scholarly journals H3ABioNet genomic medicine and microbiome data portals hackathon proceedings

Database ◽  
2021 ◽  
Vol 2021 ◽  
Author(s):  
Faisal M Fadlelmola ◽  
Kais Ghedira ◽  
Yosr Hamdi ◽  
Mariem Hanachi ◽  
Fouzia Radouani ◽  
...  
Keyword(s):  
Ethnic Groups ◽  
Genomic Medicine ◽  
Lessons Learned ◽  
Team Work ◽  
Significant Progress ◽  
Team Members ◽  
Pan African ◽  
Scientific Expertise ◽  
Microbiome Data ◽  
Made In

Abstract African genomic medicine and microbiome datasets are usually not well characterized in terms of their origin, making it difficult to find and extract data for specific African ethnic groups or even countries. The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for developing data portals for African genomic medicine and African microbiomes to address this and ran a hackathon to initiate their development. The two portals were designed and significant progress was made in their development during the hackathon. All the participants worked in a very synergistic and collaborative atmosphere in order to achieve the hackathon's goals. The participants were divided into content and technical teams and worked over a period of 6 days. In response to one of the survey questions of what the participants liked the most during the hackathon, 55% of the hackathon participants highlighted the familial and friendly atmosphere, the team work and the diversity of team members and their expertise. This paper describes the preparations for the portals hackathon and the interaction between the participants and reflects upon the lessons learned about its impact on successfully developing the two data portals as well as building scientific expertise of younger African researchers. Database URL: The code for developing the two portals was made publicly available in GitHub repositories: [https://github.com/codemeleon/Database; https://github.com/codemeleon/AfricanMicrobiomePortal].

scholarly journals Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience

2019 ◽  
Vol 1 ◽  
pp. 9
Author(s):  
Azza E. Ahmed ◽  
Phelelani T. Mpangase ◽  
Sumir Panji ◽  
Shakuntala Baichoo ◽  
Yassine Souilmi ◽  
...  
Keyword(s):  
Cloud Computing ◽  
Heterogeneous Computing ◽  
Lessons Learned ◽  
Technical Expertise ◽  
Research Projects ◽  
Pan African ◽  
Genomic Analyses ◽  
Standard Operating ◽  
Computing Environments ◽  
Scientific Expertise

The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines adapted to heterogeneous computing environments, and for the nurturing of technical expertise in workflow languages and containerization technologies. Building on the network’s Standard Operating Procedures (SOPs) for common genomic analyses, H3ABioNet arranged its first Cloud Computing and Reproducible Workflows Hackathon in 2016, with the purpose of translating those SOPs into analysis pipelines able to run on heterogeneous computing environments and meeting the needs of H3Africa research projects. This paper describes the preparations for this hackathon and reflects upon the lessons learned about its impact on building the technical and scientific expertise of African researchers. The workflows developed were made publicly available in GitHub repositories and deposited as container images on Quay.io.

scholarly journals Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience

2018 ◽  
Vol 1 ◽  
pp. 9 ◽  
Author(s):  
Azza E. Ahmed ◽  
Phelelani T. Mpangase ◽  
Sumir Panji ◽  
Shakuntala Baichoo ◽  
Yassine Souilmi ◽  
...  
Keyword(s):  
Cloud Computing ◽  
Human Health ◽  
Heterogeneous Computing ◽  
Lessons Learned ◽  
Technical Expertise ◽  
Research Projects ◽  
Pan African ◽  
Computing Environments ◽  
Scientific Expertise

The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines adapted to heterogeneous compute environments, and for the nurturing of technical expertise in workflow languages and containerization technologies. To address this need, in 2016 H3ABioNet arranged its first Cloud Computing and Reproducible Workflows Hackathon, with the purpose of building key genomics analysis pipelines able to run on heterogeneous computing environments and meeting the needs of H3Africa research projects. This paper describes the preparations for this hackathon and reflects upon the lessons learned about its impact on building the technical and scientific expertise of African researchers. The workflows developed were made publicly available in GitHub repositories and deposited as container images on quay.io.

Toward quantitative defect analysis using HREM

1994 ◽  
Vol 52 ◽  
pp. 714-715
Author(s):  
David J. Smith
Keyword(s):  
Electron Microscope ◽  
Unit Cell ◽  
Defect Analysis ◽  
Significant Progress ◽  
Detailed Characterization ◽  
Small Unit ◽  
Resolution Electron ◽  
High Resolution Electron Microscope ◽  
Large Unit Cell ◽  
Made In

The electron microscope has evolved to the level where it is now straightforward to record highresolution images from thin samples (t∼10 to 20nm) that are directly interpretable in terms of atomic arrangements. Whilst recorded images necessarily represent two-dimensional projections of the structure, many defects such as dislocations and interfaces may be linear or planar in nature and thus might be expected to be amenable to detailed characterization. In this review, we briefly consider the recent significant progress that has been made in quantitative defect analysis using the high-resolution electron microscope and then discuss some drawbacks to the technique as well as potential scope for further improvements. Surveys of defect modelling for some small-unit-cell materials and interfaces have recently been published, and reference should be made to other papers in this symposium for further examples.The technique of structure imaging originated in the early '70s with observations of large-unit-cell block oxides.

Biomarkers for Early Detection of Colitis-associated Colorectal Cancer - Current Concepts, Future Trends

2020 ◽  
Vol 22 (1) ◽  
pp. 137-145
Author(s):  
Tomasz Mackiewicz ◽  
Aleksander Sowa ◽  
Jakub Fichna
Keyword(s):  
Colorectal Cancer ◽  
Early Detection ◽  
Cancer Development ◽  
Sporadic Colorectal Cancer ◽  
Future Trends ◽  
Significant Progress ◽  
Current Standard ◽  
Risk Of Cancer ◽  
Histological Testing ◽  
Made In

: Colitis-associated colorectal cancer (CAC) remains a critical complication of ulcerative colitis (UC) with mortality of approximately 15%, which makes early CAC diagnosis crucial. The current standard of surveillance, with repetitive colonoscopies and histological testing of biopsied mucosa samples is burdensome and expensive, and therefore less invasive methods and reliable biomarkers are needed. Significant progress has been made thanks to continuous extensive research in this field, however no clinically relevant biomarker has been established so far. This review of the current literature presents the genetic and molecular differences between CAC and sporadic colorectal cancer and covers progress made in the early detection of CAC carcinogenesis. It focuses on biomarkers under development, which can be easily tested in samples of body fluids or breath and, once made clinically available, will help to differentiate between progressors (UC patients who will develop dysplasia) from non-progressors and enable early intervention to decrease the risk of cancer development.

scholarly journals Rational design of photocatalysts for ammonia production from water and nitrogen gas

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Seokwoo Choe ◽  
Sung Min Kim ◽  
Yeji Lee ◽  
Jin Seok ◽  
Jiyong Jung ◽  
...  
Keyword(s):  
Energy Source ◽  
Rational Design ◽  
Future Research ◽  
Ammonia Production ◽  
Significant Progress ◽  
Nitrogen Gas ◽  
Research Directions ◽  
Effective Strategies ◽  
Future Research Directions ◽  
Made In

AbstractPhotocatalytic N2 reduction has emerged as one of the most attractive routes to produce NH3 as a useful commodity for chemicals used in industries and as a carbon-free energy source. Recently, significant progress has been made in understanding, exploring, and designing efficient photocatalyst. In this review, we outline the important mechanistic and experimental procedures for photocatalytic NH3 production. In addition, we review effective strategies on development of photocatalysts. Finally, our analyses on the characteristics and modifications of photocatalysts have been summarized, based on which we discuss the possible future research directions, particularly on preparing more efficient catalysts. Overall, this review provides insights on improving photocatalytic NH3 production and designing solar-driven chemical conversions.

scholarly journals The COVID Army: Experiences from the Deployment of Non-Hospitalist Physician Volunteers during the 2020 COVID Pandemic

2021 ◽  
pp. 1-15
Author(s):  
Kevin Hauck ◽  
Katherine Hochman ◽  
Mark Pochapin ◽  
Sondra Zabar ◽  
Jeffrey A Wilhite ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
Medical Center ◽  
The United States ◽  
Lessons Learned ◽  
Front Line ◽  
Clinical Leadership ◽  
Team Members ◽  
Medical Centers ◽  
Hospitalist Physician

Abstract Objective New York City was the epicenter of the outbreak of the 2020 COVID-19 pandemic in the United States. As a large, quaternary care medical center, NYU Langone Medical Center was one of many New York medical centers that experienced an unprecedented influx of patients during this time. Clinical leadership effectively identified, oriented, and rapidly deployed a “COVID Army”, consisting of non-hospitalist physicians, to meet the needs of this patient influx. We share feedback from our providers on our processes and offer specific recommendations for systems experiencing a similar influx in the current and future pandemics. Methods In order to assess the experiences and perceived readiness of these physicians (n=183), we distributed a 32-item survey between March and June of 2020. Thematic analyses and response rates were examined in order to develop results. Results Responses highlighted varying experiences and attitudes of our front-line physicians during an emerging pandemic. Thematic analyses revealed a series of lessons learned, including the need to: (1) provide orientations, (2) clarify roles/ workflow, (3) balance team workload, (4) keep teams updated on evolving policies, (5) make team members feel valued, and (6) ensure they have necessary tools available. Conclusions Lessons from our deployment and assessment are scalable at other institutions.

scholarly journals Identification and Validation of New Cancer Stem Cell-Related Genes and Their Regulatory microRNAs in Colorectal Cancerogenesis

Biomedicines ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 179
Author(s):  
Kristian Urh ◽  
Margareta Žlajpah ◽  
Nina Zidar ◽  
Emanuela Boštjančič
Keyword(s):  
Experimental Validation ◽  
Target Gene ◽  
Bioinformatics Analysis ◽  
Early Carcinoma ◽  
Significant Progress ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Node Metastases ◽  
Formalin Fixed ◽  
Made In

Significant progress has been made in the last decade in our understanding of the pathogenetic mechanisms of colorectal cancer (CRC). Cancer stem cells (CSC) have gained much attention and are now believed to play a crucial role in the pathogenesis of various cancers, including CRC. In the current study, we validated gene expression of four genes related to CSC, L1TD1, SLITRK6, ST6GALNAC1 and TCEA3, identified in a previous bioinformatics analysis. Using bioinformatics, potential miRNA-target gene correlations were prioritized. In total, 70 formalin-fixed paraffin-embedded biopsy samples from 47 patients with adenoma, adenoma with early carcinoma and CRC without and with lymph node metastases were included. The expression of selected genes and microRNAs (miRNAs) was evaluated using quantitative PCR. Differential expression of all investigated genes and four of six prioritized miRNAs (hsa-miR-199a-3p, hsa-miR-335-5p, hsa-miR-425-5p, hsa-miR-1225-3p, hsa-miR-1233-3p and hsa-miR-1303) was found in at least one group of CRC cancerogenesis. L1TD1, SLITRK6, miR-1233-3p and miR-1225-3p were correlated to the level of malignancy. A negative correlation between miR-199a-3p and its predicted target SLITRK6 was observed, showing potential for further experimental validation in CRC. Our results provide further evidence that CSC-related genes and their regulatory miRNAs are involved in CRC development and progression and suggest that some them, particularly miR-199a-3p and its SLITRK6 target gene, are promising for further validation in CRC.

scholarly journals Whither Magnetic Hyperthermia? A Tentative Roadmap

Materials ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 706
Author(s):  
Irene Rubia-Rodríguez ◽  
Antonio Santana-Otero ◽  
Simo Spassov ◽  
Etelka Tombácz ◽  
Christer Johansson ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Nanoparticle Synthesis ◽  
Careful Analysis ◽  
Magnetic Hyperthermia ◽  
Lessons Learned ◽  
In Vivo Testing ◽  
Evolution Of Science ◽  
Made In ◽  
Critical Aspects

The scientific community has made great efforts in advancing magnetic hyperthermia for the last two decades after going through a sizeable research lapse from its establishment. All the progress made in various topics ranging from nanoparticle synthesis to biocompatibilization and in vivo testing have been seeking to push the forefront towards some new clinical trials. As many, they did not go at the expected pace. Today, fruitful international cooperation and the wisdom gain after a careful analysis of the lessons learned from seminal clinical trials allow us to have a future with better guarantees for a more definitive takeoff of this genuine nanotherapy against cancer. Deliberately giving prominence to a number of critical aspects, this opinion review offers a blend of state-of-the-art hints and glimpses into the future of the therapy, considering the expected evolution of science and technology behind magnetic hyperthermia.

scholarly journals The Pivotal Player: Components of NF-κB Pathway as Promising Biomarkers in Colorectal Cancer

2021 ◽  
Vol 22 (14) ◽  
pp. 7429
Author(s):  
Matthew Martin ◽  
Mengyao Sun ◽  
Aishat Motolani ◽  
Tao Lu
Keyword(s):  
Colorectal Cancer ◽  
Biological Response ◽  
Significant Progress ◽  
Therapeutic Approaches ◽  
Successful Development ◽  
Diagnostic Screening ◽  
Proteomic Data ◽  
Large Groups ◽  
Made In

Over the last several decades, colorectal cancer (CRC) has been one of the most prevalent cancers. While significant progress has been made in both diagnostic screening and therapeutic approaches, a large knowledge gap still remains regarding the early identification and treatment of CRC. Specifically, identification of CRC biomarkers that can help with the creation of targeted therapies as well as increasing the ability for clinicians to predict the biological response of a patient to therapeutics, is of particular importance. This review provides an overview of CRC and its progression stages, as well as the basic types of CRC biomarkers. We then lay out the synopsis of signaling pathways related to CRC, and further highlight the pivotal and multifaceted role of nuclear factor (NF) κB signaling in CRC. Particularly, we bring forth knowledge regarding the tumor microenvironment (TME) in CRC, and its complex interaction with cancer cells. We also provide examples of NF-κB signaling-related CRC biomarkers, and ongoing efforts made at targeting NF-κB signaling in CRC treatment. We conclude and anticipate that with more emerging novel regulators of the NF-κB pathway being discovered, together with their in-depth characterization and the integration of large groups of genomic, transcriptomic and proteomic data, the day of successful development of more ideal NF-κB inhibitors is fast approaching.

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