+ T-cell recovery, but that only IEL NK cells may be involved in providing durable control of HIV in the gut

Rival male chemical cues evoke changes in male pre- and post-copulatory investment in a flour beetle.

This is the final version of the article. Available from Oxford University Press via the DOI in this record.Males can gather information on the risk and intensity of sperm competition from their social environment. Recent studies have implicated chemosensory cues, for instance cuticular hydrocarbons (CHCs) in insects, as a key source of this information. Here, using the broad-horned flour beetle (Gnatocerus cornutus), we investigated the importance of contact-derived rival male CHCs in informing male perception of sperm competition risk and intensity. We experimentally perfumed virgin females with male CHCs via direct intersexual contact and measured male pre- and post-copulatory investment in response to this manipulation. Using chemical analysis, we verified that this treatment engendered changes to perfumed female CHC profiles, but did not make perfumed females "smell" mated. Despite this, males responded to these chemical changes. Males increased courtship effort under low levels of perceived competition (from 1-3 rivals), but significantly decreased courtship effort as perceived competition rose (from 3-5 rivals). Furthermore, our measurement of ejaculate investment showed that males allocated significantly more sperm to perfumed females than to control females. Together, these results suggest that changes in female chemical profile elicited by contact with rival males do not provide males with information on female mating status, but rather inform males of the presence of rivals within the population and thus provide a means for males to indirectly assess the risk of sperm competition.S.M.L.  was funded by a Natural Environment Research Council (NERC) studentship, J.H.S. was funded by NERC, a Royal Society Fellowship, and a Royal Society Equipment Grant (UF120087), and C.M.H. by a Leverhulme Early Career Fellowship (ECF/2010/0067)

The origin of [C II] 157 μm emission in a five-component interstellar medium : the case of NGC 3184 and NGC 628

With its relatively low ionization potential, C+ can be found throughout the interstellar medium (ISM) and provides one of the main cooling channels of the ISM via the [C II] 157 mu m emission. While the strength of the [C II] line correlates with the star formation rate, the contributions of the various gas phases to the [C II] emission on galactic scales are not well established. In this study we establish an empirical multi-component model of the ISM, including dense H II regions, dense photon dissociation regions (PDRs), the warm ionized medium (WIM), low density and G(0). surfaces of molecular clouds (SfMCs), and the cold neutral medium (CNM). We test our model on ten luminous regions within the two nearby galaxies NGC 3184 and NGC 628. on angular scales of 500-600 pc. Both galaxies are part of the Herschel. key program. KINGFISH,. and are complemented by a large set of ancillary ground-and space-based data. The five modeled phases together reproduce the observed [C II] emission quite well, overpredicting the total flux slightly (about 45%) averaged over all regions. We find that dense PDRs are the dominating component, contributing 68% of the [C II] flux on average, followed by the WIM and the SfMCs, with mean contributions of about half of the contribution from dense PDRs, each. CNM and dense H II regions are only minor contributors with less than 5% each. These estimates are averaged over the selected regions, but the relative contributions of the various phases to the [C II] flux vary significantly between these regions

Using the jet stream for sustainable airship and balloon transportation of cargo and hydrogen

© 2019 The Author(s) The maritime shipping sector is a major contributor to CO2 emissions and this figure is expected to rise in coming decades. With the intent of reducing emissions from this sector, this research proposes the utilization of the jet stream to transport a combination of cargo and hydrogen, using airships or balloons at altitudes of 10–20 km. The jet streams flow in the mid-latitudes predominantly in a west–east direction, reaching an average wind speed of 165 km/h. Using this combination of high wind speeds and reliable direction, hydrogen-filled airships or balloons could carry hydrogen with a lower fuel requirement and shorter travel time compared to conventional shipping. Jet streams at different altitudes in the atmosphere were used to identify the most appropriate circular routes for global airship travel. Round-the-world trips would take 16 days in the Northern Hemisphere and 14 in the Southern Hemisphere. Hydrogen transport via the jet stream, due to its lower energy consumption and shorter cargo delivery time, access to cities far from the coast, could be a competitive alternative to maritime shipping and liquefied hydrogen tankers in the development of a sustainable future hydrogen economy

Effects of food type, feeding frequency, and temperature on juvenile survival and growth of Marisa cornuarietis (Mollusca: Gastropoda)

The present experiments are part of a larger study designed to investigate the influence of husbandry parameters on the life history of the ramshorn snail, Marisa cornuarietis, in order to identify suitable husbandry conditions for maintaining multi-generation populations in the laboratory for use in ecotoxicological testing. In this paper we focus on the effects of a combination of food types and feeding frequencies (i.e., the frequency with which the snails were offered food) on juvenile growth and survival at different temperatures. Offspring produced in the laboratory by wild specimens of M. cornuarietis, from Puerto Rico, were used to test the effects of three types of food (lettuce, alginate with fish food, alginate with snail mix) fed at three frequencies (given ad libitum on 4/4, 2/4, or 1/4 d) on juvenile survival and growth. The 4-d feeding regimens were repeated four times, giving a total of 16 d for the experiments. The experiments were conducted at two temperatures (22° and 25°C) under a 12 h light:12 h dark photoperiod. Juvenile growth rates increased with increasing feeding frequency for all food types. The most rapid growth rates occurred in the high-frequency lettuce treatments and the slowest growth rates in the low-frequency lettuce and alginate with snail mix treatments. Juvenile snails grew faster at 25° than at 22°C, and mortality was about twice as high at the lower temperature. Growth rates were used to provide a rough estimate of time to maturity, which was determined to take about twice as long at 22° than at 25°C. The results showed that lettuce is the best food if supplied in abundance, but effects on growth are very dependent on feeding frequency and temperature. We conclude that 25°C is a more appropriate temperature for maintaining populations than 22°C, that lettuce provides a suitable food source, and that food should be supplied continuously for husbandry and toxicity testing of populations of M. cornuarietis