Impacts of Recreational Diving on Hawksbill Sea Turtles (Eretmochelys imbricata) in the Roatán Marine Park, Honduras: Summer 2014

This report represents the ongoing work of the Protective Turtle Ecology Center for Training, Outreach, and Research, Inc. (ProTECTOR Inc.) in Honduras during the 2014 season and is provided in partial fulfillment of research agreements with the Roatán Marine Park

Elucidation of time-dependent systems biology cell response patterns with time course network enrichment

Advances in OMICS technologies emerged both massive expression data sets and huge networks modelling the molecular interplay of genes, RNAs, proteins and metabolites. Network enrichment methods combine these two data types to extract subnetwork responses from case/control setups. However, no methods exist to integrate time series data with networks, thus preventing the identification of time-dependent systems biology responses. We close this gap with Time Course Network Enrichment (TiCoNE). It combines a new kind of human-augmented clustering with a novel approach to network enrichment. It finds temporal expression prototypes that are mapped to a network and investigated for enriched prototype pairs interacting more often than expected by chance. Such patterns of temporal subnetwork co-enrichment can be compared between different conditions. With TiCoNE, we identified the first distinguishing temporal systems biology profiles in time series gene expression data of human lung cells after infection with Influenza and Rhino virus. TiCoNE is available online (https://ticone.compbio.sdu.dk) and as Cytoscape app in the Cytoscape App Store (http://apps.cytoscape.org/)

Microwave synthesis of high-quality and uniform 4 nm ZnFe₂O₄ nanocrystals for application in energy storage and nanomagnetics

Magnetic nanocrystals with a narrow size distribution hold promise for many applications in different areas ranging from biomedicine to electronics and energy storage. Herein, the microwave-assisted sol–gel synthesis and thorough characterization of size-monodisperse zinc ferrite nanoparticles of spherical shape is reported. X-ray diffraction, 57Fe Mössbauer spectroscopy and X-ray photoelectron spectroscopy all show that the material is both chemically and phase-pure and adopts a partially inverted spinel structure with Fe3+ ions residing on tetrahedral and octahedral sites according to (Zn0.32Fe0.68)tet[Zn0.68Fe1.32]octO4±δ. Electron microscopy and direct-current magnetometry confirm the size uniformity of the nanocrystals, while frequency-dependent alternating-current magnetic susceptibility measurements indicate the presence of a superspin glass state with a freezing temperature of about 22 K. Furthermore, as demonstrated by galvanostatic charge–discharge tests and ex situ X-ray absorption near edge structure spectroscopy, the as-prepared zinc ferrite nanocrystals can be used as a high-capacity anode material for Li-ion batteries, showing little capacity fade – after activation – over hundreds of cycles. Overall, in addition to the good material characteristics, it is remarkable that the microwave-based synthetic route is simple, easily reproducible and scalable

Overnight Immune Regulation and Subjective Measures of Sleep: A Three Night Observational Study in Adolescent Track and Field Athletes

To ensure health maintenance of young athletes, immunological stress due to physical exercise has to be balanced for performance development and health maintenance. Sleep is an important influencing factor for immune regulation because of its regenerating effect. In an attempt to assess overnight immune regulation, this observational study aimed to examine associations between changes in capillary immunological blood markers and measures of sleep in adolescent athletes. Over a period of three nights, 12 male ( n = 6) and female ( n = 6) adolescent track and field athletes aged 16.4 ± 1.1 years were monitored for their sleep behavior (e.g., sleep duration, sleep depth) and immune regulation by using subjective (e.g., sleep) and objective (capillary blood markers) measurement tools. Over the 4 day (three nights), athletes followed their daily routines (school, homework, free time activities, and training). Training was performed for different disciplines (sprint, hurdles, and long-jump) following their daily training routines. Training included dynamic core stability training, coordination training, speed training, resistance training, and endurance training. Capillary blood samples were taken 30–45 min after the last training session (10:00–12:00 a.m. or 5:00–6:00 p.m.) and every morning between 7:00 and 10:00 a.m. Changes in capillary blood markers from post-training to the next morning and morning-to-morning fluctuations in capillary blood markers were analyzed over a three-night period using a generalized estimating equations (GEE) statistical approach. Associations of overnight changes with measures of sleep were analyzed using GEE. We found significant decreases in white blood cell count (WBC), granulocytes (GRAN), granulocytes% (GRAN%), monocytes (MID), and granulocyte-lymphocyte-ratio. In contrast, lymphocytes% (LYM%) increased significantly and systemic inflammation index showed no difference from post-training to the next morning. Furthermore, there was a significant decrease in WBC and GRAN between morning 1 and morning 3. At morning 4, values returned to baseline (morning 1), irrespective if athletes performed a training session or rested on day 3. Furthermore, sleep duration was significantly and negatively associated with changes in WBC (β z = −0.491) and lymphocytes (β z = −0.451). Our results indicate that overnight sleep duration is an important parameter of immunological overnight regulation for adolescent athletes

Genome Sequence Analysis of Clostridium chauvoei Strains of European Origin and Evaluation of Typing Options for Outbreak Investigations

Black quarter caused by Clostridium (C.) chauvoei is an important bacterial disease that affects cattle and sheep with high mortality. A comparative genomics analysis of 64 C. chauvoei strains, most of European origin and a few of non-European and unknown origin, was performed. The pangenome analysis showed limited new gene acquisition for the species. The accessory genome involved prophages and genomic islands, with variations in gene composition observed in a few strains. This limited accessory genome may indicate that the species replicates only in the host or that an active CRISPR/Cas system provides immunity to foreign genetic elements. All strains contained a CRISPR type I-B system and it was confirmed that the unique spacer sequences therein can be used to differentiate strains. Homologous recombination events, which may have contributed to the evolution of this pathogen, were less frequent compared to other related species from the genus. Pangenome single nucleotide polymorphism (SNP) based phylogeny and clustering indicate diverse clusters related to geographical origin. Interestingly the identified SNPs were mostly non-synonymous. The study demonstrates the possibility of the existence of polymorphic populations in one host, based on strain variability observed for strains from the same animal and strains from different animals of one outbreak. The study also demonstrates that new outbreak strains are mostly related to earlier outbreak strains from the same farm/region. This indicates the last common ancestor strain from one farm can be crucial to understand the genetic changes and epidemiology occurring at farm level. Known virulence factors for the species were highly conserved among the strains. Genetic elements involved in Nicotinamide adenine dinucleotide (NAD) precursor synthesis (via nadA, nadB, and nadC metabolic pathway) which are known as potential anti-virulence loci are completely absent in C. chauvoei compared to the partial inactivation in C. septicum. A novel core-genome MLST based typing method was compared to sequence typing based on CRISPR spacers to evaluate the usefulness of the methods for outbreak investigations

Accelerated physical emulation of Bayesian inference in spiking neural networks

The massively parallel nature of biological information processing plays an important role for its superiority to human-engineered computing devices. In particular, it may hold the key to overcoming the von Neumann bottleneck that limits contemporary computer architectures. Physical-model neuromorphic devices seek to replicate not only this inherent parallelism, but also aspects of its microscopic dynamics in analog circuits emulating neurons and synapses. However, these machines require network models that are not only adept at solving particular tasks, but that can also cope with the inherent imperfections of analog substrates. We present a spiking network model that performs Bayesian inference through sampling on the BrainScaleS neuromorphic platform, where we use it for generative and discriminative computations on visual data. By illustrating its functionality on this platform, we implicitly demonstrate its robustness to various substrate-specific distortive effects, as well as its accelerated capability for computation. These results showcase the advantages of brain-inspired physical computation and provide important building blocks for large-scale neuromorphic applications.Comment: This preprint has been published 2019 November 14. Please cite as: Kungl A. F. et al. (2019) Accelerated Physical Emulation of Bayesian Inference in Spiking Neural Networks. Front. Neurosci. 13:1201. doi: 10.3389/fnins.2019.0120

Functional treatment for fractures to the base of the 5th metatarsal - influence of fracture location and fracture characteristics

Background: Fractures to the base of the fifth metatarsal are common, but their treatment remains controversial. Especially for Lawrence and Botte (L&B) type II fractures, there is conflicting evidence and consequently no consensus. Further, many authors consider displacement, articular involvement, and number of fragments an indication for surgery, although evidence is missing. The aim of this study was to evaluate the outcome of functional treatment for all L&B type I and II fractures. Of special interest were the influence of (1) the fracture location (L&B type I vs. II) and (2) the fracture characteristics (displacement, intra-articular involvement, communition) on the subjective outcome. Methods: Retrospective registry study with a prospective follow-up. Patients with an acute, isolated, epi-metaphyseal fracture to the fifth metatarsal bone (L&B type I and II) treated by full weightbearing with a minimum follow-up of 6 months were included. Fracture location (L&B type I and II) and characteristics (displacement 2 mm, intra-articular involvement, and number of fragments) were assessed. Outcome parameters were return to work, return to sports, VAS-FA, and SF-12. The influence of the fracture (1) location and (2) -characteristics on these parameters was tested. Results: Thirty-nine patients (40 +/- 15 years, 56% female) were enrolled with a mean follow-up of 22 +/- 10 months. L&B type I fractures occurred in 59%, type II in 41%. Thirty-one percent of all fractures were dislocated, 74% intra-articular, and 41% multi-fragmentary. Patients returned to work after 17 +/- 12 days, to sports after 53 +/- 22 days. The VAS-FA score at the final follow-up was 96 +/- 4, SF-12 PCS score 57 +/- 5 and MCS score 51 +/- 8. No complications were reported, no patient required surgery. None of the assessed outcome parameters differed significantly between (1) the different fracture locations (L&B type I vs. II) or (2) the different fracture characteristics (displacement, intra-articular involvement, and number of fragments). Conclusions: (1) Both, L&B I and II fractures featured excellent results with immediate full weightbearing. Consequently, L&B type I and II fractures should be summarized as epi-metaphyseal fractures. (2) Fracture displacement, articular involvement, and number of fragments did not influence the outcome. Therefore, functional treatment should be recommended for all epi-metaphyseal fractures

A Scalable Approach to Modeling on Accelerated Neuromorphic Hardware.

Neuromorphic systems open up opportunities to enlarge the explorative space for computational research. However, it is often challenging to unite efficiency and usability. This work presents the software aspects of this endeavor for the BrainScaleS-2 system, a hybrid accelerated neuromorphic hardware architecture based on physical modeling. We introduce key aspects of the BrainScaleS-2 Operating System: experiment workflow, API layering, software design, and platform operation. We present use cases to discuss and derive requirements for the software and showcase the implementation. The focus lies on novel system and software features such as multi-compartmental neurons, fast re-configuration for hardware-in-the-loop training, applications for the embedded processors, the non-spiking operation mode, interactive platform access, and sustainable hardware/software co-development. Finally, we discuss further developments in terms of hardware scale-up, system usability, and efficiency

Role of thioredoxin reductase 1 and thioredoxin interacting protein in prognosis of breast cancer

Introduction: The purpose of this work was to study the prognostic influence in breast cancer of thioredoxin reductase 1 (TXNRD1) and thioredoxin interacting protein (TXNIP), key players in oxidative stress control that are currently evaluated as possible therapeutic targets. Methods: Analysis of the association of TXNRD1 and TXNIP RNA expression with the metastasis-free interval (MFI) was performed in 788 patients with node-negative breast cancer, consisting of three individual cohorts (Mainz, Rotterdam and Transbig). Correlation with metagenes and conventional clinical parameters (age, pT stage, grading, hormone and ERBB2 status) was explored. MCF-7 cells with a doxycycline-inducible expression of an oncogenic ERBB2 were used to investigate the influence of ERBB2 on TXNRD1 and TXNIP transcription. Results: TXNRD1 was associated with worse MFI in the combined cohort (hazard ratio = 1.955; P < 0.001) as well as in all three individual cohorts. In contrast, TXNIP was associated with better prognosis (hazard ratio = 0.642; P < 0.001) and similar results were obtained in all three subcohorts. Interestingly, patients with ERBB2-status-positive tumors expressed higher levels of TXNRD1. Induction of ERBB2 in MCF-7 cells caused not only an immediate increase in TXNRD1 but also a strong decrease in TXNIP. A subsequent upregulation of TXNIP as cells undergo senescence was accompanied by a strong increase in levels of reactive oxygen species. Conclusions: TXNRD1 and TXNIP are associated with prognosis in breast cancer, and ERBB2 seems to be one of the factors shifting balances of both factors of the redox control system in a prognostic unfavorable manner