bluuebunny/crossref_metadata_2025 huggingface dataset:
Address terms in social media requests
Authors: Ren Wei , Fukushima Saeko
Published: September 2023

Although address terms have been examined in Chinese and
Japanese, few studies have compared the use of address terms between the two
languages. This study investigates address terms in Chinese and Japanese in
social media communication, focusing on requests between university
students. Two sets of data were collected, one from social media and the
other from focus groups. The findings revealed both similarities and
differences in address terms in the two languages. Neither Chinese nor
Japanese participants use address terms frequently in social media requests
between peers. When they employ address terms between peers on social media,
both groups prefer using first names and nicknames. However, Chinese
participants tend to use kinship terms frequently, which are not used by
Japanese participants. It is argued that factors such as social distance,
pragmatic constraints, language play, preference for positive politeness,
globalisation, and new technologies all contribute to the findings here.
Continuous monitoring of cardiovascular function with a smart stent incorporating a flexible and stretchable wireless pressure sensor
Authors: Oyunbaatar Nomin-Erdene , Shanmugasundaram Arunkumar , Kwon Kyeongha , Lee Dong-Weon
Published: September 2023

The development of smart stents, capable of monitoring cardiovascular diseases and communicating vascular abnormalities to medical doctors, has garnered significant attention in the field of biomedical engineering. Various ex-situ fabrication strategies have been proposed to concurrently manufacture the smart stent and pressure sensor, thereby reducing the risk of sensor detachment caused by blood flow. However, the practical utility of these devices is still limited due to the rigidity of the wireless pressure sensor. In this study, we propose a flexible and stretchable smart self-reporting stent that incorporates a wireless pressure sensor. The fabrication process has been optimized to create a serpentine-shaped wireless pressure sensor that matches the shape and flexibility of the polymer stent struts. We thoroughly investigated the structural integrity, resonance frequency, stretchability, flexibility, and radial force of the manufactured smart self-reporting stent under different conditions. The wireless pressure sensor demonstrated a sensitivity of 0.15 MHz mmHg−1, as determined through experimental analysis. To demonstrate the feasibility of the proposed smart stent, we implanted it into the arteries of a three-dimensional phantom system. The obtained results, combined with the flexible and stretchable nature of the proposed smart self-reporting stent, highlight its potential for effective monitoring of the heart’s functional dynamics and detection of in-stent restenosis.
A noise reduction method of rolling bearing based on empirical wavelet transform and adaptive time frequency peak filtering
Authors: Lu Jiantao , Jia Bin , Li Shunming , Gong Siqi
Published: September 2023

The vibration signal of rolling bearing with variable operating conditions contains complex interference components, which will cause low fault diagnosis accuracy, especially in strong noise case. To solve this problem, we proposed a noise reduction method of rolling bearing with variable operating based on empirical wavelet transform and adaptive time-frequency peak filtering (EWT-ATFPF). Firstly, empirical wavelet transform is used to obtain different frequency intrinsic mode functions (IMFs). Secondly, a modified adaptive window length formula for time-frequency peak filtering (TFPF) is constructed by combining the sampling ratio index and a fault sensitivity indicator that calculated by kurtosis and correlation coefficients of IMFs, which can better characterize the impact components. Thirdly, to balance noise reduction effect and the fidelity of IMFs, we proposed an improved TFPF method by adaptively adjusting its windows length. The adaptive method could be carried out using the proposed fault sensitivity indicator and window length formula, and the denoising IMFs could be obtained by ATFPF. Finally, the denoising vibration signal is reconstructed by using the denoising IMFs. The performance of fault diagnosis of the proposed method is verified by using simulated signal and bearing fault test data. The results show that the proposed EWT-ATFPF method could effectively achieve noise reduction under variable operating conditions.
Nonlinear auto regressive Elman neural network combined with unscented Kalman filter for data-driven dynamic data reconciliation in dynamic systems
Authors: Zhang Zhenhui , Hong Zhihui , Zhang Zhengjiang , Guo Fengyi , Zhao Sheng , Huang Shipei
Published: September 2023

Measurement data plays an important role in the control system, but the data collected by sensors often has measurement noise, which makes the states of the system cannot be accurately revealed. Unscented Kalman filter (UKF) is a highly accurate and robust filtering algorithm, but its limitation is the requirement of prior knowledge of the exact dynamic mathematical model, which is a critical issue to be addressed in practice. In this work, a data-driven dynamic data reconciliation scheme called nonlinear auto regressive Elman neural network (ENN) with exogenous inputs combined with UKF (NARX-ENN-UKF) is proposed, where nonlinear auto regressive ENN with exogenous inputs is used for dynamic data-driven modeling, and then UKF is applied for dynamic data reconciliation of the measurements based on the trained model. The scheme is applied to a DC/AC inverter experimental system and a self-developed sliding electrical contact experimental system to verify the effectiveness of NARX-ENN-UKF.
Noise assessment of CMOS active pixel sensors for the CYGNO Experiment
Authors: Almeida B D , Amaro F D , Antonietti R , Baracchini E , Benussi L , Bianco S , Borra F , Capoccia C , Caponero M , Cardoso D S , Cavoto G , Costa I A , D’Imperio G , Danè E , Dho G , Di Giambattista F , Di Marco E , Iacoangeli F , Kemp E , Lima Júnior H P , P Lopes G S , Maccarrone G , P Mano R D , Marcelo Gregorio R R , G Marques D J , Mazzitelli G , McLean A G , Meloni P , Messina A , Monteiro C M B , Nobrega R A , Pains I F , Paoletti E , Passamonti L , Petrucci F , Piacentini S , Piccolo D , Pierluigi D , Pinci D , Prajapati A , Renga F , d C Roque R J , Rosatelli F , Russo A , Saviano G , C Spooner N J , Tesauro R , Tomassini S , Torelli S , Tozzi D , F dos Santos J M
Published: September 2023

Active Pixel sensors play a crucial role in enabling successful low-light scientific experiments due to their inherent advantages and capabilities. Such devices not only offer high spatial resolution but also feature individual pixels with integrated amplifiers, allowing for direct signal amplification at the pixel level. This results in reduced readout noise and improved signal-to-noise ratio (SNR), which are particularly vital when dealing with limited photon counts in low-light environments. This holds particularly true for scientific CMOS (sCMOS) sensors, acknowledged as an advanced evolution of Active Pixel sensors. However, despite their advantages, such sensors can still exhibit limitations such as higher cost and presence of noise artifacts that should be closely investigated. In particular, CYGNO project fits in a global effort aimed at direct detection of Dark Matter particles. CYGNO collaboration intends to build a detector based on a Time Projection Chamber making use of Gas Electron Multipliers for the amplification of ionization electrons. The GEM multiplication process produces photons that can be readout by a high-resolution sCMOS sensor. Such detection system is being designed to have enough sensitivity to detect low-energy particles and to measure released energy with enough granularity so to reconstruct direction and energy profile along their trajectories. The image sensor has an important role in the detector performance, having a direct impact on the SNR of the experiment. This work proposes a study on the performance of three different sCMOS sensors with respect to their sensitivity to low-energy particles and their intrinsic noise, which are of the utmost importance for various scientific experiments.
The Near Infrared Imager and Slitless Spectrograph for the James Webb Space Telescope. I. Instrument Overview and In-flight Performance
Authors: Doyon René , Willott Chris J. , Hutchings John B. , Sivaramakrishnan Anand , Albert Loïc , Lafrenière David , Rowlands Neil , Begoña Vila M. , Martel André R. , LaMassa Stephanie , Aldridge David , Artigau Étienne , Cameron Peter , Chayer Pierre , Cook Neil J. , Cooper Rachel A. , Darveau-Bernier Antoine , Dupuis Jean , Earnshaw Colin , Espinoza Néstor , Filippazzo Joseph C. , Fullerton Alexander W. , Gaudreau Daniel , Gawlik Roman , Goudfrooij Paul , Haley Craig , Kammerer Jens , Kendall David , Lambros Scott D. , Ignat Luminita Ilinca , Maszkiewicz Michael , McColgan Ashley , Morishita Takahiro , Ouellette Nathalie N.-Q. , Pacifici Camilla , Philippi Natasha , Radica Michael , Ravindranath Swara , Rowe Jason , Roy Arpita , Roy Niladri , Saad Karl , Sohn Sangmo Tony , Talens Geert Jan , Touahri Driss , Thatte Deepashri , Taylor Joanna M. , Vandal Thomas , Volk Kevin , Wander Michel , Warner Gerald , Zheng Sheng-Hai , Zhou Julia , Abraham Roberto , Beaulieu Mathilde , Benneke Björn , Ferrarese Laura , Jayawardhana Ray , Johnstone Doug , Kaltenegger Lisa , Meyer Michael R. , Pipher Judy L. , Rameau Julien , Rieke Marcia , Salhi Salma , Sawicki Marcin
Published: September 2023

The Near-Infrared Imager and Slitless Spectrograph (NIRISS) is the science module of the Canadian-built Fine Guidance Sensor onboard the James Webb Space Telescope (JWST). NIRISS has four observing modes: (1) broadband imaging featuring seven of the eight NIRCam broadband filters, (2) wide-field slitless spectroscopy at a resolving power of ∼150 between 0.8 and 2.2 μm, (3) single-object cross-dispersed slitless spectroscopy (SOSS) enabling simultaneous wavelength coverage between 0.6 and 2.8 μm at R ∼ 700, a mode optimized for exoplanet spectroscopy of relatively bright (J < 6.3) stars and (4) aperture masking interferometry (AMI) between 2.8 and 4.8 μm enabling high-contrast (∼10−3 − 10−4) imaging at angular separations between 70 and 400 mas for relatively bright (M < 8) sources. This paper presents an overview of the NIRISS instrument, its design, its scientific capabilities, and a summary of in-flight performance. NIRISS shows significantly better response shortward of ∼2.5 μm resulting in 10%–40% sensitivity improvement for broadband and low-resolution spectroscopy compared to pre-flight predictions. Two time-series observations performed during instrument commissioning in the SOSS mode yield very stable spectro-photometry performance within ∼10% of the expected noise. The first space-based companion detection of the tight binary star AB Dor AC through AMI was demonstrated.
Stress intensity factors of partially compressed centrally cracked disk with frictional crack surfaces
Authors: Fayed A S , Hammouda Mohammad M I
Published: September 2023

This work analytically calculates mixed-mode I/II stress intensity factors for an inclined central frictional crack in a Brazilian disc partially compressed with a uniform pressure. Wide-range controlling parameters are invoked. The analyzed parameters include the pressure angle, relative crack length, crack inclination, and friction coefficient between the two crack surfaces. For partially compressed discs, there exists a critical pressure angle at which a crack with any angle will experience pure II loading. This critical pressure angle is not affected by friction and decreases as the crack length increases. A crack of any angle becomes inactive once the pressure angle exceeds another critical value of pressure angle. This value decreases as the friction coefficient or/and crack length increases. The handling of frictional surfaces of short cracks is simplified. The analysis defines the conditions to have (1) the crack opened and (2) the two crack surfaces sticking. A close agreement is achieved with relevant findings in previous relevant investigations. The present results do not exist in relevant literature and are valuable in solving fracture mechanics problems of significance in relation to crack path in cracked brittle materials.
Pre-extensively Drug-Resistant Congenital Tuberculosis in an Extremely Premature Baby
Authors: Boast Alison , How Jeu Ann , Lau Charis , Sett Arun , Gilby Damien , Burke Andrew , McWhinney Brett , Wright Connor , Tramontana Adrian , Globan Maria , Denholm Justin , Graham Stephen M , Osowicki Joshua
Published: September 2023

We describe a case of congenital tuberculosis in an extremely premature baby, with rapid molecular detection of a pre-extensively drug-resistant (XDR) pattern of drug resistance. The baby was treated successfully with a regimen including bedaquline and delamanid, drugs not previously described in the treatment of congenital tuberculosis (TB).
Electrophysiology fellowship experience and requirements: an EHRA survey
Authors: Linz Dominik , Chun Julian , Guerra Federico , Conte Giulio , Garcia Rodrigue , Kommata Varvara , Malaczynska-Rajpold Katarzyna , Nesti Martina , Duncker David
Published: September 2023

Aims

This study aims to survey current educational experience and the individual requirements for electrophysiologists in training.

Methods and results

The European Heart Rhythm Association (EHRA) e-Communication Committee and the Scientific Initiatives Committee prepared a questionnaire and distributed it via newsletters, Twitter, LinkedIn, and Facebook. The survey consisted of 22 questions collected on an individual basis anonymously. Two hundred and forty-three responders from 35 countries (32% female, age 38 ± 6 years old) completed the survey. This EHRA electrophysiology (EP) fellowship survey showed that (i) hands-on participation and observation of EP procedures are very important; (ii) the main motivations to choose the EP fellowship institution are centre reputation and volume as well as the availability of a structured EP fellowship programme; (iii) 59% passed the EHRA exam and 46% took a national certification exam; (iv) respondents are overall satisfied with their own fellowships, but there are areas of less confidence such as conduction system pacing implantation and cardiac resynchronization therapy implantation; (v) 78% of respondents performed research during their fellowship, (vi) the optimal duration of an EP fellowship should be at least 2 years; and (viii) doing fellowships abroad is beneficial, but significant obstacles exist.

Conclusion

The results of this EHRA survey may help to refine current EP fellowship programmes to improve the quality of EP training and early career building of young electrophysiologists.
Clinicopathologic study of stage I adenosquamous carcinoma of the lung
Authors: Handa Yoshinori , Ikeda Takuhiro , Hanaki Hideaki , Miyata Yoshihiro , Mukaida Hidenori , Okada Morihito
Published: September 2023

Objective

Adenosquamous carcinoma of the lung is a characteristic tumor that has both adenocarcinoma and squamous cell carcinoma components. Adenosquamous carcinoma is reported to have an aggressive clinical course, but its clinicopathological features and prognosis are unclear in the early stage.

Methods

Patients who underwent surgical resection for pathological stage I non-small cell lung cancer between April 2009 and December 2014 were retrospectively reviewed. Preoperative and postoperative data, histologic characteristics and outcomes of patients with adenosquamous carcinoma (n = 40) were compared to adenocarcinoma (n = 598) and squamous cell carcinoma (n = 131) patients. Factors affecting prognosis, particularly on recurrence, were assessed via Cox regression analyses.

Results

Patients with adenosquamous carcinoma had a worse prognosis than did patients with adenocarcinoma and squamous cell carcinoma in terms of 5 year overall (66.7%) and recurrence-free survival rates (44.9%), as well as a significantly higher recurrence rate (13/40 patients, 32.5%). Multivariable Cox regression analysis for recurrence-free survival rates revealed that the histology of adenosquamous carcinoma was an independent factor for recurrence (hazard ratio: 2.473, 95% confidence interval: 1.328–3.367; P = 0.0004). High serum carcinoembryonic antigen levels (hazard ratio: 5.962) and vascular invasion (hazard ratio: 4.899) were identified as risk factors for recurrence, and patients with adenosquamous carcinoma tended to have distant relapses, such as in the brain.

Conclusions

Early-stage adenosquamous carcinoma of the lung is a histological type associated with severe prognosis and postoperative recurrence, often in distant sites, in approximately one-third of cases. High serum carcinoembryonic antigen levels and vascular invasion might be risk factors of recurrence.
BARD1germline variants induce haploinsufficiency and DNA repair defects in neuroblastoma
Authors: Randall Michael P , Egolf Laura E , Vaksman Zalman , Samanta Minu , Tsang Matthew , Groff David , Evans J Perry , Rokita Jo Lynne , Layeghifard Mehdi , Shlien Adam , Maris John M , Diskin Sharon J , Bosse Kristopher R
Published: September 2023

Background

High-risk neuroblastoma is a complex genetic disease that is lethal in more than 50% of patients despite intense multimodal therapy. Through genome-wide association studies (GWAS) and next-generation sequencing, we have identified common single nucleotide polymorphisms and rare, pathogenic or likely pathogenic germline loss-of-function variants in BARD1 enriched in neuroblastoma patients. The functional implications of these findings remain poorly understood.

Methods

We correlated BARD1 genotype with expression in normal tissues and neuroblastomas, along with the burden of DNA damage in tumors. To validate the functional consequences of germline pathogenic or likely pathogenic BARD1 variants, we used CRISPR-Cas9 to generate isogenic neuroblastoma (IMR-5) and control (RPE1) cellular models harboring heterozygous BARD1 loss-of-function variants (R112*, R150*, E287fs, and Q564*) and quantified genomic instability in these cells via next-generation sequencing and with functional assays measuring the efficiency of DNA repair.

Results

Both common and rare neuroblastoma-associated BARD1 germline variants were associated with lower levels of BARD1 mRNA and an increased burden of DNA damage. Using isogenic heterozygous BARD1 loss-of-function variant cellular models, we functionally validated this association with inefficient DNA repair. BARD1 loss-of-function variant isogenic cells exhibited reduced efficiency in repairing Cas9-induced DNA damage, ineffective RAD51 focus formation at DNA double-strand break sites, and enhanced sensitivity to cisplatin and poly (ADP-ribose) polymerase (PARP) inhibition both in vitro and in vivo.

Conclusions

Taken together, we demonstrate that germline BARD1 variants disrupt DNA repair fidelity. This is a fundamental molecular mechanism contributing to neuroblastoma initiation that may have important therapeutic implications.
Microbial communities associated with resin canal discoloration in mango fruit
Authors: Umar Muhammad , Bowman John P , Asis Constancio , McConchie Cameron , Eyles Alieta , Stanley Roger , Gracie Alistair
Published: September 2023

Resin canal discoloration (RCD) severely impacts the fruit quality of mango, diminishes consumer confidence, and reduces sales, but the biological cause is still unclear. Using next-generation sequencing, the overall microbial community composition of RCD+ and visually healthy mango fruits was determined for the first time to examine the possible role of bacterial and fungal pathogens in RCD. The diversity profile of bacterial and fungal communities was determined using primers targeting the 16S rRNA gene and Internal Transcribed Spacer (ITS) regions. Results showed that bacterial communities in healthy fruits are clustered together and significantly different from those in RCD+ fruits. Tatumella and Pantoea species were the most abundant bacterial taxa on RCD+ fruit, and both have been linked to disease outbreaks in a variety of fruit crops. Fungal communities were generally similar between RCD+ and normal samples, though non-pathogenic yeasts Meyerozyma and Naganishia tended to dominate the fungal communities on RCD+ fruit. The study indicates that bacteria rather than fungal organisms are more likely to be associated with RCD in mango. This finding will facilitate the isolation and confirmation of RCD-causing organisms and the development of control strategies to manage RCD problem in mango.
Autotrophic growth activity of complete ammonia oxidizers in an upflow biological contact filter for drinking water treatment
Authors: Ishizaki Yuta , Kurisu Futoshi , Furumai Hiroaki , Kasuga Ikuro
Published: September 2023

Biological filters effectively remove ammonium from drinking water via nitrification. In a pilot-scale upflow biological contact filter (U-BCF), complete ammonia oxidizers (comammox), which are capable of oxidizing ammonia to nitrate in one cell, were more abundant than ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, little information is available on the contribution of comammox to nitrification. In this study, we evaluated the autotrophic growth activity of comammox associated with biological activated carbon (BAC) in a U-BCF by DNA-stable isotope probing (DNA-SIP). BAC samples collected from the U-BCF were continuously fed mineral medium containing 0.14 mg N L−1 ammonium and 12C- or 13C-labeled bicarbonate for 20 days. DNA-SIP analysis revealed that comammox (clades A and B) as well as AOA assimilated bicarbonate after 10 days of incubation, proving that dominant comammox could contribute to nitrification. Contrarily, AOB remained inactive throughout the observation period. Amplicon sequencing of the 13C-labeled DNA fractions of comammox revealed that specific genotypes other than the most dominant genotype in the original sample were more enriched under the incubation condition for the DNA-SIP experiment. Thus, dominant genotypes of comammox in a U-BCF might utilize organic nitrogen to fuel nitrification in ammonia-limited environments.
thesan-hr: how does reionization impact early galaxy evolution?
Authors: Borrow Josh , Kannan Rahul , Garaldi Enrico , Smith Aaron , Vogelsberger Mark , Pakmor Rüdiger , Springel Volker , Hernquist Lars
Published: September 2023

The feedback loop between the galaxies producing the background radiation field for reionization and their growth is crucial, particularly for low-mass haloes. Despite this, the vast majority of galaxy formation studies employ a spatially uniform, time-varying reionizing background, with the majority of reionization studies employing galaxy formation models only required to work at high redshift. This paper uses the well-studied TNG galaxy formation model, calibrated at low redshift, coupled to the arepo-rt code, to self-consistently solve the coupled problems of galaxy evolution and reionization, evaluating the impact of patchy (and slow) reionization on early galaxies. thesan-hr is an extension of the thesan project to higher resolution (a factor of 50 increase, with a baryonic mass of mb ≈ 104 M⊙), to additionally enable the study of ‘mini-haloes’ with virial temperatures Tvir < 104 K. Comparing the self-consistent model to a uniform UV background, we show that galaxies in thesan-hr are predicted to be larger in physical extent (by a factor ∼2), less metal enriched (by ∼0.2 dex), and less abundant (by a factor ∼10 at M1500 =   − 10) by z = 5. We show that differences in star formation and enrichment patterns lead to significantly different predictions for star formation in low mass haloes, low-metallicity star formation, and even the occupation fraction of haloes. We posit that cosmological galaxy formation simulations aiming to study early galaxy formation (z ≳ 3) must employ a spatially inhomogeneous UV background to accurately reproduce galaxy properties.
FOREVER22: gas and metal outflow from massive galaxies in protocluster regions
Authors: Harada Naoki , Yajima Hidenobu , Abe Makito
Published: September 2023

We study gas and metal outflow from massive galaxies in protocluster regions at z = 3–9 by using the results of the FOREVER22 simulation project. Our simulations contain massive haloes with $M_{\rm h} \gtrsim 10^{13}\,\rm {\rm M}_{\odot }$, showing high star formation rates of ${>}100\,{\rm M}_{\odot}\,{\rm yr}^{-1}$ and hosting supermassive black holes with $M_{\rm BH} \gtrsim 10^{8}~\rm {\rm M}_{\odot }$. We show that the mass loading factor (ηM) sensitively depends on the halo mass and it is ηM = 1.2 (9.2) for $M_{\rm h}= 10^{13}\,(10^{11})\,{\rm {\rm M}_{\odot}}$. Once the halo mass exceeds ${\sim}10^{12.5}\,{\rm M}_{\odot}$, the outflow velocity of the gas rapidly decreases near a virial radius, and the gas returns to a galactic centre finally as a fountain flow. Also, the metal inflow and outflow rates sensitively depend on the halo mass and redshift. At z = 3, the inflow rate becomes larger than the outflow one if $M_{\rm h}\gtrsim 10^{13.0}\,{\rm M}_{\odot}$. Thus, we suggest that massive haloes cannot be efficient metal enrichment sources beyond virial radii that will be probed in future observations, e.g. studies of metal absorption lines with the Prime Focus Spectrograph on the Subaru telescope.
Impact of neutron star spin on Poynting–Robertson drag during a type I X-ray burst
Authors: Speicher J , Fragile P C , Ballantyne D R
Published: September 2023

External irradiation of a neutron star (NS) accretion disc induces Poynting–Robertson (PR) drag, removing angular momentum and increasing the mass accretion rate. Recent simulations show PR drag significantly enhancing the mass accretion rate during Type I X-ray bursts, which could explain X-ray spectral features such as an increase in the persistent emission and a soft excess. However, prograde spin of the NS is expected to weaken PR drag, challenging its importance during bursts. Here, we study the effect of spin on PR drag during X-ray bursts. We run four simulations, with two assuming a non-spinning NS and two using a spin parameter of a* = 0.2, corresponding to a rotation frequency of 500 Hz. For each scenario, we simulate the disc evolution subject to an X-ray burst and compare it to the evolution found with no burst. PR drag drains the inner disc region during a burst, moving the inner disc radius outwards by ≈1.6 km in the a* = 0 and by ≈2.2 km in the a* = 0.2 simulation. The burst enhances the mass accretion rate across the innermost stable circular orbit ≈7.9 times when the NS is not spinning and ≈11.2 times when it is spinning. The explanation for this seemingly contradictory result is that the disc is closer to the NS when a* = 0.2, and the resulting stronger irradiating flux offsets the weakening effect of spin on the PR drag. Hence, PR drag remains a viable explanation for the increased persistent emission and soft excess observed during X-ray bursts in spinning NS systems.
Stellar Karaoke: deep blind separation of terrestrial atmospheric effects out of stellar spectra by velocity whitening
Authors: Sedaghat Nima , Smart Brianna M , Kalmbach J Bryce , Howard Erin L , Amindavar Hamidreza
Published: September 2023

We report a study exploring how the use of deep neural networks with astronomical Big Data may help us find and uncover new insights into underlying phenomena: through our experiments towards unsupervised knowledge extraction from astronomical Big Data we serendipitously found that deep convolutional autoencoders tend to reject telluric lines in stellar spectra. With further experiments, we found that only when the spectra are in the barycentric frame does the network automatically identify the statistical independence between two components, stellar versus telluric, and rejects the latter. We exploit this finding and turn it into a proof-of-concept method for removal of the telluric lines from stellar spectra in a fully unsupervised fashion: we increase the interobservation entropy of telluric absorption lines by imposing a random, virtual radial velocity to the observed spectrum. This technique results in a non-standard form of ‘whitening’ in the atmospheric components of the spectrum, decorrelating them across multiple observations. We process more than 250 000 spectra from the High Accuracy Radial velocity Planetary Search and with qualitative and quantitative evaluations against a data base of known telluric lines, show that most of the telluric lines are successfully rejected. Our approach, ‘Stellar Karaoke’, has zero need for prior knowledge about parameters such as observation time, location, or the distribution of atmospheric molecules and processes each spectrum in milliseconds. We also train and test on Sloan Digital Sky Survey and see a significant performance drop due to the low resolution. We discuss directions for developing tools on top of the introduced method in the future.
mglens: Modified gravity weak lensing simulations for emulation-based cosmological inference
Authors: Harnois-Déraps Joachim , Hernandez-Aguayo Cesar , Cuesta-Lazaro Carolina , Arnold Christian , Li Baojiu , Davies Christopher T , Cai Yan-Chuan
Published: September 2023

We present mglens, a large series of modified gravity lensing simulations tailored for cosmic shear data analyses and forecasts in which cosmological and modified gravity parameters are varied simultaneously. Based on the forge and bridgeN-body simulation suites presented in companion papers, we construct 100 × 5000 deg2 of mock Stage-IV lensing data from two 4D Latin hypercubes that sample cosmological and gravitational parameters in f(R) and nDGP gravity, respectively. These are then used to validate our inference analysis pipeline based on the lensing power spectrum, exploiting our implementation of these modified gravity models within the cosmosis cosmological inference package. Sampling this new likelihood, we find that cosmic shear can achieve 95 per cent CL constraints on the modified gravity parameters of log$_{10}[f_{R_0}] \lt $ −4.77 and log10[H0rc] > 0.09, after marginalizing over intrinsic alignments of galaxies and including scales up to ℓ = 5000. We also investigate the impact of photometric uncertainty, scale cuts, and covariance matrices. We finally explore the consequences of analysing mglens data with the wrong gravity model, and report catastrophic biases for a number of possible scenarios. The Stage-IV mglens simulations, the forge and bridge emulators and the cosmosis interface modules will be made publicly available upon journal acceptance.
Revisiting UV/optical continuum time lags in AGN
Authors: Kammoun E S , Robin L , Papadakis I E , Dovčiak M , Panagiotou C
Published: September 2023

In this paper, we present an updated version of our model (KYNXiltr) which considers thermal reverberation of a standard Novikov–Thorne accretion disc illuminated by an X-ray point-like source. Previously, the model considered only two cases of black hole spins, and assumed a colour correction factor fcol = 2.4. Now, we extend the model to any spin value and fcol. In addition, we consider two scenarios of powering the X-ray corona, either via accretion, or external to the accretion disc. We use KYNXiltr to fit the observed time lags obtained from intense monitoring of four local Seyfert galaxies (NGC 5548, NGC 4593, Mrk 817, and Fairall 9). We consider various combinations of black hole spin, colour correction, corona height, and fraction of accretion power transferred to the corona. The model fits well the overall time-lag spectrum in these sources (for a large parameter space). For NGC 4593 only, we detect a significant excess of delays in the U band. The contribution of the diffuse BLR emission in the time-lag spectrum of this source is significant. It is possible to reduce the large best-fitting parameter space by combining the results with additional information, such as the observed Eddington ratio and average X-ray luminosity. We also provide an update to the analytic expression provided by Kammoun et al., for an X-ray source that is not powered by the accretion process, which can be used for any value of fcol, and for two values of the black hole spin (0 and 0.998).
Failed supernova simulations beyond black hole formation
Authors: Kuroda Takami , Shibata Masaru
Published: September 2023

We present an axisymmetric failed supernova simulation beyond black hole formation, for the first time with numerical relativity and two-moment multi-energy neutrino transport. To ensure stable numerical evolution, we use an excision method for neutrino radiation hydrodynamics within the inner part of black hole domain. We demonstrate that our excision method is capable of stably evolving the radiation hydrodynamics in dynamical black hole space–time. As a remarkable signature of the final moment of proto-neutron star (PNS), we find the emergence of high-energy neutrinos. Those high-energy neutrinos are associated with the PNS shock surface being swallowed by the central black hole and could be a possible observable of failed supernovae.
PL02.2.A RAPID, COMPREHENSIVE REPORTING OF MOLECULAR DIAGNOSTICS WITH RAPID-CNS2: A PROSPECTIVE VALIDATION COHORT
Authors: Patel A , Hinz F , Dogan H , Payne A , Göbel K , Schrimpf D , Ritter M , Krause E , Pfeifer L , Krech M , Blume C , Stichel D , Goidts V , Schweizer L , Unterberg A , Wick W , Pfister S , Sill M , Loose M , von Deimling A , Jones D T W , Schlesner M , Sahm F
Published: September 2023

BACKGROUND

The WHO classification of CNS tumours 2021 recommends reporting a wide range of molecular alterations for WHO-compatible diagnoses. Conventional molecular diagnostic workflows warrant considerable investment and long turnaround times limited by batching. Nanopore sequencing enables long read sequencing, real-time targeting and simultaneous base modification detection with compact devices. Rapid-CNS2- a rapid, comprehensive adaptive sampling based sequencing pipeline with a turnaround time of 5 days for CNS tumours was previously described. This study presents an optimised Rapid-CNS2 pipeline and prospective validation cohort that successfully reports hard-to-detect variants.

MATERIAL AND METHODS

We performed targeted adaptive sampling-based sequencing on 156 samples comprising a mix of archival and current diagnostic cases from the Department of Neuropathology, University Hospital Heidelberg. We tested variable conditions including minimum DNA input, target size, flowcell reuse and sequencing times. An analysis pipeline for detection of single nucleotide variants (SNV), indels, copy number alterations (CNA), fusions, complex structural variants (SV), target gene methylation and methylation classification incorporating multi-GPU optimization was deployed. Results were compared to NGS panel sequencing and EPIC array analyses.

RESULTS

Integrated diagnoses for all cases were in accordance with those issued using molecular alterations reported by conventional analyses. Rapid-CNS2 showed improved resolution over NGS panel sequencing for CNAs. Complete concordance was achieved for MGMT promoter methylation status and methylation classification. High accuracy was obtained for detection of SNV/Indels. Long reads spanning the breakpoint identified clinically relevant fusions. Subclonal SVs including EGFR vIII missed by NGS panel sequencing were detected with high confidence. The optimized workflow shortened the turnaround time to 30 hours from sample receipt to report and minimum input DNA required was reduced to 500ng. Due to the versatility of adaptive sampling, the analyses can readily be limited to a smaller set of targets or methylation and CNAs only, further reducing the turnaround time.

CONCLUSION

We present a thorough validation and prospective clinical application of Rapid-CNS2 with cases spanning a range of brain tumours and metastases. The improved custom neurooncology adaptive sampling-based sequencing pipeline enables simultaneous copy-number, mutational, structural variant and methylation analysis with flexible target selection, no additional library preparation, competitive costs and next-day reporting of RESULTS
PL02.4.A SHARED DECISION-MAKING IN NEUROSURGICAL CONSULTATIONS WITH NEWLY DIAGNOSED BRAIN TUMOR PATIENTS: A THEMATIC ANALYSIS OF PATIENT INVOLVEMENT
Authors: Bras I J M , Sitskoorn M M , Joosen M C W , Vugt I J M , Hoogendoorn A P Y , Rutten G J M , Gehring K
Published: September 2023

BACKGROUND

In shared decision-making (SDM) the patient serves as the expert on his or her own life and the health care professional serves as the medical expert. However, many SDM instruments that employ observer coding schemes primarily focus on information provision, and less on patient involvement. The items that are included on patient involvement are as follows: 1) introducing SDM to the patient, 2) providing personalized information and 3) discussing patient’s views, values and situation. These items may mark the presence of patient involvement and will be taken as a starting-point for this study, yet they do not provide information on how these items are discussed as part of the SDM process. The aim of this study is to illustrate the involvement of newly diagnosed brain tumor patients in SDM by analysing the decision-making process during neurosurgical consultations and identifying sub-themes related to patient involvement.

MATERIAL AND METHODS

This study employed a codebook thematic analysis to identify the sub-themes concerning aspects of patient involvement in the neurosurgical decision-making process. The first consultation between newly diagnosed glioma or meningioma patients and their neurosurgeons were audio-recorded, transcribed and coded. The study followed a recursive design continuing with analysis until data saturation was reached.

RESULTS

Saturation was reached after analysing 11 consultations. We identified 13 sub-themes within the three main themes, and we will support our findings with direct quotes from the consultations during the conference presentation. Theme 1 was comprised of the sub-themes inviting the patients to participate, presenting treatment options, inquiring about symptoms and daily life, asking patients about treatment preference and room for questions. Questions about patients’ personal circumstances are often asked near the end of a consultation, when the decision regarding treatment has already been made. Theme 2 was comprised of the sub-themes personalizing information, personalizing aspects of treatment and personalizing treatment recommendations. There are examples of neurosurgeons integrating information provided by the patient to personalize the decision-making process. Theme 3 was comprised of the sub-themes interference of disease, daily life, family and requested information. These sub-themes show what patients (spontaneously) share about their lives.

CONCLUSION

We illustrated how brain tumor patients contribute to the SDM process, what information patients and their decision-partners provide and how this information is integrated in the decision-making process during neurosurgical consultations. Our findings may provide handholds to further improve patient involvement and personalization of the decision-making process.
KS02.5.A OVERALL SURVIVAL ASSOCIATED WITH FIRST-LINE PCV OR TEMOZOLOMIDE IN COMBINATION WITH RADIOTHERAPY IN PATIENTS WITH IDH-MUTANT, 1P/19Q CODELETED, GRADE 3 OLIGODENDROGLIOMA: ANALYSIS FROM THE POLA COHORT
Authors: Kacimi S E O , Dehais C , Carpentier C , Chinot O , Bronnimann C , Vauleon E , Djelad A , Moyal E C , Campone M , Ducloie M , Noel G , Cuzzubbo S , Thaillandier L , Ramirez C , Colin C , Appay R , Tabouret E , Nichelli L , Mathon B , Thomas A , Tran S , Bielle F , Alentor A , Labreche K , Idbaih A , Figarella-Branger D , Ducray F , Touat M
Published: September 2023

BACKGROUND

Patients with IDH-mutant, 1p/19q codeleted, grade 3 oligodendroglioma (Olig-3) derive benefit from the addition of alkylating agent chemotherapy to radiotherapy. However, to date, the choice between Procarbazine, Lomustine, and Vincristine (PCV) or Temozolomide (TMZ) as an optimal chemotherapy regimen for these patients remains unclear due to the lack of randomized clinical trial data comparing the two regimens.

MATERIAL AND METHODS

The objective was to assess the survival outcomes associated with first-line radiotherapy and PCV compared to radiotherapy and TMZ in patients with IDH-mutant, 1p/19q codeleted Olig-3 (WHO 2021). We included patients with histologically-proven IDH-mutant, 1p/19q codeleted Olig-3 from a large prospective French network cohort (POLA). The overall survival (OS) from surgery date was computed using Kaplan-Meier methods and Cox proportional hazards regression model.

RESULTS

A total of 306 patients with IDH-mutant, 1p/19q codeleted Olig-3 treated with radiotherapy and chemotherapy between 2008 and 2022 were included. In all, 67.6% of patients (n=207, median age at diagnosis 49.3y [IQR: 40.4-58.7]) were treated with PCV and 32.4% with TMZ (n=99, 50.3y [IQR: 43.8-61.2]) as first-line chemotherapy. Baseline characteristics were comparable between patients from both groups. The median follow-up duration was 78.4 months (IQR: 44.4-103.0). Median OS was not reached (95% CI: NR-NR) and 140 months (95% CI: 110-NR) in the PCV and TMZ groups, respectively (log rank test for OS, P=0.0023). On univariate analysis, there was a significant difference in both 5-year (PCV: 89%, 95% CI: 85-94 vs TMZ: 75%, 95% CI: 67-84; P = 0.0014) and 10-year OS (PCV: 73%, 95% CI: 62-85 vs TMZ: 60%, 95%CI: 49-73; P = 0.003) in favor of PCV. In the adjusted analysis for age, extent of resection, gender and Karnofsky performance scale (n=288), a significant OS difference between TMZ and PCV was found in the Cox proportional hazards regression model (TMZ vs. PCV HR 2.01, 95% CI: 1.16-3.50, P=0.013).

CONCLUSION

In the POLA cohort, among patients with IDH-mutant, 1p/19q codeleted Olig-3 receiving first-line radiotherapy combined with chemotherapy, treatment with PCV was associated with better survival compared to TMZ in both univariate and adjusted analyses. The small sample size and event rate especially in TMZ group warrants further validation. However, these results provide preliminary data on survival outcomes associated with first-line chemotherapy with PCV or TMZ in patients with IDH-mutant, 1p/19q codeleted Olig-3.
JS08.4.A LINEAR GRADING COEFFICIENT REVEALS EMBRYONIC DEVELOPMENT GENE SIGNATURE AS TREATMENT-INDEPENDENT PROGNOSTIC FACTOR IN IDH-MUTANT ASTROCYTOMA
Authors: Ghisai S A , Hoogstrate Y , Tesileanu C M S , van Hijfte L , de Heer I , Vallentgoed W R , van den Bent M J , French P J
Published: September 2023

BACKGROUND

Diffuse gliomas are classified into grade II/III and grade IV IDH-mutant (IDHmt) astrocytoma based on histology and homozygous deletion of the CDKN2AB locus, according to the 2021 WHO classification. There is considerable variation in prognosis within these classification groups and we therefore sought to identify features that might aid further tumor grading.

MATERIAL AND METHODS

RNA sequencing was performed on IDHmt astrocytomas included in the CATNON trial and overlaid with previously generated genome-wide methylation data. This dataset was extended by multi-omics data from the TCGA and GLASS-NL studies, where the latter was used for validation. For all datasets, only IDHmt astrocytomas were selected. We defined a linear grading coefficient (LGC) based on calibrated DNA methylation-based probability scores and performed differential gene expression (DGE) regression analysis on the LGC. Statistical analyses were intersected across the CATNON and TCGA cohorts ("discovery set") and validated on the primary-recurrent GLASS-NL dataset. Single-nucleus RNA-sequencing (snRNAseq) data of high-grade IDHmt astrocytomas was used to explore the source of expression signals.

RESULTS

DGE regression analysis revealed that higher-grade IDHmt tumors (high LGC) exhibited mRNA upregulation of key embryonic developmental transcription factors (HOXA/C/D, NKX, PAX, and TBX). Although the vast majority of CpG sites in LGC high tumors were hypomethylated, homeobox genes were strongly hypermethylated in our discovery set. All HOX gene clusters showed gene-ordered (differential) expression where e.g. HOXD10>D9>D8>D4>D1 and HOXA3>A7>A9>A13 suggesting derepression of enhancer sequences up/downstream of the gene cluster. Our expression-based gene signature was positively correlated with, but not limited to, the G-CIMP-low subtype and homozygous CDKN2AB deletion. More than half of the genes from the HOX gene family were part of our signature. Our embryonic development signature was prognostic (log-rank test) on both the discovery (CATNON: p < 0.0005, TCGA: p < 0.0005) and validation set (GLASS-NL: p < 0.005). As our signature was developed on molecular data from the first resection its prognostic value is treatment-independent. SnRNAseq on high-grade IDHmt astrocytomas indicated expression of embryonic development genes from tumor cells, which was not restricted to cells from the stemness program.

CONCLUSION

Our study highlights upregulation of embryonic development genes as potential molecular mechanism associated with the malignant progression of IDH-mutant astrocytomas.
OS01.5.A THE USE OF MULTIOMICS IN THE IDENTIFICATION AND CHARACTERISATION OF TERTIARY LYMPHOID STRUCTURES IN GLIAL TUMORS
Authors: Lun J H , Singh A , Cakmak P , Köhler M , Schupp J , Macas J , Plate K H , Reiss Y , Imkeller K
Published: September 2023

BACKGROUND

Tertiary Lymphoid Structures (TLSs) are organized immune cell aggregates present in non-lymphoid tissues for the initiation and maintenance of local and systemic anti-tumor immune response. The presence of TLS has been associated with better prognosis and clinical outcome in several cancer types, including lung and melanoma. However, the formation of TLS and its potential role in intra-tumoral immune response remains unclear. TLS are particularly interesting in gliomas as tumor-infiltrating lymphocytes is inefficient possibly due to the immunosuppressive microenvironment and the presence of the blood brain barrier. This study aims to identify and characterize the presence of TLS in glioma patients, to understand its role in generating a local immune response against tumors and identify potential biomarkers. We characterized TLS in glioma by immunohistochemistry, RNA sequencing from TLS positive tumors and used spatial transcriptomics to map TLS gene expression within the tumors.

MATERIAL AND METHODS

Of the 1274 adult patients with diffuse glioma, resected between 2015 and 2021, a total of 663 FFPE-tissue samples were available for B cell infiltration IHC-screening. Subsequently, the TLS+ samples were characterized using spatial transcriptomics and Opal-TSA mIHC, a spatial proteomic method that enables a simultaneous detection of 6 antigens in FFPE tumor tissues. A selection of TLS+ and matched TLS- tumors were subjected to bulk-tissue whole RNA sequencing. Downstream analysis such as cell-type specific transcriptional deconvolution and differential gene expression were performed. Furthermore, a multimodal analysis of TLS in glioma was conducted by combining the genomic, transcriptomic, spatial proteomics and clinical data.

RESULTS

B cell accumulations were observed in 13.1% of all gliomas. Small CD20 B cells accumulation, named perivascular immune cells (PVIC), and TLS were observed in 10.7% and 2.4%, respectively. We investigated the overall survival of patients in the TLS+, TLS- and PVIC groups. So far, no significant differences were observed. The transcriptomic analyses of TLS+ with TLS- tumors revealed an upregulation of genes related to innate and adaptive immune responses, complement cascade and the extracellular matrix. Genes associated with neural differentiation were expressed higher in TLS- compared to TLS+ tumors. Moreover, our multimodal analysis revealed the presence of distinct classes of TLS in glioma which differed in their cellular and molecular compositions.

CONCLUSION

Using a multimodal analysis, this study identified B cell accumulation and TLS in glioma patients. In contrast to other cancer types, the presence of TLS in glioma did not correlate with a higher overall survival. However, the role of TLS in glioma and their prognostic and therapeutic relevance remains under investigation with further analyses currently underway.