bluuebunny/crossref_metadata_2025_split huggingface dataset:
SALT HRS Capabilities for Time Resolved Pulsation Analysis: A Test with the roAp Star α Circini*
Authors: Holdsworth D. L. , Brunsden E. 
Published: September 2020

Abstract
Spectroscopy is a powerful tool for detecting variability in the rapidly oscillating Ap (roAp) stars. The technique requires short integrations times and high resolution, and so is limited to only a few telescopes and instruments. To test the capabilities of the High Resolution Spectrograph (HRS) at the Southern African Large Telescope (SALT) for the study of pulsations in roAp stars, we collected 2.45 hr of high-resolution data of the well studied roAp star α Cir in a previously unused instrument configuration. We extracted radial velocity measurements using different rare earth elements, and the core of H
α
, via the cross correlation method. We performed the same analysis with a set of α Cir data collected with the High Accuracy Radial velocity Planet Searcher spectrograph to provide a benchmark for our SALT HRS test. We measured significant radial velocity variations in the HRS data and show that our results are in excellent agreement between the two data sets, with similar signal-to-noise ratio detections of the principal pulsation mode. With the HRS data, we report the detection of a second mode, showing the instrument is capable of detecting multiple and low-amplitude signals in a short observing window. We concluded that SALT HRS is well-suited for characterizing pulsations in Ap stars, opening a new science window for the telescope. Although our analysis focused on roAp stars, the fundamental results are applicable to other areas of astrophysics where high temporal and spectral resolution observations are required.
Anomalous

decay and its interference effects on gluon–gluon contribution at the LHC *
Authors: He Hua-Rong , Wan Xia , Wang You-Kai 
Published: September 2020

Abstract
We calculate the spinor helicity amplitudes of anomalous

decay. After embedding these analytic formulas into the MCFM package, we study the interference effects between the anomalous

process and the SM processes, which are indispensable in the Higgs off-shell region. Subsequently, the constraints on the anomalous couplings are estimated using LHC experimental data.
Two-neutron transfer reactions as a tool to study the interplay between shape coexistence and quantum phase transitions *
Authors: García-Ramos J.E. , Arias J.M. , Vitturi A. 
Published: September 2020

Abstract
The atomic mass table presents zones where the structure of the states changes rapidly as a function of the neutron or proton number. Among them, notable examples are the A ≈ 100 Zr region, the Pb region around the neutron midshell (N = 104), and the N ≈ 90 rare-earth region. The observed phenomena can be understood in terms of either shape coexistence or quantum phase transitions. The objective of this study is to find an observable that can distinguish between both shape coexistence and quantum phase transitions. As an observable to be analyzed, we selected the two-neutron transfer intensity between the 0+ states in the parent and daughter nuclei. The framework used for this study is the Interacting Boson Model (IBM), including its version with configuration mixing (IBM-CM). To generate wave functions of isotope chains of interest needed for calculating transfer intensities, previous systematic studies using IBM and IBM-CM were used without changing the parameters. The results of two-neutron transfer intensities are presented for Zr, Hg, and Pt isotopic chains using IBM-CM. Moreover, for Zr, Pt, and Sm isotopic chains, the results are presented using IBM with only a single configuration, i.e., without using configuration mixing. For Zr, the two-neutron transfer intensities between the ground states provide a clear observable, indicating that normal and intruder configurations coexist in the low-lying spectrum and cross at A = 98 → 100. This can help clarify whether shape coexistence induces a given quantum phase transition. For Pt, in which shape coexistence is present and the regular and intruder configurations cross for the ground state, there is almost no impact on the value of the two-neutron transfer intensity. Similar is the situation with Hg, where the ground state always has a regular nature. For the Sm isotope chain, which is one of the quantum phase transition paradigms, the value of the two-neutron transfer intensity is affected strongly.
Description of alpha-clustering of 8Be nucleus states in high-precision theoretical approach
Authors: Rodkin D. M. , Tchuvil’sky Yu. M. 
Published: September 2020

Abstract
Scrupulous theoretical study of 8Be nucleus states, both clustered and non-clustered, is performed over a wide range of excitation energies. The quantities that characterize the degree of the alpha-clustering of these states, i.e., spectroscopic factors, cluster form factors, and alpha-decay widths, are computed in the framework of the developed accurate ab initio approach. Other basic properties of the 8Be spectrum, including the binding and excitation energies and the mean values of the isospin, are calculated simultaneously. In the majority of instances, the results of the computation turn out to be in good agreement with the spectroscopic data. A number of predictions are made, and corresponding verification experiments are proposed. Prospects of the developed approach for nuclear spectroscopy are demonstrated.
Observational constraints on dark matter decaying via gravity portals *
Authors: Sun Xu-Dong , Dai Ben-Zhong 
Published: September 2020

Abstract
Global symmetry can guarantee the stability of dark matter particles (DMps). However, the nonminimal coupling between dark matter (DM) and gravity can break the global symmetry of DMps, which in turn leads to their decay. Under the framework of nonminimal coupling between scalar singlet dark matter (ssDM) and gravity, it is worth exploring the extent to which the symmetry of ssDM is broken. It is suggested that the total number of decay products of ssDM cannot exceed current observational constraints. Along these lines, the data obtained with satellites such as Fermi-LAT and AMS-02 suggest that the scale of ssDM global symmetry breaking can be limited. Because the mass of many promising DM candidates is likely to be in the GeV-TeV range, we determine reasonable parameters for the ssDM lifetime within this range. We find that when the mass of ssDM is around the electroweak scale (246 GeV), the corresponding 3σ lower limit of the lifetime of ssDM is

s. Our analysis of ssDM around the electroweak scale encompasses the most abundant decay channels of all mass ranges so that the analysis of the behavior of ssDM under the influence of gravity is more comprehensive.
Voronoi diagrams in quasi-2D hard sphere systems
Authors: Morley David Ormrod , Wilson Mark 
Published: September 2020

Abstract
Variants of the Voronoi construction, commonly applied to divide space, are analysed for quasi-two-dimensional hard sphere systems. Configurations are constructed from a polydisperse lognormal distribution of sphere radii, mimicking recent experimental investigations. In addition, experimental conditions are replicated where spheres lie on a surface such that their respective centres do not occupy a single plane. Significantly, we demonstrate that using an unweighted (no dependence on sphere size) two-dimensional Voronoi construction (in which the sphere centres are simply projected onto a single plane) is topologically equivalent to taking the lowest horizontal section through a three-dimensional construction in which the division of space is weighted in terms of sphere size. The problem is then generalised by considering the tessellations formed from horizontal sections through the three-dimensional construction at arbitrary cut height above the basal plane. This further suggests a definition of the commonly-applied packing fraction which avoids the counter-intuitive possibility of it becoming greater than unity. Key network and Voronoi cell properties (the fraction of six-membered rings, assortativity and cell height) and are analysed as a function of separation from the basal plane and the limits discussed. Finally, practical conclusions are drawn of direct relevance to on-going experimental investigations.
Lower bound estimate for buckling in axially graded cantilever rods
Authors: Abdalla Hassan Mohamed Abdelalim , Novak Srnec Jelena , Casagrande Daniele 
Published: September 2020

Abstract
Functionally graded beams, bars and rods have been gaining a relevant consideration in engineering practice and research, taking into account variations of the material properties either in the transverse or in the longitudinal direction. Yet existing literature dealing with analytical study of structural instability for an arbitrary material longitudinal variation is still limited. In this paper, a variational approach to the buckling in axially graded cantilevers is developed within Euler-Bernoulli beam theory. Considering the large deflection static behavior and interpreting the first variation of the corresponding Action integral as a weak form of the associated Euler–Lagrange equation, the problem of analytically finding a lower bound estimate for the buckling load is investigated and solved for arbitrary variations of mechanical properties within an imposed condition on the maximal deflection of the free end. In particular, two examples of widely used material gradient forms have been considered and their lower bound buckling forces have been estimated in a closed form, compared with numerical results from literature developed within the linearized version of governing equations and validated using nonlinear finite element forecasts, showing promising results in terms of buckling prediction.
Romosozumab: A first-in-class sclerostin inhibitor for osteoporosis
Authors: Prather Caitlin , Adams Erin , Zentgraf Whitney 
Published: September 2020

Abstract

Purpose
The purpose of this article is to review the pharmacology, efficacy, and safety of the sclerostin inhibitor romosozumab for the treatment of osteoporosis, including data from clinical trials of the drug.

Summary
A review of the literature was performed by searching PubMed and MEDLINE for all relevant articles published between January 2014 and February 2020 using the keywords romosozumab, romosozumab-aqqg, osteoporosis, and fracture. All relevant English-language articles evaluating the pharmacology, efficacy, or safety of romosozumab for the treatment of osteoporosis in humans were included; poster presentations were excluded. Romosozumab has been approved by the Food and Drug Administration and is considered both safe and effective for the treatment of osteoporosis in high-risk postmenopausal females. Phase 2 and phase 3 clinical trials have shown a statistically significant decrease in new vertebral fractures and an increase in bone mineral density with romosozumab use, as compared with both placebo use and use of alternative osteoporosis therapies. The primary safety concern is a potential risk of cardiovascular events; additionally, hypocalcemia must be corrected prior to initiation. Romosozumab is the first anabolic medication that both increases bone formation and decreases bone resorption. Data suggest that romosozumab is more effective than oral bisphosphonates in preventing osteoporotic fractures, though cost and safety concerns must be considered.

Conclusion
Romosozumab is a novel, 12-month treatment option for postmenopausal women at high risk for osteoporotic fracture that both increases bone formation and decreases bone resorption.
GuidingNet: revealing transcriptional cofactor and predicting binding for DNA methyltransferase by network regularization
Authors: Ren Lixin , Gao Caixia , Duren Zhana , Wang Yong 
Published: September 2020

AbstractThe DNA methyltransferases (DNMTs) (DNMT3A, DNMT3B and DNMT3L) are primarily responsible for the establishment of genomic locus-specific DNA methylation patterns, which play an important role in gene regulation and animal development. However, this important protein family’s binding mechanism, i.e. how and where the DNMTs bind to genome, is still missing in most tissues and cell lines. This motivates us to explore DNMTs and TF’s cooperation and develop a network regularized logistic regression model, GuidingNet, to predict DNMTs’ genome-wide binding by integrating gene expression, chromatin accessibility, sequence and protein–protein interaction data. GuidingNet accurately predicted methylation experimental data validated DNMTs’ binding, outperformed single data source based and sparsity regularized methods and performed well in within and across tissue prediction for several DNMTs in human and mouse. Importantly, GuidingNet can reveal transcription cofactors assisting DNMTs for methylation establishment. This provides biological understanding in the DNMTs’ binding specificity in different tissues and demonstrate the advantage of network regularization. In addition to DNMTs, GuidingNet achieves good performance for other chromatin regulators’ binding. GuidingNet is freely available at https://github.com/AMSSwanglab/GuidingNet.
SAIGEgds—an efficient statistical tool for large-scale PheWAS with mixed models
Authors: Zheng Xiuwen , Davis J Wade 
Published: September 2020

Abstract

Summary
Phenome-wide association studies (PheWASs) are known to be a powerful tool in discovery and replication of genetic association studies. To reduce the computational burden of PheWAS in the large cohorts, such as the UK Biobank, the SAIGE method has been proposed to control for case–control imbalance and sample relatedness in a tractable manner. However, SAIGE is still computationally intensive when deployed in analyzing the associations of thousands of ICD10-coded phenotypes with whole-genome imputed genotype data. Here, we present a new high-performance statistical R package (SAIGEgds) for large-scale PheWAS using generalized linear mixed models. The package implements the SAIGE method in optimized C++ codes, taking advantage of sparse genotype dosages and integrating the efficient genomic data structure file format. Benchmarks using the UK Biobank White British genotype data (N ≈ 430 K) with coronary heart disease and simulated cases show that the implementation in SAIGEgds is 5–6 times faster than the SAIGE R package. When used in conjunction with high-performance computing clusters, SAIGEgds provides an efficient analysis pipeline for biobank-scale PheWAS.

Availability and implementation
https://bioconductor.org/packages/SAIGEgds; vignettes included.

Supplementary information
Supplementary data are available at Bioinformatics online.
HiSCF: leveraging higher-order structures for clustering analysis in biological networks
Authors: Hu Lun , Zhang Jun , Pan Xiangyu , Yan Hong , You Zhu-Hong 
Published: September 2020

Abstract

Motivation
Clustering analysis in a biological network is to group biological entities into functional modules, thus providing valuable insight into the understanding of complex biological systems. Existing clustering techniques make use of lower-order connectivity patterns at the level of individual biological entities and their connections, but few of them can take into account of higher-order connectivity patterns at the level of small network motifs.

Results
Here, we present a novel clustering framework, namely HiSCF, to identify functional modules based on the higher-order structure information available in a biological network. Taking advantage of higher-order Markov stochastic process, HiSCF is able to perform the clustering analysis by exploiting a variety of network motifs. When compared with several state-of-the-art clustering models, HiSCF yields the best performance for two practical clustering applications, i.e. protein complex identification and gene co-expression module detection, in terms of accuracy. The promising performance of HiSCF demonstrates that the consideration of higher-order network motifs gains new insight into the analysis of biological networks, such as the identification of overlapping protein complexes and the inference of new signaling pathways, and also reveals the rich higher-order organizational structures presented in biological networks.

Availability and implementation
HiSCF is available at https://github.com/allenv5/HiSCF.

Supplementary information
Supplementary data are available at Bioinformatics online.
SEEDS: data driven inference of structural model errors and unknown inputs for dynamic systems biology
Authors: Newmiwaka Tobias , Engelhardt Benjamin , Wendland Philipp , Kahl Dominik , Fröhlich Holger , Kschischo Maik 
Published: September 2020

Abstract

Summary
Dynamic models formulated as ordinary differential equations can provide information about the mechanistic and causal interactions in biological systems to guide targeted interventions and to design further experiments. Inaccurate knowledge about the structure, functional form and parameters of interactions is a major obstacle to mechanistic modeling. A further challenge is the open nature of biological systems which receive unknown inputs from their environment. The R-package SEEDS implements two recently developed algorithms to infer structural model errors and unknown inputs from output measurements. This information can facilitate efficient model recalibration as well as experimental design in the case of misfits between the initial model and data.

Availability and implementation
For the R-package seeds, see the CRAN server https://cran.r-project.org/package=seeds.
‘She Made You Feel like There’s Hope’: Gaining a Better Understanding of How Children Negotiate Their Relationships with Social Workers from Their Own Accounts
Authors: Gorin Sarah , Baginsky Mary , Moriarty Jo , Manthorpe Jill 
Published: September 2020

Abstract
Recent years have seen a re-emergence of international interest in relationship-based social work. This article uses children’s accounts of their relationships with social workers to build on previous research to promote children’s safety and well-being. Interviews were undertaken with 111 children aged six- to eighteen-years old across ten different local authorities in England, as part of the evaluation of Munro, Turnell and Murphy’s Signs of Safety pilots within the Department for Education’s Children’s Social Care Innovation Programme. The interviews reveal four key findings: that children look for care and reciprocity in their relationships with social workers and this can be achieved through listening and small acts of kindness; that they are adept at recognising aspects of social workers’ verbal and non-verbal communications which indicate to the child whether they are listening and interested in them; that there are times in which children are particularly vulnerable especially if parents are resistant to engagement or children’s trust is broken; and that children actively use their agency to control their communication and engagement. The article concludes by highlighting children’s relational resilience and the importance of ensuring opportunities for children to develop new relationships with social workers when previous relationships have broken down.
O-GlcNAcylation regulates dopamine neuron function, survival and degeneration in Parkinson disease
Authors: Lee Byeong Eun , Kim Hye Yun , Kim Hyun-Jin , Jeong Hyeongsun , Kim Byung-Gyu , Lee Ha-Eun , Lee Jieun , Kim Han Byeol , Lee Seung Eun , Yang Yong Ryoul , Yi Eugene C , Hanover John A , Myung Kyungjae , Suh Pann-Ghill , Kwon Taejoon , Kim Jae-Ick 
Published: September 2020

Abstract
The dopamine system in the midbrain is essential for volitional movement, action selection, and reward-related learning. Despite its versatile roles, it contains only a small set of neurons in the brainstem. These dopamine neurons are especially susceptible to Parkinson’s disease and prematurely degenerate in the course of disease progression, while the discovery of new therapeutic interventions has been disappointingly unsuccessful. Here, we show that O-GlcNAcylation, an essential post-translational modification in various types of cells, is critical for the physiological function and survival of dopamine neurons. Bidirectional modulation of O-GlcNAcylation importantly regulates dopamine neurons at the molecular, synaptic, cellular, and behavioural levels. Remarkably, genetic and pharmacological upregulation of O-GlcNAcylation mitigates neurodegeneration, synaptic impairments, and motor deficits in an animal model of Parkinson’s disease. These findings provide insights into the functional importance of O-GlcNAcylation in the dopamine system, which may be utilized to protect dopamine neurons against Parkinson’s disease pathology.
There’s a time and a place: temporal aspects of place-based stigma
Authors: Butler-Warke Alice 
Published: September 2020

AbstractThis paper provides an overview of current debates and themes in literature relating to place-based stigma, including a reflection on terminology use. Generally, we rely on Loïc Wacquant’s framing of territorial stigma as a feature of advanced marginality. In this paper, drawing on my own research in Toxteth, Liverpool, I offer a critique of the Wacquantian approach, highlighting the limits of the advanced marginality framing of place-based stigma. The paper considers the global reach of placed-based stigma and the temporal aspect of stigma that must be taken into consideration when we consider how stigma is currently applied to communities. A key feature of this paper is the foregrounding of the concepts of ‘core’ and ‘event’ stigma, which have generally been a feature of literature in business and management. I argue that our understanding of how communities become stigmatized can be enhanced by framing place-based stigma in this temporal sense. Understanding how stigma becomes adhered to particular spaces, places and landscapes is necessary if we want to comprehend how this stigma transfers to the communities inhabiting these geographies. This paper suggests that we must look to the past, and to the voices who shape the past, in order to understand the present and to plan for the future.
Mechanism and interpretation of two-for-one response to premature atrial complexes during atrioventricular node re-entry tachycardia
Authors: Gilge Jasen L , Bagga Shiv , Ahmed Asim S , Clark Brad A , Patel Parin J , Prystowsky Eric N , Olson Jeff A , Steinberg Leonard A , Padanilam Benzy J 
Published: September 2020

Abstract

Aims
The response to premature atrial complexes (PACs) during tachycardia has been shown to differentiate atrioventricular nodal re-entrant tachycardia (AVNRT) from focal junctional tachycardia (JT). His refractory PAC (HrPACs) perturbing the next His (resetting with fusion) is diagnostic of AVNRT and such a late PAC fusing with the native beat cannot reset the focal source of JT. Early PAC advancing the immediate His with continuation of tachycardia suggests JT but can also occur in AVNRT due to simultaneous conduction through the AV nodal fast and slow pathways [two-for-one response (TFOR)]. The objective of this study was to evaluate the incidence and mechanism of TFOR after early premature atrial complexes (ePACs) during AVNRT and to differentiate it from the known response to ePACs during JT.

Methods and results
Typical AVNRT cases were diagnosed using standard criteria. We evaluated the responses to scanning PACs delivered during tachycardia in 100 patients undergoing AV node slow pathway modification for AVNRT. The responses to HrPACs and ePACs delivered from coronary sinus os or high right atrium were retrospectively reviewed. In 10 patients, ePACs advanced the immediate His with continuation of tachycardia. In all 10 cases, HrPACs advanced the next His, confirming AVNRT as the mechanism, and indicating a TFOR.

Conclusion
A TFOR can occur in a small number of patients during AVNRT and is therefore not diagnostic of JT. However, HrPACs always perturbed the next His in these cases, confirming the diagnosis of AVNRT and allowing for differentiation from JT.