bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subtyping Cutaneous Melanoma Matters
Authors: El Sharouni Mary-Ann , van Diest Paul Johannes , Witkamp Arjen Joost , Sigurdsson Vigfús , van Gils Carla Henrica 
Published: October 2020

Abstract

Background
Our aim was to investigate the role of melanoma subtype on survival and focus on the effects stratified by Breslow thickness and ulceration status.

Methods
Patients with cutaneous melanoma stage I, II, or III diagnosed between 2000 and 2014 were derived from the Dutch Nationwide Pathology Registry and overall survival data from the Netherlands Cancer Registry. Patients were followed until 2018. Using multivariable Cox proportional hazards models, hazard ratios were calculated for each melanoma subtype, per Breslow thickness category and ulceration status, and adjusted for age, sex, stage, and localization.

Results
A total of 48 361 patients were included: 79.3% had superficial spreading melanoma (SSM), 14.6% nodular melanoma (NM), 5.2% lentigo maligna melanoma, and 0.9% acral lentiginous melanoma (ALM). In the total patient group, using SSM as the reference category, adjusted hazard ratios were 1.06 (95% confidence interval [CI] = 1.01 to 1.12) for NM, 1.02 (95% CI = 0.93 to 1.13) for lentigo maligna melanoma, and 1.26 (95% = CI 1.06 to 1.50) for ALM. Among patients with 1.0 mm or less Breslow thickness and no ulceration, NM showed a twofold increased risk (hazard ratio = 1.96, 95% CI = 1.58 to 2.45) compared with SSM. Compared with 1.0 mm or less SSM without ulceration, the hazard ratio for 1.0 mm or less SSM with ulceration was 1.94 (95% CI = 1.55 to 2.44), and the hazard ratio for 1.0 mm or less NM with ulceration was 3.46 (95% CI = 2.17 to 5.50). NM patients with tumors greater than 1.0 mm did not show worse survival than SSM patients with tumors greater than 1.0 mm.

Conclusions
In this large nationwide study, ALM patients showed worse survival than SSM patients. Among patients with melanomas that were thin (1.0 mm or less), NM subtype patients also showed worse survival than SSM patients.
Investigating the growing population of massive quiescent galaxies at cosmic noon
Authors: Sherman Sydney , Jogee Shardha , Florez Jonathan , Stevans Matthew L , Kawinwanichakij Lalitwadee , Wold Isak , Finkelstein Steven L , Papovich Casey , Ciardullo Robin , Gronwall Caryl , Cora Sofía A , Hough Tomás , Vega-Martínez Cristian A 
Published: October 2020

ABSTRACT
We explore the build-up of quiescent galaxies using a sample of 28 469 massive (M⋆ ≥ 1011 M⊙) galaxies at redshifts 1.5 &lt; $z$ &lt; 3.0, drawn from a 17.5 deg2 area (0.33 Gpc3 comoving volume at these redshifts). This allows for a robust study of the quiescent fraction as a function of mass at 1.5 &lt; $z$ &lt; 3.0 with a sample ∼40 times larger at log(M⋆/$\rm M_{\odot })\ge 11.5$ than previous studies. We derive the quiescent fraction using three methods: specific star formation rate, distance from the main sequence, and UVJ colour–colour selection. All three methods give similar values at 1.5 &lt; $z$ &lt; 2.0, however the results differ by up to a factor of 2 at 2.0 &lt; $z$ &lt; 3.0. At redshifts 1.5 &lt; $z$ &lt; 3.0, the quiescent fraction increases as a function of stellar mass. By $z$ = 2, only 3.3 Gyr after the big bang, the universe has quenched ∼25 per cent of M⋆ = 1011 M⊙ galaxies and ∼45 per cent of M⋆ = 1012 M⊙ galaxies. We discuss physical mechanisms across a range of epochs and environments that could explain our results. We compare our results with predictions from hydrodynamical simulations SIMBA and IllustrisTNG and semi-analytic models (SAMs) SAG, SAGE, and Galacticus. The quiescent fraction from IllustrisTNG is higher than our empirical result by a factor of 2–5, while those from SIMBA and the three SAMs are lower by a factor of 1.5–10 at 1.5 &lt; $z$ &lt; 3.0.
A smoothed particle hydrodynamics algorithm for multigrain dust with separate sets of particles
Authors: Mentiplay Daniel , Price Daniel J , Pinte Christophe , Laibe Guillaume 
Published: October 2020

ABSTRACT
We present a method for simulating the dynamics of a mixture of gas and multiple species of large Stokes number dust grains, typical of evolved protoplanetary discs and debris discs. The method improves upon earlier methods, in which only a single grain size could be represented, by capturing the differential backreaction of multiple dust species on the gas. This effect is greater for large dust-to-gas ratios that may be expected in the later stages of the protoplanetary disc life. We benchmark the method against analytic solutions for linear waves, drag, and shocks in dust–gas mixtures, and radial drift in a protoplanetary disc showing that the method is robust and accurate.
Eigenspectra: a framework for identifying spectra from 3D eclipse mapping
Authors: Mansfield Megan , Schlawin Everett , Lustig-Yaeger Jacob , Adams Arthur D , Rauscher Emily , Arcangeli Jacob , Feng Y Katherina , Gupta Prashansa , Keating Dylan , Stevenson Kevin B , Beatty Thomas G 
Published: October 2020

ABSTRACT
Planetary atmospheres are inherently 3D objects that can have strong gradients in latitude, longitude, and altitude. Secondary eclipse mapping is a powerful way to map the 3D distribution of the atmosphere, but the data can have large correlations and errors in the presence of photon and instrument noise. We develop a technique to mitigate the large uncertainties of eclipse maps by identifying a small number of dominant spectra to make them more tractable for individual analysis via atmospheric retrieval. We use the eigencurves method to infer a multiwavelength map of a planet from spectroscopic secondary eclipse light curves. We then apply a clustering algorithm to the planet map to identify several regions with similar emergent spectra. We combine the similar spectra together to construct an ‘eigenspectrum’ for each distinct region on the planetary map. We demonstrate how this approach could be used to isolate hot from cold regions and/or regions with different chemical compositions in observations of hot Jupiters with the James Webb Space Telescope (JWST). We find that our method struggles to identify sharp edges in maps with sudden discontinuities, but generally can be used as a first step before a more physically motivated modelling approach to determine the primary features observed on the planet.
On the origin of low escape fractions of ionizing radiation from massive star-forming galaxies at high redshift
Authors: Yoo Taehwa , Kimm Taysun , Rosdahl Joakim 
Published: October 2020

ABSTRACT
The physical origin of low escape fractions of ionizing radiation derived from massive star-forming galaxies at z ∼ 3–4 is not well understood. We perform idealized disc galaxy simulations to understand how galactic properties such as metallicity and gas mass affect the escape of Lyman continuum (LyC) photons using radiation-hydrodynamic simulations with strong stellar feedback. We find that the luminosity-weighted escape fraction from a metal-poor (Z = 0.002) galaxy embedded in a halo of mass $M_{\rm h}\simeq 10^{11}\, \mathrm{M}_\odot$ is $\left\langle {f_{\rm esc}^{\rm 3D}}\right\rangle \simeq 10\, {{\ \rm per\ cent}}$. Roughly half of the LyC photons are absorbed within scales of 100 pc, and the other half is absorbed in the ISM ($\lesssim 2\, {\rm kpc}$). When the metallicity of the gas is increased to Z = 0.02, the escape fraction is significantly reduced to $\left\langle {f_{\rm esc}^{\rm 3D}}\right\rangle \simeq 1{{\ \rm per\ cent}}$ because young stars are enshrouded by their birth clouds for a longer time. In contrast, increasing the gas mass by a factor of 5 leads to $\left\langle {f_{\rm esc}^{\rm 3D}}\right\rangle \simeq 5\, {{\ \rm per\ cent}}$ because LyC photons are only moderately absorbed by the thicker disc. Our experiments suggest that high metallicity is likely more responsible for the low escape fractions observed in massive star-forming galaxies, supporting the scenario in which the escape fraction is decreasing with increasing halo mass. Finally, negligible correlation is observed between the escape fraction and surface density of star formation or galactic outflow rates.
Birth sites of young stellar associations and recent star formation in a flocculent corrugated disc
Authors: Quillen Alice C , Pettitt Alex R , Chakrabarti Sukanya , Zhang Yifan , Gagné Jonathan , Minchev Ivan 
Published: October 2020

ABSTRACT
With backwards orbit integration, we estimate birth locations of young stellar associations and moving groups identified in the solar neighbourhood that are younger than 70 Myr. The birth locations of most of these stellar associations are at a smaller galactocentric radius than the Sun, implying that their stars moved radially outwards after birth. Exceptions to this rule are the Argus and Octans associations, which formed outside the Sun’s galactocentric radius. Variations in birth heights of the stellar associations suggest that they were born in a filamentary and corrugated disc of molecular clouds, similar to that inferred from the current filamentary molecular cloud distribution and dust extinction maps. Multiple spiral arm features with different but near corotation pattern speeds and at different heights could account for the stellar association birth sites. We find that the young stellar associations are located in between peaks in the radial/tangential (UV) stellar velocity distribution for stars in the solar neighbourhood. This would be expected if they were born in a spiral arm, which perturbs stellar orbits that cross it. In contrast, stellar associations seem to be located near peaks in the vertical phase-space distribution, suggesting that the gas in which stellar associations are born moves vertically together with the low-velocity dispersion disc stars.
Characterizing dynamical states of Galactic open clusters with Gaia DR2
Authors: Angelo M S , Corradi W J B , Santos J F C , Maia F F S , Ferreira F A 
Published: October 2020

ABSTRACT
In this work, we investigate the dynamical properties of 38 Galactic open clusters: 34 of them are located at low Galactic latitudes (|b| &lt; 10°) and are projected against dense stellar fields; the other four comparison objects present clearer contrasts with the field population. We determine structural and time-related parameters that are associated with the clusters’ dynamical evolution: core (rc), tidal (rt), and half-mass (rhm) radii, ages (t), and crossing times (tcr). We have also incorporated results for 27 previously studied clusters, creating a sample of 65, spanning the age and Galactocentric distance (RG) ranges $7.0 \lt \textrm {log}\, t \lt 9.7$ and 6 &lt; RG (kpc) &lt; 13. We employ a uniform analysis method which incorporates photometric and astrometric data from the Gaia DR2 catalogue. Member stars are identified by employing a decontamination algorithm which operates on the 3D astrometric space of parallax and proper motion and attributes membership likelihoods for stars in the cluster region. Our results show that internal relaxation causes rc to correlate negatively with the dynamical ratio τdyn = t/tcr. This implies that dynamically older systems tend to be more centrally concentrated. The more concentrated ones tend to present smaller rhm/rt ratios, which means that they are less subject to tidal disruption. The analysis of coeval groups at compatible RG suggests that the inner structure of clusters is reasonably insensitive to variations in the external tidal field. Additionally, our results confirm, on average, an increase in rt for regions with less-intense Galactic gravitational fields.
Global H i asymmetries in IllustrisTNG: a diversity of physical processes disturb the cold gas in galaxies
Authors: Watts Adam B , Power Chris , Catinella Barbara , Cortese Luca , Stevens Adam R H 
Published: October 2020

ABSTRACT
Observations of the cold neutral atomic hydrogen (H i) in and around disc galaxies have revealed that spatial and kinematic asymmetries are common place, and are reflected in the global H i spectra. We use the TNG100 box from the IllustrisTNG suite of cosmological simulations to study the conditions under which these asymmetries may arise in current theoretical galaxy formation models. We find that more than 50 per cent of the sample has at least a 10 per cent difference in integrated flux between the high- and low-velocity half of the spectrum, thus the typical TNG100 galaxy has an H i profile that is not fully symmetric. We find that satellite galaxies are a more asymmetric population than centrals, consistent with observational results. Using halo mass as a proxy for environment, this trend appears to be driven by the satellite population within the virial radius of haloes more massive than 1013 M⊙, typical of medium/large groups. We show that, while the excess of H i asymmetry in group satellites is likely driven by ram pressure, the bulk of the asymmetric H i profiles observed in TNG100 are driven by physical processes able to affect both the central and satellite populations. Our results highlight how asymmetries are not driven solely by environment, and multiple physical processes can produce the same asymmetric shape in global H i spectra.
Enzymatic synthesis of hypermodified DNA polymers for sequence-specific display of four different hydrophobic groups
Authors: Ondruš Marek , Sýkorová Veronika , Bednárová Lucie , Pohl Radek , Hocek Michal 
Published: October 2020

Abstract
A set of modified 2′-deoxyribonucleoside triphosphates (dNTPs) bearing a linear or branched alkane, indole or phenyl group linked through ethynyl or alkyl spacer were synthesized and used as substrates for polymerase synthesis of hypermodified DNA by primer extension (PEX). Using the alkyl-linked dNTPs, the polymerase synthesized up to 22-mer fully modified oligonucleotide (ON), whereas using the ethynyl-linked dNTPs, the enzyme was able to synthesize even long sequences of &gt;100 modified nucleotides in a row. In PCR, the combinations of all four modified dNTPs showed only linear amplification. Asymmetric PCR or PEX with separation or digestion of the template strand can be used for synthesis of hypermodified single-stranded ONs, which are monodispersed polymers displaying four different substituents on DNA backbone in sequence-specific manner. The fully modified ONs hybridized with complementary strands and modified DNA duplexes were found to exist in B-type conformation (B- or C-DNA) according to CD spectral analysis. The modified DNA can be replicated with high fidelity to natural DNA through PCR and sequenced. Therefore, this approach has a promising potential in generation and selection of hypermodified aptamers and other functional polymers.
Brain metastasis detection using machine learning: a systematic review and meta-analysis
Authors: Cho Se Jin , Sunwoo Leonard , Baik Sung Hyun , Bae Yun Jung , Choi Byung Se , Kim Jae Hyoung 
Published: October 2020

Abstract

Background
Accurate detection of brain metastasis (BM) is important for cancer patients. We aimed to systematically review the performance and quality of machine-learning-based BM detection on MRI in the relevant literature.

Methods
A systematic literature search was performed for relevant studies reported before April 27, 2020. We assessed the quality of the studies using modified tailored questionnaires of the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) criteria and the Checklist for Artificial Intelligence in Medical Imaging (CLAIM). Pooled detectability was calculated using an inverse-variance weighting model.

Results
A total of 12 studies were included, which showed a clear transition from classical machine learning (cML) to deep learning (DL) after 2018. The studies on DL used a larger sample size than those on cML. The cML and DL groups also differed in the composition of the dataset, and technical details such as data augmentation. The pooled proportions of detectability of BM were 88.7% (95% CI, 84–93%) and 90.1% (95% CI, 84–95%) in the cML and DL groups, respectively. The false-positive rate per person was lower in the DL group than the cML group (10 vs 135, P &lt; 0.001). In the patient selection domain of QUADAS-2, three studies (25%) were designated as high risk due to non-consecutive enrollment and arbitrary exclusion of nodules.

Conclusion
A comparable detectability of BM with a low false-positive rate per person was found in the DL group compared with the cML group. Improvements are required in terms of quality and study design.
Population-based estimates of survival among elderly patients with brain metastases
Authors: Lamba Nayan , Kearney Rachel Brigell , Catalano Paul J , Hassett Michael J , Wen Patrick Y , Haas-Kogan Daphne A , Aizer Ayal A 
Published: October 2020

Abstract

Background
Prognostic estimates for patients with brain metastases (BM) stem from younger, healthier patients enrolled in clinical trials or databases from academic centers. We characterized population-level prognosis in elderly patients with BM.

Methods
Using Surveillance, Epidemiology, and End Results (SEER)–Medicare data, we identified 9882 patients ≥65 years old with BM secondary to lung, breast, skin, kidney, esophageal, colorectal, and ovarian primaries between 2014 and 2016. Survival was assessed by primary site and evaluated with Cox regression.

Results
In total, 2765 versus 7117 patients were diagnosed with BM at primary cancer diagnosis (synchronous BM, median survival = 2.9 mo) versus thereafter (metachronous BM, median survival = 3.4 mo), respectively. Median survival for all primary sites was ≤4 months, except ovarian cancer (7.5 mo). Patients with non-small-cell lung cancer (NSCLC) receiving epidermal growth factor receptor (EGFR)– or anaplastic lymphoma kinase (ALK)–based therapy for synchronous BM displayed notably better median survival at 12.5 and 20.1 months, respectively, versus 2.8 months exhibited by other patients with NSCLC; survival estimates in melanoma patients based on receipt of BRAF/MEK therapy versus not were 6.7 and 2.8 months, respectively. On multivariable regression, older age, greater comorbidity, and type of managing hospital were associated with poorer survival; female sex, higher median household income, and use of brain-directed stereotactic radiation, neurosurgical resection, or systemic therapy (versus brain-directed non-stereotactic radiation) were associated with improved survival (all P &lt; 0.05).

Conclusions
Elderly patients with BM have a poorer prognosis than suggested by prior algorithms. If prognosis is driven by systemic and not intracranial disease, brain-directed therapy with potential for significant toxicity should be utilized cautiously.
The long noncoding RNA lnc-HLX-2-7 is oncogenic in Group 3 medulloblastomas
Authors: Katsushima Keisuke , Lee Bongyong , Kunhiraman Haritha , Zhong Cuncong , Murad Rabi , Yin Jun , Liu Ben , Garancher Alexandra , Gonzalez-Gomez Ignacio , Monforte Hector L , Stapleton Stacie , Vibhakar Rajeev , Bettegowda Chetan , Wechsler-Reya Robert J , Jallo George , Raabe Eric , Eberhart Charles G , Perera Ranjan J 
Published: October 2020

Abstract

Background
Medulloblastoma (MB) is an aggressive brain tumor that predominantly affects children. Recent high-throughput sequencing studies suggest that the noncoding RNA genome, in particular long noncoding RNAs (lncRNAs), contributes to MB subgrouping. Here we report the identification of a novel lncRNA, lnc-HLX-2-7, as a potential molecular marker and therapeutic target in Group 3 MBs.

Methods
Publicly available RNA sequencing (RNA-seq) data from 175 MB patients were interrogated to identify lncRNAs that differentiate between MB subgroups. After characterizing a subset of differentially expressed lncRNAs in vitro and in vivo, lnc-HLX-2-7 was deleted by CRISPR/Cas9 in the MB cell line. Intracranial injected tumors were further characterized by bulk and single-cell RNA-seq.

Results
Lnc-HLX-2-7 is highly upregulated in Group 3 MB cell lines, patient-derived xenografts, and primary MBs compared with other MB subgroups as assessed by quantitative real-time, RNA-seq, and RNA fluorescence in situ hybridization. Depletion of lnc-HLX-2-7 significantly reduced cell proliferation and 3D colony formation and induced apoptosis. Lnc-HLX-2-7–deleted cells injected into mouse cerebellums produced smaller tumors than those derived from parental cells. Pathway analysis revealed that lnc-HLX-2-7 modulated oxidative phosphorylation, mitochondrial dysfunction, and sirtuin signaling pathways. The MYC oncogene regulated lnc-HLX-2-7, and the small-molecule bromodomain and extraterminal domain family‒bromodomain 4 inhibitor Jun Qi 1 (JQ1) reduced lnc-HLX-2-7 expression.

Conclusions
Lnc-HLX-2-7 is oncogenic in MB and represents a promising novel molecular marker and a potential therapeutic target in Group 3 MBs.
Vitamin D—A New Perspective in Treatment of Cerebral Vasospasm
Authors: Kashefiolasl Sepide , Leisegang Matthias S , Helfinger Valeska , Schürmann Christoph , Pflüger-Müller Beatrice , Randriamboavonjy Voahanginirina , Vasconez Andrea E , Carmeliet Geert , Badenhoop Klaus , Hintereder Gudrun , Seifert Volker , Schröder Katrin , Konczalla Juergen , Brandes Ralf P 
Published: October 2020

Abstract

BACKGROUND
Cerebral vasospasm (CVS) is a frequent complication after subarachnoid hemorrhage (SAH), with no sufficient therapy and a complex pathophysiology.

OBJECTIVE
To explore the vitamin D system as a potential treatment for CVS.

METHODS
25-vitamin D3 levels tested between 2007 and 2015 and data of SAH patients admitted during the months with a peak vs nadir of VitD3 values were analyzed, retrospectively. We prospectively correlated VitD3 and vasospasm/outcome data in SAH patients admitted in 2017. An experimental mice SAH model and cell culture model were used to investigate the effect of 1,25-dihydroxyvitamin D3 (1,25-VitD3). Additionally, the mediators acting in the VitD mechanism were researched and detected.

RESULTS
Based on the retrospective analysis demonstrating an increased frequency of vasospasm in SAH patients during the low vitamin D period in winter, we started basic research experiments. Active 1,25-VitD3 hormone attenuated CVS, neurological deficit, and inflammation after intrathecal blood injection in mice. Deletion of the vitamin D receptor in the endothelium or in myeloid cells decreased the protective 1,25-VitD3 effect. Co-culture experiments of myeloid and endothelial cells with blood confirmed the anti-inflammatory 1,25-VitD3 effect but also revealed an induction of stroma-cell-derived factor 1α (SDF1α), vascular endothelial growth factor, and endothelial nitric oxide synthase by 1,25-VitD3. In mice, SDF1α mimicked the protective effect of 1,25-VitD3 against CVS. From bench to bedside, CVS severity was inversely correlated with vitamin D plasma level, prospectively. Patients with more severe CVS exhibited attenuated expression of SDF1α and 1,25-VitD3-responsive genes on circulating myeloid cells.

CONCLUSION
1,25-VitD3 attenuates CVS after SAH by inducing SDF1α. However, VitD administration should be tested as optional treatment to prevent CVS.