bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondrial DNA Profiling Reveals Two Lineages of Sun Bears in East and West Malaysia
Authors: Lai Wai-Ling , Chew Jactty , Gatherer Derek , Ngoprasert Dusit , Rahman Sadequr , Ayub Qasim , Kannan Adrian , Vaughan Eleanor , Wong Siew Te , Kulaimi Noor Azleen Mohd , Ratnayeke Shyamala 
Published: January 2021

AbstractSun bear populations are fragmented and at risk from habitat loss and exploitation for body parts. These threats are made worse by significant gaps in knowledge of sun bear population genetic diversity, population connectivity, and taxonomically significant management units. Using a complete sun bear mitochondrial genome, we developed a set of mitochondrial markers to assess haplotype variation and the evolutionary history of sun bears from Peninsular (West) Malaysia and Sabah (East Malaysia). Genetic samples from 28 sun bears from Peninsular Malaysia, 36 from Sabah, and 18 from Thailand were amplified with primers targeting a 1800 bp region of the mitochondrial genome including the complete mitochondrial control region and adjacent genes. Sequences were analyzed using phylogenetic methods. We identified 51 mitochondrial haplotypes among 82 sun bears. Phylogenetic and network analyses provided strong support for a deep split between Malaysian sun bears and sun bears in East Thailand and Yunnan province in China. The Malaysian lineage was further subdivided into two clades: Peninsular Malaysian and Malaysian Borneo (Sabah). Sun bears from Thailand occurred in both Sabah and Peninsular Malaysian clades. Our study supports recent findings that sun bears from Sundaland form a distinct clade from those in China and Indochina with Thailand possessing lineages from the three clades. Importantly, we demonstrate a more recent and clear genetic delineation between sun bears from the Malay Peninsula and Sabah indicating historical barriers to gene flow within the Sundaic region.
Economic burden of diabetes among medicare beneficiaries with cancer
Authors: McDaniel Cassidi C , Loh F Ellen , Rockwell Devan M , McDonald Courtney P , Chou Chiahung 
Published: January 2021

Abstract

Objectives
Older adults are commonly affected by cancer and diabetes, and an investigation of the economic burden faced by these older adults remains a research gap. Therefore, the objective was to assess the economic burden of diabetes among Medicare beneficiaries with cancer by analyzing annual costs from administrative claims data.

Methods
We conducted a retrospective, serial cross-sectional study using the Medicare Current Beneficiary Survey (MCBS) from 2006 to 2012. Eligible beneficiaries must be currently or previously diagnosed with cancer (of any type), ≥65 years of age, non-institutionalized and continuously enrolled annually in Medicare Parts A, B and D. Diagnoses of cancer and diabetes were determined through self-report or claims. The primary outcome was the total economic burden of diabetes per capita annually, operationalized as the difference in total direct costs between cancer patients with and without diabetes. Simple linear regression was used to analyze trends of costs across the years. Multivariable regression estimated the effect of diabetes and covariates on total annual spending among beneficiaries with cancer from 2006–2012.

Key findings
From 2006 to 2012, 4918 beneficiaries included in MCBS had cancer, with over 25% (1275) also having diabetes. From 2006 to 2012, the mean economic burden of diabetes was $7815 per capita annually. After adjusting for covariates, beginning in 2006, diagnosis of diabetes significantly predicted higher total annual spending among cancer beneficiaries in 2007 [coefficient (SE) = 0.5768 (0.1918), P = 0.003], 2011 [coefficient (SE) = 0.4303 (0.1817), P = 0.018] and 2012 [coefficient (SE) = 0.3605 (0.1758), P = 0.040].

Conclusions
Medicare beneficiaries with cancer experienced a higher economic burden from concurrent diabetes.
The Gaia DR2 halo white dwarf population: the luminosity function, mass distribution, and its star formation history
Authors: Torres Santiago , Rebassa-Mansergas Alberto , Camisassa María E , Raddi Roberto 
Published: January 2021

ABSTRACT
We analyse the volume-limited nearly complete 100 pc sample of 95 halo white dwarf candidates identified by the second data release of Gaia. Based on a detailed population synthesis model, we apply a method that relies on Gaia astrometry and photometry to accurately derive the individual white dwarf parameters. This method is tested with 25 white dwarfs of our sample for which we took optical spectra and performed spectroscopic analysis. We build and analyse the halo white dwarf luminosity function, for which we find for the first time possible evidences of the cut-off, leading to an age estimate of ${\simeq}12\pm 0.5$ Gyr. The mass distribution of the sample peaks at $0.589\, \mathrm{ M}_{\odot }$, with $71{{\ \rm per\ cent}}$ of the white dwarf masses below $0.6\, \mathrm{ M}_{\odot }$ and just two massive white dwarfs of more than $0.8\, \mathrm{ M}_{\odot }$. From the age distribution, we find three white dwarfs with total ages above 12 Gyr, of which J1312−4728 is the oldest white dwarf known with an age of $12.41\pm 0.22\,$ Gyr. We prove that the star formation history is mainly characterized by a burst of star formation that occurred from 10 to 12 Gyr in the past, but extended up to 8 Gyr. We also find that the peak of the star formation history is centred at around 11 Gyr, which is compatible with the current age of the Gaia-Enceladus encounter. Finally, $13{{\ \rm per\ cent}}$ of our halo sample is contaminated by high-speed young objects (total age &lt;7 Gyr). The origin of these white dwarfs is unclear but their age distribution may be compatible with the encounter with the Sagittarius galaxy.
hmcode-2020: improved modelling of non-linear cosmological power spectra with baryonic feedback
Authors: Mead A J , Brieden S , Tröster T , Heymans C 
Published: January 2021

ABSTRACT
We present an updated version of the hmcode augmented halo model that can be used to make accurate predictions of the non-linear matter power spectrum over a wide range of cosmologies. Major improvements include modelling of baryon-acoustic oscillation (BAO) damping in the power spectrum and an updated treatment of massive neutrinos. We fit our model to simulated power spectra and show that we can match the results with an root mean square (RMS) error of 2.5 per cent across a range of cosmologies, scales $k \lt 10\, h\, \mathrm{Mpc}^{-1}$, and redshifts z &lt; 2. The error rarely exceeds 5 per cent and never exceeds 16 per cent. The worst-case errors occur at z ≃ 2, or for cosmologies with unusual dark energy equations of state. This represents a significant improvement over previous versions of hmcode, and over other popular fitting functions, particularly for massive-neutrino cosmologies with high neutrino mass. We also present a simple halo model that can be used to model the impact of baryonic feedback on the power spectrum. This six-parameter physical model includes gas expulsion by active galactic nuclei (AGN) feedback and encapsulates star formation. By comparing this model to data from hydrodynamical simulations, we demonstrate that the power spectrum response to feedback is matched at the &lt;1 per cent level for z &lt; 1 and $k\lt 20\, h\, \mathrm{Mpc}^{-1}$. We also present a single-parameter variant of this model, parametrized in terms of feedback strength, which is only slightly less accurate. We make code available for our non-linear and baryon models at https://github.com/alexander-mead/HMcode and it is also available within camb and soon within class.
A synergy of the velocity gradients technique and the probability density functions for identifying gravitational collapse in self-absorbing media
Authors: Hu Yue , Lazarian A 
Published: January 2021

ABSTRACT
The velocity gradients technique (VGT) and the probability density functions (PDFs) of mass density are tools to study turbulence, magnetic fields, and self-gravity in molecular clouds. However, self-absorption can significantly make the observed intensity different from the column density structures. In this work, we study the effects of self-absorption on the VGT and the intensity PDFs utilizing three synthetic emission lines of CO isotopologues 12CO (1–0), 13CO (1–0), and C18O (1–0). We confirm that the performance of VGT is insensitive to the radiative transfer effect. We numerically show the possibility of constructing 3D magnetic fields tomography through VGT. We find that the intensity PDFs change their shape from the pure lognormal to a distribution that exhibits a power-law tail depending on the optical depth for supersonic turbulence. We conclude the change of CO isotopologues’ intensity PDFs can be independent of self-gravity, which makes the intensity PDFs less reliable in identifying gravitational collapsing regions. We compute the intensity PDFs for a star-forming region NGC 1333 and find the change of intensity PDFs in observation agrees with our numerical results. The synergy of VGT and the column density PDFs confirms that the self-gravitating gas occupies a large volume in NGC 1333.
Modelling the delivery of dust from discs to ionized winds
Authors: Booth Richard A , Clarke Cathie J 
Published: January 2021

ABSTRACT
A necessary first step for dust removal in protoplanetary disc winds is the delivery of dust from the disc to the wind. In the case of ionized winds, the disc and wind are sharply delineated by a narrow ionization front where the gas density and temperature vary by more than an order of magnitude. Using a novel method that is able to model the transport of dust across the ionization front in the presence of disc turbulence, we revisit the problem of dust delivery. Our results show that the delivery of dust to the wind is determined by the vertical gas flow through the disc induced by the mass-loss, rather than turbulent diffusion (unless the turbulence is strong, i.e. α ≳ 0.01). Using these results, we provide a simple relation between the maximum size of particle that can be delivered to the wind and the local mass-loss rate per unit area from the wind. This relation is independent of the physical origin of the wind and predicts typical sizes in the 0.01–$1\, \rm{\mu m}$ range for extreme-ultraviolet- or X-ray-driven winds. These values are a factor of ∼10 smaller than those obtained when considering only whether the wind is able to carry away the grains.
A fully general, non-perturbative treatment of impulsive heating
Authors: Banik Uddipan , van den Bosch Frank C 
Published: January 2021

ABSTRACT
Impulsive encounters between astrophysical objects are usually treated using the distant tide approximation (DTA) for which the impact parameter, b, is assumed to be significantly larger than the characteristic radii of the subject, rS, and the perturber, rP. The perturber potential is then expanded as a multipole series and truncated at the quadrupole term. When the perturber is more extended than the subject, this standard approach can be extended to the case where rS ≪ b &lt; rP. However, for encounters with b of order rS or smaller, the DTA typically overpredicts the impulse, Δv, and hence the internal energy change of the subject, ΔEint. This is unfortunate, as these close encounters are the most interesting, potentially leading to tidal capture, mass stripping, or tidal disruption. Another drawback of the DTA is that ΔEint is proportional to the moment of inertia, which diverges unless the subject is truncated or has a density profile that falls off faster than r−5. To overcome these shortcomings, this paper presents a fully general, non-perturbative treatment of impulsive encounters which is valid for any impact parameter, and not hampered by divergence issues, thereby negating the necessity to truncate the subject. We present analytical expressions for Δv for a variety of perturber profiles, apply our formalism to both straight-path encounters and eccentric orbits, and discuss the mass-loss due to tidal shocks in gravitational encounters between equal-mass galaxies.
Dark matter-deficient dwarf galaxies form via tidal stripping of dark matter in interactions with massive companions
Authors: Jackson R A , Kaviraj S , Martin G , Devriendt J E G , Slyz A , Silk J , Dubois Y , Yi S K , Pichon C , Volonteri M , Choi H , Kimm T , Kraljic K , Peirani S 
Published: January 2021

ABSTRACT
In the standard ΛCDM (Lambda cold dark matter) paradigm, dwarf galaxies are expected to be dark matter-rich, as baryonic feedback is thought to quickly drive gas out of their shallow potential wells and quench star formation at early epochs. Recent observations of local dwarfs with extremely low dark matter content appear to contradict this picture, potentially bringing the validity of the standard model into question. We use NewHorizon, a high-resolution cosmological simulation, to demonstrate that sustained stripping of dark matter, in tidal interactions between a massive galaxy and a dwarf satellite, naturally produces dwarfs that are dark matter-deficient, even though their initial dark matter fractions are normal. The process of dark matter stripping is responsible for the large scatter in the halo-to-stellar mass relation in the dwarf regime. The degree of stripping is driven by the closeness of the orbit of the dwarf around its massive companion and, in extreme cases, produces dwarfs with halo-to-stellar mass ratios as low as unity, consistent with the findings of recent observational studies. ∼30 per cent of dwarfs show some deviation from normal dark matter fractions due to dark matter stripping, with 10 per cent showing high levels of dark matter deficiency (Mhalo/M⋆ &lt; 10). Given their close orbits, a significant fraction of dark matter-deficient dwarfs merge with their massive companions (e.g. ∼70 per cent merge over time-scales of ∼3.5 Gyr), with the dark matter-deficient population being constantly replenished by new interactions between dwarfs and massive companions. The creation of these galaxies is therefore a natural by-product of galaxy evolution and their existence is not in tension with the standard paradigm.
Inclination dynamics of resonant planets under the influence of an inclined external companion
Authors: Rodet Laetitia , Lai Dong 
Published: January 2021

ABSTRACT
Recent observations suggest that a large fraction of Kepler super-Earth systems have external giant planet companions (cold Jupiters), which can shape the architecture of the inner planets, in particular their mutual inclinations. The dynamical perturbation from cold Jupiters may account for the population of misaligned planets in the Kepler data. The effectiveness of this mechanism can be hindered by a strong planet–planet coupling in the inner system. In this paper, we study how mean-motion resonances (MMRs) affect this coupling and the expected misalignment. We derive approximate analytical expressions for the mutual inclination excitations in the inner planet system induced by an inclined companion, for various period ratios and perturber properties. In most cases, the mutual inclination is proportional to a dimensionless parameter that characterizes the strength of the perturber relative to the coupling in the inner system. We show that the MMR strengthens the inner coupling, reducing the mutual inclination induced by the perturber by a factor of a few. We find that the resonance is resilient to the perturbation, and derive a criterion for the libration of the resonant angle. Our results have applications for constraining unseen planetary perturbers, and for understanding the architecture of multiplanet systems.
Prospects for Galactic and stellar astrophysics with asteroseismology of giant stars in the TESS continuous viewing zones and beyond
Authors: Mackereth J Ted , Miglio Andrea , Elsworth Yvonne , Mosser Benoit , Mathur Savita , Garcia Rafael A , Nardiello Domenico , Hall Oliver J , Vrard Mathieu , Ball Warrick H , Basu Sarbani , Beaton Rachael L , Beck Paul G , Bergemann Maria , Bossini Diego , Casagrande Luca , Campante Tiago L , Chaplin William J , Chiappini Cristina , Girardi Léo , Jørgensen Andreas Christ Sølvsten , Khan Saniya , Montalbán Josefina , Nielsen Martin B , Pinsonneault Marc H , Rodrigues Thaíse S , Serenelli Aldo , Silva Aguirre Victor , Stello Dennis , Tayar Jamie , Teske Johanna , van Saders Jennifer L , Willett Emma 
Published: January 2021

ABSTRACT
The NASA Transiting Exoplanet Survey Satellite (NASA-TESS) mission presents a treasure trove for understanding the stars it observes and the Milky Way, in which they reside. We present a first look at the prospects for Galactic and stellar astrophysics by performing initial asteroseismic analyses of bright (G &lt; 11) red giant stars in the TESS southern continuous viewing zone (SCVZ). Using three independent pipelines, we detect νmax and Δν in 41 per cent of the 15 405 star parent sample (6388 stars), with consistency at a level of $\sim \! 2{{\ \rm per\ cent}}$ in νmax and $\sim \! 5{{\ \rm per\ cent}}$ in Δν. Based on this, we predict that seismology will be attainable for ∼3 × 105 giants across the whole sky and at least 104 giants with ≥1 yr of observations in the TESS-CVZs, subject to improvements in analysis and data reduction techniques. The best quality TESS-CVZ data, for 5574 stars where pipelines returned consistent results, provide high-quality power spectra across a number of stellar evolutionary states. This makes possible studies of, for example, the asymptotic giant branch bump. Furthermore, we demonstrate that mixed ℓ = 1 modes and rotational splitting are cleanly observed in the 1-yr data set. By combining TESS-CVZ data with TESS-HERMES, SkyMapper, APOGEE, and Gaia, we demonstrate its strong potential for Galactic archaeology studies, providing good age precision and accuracy that reproduces well the age of high [α/Fe] stars and relationships between mass and kinematics from previous studies based on e.g. Kepler. Better quality astrometry and simpler target selection than the Kepler sample makes this data ideal for studies of the local star formation history and evolution of the Galactic disc. These results provide a strong case for detailed spectroscopic follow-up in the CVZs to complement that which has been (or will be) collected by current surveys.
Undersurface Sequences
Authors: Reuven Ram 
Published: January 2021

AbstractAn undersurface sequence is a type of motivic parallelism that unifies parallel patterns into a single sequential unit. This article focuses on various undersurface sequences that leading Schenkerian scholars, including Schenker himself, integrated into their voice-leading graphs without explicitly pointing them out. The phenomenon is discussed according to different levels of distance from the surface, starting with sequences that lie very close to the surface and may allow for intuitive auditory perception, and ending with hidden sequences that lie deep in the middleground and are entirely analysis-dependent.
Nebula: ultra-efficient mapping-free structural variant genotyper
Authors: Khorsand Parsoa , Hormozdiari Fereydoun 
Published: January 2021

Abstract
Large scale catalogs of common genetic variants (including indels and structural variants) are being created using data from second and third generation whole-genome sequencing technologies. However, the genotyping of these variants in newly sequenced samples is a nontrivial task that requires extensive computational resources. Furthermore, current approaches are mostly limited to only specific types of variants and are generally prone to various errors and ambiguities when genotyping complex events. We are proposing an ultra-efficient approach for genotyping any type of structural variation that is not limited by the shortcomings and complexities of current mapping-based approaches. Our method Nebula utilizes the changes in the count of k-mers to predict the genotype of structural variants. We have shown that not only Nebula is an order of magnitude faster than mapping based approaches for genotyping structural variants, but also has comparable accuracy to state-of-the-art approaches. Furthermore, Nebula is a generic framework not limited to any specific type of event. Nebula is publicly available at https://github.com/Parsoa/Nebula.
PAUPARand PAX6 sequentially regulate human embryonic stem cell cortical differentiation
Authors: Xu Yanxin , Xi Jiajie , Wang Guiying , Guo Zhenming , Sun Qiaoyi , Lu Chenqi , Ma Li , Wu Yukang , Jia Wenwen , Zhu Songcheng , Guo Xudong , Bian Shan , Kang Jiuhong 
Published: January 2021

AbstractLong noncoding RNAs (lncRNAs) play a wide range of roles in the epigenetic regulation of crucial biological processes, but the functions of lncRNAs in cortical development are poorly understood. Using human embryonic stem cell (hESC)-based 2D neural differentiation approach and 3D cerebral organoid system, we identified that the lncRNA PAUPAR, which is adjacent to PAX6, plays essential roles in cortical differentiation by interacting with PAX6 to regulate the expression of a large number of neural genes. Mechanistic studies showed that PAUPAR confers PAX6 proper binding sites on the target neural genes by directly binding the genomic regions of these genes. Moreover, PAX6 recruits the histone methyltransferase NSD1 through its C-terminal PST enrichment domain, then regulate H3K36 methylation and the expression of target genes. Collectively, our data reveal that the PAUPAR/PAX6/NSD1 complex plays a critical role in the epigenetic regulation of hESC cortical differentiation and highlight the importance of PAUPAR as an intrinsic regulator of cortical differentiation.
DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing
Authors: Bhattacharya Arjun , Hamilton Alina M , Troester Melissa A , Love Michael I 
Published: January 2021

AbstractTargeted mRNA expression panels, measuring up to 800 genes, are used in academic and clinical settings due to low cost and high sensitivity for archived samples. Most samples assayed on targeted panels originate from bulk tissue comprised of many cell types, and cell-type heterogeneity confounds biological signals. Reference-free methods are used when cell-type-specific expression references are unavailable, but limited feature spaces render implementation challenging in targeted panels. Here, we present DeCompress, a semi-reference-free deconvolution method for targeted panels. DeCompress leverages a reference RNA-seq or microarray dataset from similar tissue to expand the feature space of targeted panels using compressed sensing. Ensemble reference-free deconvolution is performed on this artificially expanded dataset to estimate cell-type proportions and gene signatures. In simulated mixtures, four public cell line mixtures, and a targeted panel (1199 samples; 406 genes) from the Carolina Breast Cancer Study, DeCompress recapitulates cell-type proportions with less error than reference-free methods and finds biologically relevant compartments. We integrate compartment estimates into cis-eQTL mapping in breast cancer, identifying a tumor-specific cis-eQTL for CCR3 (C–C Motif Chemokine Receptor 3) at a risk locus. DeCompress improves upon reference-free methods without requiring expression profiles from pure cell populations, with applications in genomic analyses and clinical settings.