Excited-state electronic structure of molecules using many-body Green's functions: Quasiparticles and electron-hole excitations with VOTCA-XTP.

We present the open-source VOTCA-XTP software for the calculation of the excited-state electronic structure of molecules using many-body Green's function theory in the GW approximation with the Bethe-Salpeter equation (BSE). This work provides a summary of the underlying theory and discusses the details of its implementation based on Gaussian orbitals, including resolution-of-identity techniques and different approaches to the frequency integration of the self-energy or acceleration by offloading compute-intensive matrix operations using graphics processing units in a hybrid OpenMP/Cuda scheme. A distinctive feature of VOTCA-XTP is the capability to couple the calculation of electronic excitations to a classical polarizable environment on an atomistic level in a coupled quantum- and molecular-mechanics (QM/MM) scheme, where a complex morphology can be imported from Molecular Dynamics simulations. The capabilities and limitations of the GW-BSE implementation are illustrated with two examples. First, we study the dependence of optically active electron-hole excitations in a series of diketopyrrolopyrrole-based oligomers on molecular-architecture modifications and the number of repeat units. Second, we use the GW-BSE/MM setup to investigate the effect of polarization on localized and intermolecular charge-transfer excited states in morphologies of low-donor content rubrene-fullerene mixtures. These showcases demonstrate that our implementation currently allows us to treat systems with up to 2500 basis functions on regular shared-memory workstations, providing accurate descriptions of quasiparticle and coupled electron-hole excited states of various characters on an equal footing.

Mapping of exciton-exciton annihilation in a molecular dimer via fifth-order femtosecond two-dimensional spectroscopy.

We present a theoretical study on exciton-exciton annihilation (EEA) in a molecular dimer. This process is monitored using a fifth-order coherent two-dimensional (2D) spectroscopy as was recently proposed by Dostál et al. [Nat. Commun. 9, 2466 (2018)]. Using an electronic three-level system for each monomer, we analyze the different paths which contribute to the 2D spectrum. The spectrum is determined by two entangled relaxation processes, namely, the EEA and the direct relaxation of higher lying excited states. It is shown that the change of the spectrum as a function of a pulse delay can be linked directly to the presence of the EEA process.

FPGA-based RF interference reduction techniques for simultaneous PET-MRI.

The combination of positron emission tomography (PET) and magnetic resonance imaging (MRI) as a multi-modal imaging technique is considered very promising and powerful with regard to in vivo disease progression examination, therapy response monitoring and drug development. However, PET-MRI system design enabling simultaneous operation with unaffected intrinsic performance of both modalities is challenging. As one of the major issues, both the PET detectors and the MRI radio-frequency (RF) subsystem are exposed to electromagnetic (EM) interference, which may lead to PET and MRI signal-to-noise ratio (SNR) deteriorations. Early digitization of electronic PET signals within the MRI bore helps to preserve PET SNR, but occurs at the expense of increased amount of PET electronics inside the MRI and associated RF field emissions. This raises the likelihood of PET-related MRI interference by coupling into the MRI RF coil unwanted spurious signals considered as RF noise, as it degrades MRI SNR and results in MR image artefacts. RF shielding of PET detectors is a commonly used technique to reduce PET-related RF interferences, but can introduce eddy-current-related MRI disturbances and hinder the highest system integration. In this paper, we present RF interference reduction methods which rely on EM field coupling-decoupling principles of RF receive coils rather than suppressing emitted fields. By modifying clock frequencies and changing clock phase relations of digital circuits, the resulting RF field emission is optimised with regard to a lower field coupling into the MRI RF coil, thereby increasing the RF silence of PET detectors. Our methods are demonstrated by performing FPGA-based clock frequency and phase shifting of digital silicon photo-multipliers (dSiPMs) used in the PET modules of our MR-compatible Hyperion II (D) PET insert. We present simulations and magnetic-field map scans visualising the impact of altered clock phase pattern on the spatial RF field distribution, followed by MRI noise and SNR scans performed with an operating PET module using different clock frequencies and phase patterns. The methods were implemented via firmware design changes without any hardware modifications. This introduces new means of flexibility by enabling adaptive RF interference reduction optimisations in the field, e.g. when using a PET insert with different MRI systems or when different MRI RF coil types are to be operated with the same PET detector.

Exciton dynamics in perturbed vibronic molecular aggregates.

A site specific perturbation of a photo-excited molecular aggregate can lead to a localization of excitonic energy. We investigate this localization dynamics for laser-prepared excited states. Changing the parameters of the electric field significantly influences the exciton localization which offers the possibility for a selective control of this process. This is demonstrated for aggregates possessing a single vibrational degree of freedom per monomer unit. It is shown that the effects identified for the molecular dimer can be generalized to larger aggregates with a high density of vibronic states.

MR-compatibility assessment of the first preclinical PET-MRI insert equipped with digital silicon photomultipliers.

PET (positron emission tomography) with its high sensitivity in combination with MRI (magnetic resonance imaging) providing anatomic information with good soft-tissue contrast is considered to be a promising hybrid imaging modality. However, the integration of a PET detector into an MRI system is a challenging task since the MRI system is a sensitive device for external disturbances and provides a harsh environment for electronic devices. Consequently, the PET detector has to be transparent for the MRI system and insensitive to electromagnetic disturbances. Due to the variety of MRI protocols imposing a wide range of requirements regarding the MR-compatibility, an extensive study is mandatory to reliably assess worst-case interference phenomena between the PET detector and the MRI scanner. We have built the first preclinical PET insert, designed for a clinical 3 T MRI, using digital silicon photomultipliers (digital SiPM, type DPC 3200-22, Philips Digital Photon Counting). Since no thorough interference investigation with this new digital sensor has been reported so far, we present in this work such a comprehensive MR-compatibility study. Acceptable distortion of the B0 field homogeneity (volume RMS = 0.08 ppm, peak-to-peak value = 0.71 ppm) has been found for the PET detector installed. The signal-to-noise ratio degradation stays between 2-15% for activities up to 21 MBq. Ghosting artifacts were only found for demanding EPI (echo planar imaging) sequences with read-out gradients in Z direction caused by additional eddy currents originated from the PET detector. On the PET side, interference mainly between the gradient system and the PET detector occurred: extreme gradient tests were executed using synthetic sequences with triangular pulse shape and maximum slew rate. Under this condition, a relative degradation of the energy (⩽10%) and timing (⩽15%) resolution was noticed. However, barely measurable performance deterioration occurred when morphological MRI protocols are conducted certifying that the overall PET performance parameters remain unharmed.

Role of neuronal nicotinic receptors in the effects of nicotine and ethanol on contextual fear conditioning.

Nicotine can enhance contextual learning while ethanol impairs some forms of learning. Nicotine can overcome some of the impairing effects of ethanol when the two drugs are co-administered. The specific brain nicotinic acetylcholine receptors (nAChRs) that mediate nicotine's effects on contextual learning and whether any of ethanol's actions are mediated by nAChRs are unknown. The potential roles of nAChRs in contextual and cued fear conditioning as well as the effects of nicotine, ethanol, or co-administration of nicotine and ethanol were examined in wild type and homozygous null mutant mice from alpha7, beta2, beta3, and beta4 mouse lines at 24 h after training. Nicotine was given prior to training and testing, whereas ethanol was given only before training. Nicotine enhanced contextual learning in both alpha7 wild types and mutants when mice were trained at 0.17 mA, but not 0.35 mA. Mutants lacking the alpha7 subunit were less sensitive to the memory impairing effects of ethanol trained at 0.35 mA. beta2 Null mutants receiving saline showed a small, but significant, impairment in contextual learning compared with wild type littermates when the shock stimulus was 0.35 mA. Beta2 Null mutant mice also did not respond to the cognitive enhancing effects of nicotine alone, or after ethanol administration. beta3 and beta4 null mutants did not differ from wild types either after saline or any of drug treatments. These results show that beta2-containing nAChRs, but not beta3- or beta4-containing receptors, mediate the enhancing effects of nicotine on contextual learning and confirm previous studies implicating beta2 in other forms of learning. A new role for alpha7 nAChRs in regulating sensitivity to the cognitive disrupting effects of ethanol is proposed.

Open field activity and EtOH activation of gamma-PKC null mutants.

Null mutants of the neural-specific gamma-isotype of protein kinase C (gamma-PKC) have demonstrated differential responses to acute administration of ethanol in comparison with wild-type animals. Previous studies have shown that the mutants are less sensitive to ethanol-induced loss of righting response. Null mutants also consume more ethanol and exhibit less behavioral inhibition. In order to determine if these sensitivity differences extend to ethanol activation of locomotor activity in an open-field arena, baseline activity and the effect of two low doses of ethanol were assessed in gamma-PKC null mutants and wild-type littermates. Null mutants demonstrated higher levels of baseline activity than did their wild-type counterparts. Further analysis revealed that a 1.0 g/kg dose of ethanol increased locomotor activity in males and females of both genotypes, whereas only null mutant males were activated by a 1.25 g/kg ethanol dose. The current study demonstrates that male gamma-PKC null mutants exhibit increased sensitivity to activating doses of ethanol in contrast to previous findings of decreased sensitivity to higher, depressive doses. This reflects the pleiotropic effects of the gamma-PKC null mutation on the behavioral effects of ethanol.

Learning deficits in forebrain-restricted brain-derived neurotrophic factor mutant mice.

Brain-derived neurotrophic factor (BDNF) participates in synaptic plasticity and the adaptive changes in the strength of communication between neurons thought to underlie aspects of behavioral adaptation. By selectively deleting BDNF from the forebrain of mice using the Cre site-specific DNA recombinase, we were able to study the requirements for BDNF in behaviors such as learning and anxiety. Early-onset forebrain-restricted BDNF mutant mice (Emx-BDNF(KO)) that develop in the absence of BDNF in the dorsal cortex, hippocampus, and parts of the ventral cortex and amygdala failed to learn the Morris Water Maze task, a hippocampal-dependent visuo-spatial learning task. Freezing during all phases of cued-contextual fear conditioning, a behavioral task designed to study hippocampal-dependent associative learning, was enhanced. These mice learned a brightness discrimination task well but were impaired in a more difficult pattern discrimination task. Emx-BDNF(KO) mice did not exhibit altered sensory processing and gating, as measured by the acoustic startle response or prepulse inhibition of the startle response. Although they were less active in an open-field arena, they did not show alterations in anxiety, as measured in the elevated-plus maze, black-white chamber or mirrored chamber tasks. Combined, these data indicate that although an absence of forebrain BDNF does not disrupt acoustic sensory processing or alter baseline anxiety, specific forms of learning are severely impaired.

Mouse molecular genetic technologies: promise for psychiatric research.

Recent advances in mammalian genomics are providing unprecedented opportunities to identify genes that influence neural systems relevant to psychiatric illnesses. As a genetically tractable mammalian species in which complex behaviors may be modeled, mice have been the focus of much attention for examining relationships between genes and behavior. Many investigators are pursuing experimental strategies in which the functions of known genes are examined by studying the impact of their manipulation in mice. These studies are providing important information regarding genetic influences on behavior, as well as animal models relevant to human disease processes. Additional powerful genetic strategies have recently been initiated to search broadly for genes that influence particular clinically relevant behavioral traits. These approaches promise to uncover a large number of novel genetic influences on neuronal pathways that regulate behavior. In this review, mouse molecular genetic techniques are described and illustrative examples of their application to neurobehavioral processes relevant to clinical disorders are provided. Future directions in technology development that promise to further enhance the utility of these approaches for translational research are also described.

Ethanol consumption and behavioral impulsivity are increased in protein kinase Cgamma null mutant mice.

Etiological factors influencing the development of alcoholism are complex and, at a minimum, include an interaction between polygenic factors and personality and biological traits. Human and animal studies suggest that some genes may regulate both the traits associated with alcohol abuse, such as decreased sensitivity or anxiety, and vulnerability to alcoholism. The identification of these genes could elucidate neurochemical pathways that are important in the development of alcohol abuse. Results from the present study indicate that the gene encoding the neuronal-specific gamma subtype of protein kinase C (PKCgamma) influences both ethanol consumption and behavioral impulsivity, a personality characteristic associated with Type II alcoholics, in a pleiotropic manner. Mice lacking PKCgamma consume more ethanol in a two-bottle choice paradigm and also demonstrate increased behavioral impulsivity in an appetitive-signaled nosepoke task when compared with wild-type littermate control mice. Therefore, PKCgamma may be an important mechanism within the cell that mediates one or more neurochemical pathways relevant to an increased predisposition to alcoholism.

Staphylococcus aureus enterotoxins induce histamine and leukotriene release in patients with atopic eczema.

BACKGROUND: Chronic skin colonization with Staphylococcus aureus is a characteristic feature of atopic eczema (AE), and about 60% of S. aureus strains isolated from the skin of patients with AE secrete enterotoxins. Furthermore, IgE antibodies to S. aureus enterotoxins have been identified in 78% of patients with AE. OBJECTIVES: To examine the S. aureus enterotoxin-induced histamine and leukotriene release of basophils from patients with AE. METHODS: Peripheral blood basophils from patients with AE were stimulated with the staphylococcal enterotoxins A, B, D, E and toxic shock syndrome toxin-1. Additionally, priming experiments were performed with interleukin (IL)-3, IL-8 and granulocyte/macrophage colony-stimulating factor followed by stimulation with S. aureus enterotoxins. RESULTS: In patients with AE, basophils secreted significantly higher amounts of histamine and leukotriene C4 (LTC4) than in healthy controls. The priming experiments showed additional histamine and LTC4 release in the group of AE patients. CONCLUSIONS: Histamine and leukotriene generation from atopic basophils stimulated with staphylococcal enterotoxins may indicate a role for these toxins as possible allergens in at least a subgroup of patients with AE.

Utility of fiberoptic bronchoscopy before bronchial artery embolization for massive hemoptysis.

OBJECTIVE: We wanted to investigate the utility of performing fiberoptic bronchoscopy before bronchial artery embolization in patients with massive hemoptysis. MATERIALS AND METHODS: We retrospectively reviewed the cases of all patients with hemoptysis who had presented at either of two local hospitals, one county hospital and one community hospital, between 1988 and 2000 and who had undergone fiberoptic bronchoscopy before bronchial arteriography. All data were abstracted using a standardized coding form, and radiographs were independently reviewed by two of the authors. RESULTS: Twenty-nine patients meeting the inclusion criteria were identified; one patient was excluded because of missing radiographs. The remaining 28 patients consisted of 19 men and nine women, with an average age of 54.6 years (age range, 16-91 years). The clinically determined diagnoses of their symptoms were tuberculous bronchiectasis (n = 14; 50.0%); bronchogenic carcinoma (n = 4; 14.3%); active tuberculosis (n = 2; 7.1%); nontuberculous bronchiectasis (n = 2; 7.1%); active coccidioidomycosis, pancreaticobronchial fistula, arteriovenous malformation, and tetralogy of fallot (n =1 each; 3.6% each); and unknown cause (n = 2; 7.1%). The bleeding site determined through bronchoscopy was consistent with that determined through radiographs in 23 patients (82.1%); all had either unilateral disease (n = 15), bilateral disease with unilateral cavities (n = 5), or a preponderance of disease on one side (n = 3). Bronchoscopy was an essential tool in determining the bleeding site in only three patients (10.7%), all of whom had bronchiectasis without localizing features visible on chest radiographs. In the remaining two patients (7.1%), bronchoscopic findings were indeterminate, but radiographs were helpful. CONCLUSION: Fiberoptic bronchoscopy before bronchial artery embolization is unnecessary in patients with hemoptysis of known causation if the site of bleeding can be determined from radiographs and no bronchoscopic airways management is needed.

Quantitative genetics and mouse behavior.

Quantitative differences are observed for most complex behavioral and pharmacological traits within any population. Both environmental and genetic influences regulate such individual differences. The mouse has proven to be a superb model in which to investigate the genetic basis for quantitative differences in complex behaviors. Genetically defined populations of mice, including inbred strains, heterogeneous stocks, and selected lines, have been used effectively to document these genetic differences. Recently, quantitative trait loci methods have been applied to map the chromosomal regions that regulate variation with the goal of eventually identifying the gene polymorphisms that reside in these regions.

Differential sensitivity to the anxiolytic effects of ethanol and flunitrazepam in PKCgamma null mutant mice.

Tests of ethanol effects in PKCgamma null mutant mice have indicated that PKCgamma plays a role in initial sensitivity to ethanol-induced sedation, hypothermia, and GABA(A) receptor function and impacts neurochemical pathways mediating anxiety. The present study was undertaken to evaluate whether the decreased sensitivity to ethanol previously observed in these mice generalized to the anxiolytic effects of ethanol. PKCgamma null mutant mice and wild-type controls were tested in the elevated-plus maze, the black/white box, and the mirrored chamber after ethanol (0, 1.0, 1.25, 1.5 g/kg) or flunitrazepam (FNZ) (0, 0.015, 0.03, 0.06 mg/kg). Results indicated that although both genotypes exhibited anxiolytic responses to ethanol in the elevated plus-maze, null mutant mice were less sensitive than wild-type control mice; however, in the black/white box, PKCgamma null mutants were more sensitive than controls to the anxiolytic effects of FNZ. Neither ethanol nor FNZ produced anxiolytic responses in the mirrored chamber for either genotype. These results suggest that PKCgamma differentially mediates anxiolytic responses to ethanol and FNZ and that this relationship interacts with each drug's efficacy in reducing anxiety-related behaviors specific to each of the three mazes.

An unusual complication during central venous catheter placement.

A 31-year-old man with disseminated Coccidioides imitis infection required central catheter placement for access. The patient had an inferior vena cava (IVC) filter placed as a result of previous deep venous thrombosis of the left lower extremity. The guidewire could not be removed following placement of the right internal jugular catheter by the Seldinger technique. Fluoroscopic examination revealed entanglement of the J-tip guidewire in the apex of the IVC filter. The catheter was successfully removed by interventional radiologists using a snare tip catheter through the left femoral vein.

Nicotine enhances latent inhibition and ameliorates ethanol-induced deficits in latent inhibition.

Alcohol and nicotine are drugs of abuse that are used frequently together. One possible explanation for this co-administration is that nicotine prevents or lessens alcohol-associated impairments. The present study examined the dose-dependent effects of acute administration of nicotine, alcohol, or alcohol plus nicotine on latent inhibition as measured by lick suppression in C57BL/6 mice. Alterations in a lick suppression ratio were measured by assessing the effects of 10 pre-exposures to an auditory conditioned stimulus (CS) on formation of subsequent CS-shock unconditioned stimulus (US) associations. Mice pre-exposed to the CS were expected to develop a weaker CS-US association. Nicotine administered prior to pre-exposure to the CS produced increased suppression ratios, ethanol given prior to pre-exposure to the CS decreased suppression ratios, and nicotine reversed the effects of ethanol when the two drugs were co-administered. These opposing actions of nicotine and ethanol may have relevance to the high incidence of smoking and drinking in humans.

The role of RNA editing of kainate receptors in synaptic plasticity and seizures.

The ionotropic glutamate receptor subunit GluR6 undergoes developmentally and regionally regulated Q/R site RNA editing that reduces the calcium permeability of GluR6-containing kainate receptors. To investigate the functional significance of this editing in vivo, we engineered mice deficient in GluR6 Q/R site editing. In these mutant mice but not in wild types, NMDA receptor-independent long-term potentiation (LTP) could be induced at the medial perforant path-dentate gyrus synapse. This indicates that kainate receptors with unedited GluR6 subunits can mediate LTP. Behavioral analyses revealed no differences from wild types, but mutant mice were more vulnerable to kainate-induced seizures. Together, these results suggest that GluR6 Q/R site RNA editing may modulate synaptic plasticity and seizure vulnerability.

Point mutant mice with hypersensitive alpha 4 nicotinic receptors show dopaminergic deficits and increased anxiety.

Knock-in mice were generated that harbored a leucine-to-serine mutation in the alpha4 nicotinic receptor near the gate in the channel pore. Mice with intact expression of this hypersensitive receptor display dominant neonatal lethality. These mice have a severe deficit of dopaminergic neurons in the substantia nigra, possibly because the hypersensitive receptors are continuously activated by normal extracellular choline concentrations. A strain that retains the neo selection cassette in an intron has reduced expression of the hypersensitive receptor and is viable and fertile. The viable mice display increased anxiety, poor motor learning, excessive ambulation that is eliminated by very low levels of nicotine, and a reduction of nigrostriatal dopaminergic function upon aging. These knock-in mice provide useful insights into the pathophysiology of sustained nicotinic receptor activation and may provide a model for Parkinson's disease.

Current role of beta-adrenergic blockers in the treatment of chronic congestive heart failure.

Recent findings on the use of beta-adrenergic blockers in patients with congestive heart failure (CHF) are reviewed. CHF is a progressive, debilitating disease that afflicts 4.6 million patients in the United States. Treatment has traditionally consisted of a diuretic, an angiotensin-converting-enzyme (ACE) inhibitor, and digoxin. Despite advances in ACE-inhibitor therapy, the five-year mortality rate remains nearly 50%. Overstimulation of the sympathetic nervous system is believed to contribute to mortality. Beta-blockers have recently been added to the standard of care for patients with New York Heart Association functional class II or III heart failure. Four randomized, double-blind, placebo-controlled clinical trials were recently completed that addressed the benefits of beta-blockers in CHF. The overall mortality rate was reduced 65% by carvedilol, 34% by metoprolol, and 33% by bisoprolol; all these reductions were significant compared with placebo, and the trials were ended early. Bucindolol, however, did not have a significant effect on mortality. These drugs are hepatically metabolized and may require dosage adjustment in hepatically impaired patients. Decompensation of heart failure is another consideration; a beta-blocker should be added only for patients with stable CHF. Dosages must be slowly adjusted to targeted levels. Adverse effects do not differ significantly among beta-blockers. In addition to their effect on mortality, beta-blockers reduce CHF-related morbidity, such as all-cause hospitalization. Carvedilol, metoprolol, and bisoprolol decrease the mortality and morbidity associated with CHF and can be used with limited adverse effects. The choice among these agents does not affect clinical outcomes; bucindolol, however, has proven ineffective.

Protection of bacterial spores in space, a contribution to the discussion on Panspermia.

Spores of Bacillus subtilis were exposed to space in the BIOPAN facility of the European Space Agency onboard of the Russian Earth-orbiting FOTON satellite. The spores were exposed either in dry layers without any protecting agent, or mixed with clay, red sandstone, Martian analogue soil or meteorite powder, in dry layers as well as in so-called 'artificial meteorites', i.e. cubes filled with clay and spores in naturally occurring concentrations. After about 2 weeks in space, their survival was tested from the number of colony formers. Unprotected spores in layers open to space or behind a quartz window were completely or nearly completely inactivated (survival rates in most cases < or = 10(-6)). The same low survival was obtained behind a thin layer of clay acting as an optical filter. The survival rate was increased by 5 orders of magnitude and more, if the spores in the dry layer were directly mixed with powder of clay, rock or meteorites, and up to 100% survival was reached in soil mixtures with spores comparable to the natural soil to spore ratio. These data confirm the deleterious effects of extraterrestrial solar UV radiation. Thin layers of clay, rock or meteorite are only successful in UV-shielding, if they are in direct contact with the spores. The data suggest that in a scenario of interplanetary transfer of life, small rock ejecta of a few cm in diameter could be sufficiently large to protect bacterial spores against the intense insolation; however, micron-sized grains, as originally requested by Panspermia, may not provide sufficient protection for spores to survive. The data are also pertinent to search for life on Mars and planetary protection considerations for future missions to Mars.