bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel role of prostate cancer risk variant rs7247241 on PPP1R14A isoform transition through allelic TF binding and CpG methylation
Authors: Tian Yijun , Soupir Alex , Liu Qian , Wu Lang , Huang Chiang-Ching , Park Jong Y , Wang Liang 
Published: November 2021

Abstract
Although previous studies identified numerous single nucleotide polymorphisms (SNPs) and their target genes predisposed to prostate cancer (PrCa) risks, SNP-related splicing associations are rarely reported. In this study, we applied distance-based sQTL analysis (sQTLseekeR) using RNA-seq and SNP genotype data from benign prostate tissue (n = 467) and identified significant associations in 3344 SNP-transcript pairs (P ≤ 0.05) at PrCa risk loci. We characterized a common SNP (rs7247241) and its target gene (PPP1R14A) located in chr19q13, an sQTL with risk allele T associated with upregulation of long isoform (P = 9.99E−7). We confirmed the associations in both TCGA (P = 2.42E−24) and GTEX prostate cohorts (P = 9.08E−78). To functionally characterize this SNP, we performed chromatin immunoprecipitation qPCR and confirmed stronger CTCF and PLAGL2 binding in rs7247241 C than T allele. We found that CTCF binding enrichment was negatively associated with methylation level at the SNP site in human cell lines (r = −0.58). Bisulfite sequencing showed consistent association of rs7247241-T allele with nearby sequence CpG hypermethylation in prostate cell lines and tissues. Moreover, the methylation level at CpG sites nearest to the CTCF binding and first exon splice-in (ψ) of PPP1R14A was significantly associated with aggressive phenotype in the TCGA PrCa cohort. Meanwhile, the long isoform of the gene also promoted cell proliferation. Taken together, with the most updated gene annotations, we reported a set of sQTL associated with multiple traits related to human prostate diseases and revealed a unique role of PrCa risk SNP rs7247241 on PPP1R14A isoform transition.
A random survey of the prevalence of falsified and substandard antibiotics in the Lao PDR
Authors: Tabernero Patricia , Swamidoss Isabel , Mayxay Mayfong , Khanthavong Maniphone , Phonlavong Chindaphone , Vilayhong Chanthala , Sichanh Chanvilay , Sengaloundeth Sivong , Green Michael D , Newton Paul N 
Published: November 2021

Abstract

Objectives
In 2012, a stratified random survey, using mystery shoppers, was conducted to investigate the availability and quality of antibiotics sold to patients in the private sector in five southern provinces of the Lao People’s Democratic Republic (Laos).

Methods
A total of 147 outlets were sampled in 10 districts. The active pharmaceutical ingredient (API) content measurements for 909 samples, including nine APIs (amoxicillin, ampicillin, ceftriaxone, ciprofloxacin, doxycycline, ofloxacin, sulfamethoxazole, tetracycline and trimethoprim), were determined using HPLC.

Results
All the analysed samples contained the stated API and we found no evidence for falsification. All except one sample had all the units tested with %API values between 75% and 125% of the content stated on the label. However, we identified the presence of substandard antibiotics: 19.6% (201/1025) of samples had their units outside the 90%–110% content of the label claim and 18.3% (188/1025) of the samples had units outside the International Pharmacopoeia/United States Pharmacopoeia assay (percentage of label claim) specifications. Trimethoprim had a high number of samples [51.6% (64)] with units below the limit range, followed by ceftriaxone [42.9% (3)] and sulfamethoxazole [34.7% (43)]. Doxycycline, ofloxacin and ciprofloxacin had the highest number of samples with high API content: 43.7% (38), 14.7% (10) and 11.8% (2), respectively. Significant differences in %API were found between stated countries of manufacture and stated manufacturers.

Conclusions
With the global threat of antimicrobial resistance on patient outcomes, greater understanding of the role of poor-quality antibiotics is needed. Substandard antibiotics will have reduced therapeutic efficacy, impacting public health and control of bacterial infections.
Toxicological Analysis of Cases of Mixed Poisonings with Synthetic Cathinones and Other Drugs of Abuse
Authors: Pieprzyca Ewelina , Skowronek Rafał , Czekaj Piotr 
Published: November 2021

Abstract
Some of the most commonly used new psychoactive substances (NPSs) are synthetic cathinones (SCs). The literature increasingly indicates that SCs have a significant addictive potential and pose a high risk to human health and life. The vast majority of SC users take a number of substances simultaneously. This article lists the detected concentrations in 26 fatal and 2 non-fatal real cases, in which SCs or an SC along with other substances were determined in blood and other biological materials. The following SCs were found most often: α-pyrrolidinohexiophenone, α-pyrrolidinopentiophenone, N-ethylpentedrone (NEP), 4-methyl-α-ethylaminopentiophenone and N-ethylhexedrone. In addition to detected SCs, the analyzed samples showed the presence of conventional drugs such as methamphetamine, 3,4-methylenedioxymethamphetamine, 3,4-methylenedioxyamphetamine, amphetamine and NPSs from groups other than SCs, such as synthetic cannabinoids (UR-144 and 5F-AMB), synthetic opioids (AH-7921, U-47700 and 4-fluorobutyrfentanyl) and others (desoxypipradrol and etizolam). The quantitative analyses were carried out by liquid chromatography with tandem mass spectrometry (LC–MS-MS). This study presents pioneering data on concentrations and effects of 4-ethylmethcathinone, NEP, N-ethylbuphedrone and mexedrone. Also noteworthy are the data on SCs that until now have rarely been described in the literature together with specified blood concentrations. The analyzed cases of taking SCs were associated with fatal intoxication (n = 26), driving under the influence of drugs (n = 2) and death caused by beating (n = 1). Taking SCs has serious side effects that can lead to multiple organ failure and death. The use of more than one psychoactive substance simultaneously (including at least one SC) contributes to increased SC toxicity. These data could be valuable for further interpretation of other results from toxicological analyses.
New species of deep-sea squat lobsters (Decapoda: Anomura: Galatheoidea) from Guadeloupe, French West Indies, unveiled through integrative taxonomy
Authors: Rodríguez-Flores Paula C , Macpherson Enrique , Machordom Annie 
Published: November 2021

AbstractDuring two deep-sea expeditions off the island of Guadeloupe, French West Indies, several specimens belonging to MunidaLeach, 1820 and MunidopsisWhiteaves, 1874 (Galatheoidea) were collected. Further study, integrating morphological and molecular data, indicated that some of the specimens belonged to three undescribed species, one to Munida and two to Munidopsis. Munida anteaen. sp. is morphologically closely related to the Atlantic species M. microphthalma A. Milne-Edwards, 1880. Both species can be easily distinguished morphologically and represent independent evolutionary lineages. The closest relative to Munidopsis balconin. sp. is M. glabraPequegnat & Williams, 1995 from the Gulf of Mexico. They can be distinguished by the armature of the carapace and pereiopods, among other differences. Munidopsis pholidotan. sp. is sister to M. squamosa (A. Milne-Edwards, 1880) and both are considered cryptic species, distinguished only by molecular characters and subtle morphological differences like the number of epipodites. Our phylogenetic results show some monophyletic groups within Munidopsis and Munida, and the existence of morphological convergences.
Research policy in supportive care and palliative care for cancer dyspnea
Authors: Matsuda Yoshinobu , Yamaguchi Takashi , Matsumoto Yoshihisa , Ishiki Hiroto , Usui Yuko , Kako Jun , Suzuki Kozue , Matsunuma Ryo , Mori Masanori , Watanabe Hiroaki , Zenda Sadamoto 
Published: November 2021

Abstract

Background
Dyspnea is a common and distressing symptom in patients with cancer. To improve its management, multicenter confirmatory studies are necessary. Research policy would be useful in conducting these studies. Here, we propose a new research policy for the management of dyspnea in patients with cancer.

Methods
The first draft was developed by a policy working group of 11 specialists in the field of supportive care or palliative care for dyspnea. Then, a provisional draft was developed after review by a research support group (the Japanese Supportive, Palliative and Psychosocial Care Study Group) and five Japanese scientific societies (Japanese Association of Supportive Care in Cancer, Japanese Society of Medical Oncology, Japanese Society of Palliative Medicine, Japanese Association of Rehabilitation Medicine and Japanese Society of Clinical Oncology), and receipt of public comments.

Results
The policy includes the following components of research policy on dyspnea: (i) definition of dyspnea, (ii) scale for assessment of dyspnea, (iii) reason for dyspnea or factors associated with dyspnea and (iv) treatment effectiveness outcomes/adverse events. The final policy (Ver1.0) was completed on 1 March 2021.

Conclusions
This policy could help researchers plan and conduct studies on the management of cancer dyspnea.
BREVIPEDICELLUSandERECTAcontrol the expression ofAtPRX17to prevent Arabidopsis callus browning
Authors: Xie Junyan , Qi Bin , Mou Chenghong , Wang Lihua , Jiao Yuwei , Dou Yanhui , Zheng Huiqiong 
Published: November 2021

AbstractEfficient in vitro callus generation is required for tissue culture propagation, a process that allows for plant regeneration and transgenic breeding for desired phenotypes. Identifying genes and regulatory elements that prevent impaired callus growth and callus browning is essential for the development of in vitro callus systems. Here, we show that the BREVIPEDICELLUS and ERECTA pathways in Arabidopsis calli converge to prevent callus browning, and positively regulate the expression of the isoperoxidase gene AtPRX17 in rapidly growing calli. Loss-of-function mutations in both BREVIPEDICELLUS and ERECTA resulted in markedly increased callus browning. Transgenic lines expressing 35S pro::AtPRX17 in the bp-5 er105 double mutant background fully rescued this phenotypic abnormality. Using in vivo (chromatin immunoprecipitation-PCR and transient expression) and in vitro (electrophoretic mobility shift assays) assays, we observed that the BREVIPEDICELLUS protein binds directly to the upstream sequence of AtPRX17 to promote its transcription during callus growth. ERECTA is a ubiquitous factor required for cell proliferation and growth. We show that ERECTA positively regulates the expression of the transcription factor WRKY6, which directly binds to a separate site on the AtPRX17 promoter, further increasing its expression. Our data reveal an important molecular mechanism involved in the regulation of peroxidase isozyme expression to reduce Arabidopsis callus browning.
Distances, extinctions, and stellar parameters for stars in SkyMapper DR3
Authors: Lin Jane , Casagrande Luca , Asplund Martin 
Published: November 2021

ABSTRACT
We present a Bayesian isochrone fitting machinery to derive distances, extinctions, and stellar parameters (Teff, log g, and $\rm [Fe/H]$) for stars in the SkyMapper data release 3 (DR3) survey. We complement the latter with photometry from Gaia, 2MASS, and AllWISE, in addition to priors on parallaxes and interstellar extinction. We find our results to be in agreement with smaller samples of literature values derived using spectroscopic/photometric method, with typical uncertainties of order 130 K in effective temperature and 0.2 dex in surface gravity and metallicity. We demonstrate the quality of our stellar parameters by benchmarking our results against various spectroscopic surveys. We highlight the potential that SkyMapper bears for stellar population studies showing how we are able to clearly differentiate metallicities along the Gaia red (∼−0.4 dex) and blue (∼−1.1 dex) sequences using both dwarf and giant stars.
AbacusHOD: a highly efficient extended multitracer HOD framework and its application to BOSS and eBOSS data
Authors: Yuan Sihan , Garrison Lehman H , Hadzhiyska Boryana , Bose Sownak , Eisenstein Daniel J 
Published: November 2021

ABSTRACT
We introduce the AbacusHOD model and present two applications of AbacusHOD and the AbacusSummit simulations to observations. AbacusHOD is a Halo Occupation Distribution (HOD) framework written in Python that is particle-based, multitracer, highly generalized, and highly efficient. It is designed specifically with multitracer/cosmology analyses for next-generation large-scale structure surveys in mind, and takes advantage of the volume and precision offered by the new state-of-the-art AbacusSummit cosmological simulations. The model is also highly customizable and should be broadly applicable to any upcoming surveys and a diverse range of cosmological analyses. In this paper, we demonstrate the capabilities of the AbacusHOD framework through two example applications. The first example demonstrates the high efficiency and the large HOD extension feature set through an analysis of full-shape redshift-space clustering of BOSS galaxies at intermediate to small scales ($\lt 30\, h^{-1}$ Mpc), assessing the necessity of introducing secondary galaxy biases (assembly bias). We find strong evidence for using halo environment instead of concentration to trace secondary galaxy bias, a result which also leads to a moderate reduction in the ‘lensing is low’ tension. The second example demonstrates the multitracer capabilities of the AbacusHOD package through an analysis of the extended Baryon Oscillation Spectroscopic Survey cross-correlation measurements between three different galaxy tracers: luminous red galaxies, emission-line galaxies, and quasi-stellar objects. We expect the AbacusHOD framework, in combination with the AbacusSummit simulation suite, to play an important role in a simulation-based analysis of the upcoming Dark Energy Spectroscopic Instrument data sets.
The acoustic resonant drag instability with a spectrum of grain sizes
Authors: Squire Jonathan , Moroianu Stefania , Hopkins Philip F 
Published: November 2021

ABSTRACT
We study the linear growth and non-linear saturation of the ‘acoustic Resonant Drag Instability’ (RDI) when the dust grains, which drive the instability, have a wide, continuous spectrum of different sizes. This physics is generally applicable to dusty winds driven by radiation pressure, such as occurs around red-giant stars, star-forming regions, or active galactic nuclei. Depending on the physical size of the grains compared to the wavelength of the radiation field that drives the wind, two qualitatively different regimes emerge. In the case of grains that are larger than the radiation’s wavelength – termed the constant-drift regime – the grain’s equilibrium drift velocity through the gas is approximately independent of grain size, leading to strong correlations between differently sized grains that persist well into the saturated non-linear turbulence. For grains that are smaller than the radiation’s wavelength – termed the non-constant-drift regime – the linear instability grows more slowly than the single-grain-size RDI and only the larger grains exhibit RDI-like behaviour in the saturated state. A detailed study of grain clumping and grain–grain collisions shows that outflows in the constant-drift regime may be effective sites for grain growth through collisions, with large collision rates but low collision velocities.
Towards a universal model for the density profiles of dark matter haloes
Authors: Brown Shaun T , McCarthy Ian G , Stafford Sam G , Font Andreea S 
Published: November 2021

ABSTRACT
It is well established from cosmological simulations that dark matter (DM) haloes are not precisely self-similar and an additional parameter, beyond their concentration, is required to accurately describe their spherically averaged mass density profiles. We present, for the first time, a model to consistently predict both halo concentration, c, and this additional ‘shape’ parameter, α, for a halo of given mass and redshift for a specified cosmology. Following recent studies, we recast the dependence on mass, redshift, and cosmology to a dependence on ‘peak height’. We show that, when adopting the standard definition of peak height, which employs the so-called spherical top hat (STH) window function, the concentration–peak height relation has a strong residual dependence on cosmology (i.e. it is not uniquely determined by peak height), whereas the α–peak height relation is approximately universal when employing the STH window function. Given the freedom in the choice of window function, we explore a simple modification of the STH function, constraining its form so that it produces universal relations for concentration and α as a function of peak height using a large suite of cosmological simulations. It is found that universal relations for the two density profile parameters can indeed be derived and that these parameters are set by the linear power spectrum, P(k), filtered on different scales. We show that the results of this work generalize to any (reasonable) combination of P(k) and background expansion history, H($z$), resulting in accurate predictions of the density profiles of DM haloes for a wide range of cosmologies.
The steady-state hydrodynamics of a long-lived disc: planetary system architecture and prospects of observing a circumplanetary disc shadow in V4046 Sgr
Authors: Weber Philipp , Casassus Simon , Pérez Sebastián 
Published: November 2021

ABSTRACT
Recent imaging of the disc around the V4046 Sgr spectroscopic binary revealed concentric regions of dust rings and gaps. The object’s proximity and expected equilibrated state due to its old age (&gt;20 Myr) make it a superb testbed for hydrodynamical studies in direct comparison to observations. We employ two-dimensional hydrodynamical simulations of gas and multiple dust species to test whether the observed structure conforms with the presence of giant planets embedded in the disc. We then perform radiative transfer (RT) calculations of sky images, which we filter for the telescope response for comparison with near-infrared (NIR) and millimetre observations. We find that the existing data are in excellent agreement with a flared disc and the presence of two giant planets, at $9$ and $20\, {\rm au}$, respectively. The different ring widths are recovered by diffusion-balanced dust trapping within the gas pressure maxima. In our RT model, the diffusion in vertical direction is reduced in comparison to the radial value by a factor of 5 to recover the spectral energy distribution. Further, we report a previously unaddressed, azimuthally confined intensity decrement on the bright inner ring in the NIR scattered light observation. Our model shows that this decrement can be explained by a shadow cast by a circumplanetary disc around the same giant planet that creates the inner cavity in the hydrodynamical simulations. We examine the shape of the intensity indentation and discuss the potential characterization of a giant planet and its associated disc by its projected shadow in scattered light observations.
High-resolution ALMA observations of V4046 Sgr: a circumbinary disc with a thin ring
Authors: Martinez–Brunner Rafael , Casassus Simon , Pérez Sebastián , Hales Antonio , Weber Philipp , Cárcamo Miguel , Arce-Tord Carla , Cieza Lucas , Garufi Antonio , Marino Sebastián , Zurlo Alice 
Published: November 2021

ABSTRACT
The nearby V4046 Sgr spectroscopic binary hosts a gas-rich disc known for its wide cavity and dusty ring. We present high resolution (∼20 mas or 1.4 au) ALMA observations of the 1.3 mm continuum of V4046 Sgr which, combined with SPHERE–IRDIS polarised images and a well-sampled spectral energy distribution (SED), allow us to propose a physical model using radiative transfer predictions. The ALMA data reveal a thin ring at a radius of 13.15 ± 0.42 au (Ring13), with a radial width of 2.46 ± 0.56 au. Ring13 is surrounded by a ∼10 au-wide gap, and it is flanked by a mm-bright outer ring (Ring24) with a sharp inner edge at 24 au. Between 25 and ∼35 au the brightness of Ring24 is relatively flat and then breaks into a steep tail that reaches out to ∼60 au. In addition, central emission is detected close to the star which we interpret as a tight circumbinary ring made of dust grains with a lower size limit of 0.8 mm at 1.1 au. In order to reproduce the SED, the model also requires an inner ring at ∼5 au (Ring5) composed mainly of small dust grains, hiding under the IRDIS coronagraph, and surrounding the inner circumbinary disc. The surprisingly thin Ring13 is nonetheless roughly 10 times wider than its expected vertical extent. The strong near-far disc asymmetry at 1.65 $\rm{\mu m}$ points at a very forward-scattering phase function, and requires grain radii of no less than 0.4 $\rm{\mu m}$.
On the rise times in FU Orionis events
Authors: Borchert Elisabeth M A , Price Daniel J , Pinte Christophe , Cuello Nicolás 
Published: November 2021

ABSTRACT
We examine whether stellar flyby simulations can initiate FU Orionis outbursts using 3D hydrodynamics simulations coupled to live Monte Carlo radiative transfer. We find that a flyby where the secondary penetrates the circumprimary disc triggers a 1–2 yr rise in the mass accretion rate to 10−4 M⊙ yr−1 that remains high (≳10−5 M⊙ yr−1) for more than a hundred years, similar to the outburst observed in FU Ori. Importantly, we find that the less massive star becomes the dominant accretor, as observed.
Structural basis of DNA methylation-dependent site selectivity of the Epstein–Barr virus lytic switch protein ZEBRA/Zta/BZLF1
Authors: Bernaudat Florent , Gustems Montse , Günther Johannes , Oliva Mizar F , Buschle Alexander , Göbel Christine , Pagniez Priscilla , Lupo Julien , Signor Luca , Müller Christoph W , Morand Patrice , Sattler Michael , Hammerschmidt Wolfgang , Petosa Carlo 
Published: November 2021

Abstract
In infected cells, Epstein–Barr virus (EBV) alternates between latency and lytic replication. The viral bZIP transcription factor ZEBRA (Zta, BZLF1) regulates this cycle by binding to two classes of ZEBRA response elements (ZREs): CpG-free motifs resembling the consensus AP-1 site recognized by cellular bZIP proteins and CpG-containing motifs that are selectively bound by ZEBRA upon cytosine methylation. We report structural and mutational analysis of ZEBRA bound to a CpG-methylated ZRE (meZRE) from a viral lytic promoter. ZEBRA recognizes the CpG methylation marks through a ZEBRA-specific serine and a methylcytosine-arginine-guanine triad resembling that found in canonical methyl-CpG binding proteins. ZEBRA preferentially binds the meZRE over the AP-1 site but mutating the ZEBRA-specific serine to alanine inverts this selectivity and abrogates viral replication. Our findings elucidate a DNA methylation-dependent switch in ZEBRA’s transactivation function that enables ZEBRA to bind AP-1 sites and promote viral latency early during infection and subsequently, under appropriate conditions, to trigger EBV lytic replication by binding meZREs.
Fractal construction of constrained code words for DNA storage systems
Authors: Löchel Hannah F , Welzel Marius , Hattab Georges , Hauschild Anne-Christin , Heider Dominik 
Published: November 2021

Abstract
The use of complex biological molecules to solve computational problems is an emerging field at the interface between biology and computer science. There are two main categories in which biological molecules, especially DNA, are investigated as alternatives to silicon-based computer technologies. One is to use DNA as a storage medium, and the other is to use DNA for computing. Both strategies come with certain constraints. In the current study, we present a novel approach derived from chaos game representation for DNA to generate DNA code words that fulfill user-defined constraints, namely GC content, homopolymers, and undesired motifs, and thus, can be used to build codes for reliable DNA storage systems.