bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of the injection beam line at the Cooler Synchrotron COSY using Bayesian Optimization
Authors: Awal A. , Hetzel J. , Gebel R. , Kamerdzhiev V. , Pretz J. 
Published: April 2023

Abstract
The complex non-linear processes in multi-dimensional
parameter spaces, that are typical for an accelerator, are a natural
application for machine learning algorithms. This paper reports on
the use of Bayesian optimization for the optimization of the
Injection Beam Line (IBL) of the Cooler Synchrotron storage ring
COSY at the Forschungszentrum Jülich, Germany. Bayesian
optimization is a machine learning method that optimizes a
continuous objective function using limited observations. The IBL is
composed of 15 quadrupoles and 28 steerers. The goal is to increase
the beam intensity inside the storage ring. The results showed the
effectiveness of the Bayesian optimization in achieving
better/faster results compared to manual optimization.
Measurement of the Compton scattering in germanium with a p-type point-contact germanium detector for dark matter detection
Authors: Hu J.W. , Yang L.T. , Yue Q. , Geng X.P. , Li H.B. , Liang Y.F. , Lin S.T. , Liu S.K. , Ma H. , Wang L. , Wong H.T. , Zhang B.T. 
Published: April 2023

Abstract
Low-energy background through Compton scattering from the
ambient γ rays can be contaminated in direct dark matter
search experiments. In this paper, we report comparable measurements
on low-energy spectra via Compton scattering from several
γ-ray sources with a p-type point-contact germanium
detector. The spectra between 500 eV and 18 keV have been measured
and analyzed. Moreover, the features of the electron binding effect,
particularly at the edges of the K- and L-shells in the germanium
atom, were observed with different gamma sources and were consistent
with the models in the Geant4 simulation. An empirical background
model is proposed that provides insights into understanding the
low-energy background in germanium for direct dark matter
experiments.
Evaluation of a method for time-of-flight, wavelength and neutron flight path calibration for neutron scattering instruments by means of a mini-chopper and standard neutron monitors
Authors: Vergara L. , Arai M. , Woracek R. , Olsson M. , Quintanilla A. , Alcock S. , Nilsson J. , Kanaki K. , Kadletz P.M. , Kirstein O. , Hall-Wilton R. , Tsapatsaris N. 
Published: April 2023

Abstract
Accurate conversion of neutron time-of-flight (TOF) to wavelength is of fundamental importance to neutron scattering measurements in order to ensure the accuracy of the instruments and the experimental results. Equally important in these measurements is the determination of uncertainties, and with the appropriate precision. Especially in cases where instruments are highly configurable, the determination of the absolute wavelength after any change must always be performed (e.g. change of detector position). Inspired by the manner with which neutron spectrometers determine the absolute wavelength, we evaluate for the first time, in the author's knowledge, a commonly used method for converting TOF to neutron wavelength by measuring the neutron flight path length from the source of neutrons to a monitor and we proceed to analytically calculate the uncertainty contributions that limit the precision of the conversion. The method was evaluated at the V20 test beamline at the Helmholtz Zentrum Berlin (HZB), emulating the ESS source with a long pulse of 2.86 ms length and 14 Hz repetition rate, by using a mini-chopper operated at 140 Hz and two portable beam monitors (BMs), as well as accompanied data acquisition infrastructure. The mini-chopper created well-defined neutron pulses and the BM was placed at two positions, enabling the average wavelength of each of the pulses created to be determined. The used experimental setup resulted in absolute wavelength determination at the monitor positions with a δλ
mean / λ
mean of ∼1.8% for λ > 4 Å. With the use of a thinner monitor, a δλ
mean / λ
mean of ∼1% can be reached and with a modest increase of the distance between the reference monitor positions a δλ
mean / λ
mean of below 0.5% can be achieved. Further improvements are possible by using smaller chopper disc openings and a higher rotational speed chopper. The method requires only two neutron measurements and doesn't necessitate the use of crystals or complex fitting with sigmoid functions and multiple free variables, and could constitute a suitable addition to imaging, diffraction, reflectometers and small angle neutron scattering instruments, at spallation sources, that do not normally utilise fast choppers.
Spherical winding and helicity
Authors: Xiao Daining , Prior Christopher B , Yeates Anthony R 
Published: April 2023

Abstract
In ideal magnetohydrodynamics, magnetic helicity is a conserved dynamical quantity and a topological invariant closely related to Gauss linking numbers. However, for open magnetic fields with non-zero boundary components, the latter geometrical interpretation is complicated by the fact that helicity varies with non-unique choices of a field’s vector potential or gauge. Evaluated in a particular gauge called the winding gauge, open-field helicity in Cartesian slab domains has been shown to be the average flux-weighted pairwise winding numbers of field lines, a measure constructed solely from field configurations that manifest its topological origin. In this paper, we derive the spherical analogue of the winding gauge and the corresponding winding interpretation of helicity, in which we formally define the concept of spherical winding of curves. Using a series of examples, we demonstrate novel properties of spherical winding and the validity of spherical winding helicity. We further argue for the canonical status of the winding gauge choice among all vector potentials for magnetic helicity by exhibiting equivalences between local coordinate changes and gauge transformations.
Achromatic polymer-dispersed liquid crystal lens with diffractive–refractive hybrid structure
Authors: Liang Binming , An Jing , Su Xin 
Published: April 2023

Abstract
The focal length of liquid crystal Fresnel lens is electrically controllable, but the disadvantage is the chromatic aberration is obvious. In this paper, the electrically controlled zoom characteristics of liquid crystal lens and the basic theory of Fresnel lens achromatic are analyzed, and a diffractive–refractive hybrid lens model made of polymer-dispersed liquid-crystal (PDLC) material is proposed. Fresnel liquid crystal lenses and PDLC hybrid lenses are tested with light at R (700.0 nm), G (546.1 nm) and B (435.8 nm) wavelengths, respectively. The simulation results show that the hybrid lens provides a greater range of adjustment of the focus position. After voltage modulation, the measured light with three different wavelengths have the same focal length, which means that the axial chromatic aberration is eliminated. In addition, with the elimination of axial chromatic aberration, the zoom range of the hybrid lens is doubled by further accurately controlling the electrode, which breaks through the limitation that the traditional liquid crystal lens can only work in monochromatic light spectrum.
Thermal/kinetic study of the formation mechanism of NbC-Fe composite layer on the surface of GCr15 prepared by hot pressure diffusion
Authors: Zhao Nana , Yao Teli , Wang Zihan , Shan Rui , Ren Congcong , Liu Heguang , Li Shujuan , Xu Yunhua , Cui Zhen 
Published: April 2023

Abstract
In this study, an NbC-Fe composite layer is in situ prepared on the surface of GCr15 bearing steel. The formation mechanism of the composite layer was investigated in terms of thermodynamics, dynamics, and crystal structure transformation processes during the in situ reaction. According to computational thermodynamics, the reaction at 1150 °C–1200 °C allows NbC, Fe3C, Cr3C2, Cr7C3, and Cr23C6 phases to spontaneously react and stabilize in the Fe-C-Nb-CR system. The functional relationship between the growth thickness, time, and temperature of the NbC-Fe composite layer was obtained experimentally and via computational dynamics. Particularly, the growth activation energy, Q, of the NbC-Fe composite layer was calculated to be 367.06 kJ mol−1. The combination of computational thermodynamic/kinetic research and experimental observation of crystal transformation data revealed that the formation mechanism of NbC in the NbC-Fe layer on the surface of GCr15 caused the C atoms in the bearing steel diffuse into the Nb plate and occupy the octahedral gap of the Nb unit cell to form NbC. In the formation mechanism of the NbC-Fe composite layer, C and Fe atoms partially migrated from the pearlite and diffused towards the direction of the Nb plate to form the NbC-Fe composite layer.
Phthonosand Misfortune
Authors: Eidinow Esther 
Published: April 2023

AbstractIn ancient Greek society, episodes of good fortune prompted expectations and obligations that fostered social networks of reciprocity. This chapter of the book argues that phthonos was an emotion that expressed a spectrum of negative responses to that system of reciprocity between mortals. Moreover, it suggests that this model can help to explain the phenomenon of divine phthonos, and explores in what ways this is different from its mortal counterpart. Finally, it examines the links between phthonos and occult aggression, using case studies from later periods that offer some first-person insights into these experiences.
Dependence and Vulnerability
Authors: Eidinow Esther 
Published: April 2023

AbstractThis chapter examines the likely position of female dependents in Athenian society in the aftermath of war. It presents the evidence for the status of and support provided for widows, orphans and girl children, and unmarried women, and considers possible sources of livelihood. Some might follow the armies, perhaps involved in food preparation, although it was more likely that many went along as personal attendants, entertainers, and sexual partners; others traded in the markets, took part in various crafts, or worked in the fields at agricultural tasks. Grave epigraphs show other professions were possible. Prostitution was also a possibility—and could be lucrative, but dangerous. Finally, some women sold ritual practices as a way of making a living.
epitope1D: accurate taxonomy-aware B-cell linear epitope prediction
Authors: da Silva Bruna Moreira , Ascher David B , Pires Douglas E V 
Published: April 2023

Abstract
The ability to identify B-cell epitopes is an essential step in vaccine design, immunodiagnostic tests and antibody production. Several computational approaches have been proposed to identify, from an antigen protein or peptide sequence, which residues are more likely to be part of an epitope, but have limited performance on relatively homogeneous data sets and lack interpretability, limiting biological insights that could otherwise be obtained. To address these limitations, we have developed epitope1D, an explainable machine learning method capable of accurately identifying linear B-cell epitopes, leveraging two new descriptors: a graph-based signature representation of protein sequences, based on our well-established Cutoff Scanning Matrix algorithm and Organism Ontology information. Our model achieved Areas Under the ROC curve of up to 0.935 on cross-validation and blind tests, demonstrating robust performance. A comprehensive comparison to alternative methods using distinct benchmark data sets was also employed, with our model outperforming state-of-the-art tools. epitope1D represents not only a significant advance in predictive performance, but also allows biologically meaningful features to be combined and used for model interpretation. epitope1D has been made available as a user-friendly web server interface and application programming interface at https://biosig.lab.uq.edu.au/epitope1d/.
Accurate and interpretable gene expression imputation on scRNA-seq data using IGSimpute
Authors: Xu Ke , Cheong ChinWang , Veldsman Werner P , Lyu Aiping , Cheung William K , Zhang Lu 
Published: April 2023

Abstract
Single-cell ribonucleic acid sequencing (scRNA-seq) enables the quantification of gene expression at the transcriptomic level with single-cell resolution, enhancing our understanding of cellular heterogeneity. However, the excessive missing values present in scRNA-seq data hinder downstream analysis. While numerous imputation methods have been proposed to recover scRNA-seq data, high imputation performance often comes with low or no interpretability. Here, we present IGSimpute, an accurate and interpretable imputation method for recovering missing values in scRNA-seq data with an interpretable instance-wise gene selection layer (GSL). IGSimpute outperforms 12 other state-of-the-art imputation methods on 13 out of 17 datasets from different scRNA-seq technologies with the lowest mean squared error as the chosen benchmark metric. We demonstrate that IGSimpute can give unbiased estimates of the missing values compared to other methods, regardless of whether the average gene expression values are small or large. Clustering results of imputed profiles show that IGSimpute offers statistically significant improvement over other imputation methods. By taking the heart-and-aorta and the limb muscle tissues as examples, we show that IGSimpute can also denoise gene expression profiles by removing outlier entries with unexpectedly high expression values via the instance-wise GSL. We also show that genes selected by the instance-wise GSL could indicate the age of B cells from bladder fat tissue of the Tabula Muris Senis atlas. IGSimpute can impute one million cells using 64 min, and thus applicable to large datasets.
Sars-escape network for escape prediction of SARS-COV-2
Authors: Singh Bist Prem , Tayara Hilal , To Chong Kil 
Published: April 2023

Abstract

Motivation
Viruses have coevolved with their hosts for over millions of years and learned to escape the host’s immune system. Although not all genetic changes in viruses are deleterious, some significant mutations lead to the escape of neutralizing antibodies and weaken the immune system, which increases infectivity and transmissibility, thereby impeding the development of antiviral drugs or vaccines. Accurate and reliable identification of viral escape mutational sequences could be a good indicator for therapeutic design. We developed a computational model that recognizes significant mutational sequences based on escape feature identification using natural language processing along with prior knowledge of experimentally validated escape mutants.

Results
Our machine learning-based computational approach can recognize the significant spike protein sequences of severe acute respiratory syndrome coronavirus 2 using sequence data alone. This modelling approach can be applied to other viruses, such as influenza, monkeypox and HIV using knowledge of escape mutants and relevant protein sequence datasets.

Availability
Complete source code and pre-trained models for escape prediction of severe acute respiratory syndrome coronavirus 2 protein sequences are available on Github at https://github.com/PremSinghBist/Sars-CoV-2-Escape-Model.git. The dataset is deposited to Zenodo at: doi: 10.5281/zenodo.7142638. The Python scripts are easy to run and customize as needed.

Contact
premsing212@jbnu.ac.kr
Non-human primate models for understanding the impact of the microbiome on pregnancy and the female reproductive tract
Authors: Hugon Anna Marie , Golos Thaddeus G 
Published: April 2023

Abstract
The microbiome has been shown, or implicated to be involved, in multiple facets of human health and disease, including not only gastrointestinal health but also metabolism, immunity, and neurology. Although the predominant focus of microbiome research has been on the gut, other microbial communities such as the vaginal or cervical microbiome are likely involved in physiological homeostasis. Emerging studies also aim to understand the role of different microbial niches, such as the endometrial or placental microbial communities, on the physiology and pathophysiology of reproduction, including their impact on reproductive success and the etiology of adverse pregnancy outcomes (APOs). The study of the microbiome during pregnancy, specifically how changes in maternal microbial communities can lead to dysfunction and disease, can advance the understanding of reproductive health and the etiology of APOs. In this review, we will discuss the current state of non-human primate (NHP) reproductive microbiome research, highlight the progress with NHP models of reproduction, and the diagnostic potential of microbial alterations in a clinical setting to promote pregnancy health. NHP reproductive biology studies have the potential to expand the knowledge and understanding of female reproductive tract microbial communities and host–microbe or microbe–microbe interactions associated with reproductive health through sequencing and analysis. Furthermore, in this review, we aim to demonstrate that macaques are uniquely suited as high-fidelity models of human female reproductive pathology.
SIAH1/CTR9 axis promotes the epithelial–mesenchymal transition of hepatocellular carcinoma
Authors: Liu Zhiyi , Luo Pengchao , Cao Kuan , Hu Qinghe , Hu Bin , Cui Licheng , Wang Xiaotian , Shi Hengliang , Zhang Bin , Wang Renhao 
Published: April 2023

Abstract
SIAH1 has been reported to participate in several human cancers, including hepatocellular carcinoma (HCC). However, the effect of SIAH1 on the epithelial–mesenchymal transition (EMT) has not been reported in HCC cells. Here, we discovered the inhibitory effect of SIAH1 on HCC cell migration and invasion, which was related with regulating EMT. Molecularly, a yeast two-hybrid experiment indicated that Cln Three Requiring 9 (CTR9) was a potential interacting protein of SIAH1, which was further verified by co-immunoprecipitation assays. Furthermore, SIAH1 inhibited the EMT of HCC cells through negatively regulating CTR9. Importantly, CTR9 was ubiquitinated and degraded by SIAH1 via the proteasome pathway in HCC cells. Additionally, it was showed that SIAH1 mainly mediated the K48-linked polyubiquitination on CTR9. Finally, the protein level of CTR9 was found to be inversely correlated with SIAH1 in human HCC tissues. Summed up all together, these findings reveal that SIAH1/CTR9 axis promotes the EMT of HCC cells and is a promising therapeutic target for HCC therapy.
The most hated tree in America: negative difference, the White imaginary, and the Bradford pear
Authors: Neville-Shepard Ryan , Kelly Casey Ryan 
Published: April 2023

AbstractAgainst claims that we now live in a post-racial era, this article argues that panic over so-called “invasive species” illustrates how negative conceptions of difference are built into the White imaginary. We argue that the calls to exterminate the infamous Bradford pear tree across the US function as a kind of nanoracism, or what Achilles Mbembe defines as the organization of everyday affairs according to us–them logics that further justify overt racist practices. Performing a close reading of the discourse about the tree, we show how xenophobia and anti-Blackness lurk in a debate about non-human biota, specifically by normalizing inferential racist language that attacks difference, expressing fears of racial impurity, and calling for exterminating the Other.
(Hash)tagging intersection(ality): Black and Palestinian experiences on Twitter
Authors: Edwards Emily Lynell , Stephens David F 
Published: April 2023

AbstractIn this article, we examine how Twitter users discuss intersections of the Black American and Palestinian experience in 2021 through the lens of intersectionality. We explore two questions; how is intersectionality discussed and performed by Twitter users in relation to the Palestinian and Black experience against the backdrop of this particular crisis in Gaza? And how do users engage with the language of intersectionality to either reify, contradict, or complicate the intersection of the Palestinian and Black experiences on the platform? We find that intersectionality is mediated by elite users via branded communication, as well as invoked to highlight or deny the intersections of the Black and Palestinian experience by the most peripheral users on the platform.
Estimation of glomerular filtration rate in cardiorenal patients: a step forward
Authors: Quiroga Borja , Díez Javier 
Published: April 2023

ABSTRACT
The progressive reduction in estimated glomerular filtration rate (eGFR) resulting in chronic kidney disease (CKD) is associated with increased risk of cardiovascular disease (CVD) (i.e., cardiorenal disease). Cardiorenal disease is associated with poor outcomes, mainly due to increased cardiovascular (CV) complications and CV death. Data from general population–based studies and studies of cohorts with CKD and/or CVD show that compared with creatinine-based eGFR, cystatin C–based eGFR and creatinine plus cystatin C–based eGFR detect higher risks of adverse CV outcomes and add predictive discrimination to current CVD risk scores. On the other hand, growing clinical evidence supports kidney and CV protective effects of sodium–glucose cotransporter-2 (SGLT2) inhibitors in cardiorenal patients. However, recent data suggest that some detrimental effects of SGLT2 inhibitors on skeletal muscle mass may lead to overestimation of creatinine-based eGFR and subsequent misinterpretation of associated CV risk in patients treated with these agents. Within this framework, we suggest the advisability of using cystatin C and/or creatinine plus cystatin C–based eGFR for routine clinical practice in cardiorenal patients to more accurately stratify CV risk and evaluate the kidney and CV protective effects of SGLT2 inhibitors. In this regard, we make a call to action to investigate the protective effects of these pharmacological agents using cystatin C–based eGFR.
Regional contributions to impaired myocardial mechanical function in heart failure with preserved ejection fraction
Authors: Biering-Sørensen Tor , Cikes Maja , Lassen Mats C H , Claggett Brian , Minamisawa Masatoshi , Santos Angela B S , Pieske-Kraigher Elisabeth , Shah Amil M , Zile Michael R , McMurray John J V , Solomon Scott D , Cheng Susan 
Published: April 2023

Abstract

Aims
Hypertensive heart disease (HHD) is recognized as a key clinical precursor to heart failure with preserved ejection fraction (HFPEF). However, pathophysiological transition from HHD to HFPEF is not well understood. We sought determine whether regional differences in impaired myocardial function may underlie the greater mechanical dysfunction seen in HFPEF compared to HHD.

Methods and results
We used standardized echocardiography to assess regional myocardial deformation in a cohort of n = 327 adults with preserved left ventricular (LV) ejection fraction (≥45%), including: n = 129 with HFPEF, n = 158 with HHD and no heart failure, and n = 40 normotensive controls. From detailed measurements of LV systolic strain performed in multiple views, we derived and then compared regional measures of basal, mid-ventricular, and apical longitudinal strains. In models adjusting for clinical covariates, basal and mid-ventricular LV myocardial deformation was more impaired in HHD than in controls (P ≤ 0.003), whereas apical deformation was more impaired in HFPEF than in HHD (P = 0.005). In multivariable-adjusted analyses, only apical strain remained independently associated with HFPEF vs. HHD status [odds ratio 1.18 (1.02–1.37), P = 0.030 per 1% decrease in apical strain]. Compared to other regional strains, apical longitudinal strain optimally differentiated HFPEF from HHD (area under the receiver operating curve: apical longitudinal strain = 0.67; mid-ventricular longitudinal strain = 0.59; basal longitudinal strain = 0.60).

Conclusion
We found that while apical mechanical function is preserved in HHD, it was impaired in HFPEF and may contribute to the transition from an asymptomatic heart disease to a symptomatic heart disease.