Time-Dependent Resonant Inelastic X-ray Scattering of Pyrazine at the Nitrogen K-Edge: A Quantum Dynamics Approach.

We calculate resonant inelastic X-ray scattering spectra of pyrazine at the nitrogen K-edge in the time domain including wavepacket dynamics in both the valence and core-excited state manifolds. Upon resonant excitation, we observe ultrafast non-adiabatic population transfer between core-excited states within the core-hole lifetime, leading to molecular symmetry distortions. Importantly, our time-domain approach inherently contains the ability to manipulate the dynamics of this process by detuning the excitation energy, which effectively shortens the scattering duration. We also explore the impact of pulsed incident X-ray radiation, which provides a foundation for state-of-the-art time-resolved experiments with coherent pulsed light sources.

Estradiol-mediated modulation of memory and of the underlying dendritic spine plasticity through the life span.

The morphophysiology of the nervous system changes and adapts in response to external environmental inputs and the experiences of individuals throughout their lives. Other changes in the organisms internal environment can also contribute to nervous system restructuring in the form of plastic changes that underlie its capacity to adapt to emerging psychophysiological conditions. These adaptive processes lead to subtle modifications of the organisms internal homeostasis which is closely related with the activity of chemical messengers, such as neurotransmitters and hormones. Hormones reach the brain through the bloodstream, where they activate specific receptors through which certain biochemical, physiological, and morphological changes take place in numerous regions. Fetal development, infancy, puberty, and adulthood are all periods of substantial hormone-mediated brain remodeling in both males and females. Adulthood, specifically, is associated with a broad range of life events, including reproductive cycles in both sexes, and pregnancy and menopause in women. Events of this kind occur concomitantly with eventual modifications in behavioral performance and, especially, in cognitive abilities like learning and memory that underlie, at least in part, plastic changes in the dendritic spines of the neuronal cells in cerebral areas involved in processing cognitive information. Estrogens form a family that consists of three molecules [17ß-estradiol (E2), estrone, estriol] which are deeply involved in regulating numerous bodily functions in different stages of the life-cycle, including the modulation of cognitive performance. This review addresses the effects of E2 on the dendritic spine-mediated synaptic organization of cognitive performance throughout the life span.

Coupling Molecular Systems with Plasmonic Nanocavities: A Quantum Dynamics Approach.

Plasmonic nanoparticles have the capacity to confine electromagnetic fields to the subwavelength regime and provide strong coupling with few or even a single emitter at room temperature. The photophysical properties of the emitters are highly dependent on the relative distance and orientation between them and the nanocavity. Therefore, there is a need for accurate and general light-matter interaction models capable of guiding their design in application-oriented devices. In this work, we present a Hermitian formalism within the framework of quantum dynamics and based on first-principles electronic structure calculations. Our vibronic approach considers the quantum nature of the plasmonic excitations and the dynamics of nonradiative channels to model plasmonic nanocavities and their dipolar coupling to molecular electronic states. Thus, the quantized and dissipative nature of the nanocavity is fully addressed.

Optimal Mode Combination in the Multiconfiguration Time-Dependent Hartree Method through Multivariate Statistics: Factor Analysis and Hierarchical Clustering.

The multiconfiguration time-dependent Hartree (MCTDH) method and its multilayer extension (ML-MCTDH) are powerful algorithms for the efficient computation of nuclear quantum dynamics in high-dimensional systems. By providing time-dependent variational orbitals and an optimal choice of layered effective degrees of freedom, one is able to reduce the computational cost to an amenable number of configurations. However, choices related to selecting properly the mode grouping and tensor tree are strongly system dependent and, thus far, subjectively based on intuition and/or experience. Therefore, herein we detail a new protocol based on multivariate statistics─more specifically, factor analysis and hierarchical clustering─for a reliable and convenient guiding in the optimal design of such complex "system-of-systems" tensor-network decompositions. The advantages of employing the new algorithm and its applicability are tested on water and two floppy protonated water clusters with large amplitude motions.

Rational Design of Phe-BODIPY Amino Acids as Fluorogenic Building Blocks for Peptide-Based Detection of Urinary Tract Candida Infections.

Fungal infections caused by Candida species are among the most prevalent in hospitalized patients. However, current methods for the detection of Candida fungal cells in clinical samples rely on time-consuming assays that hamper rapid and reliable diagnosis. Herein, we describe the rational development of new Phe-BODIPY amino acids as small fluorogenic building blocks and their application to generate fluorescent antimicrobial peptides for rapid labelling of Candida cells in urine. We have used computational methods to analyse the fluorogenic behaviour of BODIPY-substituted aromatic amino acids and performed bioactivity and confocal microscopy experiments in different strains to confirm the utility and versatility of peptides incorporating Phe-BODIPYs. Finally, we have designed a simple and sensitive fluorescence-based assay for the detection of Candida albicans in human urine samples.

A Rare Dirhamnosyl Flavonoid and Other Radical-Scavenging Metabolites from Cynophalla mollis (Kunth) J.†Presl and Colicodendron scabridum (Kunt) Seem. (Capparaceae) of Ecuador.

The phytochemistry of Cynophalla mollis (Kunth) J. Presl and Colicodendron scabridum (Kunth), both belonging to the family Capparaceae, were investigated in this study for the first time. Lupeol, betulin, lutein, stachydrine and quercetin-3,4'-di-O-rhamnoside were isolated from C. mollis, whereas C. scabridum afforded lupeol, lutein, stachydrine, ß-sitosterol, stigmasterol, betonicine and narcissoside. All these compounds were purified by preparative liquid chromatography, in both open column and instrumental (MPLC) separation systems. Preparative TLC was also applied. They were all identified by 1 H- and 13 C-NMR experiments. The complete structure of the very rare flavonoid quercetin-3,4'-di-O-rhamnoside was fully elucidated through DEPT-135, COSY, HMQC and HMBC experiments, together with UV/VIS and FT-IR spectrophotometry. Complete NMR data for quercetin-3,4'-di-O-rhamnoside in deuterated methanol were presented here for the first time. All the extracts did not exert antioxidant activity at the maximum tested dose of 1 mg/mL. Three out of the nine isolated compounds exerted a good spectrum of antioxidant capacity, being narcissoside the most active against ABTS radicals, with SC50 =12.43 µM. It was followed by lutein and quercetin-3,4'-di-O-rhamnoside, with 40.92 µM and 46.10 µM, respectively.

Evidence of influenza infection in dogs and cats in central Chile.

As companion animals, dogs and cats live in close contact with humans, generating the possibility of interspecies pathogen transmission events. Equine origin H3N8 and avian origin H5N1 influenza virus have been reported in dogs and cats respectively since 2004 with outbreaks associated with different strains recorded for both species in Asia and North America. To date, there have been no reports of influenza viruses from companion animals in South America. To fill this gap in knowledge, we performed active epidemiological surveillance in shelters that received abandoned animals, backyard production systems and veterinary clinics between May 2017 and January 2019 to estimate the burden of influenza infection in cats and dogs in the central region of Chile. Blood samples, oropharyngeal swabs or both were collected for influenza A virus detection by RT-qPCR, NP-ELISA, and hemagglutination inhibition assay. Logistic regression models were performed to assess the association between NP-ELISA-positivity and variables including sex and animal origin. The percentage of ELISA-positive samples was 43.5 % (95 % CI: 37.0-50.1) and 23.3 % (95 % CI: 10.6-42.7) for dogs and cats, respectively. No association was found between NP-ELISA results and sex or animal origin for either dogs or cats. Two ELISA positive samples showed hemagglutination inhibition titers against pandemic H1N1 influenza. One dog sample tested positive by RT-qPCR, indicating an overall RT-qPCR positivity in dogs of 1.1 % (95 % CI: 0.05-6.7). None of the tested cat samples were positive by this assay.

Differential Transcriptomic Response of Rainbow Trout to Infection with Two Strains of IPNV.

The IPN virus (IPNV) causes a highly contagious disease that affects farmed salmonids. IPNV isolates have been phylogenetically classified into seven genogroups, of which two are present in Chile, genogroups 1 and 5. This study aimed to compare the transcriptomic response of rainbow trout fry challenged with two Chilean isolates of IPNV, RTTX (genogroup 1), and ALKA (genogroup 5). Tissue samples from challenged individuals and controls were taken at 1, 7, and 20 days post-challenge and analyzed by RNA-Seq. The results revealed that infection with RTTX elicited a greater modulation of the trout transcriptome compared to ALKA infection, generating a greater number of highly differentially expressed genes in relation to the control fish. Gene Ontology enrichment indicated that functions related to the inflammatory and immune responses were modulated in fish challenged with both isolates throughout the trial, but with different regulation patterns. On day 1 post challenge, these functions were activated in those challenged with ALKA, but suppressed in RTTX-challenged fish. These results suggest that rainbow trout exhibit a differential transcriptomic response to infection with the two genetically distinct IPNV isolates, especially at early times post-infection.

VANGUARD®crLyme: A next generation Lyme disease vaccine that prevents B. burgdorferi infection in dogs.

Lyme disease, a public health threat of significance to both veterinary and human medicine, is caused by the tick (Ixodes) transmitted spirochete, Borreliella burgdorferi. Here we report on the immunogenicity and efficacy of VANGUARD®crLyme (Zoetis), the most recent canine Lyme disease vaccine to be approved by the United States Department of Agriculture. VANGUARD®crLyme is a subunit vaccine consisting of outer surface protein A (OspA) and a recombinant outer surface protein C (OspC) based-chimeric epitope protein (chimeritope) that consists of at least 14 different linear epitopes derived from diverse OspC proteins. The combination of OspA and the OspC chimeritope (Ch14) in the vaccine formulation allows for the development of humoral immune responses that work synergistically to target spirochetes in both ticks and in mammals. Immunogenicity was assessed in purpose-bred dogs. A two-dose vaccination protocol resulted in high antibody titers to OspA and Ch14 and vaccinal antibody reacted with 25 different recombinant OspC variants. Efficacy was demonstrated using an Ixodes scapularis -purpose bred dog challenge model. Vaccination with VANGUARD®crLyme provided protection against infection and prevented the development of clinical manifestations and histopathological changes associated with Lyme disease.

Regularizing the MCTDH equations of motion through an optimal choice on-the-fly (i.e., spawning) of unoccupied single-particle functions.

The multi-configuration time-dependent Hartree method is a general algorithm to solve the time-dependent Schrödinger equation, in which the wavefunction is expanded in a direct product of self-adapting time-dependent Single-Particle Functions (SPFs) that are propagated in time according to the Dirac-Frenkel variational principle. In the current version of this approach, the size of the SPF basis is fixed at the outset so that singularities in the working equations resulting from unoccupied functions have to be removed by a regularization procedure. Here, an alternative protocol is presented, in which we gradually increase the number of unoccupied SPFs on-the-fly (i.e., spawning) and optimize their shape by variationally minimizing the error made by the finite size of the basis. An initial estimate for the respective new expansion coefficients is also computed, thus avoiding the need to regularize the equations of motion. The advantages of employing the new algorithm are tested and discussed in some illustrative examples.

Influence of testing environment and loading rate on intervertebral disc compressive mechanics: An assessment of repeatability at three different laboratories.

In vitro mechanical testing of intervertebral discs is crucial for basic science and pre-clinical testing. Generally, these tests aim to replicate in vivo conditions, but simplifications are necessary in specimen preparation and mechanical testing due to complexities in both structure and the loading conditions required to replicate in vivo conditions. There has been a growing interest in developing a consensus of testing protocols within the spine community to improve comparison of results between studies. The objective of this study was to perform axial compression experiments on bovine bone-disc-bone specimens at three institutions. No differences were observed between testing environment being air, with PBS soaked gauze, or a PBS bath (P > .206). A 100-fold increase in loading rate resulted in a small (2%) but significant increase in compressive mechanics (P < .017). A 7% difference in compressive stiffness between Labs B and C was eliminated when values were adjusted for test system compliance. Specimens tested at Lab A, however, were found to be stiffer than specimens from Lab B and C. Even after normalizing for disc geometry and adjusting for system compliance, an ∼35% difference was observed between UK based labs (B and C) and the USA based lab (A). Large differences in specimen stiffness may be due to genetic differences between breeds or in agricultural feed and use of growth hormones; highlighting significant challenges in comparing mechanics data across studies. This research provides a standardized test protocol for the comparison of spinal specimens and provides steps towards understanding how location and test set-up may affect biomechanical results.

Tg.rasH2 Mouse Model for Assessing Carcinogenic Potential of Pharmaceuticals: Industry Survey of Current Practices.

The Tg.rasH2 mouse was developed as an alternative model to the traditional 2-year mouse bioassay for pharmaceutical carcinogenicity testing. This model has found extensive use in support of pharmaceutical drug development over the last few decades. It has the potential to improve quality and timeliness, reduce animal usage, and in some instances allow expedient decision-making regarding the human carcinogenicity potential of a drug candidate. Despite the increased use of the Tg.rasH2 model, there has been no systematic survey of current practices in the design, interpretation of results from the bioassay, and global health authority perspectives. Therefore, the aim of this work was to poll the pharmaceutical industry on study design practices used in the dose range finding and definitive 6-month studies and on results relative to the ongoing negotiations to revise The International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use S1 Guidance. Twenty-two member companies of International Consortium for Innovation and Quality in Pharmaceutical Development DruSafe Leadership Group participated in the survey, sharing experiences from studies conducted with 55 test compounds between 2010 and 2018. The survey results provide very useful insights into study design and interpretation. Importantly, the results identified several key opportunities for reducing animal use and increasing the value of testing for potential human carcinogenicity using this model. Recommended changes to study designs that would reduce animal usage include eliminating the requirement to include positive control groups in every study, use of nontransgenic wild-type littermates in the dose range finding study, and use of microsampling to reduce or eliminate satellite groups for toxicokinetics.

Modifications to cytoskeleton-associated proteins in dendritic spines underlie the adaptive plasticity involved in long term reference memory.

Spatial learning and memory enables individuals to orientate themselves in an external environment. Synaptic stimulation of dendritic spines on hippocampal place cells underlies adaptive cognitive performance, inducing plastic changes such as spinogenesis, pruning and structural interconversion. Such plastic changes are driven by complex molecular machinery that relies on several actin cytoskeleton-associated proteins (ACAP's), these interacting with actin filaments in the postsynaptic density to guide the conformational changes to spines in accordance with the synaptic information they receive. However, the specific dynamics of the plastic changes in spines driven by ACAP's are poorly understood. Adult rats exhibit efficient allocentric reference memory 30 days after training in a spatial learning paradigm in the Morris water maze. A Golgi study revealed this behavior to be associated with a reduction in both spine density and in mushroom spines, as well as a concomitant increase in thin spines. These changes were accompanied by the overexpression of mRNA encoding ß-actin, Spinophilin and Cortactin, whilst the expression of Profilin, α-actinin, Drebrin, Synaptopodin and Myosin decreased. By contrast, no changes were evident in Cofilin, Gelsolin and Arp2/3 mRNA. From this analysis, it appears that neither spinogenesis nor new mushroom spines are necessary for long-term spatial information retrieval, while thin spines could be potentiated to retrieve pre-learned spatial information. Further studies that focus on the signaling pathways and their related molecules may shed further light on the molecular dynamics of the plastic changes to dendritic spines that underlie cognitive performance, both under normal and pathological conditions.

Comparison of mortality and viral load in rainbow trout (Oncorhynchus mykiss) infected with infectious pancreatic necrosis virus (IPNV) genogroups 1 and 5.

Infectious pancreatic necrosis virus (IPNV) is the aetiological agent of a highly contagious disease that affects farmed salmonids. IPNV isolates have been phylogenetically classified into eight genogroups, of which two are present in Chile, genogroups 1 and 5. Here, we compare the mortality rate caused by isolates from both genogroups in rainbow trout (Oncorhynchus mykiss) fry to determine if there is an association between host susceptibility and phylogenetic characterization of IPNV. Fish were challenged by immersion with one of four isolates (two for each genogroup), and mortality curves were assessed after 30 days. Viral load was measured in all mortalities and in live fish sampled at 1, 7 and 20 days post-infection. Although mortality was low throughout the challenge, differences were found between fish infected with different isolates. Both isolates from genogroup 1 caused greater cumulative mortalities than either of the isolates from genogroup 5. When combined, the overall mortality rate of fish challenged with genogroup 1 isolates was significantly higher than those infected with genogroup 5. However, viral load was lower on trout infected with genogroup 1 isolates. These results suggest that rainbow trout are more susceptible to IPNV isolates from genogroup 1 than genogroup 5.

Atomoxetine prevents working memory loss in hyperactive rats, mediating plastic changes in prefrontal cortex pyramidal neurons.

Attention Deficit Hyperactivity Disorder (ADHD) causes impaired visuospatial working memory (VWM), which primarily maps to the prefrontal cortex. However, little is known about the synaptic processes underlying cognitive loss in ADHD, or those ultimately involved in the preventive effect observed through the clinical use of Atomoxetine (ATX). To investigate the plasticity underlying ADHD related cognitive loss, and that potentially involved in the preventive action of Atomoxetine, allocentric VWM was assessed, as well as the dendritic spine number and proportional density on pyramidal neurons in the prefrontal cerebral cortex layer III of neonatal 6-hydroxydopamine-lesioned rats. The effect of acute ATX treatment was also assessed at 28 days of age. 6-OHDA induced lesions produced increased motor activity and a loss of VWM, concomitant with a reduction in thin spine density. ATX administration reversed cognitive loss, in conjunction with a decrease in thin spines and an increase in mushroom spines. A reduction in the proportion of spines involved in learning in hyperactive animals could account for the loss in cognitive function observed. Considering thin spine density was also reduced after ATX administration, we hypothesized that the restoration in cognitive function recorded could be brought about by an increase in memory related mushroom spines.

Multidimensional Quantum Mechanical Modeling of Electron Transfer and Electronic Coherence in Plant Cryptochromes: The Role of Initial Bath Conditions.

A multidimensional quantum mechanical protocol is used to describe the photoinduced electron transfer and electronic coherence in plant cryptochromes without any semiempirical, e.g., experimentally obtained, parameters. Starting from a two-level spin-boson Hamiltonian we look at the effect that the initial photoinduced nuclear bath distribution has on an intermediate step of this biological electron transfer cascade for two idealized cases. The first assumes a slow equilibration of the nuclear bath with respect to the previous electron transfer step that leads to an ultrafast decay with little temperature dependence; while the second assumes a prior fast bath equilibration on the donor potential energy surface leading to a much slower decay, which contrarily displays a high temperature dependence and a better agreement with previous theoretical and experimental results. Beyond Marcus and semiclassical pictures these results unravel the strong impact that the presence or not of equilibrium initial conditions has on the electronic population and coherence dynamics at the quantum dynamics level in this and conceivably in other biological electron transfer cascades.

Different patterns of motor activity induce differential plastic changes in pyramidal neurons in the motor cortex of rats: A Golgi study.

Rehabilitation is a process which favors recovery after brain damage involving motor systems, and neural plasticity is the only real resource the brain has for inducing neurobiological events in order to bring about re-adaptation. Rats were placed on a treadmill and made to walk, in different groups, at different velocities and with varying degrees of inclination. Plastic changes in the spines of the apical and basal dendrites of fifth-layer pyramidal neurons in the motor cortices of the rats were detected after study with the Golgi method. Numbers of dendritic spines increased in the three experimental groups, and thin, mushroom, stubby, wide, and branched spines increased or decreased in proportion depending on the motor demands made of each group. Along with the numerical increase of spines, the present findings provide evidence that dendritic spines' geometrical plasticity is involved in the differential performance of motor activity.

Inter-laboratory ring trial to evaluate real-time reverse transcription polymerase chain reaction methods used for detection of infectious pancreatic necrosis virus in Chile

Background: Infectious Pancreatic Necrosis Virus (IPNV) is the etiological agent of a highly contagious disease that affects salmonids. In Chile, the second worldwide salmon producer, IPNV causes great economic loss and is one of the most frequently detected pathogens. Due to its high level of persistence and the lack of information about the efficiency of its diagnostic techniques, the National Reference Laboratory (NRL) for IPNV in Chile performed the first inter-laboratory ring trial, to evaluate the sensitivity, specificity and repeatability of the qRT-PCR detection methods used in the country. Results: Results showed 100% in sensitivity and specificity in most of the laboratories. Only three of the twelve participant laboratories presented problems in sensitivity and one in specificity. Problems in specificity (false positives) were most likely caused by cross contamination of the samples, while errors in sensitivity (false negatives) were due to detection problems of the least concentrated viral sample. Regarding repeatability, many of the laboratories presented great dispersion of the results (Ct values) for replicate samples over the three days of the trial. Moreover, large differences in the Ct values for each sample were detected among all the laboratories. Conclusions: Overall, the ring trial showed high values of sensitivity and specificity, with some problems of repeatability and inter-laboratory variability. This last issue needs to be addressed in order to allow harmonized diagnostic of IPNV within the country. We recommend the use of the NRL methods as validated and reliable qRT-PCR protocols for the detection of IPNV.

Spinogenesis and Plastic Changes in the Dendritic Spines of Spinal Cord Motoneurons After Traumatic Injury in Rats.

BACKGROUND: Spinal cord injury (SCI) is highly incapacitating, and the neurobiological factors involved in an eventual functional recovery remain uncertain. Plastic changes to dendritic spines are closely related with the functional modifications of behavior. AIM OF THE STUDY: To explore the plastic response of dendritic spines in motoneurons after SCI. METHODS: Female rats were assigned to either of three groups: Intact (no manipulations), Sham (T9 laminectomy), and SCI (T9 laminectomy and spinal cord contusion). RESULTS: Motor function according to a BBBscale was progressively recovered from 2 week through 8 week postinjury, reaching a plateau through week 16. Dendritic spine density was greater in SCI vs. control groups, rostral as well as caudal to the lesion, at 8 and 16 weeks postinjury. Thin and stubby/wide spines were more abundant at both locations and time points, whereas mushroom spines predominated at 2 and 4 months in rostral to the lesion. Filopodia and atypical structures resembling dendritic spines were observed. Synaptophysin expression was lower in SCI at the caudal portion at 8 weeks, and was higher at week 16. CONCLUSION: Spinogenesis in spinal motoneurons may be a crucial plastic response to favor spontaneous recovery after SCI.