WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data [version 3; peer review: 2 approved]
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ABSTRACT:
SUBMITTER: Geles K
PROVIDER: S-EPMC8276195 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:WIND: A Workflow for pIRNAs aNd beyonD, for the evaluation of the performance in piRNAs high expression and low expression conditions, we used Human Testis RNAs (BioChain Institute Inc, Newark, CA, USA) and COLO 205 cell line RNAs (samples are available on ArrayExpress (E-MTAB-8115: Non_treated_Testis_1 and Non_treated_COLO205_1, Non_treated_COLO205_2, Non_treated_COLO205_3).
2020-11-25 | E-MTAB-9782 | biostudies-arrayexpress
Project description:For the evaluation of "WIND: A Workflow for pIRNAs aNd beyonD" performance and the transcriptomic approach on small-RNA identification, and particularly on piRNAs, two mouse Adult Cardiomyocytes (aCMs) were used.
2020-11-28 | E-MTAB-9866 | biostudies-arrayexpress
Project description:For the evaluation of \\"WIND: A Workflow for pIRNAs aNd beyonD\\" performance and the transcriptomic approach on small-RNA identification, and particularly on piRNAs, a synthetic set of 4 piRNA-like molecules was used. Two non-methylated (SS-22 and SS-28) and two methylated (mSS-22 and mSS-28) of two different lengths (22 nt and 28 nt) were included. Spike-ins were chemically synthesised at Exiqon, the pool of 4 molecules was used at three different concentrations, with a final amount of 0.3 x 10^9 (dil_A), 0.3 x 10^10 (dil_B) and 0.3 x 10^11 (dil_C) molecules/ug of RNA. Library preparation and sequencing were done as previously described in Sellitto et al 2019 (doi: https://doi.org/10.3390/cells8111390)
2020-11-25 | E-MTAB-9772 | biostudies-arrayexpress
Project description:Cohort studies collect, generate and distribute data over long periods of time – often over the lifecourse of their participants. It is common for these studies to host a list of publications (which can number many thousands) on their website to demonstrate the impact of the study and facilitate the search of existing research to which the study data has contributed. The ability to search and explore these publication lists varies greatly between studies. We believe a lack of rich search and exploration functionality of study publications is a barrier to entry for new or prospective users of a study’s data, since it may be difficult to find and evaluate previous work in a given area. These lists of publications are also typically manually curated, resulting in a lack of rich metadata to analyse, making bibliometric analysis difficult. We present here a software pipeline that aggregates metadata from a variety of third-party providers to power a web based search and exploration tool for lists of publications. Alongside core publication metadata (i.e. author lists, keywords etc.), we include geocoding of first authors and citation counts in our pipeline. This allows a characterisation of a study as a whole based on common locations of authors, frequency of keywords, citation profile etc. This enriched publications metadata can be useful for generating study impact metrics and web-based graphics for public dissemination. In addition, the pipeline produces a research data set for bibliometric analysis or social studies of science. We use a previously published list of publications from a cohort study as an exemplar input data set to show the output and utility of the pipeline here.
| S-EPMC8108552 | biostudies-literature
Project description:Mounting evidence indicates that worldwide, innovation systems are increasing unsustainable. Equally, concerns about inequities in the science and innovation process, and in access to its benefits, continue. Against a backdrop of growing health, economic and scientific challenges global stakeholders are urgently seeking to spur innovation and maximize the just distribution of benefits for all. Open Science collaboration (OS) - comprising a variety of approaches to increase open, public, and rapid mobilization of scientific knowledge - is seen to be one of the most promising ways forward. Yet, many decision-makers hesitate to construct policy to support the adoption and implementation of OS without access to substantive, clear and reliable evidence. In October 2017, international thought-leaders gathered at an Open Science Leadership Forum in the Washington DC offices of the Bill and Melinda Gates Foundation to share their views on what successful Open Science looks like. Delegates from developed and developing nations, national governments, science agencies and funding bodies, philanthropy, researchers, patient organizations and the biotechnology, pharma and artificial intelligence (AI) industries discussed the outcomes that would rally them to invest in OS, as well as wider issues of policy and implementation. This first of two reports, summarizes delegates' views on what they believe OS will deliver in terms of research, innovation and social impact in the life sciences. Through open and collaborative process over the next months, we will translate these success outcomes into a toolkit of quantitative and qualitative indicators to assess when, where and how open science collaborations best advance research, innovation and social benefit. Ultimately, this work aims to develop and openly share tools to allow stakeholders to evaluate and re-invent their innovation ecosystems, to maximize value for the global public and patients, and address long-standing questions about the mechanics of innovation.
| S-EPMC7839829 | biostudies-literature
Project description:Background: Bladder adenocarcinoma (AC) is a scarce histological variant and there are few studies on its proper management. No previous case reports present the management of a urachal tumor and the incidental finding of bladder adenocarcinoma. Clinical case: We present the case of a young woman with nonspecific symptoms, who presented with a prior history of dysuria, bladder tenesmus, suprapubic pain and urinary urgency for one year, which had been treated as recurrent urinary tract infection. A partial cystectomy plus extended lymphadenectomy was scheduled. We found a bladder tumor with characteristics of a urachal tumor and the pathological report indicated a primary bladder AC. The patient had a complete recovery at one year of follow-up. Conclusions: A patient can present with a tumor with urachal characteristics; however, the pathology report can show primary AC. The decision to perform partial cystectomy was an appropriate option for the location of this tumor, with optimal surgical results. Still, a long-term follow-up is necessary. More specific management guidelines are required for the treatment of AC.
| S-EPMC7416577 | biostudies-literature
Project description:Areas of open science (OS) policy and practice are already relatively well-advanced in several countries and sectors through the initiatives of some governments, funders, philanthropy, researchers and the community. Nevertheless, the current research and innovation system, including in the focus of this report, the life sciences, remains weighted against OS. In October 2017, thought-leaders from across the world gathered at an Open Science Leadership Forum in the Washington DC office of the Bill and Melinda Gates Foundation to share their views on what successful OS looks like. We focused on OS partnerships as this is an emerging model that aims to accelerate science and innovation. These outcomes are captured in a first meeting report: Defining Success in Open Science. On several occasions, these conversations turned to the challenges that must be addressed and new policies required to effectively and sustainably advance OS practice. Thereupon, in this report, we describe the concerns raised and what is needed to address them supplemented by our review of the literature, and suggest the stakeholder groups that may be best placed to begin to take action. It emerges that to be successful, OS will require the active engagement of all stakeholders: while the research community must develop research questions, identify partners and networks, policy communities need to create an environment that is supportive of experimentation by removing barriers. This report aims to contribute to ongoing discussions about OS and its implementation. It is also part of a step-wise process to develop and mobilize a toolkit of quantitative and qualitative indicators to assist global stakeholders in implementing high value OS collaborations. Currently in co-development through an open and international process, this set of measures will allow the generation of needed evidence on the influence of OS partnerships on research, innovation, and critical social and economic goals.
| S-EPMC7845503 | biostudies-literature
Project description:For decades, the supra-inflation increase of subscription prices for scholarly journals has concerned scholarly institutions. After years of fruitless efforts to solve this “serials crisis”, open access has been proposed as the latest potential solution. However, also the prices for open access publishing are high and are rising well beyond inflation. What has been missing from the public discussion so far is a quantitative approach to determine the actual
| S-EPMC8276192 | biostudies-literature
Project description:Background: The lack of real-time monitoring is one of the reasons for the lack of awareness among drivers of their dangerous driving behavior. This work aims to develop a driver profiling system where a smartphone’s built-in sensors are used alongside machine learning algorithms to classify different driving behaviors. Methods: We attempt to determine the optimal combination of smartphone sensors such as accelerometer, gyroscope, and GPS in order to develop an accurate machine learning algorithm capable of identifying different driving events (e.g. turning, accelerating, or braking). Results: In our preliminary studies, we encountered some difficulties in obtaining consistent driving events, which had the potential to add “noise” to the observations, thus reducing the accuracy of the classification. However, after some pre-processing, which included manual elimination of extraneous and erroneous events, and with the use of the Convolutional Neural Networks (CNN), we have been able to distinguish different driving events with an accuracy of about 95%. Conclusions: Based on the results of preliminary studies, we have determined that the proposed approach is effective in classifying different driving events, which in turn will allow us to determine driver’s driving behavior.
| S-EPMC10111143 | biostudies-literature
Project description:Background: The purpose of this work is to study the prospects of using charity lotteries as a marketing tool for involving consumers and employees in charitable activities. Methods: The research methodology is based on the principles of the theory of planned behavior by Ajzen. Results: The study confirmed that behavioral intention is correlated with actual behavior. Subjective norms factors have the most significant influence on behavioral intention. Conclusions: Correlation analysis allowed us to establish a weak effect of socio-demographic characteristics (Age, Gender, Capital Status, Ownership of Home, Educational Qualification, Employment, Annual Income) on behavior. The experience of participating in the lottery in the past also turned out to be insignificant. There is reason to believe that Russian consumers' decision to participate in the charity lottery is impulsive or due to pressure from their surroundings.
| S-EPMC9350437 | biostudies-literature