ResearchPad - notes https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Impact of the COVID-19 Pandemic on HIV Testing and Assisted Partner Notification Services, Western Kenya]]> https://www.researchpad.co/article/elastic_article_16968 <![CDATA[COVID-19 Lockdowns: Impact on Facility-Based HIV Testing and the Case for the Scaling Up of Home-Based Testing Services in Sub-Saharan Africa]]> https://www.researchpad.co/article/elastic_article_16909 <![CDATA[Sellar trough technique for endoscopic endonasal transclival repair]]> https://www.researchpad.co/article/elastic_article_16875 Endoscopic endonasal transclival approaches provide direct access to the ventral skull base allowing the treating of clival and paraclival pathology without the manipulation of the brain or neurovascular structures. Postoperative spinal fluid leak, however, remains a challenge and various techniques have been described to reconstruct the operative defect. The “gasket seal” has been well-described, but has anatomic challenges when applied to clival defects. We describe a modification of this technique for use in endonasal transclival approaches.Methods: Two patients who underwent an endoscopic endonasal transclival approach for tumor resection with an intraoperative spinal fluid leak underwent a modified “gasket seal” closure technique for skull base reconstruction.Results: A 71-year-old woman with a petroclival meningioma and a 22 year old with a clival chordoma underwent endoscopic endonasal transclival resection with the modified repair. No new postoperative deficits occurred and no postoperative spinal fluid leak was seen with a follow-up of 17 and 23 months, respectively.Conclusion: We describe the successful use of a simple, low risk, and technique modification of the “gasket seal” technique adapted to the clivus that allows for hard reconstruction and facilitates placement of the nasoseptal flap. ]]> <![CDATA[Implication of image guidance in endoscopic third ventriculostomy: Technical note]]> https://www.researchpad.co/article/elastic_article_16863 Endoscopic third ventriculostomy (ETV) is an advanced surgical procedure and plays a major role in the management of hydrocephalus. The complications associated with this procedure are grave and unforgiving. Image guidance system (IGS) can help reduce these complications. This technical note describes the technique for utilizing image guidance in carrying out ETV with safety and efficacy.Methods: The authors have performed ETV on more than 75 cases. We describe a step-by-step technique for the implication of image guidance while performing ETV including the trajectory planning, coregistration, approach, and third ventricular floor perforation. For illustration, we present the case of a 54-year-old female with moderate-intensity headache and central vertigo for 2 months presented with no significant findings on examination. Magnetic resonance imaging (MRI) showed dilated lateral and third ventricles with normal sized fourth ventricle. A diagnosis of aqueductal stenosis was made and ETV was performed under image guidance.Results: Since 2012, we performed 78 cases of ETV with the help of image guidance. None of the patients had any episode of intraoperative hemorrhage. Two patients (2.56%) had fornix contusions.Conclusion: Image guidance can help reduce complications and is becoming an essential tool in performing ETV. IGS ETV technique may benefit young neurosurgeons the most and can help them overcome the learning curve with safety. ]]> <![CDATA[Trial by Zoom? The Response to COVID-19 by Canada's Courts]]> https://www.researchpad.co/article/elastic_article_16551 COVID-19 has made videoconferencing a regular occurrence in the lives of Canadians. Videoconferencing is being used to maintain social ties, run business meetings—and to uphold responsible government. On April 28, 2020, Members of the House of Commons sat virtually using Zoom. The virtual sitting was the first of what will become a stand-in for regular proceedings, allowing the Members to fulfill some of their parliamentary duties while complying with physical distancing (see Malloy, 2020). As the legislative and executive branches look to digital technology to allow the business of government to continue, what about the judicial branch of Canada's government? Courts are an essential service. This is best articulated by the Chief Justice of Nova Scotia: “The fact is, the Courts cannot close. As the third branch of government, an independent judiciary is vital for our Canadian democracy to function. It is never more important than in times of crisis” (Wood, 2020). In this analysis, we seek to understand how courts have responded to COVID-19 and the challenges of physical distancing through the use of digital technologies. This is accomplished through a systematic review of COVID-19 statements and directives issued from all levels of court across Canada. We briefly compare Canada to the United States, a jurisdiction that demonstrates greater openness to technology.

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<![CDATA[Does Collective Interest or Self-Interest Motivate Mask Usage as a Preventive Measure Against COVID-19?]]> https://www.researchpad.co/article/elastic_article_16547 The revised guidance on masks from public health officials has been one of the most significant COVID-19 policy reversals to date. Statements made at the outset of the pandemic, including those from the World Health Organization (WHO), the United States Surgeon General, and the Chief Public Health Officer of Canada, all actively discouraged asymptomatic members of the general public from wearing masks. However, on April 3, 2020, the United States Center for Disease Control and Prevention (CDC) issued new recommendations that called for nonmedical masks, such as cloth face coverings, to be worn in public settings where other social distancing measures are difficult to maintain (Adams, 2020). Canadian public health officials quickly followed with their own guidance for wearing nonmedical masks or face coverings when out in public; however, they have stressed that doing so is optional for asymptomatic persons and should be seen as a complement to existing precautionary measures such as physical distancing and hand hygiene, particularly in cases where physical distancing may not be feasible (Public Health Agency of Canada, 2020). Emphasis was placed on nonmedical masks serving not to protect the wearer, but rather others who come within close proximity of the wearer. Echoing her public statements on the matter, Canada's chief public health officer Tweeted that “[w]earing a NON-MEDICAL mask in public settings has not been proven to add any protection TO the person wearing it, but it can be an additional way to prevent spread FROM an infected person to others” (Tam, 2020).

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<![CDATA[Adapting Substance Use Treatment for HIV Affected Communities During COVID-19: Comparisons Between a Sexually Transmitted Infections (STI) Clinic and a Local Community Based Organization]]> https://www.researchpad.co/article/elastic_article_12813 <![CDATA[From natural disaster to pandemic: A health-system pharmacy rises to the challenge]]> https://www.researchpad.co/article/elastic_article_12448 This report describes a health-system pharmacy’s response to a natural disaster while staff members simultaneously prepared for the coronavirus disease 2019 (COVID-19) pandemic. By detailing our experience, we hope to help other institutions that are current facing or could encounter similar crises.SummaryIn early March 2020, a tornado destroyed the health system’s warehouse for storage of most clinical supplies, including personal protective equipment and fluids. The pharmacy purchasing team collaborated with suppliers and manufacturers to recover losses and establish alternative storage areas. Days later, the pharmacy department was forced to address the impending COVID-19 pandemic. Key elements of the COVID-19 response included reducing the potential for virus exposure for patients and staff; overcoming challenges in sourcing of staff, personal protective equipment, and medications; and changing care delivery practices to maintain high-quality patient care while maximizing social distancing. The pharmacy department also created distance learning opportunities for 70 pharmacy students on rotations. After an initial plan, ongoing needs include adjustment in patient care activities if significant staff losses occur, when and how to resume clinical activities, and how to best utilize the resources accumulated. Elements of practice changes implemented to reduce COVID-19 threats to patients and pharmacy personnel have proven beneficial and will be further evaluated for potential continuation.ConclusionThe pharmacy department’s efforts to respond to a natural disaster and unprecedented pandemic have proven successful to this point and have illuminated several lessons, including the necessity of cohesive department communication, staff flexibility, prioritization of teamwork, and external collaboration. ]]> <![CDATA[Measuring and Comparing Municipal Policy Responses to COVID-19]]> https://www.researchpad.co/article/elastic_article_11121 Municipal governments are experts in social non-distancing. From swimming pools to libraries, streetcars to public parks, municipalities bring residents together and move them around—services vital to a vibrant community in ordinary times, but potentially disastrous in a pandemic. Municipal decisions to shutter these services and enforce social distancing are thus crucial for a successful COVID-19 response.

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<![CDATA[How Right-Leaning Media Coverage of COVID-19 Facilitated the Spread of Misinformation in the Early Stages of the Pandemic in the U.S.]]> https://www.researchpad.co/article/elastic_article_11119 We have yet to know the ultimate global impact of the novel coronavirus pandemic. However, we do know that delays, denials and misinformation about COVID-19 have exacerbated its spread and slowed pandemic response, particularly in the U.S. (e.g., Abutaleb et al., 2020).

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<![CDATA[Modeling an equivalent b‐value in diffusion‐weighted steady‐state free precession]]> https://www.researchpad.co/article/elastic_article_6791 Diffusion‐weighted steady‐state free precession (DW‐SSFP) is shown to provide a means to probe non‐Gaussian diffusion through manipulation of the flip angle. A framework is presented to define an effective b‐value in DW‐SSFP.TheoryThe DW‐SSFP signal is a summation of coherence pathways with different b‐values. The relative contribution of each pathway is dictated by the flip angle. This leads to an apparent diffusion coefficient (ADC) estimate that depends on the flip angle in non‐Gaussian diffusion regimes. By acquiring DW‐SSFP data at multiple flip angles and modeling the variation in ADC for a given form of non‐Gaussianity, the ADC can be estimated at a well‐defined effective b‐value.MethodsA gamma distribution is used to model non‐Gaussian diffusion, embedded in the Buxton signal model for DW‐SSFP. Monte‐Carlo simulations of non‐Gaussian diffusion in DW‐SSFP and diffusion‐weighted spin‐echo sequences are used to verify the proposed framework. Dependence of ADC on flip angle in DW‐SSFP is verified with experimental measurements in a whole, human postmortem brain.ResultsMonte‐Carlo simulations reveal excellent agreement between ADCs estimated with diffusion‐weighted spin‐echo and the proposed framework. Experimental ADC estimates vary as a function of flip angle over the corpus callosum of the postmortem brain, estimating the mean and standard deviation of the gamma distribution as 1.50·10-4 mm2/s and 2.10·10-4 mm2/s.ConclusionDW‐SSFP can be used to investigate non‐Gaussian diffusion by varying the flip angle. By fitting a model of non‐Gaussian diffusion, the ADC in DW‐SSFP can be estimated at an effective b‐value, comparable to more conventional diffusion sequences. ]]> <![CDATA[Magnetization transfer and frequency distribution effects in the SSFP ellipse]]> https://www.researchpad.co/article/elastic_article_6701 To demonstrate that quantitative magnetization transfer (qMT) parameters can be extracted from steady‐state free‐precession (SSFP) data with no external T 1 map or banding artifacts.MethodsSSFP images with multiple MT weightings were acquired and qMT parameters fitted with a two‐stage elliptical signal model.ResultsMonte Carlo simulations and data from a 3T scanner indicated that most qMT parameters could be recovered with reasonable accuracy. Systematic deviations from theory were observed in white matter, consistent with previous literature on frequency distribution effects.ConclusionsqMT parameters can be extracted from SSFP data alone, in a manner robust to banding artifacts, despite several confounds. ]]> <![CDATA[“Keep It Going if You Can”: HIV Service Provision for Priority Populations During the COVID-19 Pandemic in Seattle, WA]]> https://www.researchpad.co/article/Na8926f87-b574-4968-8076-1f1ceeaeff40 <![CDATA[RiboFlow, RiboR and RiboPy: an ecosystem for analyzing ribosome profiling data at read length resolution]]> https://www.researchpad.co/article/N1e190294-f8f0-4e62-8bfe-9beb97a99364 Ribosome occupancy measurements enable protein abundance estimation and infer mechanisms of translation. Recent studies have revealed that sequence read lengths in ribosome profiling data are highly variable and carry critical information. Consequently, data analyses require the computation and storage of multiple metrics for a wide range of ribosome footprint lengths. We developed a software ecosystem including a new efficient binary file format named ‘ribo’. Ribo files store all essential data grouped by ribosome footprint lengths. Users can assemble ribo files using our RiboFlow pipeline that processes raw ribosomal profiling sequencing data. RiboFlow is highly portable and customizable across a large number of computational environments with built-in capabilities for parallelization. We also developed interfaces for writing and reading ribo files in the R (RiboR) and Python (RiboPy) environments. Using RiboR and RiboPy, users can efficiently access ribosome profiling quality control metrics, generate essential plots and carry out analyses. Altogether, these components create a software ecosystem for researchers to study translation through ribosome profiling.Availability and implementationFor a quickstart, please see https://ribosomeprofiling.github.io. Source code, installation instructions and links to documentation are available on GitHub: https://github.com/ribosomeprofiling.Supplementary information Supplementary data are available at Bioinformatics online. ]]> <![CDATA[3D-Cell-Annotator: an open-source active surface tool for single-cell segmentation in 3D microscopy images]]> https://www.researchpad.co/article/N3373eae5-e76e-493f-9197-c6f496095c01 Segmentation of single cells in microscopy images is one of the major challenges in computational biology. It is the first step of most bioimage analysis tasks, and essential to create training sets for more advanced deep learning approaches. Here, we propose 3D-Cell-Annotator to solve this task using 3D active surfaces together with shape descriptors as prior information in a semi-automated fashion. The software uses the convenient 3D interface of the widely used Medical Imaging Interaction Toolkit (MITK). Results on 3D biological structures (e.g. spheroids, organoids and embryos) show that the precision of the segmentation reaches the level of a human expert.Availability and implementation3D-Cell-Annotator is implemented in CUDA/C++ as a patch for the segmentation module of MITK. The 3D-Cell-Annotator enabled MITK distribution can be downloaded at: www.3D-cell-annotator.org. It works under Windows 64-bit systems and recent Linux distributions even on a consumer level laptop with a CUDA-enabled video card using recent NVIDIA drivers.Supplementary information Supplementary data are available at Bioinformatics online. ]]> <![CDATA[The open targets post-GWAS analysis pipeline]]> https://www.researchpad.co/article/Na8d251ed-6620-4a18-bb78-564e7e8d3f79 Genome-wide association studies (GWAS) are a powerful method to detect even weak associations between variants and phenotypes; however, many of the identified associated variants are in non-coding regions, and presumably influence gene expression regulation. Identifying potential drug targets, i.e. causal protein-coding genes, therefore, requires crossing the genetics results with functional data.ResultsWe present a novel data integration pipeline that analyses GWAS results in the light of experimental epigenetic and cis-regulatory datasets, such as ChIP-Seq, Promoter-Capture Hi-C or eQTL, and presents them in a single report, which can be used for inferring likely causal genes. This pipeline was then fed into an interactive data resource.Availability and implementationThe analysis code is available at www.github.com/Ensembl/postgap and the interactive data browser at postgwas.opentargets.io. ]]> <![CDATA[PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins]]> https://www.researchpad.co/article/N981a32bd-a37b-4315-9117-3eabfe7b2b1c Two-dimensional [15N-1H] separated local field solid-state nuclear magnetic resonance (NMR) experiments of membrane proteins aligned in lipid bilayers provide tilt and rotation angles for α-helical segments using Polar Index Slant Angle (PISA)-wheel models. No integrated software has been made available for data analysis and visualization.ResultsWe have developed the PISA-SPARKY plugin to seamlessly integrate PISA-wheel modeling into the NMRFAM-SPARKY platform. The plugin performs basic simulations, exhaustive fitting against experimental spectra, error analysis and dipolar and chemical shift wave plotting. The plugin also supports PyMOL integration and handling of parameters that describe variable alignment and dynamic scaling encountered with magnetically aligned media, ensuring optimal fitting and generation of restraints for structure calculation.Availability and implementation PISA-SPARKY is freely available in the latest version of NMRFAM-SPARKY from the National Magnetic Resonance Facility at Madison (http://pine.nmrfam.wisc.edu/download_packages.html), the NMRbox Project (https://nmrbox.org) and to subscribers of the SBGrid (https://sbgrid.org). The pisa.py script is available and documented on GitHub (https://github.com/weberdak/pisa.py) along with a tutorial video and sample data.Supplementary information Supplementary data are available at Bioinformatics online. ]]> <![CDATA[Identifying and removing haplotypic duplication in primary genome assemblies]]> https://www.researchpad.co/article/Ne6d65ccc-49b2-4db7-a8a2-89a52f6f955b Rapid development in long-read sequencing and scaffolding technologies is accelerating the production of reference-quality assemblies for large eukaryotic genomes. However, haplotype divergence in regions of high heterozygosity often results in assemblers creating two copies rather than one copy of a region, leading to breaks in contiguity and compromising downstream steps such as gene annotation. Several tools have been developed to resolve this problem. However, they either focus only on removing contained duplicate regions, also known as haplotigs, or fail to use all the relevant information and hence make errors.ResultsHere we present a novel tool, purge_dups, that uses sequence similarity and read depth to automatically identify and remove both haplotigs and heterozygous overlaps. In comparison with current tools, we demonstrate that purge_dups can reduce heterozygous duplication and increase assembly continuity while maintaining completeness of the primary assembly. Moreover, purge_dups is fully automatic and can easily be integrated into assembly pipelines.Availability and implementationThe source code is written in C and is available at https://github.com/dfguan/purge_dups.Supplementary information Supplementary data are available at Bioinformatics online. ]]> <![CDATA[CytoSeg 2.0: automated extraction of actin filaments]]> https://www.researchpad.co/article/N6afbaa1f-2cf1-43b9-ad3f-012a20bb56e4 Actin filaments (AFs) are dynamic structures that substantially change their organization over time. The dynamic behavior and the relatively low signal-to-noise ratio during live-cell imaging have rendered the quantification of the actin organization a difficult task.ResultsWe developed an automated image-based framework that extracts AFs from fluorescence microscopy images and represents them as networks, which are automatically analyzed to identify and compare biologically relevant features. Although the source code is freely available, we have now implemented the framework into a graphical user interface that can be installed as a Fiji plugin, thus enabling easy access by the research community.Availability and implementationCytoSeg 2.0 is open-source software under the GPL and is available on Github: https://github.com/jnowak90/CytoSeg2.0.Supplementary information Supplementary data are available at Bioinformatics online. ]]> <![CDATA[GSOAP: a tool for visualization of gene set over-representation analysis]]> https://www.researchpad.co/article/N16a33cc8-828a-4a96-aeb8-a489b2870d93 Gene sets over-representation analysis (GSOA) is a common technique of enrichment analysis that measures the overlap between a gene set and selected instances (e.g. pathways). Despite its popularity, there is currently no established standard for visualization of GSOA results.ResultsHere, we propose a visual exploration of the GSOA results by showing the relationships among the enriched instances, while highlighting important instance attributes, such as significance, closeness (centrality) and clustering.Availability and implementationGSOAP is implemented as an R package and is available at https://github.com/tomastokar/gsoap. ]]>