bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interscale entanglement production in a quantum system simulating classical chaos
Authors: Haga Taiki , Sasa Shin-ich 
Published: December 2022

Abstract
It is a fundamental problem how the universal concept of classical chaos emerges from the microscopic description of quantum mechanics. We here study standard classical chaos in a framework of quantum mechanics. In particular, we design a quantum lattice system that exactly simulates classical chaos after an appropriate continuum limit, which is called the ‘Hamiltonian equation limit’. The key concept of our analysis is an entanglement entropy defined by dividing the lattice into many blocks of equal size and tracing out the degrees of freedom within each block. We refer to this entropy as the ‘interscale entanglement entropy (IEE)’ because it measures the amount of entanglement between the microscopic degrees of freedom within each block and the macroscopic degrees of freedom that define the large-scale structure of the wave function. By numerically simulating a quantum lattice system corresponding to the Hamiltonian of the kicked rotor, we find that the long-time average of the IEE becomes positive only when chaos emerges in the Hamiltonian equation limit, and the growth rate of the entropy in the initial stage is proportional to that of the coarse-grained Gibbs entropy of the corresponding classical system.
Charged particle tracking in real-time using a full-mesh data delivery architecture and associative memory techniques
Authors: Ajuha Sudha , Akira Shinoda Ailton , Arruda Ramalho Lucas , Baulieu Guillaume , Boudoul Gaelle , Casarsa Massimo , Cascadan Andre , Clement Emyr , Costa de Paiva Thiago , Das Souvik , Dutta Suchandra , Eusebi Ricardo , Fedi Giacomo , Finotti Ferreira Vitor , Hahn Kristian , Hu Zhen , Jindariani Sergo , Konigsberg Jacobo , Liu Tiehui , Fu Low Jia , MacDonald Emily , Olsen Jamieson , Palla Fabrizio , Pozzobon Nicola , Rathjens Denis , Ristori Luciano , Rossin Roberto , Sung Kevin , Tran Nhan , Trovato Marco , Ulmer Keith , Vaz Mario , Viret Sebastien , Wu Jin-Yuan , Xu Zijun , Zorzetti Silvia 
Published: December 2022

Abstract
We present a flexible and scalable approach to address the
challenges of charged particle track reconstruction in real-time
event filters (Level-1 triggers) in collider physics
experiments. The method described here is based on a full-mesh
architecture for data distribution and relies on the Associative
Memory approach to implement a pattern recognition algorithm that
quickly identifies and organizes hits associated to trajectories of
particles originating from particle collisions. We describe a
successful implementation of a demonstration system composed of
several innovative hardware and algorithmic elements. The
implementation of a full-size system relies on the assumption that
an Associative Memory device with the sufficient pattern density
becomes available in the future, either through a dedicated ASIC or
a modern FPGA. We demonstrate excellent performance in terms of
track reconstruction efficiency, purity, momentum resolution, and
processing time measured with data from a simulated LHC-like
tracking detector.
A comparative study on different background estimation methods for extensive air shower arrays
Authors: Wang Yan-Jin , Zha Min , Hu Shi-Cong , Gao Chuan-Dong , Zhang Jian-Li , Zhang Xin 
Published: December 2022

Abstract
Background estimation is essential when studying TeV
γ-ray astronomy for extensive air shower arrays. In this
work, by applying four different methods including equi-zenith angle
method, surrounding window method, direct integration method, and
time-swapping method, the number of the background events is
calculated. Based on simulation samples, the statistical
significance of the excess signal from different background
estimation methods is determined. Following this, we discuss the
limitations and the applicability of the four methods under
different conditions. Under the detector stability assumption with
signals, the results from the above four methods are consistent at
the 1σ level. In the no signal condition, when the acceptance
of the detector changes with both space and time, the surrounding
window method is the most stable and hardly affected. In this
acceptance assumption, we find that the background estimation in the
direct integration and time-swapping methods are sensitive to the
selection of time window, and the shorter time window can reduce the
impact on the background estimation to some extent.
South Florida estuaries are warming faster than global oceans
Authors: Shi Jing , Hu Chuanmin 
Published: December 2022

Abstract
From extensive evaluations, it is found that, of all satellite data products of sea surface temperature (SST), MODIS SST is the most appropriate in assessing long-term trends of water temperature in the South Florida estuaries. Long-term SST data show significant warming trends in these estuaries during both daytime (0.55 °C/decade) and nighttime (0.42 °C/decade) between 2000 and 2021. The warming rates are faster during winter (0.70 °C/decade and 0.67 °C/decade for daytime and nighttime, respectively) than during summer (0.48 °C/decade and 0.28 °C/decade for daytime and nighttime, respectively). Overall, the South Florida estuaries experienced rapid warming over the past two decades, 1.7 and 1.3 times faster than the Gulf of Mexico (0.33 °C/decade and 0.32 °C/decade for daytime and nighttime), and 6.9 and 4.2 times faster than the global oceans (0.08 °C/decade and 0.10 °C/decade for daytime and nighttime).
Maxwell’s disappointment and Sutton’s accident
Authors: Klein Susanne , Elter Paul , Trujillo Vazquez Abigail 
Published: December 2022

AbstractIt has almost become somewhat of an urban legend or internet myth that James Clerk Maxwell created the first colour image and had demonstrated this at the Royal Institution in London in May 1861. He did present something, but what? In ‘The scientific papers of James Clerk Maxwell’ the experiment and resulting colour projection was regarded as a failure and barely mentioned. Thomas Sutton, a well-established and respected photographer, was tasked with carrying out Maxwell’s thought-experiment using the latest photographic processes. Sutton, himself author of various books on photography, does not mention the experiment in any of his publications. Move forward to the 1930’s and enter the photo-chemist Douglas Arthur Spencer, who gained access to the original lanternslides and made copies of the three colour separations. He made the first and only physical print of the 1861 tartan ribbon and it is this colour print that we now see everywhere as Maxwell’s first colour photograph. In 1961, the 100th anniversary, Ralph M Evans published a paper in Scientific American trying to solve the riddle of the famous tartan ribbon. The original glass plate photographs were made using the wet-collodion process which has a very narrow spectral sensitivity centered in the blue light wavelength. Sutton could not have recorded in the green and red part of the spectrum. Evans deduced from an experiment with modern materials that Sutton had possibly recorded the ultraviolet reflection present in the red of the tartan ribbon and ‘accidently’ presenting itself as the red slide and the resulting image can be considered a ‘false colour’ image. Now, 160 yr since that first experiment, we are exploring and executing some of the material and technical truths about wet-plate collodion and what might have actually been recorded and why is it that both Maxwell and Sutton regarded the experiment such a failure, but the rest of the world did not.
Structural and electronic properties of two-dimensional titanium carbo-oxides
Authors: Hu Yong-Jie , Tandoc Christopher , Barsoum Michel W , Rosen Johanna , Björk Jonas 
Published: December 2022

Abstract
This work was inspired by new experimental findings where we discovered a two-dimensional (2D) material comprised of titanium-oxide-based one-dimensional (1D) sub-nanometer filaments. Preliminary results suggest that the 2D material contains considerable amounts of carbon, C, in addition to titanium, Ti, and oxygen, O. The aim of this study is to investigate the low-energy, stable atomic forms of 2D titanium carbo-oxides as a function of C content. Via a combination of first-principles calculations and an effective structure sampling scheme, the stable configurations of C-substitutions are comprehensively searched by templating different 2D TiO2 polymorphs and considering a two O to one C replacement scheme. Among the searched stable configurations, a structure where the (101) planes of anatase bound the top and bottom surfaces with a chemical formula of

Ti

C

1

/

4

O

3

/

2

was of particularly low energy. Furthermore, the variations in the electronic band structure and chemical bonding environments caused by the high-content C substitution are investigated via additional calculations using a hybrid exchange-correlation functional.
Novel Ni3S4/NiS/NC composite with multiple heterojunctions synthesized through space-confined effect for high-performance supercapacitors
Authors: Wei Wutao , Guo Zijie , Xu Jiaqiang , Fang Zhe , Zhang Jiujun , Jia Yu , Mi Liwei 
Published: December 2022

Abstract
The construction of heterojunctions in composite materials to optimize the electronic structures and active sites of energy materials is considered to be the promising strategy for the fabrication of high-performance electrochemical energy devices. In this paper, a one-step, easy processing and cost-effective technique for generating composite materials with heterojunctions was successfully developed. The composite containing Ni3S4, NiS, and N-doped amorphous carbon (abbreviated as Ni3S4/NiS/NC) with multiple heterojunction nanosheets are synthesized via the space-confined effect of molten salt interface of recrystallized NaCl. Several lattice matching forms of Ni3S4 with cubic structure and NiS with hexagonal structure are confirmed by the detailed characterization of heterogeneous interfaces. The C–S bonds are the key factor in realizing the chemical coupling between nickel sulfide and NC and constructing the stable heterojunction. Density functional theory calculations further revealed that the electronic interaction on the heterogeneous interface of Ni3S4/NiS can contribute to high electronic conductivity. The heterogeneous interfaces are identified to be the good electroactive region with excellent electrochemical performance. The synergistic effect of abundant active sites, the enhanced kinetic process and valid interface charge transfer channels of Ni3S4/NiS/NC multiple heterojunction can guarantee high reversible redox activity and high structural stability, resulting in both high specific capacitance and energy/power densities when it is used as the electrode for supercapacitors. This work offers a new avenue for the rational design of the heterojunction materials with improved electrochemical performance through space-confined effect of NaCl.
Near-unity efficiency in ridge waveguide-based, on-chip single-photon sources
Authors: Wang Y J , Vannucci L , Burger S , Gregersen N 
Published: December 2022

Abstract
We report a numerical design procedure for pursuing a near-unity coupling efficiency in quantum dot (QD)-cavity ridge waveguide single-photon sources (SPSs) by performing simulations with the finite element method. Our optimum design which is based on a 1D nanobeam cavity, achieves a high source efficiency ε

xy
of 97.7% for an isotropic in-plane dipole, together with a remarkable Purcell factor of 38.6. Such a good performance is mainly attributed to the high index contrast of GaAs/SiO2 and a careful cavity design achieving constructive interference and low scattering losses. Furthermore, we analyze the bottleneck of the proposed platform, which is the mode mismatch between the cavity mode and the Bloch mode in the nanobeam. Accordingly, we present the optimization recipe of an arbitrarily high-efficiency on-chip SPS by implementing a taper section, whose high smoothness is beneficial to gradually overcoming the mode mismatch, and therefore leading to a higher Purcell factor and source efficiency. Finally, we see good robustness of the source properties in the taper-nanobeam system under the consideration of realistic fabrication imperfections on the hole variation and QD position deviation.
The trajectory of family caregiving for older adults with dementia: difficulties and challenges
Authors: Tu Jiong , Li Haiyan , Ye Bei , Liao Jing 
Published: December 2022

AbstractIntroductionAs the main source of informal care in China, family members bear a tremendous caregiving burden, particularly in relation to older people with dementia (PwDs). However, the continuous caregiving trajectory of family caregivers was unclear.ObjectivesTo investigate the trajectory of PwDs’ family caregivers’ struggles from home care to institutional care, and identify the common tipping points leading to institutional care from their perspectives.MethodsAn ethnographic study was conducted in a long-term care institution in Chengdu, China, from 2019 to 2020. Face-to-face, semi-structured interviews were carried out with 13 family members (i.e. 5 spouses and 8 adult children) of older PwDs during family caregivers’ visits. The interviews were recorded and transcribed, after which the transcripts were analysed using thematic analysis.ResultsThe family caregivers’ experiences before and after the PwDs’ institutionalization fell into two distinctive parts, and three subthemes about their caregiving experiences in each period were identified: the mental stress, the physical care burden, and the social and emotional pressure connected to home-based care; the moral pressure and emotional torment, the financial burden, and new worries after institutionalization. The tipping points in between the two stages were major changes or incidents related to the PwDs’ status. Variations in the spouse and older children’s care experiences also emerged.ConclusionOur study provides a nuanced analysis of the trajectory of family caregiving for PwDs. The plight of family caregivers at all stages should be recognized and supported with adequate medical and social resources, with a further consideration of the caregivers’ relationships with the older PwDs.
Microbiome Toolbox: methodological approaches to derive and visualize microbiome trajectories
Authors: Banjac Jelena , Sprenger Norbert , Dogra Shaillay Kumar 
Published: December 2022

Abstract

Motivation
The gut microbiome changes rapidly under the influence of different factors such as age, dietary changes or medications to name just a few. To analyze and understand such changes, we present a Microbiome Toolbox. We implemented several methods for analysis and exploration to provide interactive visualizations for easy comprehension and reporting of longitudinal microbiome data.

Results
Based on the abundance of microbiome features such as taxa as well as functional capacity modules, and with the corresponding metadata per sample, the Microbiome Toolbox includes methods for (i) data analysis and exploration, (ii) data preparation including dataset-specific preprocessing and transformation, (iii) best feature selection for log-ratio denominators, (iv) two-group analysis, (v) microbiome trajectory prediction with feature importance over time, (vi) spline and linear regression statistical analysis for testing universality across different groups and differentiation of two trajectories, (vii) longitudinal anomaly detection on the microbiome trajectory and (viii) simulated intervention to return anomaly back to a reference trajectory.

Availability and implementation
The software tools are open source and implemented in Python. For developers interested in additional functionality of the Microbiome Toolbox, it is modular allowing for further extension with custom methods and analysis. The code, python package and the link to the interactive dashboard of Microbiome Toolbox are available on GitHub https://github.com/JelenaBanjac/microbiome-toolbox

Supplementary information
Supplementary data are available at Bioinformatics online.
Poisson hurdle model-based method for clustering microbiome features
Authors: Qiao Zhili , Barnes Elle , Tringe Susannah , Schachtman Daniel P , Liu Peng 
Published: December 2022

AbstractMotivationHigh-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality.ResultsWe propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation–maximization algorithm and a modified version using simulated annealing to conduct the cluster analysis. Moreover, we provide algorithms for initialization and choosing the number of clusters. Simulation results demonstrate that our proposed methods provide better clustering results than alternative methods under a variety of settings. We also apply the proposed method to a sorghum rhizosphere microbiome dataset that results in interesting biological findings.Availability and implementationR package is freely available for download at https://cran.r-project.org/package=PHclust.Supplementary informationSupplementary data are available at Bioinformatics online.
TransFlow: a Snakemake workflow for transmission analysis ofMycobacterium tuberculosiswhole-genome sequencing data
Authors: Pan Junhang , Li Xiangchen , Zhang Mingwu , Lu Yewei , Zhu Yelei , Wu Kunyang , Wu Yiwen , Wang Weixin , Chen Bin , Liu Zhengwei , Wang Xiaomeng , Gao Junshun 
Published: December 2022

AbstractMotivationWhole-genome sequencing (WGS) is increasingly used to aid the understanding of Mycobacterium tuberculosis (MTB) transmission. The epidemiological analysis of tuberculosis based on the WGS technique requires a diverse collection of bioinformatics tools. Effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts.ResultsHere, we present TransFlow (Transmission Workflow), a user-friendly, fast, efficient and comprehensive WGS-based transmission analysis pipeline. TransFlow combines some state-of-the-art tools to take transmission analysis from raw sequencing data, through quality control, sequence alignment and variant calling, into downstream transmission clustering, transmission network reconstruction and transmission risk factor inference, together with summary statistics and data visualization in a summary report. TransFlow relies on Snakemake and Conda to resolve dependencies among consecutive processing steps and can be easily adapted to any computation environment.Availability and implementationTransFlow is free available at https://github.com/cvn001/transflow.Supplementary informationSupplementary data are available at Bioinformatics online.
Cervical cancer screening history among women diagnosed with cervical cancer in Estonia 2017–18
Authors: Orumaa Madleen , Innos Kaire , Suurna Maria , Veerus Piret 
Published: December 2022

Abstract

Background
Despite the national cervical cancer screening programme launched in 2006, Estonia has one of the highest cervical cancer incidence rates in Europe. While the overall coverage of cervical cytology is high, the factors related to cancer screening history prior to cancer diagnosis need to be studied.

Methods
In this study, we aimed to examine the 10-year screening history of women diagnosed with cervical cancer in Estonia in 2017–18, using data collected from laboratory reports from 2007 to 2018. From each report, we extracted information on the date and result of cytology and on the laboratory where the sample was assessed. We analysed these data across cancer histology, the time interval between the last test result and cancer diagnosis and the laboratory type (local or regional).

Results
Among 319 women with cervical cancer, 181 (56.7%) did not have any cytology reports available. Among 138 women with at least one cytology, 60% had 1–3, 24% 4–6 and 16% ≥7 tests (mean 3.7) before cancer. In 78% of women, the last test was performed less than 5 years before cancer diagnosis and 62% of these tests did not report any abnormalities. The last cytology results differed significantly between the regional and local laboratories (P = 0.028).

Conclusion
Women received the cervical cancer diagnosis in Estonia despite having several screening tests 10 years prior to the diagnosis. The proportion of cytology tests without any abnormalities less than 5 years before the diagnosis was worryingly high and needs further investigation together with the difference between laboratory types.
Determining Whether Older Adults Use Similar Strategies to Young Adults in Theory of Mind Tasks
Authors: Krendl Anne C , Mannering Willa , Jones Michael N , Hugenberg Kurt , Kennedy Daniel P 
Published: December 2022

Abstract

Objectives
Theory of mind—the ability to infer others’ mental states—declines over the life span, potentially due to cognitive decline. However, it is unclear whether deficits emerge because older adults use the same strategies as young adults, albeit less effectively, or use different or no strategies. The current study compared the similarity of older adults’ theory of mind errors to young adults’ and a random model.

Methods
One hundred twenty older adults (MAge = 74.68 years; 64 female) and 111 young adults (MAge = 19.1; 61 female) completed a novel theory of mind task (clips from an episode of the sitcom The Office®), and a standard measure of cognitive function (Logical Memory II). Monte Carlo resampling estimated the likelihood that older adults’ error patterns were more similar to young adults’ or a random distribution.

Results
Age deficits emerged on the theory of mind task. Poorer performance was associated with less similarity to young adults’ response patterns. Overall, older adults’ response patterns were ~2.7 million times more likely to match young adults’ than a random model. Critically, one fourth of older adults’ errors were more similar to the random distribution. Poorer memory ability contributed to this relationship.

Discussion
Age deficits in theory of mind performance may be driven by a subset of older adults and be related to disparities in strategy use. A certain amount of cognitive ability may be necessary for older adults to engage similar strategies to young adults’ during theory of mind.