scholarly journals Improving the completeness of public metadata accompanying omics studies

2021 ◽  
Author(s):  
Anushka Rajesh ◽  
Yutong Chang ◽  
Malak S Abedalthagafi ◽  
Annie Wong-Beringer ◽  
Michael I Love ◽  
...  
Keyword(s):  
Gene Expression Omnibus ◽  
Published Data ◽  
Omics Data ◽  
Raw Data ◽  
Systematic Assessment ◽  
Tremendous Progress ◽  
Study Results ◽  
Wide Range ◽  
Public Repositories

Over the last decade there has been tremendous progress to improve the sharing of genomics data, which allows researchers to easily access the various types of data across a wide range of phenotypes. Some of the most well known public repositories are Gene Expression Omnibus, Sequence Read Archive and ArrayExpress. However, despite the availability of raw data, metadata accompanying the raw data is often unavailable. Incomplete and improperly annotated metadata on repositories proves to be a hindrance to reusing and reproducing existing data, especially for making novel discoveries. Leveraging previously published data for novel biological discoveries is only possible to its maximum extent if the metadata that accompanies raw omics data is complete and present in a standardized format. Existing literature has explored how sharing of data should be FAIR - Findable, Accessible, Interoperable and Reusable, and considered accuracy, completeness and consistency as three vital parameters to assess the quality of available metadata, although not many have examined it exclusively as an appendage to omics studies. In our study, we perform a systematic assessment of completeness of public metadata accompanying omics data. We have performed our analysis on sepsis cohorts and are currently extending the same to tuberculosis and cystic fibrosis cohorts. On comparing the data available on both platforms, we observed discrepancies between omics data and the corresponding metadata on public repositories. The results we have for the sepsis cohorts are intriguing and advocate the need to have a standardized "checklist" for researchers to submit their study results and data to public repositories. Our study opens a wide discussion about this being a potential solution to bridge the gap between omics data and metadata on repositories.

Simultaneous compared to interval administration of mifepristone and misoprostol for medical abortion up to 10+0 weeks' gestation: a systematic review with meta-analyses

2020 ◽  
pp. bmjsrh-2019-200448
Author(s):  
Mia Schmidt-Hansen ◽  
Jonathan Lord ◽  
Elise Hasler ◽  
Sharon Cameron
Keyword(s):  
Systematic Review ◽  
Meta Analysis ◽  
Cochrane Collaboration ◽  
Medical Abortion ◽  
Cochrane Library ◽  
Published Data ◽  
Study Results ◽  
Randomised Controlled ◽  
Meta Analyses

BackgroundMedical abortion with mifepristone and misoprostol usually involves an interval of 36–48 hours between administering these drugs; however, it is possible that the clinical efficacy at early gestations may be maintained when the drugs are taken simultaneously. The objective of this systematic review was to determine the safety and effectiveness of simultaneous compared with interval administration of mifepristone and misoprostol for abortion up to 10+0 weeks’ gestation.MethodsWe searched Embase Classic, Embase; Ovid MEDLINE(R) including Daily, and Epub Ahead-of-Print, In-Process & Other Non-Indexed Citations; and Cochrane Library on 11 December 2019. We included randomised controlled trials (RCTs), published in English from 1985, comparing simultaneous to interval administration of mifepristone and misoprostol for early abortion. Risk of bias was assessed using the Cochrane Collaboration checklist for RCTs. Meta-analysis of risk ratios (RRs) using the Mantel-Haenszel method were performed. The quality of the evidence was assessed using GRADE.ResultsMeta-analyses of three RCTs (n=1280) showed no differences in ‘ongoing pregnancy’ (RR 1.78, 95% CI 0.38 to 8.36), ‘haemorrhage requiring transfusion or ≥500 mL blood loss’ (RR 0.11, 95% CI 0.01 to 2.03) and ‘incomplete abortion with the need for surgical intervention’ (RR 1.30, 95% CI 0.76 to 2.25) between the interventions. Individual study results showed no difference in patient satisfaction, or ‘need for repeat misoprostol’, although ‘time to onset of bleeding or cramping’ was longer after simultaneous than interval administration. The quality of evidence was very low to moderate.ConclusionThe published data support the use of simultaneous mifepristone and misoprostol for medical abortion up to 9+0 weeks in women who prefer this method of administration.

Lean manufacturing as a way to optimize costs: Principles, tools, and implementation practices

2021 ◽  
Vol 22 (11) ◽  
pp. 1243-1261
Author(s):  
Anna A. VEKSHINA
Keyword(s):  
Lean Manufacturing ◽  
Staff Members ◽  
Economic Entity ◽  
Study Results ◽  
Wide Range ◽  
Tabular Method ◽  
Entire Country ◽  
Quality Of Products ◽  
Methodological Aspects

Subject. This article deals with the tools of lean manufacturing concept that seek to eliminate losses or minimize them as much as possible while improving the quality of products provided. Objectives. The article aims to examine the theoretical and methodological aspects of the lean concept, and describe the foreign experience of using lean technologies. Methods. For the study, I used the methods of analysis, retrospection, comparison, and generalization. To present the study results, I used the tabular method. Results. The article defines the notion of Loss (Muda) and types of losses specified in dedicated sources. It describes the techniques that help companies eliminate losses and maximize market orientation through their staff members’ participation. The article defines the content and discusses the implications of implementing various key tools of the lean concept. Conclusions. Lean technologies can be implemented both individually and in combination with one another. When combined, the technologies can help both optimize labor and tangible costs, and meet the needs of customers. The use of a wide range of lean concepts can contribute to solving socioeconomic challenges faced by an individual economic entity and the entire country.

scholarly journals Incidence of omental metastasis in uterine serous carcinoma: study protocol for a systematic review and meta-analysis

BMJ Open ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. e043141
Author(s):  
Cui Hu ◽  
Lin-Lin Zhang ◽  
Yu Cheng ◽  
Fei-Xue Xue ◽  
Ya Jia ◽  
...  
Keyword(s):  
Systematic Review ◽  
Meta Analysis ◽  
Gynecologic Oncology ◽  
Serous Carcinoma ◽  
Published Data ◽  
Wide Range ◽  
Uterine Serous Carcinoma ◽  
Endometrial Cancers ◽  
Omental Metastasis

IntroductionUterine serous carcinoma accounts for only about 10% of all endometrial cancers but this subtype is the most common amongst non-endometrioid endometrium cancers and contributes to more than half of recurrence and deaths attributed to endometrial cancers. A more extensive surgical staging and adjuvant therapies for uterine serous carcinoma are recommended by many guidelines. However, guidelines vary on recommendations for the methods that should be used for omentum assessment in uterine serous carcinoma and the previously reported incidence of omental metastasis in uterine serous carcinoma had a wide range because of the heterogeneity among these studies. As far as we know, there are no systematic review and meta-analysis available on this topic. The aim of our proposed study is to statistically synthesise the data examining the incidence of omental metastasis in uterine serous carcinoma.Methods and analysisSystematic searches of three databases (PubMed, Embase and Web of Science) will be performed using prespecified search strategies. We will include original studies that reported incidence of omental metastasis in uterine serous carcinoma and are published before 30 August 2020. Our different investigators will independently conduct the eligible study selection, assess the quality of included studies and extract the needed data. If appropriate, the relevant data will be pooled through a random-effect or fixed-effect meta-analysis based on the heterogeneity among included studies. We will evaluate the overall quality of evidence using appropriate methods.Ethics and disseminationThis proposed study will be based on published data, and thus, there is no requirement for ethics approval. We aim to publish the results of this study in a peer-reviewed journal with good visibility for the fields of gynaecology and gynecologic oncology.PROSPERO registration numberCRD42020200891.

scholarly journals Amazonia!: An Online Resource to Google and Visualize Public Human whole Genome Expression Data

2010 ◽  
Vol 4 (1) ◽  
pp. 5-10 ◽  
Author(s):  
Tanguy Le Carrour ◽  
Said Assou ◽  
Sylvie Tondeur ◽  
Ludovic Lhermitte ◽  
Ned Lamb ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem ◽  
Published Data ◽  
Transcriptome Data ◽  
Specific Expression ◽  
Human Transcriptome ◽  
Normal Tissues ◽  
Junction Protein ◽  
Wide Range ◽  
Public Repositories

Available transcriptome data accumulate in public repositories, individual web pages or as various supplemental data, but these published data cannot be routinely accessed. We have developed the web based tool Amazonia! to overcome this hurdle and provide the possibility to query and to visualize the expression of a given gene in representative and selected human transcriptome datasets. This expression atlas provides expression bar plots for single genes, across samples selected from a wide range of normal tissues and malignancies, including pluripotent stem cells. When produced by the same platform type, datasets were renormalized and combined in order to generate series of several hundreds samples. Samples types are colored and ordered, and grouped in thematic pages for ease of navigation. We also integrated gene lists provided by original publications describing these microarray data, allowing the scientific community to challenge the expression of genes in datasets other than those for which they were initially published. To illustrate the powerfulness of this simple tool, we show how Amazonia! reveals the specific expression of the tight junction protein Claudin 6 in human embryonic stem cells and human induced stem cells (iPS), or the tissue specific expression of some chemokines and their receptors such as CCL16 in liver and CX3CR1 in central nervous system samples. Thus, Amazonia! advantageously complements large public repositories by providing a simple way to query a compilation of selected human transcriptome data. The tool is freely available at http://www.amazonia.transcriptome.eu/

scholarly journals 3D INDOOR MAPPING WITH THE MICROSOFT HOLOLENS: QUALITATIVE AND QUANTITATIVE EVALUATION BY MEANS OF GEOMETRIC FEATURES

2020 ◽  
Vol V-1-2020 ◽  
pp. 165-172
Author(s):  
M. Weinmann ◽  
M. A. Jäger ◽  
S. Wursthorn ◽  
B. Jutzi ◽  
M. Weinmann ◽  
...  
Keyword(s):  
Rapid Development ◽  
Semantic Segmentation ◽  
Random Forest Classifier ◽  
Geometric Features ◽  
Qualitative And Quantitative ◽  
Fast Acquisition ◽  
Tremendous Progress ◽  
Wide Range ◽  
Microsoft Hololens

Abstract. 3D indoor mapping and scene understanding have seen tremendous progress in recent years due to the rapid development of sensor systems, reconstruction techniques and semantic segmentation approaches. However, the quality of the acquired data strongly influences the accuracy of both reconstruction and segmentation. In this paper, we direct our attention to the evaluation of the mapping capabilities of the Microsoft HoloLens in comparison to high-quality TLS systems with respect to 3D indoor mapping, feature extraction and semantic segmentation. We demonstrate how a set of rather interpretable low-level geometric features and the resulting semantic segmentation achieved with a Random Forest classifier applied on these features are affected by the quality of the acquired data. The achieved results indicate that, while allowing for a fast acquisition of room geometries, the HoloLens provides data with sufficient accuracy for a wide range of applications.

Microsurgery Fellowship Website and Social Media Presence: Are Programs Optimizing Recruitment Strategy?

2020 ◽  
Author(s):  
Andrew Atia ◽  
Hannah C. Langdell ◽  
Andrew Hollins ◽  
Ronnie L. Shammas ◽  
Adam Glener ◽  
...  
Keyword(s):  
Social Media ◽  
Plastic Surgery ◽  
San Francisco ◽  
Selection Process ◽  
Recruitment Strategy ◽  
Published Data ◽  
Social Media Presence ◽  
Eligibility Requirements ◽  
Program Description

Abstract Background Microsurgery fellowship applicants make decisions for future training based on information obtained from colleagues, mentors, and microsurgery fellowship program Websites (MFWs). In this study, we sought to evaluate the accessibility and quality of available information by microsurgery programs by analyzing the most commonly used web resources and social media outlets for applicants. Methods The San Francisco (SF) Match and American Society of Reconstructive Microsurgery Websites were queried in April 2020 for microsurgery fellowship programs (MFPs) participating in the SF Match. Twenty-two independent variables of information were assessed on MFWs based on previously published data. Social media presence was also assessed by querying Facebook, Instagram, and Twitter for official hospital, plastic surgery residency, and microsurgery fellowship accounts. Results All 24 MFWs participating in the SF Match had a webpage. Program description, faculty listing, operative volume, and eligibility requirements were listed for all programs (100%). The majority of MFWs listed affiliated hospitals (75%), provided a link to the fellowship application (66.7%), listed interview dates (66.7%), and highlighted research interests (50%). A minority of MFWs provided information on conference schedule (37.5%), current fellow listing (25%), previous fellow listing (16.67%), and positions held by previous fellows (8.33%). No MFWs (0%) presented information on selection process, or rotation schedule.All hospitals with an MFP had a Facebook page and nearly all had Instagram (83.3%) and Twitter accounts (95.8%). Plastic surgery residency programs at the same institution of an MFP had social media presence on Facebook (38.9%), Twitter (38.9%), and Instagram (66.7%). Only three MFPs had Facebook accounts (12.5%) and none had Instagram or Twitter accounts. Conclusion As the field of microsurgery continues to grow, the need for effective recruitment and training of microsurgeons continues to be essential. Overall, we conclude that both the accessibility and quality of information available to applicants are limited, which is a missed opportunity for recruitment.

COMBINATORIAL POLYNOMIALLY COMPUTABLE CHARACTERISTICS OF SUBSTITUTIONS AND THEIR PROPERTIES

2020 ◽  
Vol 7 (2) ◽  
pp. 34-41
Author(s):  
VLADIMIR NIKONOV ◽  
◽  
ANTON ZOBOV ◽  
Keyword(s):  
Mathematical Expectation ◽  
Point Of View ◽  
Small Range ◽  
Computational Point ◽  
Wide Range ◽  
Bijective Function ◽  
The Difference ◽  
Element Base ◽  
Selection Of

The construction and selection of a suitable bijective function, that is, substitution, is now becoming an important applied task, particularly for building block encryption systems. Many articles have suggested using different approaches to determining the quality of substitution, but most of them are highly computationally complex. The solution of this problem will significantly expand the range of methods for constructing and analyzing scheme in information protection systems. The purpose of research is to find easily measurable characteristics of substitutions, allowing to evaluate their quality, and also measures of the proximity of a particular substitutions to a random one, or its distance from it. For this purpose, several characteristics were proposed in this work: difference and polynomial, and their mathematical expectation was found, as well as variance for the difference characteristic. This allows us to make a conclusion about its quality by comparing the result of calculating the characteristic for a particular substitution with the calculated mathematical expectation. From a computational point of view, the thesises of the article are of exceptional interest due to the simplicity of the algorithm for quantifying the quality of bijective function substitutions. By its nature, the operation of calculating the difference characteristic carries out a simple summation of integer terms in a fixed and small range. Such an operation, both in the modern and in the prospective element base, is embedded in the logic of a wide range of functional elements, especially when implementing computational actions in the optical range, or on other carriers related to the field of nanotechnology.

Penatalaksanaan IMD pada Ibu Postpartum Sectio Caesarea Mempengaruhi Status Gizi dan Kecepatan Produksi ASI

2020 ◽  
Vol 2 (2) ◽  
pp. 112-120
Author(s):  
Nursari Abdul Syukur ◽  
Susi Purwanti
Keyword(s):  
Breast Milk ◽  
Nutritional Status ◽  
Milk Production ◽  
Quantitative Research ◽  
Milk Protein ◽  
Sectio Caesarea ◽  
Control Group ◽  
P Value ◽  
Study Results

Many mothers who give birth to Sectio Caesarea (SC) do not Initiate Early Breastfeeding (IMD), which fails exclusive breastfeeding. This study aimed to determine the effect of IMD management in postpartum SC mothers on nutritional status, speed of milk production, and quality of breast milk protein. Method: quantitative research with quasi approach experiment. The research design used was a pre-post-test control non-equivalent control group. A sampling of this study used the Consecutive method sampling with a sample of 20 mothers who gave birth by cesarean section (SC). Hypothesis testing uses the independent t-test and the Mann-Whitney test. The study results showed an influence on the management of IMD in postpartum SC mothers on the speed of ASI production (p-value=0.004) and nutritional status (p-value=0.028). There was no effect of IMD management on postpartum SC mothers on the quality of breast milk protein (p-value = 0.543). This study recommends that the hospital implement an IMD promotion program before the abdominal wall is closed as a form of intervention to increase milk production and maternal nutritional status

INFLUENCE OF FORCED CONVECTION IN LIQUID INSIDE THE TIN ON DURATION OF STERILIZATION IN THE COURSE OF FISH PROCESSING

2017 ◽  
pp. 137-144
Author(s):  
Gennadiy Valentinovich Alexeev ◽  
Elena Igorevna Verboloz
Keyword(s):  
High Temperature ◽  
Liquid Phase ◽  
Forced Convection ◽  
Thermal Process ◽  
Processing Time ◽  
Fish Processing ◽  
Study Results ◽  
Equipment Modernization ◽  
Bottom To Top

The article focuses on the process of intensive mixing of liquid phase in the tin during high-temperature sterilization, i.e. sterilization when temperature of the heat carrier reaches 150-160°C. It has been stated that for intensification of the thermal process during sterilization of tinned fish with liquid filling it is preferable to turn a tin from bottom to top. This operation helps to increase the driving power of the process and to shorten warming time. Besides, high-temperature sterilization carried out according to experimental modes, where the number of tin turnovers is calculated, greatly shortens processing time and improves quality of the product. In this case there is no superheating, all tins are evenly heated. The study results will contribute to equipment modernization and to preserving valuable food qualities.

The Influence of Barrier and Applied Voltage Parameters on the Impulse Surface Discharge Characteristics

2020 ◽  
Vol 11 (11) ◽  
pp. 17-27
Author(s):  
Vadim V. VOEVODIN ◽  
◽  
Marina V. SOKOLOVA ◽  
Viktor R. SOLOV’YEV ◽  
Nikolay Yu. LYSOV ◽  
...  
Keyword(s):  
Applied Voltage ◽  
Voltage Pulse ◽  
Discharge Zone ◽  
Surface Discharge ◽  
Initial Surface ◽  
Barrier Material ◽  
Dielectric Barrier ◽  
Discharge Ignition ◽  
Study Results ◽  
Wide Range

The results from an experimental study of impulse surface discharge occurring in an electrode system containing a dielectric plate are presented. On one of its sides, the plate had a corona-producing electrode made of 50 mm thick copper foil grounded through a current shunt for measuring the discharge current. On its other side, the plate had a high-voltage electrode, to which the voltage from a pulse generator was applied. The article presents the results from measurements of the initial voltage and the sizes of the surface discharge area in air when applying single voltage pulses with different pulse front steepness in the range 0,1–3,4 kV/ms and amplitude in the range 7–15 kV. The measurements were carried out for different dielectric barrier materials with the e values from 2 to 35. The dielectric barrier thickness was 0,9–1,8 mm. The study results have shown that the initial surface discharge ignition voltage depends essentially on the voltage pulse parameters, whereas the barrier characteristics have a weaker effect on this voltage. It has been determined that the discharge has different discharge zone length and different structure depending on the dielectric barrier properties and applied voltage parameters. The streamer zone sizes decrease with increasing the barrier material e value at the same voltage pulse steepness and increase with increasing the steepness for each barrier material. The data obtained for a wide range of external conditions can be used in numerical modeling of discharge.

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