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 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 Evaluation of the Quality of Irrigation Machinery by Monitoring Changes in the Coefficients of Uniformity and Non-Uniformity of Irrigation

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1499
Author(s):  
Ján Jobbágy ◽  
Peter Dančanin ◽  
Koloman Krištof ◽  
Juraj Maga ◽  
Vlastimil Slaný
Keyword(s):  
Repeated Measurements ◽  
Joint Stock Company ◽  
Stock Company ◽  
Uniformity Coefficient ◽  
Quality Of Work ◽  
Total Length ◽  
Irrigation Uniformity ◽  
Wide Range ◽  
The Impact

Recently, the development of agricultural technology has been focused on achieving higher reliability and quality of work. The aim of the presented paper was to examine the possibilities of evaluating the quality of work of wide-area irrigation machinery by monitoring the coefficients of uniformity and non-uniformity of irrigation. The object of the research was pivot irrigation machinery equipped with sprinklers with a total length from 230 to 540 m. The commonly applied quality of work parameter for wide-range irrigators is the irrigation uniformity coefficient according to Heermann and Hein CUH. Work quality evaluations were also carried out through other parameters applicable in practice, such as irrigation uniformity coefficients calculated according to Christiansen CU, Wilcox and Swailes Cws, and our introduced parameters, the coefficient ar (derived from the degree of unevenness according to Oehler) and the degree of uniformity γr (derived from the degree of non-uniformity according to Voight). Other applied parameters for determining the quality of work of wide-range irrigation machinery were the coefficients of irrigation uniformity according to Hart and Reynolds CUhr, further according to Criddle CUcr and subsequently according to Beale and Howell CUbr. Next, the parameters of the non-uniformity coefficient according to Oehler a, the coefficient of variation according to Stefanelli Cv, the degree of non-uniformity according to Voigt γ and the degree of non-uniformity according to Hofmeister Ef were evaluated. Field tests were performed during the growing season of cultivated crops (potatoes, corn and sugar beet) in the village of Trakovice (agricultural enterprise SLOV-MART, southwest of the Slovakia) and in the district of Piešťany (Agrobiop, joint stock company). During the research, the inlet operating parameters (speed stage, inlet pressure, irrigation dose), technical parameters (number of sprayers, total length, number of chassis) and weather conditions (wind speed and temperature) were recorded. The obtained results were examined by one-way ANOVA analysis depending on the observed coefficient or input conditions and subsequently verified by Tukey and Duncan tests as needed. Irrigation uniformity values ranged from 67.58% (Cws) to 95.88% (CUbh) depending on the input conditions. Irrigation non-uniformity values ranged from 8.58 (a, Ef) to 32.42% (Cv). The results indicate a statistically significant effect of the site of interest and thus the impact of particular field conditions (p < 0.05). When evaluating the application of different coefficients of irrigation uniformity, the results showed a statistically significant effect only in the first test (p = 0.03, p < 0.05). During further repeated measurements, the quality of work increased due to the performed inspection of all sprayers and the reduction in the influence of the wind.

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 An Adaptive Bitrate Switching Algorithm for Speech Applications in Context of WebRTC

2021 ◽  
Vol 17 (4) ◽  
pp. 1-21
Author(s):  
Mohannad Alahmadi ◽  
Peter Pocta ◽  
Hugh Melvin
Keyword(s):  
Real Time ◽  
Data Exchange ◽  
Quality Of Experience ◽  
End User ◽  
High Quality ◽  
Content Type ◽  
Switching Algorithm ◽  
Wide Range ◽  
The Impact

Web Real-Time Communication (WebRTC) combines a set of standards and technologies to enable high-quality audio, video, and auxiliary data exchange in web browsers and mobile applications. It enables peer-to-peer multimedia sessions over IP networks without the need for additional plugins. The Opus codec, which is deployed as the default audio codec for speech and music streaming in WebRTC, supports a wide range of bitrates. This range of bitrates covers narrowband, wideband, and super-wideband up to fullband bandwidths. Users of IP-based telephony always demand high-quality audio. In addition to users’ expectation, their emotional state, content type, and many other psychological factors; network quality of service; and distortions introduced at the end terminals could determine their quality of experience. To measure the quality experienced by the end user for voice transmission service, the E-model standardized in the ITU-T Rec. G.107 (a narrowband version), ITU-T Rec. G.107.1 (a wideband version), and the most recent ITU-T Rec. G.107.2 extension for the super-wideband E-model can be used. In this work, we present a quality of experience model built on the E-model to measure the impact of coding and packet loss to assess the quality perceived by the end user in WebRTC speech applications. Based on the computed Mean Opinion Score, a real-time adaptive codec parameter switching mechanism is used to switch to the most optimum codec bitrate under the present network conditions. We present the evaluation results to show the effectiveness of the proposed approach when compared with the default codec configuration in WebRTC.

scholarly journals The importance of anemia and health-related quality of life in the elderly

2020 ◽  
Vol 39 (2) ◽  
pp. 135
Author(s):  
Raditya Wratsangka ◽  
Rully Ayu Nirmalasari Haryadi Putri
Keyword(s):  
Quality Of Life ◽  
Hemoglobin Concentration ◽  
The Elderly ◽  
World Population ◽  
Health Related Quality ◽  
Wide Range ◽  
Related Quality ◽  
Health Related ◽  
The Impact

Anemia is a global health problem with an extremely high prevalence and occurring in nearly 25% of the world population, particularly in the elderly group. Currently Indonesia is facing a rapid growth of the elderly population, with around 21 million elderly (8.2% of the total population), that is projected to increase to 33.7 million (11.8%) in the year 2025. Anemia in the elderly is frequently neglected, although the facts show that low hemoglobin concentration is an important marker of physiological decline and functional limitations. Although the factor of intrinsic aging may cause low hemoglobin concentration, anemia in the elderly is known to have a wide range w88ith regard to etiology, underlying disorders, and  possible mechanisms, such that it should be clinically followed up. Whatever its causes or underlying pathophysiological, anemia in the elderly has been proven to play a role in their morbidity and mortality, and may decrease their quality of life, that comprises all aspects of physical, mental, and social health, known as health-related quality of life (HRQoL). The impact of anemia on HRQoL has been studied in various populations, and most studies report the presence of an association between HRQoL and anemia in elderly individuals, which on the subscale level is particularly associated with physical health. Early diagnosis of anemia is important to prevent aggravation of the condition, to retard the progress of the disease, and to improve the health-related quality of life (HRQoL) of the patient. Prior to determining the treatment plan, the primary diagnosis and the comorbidities, especially treatable disorders, had better be identified first. The available data show that the overall prognosis will improve for anemia in patients with well-managed and corrected chronic disorders.

scholarly journals Congenital Micropenis: Aetiology And Management

2021 ◽  
Author(s):  
Marianna Rita Stancampiano ◽  
Kentaro Suzuki ◽  
Stuart O’Toole ◽  
Gianni Russo ◽  
Gen Yamada ◽  
...  
Keyword(s):  
Racial Differences ◽  
Small Sample Size ◽  
Small Sample ◽  
Long Term Outcomes ◽  
Penile Length ◽  
Appearance Quality ◽  
Wide Range ◽  
The Impact

Abstract In the newborn, penile length is determined by a number of androgen dependent and independent factors. The current literature suggests that there are inter-racial differences in stretched penile length in the newborn and although congenital micropenis should be defined as a stretched penile length of less than 2.5SDS of the mean for the corresponding population and gestation, a pragmatic approach would be to evaluate all boys with a stretched penile length below 2 cm, as congenital micropenis can be a marker for a wide range of endocrine conditions. However, it remains unclear as to whether the state of micropenis, itself, is associated with any long-term consequences. There is a lack of systematic studies comparing the impact of different therapeutic options on long-term outcomes, in terms of genital appearance, quality of life and sexual satisfaction. To date, research has been hampered by a small sample size and inclusion of a wide range of heterogeneous diagnoses; for these reasons, condition specific outcomes have been difficult to compare between studies. Lastly, there is a need for a greater collaborative effort in collecting standardized data so that all real-world or experimental interventions performed at an early age can be studied systematically into adulthood.

scholarly journals Withaferin A Inhibits Nuclear Factor-κB-Dependent Pro-Inflammatory and Stress Response Pathways in the Astrocytes

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Francesca Martorana ◽  
Giulia Guidotti ◽  
Liliana Brambilla ◽  
Daniela Rossi
Keyword(s):  
Stress Response ◽  
Cell Types ◽  
Nuclear Factor Κb ◽  
Withaferin A ◽  
Nuclear Factor ◽  
Lps Challenge ◽  
Wide Range ◽  
Cox 2 ◽  
The Impact ◽  
Stimulation Of

Several lines of evidence suggest that astrocytes play a key role in modulating the immune responses of the central nervous system (CNS) to infections, injuries, or pathologies. Yet, their contribution to these processes remains mostly elusive. Astroglia are endowed with a wide range of toll-like receptors (TLR) by which they can sense infectious agents as well as endogenous danger signals released by damaged cells. Here we demonstrate that the activation of astrocytic TLR4 by bacterial lipopolysaccharide (LPS) challenge can promote nuclear factorκB (NF-κB)-dependent induction of pro-inflammatory and stress response mediators, particularly Tumor Necrosis Factorα(TNFα), cyclooxygenase 2 (COX-2), and inducible nitric oxide synthase (iNOS). Since the steroid lactone Withaferin A was described to inhibit NF-κB activity in different cell types, we next determined the impact of this natural compound towards the identified astrocytic signalling pathway. Innate immune activation was induced by stimulation of the LPS/TLR4 axis in spinal cord astrocytes. We provide evidence that both pre-treating and post-treating the cells with Withaferin A attenuate astrocytic NF-κB activity as well as the consequent production of TNFα, COX-2, and iNOS induced by stimulation of the LPS/TLR4 pathway. This study suggests that Withaferin A may be an eligible candidate for the treatment of neuroinflammatory and stress conditions characterized by an important astrocytic input.

Epilepsy and Stroke Emerging From Climate Change-Related Neurotoxicity

2019 ◽  
pp. 322-347
Author(s):  
Hind Benammi ◽  
Omar El Hiba ◽  
Abdelmohcine Aimrane ◽  
Nadia Zouhairi ◽  
Hicham Chatoui ◽  
...  
Keyword(s):  
Climate Change ◽  
Heavy Metals ◽  
Nervous System ◽  
Toxic Elements ◽  
Neurological Diseases ◽  
Quality Of Water ◽  
Wide Range ◽  
The Impact ◽  
Shed Light

Climate change has an important impact on the environment. As it degrades the quality of water, soil, and area, it also spreads the distribution of many toxic elements, specifically heavy metals and pesticides. The impact of climate change on contamination with heavy metals and pesticides has been well investigated and discussed. The influence of these elements on human health is obviously exacerbated following their extended distribution. Moreover, a wide range of health problems have been associated to such intoxication, among which impairment and dysfunction of the nervous system are prominent. In this chapter, the authors will shed light on two most common neurological diseases such as epilepsy and stroke affecting people worldwide arising from food and water contaminations, mainly with heavy metals and pesticides.

Mcl-1 in Transgenic Mice Promotes Survival in a Spectrum of Hematopoietic Cell Types and Immortalization in the Myeloid Lineage

Blood ◽  
1998 ◽  
Vol 92 (9) ◽  
pp. 3226-3239 ◽  
Author(s):  
Ping Zhou ◽  
Liping Qian ◽  
Christine K. Bieszczad ◽  
Randolph Noelle ◽  
Michael Binder ◽  
...  
Keyword(s):  
Myeloid Cells ◽  
Myeloid Cell ◽  
Cell Types ◽  
Cell Number ◽  
Hematopoietic Cell ◽  
Viable Cell Number ◽  
Wide Range ◽  
Transgenic Cells

Abstract Mcl-1 is a member of the Bcl-2 family that is expressed in early monocyte differentiation and that can promote viability on transfection into immature myeloid cells. However, the effects of Mcl-1 are generally short lived compared with those of Bcl-2 and are not obvious in some transfectants. To further explore the effects of this gene, mice were produced that expressed Mcl-1 as a transgene in hematolymphoid tissues. The Mcl-1 transgene was found to cause moderate viability enhancement in a wide range of hematopoietic cell types, including lymphoid (B and T) as well as myeloid cells at both immature and mature stages of differentiation. However, enhanced hematopoietic capacity in transgenic bone marrow and spleen was not reflected in any change in pool sizes in the peripheral blood. In addition, among transgenic cells, mature T cells remained long lived compared with B cells and macrophages could live longer than either of these. Interestingly, when hematopoietic cells were maintained in tissue culture in the presence of interleukin-3, Mcl-1 enhanced the probability of outgrowth of continuously proliferating myeloid cell lines. Thus, Mcl-1 transgenic cells remained subject to normal in vivo homeostatic mechanisms controlling viable cell number, but these constraints could be overridden under specific conditions in vitro. Within the organism, Bcl-2 family members may act at “viability gates” along the differentiation continuum, functioning as part of a system for controlled hematopoietic cell amplification. Enforced expression of even a moderate viability-promoting member of this family such as Mcl-1, within a conducive intra- and extracellular environment in isolation from normal homeostatic constraints, can substantially increase the probability of cell immortalization. © 1998 by The American Society of Hematology.

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