Function Transformations and the Desmos Activity Builder

2017 ◽  
Vol 110 (7) ◽  
pp. 549-551 ◽  
Author(s):  
Jon Orr
Keyword(s):  
Student Understanding ◽  
Link Type ◽  
Error Check ◽  
Set Up ◽  
Algebraic Representations ◽  
Game Changer

In my classroom, the Desmos® calculator has been a game-changer for student understanding of relationships between graphs and algebraic representations of functions. We use this beautifully designed website every day. Lately, the Desmos class activity site (https://teacher.demos.com) and the new Activity Builder tool have proven especially useful by allowing me to provide my students with opportunities to struggle productively, create, error-check, and think deeply to learn mathematics. Activity Builder is the easiest tool I have found to set up and to run an activity that promotes these ideas in your classroom.

scholarly journals Clinical and multi-omics cross-phenotyping of patients with autoimmune and autoinflammatory diseases: the observational TRANSIMMUNOM protocol

BMJ Open ◽  
2018 ◽  
Vol 8 (8) ◽  
pp. e021037 ◽  
Author(s):  
Roberta Lorenzon ◽  
Encarnita Mariotti-Ferrandiz ◽  
Caroline Aheng ◽  
Claire Ribet ◽  
Ferial Toumi ◽  
...  
Keyword(s):  
Systems Biology ◽  
Good Clinical Practice ◽  
Autoinflammatory Diseases ◽  
Case Report Form ◽  
Sample Collection ◽  
Clinical Protocol ◽  
Link Type ◽  
Systems Immunology ◽  
Hospital Ethics ◽  
Set Up

IntroductionAutoimmune and autoinflammatory diseases (AIDs) represent a socioeconomic burden as the second cause of chronic illness in Western countries. In this context, the TRANSIMMUNOM clinical protocol is designed to revisit the nosology of AIDs by combining basic, clinical and information sciences. Based on classical and systems biology analyses, it aims to uncover important phenotypes that cut across diagnostic groups so as to discover biomarkers and identify novel therapeutic targets.Methods and analysisTRANSIMMUNOM is an observational clinical protocol that aims to cross-phenotype a set of 19 AIDs, six related control diseases and healthy volunteers . We assembled a multidisciplinary cohort management team tasked with (1) selecting informative biological (routine and omics type) and clinical parameters to be captured, (2) standardising the sample collection and shipment circuit, (3) selecting omics technologies and benchmarking omics data providers, (4) designing and implementing a multidisease electronic case report form and an omics database and (5) implementing supervised and unsupervised data analyses.Ethics and disseminationThe study was approved by the institutional review board of Pitié-Salpêtrière Hospital (ethics committee Ile-De-France 48–15) and done in accordance with the Declaration of Helsinki and good clinical practice. Written informed consent is obtained from all participants before enrolment in the study. TRANSIMMUNOM’s project website provides information about the protocol (https://www.transimmunom.fr/en/) including experimental set-up and tool developments. Results will be disseminated during annual scientific committees appraising the project progresses and at national and international scientific conferences.DiscussionSystems biology approaches are increasingly implemented in human pathophysiology research. The TRANSIMMUNOM study applies such approach to the pathophysiology of AIDs. We believe that this translational systems immunology approach has the potential to provide breakthrough discoveries for better understanding and treatment of AIDs.Trial registration numberNCT02466217; Pre-results.

scholarly journals PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens

2017 ◽  
Author(s):  
Philipp N. Spahn ◽  
Tyler Bath ◽  
Ryan J. Weiss ◽  
Jihoon Kim ◽  
Jeffrey D. Esko ◽  
...  
Keyword(s):  
Web Application ◽  
Large Scale ◽  
Sequencing Data ◽  
Bioinformatic Tools ◽  
Link Type ◽  
Screening Experiments ◽  
Independent Analysis ◽  
Wide Range ◽  
Set Up ◽  
Sequence Quality

AbstractBackgroundLarge-scale genetic screens using CRISPR/Cas9 technology have emerged as a major tool for functional genomics. With its increased popularity, experimental biologists frequently acquire large sequencing datasets for which they often do not have an easy analysis option. While a few bioinformatic tools have been developed for this purpose, their utility is still hindered either due to limited functionality or the requirement of bioinformatic expertise.ResultsTo make sequencing data analysis of CRISPR/Cas9 screens more accessible to a wide range of scientists, we developed a Platform-independent Analysis of Pooled Screens using Python (PinAPL-Py), which is operated as an intuitive web-service. PinAPL-Py implements state-of-the-art tools and statistical models, assembled in a comprehensive workflow covering sequence quality control, automated sgRNA sequence extraction, alignment, sgRNA enrichment/depletion analysis and gene ranking. The workflow is set up to use a variety of popular sgRNA libraries as well as custom libraries that can be easily uploaded. Various analysis options are offered, suitable to analyze a large variety of CRISPR/Cas9 screening experiments. Analysis output includes ranked lists of sgRNAs and genes, and publication-ready plots.ConclusionsPinAPL-Py helps to advance genome-wide screening efforts by combining comprehensive functionality with user-friendly implementation. PinAPL-Py is freely accessible at http://pinapl-py.ucsd.edu with instructions, documentation and test datasets. The source code is available at https://github.com/LewisLabUCSD/PinAPL-Py

scholarly journals CRISPR-RT: A web service for designing CRISPR-C2c2 crRNA with improved target specificity

2017 ◽  
Author(s):  
Houxiang Zhu ◽  
Emily Richmond ◽  
Chun Liang
Keyword(s):  
Web Service ◽  
Genome Editing ◽  
Rna Editing ◽  
Model Organisms ◽  
Future Research ◽  
Target Specificity ◽  
Link Type ◽  
Wide Range ◽  
Set Up

AbstractCRISPR-Cas systems have been successfully applied in genome editing. Recently, the CRISPR-C2c2 system has been reported as a tool for RNA editing. Here we describe CRISPR-RT (CRISPR RNA-Targeting), the first web service to help biologists design the crRNA with improved target specificity for the CRISPR-C2c2 system. CRISPR-RT allows users to set up a wide range of parameters, making it highly flexible for current and future research in CRISPR-based RNA editing. CRISPR-RT covers major model organisms and can be easily extended to cover other species. CRISPR-RT will empower researchers in RNA editing. It is available at http://bioinfolab.miamioh.edu/CRISPR-RT.

scholarly journals Improved Understanding of Student Concepts and Skills in Volleyball Learning through Mobile Learning

2020 ◽  
Vol 20 (2) ◽  
pp. 99-110
Author(s):  
Widha Sismahendra ◽  
Agus Rusdiana ◽  
Yunyun Yudiana
Keyword(s):  
Mobile Learning ◽  
Student Motivation ◽  
Student Understanding ◽  
Learning Activities ◽  
School Level ◽  
Control Group ◽  
Control Group Design ◽  
Group Design ◽  
Quasi Experimental ◽  
Set Up

The development of information systems that is increasingly influential in various aspects of life, one of which is the world of education. One result of the development of information technology that can be utilized in education is mobile learning (M-Learning). The use of M-Learning in volleyball learning at the elementary school level is still rarely developed and used. Though this media can be a means of supporting education can make the learning process active, creative and innovative. M-Learning can enhance learning activities so that it can foster enthusiasm and student motivation. This can help improve students' understanding and volleyball skills which include volleyball, service, passing, and set-up techniques. The research method used is a quasi-experimental method with a nonequivalent control group design. The results showed that M-Learning can improve student understanding and student skills in volleyball learning. M-Learning can improve learning communication between students, both with friends and teachers so that learning creates active and conducive relationships. This has an impact on increasing student motivation. This improvement can improve students' understanding and skills in volleyball learning.

scholarly journals Dirichlet baths and the not-so-fine-grained Page curve

2021 ◽  
Vol 2021 (8) ◽  
Author(s):  
Kausik Ghosh ◽  
Chethan Krishnan
Keyword(s):  
Black Hole ◽  
Entanglement Entropy ◽  
Flat Space ◽  
Information Paradox ◽  
Braneworld Cosmology ◽  
Fine Grained ◽  
Link Type ◽  
Related Approach ◽  
Set Up ◽  
Weak Gravity

Abstract We present a doubly holographic prescription for computing entanglement entropy on a gravitating brane. It involves a Ryu-Takayanagi surface with a Dirichlet anchoring condition. In braneworld cosmology, a related approach was used previously in arXiv:2007.06551. There, the prescription naturally computed a co-moving entanglement entropy, and was argued to resolve the information paradox for a black hole living in the cosmology. In this paper, we show that the Dirichlet prescription leads to reasonable results, when applied to a recently studied wedge holography set up with a gravitating bath. The nature of the information paradox and its resolution in our Dirichlet problem have a natural understanding in terms of the strength of gravity on the two branes and at the anchoring location. By sliding the anchor to the defect, we demonstrate that the limit where gravity decouples from the anchor is continuous — in other words, as far as island physics is considered, weak gravity on the anchor is identical to no gravity. The weak and (moderately) strong gravity regions on the brane are separated by a “Dirichlet wall”. We find an intricate interplay between various extremal surfaces, with an island coming to the rescue whenever there is an information paradox. This is despite the presence of massless gravitons in the spectrum. The overall physics is consistent with the slogan that gravity becomes “more holographic”, as it gets stronger. Our observations strengthen the case that the conventional Page curve is indeed of significance, when discussing the information paradox in flat space. We work in high enough dimensions so that the graviton is non-trivial, and our results are in line with the previous discussions on gravitating baths in arXiv:2005.02993 and arXiv:2007.06551.

scholarly journals The Political Economy of Private Law: Comment on ‘The code of capital – how the law creates wealth and inequality’

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Matthias Thiemann
Keyword(s):  
New York ◽  
Social Systems ◽  
Frankfurt Am Main ◽  
Legal Form ◽  
Link Type ◽  
Princeton University ◽  
Corporate Form ◽  
The Law ◽  
Set Up

AbstractKatharina Pistor’s book The code of capital – how the law creates wealth and inequality (Pistor, K. (2019). The code of capital – How the law creates wealth and inequality. Princeton: Princeton University Press) is an original and insightful intervention in the quest to understand both the rising inequality of the last 40 years, as well as the inner dynamics of capitalism, a social formation that has ruled in western societies for about 200 years now. Pistor shares many of the convictions of the publications in the journal Accounting, Economics and Law, such as the dangers to democracy inherent in the corporate form (Robé, J. P. (2011). The legal structure of the firm. Accounting, Economics and Law, 1(1). https://doi.org/10.2202/2152-2820.1001; Strasser, K., & Blumberg, P. (2011). Legal form and economic substance of enterprise groups: Implications for legal policy. Accounting, Economics and Law, 1(1). https://doi.org/10.2202/2152-2820.1000), the fact that firms and corporate form need to be distinguished (Y. Biondi, A. Canziani, & T. Kirat (Eds), (2007). The firm as an entity: Implications for economics, accounting and law. New York and London: Routledge) and that shareholders do not own corporations, but just their shares, it is only appropriate to discuss and present it to the wider audience of the journal, pointing to its fundamental insights and potential for follow-up research. The title of the book and its set-up evoke both Luhmann’s system theory with its penchant for binary code as well as Marx’s capital (Marx, K. (1955[1867]). Das Kapital. Berlin: Dietz Verlag, Vol. 1). Combining the coding of social systems and their relentless dynamic in innovating and generating new forms by recursively referring to established elements (Luhmann, N. (1984). Soziale Systeme. Frankfurt am Main: Suhrkamp Verlag; Luhmann, N. (1995). Das Recht der Gesellschaft. Frankfurt am Main: Suhrkamp Verlag) with Marx’s focus on the structuring effects capital has on society is making this a very inspiring book, which at the same time evokes many follow-up questions.

scholarly journals A trial platform to assess approved SARS-CoV-2 vaccines in immunocompromised patients: first sub-protocol for a pilot trial comparing the mRNA vaccines Comirnaty® and COVID-19 mRNA Vaccine Moderna®

Trials ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Benjamin Speich ◽  
Frédérique Chammartin ◽  
Daniel Smith ◽  
Marcel P. Stoeckle ◽  
Patrizia Amico ◽  
...  
Keyword(s):  
Cohort Study ◽  
Antibody Response ◽  
Pilot Trial ◽  
Type I ◽  
Immunocompromised Patients ◽  
Efficacy And Safety ◽  
Randomized Controlled ◽  
Link Type ◽  
Patient Consent ◽  
Set Up

Abstract Background Late 2019, a new highly contagious coronavirus SARS-CoV-2 has emerged in Wuhan, China, causing within 2 months a pandemic with the highest disease burden in elderly and people with pre-existing medical conditions. The pandemic has highlighted that new and more flexible clinical trial approaches, such as trial platforms, are needed to assess the efficacy and safety of interventions in a timely manner. The two existing Swiss cohorts of immunocompromised patients (i.e., Swiss HIV Cohort Study (SHCS) and Swiss Transplant Cohort Study (STCS)) are an ideal foundation to set-up a trial platform in Switzerland leveraging routinely collected data. Within a newly founded trial platform, we plan to assess the efficacy of the first two mRNA SARS-CoV-2 vaccines that reached market authorization in Switzerland in the frame of a pilot randomized controlled trial (RCT) while at the same time assessing the functionality of the trial platform. Methods We will conduct a multicenter randomized controlled, open-label, 2-arm sub-study pilot trial of a platform trial nested into two Swiss cohorts. Patients included in the SHCS or the STCS will be eligible for randomization to either receiving the mRNA vaccine Comirnaty® (Pfizer/BioNTech) or the COVID-19 mRNA Vaccine Moderna®. The primary clinical outcome will be change in pan-lg antibody response (pan-Ig anti-S1-RBD; baseline vs. 3 months after first vaccination; binary outcome, considering ≥ 0.8 units/ml as a positive antibody response). The pilot study will also enable us to assess endpoints related to trial conduct feasibility (i.e., duration of RCT set-up; time of patient recruitment; patient consent rate; proportion of missing data). Assuming vaccine reactivity of 90% in both vaccine groups, we power our trial, using a non-inferiority margin such that a 95% two-sided confidence interval excludes a difference in favor of the reference group of more than 10%. A sample size of 380 (190 in each treatment arm) is required for a statistical power of 90% and a type I error of 0.025. The study is funded by the Swiss National Science Foundation (National Research Program NRP 78, “COVID-19”). Discussion This study will provide crucial information about the efficacy and safety of the mRNA SARS-CoV-2 vaccines in HIV patients and organ transplant recipients. Furthermore, this project has the potential to pave the way for further platform trials in Switzerland. Trial registration ClinicalTrials.govNCT04805125. Registered on March 18, 2021

scholarly journals Endurance-oriented training program with children and adolescents on maintenance hemodialysis to enhance dialysis efficacy—DiaSport

2021 ◽  
Author(s):  
Markus Feldkötter ◽  
Sarah Thys ◽  
Anne Adams ◽  
Ingrid Becker ◽  
Rainer Büscher ◽  
...  
Keyword(s):  
Children And Adolescents ◽  
Controlled Trial ◽  
Bicycle Ergometer ◽  
Maintenance Hemodialysis ◽  
Control Group ◽  
Intention To Treat ◽  
Link Type ◽  
Secondary Endpoints ◽  
Set Up ◽  
Bicycle Ergometer Training

Abstract Objective Pediatric patients spend significant time on maintenance hemodialysis (HD) and traveling. They are often not capable of participating in sports activities. To assess the effects of exercise training during HD on dialysis efficacy in children and adolescents, we set up a multi-center randomized controlled trial (RCT). Methods Patients on HD, age 6 to 18 years, were randomized either to 3× weekly bicycle ergometer training or to no training during HD for 12 weeks. Change in single-pool Kt/V (spKt/V) was the primary outcome parameter. Results We randomized 54 patients of whom 45 qualified (23 in the intervention and 22 in the waiting control group, 14.5 ± 3.01 years, 32 male and 13 female) for the intention-to-treat (ITT) population. Only 26 patients finished study per-protocol (PP). Training was performed for an average of 11.96 weeks (0.14–13.14) at 2.08 ± 0.76 times per week and for a weekly mean of 55.52 ± 27.26 min. Single-pool Kt/V was similar in the intervention compared to the control group (1.70 [0.33] vs. 1.79 [0.55]) at V0 and (1.70 [0.36] vs. 1.71 [0.51]) at V1; secondary endpoints also showed no difference in both ITT and PP analysis. No significant adverse events were reported. No bleeding or needle dislocation occurred in 1670 training sessions. Conclusions Intradialytic bicycle training is safe, but does not improve dialysis efficacy and physical fitness. However, the study can be considered underpowered, particularly because of high dropout rates. Future studies need better strategies to increase motivation and compliance and other more effective/intensive exercise measures should be evaluated. Trial registration The trial was registered in ClinicalTrials.Gov (Clinicaltrials.gov identifier: NCT01561118) on March 22, 2012.

scholarly journals GenIE-Sys: Genome Integrative Explorer System

2019 ◽  
Author(s):  
Chanaka Mannapperuma ◽  
John Waterworth ◽  
Nathaniel Street
Keyword(s):  
Source Code ◽  
Genome Project ◽  
Data Repositories ◽  
Web Resources ◽  
Link Type ◽  
Maximum Benefit ◽  
A Genome ◽  
Set Up ◽  
User Friendly ◽  
Mining Tools

AbstractThere are an ever-increasing number of genomes being sequenced, many of which have associated RNA sequencing and other genomics data. The availability of user-friendly web-accessible mining tools ensures that these data repositories provide maximum benefit to the community. However, there are relatively few options available for setting up such standalone frameworks. We developed the Genome Integrative Explorer System (GenIE-Sys) to set up web resources to enable search, visualization and exploration of genomics data typically generated by a genome project.GenIE-Sys is implemented in PHP, JavaScript and Python and is freely available under the GNU GPL 3 public license. All source code is freely available at the GenIE-Sys website (https://geniesys.org) or GitHub (http://github.com/plantgenie/geniesys.git). Documentation is available at http://geniesys.readthedocs.io.

scholarly journals PyMethylProcess - highly parallelized preprocessing for DNA methylation array data

2019 ◽  
Author(s):  
Joshua J. Levy ◽  
Alexander J. Titus ◽  
Lucas A. Salas ◽  
Brock C. Christensen
Keyword(s):  
Large Scale ◽  
Scale Production ◽  
Data Preparation ◽  
Methylation Array ◽  
Array Data ◽  
Link Type ◽  
Project Home Page ◽  
Large Scale Production ◽  
Set Up ◽  
Dna Methylation Array

AbstractSummaryThe ability to perform high-throughput preprocessing of methylation array data is essential in large scale methylation studies. While R is a convenient language for methylation analyses, performing highly parallelized preprocessing using Python can accelerate data preparation for downstream methylation analyses, including large scale production-ready machine learning pipelines. Here, we present a methylation data preprocessing pipeline called PyMethylProcess that is highly reproducible, scalable, and that can be quickly set-up and deployed through Docker and PIP.Availability and ImplementationProject Name: PyMethylProcessProject Home Page:https://github.com/Christensen-Lab-Dartmouth/PyMethylProcess. Available on PyPI aspymethylprocess.Available on DockerHub viajoshualevy44/pymethylprocess.Help Documentation:https://christensen-lab-dartmouth.github.io/PyMethylProcess/Operating Systems: Linux, MacOS, Windows (Docker)Programming Language: Python, ROther Requirements: Python 3.6, R 3.5.1, Docker (optional) License: [email protected]

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