GPflux: A Library for Deep Gaussian Processes

We introduce GPflux, a Python library for Bayesian deep learning with a strong emphasis on deep Gaussian processes (DGPs). Implementing DGPs is a challenging endeavour due to the various mathematical subtleties that arise when dealing with multivariate Gaussian distributions and the complex bookkeeping of indices. To date, there are no actively maintained, open-sourced and extendable libraries available that support research activities in this area. GPflux aims to fill this gap by providing a library with state-of-the-art DGP algorithms, as well as building blocks for implementing novel Bayesian and GP-based hierarchical models and inference schemes. GPflux is compatible with and built on top of the Keras deep learning eco-system. This enables practitioners to leverage tools from the deep learning community for building and training customised Bayesian models, and create hierarchical models that consist of Bayesian and standard neural network layers in a single coherent framework. GPflux relies on GPflow for most of its GP objects and operations, which makes it an efficient, modular and extensible library, while having a lean codebase

Suizid und Internet

The number of people aged 14 and older that use the Internet in Germany has doubled to 35.7 millions (55.3%) since the year 2000. The Internet also more and more expands into the domain of psychiatry and psychotherapy, and is used by psychiatric patients for information, communication and therapeutic purposes. Nevertheless, the infinite possibilities of the World Wide Web are linked with several advantages and disadvantages. Easily accessible information, numerous opportunities for exchange among like-minded people and therapeutic support from online therapies are juxtaposed with such risks as frequently lacking quality and transparency of the available information, possible enhancement of social withdrawal and certain Websites concerning suicide. If the mentioned risks of the Internet rather provoke new problems and trigger suicidality or if the chance of an easily accessible online discussion rather results in mental relief cannot be answered generally

Expanding the set of rhodococcal Baeyer–Villiger monooxygenases by high-throughput cloning, expression and substrate screening

To expand the available set of Baeyer–Villiger monooxygenases (BVMOs), we have created expression constructs for producing 22 Type I BVMOs that are present in the genome of Rhodococcus jostii RHA1. Each BVMO has been probed with a large panel of potential substrates. Except for testing their substrate acceptance, also the enantioselectivity of some selected BVMOs was studied. The results provide insight into the biocatalytic potential of this collection of BVMOs and expand the biocatalytic repertoire known for BVMOs. This study also sheds light on the catalytic capacity of this large set of BVMOs that is present in this specific actinomycete. Furthermore, a comparative sequence analysis revealed a new BVMO-typifying sequence motif. This motif represents a useful tool for effective future genome mining efforts.

Potentially inappropriate medication in older participants of the Berlin Aging Study II (BASE-II) - Sex differences and associations with morbidity and medication use

INTRODUCTION: Multimorbidity in advanced age and the need for drug treatment may lead to polypharmacy, while pharmacokinetic and pharmacodynamic changes may increase the risk of adverse drug events (ADEs). OBJECTIVE: The aim of this study was to determine the proportion of subjects using potentially inappropriate medication (PIM) in a cohort of older and predominantly healthy adults in relation to polypharmacy and morbidity. METHODS: Cross-sectional data were available from 1,382 study participants (median age 69 years, IQR 67-71, 51.3% females) of the Berlin Aging Study II (BASE-II). PIM was classified according to the EU(7)-PIM and German PRISCUS (representing a subset of the former) list. Polypharmacy was defined as the concomitant use of at least five drugs. A morbidity index (MI) largely based on the Charlson Index was applied to evaluate the morbidity burden. RESULTS: Overall, 24.1% of the participants were affected by polypharmacy. On average, men used 2 (IQR 1-4) and women 3 drugs (IQR 1-5). According to PRISCUS and EU(7)-PIM, 5.9% and 22.6% of participants received at least one PIM, while use was significantly more prevalent in females (25.5%) compared to males (19.6%) considering EU(7)-PIM (p = 0.01). In addition, morbidity in males receiving PIM according to EU(7)-PIM was higher (median MI 1, IQR 1-3) compared to males without PIM use (median MI 1, IQR 0-2, p<0.001). CONCLUSION: PIM use occurred more frequently in women than in men, while it was associated with higher morbidity in males. As expected, EU(7)-PIM identifies more subjects as PIM users than the PRISCUS list but further studies are needed to investigate the differential impact of both lists on ADEs and outcome. KEY POINTS: We found PIM use to be associated with a higher number of regular medications and with increased morbidity. Additionally, we detected a higher prevalence of PIM use in females compared to males, suggesting that women and people needing intensive drug treatment are patient groups, who are particularly affected by PIM use

Dose-response model of murine typhus (Rickettsia typhi): time post inoculation and host age dependency analysis

<p>Abstract</p> <p>Background</p> <p><it>Rickettsia typhi (R. mooseri) </it>is the causative agent of murine typhus. It is one of the most widely distributed flea-borne diseases with a relatively mild febrile initial illness with six to 14 days of incubation period. The bacterium is gram negative and an obligate intracellular pathogen. The disease is transmitted to humans and vertebrate host through fleabites or via contact with infected feces. This paper develops dose-response models of different routes of exposure for typhus in rodents.</p> <p>Methods</p> <p>Data from published articles were analyzed using parametric dose-response relationship models. Dose-response relationships were fit to data using the method of maximum likelihood estimation (MLE).</p> <p>Results</p> <p>Dose-response models quantifying the effects of different ages of rats and time post inoculation in BALB/c mice were analyzed in the study. Both the adult rats (inoculated intradermally) and newborn rats (inoculated subcutaneously) were best fit by exponential models and both distributions could be described by a single dose-response relationship. The BALB/C mice inoculated subcutaneously were best fit by Beta-Poisson models. The time post inoculation analysis showed that there was a definite time and response relationship existed in this case.</p> <p>Conclusions</p> <p>Intradermally or subcutaneously inoculated rats (adult and newborn) models suggest that less than 1 plaque-forming unit (PFU) (1.33 to 0.38 in 95% confidence limits) of the pathogen is enough to seroconvert 50% of the exposed population on average. For the BALB/c mouse time post inoculation model, an average dose of 0.28 plaque-forming units (PFU) (0.75 to 0.11 in 95% confidence limits) will seroconvert 50% of the exposed mice.</p

3D laser nano-printing on fibre paves the way for super-focusing of multimode laser radiation

Multimode high-power laser diodes suffer from inefficient beam focusing, leading to a focal spot 10–100 times greater than the diffraction limit. This inevitably restricts their wider use in ‘direct-diode’ applications in materials processing and biomedical photonics. We report here a ‘super-focusing’ characteristic for laser diodes, where the exploitation of self-interference of modes enables a significant reduction of the focal spot size. This is achieved by employing a conical microlens fabricated on the tip of a multimode optical fibre using 3D laser nano-printing (also known as multi-photon lithography). When refracted by the conical surface, the modes of the fibre-coupled laser beam self-interfere and form an elongated narrow focus, usually referred to as a ‘needle’ beam. The multiphoton lithography technique allows the realisation of almost any optical element on a fibre tip, thus providing the most suitable interface for free-space applications of multimode fibre-delivered laser beams. In addition, we demonstrate the optical trapping of microscopic objects with a super-focused multimode laser diode beam thus rising new opportunities within the applications sector where lab-on-chip configurations can be exploited. Most importantly, the demonstrated super-focusing approach opens up new avenues for the ‘direct-diode’ applications in material processing and 3D printing, where both high power and tight focusing is required

Mutations in the latent TGF-beta binding protein 3 (LTBP3) gene cause brachyolmia with amelogenesis imperfecta

Inherited dental malformations constitute a clinically and genetically heterogeneous group of disorders. Here, we report on four families, three of them consanguineous, with an identical phenotype, characterized by significant short stature with brachyolmia and hypoplastic amelogenesis imperfecta (AI) with almost absent enamel. This phenotype was first described in 1996 by Verloes et al. as an autosomal recessive form of brachyolmia associated with AI. Whole-exome sequencing resulted in the identification of recessive hypomorphic mutations including deletion, nonsense and splice mutations, in the LTBP3 gene, which is involved in the TGF-beta signaling pathway. We further investigated gene expression during mouse development and tooth formation. Differentiated ameloblasts synthesizing enamel matrix proteins and odontoblasts expressed the gene. Study of an available knockout mouse model showed that the mutant mice displayed very thin to absent enamel in both incisors and molars, hereby recapitulating the AI phenotype in the human disorder