bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutation bias shapes the spectrum of adaptive substitutions
Authors: Cano Alejandro V. , Rozhoňová Hana , Stoltzfus Arlin , McCandlish David M. , Payne Joshua L. 
Published: February 2022

SignificanceHow do mutational biases influence the process of adaptation? A common assumption is that selection alone determines the course of adaptation from abundant preexisting variation. Yet, theoretical work shows broad conditions under which the mutation rate to a given type of variant strongly influences its probability of contributing to adaptation. Here we introduce a statistical approach to analyzing how mutation shapes protein sequence adaptation. Using large datasets from three different species, we show that the mutation spectrum has a proportional influence on the types of changes fixed in adaptation. We also show via computer simulations that a variety of factors can influence how closely the spectrum of adaptive substitutions reflects the spectrum of variants introduced by mutation.
Comparison of thermodynamic behaviors of two regular-AdS black holes
Authors: Guo Sen , Huang Ya-Ling , Liang En-Wei 
Published: February 2022

Abstract
Considering the negative cosmological constant of an anti-de Sitter (AdS) background as a positive thermodynamic pressure in the extended phase space, we investigate the P−υ critical behavior and of the cooling–heating phase transition of the regular Hayward-AdS (HAdS) black hole (BH), and compare the difference of some thermodynamic processes in both the HAdS BH and the Bardeen-AdS (BAdS) BH. We found that the phase transition of the BAdS BH tends to be more the van der Waals (vdW) phase transition. For the cooling–heating phase transition, we obtained the inversion curves of the HAdS BH are always higher than the BAdS BH under the same pressure and magnetic charge. We also compare the smallest existence mass, the zero-temperature remnant, and the critical magnetic charge for these two BHs. The results suggested that the inner horizon and the outer horizon of the Hayward BH are easier to merge, and the singularity is easier to expose.
Detection of genuine multipartite entanglement based on principal basis matrix representations
Authors: Zhao Hui , Liu Yu-Qiu , Fei Shao-Ming , Wang Zhi-Xi , Jing Naihuan 
Published: February 2022

Abstract
We study the genuine multipartite entanglement in tripartite quantum systems by using the principal basis matrix representations of density matrices. Using the Schmidt decomposition and local unitary transformation, we first convert the general states to simpler forms and then construct some special matrices from the correlation tensors of the simplified density matrices. Based on the different linear combinations of these matrices, necessary conditions are presented to detect genuine multipartite entanglement of tripartite states. Detailed examples show that our method can detect more entangled states than previous ones.
Optical and X-Ray Observations of MAXI J1820+070 During the Early Outburst Phase in 2018: Zooming in the Low Frequency QPOs*
Authors: Mao Dong-Ming , Yu Wen-Fei , Zhang Ju-Jia , Yan Zhen , Rapisarda Stefano , Wang Xiao-Feng , Bai Jin-Ming 
Published: February 2022

Abstract
We report a further investigation of the optical low frequency quasi periodic oscillations (LF QPOs) detected in the black hole transient MAXI J1820+070 in the 2018 observations with the YFOSC mounted on Lijiang 2.4 m telescope (LJT). In addition, we make use of the Insight-HXMT/HE observations to measure the properties of the quasi-simultaneous X-ray LF QPOs of MAXI J1820+070 on the same day. We compared the centroid frequency, the full width at half maximum (FWHM) and the fractional rms of the LF QPOs in both wavelength ranges. We found that the centroid frequency of the optical QPO is at a frequency of 51.58 mHz, which is consistent with that of the X-ray LF QPO detected on the same day within 1 mHz. We also found that the FWHM of the optical LF QPO is significantly smaller than that of the X-ray LF QPO, indicating that the optical QPO has a higher coherence. The quasi-simultaneous optical and the X-ray LF QPO at a centroid frequency of about 52 mHz suggests that the actual mechanisms of these LF QPOs as the Lense–Thirring precession should work in the vicinity of a radius of about 80–117 gravitational radii (R

g
= GM/c
2, M is the mass of the black hole) from the black hole if the QPO frequency is related to a proxy of the orbital frequency in the accretion flow as the Lense–Thirring precession model suggests. Furthermore, the apparent higher coherence of the optical QPO favors that it is a more original signal as compared with the X-ray QPO.
ACDM cosmology with a quiescent anisotropy in a higher dimensional steady state universe
Authors: Akarsu Ozgür , Dereli Tekin , Katırcı Nihan 
Published: February 2022

Abstract
In this work, which follows a series of studies on the higher-dimensional steady state universe idea and prepared for Professor Tekin Dereli’s Festschrift, we show the infuence of the dynamical internal (unobservable) space on the evolution of the possible anisotropy of the external (observable) space. We obtain mathematically exactly the same Friedmann equation of the standard ΛCDM model for the external space, but with some remarkable physical diferences. In particular, the higher-dimensional negative cosmological constant plays the role of the four-dimensional positive cosmological constant and the expansion anisotropy, viz., the shear scalar, of the external space mimics a negative cosmological constant; it would mimic a stif fuid when allowed on top of the standard ΛCDM model. This latter feature gives us the opportunity to manipulate the CMB quadrupole temperature fuctuation, suggesting a possible answer to the fact that its observed value is lower than that predicted by the standard ΛCDM model.
Dynamics of a fermion with dipole moments in external wave fields
Authors: Obukhov Yuri N. 
Published: February 2022

Abstract
We discuss the motion of a massive fermion spin 1/2 particle in external wave field configurations when the Pauli type non-minimal interaction of the gauge field strengths with particle’s dipole moments is taken into account. The exact solution of the relativistic Dirac-Pauli equation is presented for the case of the plane electromagnetic wave.
A model of non-minimally coupled gravitation and electromagnetism in (1+2) dimensions
Authors: Ünlütürk Kıvanç İ. , Yetişmişoğlu Cem 
Published: February 2022

Abstract
Following earlier works of Dereli and collaborators, we study a three dimensional toy model where we extend the topologically massive gravity with electrodynamics by the most general RF
2-type non-minimal coupling terms. Here R denotes the possible curvature terms and F denotes the electromagnetic 2-form. We derive the variational feld equations and look for exact solutions on constant negative curvature space-times with a constant, self-dual electromagnetic feld. The notion of self-dual electromagnetic felds in three dimensions is introduced by Dereli and collaborators in the study of exact solutions of models with gravity-electromagnetism couplings. We note the conditions that the parameters of the model have to satisfy for these self-dual solutions to exist.
Efficiency and time resolution of monolithic silicon pixel detectors in SiGe BiCMOS technology
Authors: Iacobucci G. , Paolozzi L. , Valerio P. , Moretti T. , Cadoux F. , Cardarelli R. , Cardella R. , Débieux S. , Favre Y. , Ferrere D. , Gonzalez-Sevilla S. , Gurimskaya Y. , Kotitsa R. , Magliocca C. , Martinelli F. , Milanesio M. , Münker M. , Nessi M. , Picardi A. , Saidi J. , Rücker H. , Vicente Barreto Pinto M. , Zambito S. 
Published: February 2022

Abstract
A monolithic silicon pixel detector prototype has been
produced in the SiGe BiCMOS SG13G2 130 nm node technology by
IHP. The ASIC contains a matrix of hexagonal pixels with pitch of
approximately 100 μm. Three analog pixels were calibrated in
laboratory with radioactive sources and tested in a 180 GeV/c pion
beamline at the CERN SPS. A detection efficiency of
(99.9-0.2
+0.1)% was measured together with a time
resolution of (36.4 ± 0.8) ps at the highest preamplifier bias
current working point of 150 μA and at a sensor bias voltage
of 160 V. The ASIC was also characterized at lower bias voltage and
preamplifier current.
Design of front-end electronics for HXI spectrometer flight model on-board ASO-S satellite
Authors: Wan Q. , Zhang Y. , Guo J.H. , Zhang Y.Q. , Xu X. 
Published: February 2022

Abstract
Advanced Space-based Solar Observatory (ASO-S), developed by
Chinese Academy of Sciences, is utilized for observing the solar
magnetic field, coronal mass ejection, and solar flare, as well as
studying the relationships among them. As one of the three
scientific payloads on ASO-S, Hard X-ray Imager (HXI) is designed
for solar hard X-ray imaging with outstanding temporal and spatial
resolutions. The spectrometer is an important part of HXI and used
to measure the incident photon with a dynamic range of 30–200 keV
after Fourier modulation by the collimator. It consists of 99
detector units and front-end electronics (FEE). The FEE can process
all the 99 detector units' signals independently in less than
2 μs. The noise of charge measure is less than 500 fC for a
dynamic range of 20 pC–900 pC. In this paper, the implementation
of FEE is introduced, including the design of electronics, quality
control, and performance tests. All these tests show that the FEE
can meet the HXI mission requirements.
Influences of cryogenically treated work material on near-dry wire-cut electrical discharge machining process
Authors: Kannan Elango , Trabelsi Youssef , Boopathi Sampath , Alagesan Sivapragasam 
Published: February 2022

Abstract
In this research, influences of cryogenically treated Inconel 718 work material in near-dry wire-cut electrical discharge machining (WEDM) characteristics have been studied using argon-mist (mixing of pressurized argon gas and minimum amount of tap-water) and a reusable Molybdenum wire tool. The effect of cutting parameters (pulse width (PW), spark current(C), pulse interval (PI), and flow rate(F)) on surface roughness (SR) and cutting rate (CR) and using Box-Behnken response surface analysis. It was observed that CR and SR are increased by increasing PW, and C; conversely, reduced by increasing PI. The technique for order of preference by similarity to ideal solution (TOPSIS) method has been utilized to estimate the best parameters’ settings for improving both machining characteristics. The optimum CR (9.81 mm3 min)−1 and SR (1.9 μm) have been obtained by optimum settings of 4 Ampere spark current, PW of 20 μs, PI of 72 μs, and 18 ml min−1 of the flow rate of mixing water using the TOPSIS method. The best settings of cutting parameters obtained from the TOPSIS method were considered to compare the near-dry WEDM performance using cryogenically treated/untreated work materials. It was observed that CR and SR of the cryogenically treated work material are 9.17% increased and 21.58% reduced than the untreated work material due to an increase in electrical and thermal conductivities.
The structure and properties of OMt prepared by a synergistic modification strategy using the emulsifier OP-10 and hexadecyltrimethylammonium chloride as comodifiers
Authors: Zhang Jingdan , Zhai Yongqing 
Published: February 2022

Abstract
To improve the application performance of organic montmorillonite (OMt) and meet the OMt performance requirements of different fields, herein, we developed a synergistic modification method to prepare cationic–nonionic OMt (CN-Mt) using the emulsifier OP-10 and hexadecyltrimethylammonium chloride (CTAC) as comodifiers. The structure, morphology and properties of CN-Mt, cationic-OMt (C-Mt) and nonionic OMt (N-Mt) were studied by XRD, SEM, DSC, and contact angle and swell index measurements. CN-Mt has a larger layer spacing and thinner lamellae, which are obviously different from those of C-Mt and N-Mt. Moreover, CN-Mt was hydrophobic due to its denser organic surface molecules. The interlayer spacing of CN-Mt is positively related to the amount of modifier, and the amount of OP-10 contributes more to the interlayer spacing than CTAC. When the amounts of OP-10 and CTAC are 1.3 and 0.8 times the Mt cation exchange capacity (CEC), the interlayer spacing of the optimal CN-Mt is 4.49 nm, which is significantly higher than that of C-Mt (4.11 nm) at a 2.9 CEC, N-Mt (4.26 nm) at a 1.7 CEC and CN-Mt (4.20 nm) at a 0.9OP-10 + 1.5CTAC CEC. Benefitting from its structural merits, CN-Mt shows a higher degree of lamella separation, peeling and dispersion than C-Mt and N-Mt, as well as good thermal stability. Moreover, the lipophilicity and expansion of CN-Mt in medium- and low-polarity media are better than those of single-component OMt. Therefore, the structure and properties of CN-Mt can be controlled by adjusting the types and amount of modifier, further meeting the performance requirements of various application fields.
New Methods for Tracking Development of Sociophonetic Competence: Exploring a Preference Task for Spanish /d/ Deletion
Authors: Solon Megan , Kanwit Matthew 
Published: February 2022

AbstractBeyond language use, an important component of communicative competence is the ability to attend to sociolinguistic variation in the input, which requires knowledge regarding when to expect a particular form over another variant according to linguistic or extralinguistic factors. This study explores the acquisition of sociophonetic competence, employing a novel contextualized preference task with an aural component to examine second language (L2) learners’ knowledge of variable Spanish /d/ deletion—a sociolinguistic phenomenon constrained by linguistic, social, and contextual factors—regardless of whether learners produce the deleted variant in their speech. Fifty learners completed a background questionnaire, an elicited imitation task, and the contextualized preference task. Learners’ preference for a deleted variant tended to increase as proficiency level increased, as did sensitivity to variables previously shown to constrain native speaker patterns of variation, including speaker gender, surrounding phonetic context, and grammatical category of the lexical item containing /d/. Overall, findings suggest that this contextualized preference task provides an additional tool for accessing evidence of learners’ developing sociophonetic awareness, tapping an important skill as learners build communicative competence.
Deep learning-based identification of genetic variants: application to Alzheimer’s disease classification
Authors: Jo Taeho , Nho Kwangsik , Bice Paula , Saykin Andrew J ,   For The Alzheimer’s Disease Neuroimaging Initiative
Published: February 2022

AbstractDeep learning is a promising tool that uses nonlinear transformations to extract features from high-dimensional data. Deep learning is challenging in genome-wide association studies (GWAS) with high-dimensional genomic data. Here we propose a novel three-step approach (SWAT-CNN) for identification of genetic variants using deep learning to identify phenotype-related single nucleotide polymorphisms (SNPs) that can be applied to develop accurate disease classification models. In the first step, we divided the whole genome into nonoverlapping fragments of an optimal size and then ran convolutional neural network (CNN) on each fragment to select phenotype-associated fragments. In the second step, using a Sliding Window Association Test (SWAT), we ran CNN on the selected fragments to calculate phenotype influence scores (PIS) and identify phenotype-associated SNPs based on PIS. In the third step, we ran CNN on all identified SNPs to develop a classification model. We tested our approach using GWAS data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) including (N = 981; cognitively normal older adults (CN) = 650 and AD = 331). Our approach identified the well-known APOE region as the most significant genetic locus for AD. Our classification model achieved an area under the curve (AUC) of 0.82, which was compatible with traditional machine learning approaches, random forest and XGBoost. SWAT-CNN, a novel deep learning–based genome-wide approach, identified AD-associated SNPs and a classification model for AD and may hold promise for a range of biomedical applications.
Phylogenetics of Gratioleae (Plantaginaceae): paraphyly of Stemodia and its implications for generic circumscriptions, with insights from floral evolution
Authors: Scatigna André Vito , Souza Vinicius Castro , Sosa Maria de las Mercedes , Colletta Gabriel Dalla , Machado Raquel Moura , Simões André Olmos 
Published: February 2022

Abstract
Gratioleae are the most species-rich tribe of Plantaginaceae in the tropics, spanning c. 30 genera and &gt; 300 species, with a wide range of morphological variation and ecological strategies. As a first effort towards a phylogenetic classification of Gratioleae we generated a new phylogenetic hypothesis with improved taxa sampling, based on one nuclear and three plastid markers, using maximum parsimony and Bayesian inference approaches, and performed ancestral state reconstructions of ten morphological characters of flowers. The paraphyly of Stemodia s.l. was corroborated with members being retrieved in four clades; Bacopa, Conobea, Leucospora and Schistophragma are non-monophyletic. As actions towards recognizing only monophyletic genera in Gratioleae, we propose Stemodia s.s. as a monophyletic and morphological cohesive group, describe Umbraria as a new genus to accommodate two species segregated from Stemodia, transfer Stemodia vandelliodes to Darcya, merge Conobea with Bacopa and re-establish the names Chodaphyton ericifolium and Geochorda glechomoides. Traits used to define Stemodia s.l. are plesiomorphic in the tribe; the flower type (composed of seven floral characters) constitutes a good diagnostic set of traits for almost all genera in the tribe. Our study sheds light on the urgent need to reassess generic circumscriptions towards a unified classification in Gratioleae.
Fitness benefits play a vital role in the retention of the Pi-ta susceptible alleles
Authors: Liu Jia , Zhang Suobing , Xie Pengfei , Wang Long , Xue Jia-Yu , Zhang Yanmei , Lu Ruisen , Hang Yueyu , Wang Yue , Sun Xiaoqin 
Published: February 2022

Abstract
In plants, large numbers of R genes, which segregate as loci with alternative alleles conferring different levels of disease resistance to pathogens, have been maintained over a long period of evolution. The reason why hosts harbor susceptible alleles in view of their null contribution to resistance is unclear. In rice, a single copy gene, Pi-ta, segregates for 2 expressed clades of alleles, 1 resistant and the other susceptible. We simulated loss-of-function of the Pi-ta susceptible allele using the CRISPR/Cas9 system to detect subsequent fitness changes and obtained insights into fitness effects related to the retention of the Pi-ta susceptible allele. Our creation of an artificial knockout of the Pi-ta susceptible allele suffered fitness-related trait declines of up to 49% in terms of filled grain yield upon the loss of Pi-ta function. The Pi-ta susceptible alleles might serve as an off-switch to downstream immune signaling, thus contributing to the fine-tuning of plant defense responses. The results demonstrated that the susceptible Pi-ta alleles should have evolved pleiotropic functions, facilitating their retention in populations. As Pi-ta is a single copy gene with no paralogs in the genome, its function cannot be compensated by an alternative gene; whereas most other R genes form gene clusters by tandem duplications, and the function could be compensated by paralogs with high sequence similarity. This attempt to evaluate the fitness effects of the R gene in crops indicates that not all disease resistance genes incur fitness costs, which also provides a plausible explanation for how host genomes can tolerate the possible genetic load associated with a vast repertoire of R genes.
CHAMP1 disorder is associated with a complex neurobehavioral phenotype including autism, ADHD, repetitive behaviors and sensory symptoms
Authors: Levy Tess , Lerman Bonnie , Halpern Danielle , Frank Yitzchak , Layton Christina , Zweifach Jessica , Siper Paige M , Buxbaum Joseph D , Kolevzon Alexander 
Published: February 2022

Abstract
CHAMP1-related neurodevelopmental disorder, or CHAMP1 disorder, is a recently described genetic syndrome associated with developmental delay, intellectual disability, behavioral symptoms, medical comorbidities, and dysmorphic features. To date, literature has focused on medical review and dysmorphology but has yet to prospectively assess neurobehavioral core domains such as autism, or behavioral, language, cognitive, and sensory features. Here, we present deep phenotyping results for 11 individuals with CHAMP1 disorder, based on approximately 12 hours of remote clinician-administered assessments and standardized caregiver questionnaires. Diagnoses of autism spectrum disorder were given to 33% of participants; repetitive behaviors and sensory-seeking symptoms were prominent in this cohort. In addition, 60% of participants met the criteria for attention-deficit/hyperactivity disorder (ADHD). High rates of ADHD and relatively low rates of treatment suggest potential areas for intervention. This study represents the first prospective phenotyping analysis of individuals with CHAMP1 disorder. The utility of specific measures as clinical endpoints, as well as benefits and limitations of remote phenotyping, are described.
Experiences and Stressors of Parents of Trans and Gender-Diverse Youth in Clinical Care from Trans Youth CAN!
Authors: Pullen Sansfaçon Annie , Temple Newhook Julia , Douglas Laura , Gotovac Sandra , Raiche Joe , Speechley Kathy Nixon , Lawson Margaret L , Bauer Greta R 
Published: February 2022

Abstract
Parents of trans and gender-diverse youth can experience challenges navigating gender-affirming (GA) care such as stigma, transphobia, and lack of support. There is little information available about stressors, worries, and positive feelings of parents as they try to support their youth accessing GA care. This article presents baseline survey data on experiences and stressors of 160 parents/caregivers in the Trans Youth CAN! cohort study, which examined medical, social, and family outcomes in youth age 16 years or younger considering puberty blockers or GA hormones. Data were collected at 10 Canadian gender clinics. Authors report on participating parents’ characteristics, levels of support toward youth, stressors, worries, concerns, and positive feelings related to youth’s gender. Most parent participants were White (85.1 percent), female (85.1 percent), birth or adoptive parents (96.1 percent), and reported strong support for youth’s gender. Participants’ concerns included their youth facing rejection (81.9 percent), generalized transphobia (74.6 percent), or encountering violence (76.4 percent). Parents also reported positive feelings about seeing their youth grow more confident. Most parental worries and stressors were situated outside the family, reflecting the systemic discrimination faced by youth and their families. Social workers could address these by developing systems-focused interventions and by further taking into account intersectional health disparities.