bluuebunny/crossref_metadata_2025 huggingface dataset:
On teaching experimental reactor physics in times of pandemic
Authors: Malec Jan , Österlund Michael , Solders Andreas , Al-Adili Ali , Jazbec Anže , Rupnik Sebastjan , Radulović Vladimir , Lengar Igor , Snoj Luka
Published: November 2021

The COVID-19 induced restrictions have prevented reactor physics students from attending in-person reactor physics exercises which are a vital part of their education. Jožef Stefan Institute has organized remote exercises with the help of off-the-shelf technology, including multiple videoconferencing setups, remote desktop software, portable cameras, a dome camera, shared spreadsheets, and a common whiteboard. The students were encouraged to actively participate in the exercises by giving instructions to the reactor operator, asking and answering questions, logging data, operating digital acquisition systems, and performing analysis during the exercise. The first remote exercises were organized as a five-day course of experimental reactor physics for students from Uppsala University. The feedback was collected after the course using an anonymous online form and was generally positive but has revealed some problems with sound quality which were resolved later. The Jožef Stefan Institute can also organize a remote course during a full lockdown when the reactor is not able to operate using the in-house developed Research Reactor Simulator based on a point kinetics approximation and a simple thermohydraulic module.
Pre-heating by defocusation of the CO2-Laser polishing beam: an experimental report from the lab-floor -INVITED
Authors: Bliedtner Jens , Faehnle Oliver , Layher Anne-Marie , Hassel Robin , Barz Andrea
Published: November 2021

The laser beam polishing for glass and plastics is a purely thermal process and melts the ground or lapped structures to a depth of limited extent. This results in a smoothing of the surface, whereby the 1st - 4th order shape deviations can be corrected very well and transparent surfaces are
created. The process is excellently suited for quartz glasses and other optical glasses with a low coefficient of expansion α. Furthermore, thermoplastics or metallic molds for injection molding and precision molding applications can also be polished with the laser beam. On the other hand, special measures are required for glasses with a high α, e.g. preheating of the component. For the investigations, a defocused laser beam was used for the defined preheating of glasses with high linear expansion coefficients. After reaching the material-specific preheating temperature, the laser beam
was focused and the polishing process started. A defined cooling process follows again with a defocused beam. In this way, a ground biconvex lens made of boron crown glass was successfully polished. The laser-polished surfaces have an RMS value of 1- 3 nm. The polishing process can be used very flexibly. Likewise, very differently shaped optical components can be polished.

The newly developed polishing regime is transferable to other optical glasses with high linear expansion coefficients.
Multiplexed fiber-optic Fabry-Pérot cavities for refractive index and temperature sensing fabricated using diamond-blade dicing
Authors: Pfalzgraf Ivonne , Suntsov Sergiy , Hasse Kore , Kip Detlef
Published: November 2021

We report on multiplexing several Fabry-Pérot (FP) cavities in single-mode optical fibers for highprecision spatially resolved sensing of refractive indices (RI) of liquids. Resonators are fabricated by cutting small slots into fibers using a diamond-blade dicing saw and additional coating with thin Ta2O5 layers to increase cavity reflectance. Temperature compensation of RI measurements is achieved either by evaluating the reflection signals resulting from the solid core parts between different open-cavity sensor elements, or by using a thin Si inlay glued into one of the open cavities. The multiplexing performance and accuracy of the fabricated sensors with up to four open cavities were tested on sucrose solutions over a range of temperatures.
A Spectral Resolution study in Femtosecond Stimulated Raman Scattering Microscopy
Authors: Ranjan Rajeev , Ferrara Maria Antonietta , Sirleto Luigi
Published: November 2021

The simultaneous mapping and the specificity of different chemical species are desirable in several biological and biomedical applications. The stimulated Raman Scattering technique is a proven and well-established label-free method to map the distributions of individual species in a multi-component-based system due to the linear dependence of signals on concentration and its chemical selectivity. In this framework, spectral resolution, i.e., the ability to distinguish closely lying resonances, plays a fundamental role. Here in this work, the cross-correlation of Ti:Sa & OPO femtosecond laser beams in a stimulated Raman scattering microscope is measured. The separation between protein and lipid bands in the C-H region is important for biochemical research and is successfully classified.
Femtosecond laser writing of integrated photonic circuits in diamond
Authors: Coccia Giulio , Giakoumaki Argyro N. , Bharadwaj Vibhav , Jedrkiewicz Ottavia , Ramponi Roberta , Eaton Shane M.
Published: November 2021

Integrated photonic circuits pave the way for next generation technologies for quantum information and sensing applications. Femtosecond laser writing has emerged as a valuable technique for fabricating such devices when combined with diamond’s properties and its nitrogen vacancy color center. Such color centers are fundamental for sensing applications, being possible to excite them and read them out optically through the fabrication of optical waveguides in the bulk of diamond. We show how to integrate these building blocks in diamond, to develop proof-of-concept devices with unprecedented electric and magnetic field sensitivities.
Ultrafast exciton dynamics reconstruction with a ptychographic approach
Authors: Dolso Gian Luca , Moio Bruno , Inzani Giacomo , Di Palo Nicola , Borrego-Varillas Rocío , Nisoli Mauro , Lucchini Matteo
Published: November 2021

Excitons characterize the ultrafast response of many materials of technological interest. While the development of attosecond science has unlocked the possibility of performing experiments with a suitable timeresolution, the access to the exciton properties remains a non-trivial step. We propose therefore a novel approach to disclose the physical properties behind the ultrafast exciton dynamics based on a phase-retrieval method.
Maria Mitchell
Authors: Leboulleux Lucie
Published: November 2021

Maria Mitchell was a pioneer in many aspects: first observer of a comet with a telescope, she received the Gold Medal from the King of Denmark and became the first female astronomer and astronomy professor in the United States of America. But she also got involved in feminism, participating in the foundation of the Association for the Advancement of Women in 1873 as well as promoting the access to higher education for women and their inclusion in science.
Axial Spondyloarthritis and New Bone Formation
Authors: Syrbe Uta
Published: November 2021

Axial spondyloarthritis is an inflammatory disease of the axial skeleton. Its
pathogenesis is only partly understood. At the beginning, there are inflammatory
changes in the sacroiliac joints which are followed by inflammation in vertebral
bodies and in facet joints. Low back pain occurring in the morning hours is the
dominant clinical symptom. In the early phase, inflammatory changes are
detectably by MRI. Inflammation promotes a process of joint remodelling in the
sacroiliac joints which leads to erosions, sclerosis and bony bridging,
i. e. ankylosis, which are detectable by X-ray. In the spine, vertical
osteophytes developing at sites of previous inflammation connect vertebral
bodies as syndesmophytes. Additional ossification of longitudinal ligaments
contributes to the so-called bamboo spine. Ossification of the spine promotes
fixation of a severe kyphosis of the thoracic spine which strongly impairs spine
mobility and quality of life. High disease activity seems a prominent risk
factor for development of structural damage. However, although NSAIDs improve
clinical symptoms, they do not reduce new bone formation. In contrast,
TNFα and IL-17 inhibitors seem to retard new bone formation apart from
their clinical efficacy. Research work of the last years identified
immunological pathways of inflammation. However, the trigger and cellular
components of the immune reaction in the bone marrow are still poorly defined.
Osteoclasts are involved in the destruction of the subchondral bone, while
osteoblasts facilitate new bone formation and cartilage ossification. This
review gives an overview about diagnostics and therapy of axSpA and about risk
factors for the development of structural damage. Concepts about the immune
pathogenesis and joint remodeling in AS are given under recognition of genetic
and histopathological studies.
Prinzipien aus Gestalttheorie und Gestalttherapie in Beziehung zur Homöopathie Samuel Hahnemanns
Authors: Menhard Konrad
Published: November 2021

Ziel dieser Arbeit ist es, die wesentlichen Elemente der Gestalttheorie und Gestalttherapie für die Homöopathie fruchtbar zu machen. Dafür werden grundlegende Gemeinsamkeiten im Denken, im methodischen Vorgehen, in Diagnostik und Therapie der Homöopathie mit Gestalttheorie und Gestalttherapie beschrieben.
Novel Insights into the Ontogenetic and Functional Heterogeneity of
Macrophages in Synovial Tissue and Bone
Authors: Percin Gulce Itir , Grüneboom Anika , Waskow Claudia , Culemann Stephan
Published: November 2021

Inflammatory joint diseases like rheumatoid arthritis (RA) belong to the most
prevalent autoimmune disorders. RA is characterized by a massive infiltration of
immune cells into synovial tissue, cartilage destruction and bone erosion. The
perpetuating inflammatory and destructive milieu is associated with severe pain
and culminates in complete disability of synovial joints. The events initiating
RA are still not fully understood and the treatments are mainly confined to
strategies that modify and inhibit the body’s immune system. Macrophages
and osteoclasts (OC) are myeloid cells of the innate immune system and are
considered to play a central role in the inflammatory and destructive events of
arthritis by production of inflammatory cytokines and mediating pathological
bone resorption. In recent years, the use of novel fate mapping strategies
identifying the origin and cellular development (ontogeny) of OC and macrophages
in conjunction with new genetically modified mouse models, single cell analysis
and advanced imaging techniques substantially changed our understanding on the
ontogenetic and functional heterogeneity of these cells.
Young British tourists' tourism-related information sources.
Authors: Zaim Ilma Aulia
Published: November 2021

This chapter is the work of Ilma Aulia Zaim and studies a specific market segment, young British tourists aged 18-35, and how these pursue tourism-related information sources that eventually affect their travel decision-making prior to visiting a destination. The study offers significant insight into destination management organizations(DMO)regarding young British travellers' characteristics and offers suggestions to them such as the types of information they should share on their websites and which of them are really valuable for the particular tourism market segment.
New tourism experiences and mature destinations: the role of participatory planning in repositioning a southern Italy destination.
Authors: Calza Francesco , Simoni Michele , Sorrentino Annarita , Trunfio Mariapina
Published: November 2021

This chapter is the work of Francesco Calza, Michele Simoni, Annarita Sorrentino and Mariapina Trunfio, who study the role of participatory planning in repositioning a southern Italy destination, Centola-Palinuro in the Campania region. This contribution deals with a demand-driven destination that suffers from several challenges such as seaside seasonality, mass-market demand and low spending. The case argues that a participatory planning process that involves local stakeholders can have a significant impact in the repositioning of the destination by reshaping the tourism offering in the area through stakeholder engagement.
Managing hybrid destinations: challenges and lessons from the Alps.
Authors: Bausch Thomas
Published: November 2021

Using the example of the Alps, it was shown that hybridity in tourism touches primarily three marketing fields: (a) Product. Because of attractions that change their character and level of appeal throughout the year or are linked to yearly events and habits, the perception of the core elements of the destination's image varies; (b) Communication. The hybridity of the product implies the need to address different target groups, as the changing focus of the destination image attracts different, often disjunctive or mutually exclusive, consumer groups; and (c) Pricing. Similar to all fields of consumption, an increasing polarization between low cost or bargain trips and high priced luxury travelling can be found. Some travellers prefer either lowcost or luxury travelling, while others change their expenditure from trip to trip.
Nazi past and destination image: the case of Linz, Austria.
Authors: Iordanova Elitza
Published: November 2021

Positioning or repositioning a destination on the already overcrowded market is a challenging task in normal circumstances but paired with difficult heritage it could be a major obstacle for any DMO. The current study tentatively suggests that nationality influences the richness and intensity of respondents' associations with Linz where the internationals were more likely to have a higher number of spontaneous associations (keywords) than Austrians, which is in contrast with that of Reilly (1990) reporting that respondents living far away from a destination were found to lack a vivid image of it. Moreover, the Nazi past appears to be still deeply rooted in Linz's brand despite the DMO's continuous attempts to reposition the destination's image by consciously or subconsciously trying to refute its difficult heritage and focusing its marketing efforts on promoting Linz's vivid cultural life.
Promoting intangible cultural heritage through social networks: a case study of the Fête de l'ours in France.
Authors: Arcos-Pumarola Jordi , Conill-Tetuà Marta
Published: November 2021

Considering the cultural relevance of ICH and its meanings for communities, and the fact that it is increasingly becoming an asset of destinations in promoting tourism, the use of ICH in social networks must be put in the spotlight to identify best practices of transmitting the meanings of ICH through social networks. An analysis of the use of ICH in the context of social networks will also illuminate which particular tourist image is being transmitted by the various agents and stakeholders that interact with social networks. In this vein, this chapter will present a case study based on the Fête de l'Ours, a celebration performed in three rural villages in the south of France, looking at how it is explained within a particular social network, namely, Instagram. In this way, the case study will aim to: (i) identify the elements of the festivity that are highlighted by locals and visitors in their Fête de l'Ours account on Instagram; and (ii) analyse how locals, visitors and stakeholders explain and share the experience of the festival.
Conclusion.
Authors: Stylidis Dimitrios , Boukas Nikolaos
Published: November 2021

This chapter summarizes the whole volume by including the highlights of all eleven chapters. It also discusses the scope and limitations of the volume as well as recommendations for further studies on tourism marketing. It states that useful key lessons can be drawn from the volume, for country, region and city destination marketers, managers and policymakers.
Phytophthora hedraiandra
. [Distribution map].
Authors: CABI  , EPPO
Published: November 2021

A new distribution map is provided for
Phytophthora hedraiandra
De Cock & Man in 't Veld. Oomycetes: Peronosporales: Peronosporaceae. Hosts:
Viburnum
spp.,
Rhododendron
spp. Information is given on the geographical distribution in Asia (Japan), Europe (Czechia, Hungary, Italy, Mainland, Netherlands, Slovenia, Spain, Balearic Islands, Switzerland, UK, England), North America (USA, California, Minnesota, Virginia), Oceania (Australia, Victoria).
Cherry rasp leaf virus. [Distribution map].
Authors: CABI  , EPPO
Published: November 2021

A new distribution map is provided for Cherry rasp leaf virus. Picornovirales: Secoviridae: Cheravirus. Hosts:
Prunus
spp.,
Malus
spp. Information is given on the geographical distribution in Asia (China, Liaoning, Shandong) and North America (Canada, British Columbia, Quebec, USA, California, Colorado, Minnesota, Montana, Nebraska, New Mexico, Oregon, Utah, Washington, Wisconsin).
How strong can the Parrondo effect be? II
Authors: Ethier S. , Lee Jiyeon
Published: November 2021

Parrondo’s coin-tossing games comprise two games,

A
A

and

B
B

. The result of game

A
A

is determined by the toss of a fair coin. The result of game

B
B

is determined by the toss of a

p
0

p_0

-coin if capital is a multiple of

r
r

, and by the toss of a

p
1

p_1

-coin otherwise. In either game, the player wins one unit with heads and loses one unit with tails. Game

B
B

is fair if

(
1
−

p
0

)
(
1
−

p
1

)

r
−
1

=

p
0

p
1

r
−
1

(1-p_0)(1-p_1)^{r-1}=p_0\,p_1^{r-1}

. In a previous paper we showed that, if the parameters of game

B
B

, namely

r
r

,

p
0

p_0

, and

p
1

p_1

, are allowed to be arbitrary, subject to the fairness constraint, and if the two (fair) games

A
A

and

B
B

are played in an arbitrary periodic sequence, then the rate of profit can not only be positive (the so-called Parrondo effect), but also be arbitrarily close to 1 (i.e., 100%). Here we prove the same conclusion for a random sequence of the two games instead of a periodic one, that is, at each turn game

A
A

is played with probability

γ
\gamma

and game

B
B

is played otherwise, where

γ
∈
(
0
,
1
)

\gamma \in (0,1)

is arbitrary.
Seromas: How to Prevent and Treat Them—a 20-Year Experience
Authors: Turer David M , Aly Al
Published: November 2021

Seromas are a common complication in plastic surgery. In this article, the authors describe their approach to the prevention and treatment of seromas and include a discussion of the evolution of their techniques. They provide specific technical details for many body contouring operations, including abdominoplasty, belt lipectomy, brachioplasty, and thighplasty. Many of the authors’ techniques question the traditional dictums of plastic surgery, and they hope to encourage others to consider novel techniques for the treatment and prevention of seromas.

Level of Evidence: 4
Exoplanet biosignatures
Authors: Janin Estelle
Published: November 2021

Biosignature science has come a long way in half a century, but its future depends on more interdisciplinary feeback and conceptual innovation.
Serum potassium variability as a predictor of clinical outcomes in patients with cardiorenal disease or diabetes: a retrospective UK database study
Authors: James Glen , Kim Jennifer , Mellström Carl , Ford Kerrie L , Jenkins Nia C , Tsang Carmen , Evans Marc , McEwan Phil
Published: November 2021

Background

Hyperkalaemia is an electrolyte abnormality associated with adverse clinical outcomes; however, few studies have investigated the relationship with patterns of hyperkalaemia over time. This study explored the impact of time spent in a hyperkalaemic state and variability of serum potassium (sK+) on major adverse cardiovascular events (MACE) and all-cause mortality in patients with chronic kidney disease (CKD), resistant hypertension, heart failure and diabetes.

Methods

Cohorts comprised adult patients diagnosed with CKD stage 3+, resistant hypertension, heart failure or diabetes, and/or renin–angiotensin–aldosterone system inhibitor prescription, between 1 January 2003 and 30 June 2018, from the UK Clinical Practice Research Datalink. Associations between percentage of follow-up spent in a hyperkalaemic state (sK+ ≥5.0 mmol/L, ≥5.5 mmol/L, ≥6.0 mmol/L) or sK+ variability (standard deviation above or below median standard deviation) and all-cause mortality or MACE were investigated.

Results

For sK+ ≥5.0 mmol/L, time spent in a hyperkalaemic state was associated with reduced risk of all-cause mortality across all cohorts. For higher sK+ thresholds, this trend was attenuated or reversed; for time spent in a hyperkalaemic state at sK+ ≥6.0 mmol/L, an increased risk of mortality was seen in the overall cohort and for patients with diabetes, resistant hypertension or prescribed renin–angiotensin–aldosterone system inhibitors, with no consistent association seen for patients with CKD or heart failure. Risk of MACE in the overall cohort and in patients with CKD, diabetes or resistant hypertension increased with time spent in a hyperkalaemic state at all sK+ thresholds; however, no correlation was seen in patients with heart failure or those receiving dialysis. High sK+ variability was associated with a higher risk of MACE compared with low sK+ variability across most sK+ categories in the overall population and in all disease cohorts, except patients on dialysis; however, no association between sK+ variability and all-cause mortality was observed.

Conclusions

Patterns of hyperkalaemia, including time spent in hyperkalaemia and sK+ variability, are associated with adverse clinical outcomes. Regular monitoring of sK+ in high-risk populations in broader community, primary care and outpatient settings may enable guideline-recommended management of hyperkalaemia and help avoid adverse events.
Optimization of BSA-seq experiment for QTL mapping
Authors: Huang Likun , Tang Weiqi , Wu Weiren
Published: November 2021

Deep sequencing-based bulked segregant analysis (BSA-seq) has become a popular approach for quantitative trait loci (QTL) mapping in recent years. Effective statistical methods for BSA-seq have been developed, but how to design a suitable experiment for BSA-seq remains unclear. In this paper, we show in theory how the major experimental factors (including population size, pool proportion, pool balance, and generation) and the intrinsic factors of a QTL (including heritability and degree of dominance) affect the power of QTL detection and the precision of QTL mapping in BSA-seq. Increasing population size can improve the power and precision, depending on the QTL heritability. The best proportion of each pool in the population is around 0.25. So, 0.25 is generally applicable in BSA-seq. Small pool proportion can greatly reduce the power and precision. Imbalance of pool pair in size also causes decrease of the power and precision. Additive effect is more important than dominance effect for QTL mapping. Increasing the generation of filial population produced by selfing can significantly increase the power and precision, especially from F2 to F3. These findings enable researchers to optimize the experimental design for BSA-seq. A web-based program named BSA-seq Design Tool is available at http://124.71.74.135/BSA-seqDesignTool/ and https://github.com/huanglikun/BSA-seqDesignTool.
Transcriptional profile and chromatin accessibility in zebrafish melanocytes and melanoma tumors
Authors: Kramer Eva T , Godoy Paula M , Kaufman Charles K
Published: November 2021

Transcriptional and epigenetic characterization of melanocytes and melanoma cells isolated from their in vivo context promises to unveil key differences between these developmentally related normal and cancer cell populations. We therefore engineered an enhanced Danio rerio (zebrafish) melanoma model with fluorescently labeled melanocytes to allow for isolation of normal (wild type) and premalignant (BRAFV600E-mutant) populations for comparison to fully transformed BRAFV600E-mutant, p53 loss-of-function melanoma cells. Using fluorescence-activated cell sorting to isolate these populations, we performed high-quality RNA- and ATAC-seq on sorted zebrafish melanocytes vs. melanoma cells, which we provide as a resource here. Melanocytes had consistent transcriptional and accessibility profiles, as did melanoma cells. Comparing melanocytes and melanoma, we note 4128 differentially expressed genes and 56,936 differentially accessible regions with overall gene expression profiles analogous to human melanocytes and the pigmentation melanoma subtype. Combining the RNA- and ATAC-seq data surprisingly revealed that increased chromatin accessibility did not always correspond with increased gene expression, suggesting that though there is widespread dysregulation in chromatin accessibility in melanoma, there is a potentially more refined gene expression program driving cancerous melanoma. These data serve as a resource to identify candidate regulators of the normal vs. diseased states in a genetically controlled in vivo context.
A high-resolution genome of an euryhaline and eurythermal rhinogoby (Rhinogobius similis Gill 1895)
Authors: Hu Yun , Lu Liang , Zhou Tao , Sarker Kishor Kumar , Huang Junman , Xia Jianhong , Li Chenhong
Published: November 2021

Rhinogobius similis is distributed in East and Southeast Asia. It is an amphidromous species found mostly in freshwater and sometimes brackish waters. We have obtained a high-resolution assembly of the R. similis genome using nanopore sequencing, high-throughput chromosome conformation capture (Hi-C), and transcriptomic data. The assembled genome was 890.10 Mb in size and 40.15% in GC content. Including 1373 contigs with contig N50 is 1.54 Mb, and scaffold N50 is 41.51 Mb. All of the 1373 contigs were anchored on 22 pairs of chromosomes. The BUSCO evaluation score was 93.02% indicating high quality of genome assembly. The repeat sequences accounted for 34.92% of the whole genome, with retroelements (30.13%), DNA transposons (1.64%), simple repeats (2.34%), and so forth. A total of 31,089 protein-coding genes were predicted in the genome and functionally annotated using Maker, of those genes, 26,893 (86.50%) were found in InterProScan5. There were 1910 gene families expanded in R. similis, 1171 gene families contracted and 170 gene families rapidly evolving. We have compared one rapidly change gene family (PF05970) commonly found in four species (Boleophthalmus pectinirostris, Neogobius melanostomus, Periophthalmus magnuspinnatus, and R. similis), which was found probably related to the lifespan of those species. During 400–10 Ka, the period of the Guxiang Ice Age, the population of R. similis decreased drastically, and then increased gradually following the last interglacial period. A high-resolution genome of R. similis should be useful to study taxonomy, biogeography, comparative genomics, and adaptive evolution of the most speciose freshwater goby genus, Rhinogobius.
EPCO-02. GERMLINE SINGLE NUCLEOTIDE POLYMORPHISM rs55705857 AT 8q24 INTERACTS WITH SOMATIC IDH1 MUTATION TO ENHANCE HUMAN GLIOMA FORMATION
Authors: Drucker Kristen , Yanchus Connor , Kollmeyer Thomas , Ali Asma , Paul Decker , Kosel Matthew , Panda Arijit , Caron Alissa , Giannini Caterina , Burns Terence , Abyzov Alexej , Wang Liguo , Wrensch Margaret , Wiencke John , Eckel-Passow Jeanette , Lachance Daniel , Schramek Daniel , Jenkins Robert
Published: November 2021

BACKGROUND

Determination of the causation of germline single nucleotide polymorphisms (SNPs) located in non-coding regions of the genome is challenging. The genomic region of 8q24 has been identified as important in many kinds of cancer, linked to a topologically associated domain (TAD) encompassing MYC; this TAD contains a GWAS SNP (rs55705857) associated with IDH-mutant glioma.

METHODS

Germline genotyping data from 622 IDH-mutant glioma and 668 controls were used to fine map the rs55705857 locus by detailed haplotype analysis. Chromatin immunoprecipitation sequencing (ChIP-seq) of histone markers H3K4me1, H3K4me3, H3K27ac and H3K36me3 was performed on normal brain samples (n=8) and human glioma samples (n=11 IDH-wt and 52 IDH-mut). RNAseq from 9 normal and 83 brain tumors (n=26 IDH-wt and 55 IDH-mut) were used to assess differential gene expression.

RESULTS

Fine-mapping identified rs55705857 SNP as the most likely causative allele (OR=8.69; p<0.001) within 8q24 for the development of IDH-mutant glioma. At rs55705857, both H3K27ac and H3K4me1 in IDH-mutant vs IDH-wt tumors were increased 3.05- and 1.58-fold, respectively (DiffBind; p=5.81×10-7 and p=2.31×10-3). ChromHMM analysis of the marks indicated that promoter and enhancer functions were significantly increased, and the activity broadened at rs55705857 in IDH-mut gliomas compared to IDH-wt tumors and normal brain samples. This enhancement correlated with significant increased MYC expression in IDH-mut gliomas (p=3.1×10-13), as well as alterations of Myc signaling targets. Publicly available ATACseq, ChIPseq and long-range DNA interaction data demonstrated that the rs55705857 locus is open and interacts with the MYC promoter.

CONCLUSIONS

Fine-mapping of the 8q24 locus provided strong evidence that rs55705857 is the causative 8q24 locus associated with IDH-mut glioma. Functional experiments suggest that IDH mutation facilitates rs55705857 interaction with MYC to alter downstream MYC targets.
EPCO-06. AGE- AND REGION-SPECIFIC MULTI-OMIC CHARACTERIZATION OF H3-K27M MUTANT DIFFUSE MIDLINE GLIOMA
Authors: Liu Ilon , Li Jiang , Jeong Daeun , Hack Olivia A , Shaw McKenzie , Englinger Bernhard , Avihai Byron , Ernst Kati , Resnick Adam , Diaz Aaron , Jones David , Koschmann Carl , Kleinman Claudia , Jabado Nada , Cotter Jennifer , Ligon Keith , Alexandrescu Sanda , Yung W K Alfred , Czech Thomas , Arrillaga-Romany Isabel , Gojo Johannes , Slavc Irene , Monje Michelle , Filbin Mariella G
Published: November 2021

Diffuse midline gliomas driven by lysine27-to-methionine mutations in histone 3 (H3-K27M DMGs) are among the most fatal brain tumors. Molecular studies including single cell RNA-sequencing (scRNA-seq) of pediatric and predominantly pontine H3-K27M DMGs have shown that the H3-K27M oncohistone keeps glioma cells locked in a stem-like oligodendrocyte precursor cell (OPC) state that is capable of self-renewal and tumor-initiation. However, a comprehensive dissection of the cellular architecture of H3-K27M DMGs across different midline regions and age groups is required to better understand the cell-intrinsic and contextual regulation of H3-K27M DMG cell identities. In particular, the more recently described group of adult H3-K27M DMGs remains understudied. Here, we have collected and characterized 45 H3-K27M mutant patient tumors, spanning pontine (n=26), thalamic (n=17), and spinal (n=2) locations. Median age at surgery was 12 (2-68) years, encompassing 21 early childhood (0-10 years), 12 adolescent (11-20 years), and 12 adult (≥ 21 years) tumors. The majority of samples were obtained pre-treatment (n=28), as opposed to post-treatment or at autopsy (n=17). We profiled all 45 tumors by single cell/single nucleus RNA-seq and selected tumors were further characterized by the single cell assay for transposase-accessible chromatin (scATAC-seq). Our integrated analyses highlight the predominance of transcriptionally and epigenetically defined OPC-like tumor cells as the main cell population of H3-K27M DMGs across all age groups and locations. We further identify distinct age- and location-specific OPC-like cell subpopulations. Comparison of pediatric and adult tumors further demonstrates a significant increase of mesenchymal cell states in adult H3-K27M DMGs, which we link to differences in glioma-associated immune cell compartments between age groups. Together, this study sheds light on the effects of age- and region-dependent microenvironments in shaping cellular identities in H3-K27M DMGs.
EPCO-09. LONGITUDINAL ANALYSIS OF DIFFUSE GLIOMA REVEALS CELL STATE DYNAMICS AT RECURRENCE ASSOCIATED WITH CHANGES IN GENETICS AND THE MICROENVIRONMENT
Authors: Varn Frederick , Johnson Kevin , Wade Taylor , Malta Tathiane , Sabedot Thais , Barthel Floris , Kim Hoon , Ahmed Nazia , Datta Indrani , Barnholtz-Sloan Jill , Bakas Spyridon , D'Angelo Fulvio , Gan Hui , Garofano Luciano , Huse Jason , Khasraw Mustafa , Kocakavuk Emre , Migliozzi Simona , Ormond David , Paek Sun Ha , Van Meir Erwin , Walenkamp Annemiek , Watts Colin , Weller Michael , Weiss Tobias , Wesseling Pieter , Stead Lucy , Poisson Laila , Noushmehr Houtan , Iavarone Antonio , Verhaak Roel
Published: November 2021

Diffuse glioma is characterized by a poor prognosis and a universal resistance to therapy, though the evolutionary processes behind this resistance remain unclear. The Glioma Longitudinal Analysis (GLASS) Consortium has previously demonstrated that therapy-induced selective pressures shape the genetic evolution of glioma in a stochastic manner. However, single-cell studies have revealed that malignant glioma cells are highly plastic and transition their cell state in response to diverse challenges, including changes in the microenvironment and the administration of standard-of-care therapy. To interrogate the factors driving therapy resistance in diffuse glioma, we collected and analyzed RNA- and/or DNA-sequencing data from temporally separated tumor pairs of over 300 adult patients with IDH-wild-type or IDH-mutant glioma. In a subset of these tumor pairs, we complemented these data with single-nucleus RNAseq and multiplex imaging mass cytometry at each time point. Recurrent tumors exhibited diverse changes that were attributable to changes in histological features, somatic alterations, and microenvironment interactions. IDH-wild-type tumors overall were more invasive at recurrence and exhibited increased expression of neuronal signaling programs that reflected a possible role for neuronal interactions in promoting glioma progression. In contrast, recurrent IDH-mutant tumors exhibited a significant increase in proliferative expression programs that correlated with discrete genetic changes. Hypermutation and acquired CDKN2A homozygous deletions associated with an increase in proliferating stem-like malignant cells at recurrence in both glioma subtypes, reflecting active tumor expansion. A transition to the mesenchymal phenotype was associated with the presence of a specific myeloid cell state defined by unique ligand-receptor interactions with malignant cells, providing opportunities to target this transition through therapy. Collectively, our results uncover recurrence-associated changes in genetics and the microenvironment that can be targeted to shape disease progression following initial diagnosis.
EPCO-27. SINGLE-CELL ANALYSIS OF ETMR PATIENT SAMPLES LINKS TRANSCRIPTIONAL PHENOTYPES TO GENETIC DRIVER ALTERATIONS AND INFORMS NOVEL THERAPEUTIC STRATEGIES
Authors: Hovestadt Volker , Beck Alexander , Lambo Sander , Shaw McKenzie , Hack Olivia A , Englinger Bernhard , Gojo Johannes , Madlener Sibylle , Alexandrescu Sanda , Pfister Stefan , Kool Marcel , Filbin Mariella G
Published: November 2021

Embryonal tumor with multilayered rosettes (ETMR) is a malignant brain tumor that typically occurs in children under the age of three. Most patients die within two years of diagnosis, and more effective, targeted therapies are urgently needed. To better characterize the oncogenic mechanisms of key driver alterations and identify novel therapeutic targets, we studied the cellular heterogeneity of ETMR using single-cell RNA sequencing. Analyses conducted on >3,000 high-quality cells collected from ten primary and relapse specimens revealed a common cellular hierarchy across all tumors: A highly proliferative neural stem cell-like population (SOX2+) gives rise to intermediate progenitors (ASCL1+) and more differentiated neuron-like cells (STMN2/4+). These malignant populations closely match histological patterns of ETMR (i.e. rosettes, neuropil), as observed by immunofluorescence microscopy. Comparison to single-cell datasets from human embryos indicates resemblance to cell populations of the developing brain, but also reveals key ETMR-specific differences, including expression of the chromosome 19 miRNA cluster (C19MC, the presumed genetic driver of most ETMRs), which is restricted to the stem cell-like population. We next investigated if targeting C19MC is a viable strategy to disrupt the cellular hierarchy of ETMR. Silencing with antisense oligonucleotides shows pronounced reduction of cell line growth for a specific subset of the 46 members of C19MC. These miRNAs share seed sequences with evolutionary conserved miRNAs that have been shown to regulate pluripotency and self-renewal of embryonic stem cells. We hypothesize that select C19MC members play similar roles in ETMR and represent bona fide targets for therapeutic targeting using antisense technology.
EPCO-28. SINGLE-CELL RNA SEQUENCING IDENTIFIES INTRATUMORAL HETEROGENEITY AND ACTIVATION OF PRO-INVASIVE PATHWAYS IN NON-FUNCTIONING PITUITARY ADENOMAS
Authors: Jain Saket , Wang Elaina , Babikir Husam , Shamardani Karin , Diaz Aaron , Aghi Manish K
Published: November 2021

Pituitary adenomas (PA) are one of the most common primary brain tumors and comprise 15% of brain neoplasms. Most PAs are histologically benign but can cause significant morbidity. The genetic profile of PAs is poorly understood. We used single-cell RNA sequencing using the 10X genomic platform to investigate cellular heterogeneity in twelve non-functioning pituitary adenoma samples from nine patients including site-specific (core vs edge) samples from three patients. Our analysis identified discrete clusters of cells associated with activation of specific functional pathways including lipid metabolism, angiogenic, and antigen presentation and processing pathways regardless of location within the tumor. MALT1, a lncRNA associated with increased proliferation and metastasis was ubiquitously expressed amongst these samples. Analysis of the core vs edge samples showed two specific clusters with activated invasion-promoting pathways including PI3k/AKT signaling, Wnt signaling (Wnt6 and FZD4), and epithelial-mesenchymal transition (TGFB1, SMAD1, ZEB1, and SNAI2) in the edge of the tumors. The activated Wnt signaling cascade drove a proinflammatory tumor microenvironment induced by the expression of IL-1, IL-17, and Toll-like receptors (TLR6 and TLR7/8) resulting in suppression of Tregs. Copy number variation analysis using the CONICS-CNV algorithm highlighted distinct chromosomal alterations within our samples that led to insight into clonal variations within each tumor with loss of chromosome 2 an early event in tumorigenesis and gain/loss of chromosome 19 as late events. Mapping the copy number variation analysis with the somatic variant analysis using the Vartrix algorithm identified novel driver mutations within these tumors. These findings help define the molecular fingerprint of pituitary adenomas and provide insights which could be utilized for better management of these tumors.
BIOM-07. QUANTITATIVE MGMT PROMOTER METHYLATION INDEX INDICATES A NON-LINEAR PROGNOSTIC EFFECT IN GLIOBLASTOMA, SUGGESTING THAT USE OF OPTIMAL CUTOFF POINTS MAY BE CLINICALLY DISADVANTAGEOUS
Authors: Gibson David , Ravi Akshay , Almaraz Eduardo Rodriguez , Chang Susan , Oberheim-Bush Nancy Ann , Taylor Jennie , Clarke Jennifer , Solomon David , Scheffler Aaron , Witte John , Lambing Hannah , Berger Mitchel , Okada Hideho , Chehab Farid , Butowski Nicholas
Published: November 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 approaches that measure methylation, providing 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 240 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 16 and 9 months, respectively. 176 subjects experienced death. A one-unit increase in CpG methylation on a scale of 1-17 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 sites) 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 CpG 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

This novel approach offers greater bisulfite conversion efficiency when compared to alternative methods, reducing the likelihood of false positives. Analysis of the resulting methylation index scores demonstrates a non-linear relationship between MGMT methylation and survival, suggesting conformation of the marker’s protective effect. These findings challenge the current understanding of MGMT’s functional form and underline why implementing an “optimal cutoff point” may be disadvantageous.
BIOM-13. DEVELOPMENT AND VALIDATION OF AN LC-MS/MS ASSAY TO MEASURE GLUTATHIONE, GLUTATHIONE DISULFIDE, CYSTEINE, AND CYSTINE IN HUMAN BRAIN AND HUMAN GLIOBLASTOMA
Authors: Liu Miao , Margaryan Tigran , Sanai Nader , Tovmasyan Artak
Published: November 2021

BACKGROUND

Oxidative stress is implicated in many pathological conditions. Herein, we report on our development and validation of a sensitive and rapid LC-MS/MS method for the determination of oxidative stress biomarkers glutathione (GSH), glutathione disulfide (GSSG), cysteine (Cys) and cystine (CySS) in human brain and glioblastoma tissue.

METHODS

Freshly-acquired human glioblastoma tissue was homogenized with N-ethylmaleimide solution to prevent thiol oxidation. Analytes were then extracted from homogenate samples by protein precipitation with 2% sulfosalicylic acid (SSA). Stable isotope-labeled analytes were used as internal standards. Independent calibration curves for thiols and disulfides were prepared in analytical solutions. Three levels of quality controls were prepared in human brain homogenate. The detection was performed on Sciex QTRAP 6500+ mass spectrometer in positive electrospray ionization mode.

RESULTS

Linear regression model was used to cover a concentration ranging 0.4-100 µmol/L for GSSG/CySS and 1-400 µmol/L for GSH/Cys. Chromatographic separation was optimized on Intrada Amino Acid column with total run time of 5 min using gradient elution. For all analytes the maximum coefficient of variation for intra- and inter-day precision was 11.4% and the accuracy was within 80.9-113.7% in analytical solution and matrix. The analytes were stable in brain homogenate for 1 hour and 3 hours at room temperature (RT) and 4 °C, respectively. Stability at -80°C was demonstrated for at least 35 days in human brain homogenate. Stability of stock and working solutions was demonstrated for at least 4 hours (RT) and 25 days (-20°C).

CONCLUSIONS

A bioanalytical method to quantify GSH, GSSG, Cys, and CySS is successfully developed and validated. The method is currently applied to measure thiols and related disulfides in human glioblastoma tissue undergoing 5-aminolevulinic acid sonodynamic therapy (NCT04559685).
BIOM-25. ADULT GANGLIOGLIOMA: A 4-PATIENT CASE SERIES WITH MOLECULAR PROFILING
Authors: Shen Erica , Shams Alireza , Song Xianyuan , Daher Ahmad
Published: November 2021

Accounting for only 2% of all primary brain tumors, ganglioglioma is a rare neoplasm that most frequently arises in the temporal lobe in children or young adults. Ganglioglioma is the most common epilepsy-associated neoplasm and is typically composed of dysplastic ganglion cells and neoplastic glial cells. Recent publications have revealed that the activating p.V600E mutation in the BRAF oncogene is seen in 20-60% of gangliogliomas. However, the genetic landscape of ganglioglioma requires further elucidation, especially in gangliogliomas that arise from outside of the temporal lobe in adults. In this case series, we describe the genetic mutations of adult gangliogliomas originating outside of the temporal lobe in four patients aged 21 to 56 years. Targeted next generation sequencing via the MSK-IMPACT panel covering ~ 500 actionable mutations was used in all cases. None of the cases had the BRAF p.V600E mutation. Case 1 describes a left cerebellar cystic ganglioglioma with NTRK2 fusion mutation (NTRK2-DST) and a tumor mutation burden (TMB) = 0 mutation/megabase (mut/Mb). Case 2 describes a right parietal lobe cystic ganglioglioma with a BRAF-CLEC2Linversion mutation and TMB = 0 mut/Mb. Case 3 describes a cerebellar vermis ganglioglioma with a BRAF fusion mutation (BRAF-KIAA1549) and TMB = 0 mut/Mb. The last case describes a right cerebellopontine angle ganglioglioma with a MAP2K1 splicing mutation and TMB = 0.9 mut/Mb. To the best of our knowledge, the mutations identified in this case series have not been previously described in adult brain gangliogliomas. The BRAF-KIAA1549 fusion mutation has been found in spinal cord gangliogliomas, but not in brain gangliogliomas. MAP2K1 splicing mutations, unlike MAP2K1 in-frame deletions, have not been found in gangliogliomas. Finally, a different NTRK2 mutation (NTRK2-TLE4) has been described in a pediatric ganglioglioma, but NTRK2-DST has not been found in any adult gangliogliomas.