bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photon-noise: is a single-pixel camera better than point scanning? A signal-to-noise ratio analysis for Hadamard and Cosine positive modulation
Authors: Scotté Camille , Galland Frédéric , Rigneault Hervé 
Published: March 2023

Abstract
In a single-pixel camera, an unknown object is sequentially illuminated by intensity patterns. The total reflected or transmitted intensity is summed in a single-pixel detector from which the object is computationally reconstructed. In the situation where the measurements are limited by photon-noise, it is questionable whether a single-pixel camera performs better or worse than simply scanning the object with a focused intensity spot—a modality known as point raster scanning and employed in many laser scanning systems. Here, we solve this general question and report that positive intensity modulation based on Hadamard or Cosine patterns does not necessarily improve the single-to-noise ratio (SNR) of single-pixel cameras, as compared to point raster scanning (RS). Instead, we show that the SNR is only improved on object pixels at least k times brighter than the object mean signal

x
ˉ

, where k is a constant that depends on the modulation scheme (modulation matrix, number of detectors, etc). The constant k is derived for several widespread cases and has important consequences on the choice of the optical deign. This fundamental property is demonstrated theoretically, numerically, and is experimentally confirmed in the spatial domain (widefield fluorescence imaging) and in the spectral domain (spontaneous Raman spectral measurements). Finally, we provide user-oriented guidelines that help decide when and how multiplexing under photon-noise should be used instead of point RS.
Wearable upper limb robotics for pervasive health: a review
Authors: Ochieze Chukwuemeka , Zare Soroush , Sun Ye 
Published: March 2023

Abstract
Wearable robotics, also called exoskeletons, have been engineered for human-centered assistance for decades. They provide assistive technologies for maintaining and improving patients’ natural capabilities towards self-independence and also enable new therapy solutions for rehabilitation towards pervasive health. Upper limb exoskeletons can significantly enhance human manipulation with environments, which is crucial to patients’ independence, self-esteem, and quality of life. For long-term use in both in-hospital and at-home settings, there are still needs for new technologies with high comfort, biocompatibility, and operability. The recent progress in soft robotics has initiated soft exoskeletons (also called exosuits), which are based on controllable and compliant materials and structures. Remarkable literature reviews have been performed for rigid exoskeletons ranging from robot design to different practical applications. Due to the emerging state, few have been focused on soft upper limb exoskeletons. This paper aims to provide a systematic review of the recent progress in wearable upper limb robotics including both rigid and soft exoskeletons with a focus on their designs and applications in various pervasive healthcare settings. The technical needs for wearable robots are carefully reviewed and the assistance and rehabilitation that can be enhanced by wearable robotics are particularly discussed. The knowledge from rigid wearable robots may provide practical experience and inspire new ideas for soft exoskeleton designs. We also discuss the challenges and opportunities of wearable assistive robotics for pervasive health.
A review on mechanical and material characterisation through molecular dynamics using large-scale atomic/molecular massively parallel simulator (LAMMPS)
Authors: Gowthaman S 
Published: March 2023

Abstract
Molecular dynamics (MD) simulation continues to be one of the most advanced tools in a wide range of fields and applications. The motion of atoms or molecules at various temperatures and pressures was analysed and visualised using the MD simulation through large-scale atomic/molecular massively parallel simulator (LAMMPS). This research focuses on a basic introduction to MD, as well as their determination and MD methods. LAMMPS works with a variety of external packages to determine the position of atoms and molecules over time. As the simulation has various procedures such as algorithm to step processing and results, the developers of MD are constantly pushing for the reduction of pre-steps. This classifies the performance competence that should be approached for increased portability of performance on a programmatic level, a key to implementing the solution for various problems that would come from inventors and possibly new research in programming languages.
Quantum Kerr learning
Authors: Liu Junyu , Zhong Changchun , Otten Matthew , Chandra Anirban , Cortes Cristian L , Ti Chaoyang , K Gray Stephen , Han Xu 
Published: March 2023

Abstract
Quantum machine learning is a rapidly evolving field of research that could facilitate important applications for quantum computing and also significantly impact data-driven sciences. In our work, based on various arguments from complexity theory and physics, we demonstrate that a single Kerr mode can provide some ‘quantum enhancements’ when dealing with kernel-based methods. Using kernel properties, neural tangent kernel theory, first-order perturbation theory of the Kerr non-linearity, and non-perturbative numerical simulations, we show that quantum enhancements could happen in terms of convergence time and generalization error. Furthermore, we make explicit indications on how higher-dimensional input data could be considered. Finally, we propose an experimental protocol, that we call quantum Kerr learning, based on circuit QED.
Vatican II: A Very Short Introduction
Authors: Blanchard Shaun , Bullivant Stephen 
Published: March 2023

Abstract
The Second Vatican Council (1962–5), or Vatican II, is arguably the most significant event in the life of the Catholic Church since the age of the Reformation in the 1500s. The Council initiated, intentionally or not, profound changes not simply within Catholic theology, but in the religious, social, and moral lives of the world’s c.1 billion Catholics. It also reconfigured, intellectually and practically, the Church’s engagements with those outside it—most obviously with regard to the Jews and members of other Christian denominations. The 16 documents formally issued by Vatican II constitute some of the most influential, concretely impactful, and most-cited theological writings of the whole 20th century. Debates over their correct interpretation and authority are constant, but they remain an indispensable point of reference for all areas of Catholic life, from liturgy and sacraments to the Church’s vast network of charitable and educational endeavours the world over. In this Very Short Introduction, Shaun Blanchard and Stephen Bullivant present the backstory, event, and reception with freshness and dynamism. Vatican II is explored in light of the wider history of the Catholic Church and placed in the exciting and tumultuous context of the 1960s. The perfect introduction for academics and for undergrad or postgrad classrooms, this Very Short Introduction distils the best research on Vatican II, employing cartoons, the first-hand accounts of participants and observers, and the official proceedings of the Council to paint an exciting and rich picture of one of the most important events of the last century.
What is an ‘ecumenical council’?
Authors: Blanchard Shaun , Bullivant Stephen 
Published: March 2023

Abstract
Vatican II is the most important Catholic event of the past century, if not the past half-millennium. It also had, and has, ramifications far beyond the lives of the world’s billion-or-so Catholics. To understand why, this chapter introduces both the theological meaning of a ‘general ecumenical council’, and the critical historical context in which this specific one played out. Parallels are drawn to previous such events in the history of the Church, including the so-called ‘Council of Jerusalem’ (Acts 15), the formal ecumenical councils of Nicaea (ad 325), Trent (1545‒63), and Vatican I (1869‒70). It also highlights the wider religious, social, cultural, and political currents to which Vatican II was both reacting and, soon enough, actively contributing.
Liturgy
Authors: Blanchard Shaun , Bullivant Stephen 
Published: March 2023

Abstract
Sacrosanctum Concilium, the Constitution on the liturgy, was the Council’s first document, and had the most immediate, visible, and far-reaching impact on the lives of ordinary Catholics. It ignited a period of sweeping (and often bitterly contentious) changes to how Catholics worship. More broadly, it also functions as a kind of manifesto for the Council’s own pastoral and reforming vision. This chapter considers the main hallmarks of Sacrosanctum Concilium’s teachings, e.g. regarding active participation, the use of the vernacular, different musical styles, the need to simplify (and make more explicitly biblical) liturgical texts and the calendar. Attention is also given to how the liturgical reforms were, in practice, rolled out and received in dioceses and parishes across the world, with very variable results.
Dei Verbum and divine revelation
Authors: Blanchard Shaun , Bullivant Stephen 
Published: March 2023

Abstract
Frequently cited among Vatican II’s greatest achievements is the new scriptural focus it engendered in all areas of Catholic life and thought, from the liturgy and personal devotion, to a reinvigoration of biblical criticism and theology. Hence this chapter explores the teaching and historical significance of Dei Verbum (Vatican II’s ‘Dogmatic Constitution on Divine Revelation’). While the Constitution was not formally promulgated until the Council’s fourth and final session (8 December 1965), the key turning point in the Council’s first session was the conciliar majority’s rejection of a draft text (a ‘schema’) on Revelation which reflected the neo-scholastic theology and method of the day. The document that eventually replaced it, Dei Verbum, reflected the majority’s desire for ressourcement—a ‘return to the sources’: scriptural, patristic, and liturgical. This chapter also discusses how this ‘reformist orientation’ grounded in ressourcement set the tone for later debates. This discussion also sheds further light on the roots of Vatican II, since it is in the debate over Dei verbum that we see the triumph of the biblical and patristic movements which began to gain momentum earlier in the century. Additionally, the Council made a strong comment on the development of doctrine (Dei Verbum 8), the centrality of Jesus Christ, and the relationship between scripture and tradition. The chapter closes by briefly recounting how Dei Verbum stimulated biblical renewal among the laity, scholarly biblical criticism among Catholics, and, in the words of Joseph Ratzinger, a ‘new view of the phenomenon of tradition’.
HTRX: an R package for learning non-contiguous haplotypes associated with a phenotype
Authors: Yang Yaoling , Lawson Daniel John 
Published: March 2023

AbstractSummaryHaplotype Trend Regression with eXtra flexibility (HTRX) is an R package to learn sets of interacting features that explain variance in a phenotype. Genome-wide association studies (GWAS) have identified thousands of single nucleotide polymorphisms (SNPs) associated with complex traits and diseases, but finding the true causal signal from a high linkage disequilibrium block is challenging. We focus on the simpler task of quantifying the total variance explainable not just with main effects but also interactions and tagging, using haplotype-based associations. HTRX identifies haplotypes composed of non-contiguous SNPs associated with a phenotype and can naturally be performed on regions with a GWAS hit before or after fine-mapping. To reduce the space and computational complexity when investigating many features, we constrain the search by growing good feature sets using ‘Cumulative HTRX’, and limit the maximum complexity of a feature set. As the computational time scales linearly with the number of SNPs, HTRX has the potential to be applied to large chromosome regions.Availability and implementationHTRX is implemented in R and is available under GPL-3 licence from CRAN (https://cran.r-project.org/web/packages/HTRX/readme/README.html). The development version is maintained on GitHub (https://github.com/YaolingYang/HTRX).Contactyaoling.yang@bristol.ac.ukSupplementary informationSupplementary data are available at Bioinformatics Advances online.
Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format
Authors: Mutsuddy Arnab , Erdem Cemal , Huggins Jonah R , Salim Misha , Cook Daniel , Hobbs Nicole , Feltus F Alex , Birtwistle Marc R 
Published: March 2023

AbstractSummaryLarge-scale and whole-cell modeling has multiple challenges, including scalable model building and module communication bottlenecks (e.g. between metabolism, gene expression, signaling, etc.). We previously developed an open-source, scalable format for a large-scale mechanistic model of proliferation and death signaling dynamics, but communication bottlenecks between gene expression and protein biochemistry modules remained. Here, we developed two solutions to communication bottlenecks that speed-up simulation by ∼4-fold for hybrid stochastic-deterministic simulations and by over 100-fold for fully deterministic simulations. Fully deterministic speed-up facilitates model initialization, parameter estimation and sensitivity analysis tasks.Availability and implementationSource code is freely available at https://github.com/birtwistlelab/SPARCED/releases/tag/v1.3.0 implemented in python, and supported on Linux, Windows and MacOS (via Docker).
HiCube: interactive visualization of multiscale and multimodal Hi-C and 3D genome data
Authors: Ye Tiantian , Hu Yangyang , Pun Sydney , Ma Wenxiu 
Published: March 2023

AbstractSummaryHiCube is a lightweight web application for interactive visualization and exploration of diverse types of genomics data at multiscale resolutions. Especially, HiCube displays synchronized views of Hi-C contact maps and 3D genome structures with user-friendly annotation and configuration tools, thereby facilitating the study of 3D genome organization and function.Availability and implementationHiCube is implemented in Javascript and can be installed via NPM. The source code is freely available at GitHub (https://github.com/wmalab/HiCube).
De novodrug design by iterative multiobjective deep reinforcement learning with graph-based molecular quality assessment
Authors: Fang Yi , Pan Xiaoyong , Shen Hong-Bin 
Published: March 2023

AbstractMotivationGenerating molecules of high quality and drug-likeness in the vast chemical space is a big challenge in the drug discovery. Most existing molecule generative methods focus on diversity and novelty of molecules, but ignoring drug potentials of the generated molecules during the generation process.ResultsIn this study, we present a novel de novo multiobjective quality assessment-based drug design approach (QADD), which integrates an iterative refinement framework with a novel graph-based molecular quality assessment model on drug potentials. QADD designs a multiobjective deep reinforcement learning pipeline to generate molecules with multiple desired properties iteratively, where a graph neural network-based model for accurate molecular quality assessment on drug potentials is introduced to guide molecule generation. Experimental results show that QADD can jointly optimize multiple molecular properties with a promising performance and the quality assessment module is capable of guiding the generated molecules with high drug potentials. Furthermore, applying QADD to generate novel molecules binding to a biological target protein DRD2 also demonstrates the algorithm’s efficacy.Availability and implementationQADD is freely available online for academic use at https://github.com/yifang000/QADD or http://www.csbio.sjtu.edu.cn/bioinf/QADD.
Diagnosis and treatment of lupus nephritis: a summary of the Consensus Document of the Spanish Group for the Study of Glomerular Diseases (GLOSEN)
Authors: Rojas-Rivera Jorge E , García-Carro Clara , Ávila Ana I , Espino Mar , Espinosa Mario , Fernández-Juárez Gema , Fulladosa Xavier , Goicoechea Marian , Macía Manuel , Morales Enrique , Quintana Luis F , Praga Manuel 
Published: March 2023

ABSTRACT
Lupus nephritis (LN) is the most frequent serious manifestation of patients with systemic lupus erythematosus (SLE). Up to 60% of SLE patients develop LN, which has a significant impact on their quality of life and prognosis. Recent advances have improved the diagnostic approach to LN, and new drugs that block specific pathways and kidney damage progression have been developed. Several randomized and well-powered clinical trials have confirmed the efficacy of these agents in terms of proteinuria remission and preservation of kidney function in the medium and long term, with an acceptable safety profile and good tolerance. The combination of different therapies allows for reduction of the dose and duration of corticosteroids and other potentially toxic therapies and leads to an increase in the number of patients achieving complete remission of the disease. This consensus document carried out by the Spanish Group for the Study of Glomerular Diseases (GLOSEN) provides practical and updated recommendations, based on the best available evidence and clinical expertise of participating nephrologists.
VEGF-B hypertrophy predisposes to transition from diastolic to systolic heart failure in hypertensive rats
Authors: Samuelsson Anne-Maj , Bartolomaeus Theda Ulrike Patricia , Anandakumar Harithaa , Thowsen Irene , Nikpey Elham , Han Jianhua , Marko Lajos , Finne Kenneth , Tenstad Olav , Eckstein Johannes , Berndt Nikolaus , Kühne Titus , Kedziora Sarah , Sultan Ibrahim , Skogstrand Trude , Karlsen Tine V , Nurmi Harri , Forslund Sofia K , Bollano Entela , Alitalo Kari , Muller Dominik N , Wiig Helge 
Published: March 2023

Abstract

Aims
Cardiac energy metabolism is centrally involved in heart failure (HF), although the direction of the metabolic alterations is complex and likely dependent on the particular stage of HF progression. Vascular endothelial growth factor B (VEGF-B) has been shown to modulate metabolic processes and to induce physiological cardiac hypertrophy; thus, it could be cardioprotective in the failing myocardium. This study investigates the role of VEGF-B in cardiac proteomic and metabolic adaptation in HF during aldosterone and high-salt hypertensive challenges.

Methods and results
Male rats overexpressing the cardiac-specific VEGF-B transgene (VEGF-B TG) were treated for 3 or 6 weeks with deoxycorticosterone-acetate combined with a high-salt (HS) diet (DOCA + HS) to induce hypertension and cardiac damage. Extensive longitudinal echocardiographic studies of HF progression were conducted, starting at baseline. Sham-treated rats served as controls. To evaluate the metabolic alterations associated with HF, cardiac proteomics by mass spectrometry was performed. Hypertrophic non-treated VEGF-B TG hearts demonstrated high oxygen and adenosine triphosphate (ATP) demand with early onset of diastolic dysfunction. Administration of DOCA + HS to VEGF-B TG rats for 6 weeks amplified the progression from cardiac hypertrophy to HF, with a drastic drop in heart ATP concentration. Dobutamine stress echocardiographic analyses uncovered a significantly impaired systolic reserve. Mechanistically, the hallmark of the failing TG heart was an abnormal energy metabolism with decreased mitochondrial ATP, preceding the attenuated cardiac performance and leading to systolic HF.

Conclusions
This study shows that the VEGF-B TG accelerates metabolic maladaptation which precedes structural cardiomyopathy in experimental hypertension and ultimately leads to systolic HF.
Oncological and physiological impact of thoracic duct resection in esophageal cancer
Authors: Matsuda Satoru , Takeuchi Masashi , Kawakubo Hirofumi , Takeuchi Hiroya , Kitagawa Yuko 
Published: March 2023

Abstract
Despite advances in multidisciplinary treatment, esophagectomy remains the main curative treatment for esophageal cancer. The advantages and disadvantages of thoracic duct (TD) resection have been controversial for decades. We have herein reviewed relevant published literature regarding ‘thoracic duct,’ ‘esophageal cancer,’ and ‘esophagectomy’ describing the anatomy and function of the TD, and incidence of thoracic duct lymph nodes (TDLN) and TDLN metastases, as well as the oncological and physiological effects of TD resection. The presence of lymph nodes around the TD, referred to as TDLN, has been reported previously. The delineation of TDLNs is clearly defined by a thin fascial structure covering the TD and the surrounding adipose tissue. Previous studies have examined the number of TDLNs and the percentage of patients with TDLN metastasis and revealed that each patient had approximately two TDLNs. The percentage of patients with TDLN metastasis was reported to be 6–15%. Several studies have been conducted to compare the survival after TD resection with that after TD preservation. However, no consensus has been reached because all studies were retrospective, precluding firm conclusions. Although the issue of whether the risk of postoperative complications is affected by TD resection is still unclear, resecting the TD has been shown to have a long-term impact on nutritional status after surgery. In summary, TDLNs are quite common and present in most patients, while metastasis in the TDLNs occurs in a minority. However, the oncological value of TD resection in esophageal cancer surgery remains controversial due to varying findings and methodological limitations of previous comparative studies. Considering the potential but unproven oncological benefits and possible physiological drawbacks of TD resection, including postoperative fluid retention and disadvantages in the long-term nutritional outcome, clinical stage, and nutritional status should be considered before deciding whether to perform TD resection or not.