bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract

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

Abstract

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

AbstractBackgroundHigh-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.MethodsWe 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.ResultsBoth 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.ConclusionsTaken 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

Abstract
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

Abstract
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

ABSTRACT
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 &lt; 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

ABSTRACT
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 ${&gt;}100\,{\rm M}_{\odot}\,{\rm yr}^{-1}$ 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

ABSTRACT
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

ABSTRACT
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

ABSTRACT
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] &gt; 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

ABSTRACT
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

ABSTRACT
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

Abstract

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