bluuebunny/crossref_metadata_2025_split huggingface dataset:
An investigation on the factors affecting machine learning classifications in gamma-ray astronomy
Authors: Luo Shengda , Leung Alex P , Hui C Y , Li K L 
Published: January 2020

ABSTRACTWe have investigated a number of factors that can have significant impacts on the classification performance of gamma-ray sources detected by Fermi Large Area Telescope (LAT) with machine learning techniques. We show that a framework of automatic feature selection can construct a simple model with a small set of features that yields better performance over previous results. Secondly, because of the small sample size of the training/test sets of certain classes in gamma-ray, nested re-sampling and cross-validations are suggested for quantifying the statistical fluctuations of the quoted accuracy. We have also constructed a test set by cross-matching the identified active galactic nuclei (AGNs) and the pulsars (PSRs) in the Fermi-LAT 8-yr point source catalogue (4FGL) with those unidentified sources in the previous 3rd Fermi-LAT Source Catalog (3FGL). Using this cross-matched set, we show that some features used for building classification model with the identified source can suffer from the problem of covariate shift, which can be a result of various observational effects. This can possibly hamper the actual performance when one applies such model in classifying unidentified sources. Using our framework, both AGN/PSR and young pulsar (YNG)/millisecond pulsar (MSP) classifiers are automatically updated with the new features and the enlarged training samples in 4FGL catalogue incorporated. Using a two-layer model with these updated classifiers, we have selected 20 promising MSP candidates with confidence scores $\gt 98{{\ \rm per\ cent}}$ from the unidentified sources in 4FGL catalogue that can provide inputs for a multiwavelength identification campaign.
MAGMO: polarimetry of 1720-MHz OH masers towards southern star-forming regions
Authors: Ogbodo C S , Green J A , Dawson J R , Breen S L , Mao S A , McClure-Griffiths N M , Robishaw T , Harvey-Smith L 
Published: January 2020

ABSTRACT
From targeted observations of ground-state hydroxyl (OH) masers towards 702 Methanol Multibeam survey 6.7-GHz methanol masers, in the Galactic longitude range from 186° through the Galactic Centre to 20°, made as part of the ‘MAGMO’ (Mapping the Galactic Magnetic field through OH masers) project, we present the physical and polarization properties of the 1720-MHz OH maser transition, including the identification of Zeeman pairs. We present 10 new and 23 previously catalogued 1720-MHz OH maser sources detected towards star-forming regions (SFRs). In addition, we also detected 16 1720-MHz OH masers associated with supernova remnants and two sites of diffuse OH emission. Towards the 33 star formation masers, we identify 44 Zeeman pairs, implying magnetic field strengths ranging from −11.4 to +13.2 mG, and a median magnetic field strength of |BLOS| ∼ 6 mG. With limited statistics, we present the in situ magnetic field orientation of the masers and the Galactic magnetic field distribution revealed by the 1720-MHz transition. We also examine the association statistics of 1720-MHz OH SFR masers with other ground-state OH masers, excited-state OH masers, class I and class II methanol masers, and water masers, and compare maser positions with mid-infrared images of the parent SFRs. Of the 33 1720-MHz star formation masers, 10 are offset from their central exciting sources, and appear to be associated with outflow activity.
The contribution of nearby supernova remnants on the cosmic ray flux at Earth
Authors: A L-Zetoun A , Achterberg A 
Published: January 2020

ABSTRACT
We consider anisotropic diffusion of Galactic cosmic rays in the Galactic magnetic field, using the Jansson–Farrar model for the field. In this paper, we investigate the influence of source position on the cosmic ray flux at the Earth in two ways: (1) by considering the contribution from cosmic ray sources located in different intervals in Galactocentric radius, and (2) by considering the contribution from a number of specific and individual close-by supernova remnants. Our calculation is performed by using a fully three-dimensional stochastic method. This method is based on the numerical solution of a set of stochastic differential equations, equivalent to Itô formulation, that describes the propagation of the Galactic cosmic rays.
Mirror principle and the red-giant bump: the battle of entropy in low-mass stars
Authors: Hekker S , Angelou G C , Elsworth Y , Basu S 
Published: January 2020

ABSTRACT
The evolution of low-mass stars into red giants is still poorly understood. During this evolution the core of the star contracts and, simultaneously, the envelope expands – a process known as the ‘mirror’. Additionally, there is a short phase where the trend for increasing luminosity is reversed. This is known as the red giant branch bump. We explore the underlying physical reasons for these two phenomena by considering the specific entropy distribution in the star and its temporal changes. We find that between the luminosity maximum and luminosity minimum of the bump there is no mirror present and the star is fully contracting. The contraction is halted and the star regains its mirror when the hydrogen-burning shell reaches the mean molecular weight discontinuity. This marks the luminosity minimum of the bump.
Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH
Authors: Gao Ang , Vasilyev Nikita , Kaushik Abhishek , Duan Wenqian , Serganov Alexander 
Published: January 2020

AbstractAll enzymes face a challenge of discriminating cognate substrates from similar cellular compounds. Finding a correct substrate is especially difficult for the Escherichia coli Nudix hydrolase RppH, which triggers 5′-end-dependent RNA degradation by removing orthophosphate from the 5′-diphosphorylated transcripts. Here we show that RppH binds and slowly hydrolyzes NTPs, NDPs and (p)ppGpp, which each resemble the 5′-end of RNA. A series of X-ray crystal structures of RppH-nucleotide complexes, trapped in conformations either compatible or incompatible with hydrolysis, explain the low reaction rates of mononucleotides and suggest two distinct mechanisms for their hydrolysis. While RppH adopts the same catalytic arrangement with 5′-diphosphorylated nucleotides as with RNA, the enzyme hydrolyzes 5′-triphosphorylated nucleotides by extending the active site with an additional Mg2+ cation, which coordinates another reactive nucleophile. Although the average intracellular pH minimizes the hydrolysis of nucleotides by slowing their reaction with RppH, they nevertheless compete with RNA for binding and differentially inhibit the reactivity of RppH with triphosphorylated and diphosphorylated RNAs. Thus, E. coli RppH integrates various signals, such as competing non-cognate substrates and a stimulatory protein factor DapF, to achieve the differential degradation of transcripts involved in cellular processes important for the adaptation of bacteria to different growth conditions.
A crucial RNA-binding lysine residue in the Nab3 RRM domain undergoes SET1 and SET3-responsive methylation
Authors: Lee Kwan Yin , Chopra Anand , Burke Giovanni L , Chen Ziyan , Greenblatt Jack F , Biggar Kyle K , Meneghini Marc D 
Published: January 2020

AbstractThe Nrd1–Nab3–Sen1 (NNS) complex integrates molecular cues to direct termination of noncoding transcription in budding yeast. NNS is positively regulated by histone methylation as well as through Nrd1 binding to the initiating form of RNA PolII. These cues collaborate with Nrd1 and Nab3 binding to target RNA sequences in nascent transcripts through their RRM RNA recognition motifs. In this study, we identify nine lysine residues distributed amongst Nrd1, Nab3 and Sen1 that are methylated, suggesting novel molecular inputs for NNS regulation. We identify mono-methylation of one these residues (Nab3-K363me1) as being partly dependent on the H3K4 methyltransferase, Set1, a known regulator of NNS function. Moreover, the accumulation of Nab3-K363me1 is essentially abolished in strains lacking SET3, a SET domain containing protein that is positively regulated by H3K4 methylation. Nab3-K363 resides within its RRM and physically contacts target RNA. Mutation of Nab3-K363 to arginine (Nab3-K363R) decreases RNA binding of the Nab3 RRM in vitro and causes transcription termination defects and slow growth. These findings identify SET3 as a potential contextual regulator of Nab3 function through its role in methylation of Nab3-K363. Consistent with this hypothesis, we report that SET3 exhibits genetic activation of NAB3 that is observed in a sensitized context.
The molecular aetiology of tRNA synthetase depletion: induction of a GCN4 amino acid starvation response despite homeostatic maintenance of charged tRNA levels
Authors: McFarland Matthew R , Keller Corina D , Childers Brandon M , Adeniyi Stephen A , Corrigall Holly , Raguin Adélaïde , Romano M Carmen , Stansfield Ian 
Published: January 2020

AbstractDuring protein synthesis, charged tRNAs deliver amino acids to translating ribosomes, and are then re-charged by tRNA synthetases (aaRS). In humans, mutant aaRS cause a diversity of neurological disorders, but their molecular aetiologies are incompletely characterised. To understand system responses to aaRS depletion, the yeast glutamine aaRS gene (GLN4) was transcriptionally regulated using doxycycline by tet-off control. Depletion of Gln4p inhibited growth, and induced a GCN4 amino acid starvation response, indicative of uncharged tRNA accumulation and Gcn2 kinase activation. Using a global model of translation that included aaRS recharging, Gln4p depletion was simulated, confirming slowed translation. Modelling also revealed that Gln4p depletion causes negative feedback that matches translational demand for Gln-tRNAGln to aaRS recharging capacity. This maintains normal charged tRNAGln levels despite Gln4p depletion, confirmed experimentally using tRNA Northern blotting. Model analysis resolves the paradox that Gln4p depletion triggers a GCN4 response, despite maintenance of tRNAGln charging levels, revealing that normally, the aaRS population can sequester free, uncharged tRNAs during aminoacylation. Gln4p depletion reduces this sequestration capacity, allowing uncharged tRNAGln to interact with Gcn2 kinase. The study sheds new light on mutant aaRS disease aetiologies, and explains how aaRS sequestration of uncharged tRNAs can prevent GCN4 activation under non-starvation conditions.
Higher mortality risk among kidney transplant recipients than among estimated glomerular filtration rate–matched patients with CKD—preliminary results
Authors: Cheddani Lynda , Liabeuf Sophie , Essig Marie , Snanoudj Renaud , Jacquelinet Christian , Kerleau Clarisse , Metzger Marie , Balkau Beverley , Drüeke Tilman B , Hourmant Maryvonne , Massy Ziad A ,   Nantes Kidney and Pancreas Transplantation Group and the Chronic Kidney Disease-Renal Epidemiology and Information Network (CKD-REIN) Study Group, Hourmant Maryvonne , Blancho Gilles , Diego Cantarovich , Jacques Dantal , Garandeau Claire , Giral Magali , Meurette Aurélie , Chapelet Agnès , Deltombe Clément , Gourraud-Vercel Caroline , Figueres Lucile , Ville Simon , Jacquemont Lola , Branchereau Julien , Karam Georges , Kandell Christine , Moreau Anne , Renaudin Karine , Cesbron Anne , Delbos Florent , Walencik Alexandre , Devis Anne , Ayav Carole , Besson-Dubourg Vanessa , Briançon Serge , Cannet Dorothée , Combe Christian , Fouque Denis , Frimat Luc , Herpe Yves-Edouard , Laville Maurice , Pascal Christophe , Robinson Bruce M , Stengel Bénédicte , Lange Céline , Legrand Karine , Speyer Elodie 
Published: January 2020

AbstractBackgroundAlthough kidney transplantation prolongs survival relative to dialysis, it is associated with a higher death rate than in the general population. The objective of the present study was to assess and compare the risk of mortality and frequency of non-lethal cardiovascular (CV) events in kidney transplant recipients (KTRs) beyond 1 year after successful transplantation versus patients with chronic kidney disease (CKD) using propensity score–matched analysis of estimated glomerular filtration rate (eGFR) and other parameters.MethodsAfter propensity score matching, we studied 340 KTRs from the French Données Informatisées et Validées en Transplantation cohort and 605 non-transplant patients with CKD (CKDps) from the French Chronic Kidney Disease–Renal Epidemiology and Information Network cohort. The mean ± standard deviation eGFR was 42 ± 13 and 41 ± 12 mL/min/  1.73 m2, respectively (P = 0.649). Descriptive data were completed by a survival analysis with Cox regression models.ResultsAfter a median follow-up period of 2.8 years (KTRs 2.0 years, CKDp 2.9 years), 71 deaths were recorded (31 and 40 in the KTR and CKD groups, respectively). Univariate analysis showed that KTRs had a significantly greater risk of mortality than CKDps. In multivariable analysis, KTRs were found to have a 2.7-fold greater risk of mortality [hazard ratio 2.7 (95% confidence interval 1.6–4.7); P = 0.005]. There was no between-group difference concerning the risk of CV events (P = 0.448). CV death rates in KTRs (29.0%) approximated those of CKDps (22.5%), whereas death rates due to infections were higher in KTRs (19.4% versus 10.0%).ConclusionBeyond 1 year after transplantation, KTRs, who possibly had a longer CKD history, had a significantly greater mortality risk than eGFR-matched CKDps. The excess risk was not associated with CV events.
Internal Auditory Canal Variability: Anatomic Variation Affects Cisternal Facial Nerve Visualization
Authors: Cohen Michael A , Abou-Al-Shaar Hussam , Gozal Yair M , Karsy Michael , Alzhrani Gmaan , Shelton Clough , Couldwell William T 
Published: January 2020

Abstract

BACKGROUND
The internal auditory canal (IAC) is an important landmark during surgery for lesions of the cerebellopontine angle. There is significant variability in the position and orientation of the IAC radiographically, and the authors have noted differences in surgical exposure depending on the individual anatomy of the IAC.

OBJECTIVE
To test the hypothesis that IAC position and orientation affects the surgical exposure of the IAC and facial nerve, especially when performing the translabyrinthine approach.

METHODS
The authors retrospectively reviewed magnetic resonance imaging studies of 50 randomly selected patients with pathologically confirmed vestibular schwannomas. Measurements, including the anterior (APD) and posterior (PPD) petrous distances, the anterior (APA) and posterior (PPA) petro-auditory angles, and the internal auditory angle (IAA), were obtained to quantify the position and orientation of the IAC within the petrous temporal bone.

RESULTS
The results quantitatively demonstrate tremendous variability of the position and orientation of the IAC in the petrous temporal bone. The measurement ranges were APD 10.2 to 26.1 mm, PPD 15.1 to 37.2 mm, APA 104 to 157°, PPA 30 to 96°, and IAA –5 to 40°.

CONCLUSION
IAC variability can have a substantial effect on the surgical exposure of the IAC and facial and vestibulocochlear nerves. Specifically, a horizontally oriented IAC with a small IAA may have significant impact on visualization of the facial nerve within its cisternal segment with the translabyrinthine approach. The retrosigmoid approach is less affected with IAC variability in position and angle.
Art as an Asset: Evidence from Keynes the Collector
Authors: Chambers David , Dimson Elroy , Spaenjers Christophe 
Published: January 2020

Abstract
The risk-return characteristics of art as an asset have been previously studied through aggregate price indexes. By contrast, we examine the long-run buy-and-hold performance of an actual portfolio, namely, the collection of John Maynard Keynes. We find that its performance has substantially exceeded existing estimates of art market returns. Our analysis of the collection identifies general attributes of art portfolios crucial in explaining why investor returns can substantially diverge from market returns: transaction-specific risk, buyer heterogeneity, return skewness, and portfolio concentration. Furthermore, our findings highlight the limitations of art price indexes as a guide to asset allocation or performance benchmarking. (JEL B26, C43, G11, G12, G14, Z11) Received: September 7, 2018: Editorial decision: November 24, 2019 by Editor: Nikolai Roussanov
Methods for analysing lineage tracing datasets
Authors: Kostiou Vasiliki , Zhang Huairen , Hall Michael WJ , Jones Philip H , Hall Benjamin A 
Published: January 2020

AbstractA single population of stem cells maintains many epithelial tissues. Transgenic mouse cell tracking has frequently been used to study the growth dynamics of competing clones in these tissues. A mathematical model (the ‘single progenitor model’) has been argued to reproduce the observed stem cell dynamics accurately. This requires three parameters to describe the growth dynamics observed in transgenic mouse cell tracking- a division rate, a stratification rate, and the probability of dividing symmetrically. Deriving these parameters is time intensive and complex process. We compare the alternative strategies for analysing this source of experimental data, identifying an approximate Bayesian computation-based approach as the best in terms of efficiency and appropriate error estimation. We support our findings by explicitly modelling biological variation and consider the impact of different sampling regimes. All tested solutions are made available to allow new datasets to be analysed following our workflows. Based on our findings we make recommendations for future experimental design.
Shift of maternal gut microbiome of Tibetan antelope (Pantholops hodgsonii) during the perinatal period
Authors: Shi Yue , Miao Ziyan , Su Jianping , Wasser Samuel K. 
Published: January 2020

AbstractThe maternal gut microbiome can influence and be affected by the substantial physiological changes taking place during the perinatal period. However, little information is known about the changes in the maternal gut microbiome during this period. Tibetan antelope (Pantholops hodgsonii) provide a unique system to address this issue because their summer migration cycle is synchronized with the perinatal period. We used 16S rRNA gene sequencing to generate gut microbiome profiles using fecal samples collected from female migratory Tibetan antelope. We then correlated microbiome diversity with fecal hormone metabolite concentrations of glucocorticoids (GCs) and triiodothyronine (T3) extracted from the same fecal samples. The maternal gut microbiome of Tibetan antelope was dominated by Firmicutes and Bacteroidetes. There was a clear separation in gut microbial composition by female reproductive states based on both hierarchical clustering and PCoA analyses. The shift in the maternal gut microbiome likely reflects the metabolic and immune system dynamics during the perinatal period. Overall, the microbiome diversity was higher in the late pregnancy compared to the postpartum period. The negative association between T3 and microbiome diversity may be moderated by the shift of reproductive states since the correlations disappeared when considering each reproductive state separately. Integrating the microbiome dimension, migration pattern and reproduction may have direct conservation implications as by establishing a baseline of the physiological changes during the migration/perinatal period, we can have a better understanding of the impacts of increasing human activities on the Tibetan Plateau on the reproductive health of Tibetan antelope.
Complex multi-environment gene interactions linked to the interplay between polysubstance dependence and suicidal behaviors
Authors: Polimanti Renato , Levey Daniel F. , Pathak Gita A. , Wendt Frank R. , Nunez Yaira Z. , Ursano Robert J. , Kessler Ronald C. , Kranzler Henry R. , Stein Murray B. , Gelernter Joel 
Published: January 2020

AbstractBackground and AimsSubstance dependence diagnoses (SDs) are important risk factors for suicidal behaviors. We investigated the associations of multiple SDs with different suicidal behaviors and tested how genetic background moderates these associations.DesignMultivariate logistic regression to investigate the associations of SDs with suicidal behaviors; structured linear mixed model to study multivariate gene– environment interactions.SettingThe Yale-Penn cohort was recruited to investigate the genetics of SDs. The Army STARRS (Study to Assess Risk and Resilience in Servicemembers) cohort was recruited to evaluate mental health risk and resilience for suicidal behaviors among Army personnel.ParticipantsYale-Penn participants (N=15,557) were assessed via the Semi-Structured Assessment for Drug Dependence and Alcoholism. Army STARRS participants (N=11,236) were evaluated using the self-administered Composite International Diagnostic Interview Screening Scales.MeasurementLifetime self-reported suicidal behaviors (ideation, SI; planning; attempt, SA); Lifetime DSM-IV diagnoses and criteria for dependence on alcohol, cannabis, cocaine (CoD), opioid (OD), and nicotine (ND) (Yale-Penn); substance use disorder (SUD) (Army STARRS).FindingsIn Yale-Penn, lifetime polysubstance dependence was strongly associated with lifetime suicidal behaviors: individuals with five SDs showed increased odds ranging from OR=6.77 (95%CI=5.74-7.99) for SI to OR=3.61 (95%CI=2.7-4.86) for SA. In Army STARRS, SUD was associated with increased odds ranging from OR=2.88 (95%CI=2.6-3.19) for SI to OR=3.92 (95%CI=3.19-4.81) for SA. In Yale-Penn, we identified multivariate gene–environment interactions (Bayes factors, BF > 0) of SI with respect to a gene cluster on chromosome 16 (LCAT, p=1.82×10−7; TSNAXIP1, p=2.13×10−7; CENPT, p=2.32×10−7; PARD6A, p=5.57×10−7) for OD (BF=12.2), CoD (BF=12.1), ND (BF=9.2), and polysubstance dependence (BF=2.1).ConclusionsComorbidity of multiple SDs is a significant suicide risk factor and heritability of suicidal behaviors is partially moderated by multivariate gene interactions.