Indirect Dissociative Recombination of LiH+^+ Molecules Fueled by Complex Resonance Manifolds

The LiH$^{+}$ molecule is prototypical of the indirect dissociative recombination (DR) process, in which a colliding electron destroys the molecule through Rydberg capture pathways. This Letter develops the first quantitative test of the Siegert state multichannel quantum defect theory description of indirect DR for a diatomic molecular ion. The R-matrix approach is adopted to calculate ab-initio quantum defects, functions of the internuclear distance that characterize both Rydberg states and the zero-energy collisions of electrons with LiH$^{+}$ ions. The calculated DR rate coefficient agrees accurately with recent experimental data (S. Krohn et al, Phys. Rev. Lett. 86, 4005). We identify the doorways to fast indirect DR as complex resonance manifolds, which couple closed channels having both high and low principal quantum numbers. This sheds new light on the competition between direct and indirect DR pathways, and suggests the reason why previous theory underestimated the DR rate by an order of magnitude.Comment: Submitted to PR

Posttranslational modification of a neurofilament protein during axoplasmic transport: implications for regional specialization of CNS axons

The possibility that proteins are modified during axoplasmic transport in central nervous system axons was examined by analyzing neurofilament proteins (200,000, 140,000, and 70,000 mol wt) along the mouse primary optic pathway (optic nerve and optic tract). The major neurofilament proteins (NFPs) exhibited considerable microheterogeneity. At least three forms of the “ 140,000” neurofilament protein differing in molecular weight by SDS PAGE (140,000-145,000 mol wt) were identified. The “140,000” proteins, and their counterparts in purified neurofilament preparations, displayed similar isoelectric points and the same peptide maps. The “140,000” NFPs exhibited regional heterogeneity when consecutive segments of the optic pathway were separately examined on polyacrylamide gels. Two major species (145,000 and 140,000 mol wt) were present along the entire length of the optic pathway. The third protein (143,000 mol wt) was absent proximally but became increasingly prominent in distal segments. After intravitreal injection of [(3)H]proline, newly synthesized radiolabeled proteins in the “140,000” mol wt region entered proximal mouse retinal ganglion cell (RGC) axons as two major species corresponding to the 145,000 and 14,000 mol wt NFPs observed on stained gels. When transported NFPs reached more distal axonal regions (30 d postinjection or longer), a 143,000 mol wt protein appeared that was similar in isoelectric point and peptide map to the 145,000 and 140,000 mol wt species. The results suggest that (a) the composition of CNS neurofilaments, particularly the “140,000” component, is more complex than previously recognized, that (b) retinal ganglion cell axons display regional differentiation with respect to these cytoskeletal proteins, and that (c) structural heterogeneity of “140,000” NFPs arises, at least in part, from posttranslational modification during axoplasmic transport. When excised but intact optic pathways were incubated in vitro at pH 7.4, a 143,000 NFP was rapidly formed by a calcium-dependent enzymatic process active at endogenous calcium levels. Changes in major proteins other than those in the 145,000-140,000 mol wt region were minimal. In optic pathways from mice injected intravitreally with L-[(3)H]proline, tritiated 143,000 mol wt NFP formed rapidly in vitro if radioactively labeled NFPs were present in distal RGC axonal regions (31 d postinjection). By contrast, no 143,000 mol wt NFP was generated if radioactively labeled NFPs were present proximally in RGC axons (6 d postinjection). The enzymatic process that generates 143,000 mol wt NFP in vitro, therefore, appears to have a nonuniform distribution along the RGC axons. The foregoing results and other observations, including the accompanying report (J. Cell Biol., 1982, 94:159-164), imply that CNS axons may be regionally specialized with respect to structure and function

Hydrodynamic simulations of shell convection in stellar cores

Shell convection driven by nuclear burning in a stellar core is a common hydrodynamic event in the evolution of many types of stars. We encounter and simulate this convection (i) in the helium core of a low-mass red giant during core helium flash leading to a dredge-down of protons across an entropy barrier, (ii) in a carbon-oxygen core of an intermediate-mass star during core carbon flash, and (iii) in the oxygen and carbon burning shell above the silicon-sulfur rich core of a massive star prior to supernova explosion. Our results, which were obtained with the hydrodynamics code HERAKLES, suggest that both entropy gradients and entropy barriers are less important for stellar structure than commonly assumed. Our simulations further reveal a new dynamic mixing process operating below the base of shell convection zones.Comment: 8 pages, 3 figures .. submitted to a proceedings of conference about "Red Giants as Probes of the Structure and Evolution of the Milky Way" which has taken place between 15-17 November 2010 in Rom

A simple and effective method for high quality co-extraction of genomic DNA and total RNA from low biomass Ectocarpus siliculosus, the model brown alga.

The brown seaweed Ectocarpus siliculosus is an emerging model species distributed worldwide in temperate coastal ecosystems. Over 1500 strains of E. siliculosus are available in culture from a broad range of geographic locations and ecological niches. To elucidate the molecular mechanisms underlying its capacity to cope with different environmental and biotic stressors, genomic and transcriptomic studies are necessary; this requires the co-isolation of genomic DNA and total RNA. In brown algae, extraction of nucleic acids is hindered by high concentrations of secondary metabolites that co-precipitate with nucleic acids. Here, we propose a reliable, rapid and cost-effective procedure for the co-isolation of high-quality nucleic acids using small quantities of biomass (25-, 50- and 100 mg) from strains of E. siliculosus (RHO12; LIA4A; EC524 and REP10-11) isolated from sites with different environmental conditions. The procedure employs a high pH extraction buffer (pH 9.5) which contains 100 mM Tris-HCl and 150 mM NaCl, with the addition of 5 mM DTT and 1% sarkosyl to ensure maximum solubility of nucleic acids, effective inhibition of nuclease activity and removal of interfering contaminants (e.g. polysaccharides, polyphenols). The use of sodium acetate together with isopropanol shortened precipitation time and enhanced the yields of DNA/RNA. A phenol:chlorophorm:isoamyl alcohol step was subsequently used to purify the nucleic acids. The present protocol produces high yields of nucleic acids from only 25 mg of fresh algal biomass (0.195 and 0.284 µg mg(-1) fresh weigh of RNA and DNA, respectively) and the high quality of the extracted nucleic acids was confirmed through spectrophotometric and electrophoretic analyses. The isolated RNA can be used directly in downstream applications such as RT-PCR and the genomic DNA was suitable for PCR, producing reliable restriction enzyme digestion patterns. Co-isolation of DNA/RNA from different strains indicates that this method is likely to have wider applications for intra- and inter-specific studies on other brown algae

Robust and Efficient Online Auditory Psychophysics

Most human auditory psychophysics research has historically been conducted in carefully controlled environments with calibrated audio equipment, and over potentially hours of repetitive testing with expert listeners. Here, we operationally define such conditions as having high 'auditory hygiene'. From this perspective, conducting auditory psychophysical paradigms online presents a serious challenge, in that results may hinge on absolute sound presentation level, reliably estimated perceptual thresholds, low and controlled background noise levels, and sustained motivation and attention. We introduce a set of procedures that address these challenges and facilitate auditory hygiene for online auditory psychophysics. First, we establish a simple means of setting sound presentation levels. Across a set of four level-setting conditions conducted in person, we demonstrate the stability and robustness of this level setting procedure in open air and controlled settings. Second, we test participants' tone-in-noise thresholds using widely adopted online experiment platforms and demonstrate that reliable threshold estimates can be derived online in approximately one minute of testing. Third, using these level and threshold setting procedures to establish participant-specific stimulus conditions, we show that an online implementation of the classic probe-signal paradigm can be used to demonstrate frequency-selective attention on an individual-participant basis, using a third of the trials used in recent in-lab experiments. Finally, we show how threshold and attentional measures relate to well-validated assays of online participants' in-task motivation, fatigue, and confidence. This demonstrates the promise of online auditory psychophysics for addressing new auditory perception and neuroscience questions quickly, efficiently, and with more diverse samples. Code for the tests is publicly available through Pavlovia and Gorilla

Molecular footprints of the Holocene retreat of dwarf birch in Britain

© 2014 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited

Consciousness, complexity and chronic pain: Exploring the occurence and implications of incongruent beliefs about 'important' chronic pain treatment components

Background: The biological sciences have contributed an extensive volume of research in efforts to resolve the issue of chronic pain. An expanding body of research, focusing on the psycho-social aspects of chronic pain, is also now evident. Paradigms applied to chronic pain appear to compete and lack an integrative framework. Aims: The original aim of this study was to identify and explore patterns of congruence that exist between service users and providers in relation to beliefs about which treatments for chronic pain are important. At the outset this research took a constructivist position, based within existing research which demonstrates that beliefs about chronic pain and its treatment are individually constructed and that lack of agreement between people with pain and treatment providers may contribute to negative treatment outcomes. As the iterative process of the research unfolded the aims of determining if a complex adaptive systems (CAS) analysis was appropriate for chronic pain and whether recommendations for change could legitimately be generated using a CAS paradigm, emerged. Methods: The literature was reviewed to identify conceptualizations of, and interventions for, chronic pain. Based on this information the Stage one postal survey, gathering service users' and providers' opinions about important treatment components, was designed. The survey also included Skevington's standardised Beliefs About Pain Control Questionnaire (BPCQ). The second stage employed Delphi methodology. A series of iterative questionnaires explored the original questions about congruence of beliefs, perceived impact of disagreement and suggestions for action. As additional information emerging from each Delphi round the analysis employed firstly a constructivist framework and ultimately explored the usefulness ofreframing chronic pain within a CAS framework. Findings: The participants in this study had very little inter and intra-group congruence of beliefs. While service users believed that their decision-making was influenced by four domains of the Chapman's Consciousness model (coherence, purposiveness, affect and self-image) as derived from constructivist theory, service providers stated that affect and self-image were not strong influences. Participants agreed that some action should be taken when there is disagreement about important treatments and the overwhelming majority of recommendations focused on actions the service providers should take. Very few recommendations were made of actions for the service users. Participants' responses in Delphi 3 indicated that chronic pain had a number of elements consistent with a CAS but that more linear and conflicting beliefs were also strong. Discussion and Conclusions: A constructivist perspective in itself proved insufficient to explore chronic pain's resistance to change and the implications of this for intervention. By applying CAS theory to the three key features that emerged from Delphi 1 and 2 (incongruent beliefs, differential access to information and paradoxical beliefs and behaviours) the phenomenon of chronicity was reframed. Interventions, based on complexity science principles, can effect change in the highly interactive systems that constitute the chronic pain experience. A complexity science paradigm can serve as a meta-framework, integrating the currently competing theoretical models employed in chronic pain. The NHS Modernisation Agency, and other researchers and theorists, have provided complexity science based policy statements and recommendations for affecting change in a range of healthcare settings. These can be examined for patterns and examples of how dissent and conflict can be a positive generative force for change. Examples and patterns in turn, can form templates to guide reframing the practice and operating paradigm for chronic pain service delivery

Perceptions of psychological momentum of elite soccer players

The purpose of this research was to investigate elite soccer players’ perceptions and experiences of psychological momentum (PM) using a mixed methodological approach. Specifically, by comparing responses, the study aimed to provide coaches with a more appropriate method for collecting PM data. Interviews and focus groups were conducted with 10 English Academy, elite male soccer players. In addition, 75 professional male soccer players completed a 49-item measure about their experiences of PM. Interviews and focus groups were manually analysed using a combination of inductive and deductive approaches with Chi-square tests used to assess differences between responses to the PM measure. The majority of questionnaire responses were supported by themes highlighted by players interviewed. Scoring and conceding goals were the most frequently reported match variables associated with positive and negative PM, respectively. In addition, ‘feeling confident’, ‘having a positive attitude’ and ‘being cohesive as a team’ were important aspects of positive PM. A ‘perceived lack of ability’ and ‘feeling anxious’ were the most frequently reported experiences of negative PM. The similarity of results from both methods support the measure as a useful tool for coaches to collect data pertaining to players’ experiences and perceptions of PM. Overall, findings suggest that PM is a complex (dynamic) process whereby triggers, characteristics, and consequences can hardly be separated. By understanding players’ experiences and perceptions of PM, coaches may incorporate specific training methods to help players maximise positive PM, reduce negative PM as well as develop strategies to optimise PM

Evolutionary Multi-Objective Design of SARS-CoV-2 Protease Inhibitor Candidates

Computational drug design based on artificial intelligence is an emerging research area. At the time of writing this paper, the world suffers from an outbreak of the coronavirus SARS-CoV-2. A promising way to stop the virus replication is via protease inhibition. We propose an evolutionary multi-objective algorithm (EMOA) to design potential protease inhibitors for SARS-CoV-2's main protease. Based on the SELFIES representation the EMOA maximizes the binding of candidate ligands to the protein using the docking tool QuickVina 2, while at the same time taking into account further objectives like drug-likeliness or the fulfillment of filter constraints. The experimental part analyzes the evolutionary process and discusses the inhibitor candidates.Comment: 15 pages, 7 figures, submitted to PPSN 202

DNA methylation governs the dynamic regulation of inflammation by apoptotic cells during efferocytosis

Efficient clearance of apoptotic cells (AC) is pivotal in preventing autoimmunity and is a potent immunosuppressive stimulus. However, activation of cells prior to apoptosis abolishes their immunoregulatory properties. Here we show using the antigen-induced model of arthritis that the degree of DNA methylation within AC confers their immunomodulatory plasticity. DNA isolated from resting and activated AC mimicked their respective immune effects. Demethylation of DNA abrogated the protective effect of AC whereas remethylation of AC DNA reversed the effects of activation and restored the ability to inhibit inflammation. Disease suppression or lack thereof was associated with TGFβ and IL-6 production respectively. Apoptotic CD4+ T cells from patients with rheumatoid arthritis and systemic lupus erythematosus were demethylated compared to healthy controls and favoured production of IL-6 when cultured with healthy macrophages, in contrast to the TGFβ produced in response to healthy AC. Our data implicate AC DNA methylation as the molecular switch that imprints their regulatory properties