bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flows for the masses: A multi-fluid non-linear perturbation theory for massive neutrinos
Authors: Chen Joe Zhiyu , Upadhye Amol , Wong Yvonne Y.Y. 
Published: May 2023

Abstract
Velocity dispersion of the massive neutrinos presents a daunting challenge for non-linear cosmological perturbation theory. We consider the neutrino population as a collection of non-linear fluids, each with uniform initial momentum, through an extension of the Time Renormalization Group perturbation theory. Employing recently-developed Fast Fourier Transform techniques, we accelerate our non-linear perturbation theory by more than two orders of magnitude, making it quick enough for practical use. After verifying that the neutrino mode-coupling integrals and power spectra converge, we show that our perturbation theory agrees with N-body neutrino simulations to within 10% for neutrino fractions Ω
ν,0
h
2 ≤ 0.005 up to wave numbers of k = 1 h/Mpc, an accuracy consistent with ≤ 2.5% errors in the neutrino mass determination. Non-linear growth represents a > 10% correction to the neutrino power spectrum even for density fractions as low as Ω
ν,0
h
2 = 0.001, demonstrating the limits of linear theory for accurate neutrino power spectrum predictions. Our code FlowsForTheMasses is avaliable online at github.com/upadhye/FlowsForTheMasses.
Genome entropy and network centrality contrast exploration and exploitation in evolution of foodborne pathogens
Authors: Chang Sheryl L , Suster Carl J E , Rockett Rebecca J , Svahn Adam J , Cliff Oliver M , Arnott Alicia , Wang Qinning , Kim Rady , Suliman Basel , Gall Mailie , Sorrell Tania C , Sintchenko Vitali , Prokopenko Mikhail 
Published: May 2023

Abstract
Modelling evolution of foodborne pathogens is crucial for mitigation and prevention of outbreaks. We apply network-theoretic and information-theoretic methods to trace evolutionary pathways of Salmonella Typhimurium in New South Wales, Australia, by studying whole genome sequencing surveillance data over a five-year period which included several outbreaks. The study derives both undirected and directed genotype networks based on genetic proximity, and relates the network’s structural property (centrality) to its functional property (prevalence). The centrality-prevalence space derived for the undirected network reveals a salient exploration-exploitation distinction across the pathogens, further quantified by the normalised Shannon entropy and the Fisher information of the corresponding shell genome. This distinction is also analysed by tracing the probability density along evolutionary paths in the centrality-prevalence space. We quantify the evolutionary pathways, and show that pathogens exploring the evolutionary search-space during the considered period begin to exploit their environment (their prevalence increases resulting in outbreaks), but eventually encounter a bottleneck formed by epidemic containment measures.
Design of embedded software architecture for spacecraft electric propulsion system
Authors: Zhao Xingsong , Gu Bin , Dong Xiaogang , Li Xiaofeng , Zhong Ruiming 
Published: May 2023

Abstract
With the rapid growth of the number of spacecraft tasks and the complexity of the system, spacecraft software development is faced with the challenges of high-quality and rapid delivery, increased complexity, and frequent changes in requirements. The reuse rate of software assets needs to be improved urgently. In order to realize cross-platform and cross-project reuse of software design, this paper studies the design of electric propulsion software architecture. Carry out requirements decomposition and subsystem division of electric propulsion systems for different platforms, extract common requirements and variability requirements at the system level and subsystem level based on the Feature-Oriented Domain Analysis method, and establish a requirements model. Based on the requirements model, an electric propulsion software architecture integrating “event-driven + components” is proposed, and the classic event-driven model of “publish-subscribe” is adaptively improved. The architecture has been instantiated and applied to 16 projects on 4 platforms, and the reuse rate of core assets has reached 70%. This paper has certain guidance and reference significance for spacecraft software asset reuse and platform construction.
High rate studies of the ATLAS sTGC detector and optimization of the filter circuit on the input of the front-end amplifier
Authors: Sun Siyuan , Moleri Luca , Vasquez Gerardo , Teterin Peter , Corsetti Sabrina , Guan Liang , Lefebvre Benoit , Kajomovitz Enrique , Levinson Lorne , Lupu Nachman , McPherson Rob , Vdovin Alexander , Wang Rongkun , Zhou Bing , Zhu Junjie 
Published: May 2023

Abstract
The Large Hadron Collider (LHC) at CERN is expected to be upgraded to the High-Luminosity LHC (HL-LHC) by 2029 and achieve instantaneous luminosity around 5–7.5 × 10^34 cm^-2 s^-1. This represents a more than 3–4 fold increase in the instantaneous luminosity compared to what has been achieved in Run 2. The New Small Wheel (NSW) upgrade is designed to be able to operate efficiently in this high background rate environment. In this article, we summarize multiple performance studies of the small-strip Thin Gap Chamber (sTGC) at high rate using nearly final front-end electronics. We demonstrate that the efficiency versus rate distribution can be well described by an exponential decay with electronics dead-time being the primary cause of loss of efficiency at high rate. We then demonstrate several methods that can decrease the electronics dead-time and therefore minimize efficiency loss. One such method is to install either a pi-network input filter or pull-up resistor to minimize the charge input into the amplifier. We optimized the pi-network capacitance and pull-up resistor resistance using the results from our measurements. The results shown here were not only critical to finalizing the components on the front-end board, but also are critical for setting the optimal operating parameters of the sTGC detector and electronics in the ATLAS cavern.
A measure of perceived quality to secure the polishability of new paint systems
Authors: Rebeggiani Sabina , Rosén B-G 
Published: May 2023

Abstract
The automotive industry continuously strives to reduce their environmental impact. For the paint shop it means to introduce more sustainable paint concepts, while maintaining the production rate and retain the right surface appearance that is crucial for the vehicle’s perceived quality. Today most painted parts are visually inspected and, if needed, manually repaired by abrasive polishing to eliminate spot defects. The repair process consists of one sanding step to remove the defect, and one or two rubbing/polishing steps to restore the surface, but still it tends to be a non-reliable process leaving patterns or clusters of shallow micro scratches seen as three-dimensional shapes moving over the surface when viewed from different angles like holograms. These so called ‘polishing roses’ are hard to detect in artificial light but clearly visible in Sunlight and therefore they constitute a constant quality issue. Accurate polishing procedures in combination with more objective inspection techniques would secure a high surface quality—but what is ‘accurate’? The overall scope of the study was to deepen the knowledge of paint systems to develop test routines for the polishability of coatings already during the development stage, and thereby ease the implementation of new coating systems in production. The study was based on collected process data from professional polishers to define a process window based on key parameters for successful end-of-line repairs of coated surfaces, i.e. strategies minimizing the occurrence of visible polishing traces. A CNC-machine was built up for the purpose to systematically test and evaluate new coating systems and repair procedures. The surface estimation was made by visual inspections as well as by a further developed photometric stereo system providing quantitative images of remaining repair traces.
Atomic layer deposition of thin films: from a chemistry perspective
Authors: Li Jinxiong , Chai Gaoda , Wang Xinwei 
Published: May 2023

Abstract
Atomic layer deposition (ALD) has become an indispensable thin-film technology in the contemporary microelectronics industry. The unique self-limited layer-by-layer growth feature of ALD has outstood this technology to deposit highly uniform conformal pinhole-free thin films with angstrom-level thickness control, particularly on 3D topologies. Over the years, the ALD technology has enabled not only the successful downscaling of the microelectronic devices but also numerous novel 3D device structures. As ALD is essentially a variant of chemical vapor deposition, a comprehensive understanding of the involved chemistry is of crucial importance to further develop and utilize this technology. To this end, we, in this review, focus on the surface chemistry and precursor chemistry aspects of ALD. We first review the surface chemistry of the gas–solid ALD reactions and elaborately discuss the associated mechanisms for the film growth; then, we review the ALD precursor chemistry by comparatively discussing the precursors that have been commonly used in the ALD processes; and finally, we selectively present a few newly-emerged applications of ALD in microelectronics, followed by our perspective on the future of the ALD technology.
‘What is it?’ ‘It is a lewd goblin’: Taking Critical Cues from Illustrative Adaptations of Christina Rossetti’s Goblin Market
Authors: Figgins Kristen Layne 
Published: May 2023

Abstract
When adapters interpret a work over and over again, they focus on details that can shape the way we think about a text. Focusing on these adaptive details can often lead to seeing gaps in the criticism of a text. Such is the case with Goblin Market, a poem that critics have been noting is ‘ambiguous’ since its first publication in 1862. While most critics understand that this ambiguity centres on the sexual undertones of the poem, the key to understanding this allegory might be discovered by turning to illustrative adaptations. In all illustration, one detail is reproduced consistently: the goblins are visualised as animals. Yet animality is rarely discussed in criticism of the poem, and almost never with any depth. I argue that we can view adaptation as a type of meaning-making that literary and cultural critics might build upon when analysing familiar texts.
VII—Can Arguments Change Minds?
Authors: Dutilh Novaes Catarina 
Published: May 2023

AbstractCan arguments change minds? Philosophers like to think that they can. However, a wealth of empirical evidence suggests that arguments are not very efficient tools to change minds. What to make of the different assessments of the mind-changing potential of arguments? To address this issue, we must take into account the broader contexts in which arguments occur, in particular the propagation of messages across networks of attention, and the choices that epistemic agents must make between alternative potential sources of content and information, which are very much influenced by perceptions of reliability and trustworthiness. Arguments can change minds, but only under conducive, favourable socio-epistemic conditions.
Locality-preserving minimal perfect hashing of k-mers
Authors: Pibiri Giulio Ermanno , Shibuya Yoshihiro , Limasset Antoine 
Published: May 2023

Abstract

Motivation
Minimal perfect hashing is the problem of mapping a static set of n distinct keys into the address space {1,…,n} bijectively. It is well-known that n log 2(e) bits are necessary to specify a minimal perfect hash function (MPHF) f, when no additional knowledge of the input keys is to be used. However, it is often the case in practice that the input keys have intrinsic relationships that we can exploit to lower the bit complexity of f. For example, consider a string and the set of all its distinct k-mers as input keys: since two consecutive k-mers share an overlap of k−1 symbols, it seems possible to beat the classic  log 2(e) bits/key barrier in this case. Moreover, we would like f to map consecutive k-mers to consecutive addresses, as to also preserve as much as possible their relationship in the codomain. This is a useful feature in practice as it guarantees a certain degree of locality of reference for f, resulting in a better evaluation time when querying consecutive k-mers.

Results
Motivated by these premises, we initiate the study of a new type of locality-preserving MPHF designed for k-mers extracted consecutively from a collection of strings. We design a construction whose space usage decreases for growing k and discuss experiments with a practical implementation of the method: in practice, the functions built with our method can be several times smaller and even faster to query than the most efficient MPHFs in the literature.
gExcite: a start-to-end framework for single-cell gene expression, hashing, and antibody analysis
Authors: Grob Linda , Bertolini Anne , Carrara Matteo , Lischetti Ulrike , Tastanova Aizhan , Beisel Christian , Levesque Mitchell P , Stekhoven Daniel J , Singer Franziska 
Published: May 2023

Abstract

Summary
Recently, CITE-seq emerged as a multimodal single-cell technology capturing gene expression and surface protein information from the same single cells, which allows unprecedented insights into disease mechanisms and heterogeneity, as well as immune cell profiling. Multiple single-cell profiling methods exist, but they are typically focused on either gene expression or antibody analysis, not their combination. Moreover, existing software suites are not easily scalable to a multitude of samples. To this end, we designed gExcite, a start-to-end workflow that provides both gene and antibody expression analysis, as well as hashing deconvolution. Embedded in the Snakemake workflow manager, gExcite facilitates reproducible and scalable analyses. We showcase the output of gExcite on a study of different dissociation protocols on PBMC samples.

Availability and implementation
gExcite is open source available on github at https://github.com/ETH-NEXUS/gExcite_pipeline. The software is distributed under the GNU General Public License 3 (GPL3).
Multi-modal deep learning improves grain yield prediction in wheat breeding by fusing genomics and phenomics
Authors: Togninalli Matteo , Wang Xu , Kucera Tim , Shrestha Sandesh , Juliana Philomin , Mondal Suchismita , Pinto Francisco , Govindan Velu , Crespo-Herrera Leonardo , Huerta-Espino Julio , Singh Ravi P , Borgwardt Karsten , Poland Jesse 
Published: May 2023

Abstract

Motivation
Developing new crop varieties with superior performance is highly important to ensure robust and sustainable global food security. The speed of variety development is limited by long field cycles and advanced generation selections in plant breeding programs. While methods to predict yield from genotype or phenotype data have been proposed, improved performance and integrated models are needed.

Results
We propose a machine learning model that leverages both genotype and phenotype measurements by fusing genetic variants with multiple data sources collected by unmanned aerial systems. We use a deep multiple instance learning framework with an attention mechanism that sheds light on the importance given to each input during prediction, enhancing interpretability. Our model reaches 0.754 ± 0.024 Pearson correlation coefficient when predicting yield in similar environmental conditions; a 34.8% improvement over the genotype-only linear baseline (0.559 ± 0.050). We further predict yield on new lines in an unseen environment using only genotypes, obtaining a prediction accuracy of 0.386 ± 0.010, a 13.5% improvement over the linear baseline. Our multi-modal deep learning architecture efficiently accounts for plant health and environment, distilling the genetic contribution and providing excellent predictions. Yield prediction algorithms leveraging phenotypic observations during training therefore promise to improve breeding programs, ultimately speeding up delivery of improved varieties.

Availability and implementation
Available at https://github.com/BorgwardtLab/PheGeMIL (code) and https://doi.org/doi:10.5061/dryad.kprr4xh5p (data).
Heart rate variability during slow wave sleep is linked to functional connectivity in the central autonomic network
Authors: Kong Shawn D X , Gordon Christopher J , Hoyos Camilla M , Wassing Rick , D’Rozario Angela , Mowszowski Loren , Ireland Catriona , Palmer Jake R , Grunstein Ronald R , Shine James M , McKinnon Andrew C , Naismith Sharon L 
Published: May 2023

AbstractReduced heart rate variability can be an early sign of autonomic dysfunction in neurodegenerative diseases and may be related to brain dysfunction in the central autonomic network. As yet, such autonomic dysfunction has not been examined during sleep—which is an ideal physiological state to study brain–heart interaction as both the central and peripheral nervous systems behave differently compared to during wakefulness. Therefore, the primary aim of the current study was to examine whether heart rate variability during nocturnal sleep, specifically slow wave (deep) sleep, is associated with central autonomic network functional connectivity in older adults ‘at-risk’ of dementia.Older adults (n = 78; age range = 50–88 years; 64% female) attending a memory clinic for cognitive concerns underwent resting-state functional magnetic resonance imaging and an overnight polysomnography. From these, central autonomic network functional connectivity strength and heart rate variability data during sleep were derived, respectively. High-frequency heart rate variability was extracted to index parasympathetic activity during distinct periods of sleep, including slow wave sleep as well as secondary outcomes of non-rapid eye movement sleep, wake after sleep onset, and rapid eye movement sleep. General linear models were used to examine associations between central autonomic network functional connectivity and high-frequency heart rate variability.Analyses revealed that increased high-frequency heart rate variability during slow wave sleep was associated with stronger functional connectivity (F = 3.98, P = 0.022) in two core brain regions within the central autonomic network, the right anterior insular and posterior midcingulate cortex, as well as stronger functional connectivity (F = 6.21, P = 0.005) between broader central autonomic network brain regions—the right amygdala with three sub-nuclei of the thalamus. There were no significant associations between high-frequency heart rate variability and central autonomic network connectivity during wake after sleep onset or rapid eye movement sleep.These findings show that in older adults ‘at-risk’ of dementia, parasympathetic regulation during slow wave sleep is uniquely linked to differential functional connectivity within both core and broader central autonomic network brain regions. It is possible that dysfunctional brain–heart interactions manifest primarily during this specific period of sleep known for its role in memory and metabolic clearance. Further studies elucidating the pathophysiology and directionality of this relationship should be conducted to determine if heart rate variability drives neurodegeneration, or if brain degeneration within the central autonomic network promotes aberrant heart rate variability.
No Acceptable Losses: Risk, Prevention, and Justice
Authors: Scherz Paul 
Published: May 2023

AbstractBeginning in the nineteenth century, social statistics inspired a vision of society as a population characterized by a certain distribution of risks. The introduction of the risk paradigm has deep implications for central concepts in Christian social ethics like distributive justice, with this vision leading to a new concept of distributive justice as the equal distribution of risk. This essay describes tensions that arise due to the risk paradigm in relation to distributive justice: risks can always be further reduced, risk mitigation creates other risks, and there is no inherent rule of justice for balancing risks. While recognition of shared risk can create social cohesion, it also leads to interest groups struggling over which risks to confront. The essay illustrates these problems with two examples from health care: preventive health programs that manage disease risk through medication, and debates over school closures in respond to the Covid pandemic. Christian bioethics, as it wrestles with issues of justice, must address the problems created by the risk paradigm.
Identification of upper thermal thresholds during development in the endangered Nechako white sturgeon with management implications for a regulated river
Authors: Earhart Madison L , Blanchard Tessa S , Morrison Phillip R , Strowbridge Nicholas , Penman Rachael J , Brauner Colin J , Schulte Patricia M , Baker Daniel W 
Published: May 2023

Abstract
Climate change-induced warming effects are already evident in river ecosystems, and projected increases in temperature will continue to amplify stress on fish communities. In addition, many rivers globally are impacted by dams, which have many negative effects on fishes by altering flow, blocking fish passage, and changing sediment composition. However, in some systems, dams present an opportunity to manage river temperature through regulated releases of cooler water. For example, there is a government mandate for Kenney dam operators in the Nechako river, British Columbia, Canada, to maintain river temperature &lt;20°C in July and August to protect migrating sockeye salmon (Oncorhynchus nerka). However, there is another endangered fish species inhabiting the same river, Nechako white sturgeon (Acipenser transmontanus), and it is unclear if these current temperature regulations, or timing of the regulations, are suitable for spawning and developing sturgeon. In this study, we aimed to identify upper thermal thresholds in white sturgeon embryos and larvae to investigate if exposure to current river temperatures are playing a role in recruitment failure. We incubated embryos and yolk-sac larvae in three environmentally relevant temperatures (14, 18 and 21°C) throughout development to identify thermal thresholds across different levels of biological organization. Our results demonstrate upper thermal thresholds at 21°C across physiological measurements in embryo and yolk-sac larvae white sturgeon. Before hatch, both embryo survival and metabolic rate were reduced at 21°C. After hatch, sublethal consequences continued at 21°C because larval sturgeon had decreased thermal plasticity and a dampened transcriptional response during development. In recent years, the Nechako river has reached 21°C by the end of June, and at this temperature, a decrease in sturgeon performance is evident in most of the traits measured. As such, the thermal thresholds identified here suggest current temperature regulations may not be suitable for developing white sturgeon and future recruitment.