Comparison between dedicated MRI and symphyseal fluoroscopic guided contrast agent injection in the diagnosis of cleft sign in athletic groin pain and association with pelvic ring instability.

OBJECTIVE: To compare dedicated MRI with targeted fluoroscopic guided symphyseal contrast agent injection regarding the assessment of symphyseal cleft signs in men with athletic groin pain and assessment of radiographic pelvic ring instability. METHODS: Sixty-six athletic men were prospectively included after an initial clinical examination by an experienced surgeon using a standardized procedure. Diagnostic fluoroscopic symphyseal injection of a contrast agent was performed. Additionally, standing single-leg stance radiography and dedicated 3-Tesla MRI protocol were employed. The presence of cleft injuries (superior, secondary, combined, atypical) and osteitis pubis was recorded. RESULTS: Symphyseal bone marrow edema (BME) was present in 50 patients, bilaterally in 41 patients and in 28 with an asymmetrical distribution. Comparison of MRI and symphysography was as followed: no clefts: 14 cases (MRI) vs. 24 cases (symphysography), isolated superior cleft sign: 13 vs. 10, isolated secondary cleft sign: 15 vs. 21 cases and combined injuries: 18 vs. 11 cases. In 7 cases a combined cleft sign was observed in MRI but only an isolated secondary cleft sign was visible in symphysography. Anterior pelvic ring instability was observed in 25 patients and was linked to a cleft sign in 23 cases (7 superior cleft sign, 8 secondary cleft signs, 6 combined clefts, 2 atypical cleft injuries). Additional BME could be diagnosed in 18 of those 23. CONCLUSION: Dedicated 3-Tesla MRI outmatches symphysography for purely diagnostic purposes of cleft injuries. Microtearing at the prepubic aponeurotic complex and the presence of BME is a prerequisite for the development of anterior pelvic ring instability. CLINICAL RELEVANCE STATEMENT: For diagnostic of symphyseal cleft injuries dedicated 3-T MRI protocols outmatch fluoroscopic symphysography. Prior specific clinical examination is highly beneficial and additional flamingo view x-rays are recommended for assessment of pelvic ring instability in these patients. KEY POINTS: • Assessment of symphyseal cleft injuries is more accurate by use of dedicated MRI as compared to fluoroscopic symphysography. • Additional fluoroscopy may be important for therapeutic injections. • The presence of cleft injury might be a prerequisite for the development of pelvic ring instability.

Genome-wide Association and Meta-analysis of Age at Onset in Parkinson Disease: Evidence From the COURAGE-PD Consortium.

BACKGROUND AND OBJECTIVES: Considerable heterogeneity exists in the literature concerning genetic determinants of the age at onset (AAO) of Parkinson disease (PD), which could be attributed to a lack of well-powered replication cohorts. The previous largest genome-wide association studies (GWAS) identified SNCA and TMEM175 loci on chromosome (Chr) 4 with a significant influence on the AAO of PD; these have not been independently replicated. This study aims to conduct a meta-analysis of GWAS of PD AAO and validate previously observed findings in worldwide populations. METHODS: A meta-analysis was performed on PD AAO GWAS of 30 populations of predominantly European ancestry from the Comprehensive Unbiased Risk Factor Assessment for Genetics and Environment in Parkinson's Disease (COURAGE-PD) Consortium. This was followed by combining our study with the largest publicly available European ancestry dataset compiled by the International Parkinson Disease Genomics Consortium (IPDGC). RESULTS: The COURAGE-PD Consortium included a cohort of 8,535 patients with PD (91.9%: Europeans and 9.1%: East Asians). The average AAO in the COURAGE-PD dataset was 58.9 years (SD = 11.6), with an underrepresentation of females (40.2%). The heritability estimate for AAO in COURAGE-PD was 0.083 (SE = 0.057). None of the loci reached genome-wide significance (p < 5 × 10-8). Nevertheless, the COURAGE-PD dataset confirmed the role of the previously published TMEM175 variant as a genetic determinant of the AAO of PD with Bonferroni-corrected nominal levels of significance (p < 0.025): (rs34311866: ß(SE)COURAGE = 0.477(0.203), p COURAGE = 0.0185). The subsequent meta-analysis of COURAGE-PD and IPDGC datasets (Ntotal = 25,950) led to the identification of 2 genome-wide significant association signals on Chr 4, including the previously reported SNCA locus (rs983361: ß(SE)COURAGE+IPDGC = 0.720(0.122), p COURAGE+IPDGC = 3.13 × 10-9) and a novel BST1 locus (rs4698412: ß(SE)COURAGE+IPDGC = -0.526(0.096), p COURAGE+IPDGC = 4.41 × 10-8). DISCUSSION: Our study further refines the genetic architecture of Chr 4 underlying the AAO of the PD phenotype through the identification of BST1 as a novel AAO PD locus. These findings open a new direction for the development of treatments to delay the onset of PD.

A Multi-Modular System for the Visualization and Classification of MER Data During Neurostimulation Procedures.

This paper proposes an interactive analysis and visualization tool for the accuracy improvement of electrode placement during neurostimulation therapy surgery. During the procedure, the presented system assists the surgeon in the crucial tissue type detection by providing a fused visualization of the current electrode location and the microelectrode recordings (MER). The system processes the MER in real-time and utilizes a convolutional neural network (CNN) to classify the targeted tissue type. In addition to presenting the MER in its raw waveform, the system also offers the visualization of the frequency domain and the result of the neural network. To further assist the decision-making process, additional visualization methods are integrated into the system. Using the pre-operative taken CT and MRI scans, the system offers 3D visualization in the form of direct volume rendering (DVR) and axis-aligned slice views in 2D. Both domains are enriched by the MER readings and the result of the machine learning classifier.

Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources.

The large amount of biological data available in the current times, makes it necessary to use tools and applications based on sophisticated and efficient algorithms, developed in the area of bioinformatics. Further, access to high performance computing resources is necessary, to achieve results in reasonable time. To speed up applications and utilize available compute resources as efficient as possible, software developers make use of parallelization mechanisms, like multithreading. Many of the available tools in bioinformatics offer multithreading capabilities, but more compute power is not always helpful. In this study we investigated the behavior of well-known applications in bioinformatics, regarding their performance in the terms of scaling, different virtual environments and different datasets with our benchmarking tool suite BOOTABLE. The tool suite includes the tools BBMap, Bowtie2, BWA, Velvet, IDBA, SPAdes, Clustal Omega, MAFFT, SINA and GROMACS. In addition we added an application using the machine learning framework TensorFlow. Machine learning is not directly part of bioinformatics but applied to many biological problems, especially in the context of medical images (X-ray photographs). The mentioned tools have been analyzed in two different virtual environments, a virtual machine environment based on the OpenStack cloud software and in a Docker environment. The gained performance values were compared to a bare-metal setup and among each other. The study reveals, that the used virtual environments produce an overhead in the range of seven to twenty-five percent compared to the bare-metal environment. The scaling measurements showed, that some of the analyzed tools do not benefit from using larger amounts of computing resources, whereas others showed an almost linear scaling behavior. The findings of this study have been generalized as far as possible and should help users to find the best amount of resources for their analysis. Further, the results provide valuable information for resource providers to handle their resources as efficiently as possible and raise the user community's awareness of the efficient usage of computing resources.

A Discrete Probabilistic Approach to Dense Flow Visualization.

Dense flow visualization is a popular visualization paradigm. Traditionally, the various models and methods in this area use a continuous formulation, resting upon the solid foundation of functional analysis. In this work, we examine a discrete formulation of dense flow visualization. From probability theory, we derive a similarity matrix that measures the similarity between different points in the flow domain, leading to the discovery of a whole new class of visualization models. Using this matrix, we propose a novel visualization approach consisting of the computation of spectral embeddings, i.e., characteristic domain maps, defined by particle mixture probabilities. These embeddings are scalar fields that give insight into the mixing processes of the flow on different scales. The approach of spectral embeddings is already well studied in image segmentation, and we see that spectral embeddings are connected to Fourier expansions and frequencies. We showcase the utility of our method using different 2D and 3D flows.

Genetic Architecture of Parkinson's Disease in the Indian Population: Harnessing Genetic Diversity to Address Critical Gaps in Parkinson's Disease Research.

Over the past two decades, our understanding of Parkinson's disease (PD) has been gleaned from the discoveries made in familial and/or sporadic forms of PD in the Caucasian population. The transferability and the clinical utility of genetic discoveries to other ethnically diverse populations are unknown. The Indian population has been under-represented in PD research. The Genetic Architecture of PD in India (GAP-India) project aims to develop one of the largest clinical/genomic bio-bank for PD in India. Specifically, GAP-India project aims to: (1) develop a pan-Indian deeply phenotyped clinical repository of Indian PD patients; (2) perform whole-genome sequencing in 500 PD samples to catalog Indian genetic variability and to develop an Indian PD map for the scientific community; (3) perform a genome-wide association study to identify novel loci for PD and (4) develop a user-friendly web-portal to disseminate results for the scientific community. Our "hub-spoke" model follows an integrative approach to develop a pan-Indian outreach to develop a comprehensive cohort for PD research in India. The alignment of standard operating procedures for recruiting patients and collecting biospecimens with international standards ensures harmonization of data/bio-specimen collection at the beginning and also ensures stringent quality control parameters for sample processing. Data sharing and protection policies follow the guidelines established by local and national authorities.We are currently in the recruitment phase targeting recruitment of 10,200 PD patients and 10,200 healthy volunteers by the end of 2020. GAP-India project after its completion will fill a critical gap that exists in PD research and will contribute a comprehensive genetic catalog of the Indian PD population to identify novel targets for PD.

The Phosphodiesterase Inhibitor IBMX Blocks the Potassium Channel THIK-1 from the Extracellular Side.

The two-pore domain potassium channel (K2P-channel) THIK-1 has several predicted protein kinase A (PKA) phosphorylation sites. In trying to elucidate whether THIK-1 is regulated via PKA, we expressed THIK-1 channels in a mammalian cell line (CHO cells) and used the phosphodiesterase inhibitor 3-isobutyl-1-methyl-xanthine (IBMX) as a pharmacological tool to induce activation of PKA. Using the whole-cell patch-clamp recording, we found that THIK-1 currents were inhibited by application of IBMX with an IC50 of 120 µM. Surprisingly, intracellular application of IBMX or of the second messenger cAMP via the patch pipette had no effect on THIK-1 currents. In contrast, extracellular application of IBMX produced a rapid and reversible inhibition of THIK-1. In patch-clamp experiments with outside-out patches, THIK-1 currents were also inhibited by extracellular application of IBMX. Expression of THIK-1 channels in Xenopus oocytes was used to compare wild-type channels with mutated channels. Mutation of the putative PKA phosphorylation sites did not change the inhibitory effect of IBMX on THIK-1 currents. Mutational analysis of all residues of the (extracellular) helical cap of THIK-1 showed that mutation of the arginine residue at position 92, which is in the linker between cap helix 2 and pore helix 1, markedly reduced the inhibitory effect of IBMX. This flexible linker region, which is unique for each K2P-channel subtype, may be a possible target of channel-specific blockers. SIGNIFICANCE STATEMENT: The potassium channel THIK-1 is strongly expressed in the central nervous system. We studied the effect of 3-isobutyl-1-methyl-xanthine (IBMX) on THIK-1 currents. IBMX inhibits breakdown of cAMP and thus activates protein kinase A (PKA). Surprisingly, THIK-1 current was inhibited when IBMX was applied from the extracellular side of the membrane, but not from the intracellular side. Our results suggest that IBMX binds directly to the channel and that the inhibition of THIK-1 current was not related to activation of PKA.

[Diagnostic algorithm "FAI and sports hernia" : Results of the consensus meeting for groin pain in athletes]. / Diagnostik-Algorithmus Grenzbereich "FAI und Sportlerleiste" : Ergebnisse des Konsensustreffens Leistenschmerz beim Sportler.

As a result of the complexity and diversity of diseases in the region of the groin, differentiation of the various soft-tissue and bone pathologies remains a challenge for differential diagnosis in routine clinical practice. In the case of athletes with pain localized in the area of the groin, femoroacetabular impingement (FAI) and athlete's groin must be considered as important causes of the groin pain, whereby the common occurrence of double pathologies further complicates diagnosis. Despite the importance of groin pain and its differential diagnoses in everyday clinical practice, there has been a lack of recognized recommendations for diagnostic procedure to date. To this end, a consensus meeting was held in February 2017, in which a group composed equally of groin and hip surgeons took part. With the formulation of recommendations and the establishment of a practicable diagnostic path, colleagues that are involved in treating such patients should be sensitized to this issue and the quality of the diagnosis of groin pain improved in routine clinical practice.

Deadeye Visualization Revisited: Investigation of Preattentiveness and Applicability in Virtual Environments.

Visualizations rely on highlighting to attract and guide our attention. To make an object of interest stand out independently from a number of distractors, the underlying visual cue, e.g., color, has to be preattentive. In our prior work, we introduced Deadeye as an instantly recognizable highlighting technique that works by rendering the target object for one eye only. In contrast to prior approaches, Deadeye excels by not modifying any visual properties of the target. However, in the case of 2D visualizations, the method requires an additional setup to allow dichoptic presentation, which is a considerable drawback. As a follow-up to requests from the community, this paper explores Deadeye as a highlighting technique for 3D visualizations, because such stereoscopic scenarios support dichoptic presentation out of the box. Deadeye suppresses binocular disparities for the target object, so we cannot assume the applicability of our technique as a given fact. With this motivation, the paper presents quantitative evaluations of Deadeye in VR, including configurations with multiple heterogeneous distractors as an important robustness challenge. After confirming the preserved preattentiveness (all average accuracies above 90%) under such real-world conditions, we explore VR volume rendering as an example application scenario for Deadeye. We depict a possible workflow for integrating our technique, conduct an exploratory survey to demonstrate benefits and limitations, and finally provide related design implications.

de.NBI Cloud federation through ELIXIR AAI.

The academic de.NBI Cloud offers compute resources for life science research in Germany.  At the beginning of 2017, de.NBI Cloud started to implement a federated cloud consisting of five compute centers, with the aim of acting as one resource to their users. A federated cloud introduces multiple challenges, such as a central access and project management point, a unified account across all cloud sites and an interchangeable project setup across the federation. In order to implement the federation concept, de.NBI Cloud integrated with the ELIXIR authentication and authorization infrastructure system (ELIXIR AAI) and in particular Perun, the identity and access management system of ELIXIR. The integration solves the mentioned challenges and represents a backbone, connecting five compute centers which are based on OpenStack and a web portal for accessing the federation.This article explains the steps taken and software components implemented for setting up a federated cloud based on the collaboration between de.NBI Cloud and ELIXIR AAI. Furthermore, the setup and components that are described are generic and can therefore be used for other upcoming or existing federated OpenStack clouds in Europe.

Deadeye: A Novel Preattentive Visualization Technique Based on Dichoptic Presentation.

Preattentive visual features such as hue or flickering can effectively draw attention to an object of interest - for instance, an important feature in a scientific visualization. These features appear to pop out and can be recognized by our visual system, independently from the number of distractors. Most cues do not take advantage of the fact that most humans have two eyes. In cases where binocular vision is applied, it is almost exclusively used to convey depth by exposing stereo pairs. We present Deadeye, a novel preattentive visualization technique based on presenting different stimuli to each eye. The target object is rendered for one eye only and is instantly detected by our visual system. In contrast to existing cues, Deadeye does not modify any visual properties of the target and, thus, is particularly suited for visualization applications. Our evaluation confirms that Deadeye is indeed perceived preattentively. We also explore a conjunction search based on our technique and show that, in contrast to 3D depth, the task cannot be processed in parallel.

TPC2 polymorphisms associated with a hair pigmentation phenotype in humans result in gain of channel function by independent mechanisms.

Two-pore channels (TPCs) are endolysosomal cation channels. Two members exist in humans, TPC1 and TPC2. Functional roles associated with the ubiquitously expressed TPCs include VEGF-induced neoangiogenesis, LDL-cholesterol trafficking and degradation, physical endurance under fasting conditions, autophagy regulation, the acrosome reaction in sperm, cancer cell migration, and intracellular trafficking of pathogens such as Ebola virus or bacterial toxins (e.g., cholera toxin). In a genome-wide association study for variants associated with human pigmentation characteristics two coding variants of TPC2, rs35264875 (encoding M484L) and rs3829241 (encoding G734E), have been found to be associated with a shift from brown to blond hair color. In two recent follow-up studies a role for TPC2 in pigmentation has been further confirmed. However, these human polymorphic variants have not been functionally characterized until now. The development of endolysosomal patch-clamp techniques has made it possible to investigate directly ion channel activities and characteristics in isolated endolysosomal organelles. We applied this technique here to scrutinize channel characteristics of the polymorphic TPC2 variants in direct comparison with WT. We found that both polymorphisms lead to a gain of channel function by independent mechanisms. We next conducted a clinical study with more than 100 blond- and brown/black-haired individuals. We performed a genotype/phenotype analysis and subsequently isolated fibroblasts from WT and polymorphic variant carriers for endolysosomal patch-clamp experimentation to confirm key in vitro findings.

Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry.

BACKGROUND: In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. These workflows are executed on computing infrastructures and may require large computing and data resources. Scientific workflows hide these infrastructures and the resources needed to run them. It requires significant efforts and specific expertise to design, implement and test these workflows. SIGNIFICANCE: Many of these workflows are complex and monolithic entities that can be used for particular scientific experiments. Hence, their modification is not straightforward and it makes almost impossible to share them. To address these issues we propose developing atomic workflows and embedding them in meta-workflows. Atomic workflows deliver a well-defined research domain specific function. Publishing workflows in repositories enables workflow sharing inside and/or among scientific communities. We formally specify atomic and meta-workflows in order to define data structures to be used in repositories for uploading and sharing them. Additionally, we present a formal description focused at orchestration of atomic workflows into meta-workflows. CONCLUSIONS: We investigated the operations that represent basic functionalities in Quantum Chemistry, developed the relevant atomic workflows and combined them into meta-workflows. Having these workflows we defined the structure of the Quantum Chemistry workflow library and uploaded these workflows in the SHIWA Workflow Repository.Graphical AbstractMeta-workflows and embedded workflows in the template representation.

Portals and Web-Based Resources for Virtual Screening.

Virtual screening for active compounds has become an essential step within the drug development pipeline. The computer based prediction of compound binding modes is one of the most time and cost efficient methods for screening ligand libraries and enrich results of potential drugs. Here we present an overview about currently available online resources regarding compound databases, docking applications, and science gateways for drug discovery and virtual screening, in order to help structural biologists in choosing the best tools for their analysis. The appearance of the user interface, authentication and security aspects, data management, and computational performance will be discussed. We anticipate a broad overview about currently available solutions, guiding computational chemists and users from related fields towards scientifically reliable results.

DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats.

Transcription Activator-Like Effectors (TALEs) of Xanthomonas bacteria are programmable DNA binding proteins with unprecedented target specificity. Comparative studies into TALE repeat structure and function are hindered by the limited sequence variation among TALE repeats. More sequence-diverse TALE-like proteins are known from Ralstonia solanacearum (RipTALs) and Burkholderia rhizoxinica (Bats), but RipTAL and Bat repeats are conserved with those of TALEs around the DNA-binding residue. We study two novel marine-organism TALE-like proteins (MOrTL1 and MOrTL2), the first to date of non-terrestrial origin. We have assessed their DNA-binding properties and modelled repeat structures. We found that repeats from these proteins mediate sequence specific DNA binding conforming to the TALE code, despite low sequence similarity to TALE repeats, and with novel residues around the BSR. However, MOrTL1 repeats show greater sequence discriminating power than MOrTL2 repeats. Sequence alignments show that there are only three residues conserved between repeats of all TALE-like proteins including the two new additions. This conserved motif could prove useful as an identifier for future TALE-likes. Additionally, comparing MOrTL repeats with those of other TALE-likes suggests a common evolutionary origin for the TALEs, RipTALs and Bats.

ballaxy: web services for structural bioinformatics.

MOTIVATION: Web-based workflow systems have gained considerable momentum in sequence-oriented bioinformatics. In structural bioinformatics, however, such systems are still relatively rare; while commercial stand-alone workflow applications are common in the pharmaceutical industry, academic researchers often still rely on command-line scripting to glue individual tools together. RESULTS: In this work, we address the problem of building a web-based system for workflows in structural bioinformatics. For the underlying molecular modelling engine, we opted for the BALL framework because of its extensive and well-tested functionality in the field of structural bioinformatics. The large number of molecular data structures and algorithms implemented in BALL allows for elegant and sophisticated development of new approaches in the field. We hence connected the versatile BALL library and its visualization and editing front end BALLView with the Galaxy workflow framework. The result, which we call ballaxy, enables the user to simply and intuitively create sophisticated pipelines for applications in structure-based computational biology, integrated into a standard tool for molecular modelling. AVAILABILITY AND IMPLEMENTATION: ballaxy consists of three parts: some minor modifications to the Galaxy system, a collection of tools and an integration into the BALL framework and the BALLView application for molecular modelling. Modifications to Galaxy will be submitted to the Galaxy project, and the BALL and BALLView integrations will be integrated in the next major BALL release. After acceptance of the modifications into the Galaxy project, we will publish all ballaxy tools via the Galaxy toolshed. In the meantime, all three components are available from http://www.ball-project.org/ballaxy. Also, docker images for ballaxy are available at https://registry.hub.docker.com/u/anhi/ballaxy/dockerfile/. ballaxy is licensed under the terms of the GPL.

Activation of lymphoma-associated MyD88 mutations via allostery-induced TIR-domain oligomerization.

Myeloid differentiation 88 (MyD88) is the key signaling adapter of Toll-like and interleukin-1 receptors. Recurrent lymphoma-associated mutations, particularly Leu265Pro (L265P), within the MyD88 Toll/interleukin-1 receptor (TIR) domain sustain lymphoma cell survival due to constitutive nuclear factor κB signaling. We found that mutated TIR domains displayed an intrinsic propensity for augmented oligomerization and spontaneous formation of cytosolic Myddosome aggregates in lymphoma cell lines, mimicking the effect of dimerized TIR domains. Blocking of MyD88 oligomerization induced apoptosis. The L265P TIR domain can recruit the endogenous wild-type MyD88 for oligomer formation and hyperactivity. Molecular dynamics simulations and analysis of additional mutations suggest that constitutive activity is caused by allosteric oligomerization.

Hybrid Rendering with Scheduling under Uncertainty.

As scientific data of increasing size is generated by today's simulations and measurements, utilizing dedicated server resources to process the visualization pipeline becomes necessary. In a purely server-based approach, requirements on the client-side are minimal as the client only displays results received from the server. However, the client may have a considerable amount of hardware available, which is left idle. Further, the visualization is put at the whim of possibly unreliable server and network conditions. Server load, bandwidth and latency may substantially affect the response time on the client. In this paper, we describe a hybrid method, where visualization workload is assigned to server and client. A capable client can produce images independently. The goal is to determine a workload schedule that enables a synergy between the two sides to provide rendering results to the user as fast as possible. The schedule is determined based on processing and transfer timings obtained at runtime. Our probabilistic scheduler adapts to changing conditions by shifting workload between server and client, and accounts for the performance variability in the dynamic system.

Performance studies on distributed virtual screening.

Virtual high-throughput screening (vHTS) is an invaluable method in modern drug discovery. It permits screening large datasets or databases of chemical structures for those structures binding possibly to a drug target. Virtual screening is typically performed by docking code, which often runs sequentially. Processing of huge vHTS datasets can be parallelized by chunking the data because individual docking runs are independent of each other. The goal of this work is to find an optimal splitting maximizing the speedup while considering overhead and available cores on Distributed Computing Infrastructures (DCIs). We have conducted thorough performance studies accounting not only for the runtime of the docking itself, but also for structure preparation. Performance studies were conducted via the workflow-enabled science gateway MoSGrid (Molecular Simulation Grid). As input we used benchmark datasets for protein kinases. Our performance studies show that docking workflows can be made to scale almost linearly up to 500 concurrent processes distributed even over large DCIs, thus accelerating vHTS campaigns significantly.