bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a fourfold dielectric-filled reentrant cavity as a beam position monitor (BPM) in a proton therapy facility
Authors: Srinivasan S. , Brandenburg S. , Schippers J.M. , Duperrex P.A. 
Published: September 2022

Abstract
At the Paul Scherrer Institute (PSI), the superconducting cyclotron “COMET” delivers a 250 MeV proton beam for radiation therapy in pulses of 1ns at the cyclotron-RF frequency of 72.85 MHz. Accurate measurement of the beam position at proton beam currents of 0.1–10 nA in the beam transport line downstream of the degrader is of crucial importance for the treatment safety and quality, beam alignment and feedback systems. This is essential for efficient operation and beam delivery. These measurements are usually performed with intercepting monitors such as ionization chambers (ICs). In this paper, we present a novel non-intercepting position sensitive cavity resonator. The resonant monitor, tuned to the second harmonic of the cyclotron's RF, is based on the detection of the transverse magnetic dipole mode of the EM field generated by the beam. This mode is only excited for off-center beam positions and is measured with the help of four floating cavities within a common grounded cylinder. This paper discusses the BPM fundamental characteristics, design optimization and the underlying parametric investigations involving the contribution of the different modes and crosstalk. We estimate the expected signals from the prototype BPM for position offsets from simulations and compare them with test-bench measurements and beam measurements with the prototype and the improvised BPM design. We conclude by summarizing the achieved position sensitivity, precision, and measurement bandwidth.
Systematic uncertainties in integrated luminosity measurement at CEPC
Authors: Smiljanic I. , Bozovic Jelisavcic I. , Kacarevic G. , Vukasinovic N. , Vidakovic I. , Rekovic V. 
Published: September 2022

Abstract
The very forward region is one of the most challenging
regions to instrument at a future e
+
e
- collider. At CEPC,
machine-detector interface includes, among others, a calorimeter
dedicated for precision measurement of the integrated luminosity at
a per mill level or better. Here we review a feasibility of such
precision, from the point of view of systematic effects arising from
luminometer mechanical precision and positioning, beam-related
requirements and physics background from two-photon processes. The
impact of the beam energy spread and its uncertainty on the
integrated luminosity precision is also discussed, as well as the
achievable beam energy spread precision with the post-CDR CEPC
beams.
Y-systems for generalised Gibbs ensembles in integrable quantum field theory
Authors: Castro-Alvaredo Olalla A 
Published: September 2022

Abstract
The thermodynamic Bethe ansatz approach to the study of integrable quantum field theories was introduced in the early 90s. Since then it has been known that the thermodynamic Bethe ansatz equations can be recast in the form of Y-systems. These Y-systems have a number of interesting properties, notably in the high-temperature limit their solutions are constants from which the central charge of the ultraviolet fixed point can be obtained and they are typically periodic functions, with period proportional to the dimension of the perturbing field. In this letter we discuss the derivation of Y-systems when the standard thermodynamic Bethe ansatz equations are replaced by generalised versions, describing generalised Gibbs ensembles. We shown that for many integrable quantum field theories, there is a large class of distinct generalised Gibbs ensembles which share the same Y-system.
The Turn to Confession Bargaining in German Criminal Procedure: Causes and Comparisons with American Plea Bargaining
Authors: Langbein John H 
Published: September 2022

Abstract
In recent decades German criminal procedure has developed a practice of confession bargaining, in which defense counsel negotiates with the trial judge for the defendant to confess the charged offense in exchange for a milder sentence than would result if the defendant were to contest the charge. The German practice resembles American plea bargaining in many respects. This Article probes the similarities and the differences between the two systems of negotiated criminal justice. The Article discusses the origins of the German practice, its tensions with historic principles of the procedure system, and the troubled efforts of the courts and the legislature to justify and to regulate the practice.
Genome-wide characterization of twoAubrietataxa:Aubrieta canescenssubsp.canescensandAu. macrostyla(Brassicaceae)
Authors: Kaya Yasin , Aydın Zübeyde Uğurlu , Cai Xu , Wang Xiaowu , Dönmez Ali A 
Published: September 2022

AbstractAubrieta canescens complex is divided into two subspecies, Au. canescens subsp. canescens, Au. canescens subsp. cilicica and a distinct species, Au. macrostyla, based on molecular phylogeny. We generated a draft assembly of Au. canescens subsp. canescens and Au. macrostyla using paired-end shotgun sequencing. This is the first attempt at genome characterization for the genus. In the presented study, ~165 and ~157 Mbp of the genomes of Au. canescens subsp. canescens and Au. macrostyla were assembled, respectively, and a total of 32 425 and 31 372 gene models were predicted in the genomes of the target taxa, respectively. We corroborated the phylogenomic affinity of taxa with some core Brassicaceae species (Clades A and B) including Arabis alpina. The orthology-based tree suggested that Aubrieta species differentiated from A. alpina 1.3–2.0 mya (million years ago). The genome-wide syntenic comparison of two Aubrieta taxa revealed that Au. canescens subsp. canescens (46 %) and Au. macrostyla (45 %) have an almost identical syntenic gene pair ratio. These novel genome assemblies are the first steps towards the chromosome-level assembly of Au. canescens and understanding the genome diversity within the genus.
Comparison of metabolism and biological properties among positional isomers of quercetin glucuronide in LPS- and RANKL-challenged RAW264.7 cells
Authors: Nishikawa Miyu , Kada Yuriko , Kimata Mirai , Sakaki Toshiyuki , Ikushiro Shinichi 
Published: September 2022

ABSTRACT
The major quercetin metabolite, quercetin-3-glucuronide, exerts various biological activities, including anti-inflammatory effects. This study aimed to evaluate the metabolic profiles and biological properties of the positional isomers of quercetin monoglucuronides (Q3G, Q7G, Q3’G, and Q4’G) in activated macrophages. In addition to quercetin aglycone, Q7G was more cytotoxic than the other quercetin monoglucuronides (QGs), which corresponded to its lower stability under neutral pH conditions. Q3G was most effective in inhibiting both LPS-dependent induction of IL-6 and RANKL-dependent activation of tartrate-resistant acid phosphatase; however, Q3’G and Q4’G may also help exert biological activities without potential cytotoxicity. The deconjugation efficacy to generate quercetin aglycone differed among QGs, with the highest efficacy in Q3G. These results suggest that the chemical or biological properties and metabolic profiles may depend on the stability of QGs to generate quercetin aglycone using β-glucuronidase.
Rice OsHAK5 is a major potassium transporter that functions in potassium uptake with high specificity but contributes less to cesium uptake
Authors: Uchiyama Minato , Fudaki Rika , Kobayashi Takuya , Adachi Yoshiko , Ukai Yuko , Yoshihara Toshihiro , Shimada Hiroaki 
Published: September 2022

ABSTRACT
Cesium (Cs) in the environment is primarily absorbed by a potassium (K) transporter. OsHAK5 is a KT/HAK/KUP family K-transporter showing a high affinity for K. We created cultured rice cells whose OsHAK5 was knocked down by RNAi (named KD). In the medium containing 1.0 m m and less K, the growth of KD was significantly suppressed, suggesting that OsHAK5 greatly contributed to K absorption under limited K conditions. Although Cs suppressed the growth of KD and WT, stronger inhibition was observed on KD. Both KD and WT accumulated similar amounts of Cs when they were cultured in a medium containing Cs, whereas lower amounts of K were detected in KD. These results suggest that OsHAK5 was less involved in the absorption of Cs, although it was essential to K absorption under limited K conditions. In contrast, this means that another transporter may contribute to cesium uptake in rice.
Integrating multi-omics summary data using a Mendelian randomization framework
Authors: Jin Chong , Lee Brian , Shen Li , Long Qi ,   for the Alzheimer’s Disease Neuroimaging Initiative,   for the Alzheimer’s Disease Metabolomics Consortium
Published: September 2022

Abstract
Mendelian randomization is a versatile tool to identify the possible causal relationship between an omics biomarker and disease outcome using genetic variants as instrumental variables. A key theme is the prioritization of genes whose omics readouts can be used as predictors of the disease outcome through analyzing GWAS and QTL summary data. However, there is a dearth of study of the best practice in probing the effects of multiple -omics biomarkers annotated to the same gene of interest. To bridge this gap, we propose powerful combination tests that integrate multiple correlated $P$-values without assuming the dependence structure between the exposures. Our extensive simulation experiments demonstrate the superiority of our proposed approach compared with existing methods that are adapted to the setting of our interest. The top hits of the analyses of multi-omics Alzheimer’s disease datasets include genes ABCA7 and ATP1B1.
Self-supervised contrastive learning for integrative single cell RNA-seq data analysis
Authors: Han Wenkai , Cheng Yuqi , Chen Jiayang , Zhong Huawen , Hu Zhihang , Chen Siyuan , Zong Licheng , Hong Liang , Chan Ting-Fung , King Irwin , Gao Xin , Li Yu 
Published: September 2022

Abstract
We present a novel self-supervised Contrastive LEArning framework for single-cell ribonucleic acid (RNA)-sequencing (CLEAR) data representation and the downstream analysis. Compared with current methods, CLEAR overcomes the heterogeneity of the experimental data with a specifically designed representation learning task and thus can handle batch effects and dropout events simultaneously. It achieves superior performance on a broad range of fundamental tasks, including clustering, visualization, dropout correction, batch effect removal, and pseudo-time inference. The proposed method successfully identifies and illustrates inflammatory-related mechanisms in a COVID-19 disease study with 43 695 single cells from peripheral blood mononuclear cells.
MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification
Authors: Tian Simon Zhongyuan , Li Guoliang , Ning Duo , Jing Kai , Xu Yewen , Yang Yang , Fullwood Melissa J , Yin Pengfei , Huang Guangyu , Plewczynski Dariusz , Zhai Jixian , Dai Ziwei , Chen Wei , Zheng Meizhen 
Published: September 2022

Abstract
The emerging ligation-free three-dimensional (3D) genome mapping technologies can identify multiplex chromatin interactions with single-molecule precision. These technologies not only offer new insight into high-dimensional chromatin organization and gene regulation, but also introduce new challenges in data visualization and analysis. To overcome these challenges, we developed MCIBox, a toolkit for multi-way chromatin interaction (MCI) analysis, including a visualization tool and a platform for identifying micro-domains with clustered single-molecule chromatin complexes. MCIBox is based on various clustering algorithms integrated with dimensionality reduction methods that can display multiplex chromatin interactions at single-molecule level, allowing users to explore chromatin extrusion patterns and super-enhancers regulation modes in transcription, and to identify single-molecule chromatin complexes that are clustered into micro-domains. Furthermore, MCIBox incorporates a two-dimensional kernel density estimation algorithm to identify micro-domains boundaries automatically. These micro-domains were stratified with distinctive signatures of transcription activity and contained different cell-cycle-associated genes. Taken together, MCIBox represents an invaluable tool for the study of multiple chromatin interactions and inaugurates a previously unappreciated view of 3D genome structure.
Implementing the Social Care Workforce Race Equality Standard in England: Early Observations
Authors: Manthorpe Jill , Samsi Kritika 
Published: September 2022

AbstractThe implementation in England of a Social Care Workforce Race Equality Standard (SCWRES), initially confined to social work, started with a first set of eighteen volunteer local authorities (LAs) in 2021. This article discusses a rapid evaluation of the SCWRES during its first year. We used Normalization Process Theory (NPT) to better understand the implementation process of this initiative. Thirty-one interviews were undertaken in 2021. Transcripts were analysed using the constant comparative approach and emerging themes were then mapped onto the NPT framework and its four main constructs. Using these we found some lack of clarity over the aims and data demands of the SCWRES (coherence), but generally substantial personal and employer investment in the intervention (cognitive participation); implementation was assisted by personal support to the LAs from senior managers at national level (collective action); and there was general constructive reflection and positive feedback about the SCWRES (reflexive monitoring). Barriers to implementation of new initiatives might be expected during a global pandemic. However, support for the SCWRES was generally high and participants considered they had learned much in its first six months despite pandemic pressures. This article highlights aspects of implementation to be addressed in any further SCWRES rollout.
Neural signatures of default mode network in major depression disorder after electroconvulsive therapy
Authors: Li Yuanyuan , Yu Xiaohui , Ma Yingzi , Su Jing , Li Yue , Zhu Shunli , Bai Tongjian , Wei Qiang , Becker Benjamin , Ding Zhiyong , Wang Kai , Tian Yanghua , Wang Jiaojian 
Published: September 2022

AbstractFunctional abnormalities of default mode network (DMN) have been well documented in major depressive disorder (MDD). However, the association of DMN functional reorganization with antidepressant treatment and gene expression is unclear. Moreover, whether the functional interactions of DMN could predict treatment efficacy is also unknown. Here, we investigated the link of treatment response with functional alterations of DMN and gene expression with a comparably large sample including 46 individuals with MDD before and after electroconvulsive therapy (ECT) and 46 age- and sex-matched healthy controls. Static and dynamic functional connectivity (dFC) analyses showed increased intrinsic/static but decreased dynamic functional couplings of inter- and intra-subsystems and between nodes of DMN. The changes of static functional connections of DMN were spatially correlated with brain gene expression profiles. Moreover, static and dFC of the DMN before treatment as features could predict depressive symptom improvement following ECT. Taken together, these results shed light on the underlying neural and genetic basis of antidepressant effect of ECT and the intrinsic functional connectivity of DMN have the potential to serve as prognostic biomarkers to guide accurate personalized treatment.
Development and Analytical Validation of a 6-Plex Reverse Transcription Droplet Digital PCR Assay for the Absolute Quantification of Prostate Cancer Biomarkers in Circulating Tumor Cells of Patients with Metastatic Castration-Resistant Prostate Cancer
Authors: Zavridou Martha , Smilkou Stavroula , Tserpeli Victoria , Sfika Aggeliki , Bournakis Evangelos , Strati Areti , Lianidou Evi 
Published: September 2022

Abstract

Background
Gene expression in circulating tumor cells (CTCs) can be used as a predictive liquid biopsy test in metastatic castration-resistant prostate cancer (mCRPC). We developed a novel 6-plex reverse transcription droplet digital PCR (RT-ddPCR) assay for the absolute quantification of 4 prostate cancer biomarkers, a reference gene, and a synthetic DNA external control (DNA-EC) in CTCs isolated from mCRPC patients.

Methods
A novel 6-plex RT-ddPCR assay was developed for the simultaneous absolute quantification of AR-FL, AR-V7, PSA, and PSMA, HPRT (used as a reference gene), and a synthetic DNA-EC that was included for quality control. The assay was optimized and analytically validated using DNA synthetic standards for each transcript as positive controls. Epithelial cellular adhesion molecule (EpCAM)-positive CTC fractions isolated from 90 mCRPC patients and 11 healthy male donors were analyzed, and results were directly compared with reverse transcription quantitative PCR (RT-qPCR) for all markers in all samples.

Results
Linear dynamic range, limit of detection, limit of quantification, intra- and interassay precision, and analytical specificity were determined for each marker. Application of the assay in EpCAM-positive CTC showed positivity for AR-FL (71/90; 78.9%), AR-V7 (28/90; 31.1%), PSA (41/90; 45.6%), PSMA (38/90; 42.2%), and HPRT (90/90; 100%); DNA-EC concentration was constant across all samples. Direct comparison with RT-qPCR for the same markers in the same samples revealed RT-ddPCR to have superior diagnostic sensitivity.

Conclusions
Our 6-plex RT-ddPCR assay was highly sensitive, specific, and reproducible, and enabled simultaneous and absolute quantification of 5 gene transcripts in minute amounts of CTC-derived cDNA. Application of this assay in clinical samples gave diagnostic sensitivity and specificity comparable to, or better than, RT-qPCR.
Threshold Homomorphic Encryption From Provably Secure NTRU
Authors: Xu Kexin , Hong Meng Tan Benjamin , Wang Li-Ping , Mi Mi Aung Khin , Wang Huaxiong 
Published: September 2022

Abstract
Homomorphic Encryption (HE) supports computation on encrypted data without the need to decrypt, enabling secure outsourcing of computing to an untrusted cloud. Motivated by application scenarios where private information is offered by different data owners, Multi-Key Homomorphic Encryption (MKHE) and Threshold Homomorphic Encryption (ThHE) were proposed. Unlike MKHE, ThHE schemes do not require expensive ciphertext extension procedures and are therefore as efficient as their underlying single-key HE schemes. In this work, we propose a novel NTRU-type ThHE scheme which caters to the computation scenarios with pre-defined participants. In addition to inheriting the simplicity of NTRU scheme, our construction has no expensive relinearization and correspondingly no costly evaluation keys. Controlling noise to make it increase linearly and then using a wide key distribution, our scheme is immune to the subfield lattice attacks and its security follows from the hardness of the standard R-LWE problem. Finally, based on the {0,1}-linear secret sharing and noise flooding techniques, we design a single round distributed threshold decryption protocol, where the decryption is able to be completed even when only given a subset (say $t$-out-of-$k$) of partial decryptions. To the best of our knowledge, our construction is the first NTRU-type ThHE scheme.
Sinus plication technique for neoaorta dilation and regurgitation in patients with repaired congenital heart diseases
Authors: Kisamori Eiri , Kotani Yasuhiro , Suzuki Hiroyuki , Kasahara Shingo 
Published: September 2022

Abstract
We report 3 cases in sinus plication technique utilized to repair aortic or neoaortic root dilation and valve regurgitation after congenital heart disease operation.
Nitrogen to phosphorus ratio shapes the bacterial communities involved in cellulose decomposition and copper contamination alters their stoichiometric demands
Authors: Wang Ziming , Cébron Aurélie , Baillard Vincent , Danger Michael 
Published: September 2022

AbstractAll living organisms theoretically have an optimal stoichiometric nitrogen: phosphorus (N: P) ratio, below and beyond which their growth is affected, but data remain scarce for microbial decomposers. Here, we evaluated optimal N: P ratios of microbial communities involved in cellulose decomposition and assessed their stability when exposed to copper Cu(II). We hypothesized that (1) cellulose decomposition is maximized for an optimal N: P ratio; (2) copper exposure reduces cellulose decomposition and (3) increases microbial optimal N: P ratio; and (4) N: P ratio and copper modify the structure of microbial decomposer communities. We measured cellulose disc decomposition by a natural inoculum in microcosms exposed to a gradient of N: P ratios at three copper concentrations (0, 1 and 15 µM). Bacteria were most probably the main decomposers. Without copper, cellulose decomposition was maximized at an N: P molar ratio of 4.7. Contrary to expectations, at high copper concentration, the optimal N: P ratio (2.8) and the range of N: P ratios allowing decomposition were significantly reduced and accompanied by a reduction of bacterial diversity. Copper contamination led to the development of tolerant taxa probably less efficient in decomposing cellulose. Our results shed new light on the understanding of multiple stressor effects on microbial decomposition in an increasingly stoichiometrically imbalanced world.
A chromosome-level assembly of the widely used Rockefeller strain of Aedes aegypti, the yellow fever mosquito
Authors: Fisher Cera R , Wilson Michael , Scott Jeffrey G 
Published: September 2022

Abstract
Aedes aegypti is the vector of important human diseases, and genomic resources are crucial in facilitating the study of A. aegypti and its ecosystem interactions. Several laboratory-acclimated strains of this mosquito have been established, but the most used strain in toxicology studies is “Rockefeller,” which was originally collected and established in Cuba 130 years ago. A full-length genome assembly of another reference strain, “Liverpool,” was published in 2018 and is the reference genome for the species (AaegL5). However, genetic studies with the Rockefeller strain are complicated by the availability of only the Liverpool strain as the reference genome. Differences between Liverpool and Rockefeller have been known for decades, particularly in the expression of genes relevant to mosquito behavior and vector control (e.g. olfactory). These differences indicate that AaegL5 is likely not fully representative of the Rockefeller genome, presenting potential impediments to research. Here, we present a chromosomal-level assembly and annotation of the Rockefeller genome and a comparative characterization vs the Liverpool genome. Our results set the stage for a pan-genomic approach to understanding evolution and diversity within this important disease vector.