bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effect of Neonatal Sepsis on Risk of Autism Diagnosis
Authors: Getahun Darios , Fassett Michael J. , Xiang Anny H. , Chiu Vicki Y. , Takhar Harpreet S. , Shaw Sally F. , Peltier Morgan R.
Published: July 2021

Objective The study aimed to examine the association between neonatal sepsis and autism risk among children and whether the risk varied with the timing of exposure, child's sex, and race/ethnicity.

Study Design We conducted a retrospective cohort study using electronic health records (EHR) extracted from Kaiser Permanente Southern California Health Care System. Mother–child dyads were constructed by linking records of children born to member mothers and continuing to receive care through the system during the follow-up period with those of their biological mothers (n = 469,789). Clinical health records were used to define neonatal sepsis. Diagnosis of autism was made by medical specialists. Potential confounders included maternal sociodemographic factors, obstetrical history, child's age, sex, race/ethnicity, and maternal and child medical history. Incident rates and adjusted hazard ratios (aHR) were used to estimate the associations.

Results Compared with children without the diagnosis of autism, children with the condition were more likely to be from Asian/Pacific Islander descent and male sex. Exposed children showed higher rates of autism as compared with unexposed children (3.43 vs. 1.73 per 1,000 person-years, aHR: 1.67–95% confidence interval [CI]: 1.39–2.00). Both preterm (aHR: 1.47; 95% CI: 1.09–1.98) and term (aHR: 1.63; 95% CI: 1.29–2.06) births were associated with increased risk for autism. Although the magnitude of the HRs and incidence ratios for neonatal sepsis to increase autism risk varied between race ethnicities, neonatal sepsis was associated with significantly increased likelihood of autism diagnosis for all race-ethic groups except for Asian/Pacific Islanders. Although neonatal sepsis was associated with significantly increased autism risk for both boys and girls, incident rates and HR point estimates suggested that the effect may be stronger in girls.

Conclusion Neonatal sepsis is associated with increased risk of autism diagnosis in preterm- and term-born children. The association was significant for both girls and boys and all race ethnicities except for Asian-Pacific Islanders.

Key Points
Strategic maneuvering in extended polylogues
Authors: Egres Dorottya
Published: July 2021

This paper presents the analysis of the Hungarian nuclear expansion controversy using a conceptual framework that
links strategic maneuvering with an extended polylogical controversy and evaluates the strategic maneuvering of political,
environmentalist and expert actors. The paper aims to show that the three aspects of strategic maneuvering (audience demand,
topical potential, presentational devices) are flexible enough that they can be analyzed when the object of study is not a
spatially and temporally localized argumentative situation, but a decade-long debate with multiple actors. In 2014, Hungary signed
a deal with Russia to finance 80% of the investment costs and supply two new reactors to maintain the 40–50% of nuclear energy in
the national energy production.
The Role of Building Sector in Preserving Occupant Health for A Sustainable Development: A Review
Authors: Mansor Razlin , Sheau-Ting Low
Published: July 2021

There has been a dramatic rise in research on sustainable development but limited attention is given to human aspects such as their needs and requirements in a sustainable building. The majority of people spend their time mostly indoor, either for working, studying or living. Therefore, it is important to understand the health implications of building on occupants. The impact of indoor environment on occupant health has been largely disregarded. It should be part of the main agenda in progressing towards sustainable development. This paper aimed to discuss the interplay between indoor environment and occupant health and highlighted the role of building sector in preserving occupant health to ensure that buildings can be optimised for the benefit of occupants. A literature search on published works of indoor environment and occupant health has identified four indoor environment parameters that contribute to occupant health. These include indoor air quality, indoor lighting, indoor cleanliness and ergonomic. The impacts of each indoor environment parameter on occupant health were discussed in this paper. The findings will serve as reference for policy makers to preserve occupant health in buildings and as enhancement strategies for sustainable building development to fulfil the human requirements.
Prediction of Coal-Fired Power Generation Cost
Authors: Wang Yixiao
Published: July 2021

China is not only a big country with coal production, but also a big country with coal consuming. The amount of coal used in coal-fired power generation in China accounts for 30% of the total production each year, but its power generation accounts for 75% of the total power generation. Although all kinds of coal is still the main energy source in China, the proportion of coal-fired power generation will gradually decrease from 2020, and the use of renewable energy will increase. CPPs in China are mainly distributed in the north and the east of China. However, coal reserves are distributed in the northern and western part on a national scale. The cost of coal-fired power generation has always been a hot topic. It is necessary to add fresh water cost and environmental cost to the total cost of coal-fired power generation. However, there are few studies to precisely consider all kinds of possible cost in the CPPs and estimate the cost of coal-fired power generation in the future. This article firstly revises the resources cost estimation in the existing literature. Water consumption for coal extraction, transportation, combustion and circulating cooling is estimated at 0.018 CNY/kWh. Based on the internal resources cost and external environmental cost, this paper established a fitting model to obtain the trend of cost over time. Lastly, it is predicted that the cost growth trend of coal-fired power generation will reach the peak in 2020 at around 0.908 CNY/kWh, and then it will rapidly decrease year by year.
Application of poly(ether imide) membranes for the removal of the aromatic sulphur compounds from gasoline
Authors: Nedeljkovic Dragutin
Published: July 2021

Organic sulphur compounds are regularly present in the crude oil and natural gasoline, mostly as mercaptanes and heterocyclic sulphur compounds. Their combustion products have negative effects to both to the performance of the devices using gasoline and to the environment. Therefore, removal of the sulphur compounds in the pre-combustion process is of a great importance. One of the most promising method is application of the polymeric membranes. Suitable membrane should provide high permeability of sulphur compounds and low permeability of other hydrocarbons. In this work, several membranes based on the poly(ether imide) were tested for the sulphur organic compounds removal from the n-heptane. The membrane separation properties were measured for various concentrations of thiophene in heptane. It was found that increase of the amount of thiophene increases the flux of both thiophene and n-heptane. As the increase of the flux of the n-heptane was higher that the increase of the flux of the thiophene, the selectivity of the polyimide based membrane decreases with the increased concentration of thiophene in the feed. The possible reason is increased mobility of the polymer chains in the active layer.
Graphene oxide composite fibres for therapeutic fabrics
Authors: Leese Hannah S , Durailingam Maveendra , Roffe Theo , Atri Ria
Published: July 2021

Topical administration of various therapeutic factors at different stages of healing has the potential to enhance wound healing rates and reduce pain of chronic wounds. Here, the potential of utilising therapeutic fibres as wound dressings and/or sutures, is demonstrated by wet-spinning graphene oxide (GO) and aspirin adsorbed GO with polyvinyl alcohol, into drug eluting composite fibres. By varying the load of GO in the composite fibres it was possible to tailor strength, stiffness and stretchability. GO loadings of 5 wt.% resulted in fibres five times stronger than polyvinyl alcohol alone. Low loadings of GO 0.2–0.4 wt.% produced super-stretchable fibres. The drug loaded composite fibres exhibited a slow release of aspirin over a period of 3 d which is attributed to the π–π interactions between the GO and aspirin. These composite fibres demonstrate promise for incorporating other biological factors using GO as a vector, as well as creating textiles that can deliver therapeutics in a sustained manner, leading to flexible wearable therapeutics and sutures in the future.
Genetic mechanisms of COVID-19 and its association with smoking and alcohol consumption
Authors: Rao Shuquan , Baranova Ancha , Cao Hongbao , Chen Jiu , Zhang Xiangrong , Zhang Fuquan
Published: July 2021

We aimed to investigate the genetic mechanisms associated with coronavirus disease of 2019 (COVID-19) outcomes in the host and to evaluate the possible associations between smoking and drinking behavior and three COVID-19 outcomes: severe COVID-19, hospitalized COVID-19 and COVID-19 infection. We described the genomic loci and risk genes associated with the COVID-19 outcomes, followed by functional analyses of the risk genes. Then, a summary data-based Mendelian randomization (SMR) analysis, and a transcriptome-wide association study (TWAS) were performed for the severe COVID-19 dataset. A two-sample Mendelian randomization (MR) analysis was used to evaluate the causal associations between various measures of smoking and alcohol consumption and the COVID-19 outcomes. A total of 26 protein-coding genes, enriched in chemokine binding, cytokine binding and senescence-related functions, were associated with either severe COVID-19 or hospitalized COVID-19. The SMR and the TWAS analyses highlighted functional implications of some GWAS hits and identified seven novel genes for severe COVID-19, including CCR5, CCR5AS, IL10RB, TAC4, RMI1 and TNFSF15, some of which are targets of approved or experimental drugs. According to our studies, increasing consumption of cigarettes per day by 1 standard deviation is related to a 2.3-fold increase in susceptibility to severe COVID-19 and a 1.6-fold increase in COVID-19-induced hospitalization. Contrarily, no significant links were found between alcohol consumption or binary smoking status and COVID-19 outcomes. Our study revealed some novel COVID-19 related genes and suggested that genetic liability to smoking may quantitatively contribute to an increased risk for a severe course of COVID-19.
Circular RNAs and complex diseases: from experimental results to computational models
Authors: Wang Chun-Chun , Han Chen-Di , Zhao Qi , Chen Xing
Published: July 2021

Circular RNAs (circRNAs) are a class of single-stranded, covalently closed RNA molecules with a variety of biological functions. Studies have shown that circRNAs are involved in a variety of biological processes and play an important role in the development of various complex diseases, so the identification of circRNA-disease associations would contribute to the diagnosis and treatment of diseases. In this review, we summarize the discovery, classifications and functions of circRNAs and introduce four important diseases associated with circRNAs. Then, we list some significant and publicly accessible databases containing comprehensive annotation resources of circRNAs and experimentally validated circRNA-disease associations. Next, we introduce some state-of-the-art computational models for predicting novel circRNA-disease associations and divide them into two categories, namely network algorithm-based and machine learning-based models. Subsequently, several evaluation methods of prediction performance of these computational models are summarized. Finally, we analyze the advantages and disadvantages of different types of computational models and provide some suggestions to promote the development of circRNA-disease association identification from the perspective of the construction of new computational models and the accumulation of circRNA-related data.
Differential network analysis by simultaneously considering changes in gene interactions and gene expression
Authors: Tu Jia-Juan , Ou-Yang Le , Zhu Yuan , Yan Hong , Qin Hong , Zhang Xiao-Fei
Published: July 2021

Motivation

Differential network analysis is an important tool to investigate the rewiring of gene interactions under different conditions. Several computational methods have been developed to estimate differential networks from gene expression data, but most of them do not consider that gene network rewiring may be driven by the differential expression of individual genes. New differential network analysis methods that simultaneously take account of the changes in gene interactions and changes in expression levels are needed.

Results

: In this article, we propose a differential network analysis method that considers the differential expression of individual genes when identifying differential edges. First, two hypothesis test statistics are used to quantify changes in partial correlations between gene pairs and changes in expression levels for individual genes. Then, an optimization framework is proposed to combine the two test statistics so that the resulting differential network has a hierarchical property, where a differential edge can be considered only if at least one of the two involved genes is differentially expressed. Simulation results indicate that our method outperforms current state-of-the-art methods. We apply our method to identify the differential networks between the luminal A and basal-like subtypes of breast cancer and those between acute myeloid leukemia and normal samples. Hub nodes in the differential networks estimated by our method, including both differentially and nondifferentially expressed genes, have important biological functions.

Availability and implementation

All the datasets underlying this article are publicly available. Processed data and source code can be accessed through the Github repository at https://github.com/Zhangxf-ccnu/chNet.

Supplementary information

Supplementary data are available at Bioinformatics online.
Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data
Authors: Lei Haoyun , Gertz E Michael , Schäffer Alejandro A , Fu Xuecong , Tao Yifeng , Heselmeyer-Haddad Kerstin , Torres Irianna , Li Guibo , Xu Liqin , Hou Yong , Wu Kui , Shi Xulian , Dean Michael , Ried Thomas , Schwartz Russell
Published: July 2021

Motivation

Computational reconstruction of clonal evolution in cancers has become a crucial tool for understanding how tumors initiate and progress and how this process varies across patients. The field still struggles, however, with special challenges of applying phylogenetic methods to cancers, such as the prevalence and importance of copy number alteration (CNA) and structural variation events in tumor evolution, which are difficult to profile accurately by prevailing sequencing methods in such a way that subsequent reconstruction by phylogenetic inference algorithms is accurate.

Results

In this work, we develop computational methods to combine sequencing with multiplex interphase fluorescence in situ hybridization to exploit the complementary advantages of each technology in inferring accurate models of clonal CNA evolution accounting for both focal changes and aneuploidy at whole-genome scales. By integrating such information in an integer linear programming framework, we demonstrate on simulated data that incorporation of FISH data substantially improves accurate inference of focal CNA and ploidy changes in clonal evolution from deconvolving bulk sequence data. Analysis of real glioblastoma data for which FISH, bulk sequence and single cell sequence are all available confirms the power of FISH to enhance accurate reconstruction of clonal copy number evolution in conjunction with bulk and optionally single-cell sequence data.

Availability and implementation

Source code is available on Github at https://github.com/CMUSchwartzLab/FISH_deconvolution.

Supplementary information

Supplementary data are available at Bioinformatics online.
2DProts: database of family-wide protein secondary structure diagrams
Authors: Hutařová Vařeková Ivana , Hutař Jan , Midlik Adam , Horský Vladimír , Hladká Eva , Svobodová Radka , Berka Karel
Published: July 2021

Secondary structures provide a deep insight into the protein architecture. They can serve for comparison between individual protein family members. The most straightforward way how to deal with protein secondary structure is its visualization using 2D diagrams. Several software tools for the generation of 2D diagrams were developed. Unfortunately, they create 2D diagrams based on only a single protein. Therefore, 2D diagrams of two proteins from one family markedly differ. For this reason, we developed the 2DProts database, which contains secondary structure 2D diagrams for all domains from the CATH and all proteins from PDB databases. These 2D diagrams are generated based on a whole protein family, and they also consider information about the 3D arrangement of secondary structure elements. Moreover, 2DProts database contains multiple 2D diagrams, which provide an overview of a whole protein family's secondary structures. 2DProts is updated weekly and is integrated into CATH.

Availability and Implementation

Freely accessible at https://2dprots.ncbr.muni.cz. The web interface was implemented in JavaScript. The database was implemented in Python.

Supplementary information

Supplementary data are available at Bioinformatics online.
Uncertainty and inequality in early financial thought: John Hicks as a reader of Knight and Keynes
Authors: Hirsch Roni
Published: July 2021

The article examines the early reception of Knight’s and Keynes’ accounts of uncertainty and their overlooked role in the development of financial economics. Knight’s famous distinction between risk and uncertainty bore a deep social and political significance, dividing humanity into risk-takers and the risk-averse. This same distinction, I argue, along with its asymmetries of power and rewards, was reproduced in Hicks’ 1939 dynamic equilibrium model. It was recast as an opposition between hedgers and speculators in a market for risk, on the one hand, and between institutional investors and the general public, on the other. Hicks’s synthesis heeds both Knightian and Keynesian notions of uncertainty, adopting the former’s idea of profit-earning uncertainty-bearers and the latter’s definition of money as an imperfect though widely used hedge against uncertainty. Closer to Knight than to Keynes, Hicks’s model raises a fundamental political question: is inequality a price worth paying for greater certainty in economic life?
British Nationals’ Preferences Over Who Gets to Be a Citizen According to a Choice-Based Conjoint Experiment
Authors: Donnaloja Victoria
Published: July 2021

This article contributes new evidence about the types of immigrants that British nationals would accept as fellow citizens. I analyse the preferences of a large, nationally representative UK sample employing a choice-based conjoint-analysis experiment. Respondents were presented with paired vignettes of applicant types characterized by a combination of attributes chosen randomly. The attributes of immigrants with the largest impact on the probability of granting citizenship were occupation and religion: respondents especially penalized applicants who were Muslim or with no occupation. Respondents granted citizenship at different rates on average (from 64 per cent to 80 per cent): rates were lower among respondents who had voted to leave the EU, were older, less educated, and earned less. The types of immigrant who were most likely to be granted citizenship did not, however, vary by respondents’ income, education, or age, and varied little between Brexit Leave and Remain voters. My findings about nationals’ citizen preferences reflect the inclusive–exclusive nature of British citizenship and national identity, whereby inclusion is conditional on productivity and on the endorsement of liberal values.
Genomic Expansions in the Human Gut Microbiome
Authors: Moeller Andrew H
Published: July 2021

Bacteria inhabiting the human body vary in genome size by over an order of magnitude, but the processes that generate this diversity are poorly understood. Here, we show that evolutionary forces drive divergence in genome size between bacterial lineages in the gut and their closest relatives in other body sites. Analyses of thousands of reference bacterial isolate genomes and metagenome-assembled genomes from the human microbiome indicated that transitions into the gut from other body sites have promoted genomic expansions, whereas the opposite transitions have promoted genomic contractions. Bacterial genomes in the gut are on average ∼127 kb larger than their closest congeneric relatives from other body sites. Moreover, genome size and relative abundance are positively associated within the gut but negatively associated at other body sites. These results indicate that the gut microbiome promotes expansions of bacterial genomes relative to other body sites.
Is a National Court Competent to Introduce a Disclaimer into a Trade Mark Registration? The Latvian Supreme Court Finally Says ‘No’
Authors: Rozenfelds JĀnis , Mantrov Vadim
Published: July 2021

It was a longstanding practice of Latvian courts to acknowledge their competence to introduce a disclaimer into a challenged trade mark registration. This had come to be considered as settled court practice. However, the Latvian Supreme Court recently decided to withdraw this practice and explicitly admitted a change of approach concerning the competence of Latvian national courts to introduce a disclaimer into a trade mark registration. In this way, the Latvian Supreme Court finally abolished a disputable practice in the Latvian courts, having formerly allowed themselves to introduce a disclaimer which could – by way of a misunderstanding of trade mark law – be introduced by a court in addition to a trade mark applicant and the Patent Office. The consequences of this Latvian case have led to the situation that only a trade mark applicant may – either on their own initiative or following a request from the Patent Office – introduce a disclaimer into a trade mark registration. This opinion discusses the situation which existed before the Latvian Supreme Court judgment in question and its consequences.
Postwar statebuilding in Burundi: ruling party elites and illiberal peace
Authors: Burihabwa Ntagahoraho Z , Curtis Devon E A
Published: July 2021

The widespread enthusiasm for internationally-supported liberal statebuilding since the 1990s has become much more tempered, due in part to the mixed record of postwar liberal statebuilding. Over time, many postwar countries have adopted more authoritarian statebuilding trajectories, despite the fact that negotiated peace agreements tend to reflect liberal principles. This is often attributed to ‘liberal’ international actors encountering resistant ‘illiberal’ domestic elites. The postwar statebuilding trajectory in Burundi appears to fit this dominant narrative, with the ruling party, the Conseil National pour la Défense de la Démocratie-Forces pour la Défense de la Démocratie (CNDD-FDD), deviating from some of the liberal principles that underpinned the Burundian peace agreement. Drawing on a detailed analysis of the internal politics of Burundi's ruling party, we show that this account is flawed. We question overly simplified accounts of ‘illiberal’ ruling party elites and we argue that tensions, competition and fragmentation within the ruling party were decisive in Burundi's statebuilding path. Rather than seeing Burundi as an inevitable failure of liberal statebuilding, we highlight how there was some commitment to liberal principles even within the ruling party. Internal struggles within the ruling CNDD-FDD led to current outcomes in Burundi, which should not be interpreted as predestined or definitive. We show that understanding the complexities, diversities and contingencies within ruling parties opens new spaces for thinking about the creation and recreation of political orders after war.
Clerical associations in Qatar and the United Arab Emirates: soft power competition in Islamic politics
Authors: Diwan Kristin
Published: July 2021

In the wake of the 2011 Arab uprisings, the wealthy Gulf states of Qatar and the United Arab Emirates began hosting and establishing associations of influential Islamic scholars. These clerical associations, the Doha-based International Union for Muslim Scholars (IUMS) and the Abu Dhabi-based Muslim Council of Elders (MCE) and associated peace initiatives, have afforded a platform for more credibly entering into religious and political debates, for cultivating new networks of influence among Muslim publics, and engaging non-Islamic countries and organizations. Drawing upon interviews and primary resources, this study investigates this exercise in religious statecraft, comparing the discourse and policy interventions of these associations, and analysing their improbable challenge to the predominant religious terms set by the traditional heavyweight in the Gulf, Saudi Arabia. It finds that the effectiveness, or resonance, of these religious soft power projects depends upon credibility—their alignment with national religious traditions and policy directions—and positioning—the targeting of particular audiences and stakeholders. It concludes that the UAE holds certain advantages over Qatar in its soft power positioning in the current nationalist moment, as states gain ground over transnational Islamic movements and relations with powers such as India, Russia, China and Israel—all hostile to independent Islamic movements—gain in importance. Policy-makers acknowledging the surprising hard power projection of these small states through military interventions and economic leverage may benefit from this study of their new religious soft power influence.
Post-Termination Responsibility of States?—The Impact of Amendment/Modification, Suspension and Termination of Investment Treaties on (Vested) Rights of Investors
Authors: Reinisch August , Mansour Fallah Sara
Published: July 2021

The recent practice of States to amend, suspend or terminate investment treaties has moved questions of potential ‘post-termination responsibility’ to the forefront of the contemporary legal discourse in international investment law. Although States have often included provisions in their respective treaties to regulate post-termination protection of investments, some aspects of the aftermath of treaty terminations are still unsettled. This article defines and discusses various types of ‘post-termination responsibility’ by reviewing current practice, doctrine and jurisprudence on the matter. In that vein, it examines terminations, modifications and suspensions that were unlawful and ineffective, or effective but not capable of releasing the State from all treaty obligations either by virtue of survival clauses or separate principles of vested or third-party rights. It then elaborates on denunciations of the ICSID Convention or terminations of BITs and their effects on pending proceedings or the right to initiate proceedings in the future. Moreover, the article discusses whether survival clauses apply solely to unilateral or also to mutual terminations of investment treaties. It will also address the question whether investor rights may continue to be protected as a result of acquired/vested rights or third-party rights. By analysing the most recent jurisprudence and practice of States, as well as more general foundations of general international law, this article aims to contribute to a clarification of these questions.
Review: optimizing genomic selection for crossbred performance by model improvement and data collection
Authors: Duenk Pascal , Bijma Piter , Wientjes Yvonne C J , Calus Mario P L
Published: July 2021

Breeding programs aiming to improve the performance of crossbreds may benefit from genomic prediction of crossbred (CB) performance for purebred (PB) selection candidates. In this review, we compared genomic prediction strategies that differed in 1) the genomic prediction model used or 2) the data used in the reference population. We found 27 unique studies, two of which used deterministic simulation, 11 used stochastic simulation, and 14 real data. Differences in accuracy and response to selection between strategies depended on i) the value of the purebred crossbred genetic correlation (rpc), ii) the genetic distance between the parental lines, iii) the size of PB and CB reference populations, and iv) the relatedness of these reference populations to the selection candidates. In studies where a PB reference population was used, the use of a dominance model yielded accuracies that were equal to or higher than those of additive models. When rpc was lower than ~0.8, and was caused mainly by G × E, it was beneficial to create a reference population of PB animals that are tested in a CB environment. In general, the benefit of collecting CB information increased with decreasing rpc. For a given rpc, the benefit of collecting CB information increased with increasing size of the reference populations. Collecting CB information was not beneficial when rpc was higher than ~0.9, especially when the reference populations were small. Collecting only phenotypes of CB animals may slightly improve accuracy and response to selection, but requires that the pedigree is known. It is, therefore, advisable to genotype these CB animals as well. Finally, considering the breed-origin of alleles allows for modeling breed-specific effects in the CB, but this did not always lead to higher accuracies. Our review shows that the differences in accuracy and response to selection between strategies depend on several factors. One of the most important factors is rpc, and we, therefore, recommend to obtain accurate estimates of rpc of all breeding goal traits. Furthermore, knowledge about the importance of components of rpc (i.e., dominance, epistasis, and G × E) can help breeders to decide which model to use, and whether to collect data on animals in a CB environment. Future research should focus on the development of a tool that predicts accuracy and response to selection from scenario specific parameters.
DNA G-quadruplex structures: more than simple roadblocks to transcription?
Authors: Robinson Jenna , Raguseo Federica , Nuccio Sabrina Pia , Liano Denise , Di Antonio Marco
Published: July 2021

It has been >20 years since the formation of G-quadruplex (G4) secondary structures in gene promoters was first linked to the regulation of gene expression. Since then, the development of small molecules to selectively target G4s and their cellular application have contributed to an improved understanding of how G4s regulate transcription. One model that arose from this work placed these non-canonical DNA structures as repressors of transcription by preventing polymerase processivity. Although a considerable number of studies have recently provided sufficient evidence to reconsider this simplistic model, there is still a misrepresentation of G4s as transcriptional roadblocks. In this review, we will challenge this model depicting G4s as simple ‘off switches’ for gene expression by articulating how their formation has the potential to alter gene expression at many different levels, acting as a key regulatory element perturbing the nature of epigenetic marks and chromatin architecture.
ECOA-4. Hypoxia alters the DNA methylation profile of glioblastoma tumor cells
Authors: Mansouri Sheila , Mamatjan Yasin , Karimi Shirin , Singh Olivia , Tung Takyee , Velasquez Carlos , Nassiri Farshad , Aldape Kenneth , Zadeh Gelareh
Published: July 2021

Glioblastoma (GBM) is the deadliest and most vascularized brain tumor in adults; however, blood circulation is highly inefficient in these tumors, contributing to areas of cell death (necrosis) within the tumor, which is likely due to oxygen deprivation (hypoxia). Hypoxia plays a major role in tumor growth, invasion, and resistance to therapy. Hypoxic stress has been linked to several changes that are fundamental to the malignant progression of GBM and other tumor types. Pimonidazole (PIMO) is an exogenous marker of hypoxia that is used to delineate hypoxic regions in several tumor types. To date, a clear hypoxia gene signature has not been specifically described for GBM. We hypothesize that specific cellular pathways are differentially regulated in hypoxic tumor niches and can serve as novel actionable targets for treatment-resistant tumor cells in GBM. Over the past 3 years, we have administered PIMO to 35 patients with primary IDH1/2 wild-type GBM and isolated PIMO-positive and PIMO-negative tumor cells by laser capture microdissection using a PIMO-specific antibody on frozen tumor specimens. Total genomic DNA was isolated and subjected to DNA methylation profiling using the Illumina Infinium Methylation EPIC array. Our preliminary results suggest that PIMO-positive (hypoxic) tumor cells display a distinct DNA methylation profile that corresponds to changes in expression of a set of genes associated with immune regulation, angiogenesis, and proliferation. Furthermore, multiple CpG sites within the promoter of some genes are differentially methylated in hypoxic cells, suggesting these genes may be epigenetically regulated under hypoxia. In conclusion, our results indicate that hypoxia is associated with distinct epigenetic alterations in tumor cells which may alter how these cells respond to low oxygen levels and can further be utilized to uncover the epigenomic vulnerabilities of hypoxic tumor cells in GBM.
ECOA-8. Lung adenocarcinoma brain metastasis prediction using tumor DNA methylation profiling
Authors: Zuccato Jeffrey , Mamatjan Yasin , Aldape Kenneth , Zadeh Gelareh
Published: July 2021

Introduction

The development of brain metastases from primary cancer profoundly impacts patient prognosis. Up to one quarter of lung cancers develop brain metastases and subsequent median overall survival is one year. Although clinical factors do not reliably predict brain metastasis development, DNA methylation signatures have been recently shown to predict outcomes in other cancers. It is hypothesized that DNA methylation signatures predicting brain metastasis development from lung cancer will be identified. This work may allow for treatment strategies that prevent brain metastasis development in high risk lung cancer patients.

Methods

DNA methylation profiling was undertaken on N=124 lung adenocarcinoma patients. In a randomly selected 70% training cohort, differentially methylated CpG sites between patients developing and not developing brain metastases were identified and used to build a generalized boosted regression model. Patients in the independent 30% testing cohort were assigned brain metastasis risk scores by the model.

Results

Brain metastases developed in 49/124 (39.5%) of patients and 2.3K CpG sites were significantly differentially methylated between patients developing and not developing metastases. Methylation-based brain metastasis risk scores predicted time to brain metastasis development in the testing cohort (Univariate cox: HR=3.2, 95% CI 1.1–9.4, p=0.03). A multivariate cox analysis assessing tumor size and nodal positivity together with methylation scores as covariates identified methylation scores as the only independent predictor of brain metastasis development in the testing cohort (HR=4.3, 95%CI 1.1–17, p=0.038).

Conclusions

DNA methylation signatures in lung adenocarcinomas predict brain metastasis development independently from the non-metastatic components of cancer stage. Future work developing a comprehensive nomogram utilizing methylation scores together with clinical factors to determine patient specific risk values may aid in treatment decisions and patient prognosis counselling.
NGMA-1. Quantification of IDH mutant alleles predicts outcome in diffuse gliomas
Authors: Voisin Mathew , Zadeh Gelareh
Published: July 2021

Background

IDH mutation is the main factor used in the prognostication of diffuse gliomas, however within IDH mutated gliomas there still remains a high variability in both tumor progression and overall survival.1 Digital droplet polymerase chain reaction (ddPCR) is one of the latest molecular amplification techniques that offers high precision in addition to the ability of absolute quantification of mutant allele copies.2

Methods

A total of 102 IDH mutant diffuse glioma tumor samples ranging from WHO grade 2 to 4 were collected. This cohort includes a total of 45 paired samples collected at two distinct surgical timepoints: initial and recurrent. All samples underwent DNA extraction. A total of 5 ng of tumor DNA from each sample was analyzed using ddPCR for the detection and quantification of IDH1 R132H mutant alleles. Sanger sequencing was performed on all samples as a gold standard.

Results

ddPCR was highly sensitive (100%) and specific (99%) for the detection of IDH mutations. Initial tumor samples with a high number of IDH mutant copies split by median demonstrated decreased overall survival (p = 0.04) and shorter progression free survival (p = 0.024). The number of IDH mutant copies was independent of WHO grade (p = 0.6) and 1p19q codeletion status (p = 0.86). Tumor pairs that had IDH mutant copies increase at recurrence were trending but not significantly related to a decrease in remaining survival (p = 0.1).

Conclusions

ddPCR is a highly sensitive and specific method of detecting IDH mutations in diffuse gliomas. The number of IDH mutant copies in tumors at initial surgery can serve as an independent prognostic factor to help guide future treatment and follow-up.
NGMA-2. Dual sgRNA-directed PD-L1 knockout in human glioblastoma cells using the CRISPR/Cas9 system
Authors: Fierro Javier , Dipasquale Jake , Aguilar Rocio , Perez Joshua , Tran An , Factoriza Chris , Dou Huanyu
Published: July 2021

Glioblastoma multiforme (GBM) is an astrocyte derived brain tumor. It induces an immunosuppressive microenvironment by exploiting immune checkpoints such as the PD-1/PD-L1 pathway. Targeting the PD-1/PD-L1 pathway for immunotherapy is a promising new avenue for treating GBM, but more work is needed to develop a safe and effective method for clinical applications. We identified two sgRNA sequences located on PD-L1 exon 3. The first sgRNA recognized the forward strand of human PD-L1 near the beginning of exon 3 and cuts at approximately base pair 82 (g82). The second sgRNA recognized the reverse strand of exon 3 and cuts at base pair 165 (g165). Two sgRNAs, g82 and g165, created an 83bp deletion in the genomic sequence that can lead to the production of a non-functional PD-L1 protein. A homology-directed repair template (HDR) containing an in-frame stop codon was designed to enhance PD-L1 knockout specificity and efficiency. Both g82 and g165 were cloned into the CRISPR/Cas9 plasmid, and was co-transfected with the added HDR template. T7E1, qRT-PCR and western blot analysis determined that the dual sgRNA CRISPR/Ca9 system knocked out both endogenous (80%) and exogenous (64%) PD-L1 in U87 cells and PD-L1 overexpression U87 cells, respectively. Deletion of PD-L1 reduced U87 migration and proliferation, while PD-L1 overexpression promoted tumor growth and tumor-associated macrophage polarization. Together, deletion of both membrane and cytoplasmic PD-L1 altered the PD-L1-associated immunosuppressive environment and prevented tumor progression and migration. Thus, a dual sgRNA CRISPR/Cas9 gene-editing system is a promising avenue for anti-GBM immunotherapy.
NGMA-3. Use of multi-omics data to initialize and validate a causal model of glioblastoma stem cell signaling
Authors: Holtzapple Emilee , Miskov-Zivanov Natasa , Cochran Brent
Published: July 2021

Glioblastomas and glioblastoma stem cells are heterogeneous with respect to mutations, gene expression, and response to drugs. To make predictive responses of individual GBM stem cell lines to drugs, we have constructed a causal model of glioblastoma stem cell signaling. The core model was built starting from pathways identified from TCGA mutation data with the addition of the Jak/STAT, Hedgehog, and Notch pathways. Elements and relations between them were validated and extended using the PCNet interaction database and the INDRA database which includes machine read extractions from the biomedical literature. The result is a high confidence executable model consisting of 209 element and 370 rules of interaction between the elements. Stochastic simulations of the model provide dynamic (quantile) changes in time and responses to perturbations. The output provides activity of individual nodes as well as a cellular output state of cell cycle progression, apoptosis, or differentiation. To simulate the responses of individual cell lines to kinase inhibitors, the model was initialized using DNA sequencing data, RNA-seq, and reverse phase protein array (RPPA) data from each cell line. Comparing the results of the simulations to the drug responses of 11 different kinase targets, the model was 88% accurate in predicting effects on growth and survival. The model was further tested by comparing the effects of Mek inhibition of each of the cell lines in model to the results observed in the RPPA data which overlap by 127 elements. In this case, there was 62% concordance between the model and data when binned into quintiles. Discrepancies between the model predictions and the data are being investigated to determine whether the model logic or extent needs to be revised to improve the model. This modeling approach is a step toward developing algorithms for personalized therapeutics for GBM based on multi-omics data.
NGMA-6. Quantitative MGMT Promoter Methylation Index Indicates Non-Linear, Prognostic Effect in Glioblastoma
Authors: Gibson David , Ravi Akshay , Rodriguez Eduardo , Chang Susan , Bush Nancy , Taylor Jennie , Clarke Jennifer , Solomon David , Scheffler Aaron , Witte John , Okada Hideho , Berger Mitchel , Chehab Farid , Butowski Nicholas
Published: July 2021

Background

Epigenetic inhibition of the O6-methylguanine-DNA-methyltransferase (MGMT) gene has emerged as a clinically relevant prognostic marker in glioblastoma (GBM). Methylation of the MGMT promoter has been shown to increase chemotherapy efficacy. While traditionally reported as a binary marker, recent methodological advancements have led to quantitative methods of measuring methylation, allowing for clearer insights into methylation’s functional relationship with survival.

Methods

A CLIA assay and bisulfite sequencing was utilized to develop a quantitative, 17-point MGMT promoter methylation index derived from the number of methylated CpG sites. Retrospective review of 242 newly diagnosed GBM patients was performed in order to discern how risk for mortality transforms as promoter methylation increases. Non-linearities were captured by fitting splines to Cox proportional hazard models, plotting smoothed residuals, and creating survival plots. Covariates included age, KPS, IDH1 mutation, and extent of resection.

Results

Median follow-up time and progression free survival were 15.9 and 9 months, respectively. 176 subjects experienced death. A one-unit increase in CpG methylation resulted in a 4% reduction in hazard (95% CI 0.93–0.99, P<0.005). Moreover, GBM patients with low levels of methylation (1–6 CpG islands) fared markedly worse (HR=1.62, 95% CI 1.03–2.54, P<0.036) than individuals who were unmethylated (reference group). Subjects with medium levels of methylation (7–12 sites) had the greatest reduction in hazard (HR=0.48, 95% CI 0.29–0.80, P<0.004), followed by individuals in the highest methylation tertile (HR=0.62, 95% CI 0.40–0.97, P<0.035).

Conclusion

The extent of MGMT methylation shares a non-linear relationship with survival, suggesting conformation of the marker’s protective effect. This finding challenges the current understanding of MGMT and underlines the clinical importance of determining its prognostic utility. Potential limitations include censoring, sample size, and extraneous mutations. Future research is warranted to examine whether the location of CpG site methylation contributes to a reduction in mortality hazard.
OPTC-1. Proteomic analysis of genetically stratified low-grade meningioma
Authors: Akther Yeasmin , Adams Claire , Sharma Vikram , Barros Claudia , Banton Matthew , Hanemann Oliver
Published: July 2021

Introduction

Meningioma are the most common primary intracranial tumour. According to WHO, ~80% tumours are benign grade I. Although, some grade I tumour clinically show aggressive behaviour. Radio-surgery are the main therapeutic approaches, chemotherapies are ineffective. Accurate biomarkers for clinical management are lacking. The mutational profile of low-grade meningioma is well-defined, with non-NF2 mutated tumours harbouring recurrent mutations in genes including TRAF7, KLF4, AKT1 and SMO. Here, we aim to identify novel biomarkers and therapeutic targets of genetically stratified low-grade meningioma by characterising the proteomic landscape.

Materials and methods

Meningioma specimens were stratified according to mutational background: AKT1E17K/TRAF7, KLF4K409Q/TRAF7 and NF2-/-. Proteins were separated by SDS-PAGE followed by in-gel tryptic digestion and sample preparation for LC-MS/MS analysis. Raw mass spectrometry data files were processed by MaxQuant and Perseus software. Quantitative phospho-proteomics was performed using TMT-10plex labelling approach followed by motif analysis using motif-X algorithm. GO enrichment analyses were performed using DAVID against all human proteins.

Results and Conclusions

We have quantified 4162 proteins across all mutational meningioma subgroups and normal meninges (n=31). Hierarchical clustering analysis showed distinct proteomic profiles of mutational subgroups revealing clusters of differentially expressed proteins (DEPs). Comparative analysis showed 10 proteins were commonly significantly upregulated (log2 fold-change≥1; p<0.05) among all mutational subtypes vs. normal meninges, indicating proteomic landscapes of mutational subtypes to be highly variable. In contrast, 257 proteins were commonly significantly downregulated (log2 fold-change≤-1; p<0.05) and enriched with molecular functions including aldehyde dehydrogenase and oxido-reductase. Mutational subtype-specific analysis identified 162 proteins significantly upregulated in AKT1E17K/TRAF7 vs. remaining sample groups to be enriched in the oxidative phosphorylation pathway. Lastly, analyses of 6600 phospho-sites (n=8) predicted regulatory kinases including EGFR and PKCα. Several of these up-regulated proteins and kinases already verified via WB. Further validation and functional verification will allow us to identify potential drug targets/biomarkers for meningioma.