scholarly journals Targeted enrichment of novel chloroplast-based probes reveals a large-scale phylogeny of 412 bamboos

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jiongliang Wang ◽  
Weixue Mu ◽  
Ting Yang ◽  
Yue Song ◽  
Yin Guang Hou ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Large Scale ◽  
Probe Design ◽  
Time Saving ◽  
Chloroplast Genomes ◽  
Representative Species ◽  
Monophyletic Lineage ◽  
Sequencing Strategy ◽  
Targeted Enrichment

Abstract Background The subfamily Bambusoideae belongs to the grass family Poaceae and has significant roles in culture, economy, and ecology. However, the phylogenetic relationships based on large-scale chloroplast genomes (CpGenomes) were elusive. Moreover, most of the chloroplast DNA sequencing methods cannot meet the requirements of large-scale CpGenome sequencing, which greatly limits and impedes the in-depth research of plant genetics and evolution. Results To develop a set of bamboo probes, we used 99 high-quality CpGenomes with 6 bamboo CpGenomes as representative species for the probe design, and assembled 15 M unique sequences as the final pan-chloroplast genome. A total of 180,519 probes for chloroplast DNA fragments were designed and synthesized by a novel hybridization-based targeted enrichment approach. Another 468 CpGenomes were selected as test data to verify the quality of the newly synthesized probes and the efficiency of the probes for chloroplast capture. We then successfully applied the probes to synthesize, enrich, and assemble 358 non-redundant CpGenomes of woody bamboo in China. Evaluation analysis showed the probes may be applicable to chloroplasts in Magnoliales, Pinales, Poales et al. Moreover, we reconstructed a phylogenetic tree of 412 bamboos (358 in-house and 54 published), supporting a non-monophyletic lineage of the genus Phyllostachys. Additionally, we shared our data by uploading a dataset of bamboo CpGenome into CNGB (https://db.cngb.org/search/project/CNP0000502/) to enrich resources and promote the development of bamboo phylogenetics. Conclusions The development of the CpGenome enrichment pipeline and its performance on bamboos recommended an inexpensive, high-throughput, time-saving and efficient CpGenome sequencing strategy, which can be applied to facilitate the phylogenetics analysis of most green plants.

scholarly journals Targeted Enrichment of Novel Chloroplast-Based Probes Reveals a Large-Scale Phylogeny of 412 Bamboos

2020 ◽  
Author(s):  
Jiongliang Wang ◽  
Weixue Mu ◽  
Ting Yang ◽  
Yue Song ◽  
YinGuang Hou ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Large Scale ◽  
Probe Design ◽  
Time Saving ◽  
Chloroplast Genomes ◽  
Representative Species ◽  
Monophyletic Lineage ◽  
Sequencing Strategy ◽  
Targeted Enrichment

Abstract Background: The subfamily Bambusoideae belongs to the grass family Poaceae and has significant roles in culture, economy, and ecology. However, the phylogenetic relationships based on large-scale chloroplast genomes (CpGenomes) were elusive. Moreover, most of the chloroplast DNA sequencing methods cannot meet the requirements of large-scale CpGenome sequencing, which greatly limits and impedes the in-depth research of plant genetics and evolution.Results: To develop a set of bamboo probes, we used 99 high-quality CpGenomes with 6 bamboo CpGenomes as representative species for the probe design, and assembled 15M unique sequences as the final pan-chloroplast genome. A total of 180,519 probes for chloroplast DNA fragments were designed and synthesized by a novel hybridization-based targeted enrichment approach. Another 468 CpGenomes were selected as test data to verify the quality of the newly synthesized probes and the efficiency of the probes for chloroplast capture. We then successfully applied the probes to synthesize, enrich, and assemble 358 non-redundant CpGenomes of woody bamboo in China. Evaluation analysis showed the probes may be applicable to chloroplasts in Magnoliales, Pinales, Poales et al. Moreover, we reconstructed a phylogenetic tree of 412 bamboos (358 in-house and 54 published), supporting a non-monophyletic lineage of the genus Phyllostachys. Additionally, we shared our data by uploading a dataset of bamboo CpGenome into CNGB (https://db.cngb.org/search/project/CNP0000502/) to enrich resources and promote the development of bamboo phylogenetics.Conclusions: The development of the CpGenome enrichment pipeline and its performance on bamboos recommended an inexpensive, high-throughput, time-saving and efficient CpGenome sequencing strategy, which can be applied to facilitate the phylogenetics analysis of most green plants.

scholarly journals Automatic Plaster Machine

2020 ◽  
Vol 6 (6) ◽  
pp. 182-185
Author(s):  
Keyur Sanjay Misar ◽  
P M Desai ◽  
Aishwarya Deepak Babar ◽  
Ankita Ramesh Ahire
Keyword(s):  
Large Scale ◽  
Labor Costs ◽  
Construction Sites ◽  
Time Saving ◽  
Total Cost ◽  
Progress Rate ◽  
Cost Of Construction

Presently, on the construction sites, because of the manual process of plastering the walls, there is large scale need of skilled labors and the higher labor costs are responsible for increasing the overall cost of construction of a building. The quality of plastering depends upon the skill of the labor in manual plastering method hence it contains irregular plastering surface which gives rise to risk and hazards to the infrastructure. The solution of the above issues is just to introduce an automatic plastering machine which automates the process so as to save the time and money and achieve better quality of paltering. The finishing of the walls obtained from automatic plaster machine is very smooth and accurate as compared to manual process. Hence the machine is time saving, money saving hence the total cost of the project reduces which ultimately increases the progress rate of our nation

Semi-automated methods for 3-D reconstruction of macromolecular complexes

1995 ◽  
Vol 53 ◽  
pp. 42-43
Author(s):  
B. Carragher ◽  
M. Whittaker
Keyword(s):  
Three Dimensional ◽  
Time Saving ◽  
Macromolecular Complexes ◽  
Symmetry Properties ◽  
Dimensional Reconstruction ◽  
Experienced Operator ◽  
Projection Images ◽  
The Individual ◽  
Natural Symmetry

Techniques for three-dimensional reconstruction of macromolecular complexes from electron micrographs have been successfully used for many years. These include methods which take advantage of the natural symmetry properties of the structure (for example helical or icosahedral) as well as those that use single axis or other tilting geometries to reconstruct from a set of projection images. These techniques have traditionally relied on a very experienced operator to manually perform the often numerous and time consuming steps required to obtain the final reconstruction. While the guidance and oversight of an experienced and critical operator will always be an essential component of these techniques, recent advances in computer technology, microprocessor controlled microscopes and the availability of high quality CCD cameras have provided the means to automate many of the individual steps.During the acquisition of data automation provides benefits not only in terms of convenience and time saving but also in circumstances where manual procedures limit the quality of the final reconstruction.

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.

scholarly journals Are “Internet+” tactics the key to poverty alleviation in China’s rural ethnic minority areas? Empirical evidence from Sichuan Province

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Xiang Yin ◽  
Zhiyi Meng ◽  
Xin Yi ◽  
Yong Wang ◽  
Xia Hua
Keyword(s):  
Ethnic Minority ◽  
Poverty Alleviation ◽  
Large Scale ◽  
Sichuan Province ◽  
Infrastructure Investment ◽  
Communication Infrastructure ◽  
Gdp Growth Rate ◽  
The Relationship ◽  
Positive Effect

AbstractChina has made great efforts to alleviate poverty in rural ethnic minority areas and targeted achieving the poverty-alleviation task by the end of 2020. Aba, Ganzi, and Liangshan, three of the poorest ethnic prefectures in Sichuan Province, Southwest China, have all implemented “Internet+” tactics since 2013, which have had the positive effect of increasing family revenues by improving communication infrastructure and encouraging the large-scale use of e-commerce. This paper aims to comprehensively investigate whether “Internet+” tactics play a key role in poverty alleviation in Sichuan’s rural ethnic minority areas and to propose further measures to enhance the efficiency of e-commerce practice. To this end, we conduct an analysis using the framework of classic growth theory and use panel data from 2000 to 2018 to examine the relationship between Communication Infrastructure Investment (CII) and a set of poverty-alleviation indicators, including local GDP growth rate (LGGR), local government revenue (LGR), and per-capita income of residents (PCIR). The results indicate that strengthening CII improves the PCIR and local economic growth, playing a key role in poverty alleviation. However, the stimulation of CII on LGGR and LGR wanes as time passes. More financial and technical actions will be needed to improve the efficiency and quality of current strategies for sustainable development in those areas.

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