bluuebunny/crossref_metadata_2025_split huggingface dataset:
FCCCSR_Glu: a semi-supervised learning model based on FCCCSR algorithm for prediction of glutarylation sites
Authors: Ning Qiao , Qi Zedong , Wang Yue , Deng Ansheng , Chen Chen 
Published: September 2022

Abstract
Glutarylation is a post-translational modification which plays an irreplaceable role in various functions of the cell. Therefore, it is very important to accurately identify the glutarylation substrates and its corresponding glutarylation sites. In recent years, many computational methods of glutarylation sites have emerged one after another, but there are still many limitations, among which noisy data and the class imbalance problem caused by the uncertainty of non-glutarylation sites are great challenges. In this study, we propose a new semi-supervised learning algorithm, named FCCCSR, to identify reliable non-glutarylation lysine sites from unlabeled samples as negative samples. FCCCSR first finds core objects from positive samples according to reverse nearest neighbor information, and then clusters core objects based on natural neighbor structure. Finally, reliable negative samples are selected according to clustering result. With FCCCSR algorithm, we propose a new method named FCCCSR_Glu for glutarylation sites identification. In this study, multi-view features are extracted and fused to describe peptides, including amino acid composition, BLOSUM62, amino acid factors and composition of k-spaced amino acid pairs. Then, reliable negative samples selected by FCCCSR and positive samples are combined to establish models and XGBoost optimized by differential evolution algorithm is used as the classifier. On the independent testing dataset, FCCCSR_Glu achieves 85.18%, 98.36%, 94.31% and 0.8651 in sensitivity, specificity, accuracy and Matthew’s Correlation Coefficient, respectively, which is superior to state-of-the-art methods in predicting glutarylation sites. Therefore, FCCCSR_Glu can be a useful tool for glutarylation sites prediction and FCCCSR algorithm can effectively select reliable negative samples from unlabeled samples. The data and code are available on https://github.com/xbbxhbc/FCCCSR_Glu.git
SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells
Authors: Moody Jonathan , Kouno Tsukasa , Chang Jen-Chien , Ando Yoshinari , Carninci Piero , Shin Jay W , Hon Chung-Chau 
Published: September 2022

Abstract

Motivation
Cell type-specific activities of cis-regulatory elements (CRE) are central to understanding gene regulation and disease predisposition. Single-cell RNA 5′end sequencing (sc-end5-seq) captures the transcription start sites (TSS) which can be used as a proxy to measure the activity of transcribed CREs (tCREs). However, a substantial fraction of TSS identified from sc-end5-seq data may not be genuine due to various artifacts, hindering the use of sc-end5-seq for de novo discovery of tCREs.

Results
We developed SCAFE—Single-Cell Analysis of Five-prime Ends—a software suite that processes sc-end5-seq data to de novo identify TSS clusters based on multiple logistic regression. It annotates tCREs based on the identified TSS clusters and generates a tCRE-by-cell count matrix for downstream analyses. The software suite consists of a set of flexible tools that could either be run independently or as pre-configured workflows.

Availability and implementation
SCAFE is implemented in Perl and R. The source code and documentation are freely available for download under the MIT License from https://github.com/chung-lab/SCAFE. Docker images are available from https://hub.docker.com/r/cchon/scafe. The submitted software version and test data are archived at https://doi.org/10.5281/zenodo.7023163 and https://doi.org/10.5281/zenodo.7024060, respectively.

Supplementary information
Supplementary data are available at Bioinformatics online.
Additive models for symmetric positive-definite matrices and Lie groups
Authors: Lin Z , Müller H -G , Park B U 
Published: September 2022

Summary
We propose and investigate an additive regression model for symmetric positive-definite matrix-valued responses and multiple scalar predictors. The model exploits the Abelian group structure inherited from either of the log-Cholesky and log-Euclidean frameworks for symmetric positive-definite matrices and naturally extends to general Abelian Lie groups. The proposed additive model is shown to connect to an additive model on a tangent space. This connection not only entails an efficient algorithm to estimate the component functions, but also allows one to generalize the proposed additive model to general Riemannian manifolds. Optimal asymptotic convergence rates and normality of the estimated component functions are established, and numerical studies show that the proposed model enjoys good numerical performance, and is not subject to the curse of dimensionality when there are multiple predictors. The practical merits of the proposed model are demonstrated through an analysis of brain diffusion tensor imaging data.
BCSCdb: a database of biomarkers of cancer stem cells
Authors: Firdous Shazia , Ghosh Abhirupa , Saha Sudipto 
Published: September 2022

AbstractCancer stem cells (CSCs) are a small heterogeneous population present within the tumor cells exhibiting self-renewal properties. CSCs have been demonstrated to elicit an important role in cancer recurrence, metastasis and drug resistance. CSCs are distinguished from cancer cell populations based on their molecular profiling or expression of distinct CSC biomarker(s). Recently, a huge amount of omics data have been generated for the characterization of CSCs, which enables distinguishing CSCs in different cancers. Here, we report biomarkers of the Cancer Stem Cells database (BCSCdb), a repository of information about CSC biomarkers. BCSCdb comprises CSC biomarkers collected from PubMed literature where these are identified using high-throughput and low-throughput methods. Each biomarker is provided with two different scores: the first is a confidence score to give confidence to reported CSC biomarkers based on the experimental method of detection in CSCs. The second is the global score to identify the global CSC biomarkers across 10 different types of cancer. This database contains three tables containing information about experimentally validated CSC biomarkers or genes, therapeutic target genes of CSCs and CSC biomarkers interactions. It contains information on three types of markers: high-throughput marker (HTM-8307), high-throughput marker validated by the low-throughput method (283) and low-throughput marker (LTM-525). A total of 171 low-throughput biomarkers were identified in primary tissue referred to as clinical biomarkers. Moreover, it contains 445 target genes for CSC therapeutics, 10 biomarkers targeted by clinical trial drugs in CSCs and 5 different types of interaction data for CSC biomarkers. BCSCdb is an online resource for CSC biomarkers, which will be immensely helpful in the cancer research community and is freely available.Database URL: http://dibresources.jcbose.ac.in/ssaha4/bcscdb
Francesco Ballerini’s opera licence for Vienna
Authors: Paczkowski Szymon 
Published: September 2022

Abstract
Around 1710, an imperial singer and favourite, the soprano castrato Francesco Ballerini, petitioned Holy Roman Emperor Joseph I for an exclusive licence to establish a public Italian opera house in Vienna that could also double as a court stage. Ballerini’s petition was successful, but his own financial resources were not sufficient to bring the project to completion. In April 1711, the death of Joseph I complicated matters even further. However, Ballerini did not give up on his ambitious undertaking, and in 1726 he invoked his privilege to announce a business plan involving the construction of a new Italian opera and comedy theatre. This announcement was made in a printed pamphlet, hitherto unknown to music historians, which offers new information about how the Italian model of theatre management being was adapted north of the Alps in the early 18th century. This article presents the newly discovered source along with a reconstruction of Ballerini’s efforts to establish Italian opera in Vienna.
Developing an Observing Air–Sea Interactions Strategy (OASIS) for the global ocean
Authors: Cronin M F , Swart S , Marandino C A , Anderson C , Browne P , Chen S , Joubert W R , Schuster U , Venkatesan R , Addey C I , Alves O , Ardhuin F , Battle S , Bourassa M A , Chen Z , Chory M , Clayson C , de Souza R B , du Plessis M , Edmondson M , Edson J B , Gille S T , Hermes J , Hormann V , Josey S A , Kurz M , Lee T , Maicu F , Moustahfid E H , Nicholson S-A , Nyadjro E S , Palter J , Patterson R G , Penny S G , Pezzi L P , Pinardi N , Reeves Eyre J E J , Rome N , Subramanian A C , Stienbarger C , Steinhoff T , Sutton A J , Tomita H , Wills S M , Wilson C , Yu L 
Published: September 2022

AbstractThe Observing Air–Sea Interactions Strategy (OASIS) is a new United Nations Decade of Ocean Science for Sustainable Development programme working to develop a practical, integrated approach for observing air–sea interactions globally for improved Earth system (including ecosystem) forecasts, CO2 uptake assessments called for by the Paris Agreement, and invaluable surface ocean information for decision makers. Our “Theory of Change” relies upon leveraged multi-disciplinary activities, partnerships, and capacity strengthening. Recommendations from &gt;40 OceanObs’19 community papers and a series of workshops have been consolidated into three interlinked Grand Ideas for creating #1: a globally distributed network of mobile air–sea observing platforms built around an expanded array of long-term time-series stations; #2: a satellite network, with high spatial and temporal resolution, optimized for measuring air–sea fluxes; and #3: improved representation of air–sea coupling in a hierarchy of Earth system models. OASIS activities are organized across five Theme Teams: (1) Observing Network Design & Model Improvement; (2) Partnership & Capacity Strengthening; (3) UN Decade OASIS Actions; (4) Best Practices & Interoperability Experiments; and (5) Findable–Accessible–Interoperable–Reusable (FAIR) models, data, and OASIS products. Stakeholders, including researchers, are actively recruited to participate in Theme Teams to help promote a predicted, safe, clean, healthy, resilient, and productive ocean.
Variable-order fractional dynamic behavior of viscoelastic damping material
Authors: Li Zhanlong , Dong Zhifei , Zhang Zheng , Han Binhui , Sun Bao , Wang Yao , Liu Fuxi 
Published: September 2022

Abstract
Viscoelastic damping material has been widely used in engineering machinery to absorb vibration and noise. Dynamic behavior of the viscoelastic damping material is mainly affected by temperature and frequency. Classical dynamic behavior equations of the viscoelastic damping material have complex structures with multiple and ambiguous parameters. So a novel variable-order fractional constitutive model (VOFC) is established based on the variable-order fractional operator. Then the viscoelastic dynamic equations are derived by Laplace transform of the VOFC model. The dynamic thermomechanical analysis tests by the three-point bending mode are carried out at variable temperatures and frequencies, and the frequency spectrum of the dynamic behavior, i.e. the loss modulus, storage modulus and loss factor are obtained. Against the test data, the VOFC model is compared with classical models such as the integer-order Maxwell model, constant fractional-order Kelvin-Voigt model, constant fractional-order Maxwell model and constant fractional-order standard linear solid model. The results show that the VOFC model can describe dynamic behavior of the viscoelastic damping material at different temperatures and frequencies more accurately. And the VOFC model has simpler structure and only two parameters with clearly physical meaning. Finally, a calculation software is designed and developed, which simplifies the process of predicting viscoelastic dynamic behavior in a wide frequency range.
Hubble Space Telescope Captures UGC 12591: bulge/disc properties, star formation and ‘missing baryons’ census in a very massive and fast-spinning hybrid galaxy
Authors: Ray Shankar , Bagchi Joydeep , Dhiwar Suraj , Pandge M B , Mirakhor Mohammad , Walker Stephen A , Mukherjee Dipanjan 
Published: September 2022

ABSTRACT
We present Hubble Space Telescope (HST) observations of the nearby, massive, highly rotating hybrid galaxy UGC 12591, along with observations in the UV to FIRbands. HST data in V, I, and H bands is used to disentangle the structural components. Surface photometry shows a dominance of the bulge over the disc with an H-band B/D ratio of $69{{\,\rm per\,cent}}$. The spectral energy distribution (SED) fitting reveals an extremely low global star formation rate (SFR) of $\rm \sim 0.1\!-\!0.2\, M_\odot \, yr^{-1}$, exceptionally low for the galaxy’s huge stellar mass of $\rm 1.6\times 10^{11}M_\odot$, implying a strong quenching of its SFR with a star formation efficiency of 3–5 per cent. For at least the past $\rm 10^{8}$ yr, the galaxy has remained in a quiescent state as a sterile, ‘red and dead’ galaxy. UGC 12591 hosts a supermassive black hole (SMBH) of $\rm 6.18\times 10^{8} \, M_\odot$, which is possibly quiescent at present, i.e. we neither see large ($\rm \gt 1 kpc$) radio jets nor the SMBH contributing significantly to the mid-IR SED, ruling out strong radiative feedback of AGN. We obtained a detailed census of all observable baryons with a total mass of $\rm 6.46\times 10^{11} \, M_\odot$ within the virial radius, amounting to a baryonic deficiency of ${\sim }85{{\,\rm per\,cent}}$ relative to the cosmological mean. Only a small fraction of these baryons reside in a warm/hot circumgalactic X-ray halo, while the majority are still unobservable. We discussed various astrophysical scenarios to explain its unusual properties. Our work is a major step forward in understanding the assembly history of such extremely massive, isolated galaxies.
Radar analysis algorithm for determining meteor head echo parameter probability distributions
Authors: Kastinen Daniel , Kero Johan 
Published: September 2022

ABSTRACT
We present an automated radar data analysis algorithm developed to calculate probability distributions of meteor- and meteoroid parameters for head echoes detected with the Middle and Upper atmosphere (MU) radar in Shigaraki, Japan. The algorithm utilizes direct Monte Carlo simulations of uncertainties, with Bayesian Markov-chain Monte Carlo estimation of meteor model parameters and N-body propagation of distributions to perform orbit determination. The implementation has been validated using raw data simulations and a comparison with previous analysis methods. The concepts are applicable on a wide range of possible head echo measurements with other radar systems. The generated probability distributions provide quantitative reliability, which enables improved statistical studies and investigating the origins of detected meteoroids. The methodology section is highly detailed in order for the methods to be reproducible and provide a solid reference foundation for future studies. One such study is presented in a companion paper called ‘High-altitude meteors detected by the interferometric MU radar’.
How narrow is the M87* ring – II. A new geometric model
Authors: Lockhart Will , Gralla Samuel E 
Published: September 2022

ABSTRACTThe 2017 Event Horizon Telescope (EHT) observations of M87* detected a ring-shaped feature ∼40 μas in diameter, consistent with the event horizon scale of a black hole of the expected mass. The thickness of this ring, however, proved difficult to measure, despite being an important parameter for constraining the observational appearance. In the first paper of this series, we asked whether the width of the ring was sensitive to the choice of likelihood function used to compare observed closure phases and closure amplitudes to model predictions. In this paper, we investigate whether the ring width is robust to changes in the model itself. We construct a more realistic geometric model with two new features: an adjustable radial falloff in brightness, and a secondary ‘photon ring’ component in addition to the primary annulus. This thin, secondary ring is predicted by gravitational lensing for any black hole with an optically thin accretion flow. Analysing the data using the new model, we find that the primary annulus remains narrow (fractional width ≤ 0.25) even with the added model freedom. This provides further evidence in favour of a narrow ring for the true sky appearance of M87*, a surprising feature that, if confirmed, would demand theoretical explanation. Comparing the Bayesian evidence for models with and without a secondary ring, we find no evidence for the presence of a lensed photon ring in the 2017 observations. However, the techniques we introduce may prove useful for future observations with a larger and more sensitive array.
XyloFUNS: Xylocaine to freeze during unpleasant nasopharyngeal swabs in children—a randomized controlled trial
Authors: Gagnon François , Gravel Jocelyn , Duranceau Camille , Vallieres Emilie , Bhatt Maala , Harman Stuart , Trottier Evelyne D 
Published: September 2022

Abstract

Objectives
To evaluate the efficacy of intranasal vaporized lidocaine in reducing pain for children undergoing a nasopharyngeal (NP) swab in the Emergency Department (ED).

Study Design
A randomized blinded clinical trial was conducted in a paediatric ED. Both participants and the researcher evaluating the primary outcome were blinded. Children aged 6 to 17 years old requiring a NP swab were eligible. Participants were randomly allocated to receive intranasal lidocaine or a sham treatment prior to their NP swab. The primary outcome measure was pain during the swab as assessed by the visual analog scale. Secondary outcome measures were pain using the verbal numeric rating scale, fear using the children fear scale, and adverse effects of the intervention.

Results
Eighty-eight participants were enrolled—45 in the lidocaine group and 43 controls. The mean visual analog scale scores for pain were 46 mm in the lidocaine group and 53 mm in the control group (mean difference 7 mm; 95% CI: −5 to 19 mm). No serious adverse events were observed.

Conclusions
Intranasal lidocaine administered prior to NP swabs in the ED failed to show an improvement in pain scores for school-aged children and youth.
Can Risk Aversion Survive the Long Run?
Authors: Wilkinson Hayden 
Published: September 2022

AbstractCan it be rational to be risk-averse? It seems plausible that the answer is yes—that normative decision theory should accommodate risk aversion. But there is a seemingly compelling class of arguments against our most promising methods of doing so. These long-run arguments point out that, in practice, each decision an agent makes is just one in a very long sequence of such decisions. Given this form of dynamic choice situation and the (Strong) Law of Large Numbers, they conclude that those theories which accommodate risk aversion end up delivering the same verdicts as risk-neutral theories in nearly all practical cases. If so, why not just accept a simpler, risk-neutral theory? The resulting practical verdicts seem to be much the same. In this paper, I show that these arguments do not in fact condemn those risk-aversion-accommodating theories. Risk aversion can indeed survive in the long run.
Chiral symmetry breaking and the quark bilinear condensate in large-N QCD
Authors: Sato Ryosuke 
Published: September 2022

Abstract
We discuss spontaneous chiral symmetry breaking and the quark bilinear condensate in large-Nc quantum chromodynamics (QCD). It is known that the existence of the η′ meson is implied in large-Nc QCD, as pointed out by Witten[27] and Veneziano[28]. First, we show that the existence of η′ and the Ward–Takahashi identities implies the existence of Nambu–Goldstone bosons from chiral symmetry breaking SU(Nf)L × SU(Nf)R → SU(Nf)V. Second, we show that a QCD inequality implies a non-zero lower bound on the quark bilinear condensate.
Daily-Living Freezing of Gait as Quantified Using Wearables in People With Parkinson Disease: Comparison With Self-Report and Provocation Tests
Authors: Denk Diana , Herman Talia , Zoetewei Demi , Ginis Pieter , Brozgol Marina , Cornejo Thumm Pablo , Decaluwe Eva , Ganz Natalie , Palmerini Luca , Giladi Nir , Nieuwboer Alice , Hausdorff Jeffrey M 
Published: September 2022

Abstract

Objective
Freezing of gait (FOG) is an episodic, debilitating phenomenon that is common among people with Parkinson disease. Multiple approaches have been used to quantify FOG, but the relationships among them have not been well studied. In this cross-sectional study, we evaluated the associations among FOG measured during unsupervised daily-living monitoring, structured in-home FOG-provoking tests, and self-report.

Methods
Twenty-eight people with Parkinson disease and FOG were assessed using self-report questionnaires, percentage of time spent frozen (%TF) during supervised FOG-provoking tasks in the home while off and on dopaminergic medication, and %TF evaluated using wearable sensors during 1 week of unsupervised daily-living monitoring. Correlations between those 3 assessment approaches were analyzed to quantify associations. Further, based on the %TF difference between in-home off-medication testing and in-home on-medication testing, the participants were divided into those responding to Parkinson disease medication (responders) and those not responding to Parkinson disease medication (nonresponders) in order to evaluate the differences in the other FOG measures.

Results
The %TF during unsupervised daily living was mild to moderately correlated with the %TF during a subset of the tasks of the in-home off-medication testing but not the on-medication testing or self-report. Responders and nonresponders differed in the %TF during the personal “hot spot” task of the provoking protocol while off medication (but not while on medication) but not in the total scores of the self-report questionnaires or the measures of FOG evaluated during unsupervised daily living.

Conclusion
The %TF during daily living was moderately related to FOG during certain in-home FOG-provoking tests in the off-medication state. However, this measure of FOG was not associated with self-report or FOG provoked in the on-medication state. These findings suggest that to fully capture FOG severity, it is best to assess FOG using a combination of all 3 approaches.

Impact
These findings suggest that several complementary approaches are needed to provide a complete assessment of FOG severity.