scholarly journals Effects of sheared chromatin length on ChIP-seq quality and sensitivity

2021 ◽  
Author(s):  
Cheryl A Keller ◽  
Alexander Q Wixom ◽  
Elisabeth F Heuston ◽  
Belinda Giardine ◽  
Chris C -S Hsiung ◽  
...  
Keyword(s):  
Transcription Factors ◽  
High Throughput Sequencing ◽  
Cell Types ◽  
Poor Quality ◽  
Erythroid Cell ◽  
On Chip ◽  
Direct And Indirect Binding ◽  
And Control ◽  
The Impact

Abstract Chromatin immunoprecipitation followed by massively parallel, high throughput sequencing (ChIP-seq) is the method of choice for genome-wide identification of DNA segments bound by specific transcription factors or in chromatin with particular histone modifications. However, the quality of ChIP-seq datasets varies widely, with a substantial fraction being of intermediate to poor quality. Thus, it is important to discern and control the factors that contribute to variation in ChIP-seq. In this study, we focused on sonication, a user-controlled variable, to produce sheared chromatin. We systematically varied the amount of shearing of fixed chromatin from a mouse erythroid cell line, carefully measuring the distribution of resultant fragment lengths prior to ChIP-seq. This systematic study was complemented with a retrospective analysis of additional experiments. We found that the level of sonication had a pronounced impact on the quality of ChIP-seq signals. Over-sonication consistently reduced quality, while the impact of under-sonication differed among transcription factors, with no impact on sites bound by CTCF but frequently leading to the loss of sites occupied by TAL1 or bound by POL2. The bound sites not observed in low quality datasets were inferred to be a mix of both direct and indirect binding. We leveraged these findings to produce a set of CTCF ChIP-seq datasets in rare, primary hematopoietic progenitor cells. Our observation that the amount of chromatin sonication is a key variable in success of ChIP-seq experiments indicates that monitoring the level of sonication can improve ChIP-seq quality and reproducibility and facilitate ChIP-seq in rare cell types.

scholarly journals Effects of sheared chromatin length on ChIP-seq quality and sensitivity

2020 ◽  
Author(s):  
Cheryl A. Keller ◽  
Elisabeth F. Heuston ◽  
Belinda Giardine ◽  
Maria R. Long ◽  
Amber Miller ◽  
...  
Keyword(s):  
Transcription Factors ◽  
High Throughput Sequencing ◽  
Cell Types ◽  
Cell Number ◽  
Poor Quality ◽  
Erythroid Cell ◽  
A Genome ◽  
Wide Range ◽  
The Impact

AbstractChromatin immunoprecipitation followed by massively parallel, high throughput sequencing (ChIP-seq) is the method of choice for identifying, on a genome-wide scale, the segments of DNA bound by specific transcription factors (TFs) or in chromatin with particular histone modifications. However, the quality of ChIP-seq datasets vary over a wide range, with a substantial fraction being of intermediate to poor quality. Such experimental variability can lead to many false positives or false negatives, impairing the ability to interpret the data. Thus, it is important to discern and control the factors that contribute to variation in ChIP-seq. In this study, we focus on the sonication step to produce sheared chromatin, a variable controllable by the user and applicable to all ChIP-seq protocols. We systematically varied the amount of shearing of fixed chromatin from a mouse erythroid cell line, carefully measured the distribution of resultant fragment lengths using the Agilent Bioanalzyer 2100, and then immunoprecipitated these batches of chromatin using highly specific antibodies against either TAL1 or CTCF. We found that the level of sonication, which was affected by both the number of sonication cycles, as well as the starting cell number, had a pronounced impact on the quality of resulting ChIP-seq signals. Specifically, over-sonication led to degradation of quality (e.g. increased background and reduction in signal), while the impact of under-sonication of chromatin differed between the two transcription factors, leading to the loss of sites occupied by TAL1 but not those bound by CTCF. We leveraged these findings to produce a set of CTCF ChIP-seq datasets in primary hematopoietic progenitor cells, including several rare cell types. Together, these results suggest that the amount of sonication is a key variable in success of ChIP-seq experiments, and that carefully monitoring the level of chromatin sonication is one way to improve ChIP-seq quality and reproducibility, which in turn facilitates low input ChIP-seq in rare cell types.

scholarly journals Quality of care in the free maternal healthcare era in sub-Saharan Africa: a scoping review of providers’ and managers’ perceptions

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Monica Ansu-Mensah ◽  
Frederick Inkum Danquah ◽  
Vitalis Bawontuo ◽  
Peter Ansu-Mensah ◽  
Tahiru Mohammed ◽  
...  
Keyword(s):  
Quality Of Care ◽  
Research Question ◽  
Healthcare Providers ◽  
Poor Quality ◽  
Sub Saharan Africa ◽  
Healthcare Financing ◽  
Maternal Healthcare ◽  
Sub Saharan ◽  
The Impact

Abstract Background Free maternal healthcare financing schemes play an essential role in the quality of services rendered to clients during antenatal care in sub-Saharan Africa (SSA). However, healthcare managers’ and providers’ perceptions of the healthcare financing scheme may influence the quality of care. This scoping review mapped evidence on managers’ and providers’ perspectives of free maternal healthcare and the quality of care in SSA. Methods We used Askey and O’Malley’s framework as a guide to conduct this review. To address the research question, we searched PubMed, CINAHL through EBSCOhost, ScienceDirect, Web of Science, and Google Scholar with no date limitation to May 2019 using keywords, Boolean terms, and Medical Subject Heading terms to retrieve relevant articles. Both abstract and full articles screening were conducted independently by two reviewers using the inclusion and exclusion criteria as a guide. All significant data were extracted, organized into themes, and a summary of the findings reported narratively. Results In all, 15 out of 390 articles met the inclusion criteria. These 15 studies were conducted in nine countries. That is, Ghana (4), Kenya (3), and Nigeria (2), Burkina Faso (1), Burundi (1), Niger (1), Sierra Leone (1), Tanzania (1), and Uganda (1). Of the 15 included studies, 14 reported poor quality of maternal healthcare from managers’ and providers’ perspectives. Factors contributing to the perception of poor maternal healthcare included: late reimbursement of funds, heavy workload of providers, lack of essential drugs and stock-out of medical supplies, lack of policy definition, out-of-pocket payment, and inequitable distribution of staff. Conclusion This study established evidence of existing literature on the quality of care based on healthcare providers’ and managers’ perspectives though very limited. This study indicates healthcare providers and managers perceive the quality of maternal healthcare under the free financing policy as poor. Nonetheless, the free maternal care policy is very much needed towards achieving universal health, and all efforts to sustain and improve the quality of care under it must be encouraged. Therefore, more research is needed to better understand the impact of their perceived poor quality of care on maternal health outcomes.

scholarly journals Scoping review of mental health in prisons through the COVID-19 pandemic

BMJ Open ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. e046547
Author(s):  
Luke Johnson ◽  
Kerry Gutridge ◽  
Julie Parkes ◽  
Anjana Roy ◽  
Emma Plugge
Keyword(s):  
Mental Health ◽  
Scoping Review ◽  
Grey Literature ◽  
Well Being ◽  
Health Impact ◽  
Poor Quality ◽  
Eligibility Criteria ◽  
Prison Staff ◽  
The Impact

ObjectiveTo examine the extent, nature and quality of literature on the impact of the COVID-19 pandemic on the mental health of imprisoned people and prison staff.DesignScoping review.Data sourcesPubMed, Embase, CINAHL, Global Health, Cochrane, PsycINFO, PsychExtra, Web of Science and Scopus were searched for any paper from 2019 onwards that focused on the mental health impact of COVID-19 on imprisoned people and prison staff. A grey literature search focused on international and government sources and professional bodies representing healthcare, public health and prison staff was also performed. We also performed hand searching of the reference lists of included studies.Eligibility criteria for selection of studiesAll papers, regardless of study design, were included if they examined the mental health of imprisoned people or prison staff specifically during the COVID-19 pandemic. Imprisoned people could be of any age and from any countries. All languages were included. Two independent reviewers quality assessed appropriate papers.ResultsOf 647 articles found, 83 were eligible for inclusion, the majority (58%) of which were opinion pieces. The articles focused on the challenges to prisoner mental health. Fear of COVID-19, the impact of isolation, discontinuation of prison visits and reduced mental health services were all likely to have an adverse effect on the mental well-being of imprisoned people. The limited research and poor quality of articles included mean that the findings are not conclusive. However, they suggest a significant adverse impact on the mental health and well-being of those who live and work in prisons.ConclusionsIt is key to address the mental health impacts of the pandemic on people who live and work in prisons. These findings are discussed in terms of implications for getting the balance between infection control imperatives and the fundamental human rights of prison populations.

scholarly journals SQoF-WEAR Project. The Use of Wearable Devices to Identify the Impact of Stress on Workers’ Quality of Life

2021 ◽  
Vol 7 (1) ◽  
pp. 25
Author(s):  
Patricia Concheiro-Moscoso ◽  
Betania Groba ◽  
Sílvia Monteiro-Fonseca ◽  
Nereida Canosa ◽  
Cristina Queirós
Keyword(s):  
Quality Of Life ◽  
Public Health Problem ◽  
Wearable Devices ◽  
Assessment Tools ◽  
Self Report ◽  
Major Public Health Problem ◽  
The University ◽  
And Control ◽  
The Impact

(1) Background: Stress is a major public health problem due to its relevant health, social and economic repercussions. Moreover, stress can be associated with work; when stress increases over time, burnout can occur, an occupational phenomenon recognized by the WHO in 2019. There is interest in the use of wearable devices to monitor and control stressors and their influence on the condition of workers. This study aims to identify the level of job stress and its influence on the quality of life of workers. (2) Methods:This longitudinal study was carried out between the end of May and mid-July 2021. Three assessment tools along with a daily and a weekly questionnaire were computerized through the RedCap platform. The participants had to fill out the diary and weekly questionnaires and wear a Xiaomi Mi Band 5 during the project. (3) Results and discussion: Thirty-six workers from the University of Coruña and from the University of Porto participated in the project. This study promotes the awareness of workers regarding their work stress and the influence of this factor on their quality of life using physiological (e.g., activity, sleep, and heart rate) and psychological indicators (self-report questionnaires in different moments).

scholarly journals THE CORRELATION OF THE CATEGORIES OF “QUALITY” AND “SAFETY” OF PRODUCTS

2019 ◽  
pp. 74-78
Author(s):  
T.V. Malanchuk ◽  
E.A. Zaitsev
Keyword(s):  
Civil Rights ◽  
Legal Regulation ◽  
Poor Quality ◽  
Product Safety ◽  
Legal Rights ◽  
Safety Issues ◽  
State Supervision ◽  
Safety Features ◽  
And Control

The article analyzes the complex state of the modern legislative regulation of quality and product safety issues in the context of ensuring consumers’ rights to the proper quality of goods (works, services). It is stated that in view of the variety of different properties that make up the notion of quality, the most important are the defects, which are capable of damaging the life, health, or property of the consumer, that is, the defects, which indicate that the goods are dangerous. The safety of goods works, and services as a legal category are of particular importance and is one of the functions of the state to ensure public safety. State measures of influence on manufacturers and sellers of goods, persons who perform work and provide services should be aimed at ensuring the protection of fundamental civil rights. In most cases, these are imperative requirements for safety, which are approved by special legal acts, as well as measures of state supervision and control to ensure the safety of manufactured goods, works, and services. The legislator, when defining security, uses the term “safety of goods (works, services)”, but it would be advisable to carry out graduation of these concepts since the safety of goods is a state of goods that allows it to be sold, used, stored, transported, disposed of without harm for life, health, the property of the consumer and the environment in normal conditions, and the safety of works and services is the quality of protection of the legal rights of the consumer in carrying out the activities of persons who perform work and provide services, danger to life, health, the property should not manifest itself either in their implementation and providing or later. It is noted that quality requirements should be made mandatory when designing production specifications. It is stated that in order to ensure the effectiveness of legal regulation, the safety of a product, work, or service must be considered as a full-fledged property within the legal notion of quality. It is concluded that product safety is an integral feature of any product, work, and service, acting as an integral element of the quality category. Lack of safety features indicates that the product is of poor quality. Keywords: quality, safety, proper quality, improper quality, specifications, consumers.

Impact of AI regulation on intention to use robots

2019 ◽  
Vol 8 (2) ◽  
pp. 97-114
Author(s):  
Sheshadri Chatterjee
Keyword(s):  
Quality Of Life ◽  
Artificial Intelligence ◽  
Design Methodology ◽  
Regulatory Control ◽  
Control Beliefs ◽  
Intention To Use ◽  
Content Type ◽  
And Control ◽  
The Impact

Purpose The purpose of this paper is to identify the factors influencing the citizens to use robots that would improve the quality of life of the citizens. Design/methodology/approach With the help of different adoption theories and models and with the support of background studies, some hypotheses have been formulated and a conceptual model has been developed with the consideration of the impact of artificial intelligence regulation (IAR) that controls the use of robots as a moderator. The model has been validated and the hypotheses have been tested by statistical analysis with the help of survey works involving consideration of feedbacks from 503 usable respondents. Findings The study reveals that the use of robots by the citizens would appreciably increase if government imposes strict artificial intelligence (AI) regulatory control concerning the use of robots, and in that case, it appears that the use of robots would improve the quality of life of the citizens. Research limitations/implications The duly validated model would help the authority to appropriately nurse and nurture the factors such as ethical dilemma, perceived risks and control beliefs for enhancing the intention of the citizens to use robots for many purposes including domestic usage in the context of appropriate restrictions imposed through AI regulation. Such use of robots would eventually improve the quality of life. Originality/value There are a few studies covering analysis of IAR as a moderator on the linkages of the predictors with the intention of the citizens to use robots. In this context, this study is claimed to have offered a novel contribution.

scholarly journals Metabolome and Microbiome Signatures in the Roots of Citrus Affected by Huanglongbing

2019 ◽  
Vol 109 (12) ◽  
pp. 2022-2032 ◽  
Author(s):  
Emily M. T. Padhi ◽  
Nilesh Maharaj ◽  
Shin-Yi Lin ◽  
Darya O. Mishchuk ◽  
Elizabeth Chin ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Water Soluble ◽  
Resonance Spectroscopy ◽  
Its Gene ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus ◽  
Citrus Leaves ◽  
Citrus Varieties ◽  
And Control ◽  
The Impact

Huanglongbing (HLB) is a severe, incurable citrus disease caused by the bacterium ‘Candidatus Liberibacter asiaticus’ (CLas). Although citrus leaves serve as the site of initial infection, CLas is known to migrate to and colonize the root system; however, little is known about the impact of CLas infection on root metabolism and resident microbial communities. Scions of ‘Lisbon’ lemon and ‘Washington Navel’ orange grafted onto ‘Carrizo’ rootstock were grafted with either CLas-infected citrus budwood or uninfected budwood. Roots were obtained from trees 46 weeks after grafting and analyzed via 1H nuclear magnetic resonance spectroscopy to identify water-soluble root metabolites and high-throughput sequencing of 16S rRNA and ITS gene amplicons to determine the relative abundance of bacterial and fungal taxa in the root rhizosphere and endosphere. In both citrus varieties, 27 metabolites were identified, of which several were significantly different between CLas(+) and control plants. CLas infection also appeared to alter the microbial community structure near and inside the roots of citrus plants. Nonmetric multidimensional scaling (NMDS) and a principal coordinate analysis (PCoA) revealed distinct metabolite and microbial profiles, demonstrating that CLas impacts the root metabolome and microbiome in a manner that is variety-specific.

scholarly journals Impact of the severity of restrictive spirometric pattern on nutrition, physical activity, and quality of life: results from a nationally representative database

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sung Jun Chung ◽  
Hwan Il Kim ◽  
Bumhee Yang ◽  
Taehee Kim ◽  
Yun Su Sim ◽  
...  
Keyword(s):  
Quality Of Life ◽  
Physical Activity ◽  
General Health ◽  
Multivariable Analysis ◽  
Caloric Intake ◽  
Health Problems ◽  
Poor Quality ◽  
Five Dimensions ◽  
The Impact

AbstractThe general disease burden associated with the restrictive spirometric pattern (RSP) is substantial. However, the impact of RSP by its severity on general health problems and quality of life has not been well elucidated. This study aimed to analyse nutrition, physical activity, and quality of life in subjects who participated in the Korea National Health and Nutrition Examination Survey 2007–2016 according to severity of RSP. Participants were classified as subjects with normal spirometry, those with mild-to-moderate RSP, and those with severe RSP. Poor quality of life was defined as 25th percentile value on the EuroQoL five dimensions (Eq5D) questionnaire index, i.e., 0.90. This study included 23,615 subjects composed of 20,742 with normal spirometry, 2758 with mild-to-moderate RSP, and 115 with severe RSP. The subjects with severe RSP were more likely to have attained lower education levels, had a lower total caloric intake, had less physical activity, had experienced a higher prevalence of comorbidities, and poorer quality of life than those with normal spirometry (P < 0.001 for all). In multivariable analysis, subjects with a mild-to-moderate RSP and severe RSP were more likely to show decreased total calories (coefficient for change in calorie = − 56.6 kcal and − 286.7 kcal, respectively) than those with normal spirometry; subjects with mild-to-moderate RSP and those with severe RSP were 1.26 times and 1.96 times more likely, respectively, to have a poorer quality of life than those with normal spirometry. Additionally, subjects with mild-to-moderate RSP and those with severe RSP were 0.84 times and 0.36 times less likely, respectively, to have high-intensity physical activity than those with normal spirometry in univariable analysis. The trends of a poorer quality of life and physical activity were only significant in the male subgroups. In conclusion, our study revealed that the severity of general health problems and quality of life reductions are correlated with the severity of RSP, especially in males.

Depressive and Bipolar Disorders

2017 ◽  
Author(s):  
Antoine Douaihy ◽  
Matthew Conlon ◽  
Maria Ferrara
Keyword(s):  
Quality Of Life ◽  
Antiretroviral Therapy ◽  
Sexual Behaviors ◽  
Depressive Disorders ◽  
Bipolar Disorders ◽  
Poor Quality ◽  
Persons Living With Hiv ◽  
The Impact ◽  
Hiv Aids

Depressive disorders are highly prevalent among persons living with HIV/AIDS. Depressive disorders significantly negatively affects adherence to antiretroviral therapy and HIV viral suppression and is associated with poor quality of life and major impairment in overall functioning. This chapter reviews the prevalence, risk factors, assessment and diagnosis of depressive and bipolar disorders. It also examines the impact of depression on sexual behaviors, adherence to antiretroviral therapy, quality of life, and mortality. This chapter also includes a comprehensive discussion of treatment approaches and considerations for HIV-infected individuals with depressive disorders. Furthermore, it reviews the bipolar disorder spectrum in HIV/AIDS as well as other psychiatric disorders co-occurring with depressive disorders.

scholarly journals High-Throughput Sequencing is a Crucial Tool to Investigate the Contribution of Human Endogenous Retroviruses (HERVs) to Human Biology and Development

Viruses ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 633 ◽  
Author(s):  
Maria Paola Pisano ◽  
Nicole Grandi ◽  
Enzo Tramontano
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Large Fraction ◽  
Expression Patterns ◽  
Cell Types ◽  
Endogenous Retroviruses ◽  
Human Endogenous Retroviruses ◽  
Retroviral Infections ◽  
The Impact

Human Endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that represent a large fraction of our genome. Their transcriptional activity is finely regulated in early developmental stages and their expression is modulated in different cell types and tissues. Such activity has an impact on human physiology and pathology that is only partially understood up to date. Novel high-throughput sequencing tools have recently allowed for a great advancement in elucidating the various HERV expression patterns in different tissues as well as the mechanisms controlling their transcription, and overall, have helped in gaining better insights in an all-inclusive understanding of the impact of HERVs in biology of the host.

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