scholarly journals Robust single-cell DNA methylome profiling with snmC-seq2

2018 ◽  
Author(s):  
Chongyuan Luo ◽  
Angeline Rivkin ◽  
Jingtian Zhou ◽  
Justin P. Sandoval ◽  
Laurie Kurihara ◽  
...  
Keyword(s):  
Single Cell ◽  
Large Scale ◽  
Cellular Reprogramming ◽  
Read Mapping ◽  
Dna Methylome ◽  
Efficient Strategy ◽  
Library Complexity

Single-cell DNA methylome profiling has enabled the study of epigenomic heterogeneity in complex tissues and during cellular reprogramming. However, broader applications of the method have been impeded by the modest quality of sequencing libraries. Here we report snmC-seq2, which provides improved read mapping, reduced artifactual reads, enhanced throughput, as well as increased library complexity and coverage uniformity compared to snmC-seq. snmC-seq2 is an efficient strategy suited for large scale single-cell epigenomic studies.

scholarly journals destiny – diffusion maps for large-scale single-cell data in R

2015 ◽  
Author(s):  
Philipp Angerer ◽  
Laleh Haghverdi ◽  
Maren Büttner ◽  
Fabian J. Theis ◽  
Carsten Marr ◽  
...  
Keyword(s):  
Single Cell ◽  
Large Scale ◽  
Cellular Reprogramming ◽  
Noise Model ◽  
Diffusion Maps ◽  
Time Resolved ◽  
Describing Functions ◽  
Link Type ◽  
Cell Expression ◽  
Cell Data

ABSTRACTSummaryDiffusion maps are a spectral method for non-linear dimension reduction and have recently been adapted for the visualization of single cell expression data. Here we present destiny, an efficient R implementation of the diffusion map algorithm. Our package includes a single-cell specific noise model allowing for missing and censored values. In contrast to previous implementations, we further present an efficient nearest-neighbour approximation that allows for the processing of hundreds of thousands of cells and a functionality for projecting new data on existing diffusion maps. We exemplarily apply destiny to a recent time-resolved mass cytometry dataset of cellular reprogramming.Availability and implementationdestiny is an open-source R/Bioconductor package http://bioconductor.org/packages/ destiny also available at https://www.helmholtz-muenchen.de/icb/destiny. A detailed vignette describing functions and workflows is provided with the [email protected], [email protected]

scholarly journals Cumulus: a cloud-based data analysis framework for large-scale single-cell and single-nucleus RNA-seq

2019 ◽  
Author(s):  
Bo Li ◽  
Joshua Gould ◽  
Yiming Yang ◽  
Siranush Sarkizova ◽  
Marcin Tabaka ◽  
...  
Keyword(s):  
Single Cell ◽  
Large Scale ◽  
Bone Marrow Cells ◽  
Low Cost ◽  
Data Generation ◽  
Rna Seq ◽  
User Friendliness ◽  
Health And Disease ◽  
Single Nucleus

AbstractMassively parallel single-cell and single-nucleus RNA-seq (sc/snRNA-seq) have opened the way to systematic tissue atlases in health and disease, but as the scale of data generation is growing, so does the need for computational pipelines for scaled analysis. Here, we developed Cumulus, a cloud-based framework for analyzing large scale sc/snRNA-seq datasets. Cumulus combines the power of cloud computing with improvements in algorithm implementations to achieve high scalability, low cost, user-friendliness, and integrated support for a comprehensive set of features. We benchmark Cumulus on the Human Cell Atlas Census of Immune Cells dataset of bone marrow cells and show that it substantially improves efficiency over conventional frameworks, while maintaining or improving the quality of results, enabling large-scale studies.

scholarly journals Aligning single-cell developmental and reprogramming trajectories identifies molecular determinants of reprogramming outcome

2017 ◽  
Author(s):  
Davide Cacchiarelli ◽  
Xiaojie Qiu ◽  
Sanjay Srivatsan ◽  
Michael Ziller ◽  
Eliah Overbey ◽  
...  
Keyword(s):  
Single Cell ◽  
Large Scale ◽  
Human Fibroblasts ◽  
Cell Types ◽  
Cellular Reprogramming ◽  
Bmp Signaling ◽  
Great Promise ◽  
Scale Production ◽  
Branch Points ◽  
Molecular Determinants

AbstractCellular reprogramming through manipulation of defined factors holds great promise for large-scale production of cell types needed for use in therapy, as well as for expanding our understanding of the general principles of gene regulation. MYOD-mediated myogenic reprogramming, which converts many cell types into contractile myotubes, remains one of the best characterized model system for direct conversion by defined factors. However, why MYOD can efficiently convert some cell types into myotubes but not others remains poorly understood. Here, we analyze MYOD-mediated reprogramming of human fibroblasts at pseudotemporal resolution using single-cell RNA-Seq. Successfully reprogrammed cells navigate a trajectory with two branches that correspond to two barriers to reprogramming, with cells that select incorrect branches terminating at aberrant or incomplete reprogramming outcomes. Differential analysis of the major branch points alongside alignment of the successful reprogramming path to a primary myoblast trajectory revealed Insulin and BMP signaling as crucial molecular determinants of an individual cell’s reprogramming outcome, that when appropriately modulated, increased efficiency more than five-fold. Our single-cell analysis reveals that MYOD is sufficient to reprogram cells only when the extracellular milieu is favorable, supporting MYOD with upstream signaling pathways that drive normal myogenesis in development.

scholarly journals Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming

2017 ◽  
Author(s):  
Geoffrey Schiebinger ◽  
Jian Shu ◽  
Marcin Tabaka ◽  
Brian Cleary ◽  
Vidya Subramanian ◽  
...  
Keyword(s):  
Single Cell ◽  
Cellular Differentiation ◽  
Large Scale ◽  
Time Course ◽  
Optimal Transport ◽  
Cellular Reprogramming ◽  
Modern Biology ◽  
Cell Class ◽  
High Resolution Map ◽  
Cell Gene Expression

AbstractUnderstanding the molecular programs that guide cellular differentiation during development is a major goal of modern biology. Here, we introduce an approach, WADDINGTON-OT, based on the mathematics of optimal transport, for inferring developmental landscapes, probabilistic cellular fates and dynamic trajectories from large-scale single-cell RNA-seq (scRNA-seq) data collected along a time course. We demonstrate the power of WADDINGTON-OT by applying the approach to study 65,781 scRNA-seq profiles collected at 10 time points over 16 days during reprogramming of fibroblasts to iPSCs. We construct a high-resolution map of reprogramming that rediscovers known features; uncovers new alternative cell fates including neuraland placental-like cells; predicts the origin and fate of any cell class; highlights senescent-like cells that may support reprogramming through paracrine signaling; and implicates regulatory models in particular trajectories. Of these findings, we highlight Obox6, which we experimentally show enhances reprogramming efficiency. Our approach provides a general framework for investigating cellular differentiation.

Assessment of quality of life in patients with the effects of transient ischemic stroke

2016 ◽  
pp. 37-39
Author(s):  
A. Babirad
Keyword(s):  
Quality Of Life ◽  
Ischemic Stroke ◽  
Large Scale ◽  
Cerebrovascular Diseases ◽  
Control Measures ◽  
Sociological Research ◽  
Cerebrovascular Events ◽  
Sf 36 ◽  
Angioplasty And Stenting

Cerebrovascular diseases are a problem of the world today, and according to the forecast, the problem of the near future arises. The main risk factors for the development of ischemic disorders of the cerebral circulation include oblique and aging, arterial hypertension, smoking, diabetes mellitus and heart disease. An effective strategy for the prevention of cerebrovascular events is based on the implementation of large-scale risk control measures, including the use of antiagregant and anticoagulant therapy, invasive interventions such as atheromectomy, angioplasty and stenting. In this connection, the efforts of neurologists, cardiologists, angiosurgery, endocrinologists and other specialists are the basis for achieving an acceptable clinical outcome. A review of the SF-36 method for assessing the quality of life in patients with the effects of transient ischemic stroke is presented. The assessment of quality of life is recognized in world medical practice and research, an indicator that is also used to assess the quality of the health system and in general sociological research.

Model and Method for Contributor’s Quality Assessment in Community Image Tagging Systems

2018 ◽  
pp. 45-51
Author(s):  
A. V. Ponomarev
Keyword(s):  
Large Scale ◽  
Wide Spectrum ◽  
Preference Relation ◽  
Pairwise Comparison ◽  
Ground Truth ◽  
Comparison Method ◽  
Characteristic Matrix ◽  
Image Tagging ◽  
Proposed Model

Introduction: Large-scale human-computer systems involving people of various skills and motivation into the information processing process are currently used in a wide spectrum of applications. An acute problem in such systems is assessing the expected quality of each contributor; for example, in order to penalize incompetent or inaccurate ones and to promote diligent ones.Purpose: To develop a method of assessing the expected contributor’s quality in community tagging systems. This method should only use generally unreliable and incomplete information provided by contributors (with ground truth tags unknown).Results:A mathematical model is proposed for community image tagging (including the model of a contributor), along with a method of assessing the expected contributor’s quality. The method is based on comparing tag sets provided by different contributors for the same images, being a modification of pairwise comparison method with preference relation replaced by a special domination characteristic. Expected contributors’ quality is evaluated as a positive eigenvector of a pairwise domination characteristic matrix. Community tagging simulation has confirmed that the proposed method allows you to adequately estimate the expected quality of community tagging system contributors (provided that the contributors' behavior fits the proposed model).Practical relevance: The obtained results can be used in the development of systems based on coordinated efforts of community (primarily, community tagging systems). 

Translation and Validation of the Thai Version of the Wisconsin Quality of Life Questionnaire (TH WISQoL) for Kidney Stone Patients

2020 ◽  
Vol 103 (11) ◽  
pp. 1194-1199
Keyword(s):  
Quality Of Life ◽  
Internal Consistency ◽  
Kidney Stone ◽  
Convergent Validity ◽  
Large Scale ◽  
Short Form ◽  
Outcome Measurement ◽  
Life Questionnaire ◽  
Sf 36

Objective: To develop and validate a Thai version of the Wisconsin Quality of Life (TH WISQoL) Questionnaire. Materials and Methods: The authors developed the TH WISQoL Questionnaire based on a standard multi-step process. Subsequently, the authors recruited patients with kidney stone and requested them to complete the TH WISQoL and a validated Thai version of the 36-Item Short Form Survey (TH SF-36). The authors calculated the internal consistency and interdomain correlation of TH WISQoL and compared the convergent validity between the two instruments. Results: Thirty kidney stone patients completed the TH WISQoL and the TH SF-36. The TH WISQoL showed acceptable internal consistency for all domains (Cronbach’s alpha 0.768 to 0.909). Interdomain correlation was high for most domains (r=0.698 to 0.779), except for the correlation between Vitality and Disease domains, which showed a moderate correlation (r=0.575). For convergent validity, TH WISQoL demonstrated a good overall correlation to TH SF-36, (r=0.796, p<0.05). Conclusion: The TH WISQoL is valid and reliable for evaluating the quality of life of Thai patients with kidney stone. A further large-scale multi-center study is warranted to confirm its applicability in Thailand. Keywords: Quality of life, Kidney stone, Validation, Outcome measurement

Evaluating Qualitative Research

2017 ◽  
Author(s):  
Jeasik Cho
Keyword(s):  
Qualitative Research ◽  
Large Scale ◽  
Academic Research ◽  
Research Community ◽  
Assessment Tools ◽  
Journal Articles ◽  
Journal Editors ◽  
The Past ◽  
Grant Proposals

This book provides the qualitative research community with some insight on how to evaluate the quality of qualitative research. This topic has gained little attention during the past few decades. We, qualitative researchers, read journal articles, serve on masters’ and doctoral committees, and also make decisions on whether conference proposals, manuscripts, or large-scale grant proposals should be accepted or rejected. It is assumed that various perspectives or criteria, depending on various paradigms, theories, or fields of discipline, have been used in assessing the quality of qualitative research. Nonetheless, until now, no textbook has been specifically devoted to exploring theories, practices, and reflections associated with the evaluation of qualitative research. This book constructs a typology of evaluating qualitative research, examines actual information from websites and qualitative journal editors, and reflects on some challenges that are currently encountered by the qualitative research community. Many different kinds of journals’ review guidelines and available assessment tools are collected and analyzed. Consequently, core criteria that stand out among these evaluation tools are presented. Readers are invited to join the author to confidently proclaim: “Fortunately, there are commonly agreed, bold standards for evaluating the goodness of qualitative research in the academic research community. These standards are a part of what is generally called ‘scientific research.’ ”

scholarly journals A standardized framework for testing the performance of sleep-tracking technology: step-by-step guidelines and open-source code

SLEEP ◽  
2020 ◽  
Author(s):  
Luca Menghini ◽  
Nicola Cellini ◽  
Aimee Goldstone ◽  
Fiona C Baker ◽  
Massimiliano de Zambotti
Keyword(s):  
Open Source ◽  
Validation Studies ◽  
Large Scale ◽  
Analytical Framework ◽  
Clinical Settings ◽  
Large Scale Data ◽  
Fast Pace ◽  
Epoch Analysis ◽  
Tracking Devices

Abstract Sleep-tracking devices, particularly within the consumer sleep technology (CST) space, are increasingly used in both research and clinical settings, providing new opportunities for large-scale data collection in highly ecological conditions. Due to the fast pace of the CST industry combined with the lack of a standardized framework to evaluate the performance of sleep trackers, their accuracy and reliability in measuring sleep remains largely unknown. Here, we provide a step-by-step analytical framework for evaluating the performance of sleep trackers (including standard actigraphy), as compared with gold-standard polysomnography (PSG) or other reference methods. The analytical guidelines are based on recent recommendations for evaluating and using CST from our group and others (de Zambotti and colleagues; Depner and colleagues), and include raw data organization as well as critical analytical procedures, including discrepancy analysis, Bland–Altman plots, and epoch-by-epoch analysis. Analytical steps are accompanied by open-source R functions (depicted at https://sri-human-sleep.github.io/sleep-trackers-performance/AnalyticalPipeline_v1.0.0.html). In addition, an empirical sample dataset is used to describe and discuss the main outcomes of the proposed pipeline. The guidelines and the accompanying functions are aimed at standardizing the testing of CSTs performance, to not only increase the replicability of validation studies, but also to provide ready-to-use tools to researchers and clinicians. All in all, this work can help to increase the efficiency, interpretation, and quality of validation studies, and to improve the informed adoption of CST in research and clinical settings.

scholarly journals Implementing an Integrated Large-Scale Clinical Information System for ISSSTE’s Hospital Network in Mexico

2021 ◽  
Vol 3 (2) ◽  
pp. 444-453
Author(s):  
Arturo Cervantes Trejo ◽  
Sophie Domenge Treuille ◽  
Isaac Castañeda Alcántara
Keyword(s):  
Health Care ◽  
Information System ◽  
Health Care Services ◽  
Large Scale ◽  
Clinical Information System ◽  
Clinical Information ◽  
Public Hospitals ◽  
Care Services ◽  
Cost Reductions

AbstractThe Institute for Security and Social Services for State Workers (ISSSTE) is a large public provider of health care services that serve around 13.2 million Mexican government workers and their families. To attain process efficiencies, cost reductions, and improvement of the quality of diagnostic and imaging services, ISSSTE was set out in 2019 to create a digital filmless medical image and report management system. A large-scale clinical information system (CIS), including radiology information system (RIS), picture archiving and communication system (PACS), and clinical data warehouse (CDW) components, was implemented at ISSSTE’s network of forty secondary- and tertiary-level public hospitals, applying global HL-7 and Digital Imaging and Communications in Medicine (DICOM) standards. In just 5 months, 40 hospitals had their endoscopy, radiology, and pathology services functionally interconnected within a national CIS and RIS/PACS on secure private local area networks (LANs) and a secure national wide area network (WAN). More than 2 million yearly studies and reports are now in digital form in a CDW, securely stored and always available. Benefits include increased productivity, reduced turnaround times, reduced need for duplicate exams, and reduced costs. Functional IT solutions allow ISSSTE hospitals to leave behind the use of radiographic film and printed medical reports with important cost reductions, as well as social and environmental impacts, leading to direct improvement in the quality of health care services rendered.

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