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Abstract Background Traditional methods for computational motif discovery often suffer from poor performance. In particular, methods that search for sequence matches to known binding motifs tend to predict many non-functional binding sites because they fail to take into consideration the biological state of the cell. In recent years, genome-wide studies have generated a lot of data that has the potential to improve our ability to identify functional motifs and binding sites, such as information about chromatin accessibility and epigenetic states in different cell types. However, it is not always trivial to make use of this data in combination with existing motif discovery tools, especially for researchers who are not skilled in bioinformatics programming. Results Here we present MotifLab, a general workbench for analysing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. MotifLab supports comprehensive motif discovery and analysis by allowing users to integrate several popular motif discovery tools as well as different kinds of additional information, including phylogenetic conservation, epigenetic marks, DNase hypersensitive sites, ChIP-Seq data, positional binding preferences of transcription factors, transcription factor interactions and gene expression. MotifLab offers several data-processing operations that can be used to create, manipulate and analyse data objects, and complete analysis workflows can be constructed and automatically executed within MotifLab, including graphical presentation of the results. Conclusions We have developed MotifLab as a flexible workbench for motif analysis in a genomic context. The flexibility and effectiveness of this workbench has been demonstrated on selected test cases, in particular two previously published benchmark data sets for single motifs and modules, and a realistic example of genes responding to treatment with forskolin. MotifLab is freely available at http://www.motiflab.org.

Abstract Background Computational discovery of regulatory elements is an important area of bioinformatics research and more than a hundred motif discovery methods have been published. Traditionally, most of these methods have addressed the problem of single motif discovery – discovering binding motifs for individual transcription factors. In higher organisms, however, transcription factors usually act in combination with nearby bound factors to induce specific regulatory behaviours. Hence, recent focus has shifted from single motifs to the discovery of sets of motifs bound by multiple cooperating transcription factors, so called composite motifs or cis-regulatory modules. Given the large number and diversity of methods available, independent assessment of methods becomes important. Although there have been several benchmark studies of single motif discovery, no similar studies have previously been conducted concerning composite motif discovery. Results We have developed a benchmarking framework for composite motif discovery and used it to evaluate the performance of eight published module discovery tools. Benchmark datasets were constructed based on real genomic sequences containing experimentally verified regulatory modules, and the module discovery programs were asked to predict both the locations of these modules and to specify the single motifs involved. To aid the programs in their search, we provided position weight matrices corresponding to the binding motifs of the transcription factors involved. In addition, selections of decoy matrices were mixed with the genuine matrices on one dataset to test the response of programs to varying levels of noise. Conclusion Although some of the methods tested tended to score somewhat better than others overall, there were still large variations between individual datasets and no single method performed consistently better than the rest in all situations. The variation in performance on individual datasets also shows that the new benchmark datasets represents a suitable variety of challenges to most methods for module discovery.

Objective: We aim to describe use of electroconvulsive therapy (ECT) to treat super refractory status epilepticus (SRSE) in pregnancy and review the literature regarding utility and safety of ECT in refractory status epilepticus., Background: Status epilepticus (SE) is a commonly encountered emergency in neuro-critical care world. Pharmacotherapy of status epilepticus in pregnancy is very challenging given the effect of the majority of antiepileptic drugs (AEDs) on fetal development. Although there has been growing evidence for use of ECT in status epilepticus, data about its utility in pregnancy is lacking., Design/method: A twenty-one year old Caucasian female with history of epilepsy presented at 8 weeks of gestation as status epilepticus (SE) after abrupt discontinuation of her AEDs. Treatment was initiated with standard regimen of benzodiazepine and levetiracetam, which was progressively expanded to include approximately 10 anti-epileptic drugs over the course of 30 days. The status epilepticus was super refractory to sedation. She underwent ECT on day 31 with remarkable improvement in electroencephalogram (EEG) pattern and resolution of status epilepticus following a single ECT session. We reviewed PubMed and collated case reports involving the use of ECT in status epilepticus with emphasis on differences in various confounding factors esp. etiology of status and age group., Conclusion: Our case is the first reported case of ECT for successful treatment of SRSE in pregnancy. While majority AEDs pose a significant maternal and fetal risk during pregnancy, ECT could be a potential frontline therapy for SE in pregnancy.

Introduction With the number of COVID cases in children increasing, the variation in presentation seen in pediatric patients compared with adults has become more apparent. The typical adult presentation of COVID-19 infection, generally associated with acute respiratory symptoms, seems to differ from that seen in children, many of whom are initially asymptomatic. Case Presentation In this case, a previously healthy female adolescent presented with insidious onset nausea and weight loss, but a broad gastrointestinal workup was unrevealing. The delayed development of vertiginous symptoms later led to the identification of prior, asymptomatic COVID-19 infection as the suspected etiology of her presenting gastrointestinal symptoms. Conclusion This case highlights the notion that COVID-19 infection in children may have a delayed manifestation in the absence of acute respiratory systems. Given this, COVID should be included in the differential diagnosis early on in an effort to limit the risks and costs associated with broad, unrevealing workups.

Background: Facial baroparesis is a palsy of the seventh cranial nerve resulting from increased pressure compressing the nerve along its course through the middle ear cavity. It is a rare condition, most commonly reported in barotraumatic environments, in particular scuba diving and high-altitude air travel. We report here an unusual case of highly frequent baroparesis, workup, and successful treatment., Case Presentation: A 57-year-old Caucasian male frequent commercial airline traveler presented with a 4-year history of recurrent episodes of right-sided facial paralysis and otalgia, increasing in both frequency and severity. Incidents occurred almost exclusively during rapid altitude changes in aircraft, mostly ascent, but also during rapid altitude change in an automobile. Self-treatment included nasal and oral decongestants, nasal corticosteroids, and warm packs. Temporal bone computed tomography (CT) scan revealed possible right-sided dehiscence of the tympanic bone segment; audiogram and magnetic resonance imaging of the internal auditory canals were unremarkable. After a diagnosis of facial nerve baroparesis was made, the patient underwent myringotomy with insertion of a pressure equalization tube (PET) into the right tympanic membrane. Despite re-exposure to altitude change multiple times weekly post-treatment, the patient reported being symptom-free for more than 6 months following intervention., Conclusions: Prompt PET insertion may represent the preferred treatment for individuals who suffer recurrent episodes of facial baroparesis. Education regarding this rare condition may prevent unnecessary testing and treatment of affected patients. Future studies should explore the pathophysiology and risk factors, compare therapeutic options, and provide follow-up data to optimize the management of affected patients.

Background: Common colorectal procedures that require access to all quadrants of the abdomen are subtotal colectomy (STC) and total proctocolectomy (TPC). These are frequently performed with a surgical robot, but multiquadrant operations have unique challenges during robot-assisted surgery., Methods: Patients who underwent robotic STC or TPC with the da Vinci Xi surgical robot at our institution from July 1, 2016 through June 30, 2019 were identified by diagnosis and procedure codes. A technical description is provided for the techniques utilized at our institution. Outcomes included operative times (OT), supply cost and length of stay. Associated morbidity and mortality was also analyzed., Results: From a review of our institution's robotic surgery data, 37 cases were identified that utilized the described technique. Of these cases, 21 were robotic STC and 16 were TPC. Total mean OT was 276.86 min (SD ± 119.49). Mean OT was further analyzed by year, which demonstrated an overall decrease in OT from 350.91 min (SD ± 46.38) in 2016 to 221.43 min (SD ± 16.46) in 2018 (p = 0.008). A total of 21 cases were performed prior to 2018. Overall OT for STC was 222.81 min (SD ± 14.54) compared to overall TPC OT 347.81 min (SD ± 34.35). Median length of stay was 5 days [25th and 75th percentiles 4, 6, respectively]. There was no 30-day mortality and only one return to operating room for mesenteric bleeding. There was a low risk of mortality associated with this technique., Conclusions: The current study provides the largest cohort of patients assessed who have undergone multiquadrant robotic STC or TPC. The study provides a detailed description of the technique utilized at our institution. There was no associated 30-day mortality and a low risk of morbidity. The data suggest that the learning curve for improved operative time is between 15 and 20 cases.

The pathophysiology of age-related hearing loss (ARHL), or presbycusis, involves a complex interplay between environmental and genetic factors. The fundamental biomolecular mechanisms of ARHL have been well described, including the roles of membrane transport, reactive oxygen species, cochlear synaptopathy, vascular insults, hormones, and microRNA, to name a few. The genetic basis underlying these mechanisms remains under-investigated and poorly understood. The emergence of genome-wide association studies has allowed for the identification of specific groups of genes involved in ARHL. This review highlights recent advances in understanding of the pathogenesis of ARHL, the genetic basis underlying these processes and suggests future directions for research and potential therapeutic avenues., (© 2019 Wiley Periodicals, Inc.)

The Norwegian e-Infrastructure for Life Sciences (NeLS) has been developed by ELIXIR Norway to provide its users with a system enabling data storage, sharing, and analysis in a project-oriented fashion. The system is available through easy-to-use web interfaces, including the Galaxy workbench for data analysis and workflow execution. Users confident with a command-line interface and programming may also access it through Secure Shell (SSH) and application programming interfaces (APIs).  NeLS has been in production since 2015, with training and support provided by the help desk of ELIXIR Norway. Through collaboration with NorSeq, the national consortium for high-throughput sequencing, an integrated service is offered so that sequencing data generated in a research project is provided to the involved researchers through NeLS. Sensitive data, such as individual genomic sequencing data, are handled using the TSD (Services for Sensitive Data) platform provided by Sigma2 and the University of Oslo. NeLS integrates national e-infrastructure storage and computing resources, and is also integrated with the SEEK platform in order to store large data files produced by experiments described in SEEK.   In this article, we outline the architecture of NeLS and discuss possible directions for further development., Competing Interests: No competing interests were disclosed.

We developed a systematic approach to map human genetic networks by combinatorial CRISPR-Cas9 perturbations coupled to robust analysis of growth kinetics. We targeted all pairs of 73 cancer genes with dual guide RNAs in three cell lines, comprising 141,912 tests of interaction. Numerous therapeutically relevant interactions were identified, and these patterns replicated with combinatorial drugs at 75% precision. From these results, we anticipate that cellular context will be critical to synthetic-lethal therapies.

An emerging therapeutic strategy for cancer is to induce selective lethality in a tumor by exploiting interactions between its driving mutations and specific drug targets. Here we use a multi-species approach to develop a resource of synthetic lethal interactions relevant to cancer therapy. First, we screen in yeast ∼169,000 potential interactions among orthologs of human tumor suppressor genes (TSG) and genes encoding drug targets across multiple genotoxic environments. Guided by the strongest signal, we evaluate thousands of TSG-drug combinations in HeLa cells, resulting in networks of conserved synthetic lethal interactions. Analysis of these networks reveals that interaction stability across environments and shared gene function increase the likelihood of observing an interaction in human cancer cells. Using these rules, we prioritize ∼10(5) human TSG-drug combinations for future follow-up. We validate interactions based on cell and/or patient survival, including topoisomerases with RAD17 and checkpoint kinases with BLM., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Chemical inhibitors of the checkpoint kinases have shown promise in the treatment of cancer, yet their clinical utility may be limited by a lack of molecular biomarkers to identify specific patients most likely to respond to therapy. To this end, we screened 112 known tumor suppressor genes for synthetic lethal interactions with inhibitors of the CHEK1 and CHEK2 checkpoint kinases. We identified eight interactions, including the Replication Factor C (RFC)-related protein RAD17. Clonogenic assays in RAD17 knockdown cell lines identified a substantial shift in sensitivity to checkpoint kinase inhibition (3.5-fold) as compared to RAD17 wild-type. Additional evidence for this interaction was found in a large-scale functional shRNA screen of over 100 genotyped cancer cell lines, in which CHEK1/2 mutant cell lines were unexpectedly sensitive to RAD17 knockdown. This interaction was widely conserved, as we found that RAD17 interacts strongly with checkpoint kinases in the budding yeast Saccharomyces cerevisiae. In the setting of RAD17 knockdown, CHEK1/2 inhibition was found to be synergistic with inhibition of WEE1, another pharmacologically relevant checkpoint kinase. Accumulation of the DNA damage marker γH2AX following chemical inhibition or transient knockdown of CHEK1, CHEK2 or WEE1 was magnified by knockdown of RAD17. Taken together, our data suggest that CHEK1 or WEE1 inhibitors are likely to have greater clinical efficacy in tumors with RAD17 loss-of-function.

Strict control of tissue-specific gene expression plays a pivotal role during lineage commitment. The transcription factor c-Myb has an essential role in adult haematopoiesis and functions as an oncogene when rearranged in human cancers. Here we have exploited digital genomic footprinting analysis to obtain a global picture of c-Myb occupancy in the genome of six different haematopoietic cell-types. We have biologically validated several c-Myb footprints using c-Myb knockdown data, reporter assays and DamID analysis. We show that our predicted conserved c-Myb footprints are highly dependent on the haematopoietic cell type, but that there is a group of gene targets common to all cell-types analysed. Furthermore, we find that c-Myb footprints co-localise with active histone mark H3K4me3 and are significantly enriched at exons. We analysed co-localisation of c-Myb footprints with 104 chromatin regulatory factors in K562 cells, and identified nine proteins that are enriched together with c-Myb footprints on genes positively regulated by c-Myb and one protein enriched on negatively regulated genes. Our data suggest that c-Myb is a transcription factor with multifaceted target regulation depending on cell type.

Background: Preeclampsia is a serious pregnancy complication, demonstrating a complex pattern of inheritance. The elucidation of genetic liability to preeclampsia remains a major challenge in obstetric medicine. We have adopted a positional cloning approach to identify maternal genetic components, with linkages previously demonstrated to chromosomes 2q, 5q and 13q in an Australian/New Zealand familial cohort. The current study aimed to identify potential functional and structural variants in the positional candidate gene TNFSF13B under the 13q linkage peak and assess their association status with maternal preeclampsia genetic susceptibility., Methodology/principal Findings: The proximal promoter and coding regions of the positional candidate gene TNFSF13B residing within the 13q linkage region was sequenced using 48 proband or founder individuals from Australian/New Zealand families. Ten sequence variants (nine SNPs and one single base insertion) were identified and seven SNPs were successfully genotyped in the total Australian/New Zealand family cohort (74 families/480 individuals). Borderline association to preeclampsia (p = 0.0153) was observed for three rare SNPs (rs16972194, rs16972197 and rs56124946) in strong linkage disequilibrium with each other. Functional evaluation by electrophoretic mobility shift assays showed differential nuclear factor binding to the minor allele of the rs16972194 SNP, residing upstream of the translation start site, making this a putative functional variant. The observed genetic associations were not replicated in a Norwegian case/control cohort (The Nord-Trøndelag Health Study (HUNT2), 851 preeclamptic and 1,440 non-preeclamptic women)., Conclusion/significance: TNFSF13B has previously been suggested to contribute to the normal immunological adaption crucial for a successful pregnancy. Our observations support TNFSF13B as a potential novel preeclampsia susceptibility gene. We discuss a possible role for TNFSF13B in preeclampsia pathogenesis, and propose the rs16972194 variant as a candidate for further functional evaluation.

Summary: Computational methods designed to discover transcription factor binding sites in DNA sequences often have a tendency to make a lot of false predictions. One way to improve accuracy in motif discovery is to rely on positional priors to focus the search to parts of a sequence that are considered more likely to contain functional binding sites. We present here a program called PriorsEditor that can be used to create such positional priors tracks based on a combination of several features, including phylogenetic conservation, nucleosome occupancy, histone modifications, physical properties of the DNA helix and many more., Availability: PriorsEditor is available as a web start application and downloadable archive from http://tare.medisin.ntnu.no/priorseditor (requires Java 1.6). The web site also provides tutorials, screenshots and example protocol scripts.

Thin films of iron cobalt oxides with spinel-type structure are made by the atomic layer deposition (ALD) technique using Fe(thd)3 (Hthd = 2,2,6,6-tetramethylheptane-3,5-dione), Co(thd)2, and ozone as precursors. Pulse parameters for ALD-type growth are established and such growth can be achieved at deposition temperatures between 185 and 310 degrees C. Films have been deposited on amorphous soda-lime glass and single-crystalline substrates of Si(100), MgO(100), and alpha-Al2O3(001) which all provide crystalline films, but with various orientations and crystallite sizes. Application of an external magnetic field during the film growth does not influence film growth characteristics (growth rate, crystallinity, topography etc.). Magnetization data are reported for phase-pure films of spinel-type structure with composition Fe2CoO4.

We have piloted a monthly series of multidisciplinary case discussions via videoconference in the area of child development. The project provided a forum for clinical discussion of complex cases, peer review, professional development and networking for allied health professionals and paediatricians. Six sites in Queensland participated in the project; each site presented at least one case for discussion. The videoconferences ran for 90 min each and were attended by an average of 26 health professionals. The response rate for a questionnaire survey was 71%. The respondents rated the effectiveness of case summaries and the follow-up newsletter very positively. Despite some early difficulties with the technical aspects of videoconferencing, the evaluation demonstrated the participants' satisfaction with the project and its relevance to their everyday practice.