A pathway towards net-zero emissions in oil refineries

Rapid industrialization and urbanization have increased the demand for both energy and mobility services across the globe, with accompanying increases in greenhouse gas emissions. This short paper analyzes strategic measures for the abatement of CO2 emissions from oil refinery operations. A case study involving a large conversion refinery shows that the use of post-combustion carbon capture and storage (CCS) may only be practical for large combined emission point sources, leaving about 30% of site-wide emissions unaddressed. A combination of post-combustion CCS with a CO2 capture rate well above 90% and other mitigation measures such as fuel substitution and emission offsets is needed to transition towards carbon-neutral refinery operations. All of these technologies must be configured to minimize environmental burden shifting and scope 2 emissions, whilst doing so cost-effectively to improve energy access and affordability. In the long run, scope 3 emissions from the combustion of refinery products and flaring must also be addressed. The use of synthetic fuels and alternative feedstocks such as liquefied plastic waste, instead of crude oil, could present a growth opportunity in a circular carbon economy

A comparative analysis of the efficiency, timing, and permanence of CO2 removal pathways

Carbon dioxide removal (CDR) is essential to deliver the climate objectives of the Paris Agreement. Whilst several CDR pathways have been identified, they vary significantly in terms of CO2 removal efficiency, elapsed time between their deployment and effective CO2 removal, and CO2 removal permanence. All these criteria are critical for the commercial-scale deployment of CDR. In this study, we evaluate a set of archetypal CDR pathways—including afforestation/reforestation (AR), bioenergy with carbon capture and storage (BECCS), biochar, direct air capture of CO2 with storage (DACCS) and enhanced weathering (EW)—through this lens. We present a series of thought experiments, considering different climates and forest types for AR, land types, e.g. impacting biomass yield and (direct and indirect) land use change, and biomass types for BECCS and biochar, capture processes for DACCS, and rock types for EW. Results show that AR can be highly efficient in delivering CDR, up to 95–99% under optimal conditions. However, regional bio-geophysical factors, such as the near-term relatively slow and limited forest growth in cold climates, or the long-term exposure to natural disturbances, e.g. wildfires in warm and dry climates, substantially reduces the overall CO2 removal efficiency of AR. Conversely, BECCS delivers immediate and permanent CDR, but its CO2 removal efficiency can be significantly impacted by any initial carbon debt associated with (direct and indirect) land use change, and thereby significantly delayed. Biochar achieves low CDR efficiency, in the range of 20–39% when it is first integrated with the soil, and that regardless of the biomass feedstock considered. Moreover, its CO2 removal efficiency can decrease to −3 to 5% with time, owing to the decay of biochar. Finally, as for BECCS, DACCS and EW deliver permanent CO2 removal, but their CO2 removal efficiencies are substantially characterized by the energy system within which they are deployed, in the range of −5 to 90% and 17–92%, respectively, if currently deployed. However, the CDR efficiency of EW can increase to 51–92% with time, owing to the carbonation rate of EW

Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.

Although promoter-associated CpG islands have been established as targets of DNA methylation changes in cancer, previous studies suggest that epigenetic dysregulation outside the promoter region may be more closely associated with transcriptional changes. Here we examine DNA methylation, chromatin marks, and transcriptional alterations to define the relationship between transcriptional modulation and spatial changes in chromatin structure. Using human papillomavirus-related oropharyngeal carcinoma as a model, we show aberrant enrichment of repressive H3K9me3 at the transcriptional start site (TSS) with methylation-associated, tumor-specific gene silencing. Further analysis identifies a hypermethylated subtype which shows a functional convergence on MYC targets and association with CREBBP/EP300 mutation. The tumor-specific shift to transcriptional repression associated with DNA methylation at TSSs was confirmed in multiple tumor types. Our data may show a common underlying epigenetic dysregulation in cancer associated with broad enrichment of repressive chromatin marks and aberrant DNA hypermethylation at TSSs in combination with MYC network activation

Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.

The original version of this Article contained an error in the author affiliations. Trey Ideker was incorrectly associated with 'Department of Medicine (Oncology), Stanford University School of Medicine, 875 Blake Wilbur Dr, Palo Alto, CA 94304, USA.' This has now been corrected in both the PDF and HTML versions of the Article

Modern temporal network theory: A colloquium

The power of any kind of network approach lies in the ability to simplify a complex system so that one can better understand its function as a whole. Sometimes it is beneficial, however, to include more information than in a simple graph of only nodes and links. Adding information about times of interactions can make predictions and mechanistic understanding more accurate. The drawback, however, is that there are not so many methods available, partly because temporal networks is a relatively young field, partly because it more difficult to develop such methods compared to for static networks. In this colloquium, we review the methods to analyze and model temporal networks and processes taking place on them, focusing mainly on the last three years. This includes the spreading of infectious disease, opinions, rumors, in social networks; information packets in computer networks; various types of signaling in biology, and more. We also discuss future directions.Comment: Final accepted versio

Exploring the Development of Playfulness among Youth with Disabilities in the HB FIRST® Robotics Program

Background: Youth with disabilities often have less opportunities to play than their typically developing peers. An adapted robotics program is a promising way to help address problems in play development while learning educational content relevant for success across the lifespan.Objective: To understand the impact of using an adapted robotics program on the development of playfulness among youth with disabilities, aged 9 to 14 years. Methods: Observational research design using a pre-post video analysis on video-recorded raw data using the normalized and standardized assessment tool, the Test of Playfulness. Results: Participants exhibited significantly more playful behaviours following the completion of the adapted robotics program (Δ=0.8, p=0.001). Prior enrollment in the program also significantly impacted playfulness (F(1.0, 25)=10.0, p=0.004) Age, gender and disability type did not improve playfulness. Conclusion: The adapted robotics program improved the playfulness scores of youth with disabilities while enrolled in the program. These findings suggest that youth with disabilities can improve their playfulness through recreational and/or leisurely means.M.Sc

Disclosure and workplace accommodations for people with autism: a systematic review

This is an Accepted Manuscript of an article published by Taylor & Francis in Disability and Rehabilitation July 7th 2019, available online: http://www.tandfonline.com/10.1080/09638288.2019.1635658Purpose: The objective of this systematic review was to describe the prevalence and processes of disability disclosure for persons with autism spectrum disorder. Methods: Systematic searches of seven international databases revealed 26 studies meeting our inclusion criteria. We analyzed these studies with respect to participant demographics, methodology, results and quality of the evidence. Results: Among the 26 studies, 7006 participants (aged 13-75, mean 28.1 years) were represented across seven countries. Our findings showed that rates of disclosure and receiving workplace accommodations varied considerably. Benefits of disclosing in the workplace included greater acceptance and inclusion, receiving accommodations, and increasing awareness about autism. Limitations of disclosing to employers involved experiencing stigma and discrimination. Factors affecting decisions to disclose included age at diagnosis, social demands of the job, and workplace policies. Types of accommodations that were received or desired included adjustments to the job interview process, schedules (i.e., flexibility, working from home), job content or working conditions, environment (i.e., lighting, quiet space); support with communication and social skills; and disability awareness training for their workplace colleagues. Conclusions: Our findings highlight that disclosing a condition of autism in the workplace and requesting accommodations is complex. More research is needed to explore processes of disclosing and accommodation and how these processes vary by autism sub-type, gender, and industry type. Implications for rehabilitation Clinicians and vocational Counselors should support people with autism to advocate for their needs in the workplace, including the potential benefits of disclosing their conditions so they can access accommodations that allow them to keep healthy and productive in workplace.Clinicians should recognize that people with autism spectrum disorder may have different workplace accommodation needs than those with other types of disabilities, in particular support with social and communication skills.Clinicians should aid people with autism to access resources and supports that are available to them to access workplace accommodations.This research was funded by a CIHR-SSHRC partnership grant and the Kimmel Family Fund

An open source and convenient method for the wide-spread testing of COVID-19 using deep throat sputum samples

Importance The rise of novel, more infectious SARS-CoV-2 variants has made clear the need to rapidly deploy large-scale testing for COVID-19 to protect public health. However, testing remains limited due to shortages of personal protective equipment (PPE), naso- and oropharyngeal swabs, and healthcare workers. Simple test methods are needed to enhance COVID-19 screening. Here, we describe a simple, and inexpensive spit-test for COVID-19 screening called Patient Self-Collection of Sample-CoV2 (PSCS-CoV2). Objective To evaluate an affordable and convenient test for COVID-19. Methods The collection method relies on deep throat sputum (DTS) self-collected by the subject without the use of swabs, and was hence termed the Self-Collection of Sample for SARS-CoV-2 (abbreviated PSCS-CoV2). We used a phenol-chloroform extraction method for the viral RNA. We then tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction with primers against at least two coding regions of the viral nucleocapsid protein (N1 and N2 or E) of SARS-CoV-2. We evaluted the sensitivity and specificity of our protocol. In addition we assess the limit of detection, and efficacy of our Viral Inactivating Solution. We also evaluated our protocol, and pooling strategy from volunteers on a local college campus. Results We show that the PSCS-CoV2 method accurately identified 42 confirmed COVID-19 positives, which were confirmed through the nasopharyngeal swabbing method of an FDA approved testing facility. For samples negative for COVID-19, we show that the cycle threshold for N1, N2, and RP are similar between the PSCS-CoV2 and nasopharynx swab collection method (n = 30). We found a sensitivity of 100% (95% Confidence Interval [CI], 92-100) and specifity of 100% (95% CI, 89-100) for our PSCS-CoV2 method. We determined our protocol has a limit of detection of 1/10,000 for DTS from a COVID-19 patient. In addition, we show field data of the PSCS-CoV2 method on a college campus. Ten of the twelve volunteers (N1 < 30) that we tested as positive were subsequently tested positive by an independent laboratory. Finally, we show proof of concept of a pooling strategy to test for COVID-19, and recommend pool sizes of four if the positivity rate is less than 15%. Conclusion and Relevance We developed a DTS-based protocol for COVID-19 testing with high sensitivity and specificity. This protocol can be used by non-debilitated adults without the assistance of another adult, or by non-debilitated children with the assistance of a parent or guardian. We also discuss pooling strategies based on estimated positivity rates to help conserve resources, time, and increase throughput. The PSCS-CoV2 method can be a key component of community-wide efforts to slow the spread of COVID-19

Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.

Although promoter-associated CpG islands have been established as targets of DNA methylation changes in cancer, previous studies suggest that epigenetic dysregulation outside the promoter region may be more closely associated with transcriptional changes. Here we examine DNA methylation, chromatin marks, and transcriptional alterations to define the relationship between transcriptional modulation and spatial changes in chromatin structure. Using human papillomavirus-related oropharyngeal carcinoma as a model, we show aberrant enrichment of repressive H3K9me3 at the transcriptional start site (TSS) with methylation-associated, tumor-specific gene silencing. Further analysis identifies a hypermethylated subtype which shows a functional convergence on MYC targets and association with CREBBP/EP300 mutation. The tumor-specific shift to transcriptional repression associated with DNA methylation at TSSs was confirmed in multiple tumor types. Our data may show a common underlying epigenetic dysregulation in cancer associated with broad enrichment of repressive chromatin marks and aberrant DNA hypermethylation at TSSs in combination with MYC network activation

Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.

The original version of this Article contained an error in the author affiliations.&nbsp;Trey Ideker was incorrectly associated with 'Department of Medicine (Oncology), Stanford University School of Medicine, 875 Blake Wilbur Dr, Palo Alto, CA 94304, USA.' This has now been corrected in both the PDF and HTML versions of the Article