bluuebunny/crossref_metadata_2025_split huggingface dataset:
2 Framing
Authors: Cobussen Marcel 
Published: November 2022

This chapter sets out the ways in which sound studies can contribute to our thinking about place; listening to a place can help us to perceive it as an active and unstable agent, participating and constituting in the moment the action takes place. The environment around us affects the absorption, reverberation, and diffraction of sound; therefore, sound gives us an indication of the space it is in. Additionally, the activities that occur in a place – along with their associated sounds – cause the place to be given meaning. In other words, a place provides a stage for a specific practice, and is an intersection of happenings.
We then discuss why sounds are impactful and important for our culture; sound offers us a possibility to explore and reveal new ways of knowing, and to gain new knowledge of how human and non-human agents relate to one another and their environment. The dominance of the eye in Western history is detailed, through to the modern rise of ‘auditory culture’ and ‘sound studies’.
The chapter also outlines the intent to sketch some contours of what sonic materialism could be(come) and how it deviates from the conceptual frameworks which have dominated Western culture and discourses. The objective behind this is to create affective relationships to places, to explore various listening attitudes, and to give a voice to the less ear-catching sounds of everyday life. The development of sonic materialism is described as being a quest into how the sonic can contribute to and participate in current philosophical discourses, without being encapsulated beforehand in the written or spoken language typical of philosophy or theorizing. In other words, it involves thinking in and through the sonic, rather than thinking about it. The identity of sounds is discussed, as well as the movement involved in creating them.
3 The Familiarity of Everyday Sounds
Authors: Cobussen Marcel 
Published: November 2022

In this chapter, sonic environments are described as characteristic traits of a place, which are perceived but not noticed, to the listener’s pleasure or annoyance. Under the topic of ‘annoyance’, misophonia and ‘the Hum’ are discussed, while under ‘pleasure’, Autonomous Sensory Meridian Response (ASMR) comes into play.
Everyday sounds are described as comparable to music, rather than inferior to it. There is a discussion of “disciplining sounds”, where sounds guide, control, and manipulate us. The use of sound in this way shows us the extent to which we do actually monitor what is going on around us aurally, even without consciously paying attention.
Finally, the chapter covers windows and doors, and the way in which they carry out sound management, preventing unwanted sounds from entering the house as best they can. As a result, windows and doors are argued to have a social, political, and ethical role which is closely connected to the sonic ambiance.
5 The Ethics and Politics of Everyday Sounds
Authors: Cobussen Marcel 
Published: November 2022

This chapter turns to solastalgia – a form of psychic or existential distress caused by changes in the home environment. Sonic solastalgia, in particular, is discussed in relation to the construction of a new highway or wind farm, the chopping down of trees, etc.
The author then discusses resonance communities, and our inability to be entirely separated from other sonic environments. This means that sound is a (co-)constituent of our social lives – it can unite or divide, include or exclude, homogenize or heterogenized. It is set out that in and through sound we can express how we live together and share our common daily experiences.
The way in which sounds are political is detailed – sounds influence modes of perception and are a means of (re)organizing private and public spaces. They also influence human agents on a cultural and pre-cultural (biological) level. Additionally, interactive sonic encounters are shown to relate to ethics.
Exploring Global Climate Model Downscaling Based on Tile-Level Output
Authors: Admasu Lualawi Mareshet , Grant Luke , Thiery Wim 
Published: November 2022

Abstract
Statistical and dynamical modeling techniques are used to downscale global climate model (GCM) outputs to practical resolutions for local- or regional-scale applications. Current techniques do not incorporate the effects of land-use and land-cover changes, although research has shown that such changes can substantially affect climate locally. Here, we explore a new downscaling technique that uses tile-level GCM outputs provided under phase 6 of the Coupled Model Intercomparison Project (CMIP6). The method, land-cover tile downscaling (LTD), spatially locates the tile-level GCM outputs by mapping them to corresponding classes in high-resolution land-cover maps. Furthermore, it applies an elevation-based correction to account for the effect of topography on the local climate. LTD is applied to near-surface temperature outputs from the Community Earth System Model, version 2 (CESM2) and U.K. Earth System Model, version 1 (UKESM1), and surface temperature output from CESM2 and evaluated against observations. In comparison with grid-averaged control data, LTD outputs show an overall bias reduction that is not spatially consistent. Moreover, LTD performs better on air temperature data than on surface temperature and better on areas dominated by primary/secondary land and crops than on urban land. This could arise from simplifications in methods, like land-cover reclassification and simplified lapse rate estimates. However, the difference in response between the two variables and land-cover types implies that biases also stem from model structural features involved in estimating their tile-level outputs. This is supported by the differences between grid average data provided by the models and the same data reconstructed from tile-level outputs. Therefore, a thorough evaluation and quality control of tile-level outputs is recommended.
Standing Eddies in Glacial Fjords and Their Role in Fjord Circulation and Melt
Authors: Zhao Ken X. , Stewart Andrew L. , McWilliams James C. , Fenty Ian G. , Rignot Eric J. 
Published: November 2022

Abstract
Glacial fjord circulation modulates the connection between marine-terminating glaciers and the ocean currents offshore. These fjords exhibit a complex 3D circulation with overturning and horizontal recirculation components, which are both primarily driven by water mass transformation at the head of the fjord via subglacial discharge plumes and distributed meltwater plumes. However, little is known about the 3D circulation in realistic fjord geometries. In this study, we present high-resolution numerical simulations of three glacial fjords (Ilulissat, Sermilik, and Kangerdlugssuaq), which exhibit along-fjord overturning circulations similar to previous studies. However, one important new phenomenon that deviates from previous results is the emergence of multiple standing eddies in each of the simulated fjords, as a result of realistic fjord geometries. These standing eddies are long-lived, take months to spin up, and prefer locations over the widest regions of deep-water fjords, with some that periodically merge with other eddies. The residence time of Lagrangian particles within these eddies are significantly larger than waters outside of the eddies. These eddies are most significant for two reasons: 1) they account for a majority of the vorticity dissipation required to balance the vorticity generated by discharge and meltwater plume entrainment and act to spin down the overall recirculation and 2) if the eddies prefer locations near the ice face, their azimuthal velocities can significantly increase melt rates. Therefore, the existence of standing eddies is an important factor to consider in glacial fjord circulation and melt rates and should be taken into account in models and observations.
Understanding Energy Pathways in the Gulf Stream
Authors: Contreras Marcela , Renault Lionel , Marchesiello Patrick 
Published: November 2022

Abstract
The Gulf Stream (GS) is one of the strongest ocean currents on the planet. Eddy-rich resolution models are needed to properly represent the dynamics of the GS; however, kinetic energy (KE) can be in excess in these models if not dissipated efficiently. The question of how and how much energy is dissipated and in particular how it flows through ocean scales thus remains an important and largely unanswered question. Using a high-resolution (∼2 km) ocean model [Coastal and Regional Ocean Community (CROCO)], we characterize the spatial and temporal distribution of turbulent cascades in the GS based on a coarse-grained method. We show that the balanced flow is associated with an inverse cascade while the forward cascade is explained by ageostrophic advection associated with frontogenesis. Downscale fluxes are dominant at scales smaller than about 20 km near the surface and most intense at the GS North Wall. There is also strong seasonal variability in KE flux, with the forward cascade intensifying in winter and the inverse cascade later in spring. The forward cascade, which represents an interior route to dissipation, is compared with both numerical and boundary dissipation processes. The contribution of interior dissipation is an order of magnitude smaller than that of the other energy sinks. We thus evaluate the sensitivity of horizontal momentum advection schemes on energy dissipation and show that the decrease in numerical dissipation in a high-order scheme leads to an increase in dissipation at the boundaries, not in the downscale flux.
Objectively Diagnosing Characteristics of Mesoscale Organization from Radar Reflectivity and Ambient Winds
Authors: Short Ewan , Lane Todd P. , Vincent Claire L. 
Published: November 2022

Abstract
In the classical model of mesoscale convective systems (MCSs), a system generates new convective cells on the downshear side of its cold pool, with the cells fed at low levels from the front, and the stratiform cloud trailing behind the system in the upshear direction, where “front” and “behind” typically refer to the system’s ground-relative velocity. In this study we present an algorithm for identifying and tracking MCSs in radar reflectivity data, and objectively diagnosing organizational characteristics related to the classical model, namely, the offset of stratiform cloud from convective cloud relative to system velocity, the low-level inflow direction, and the shear-relative tilt and propagation directions. When applied to the 15-yr radar record covering the Darwin region of northern Australia, the algorithm indicates that 65%–80% of MCS observations are consistent with the classical model, at least when the four classifications can be made unambiguously. However, these observed characteristics occur almost entirely in the drier phases of the Australian monsoon. During the humid, active monsoon phase, observed characteristics consistent with the classical model are rare, and most systems exhibit nonclassical upshear propagation.

Significance Statement
In this study we developed a computer program for tracking large storms in radar data. The program tracks storms through time and space, recording their three-dimensional structure. Knowledge of this structure allows our program to automatically put storms into different, commonly used categories. These categories provide clues about the processes that can make storms grow, persist, or decay. Our computer program is useful because the classification process is very time consuming when done by humans. Also, when applied to radar datasets from northern Australia, our program suggests most large storms are consistent with standard theories of what make storms grow and persist. However, when the air is very humid, large storms inconsistent with standard theories become common.
Sarcopenia is associated with mild-to-moderate chronic kidney disease in Chinese community-dwelling older men but not in women
Authors: Chen Xiaoyu , Zhu Xiaoyan , Han Peipei , Zhang Yuanyuan , He Mian , Zhang Yuhui , Liu Jinghuan , Tang Jiawei , Zhang Yisong , Zheng Yaqing , Zhang Ziwei , Li Ming , Guo Qi 
Published: November 2022

Objective To determine whether a relationship exists between sarcopenia, including its individual components (muscle mass, muscle strength and gait speed), and mild-to-moderate chronic kidney disease (CKD) in Chinese older adults. Methods This cross-sectional study comprised participants aged ≥60 years from Tianjin and Shanghai, China, who joined a national free physical examination program between 2014 and 2019, and consented to study inclusion. Sarcopenia was defined according to the Asian Working Group for Sarcopenia (2019 version). Mild-to-moderate CKD was defined as estimated glomerular filtration rate (eGFR) between 45 ml/min/1.73 m2 and 60 ml/min/1.73 m2. Results A total of 1627 participants were included (mean age, 69.32 ± 6.17 years; 43.8% male). Sarcopenia was significantly associated with mild-to-moderate CKD in men but not women. Among three physical performance components, slow gait speed (odds ratio 1.89, 95% confidence interval 1.38, 2.58) was associated with mild-to-moderate CKD in both men and women after adjusting for all other variables. Conclusions Sarcopenia was closely associated with mild-to-moderate CKD in older men, and slow gait speed was related to mild-to-moderate CKD in men and women. These findings may help guide better diagnosis and management of CKD in the context of slow gait speed, and facilitate earlier CKD detection and appropriate intervention in older adults.
Transfer learning for genotype–phenotype prediction using deep learning models
Authors: Muneeb Muhammad , Feng Samuel , Henschel Andreas 
Published: November 2022

Abstract
Background
For some understudied populations, genotype data is minimal for genotype-phenotype prediction. However, we can use the data of some other large populations to learn about the disease-causing SNPs and use that knowledge for the genotype-phenotype prediction of small populations. This manuscript illustrated that transfer learning is applicable for genotype data and genotype-phenotype prediction.

Results
Using HAPGEN2 and PhenotypeSimulator, we generated eight phenotypes for 500 cases/500 controls (CEU, large population) and 100 cases/100 controls (YRI, small populations). We considered 5 (4 phenotypes) and 10 (4 phenotypes) different risk SNPs for each phenotype to evaluate the proposed method. The improved accuracy with transfer learning for eight different phenotypes was between 2 and 14.2 percent. The two-tailed p-value between the classification accuracies for all phenotypes without transfer learning and with transfer learning was 0.0306 for five risk SNPs phenotypes and 0.0478 for ten risk SNPs phenotypes.

Conclusion
The proposed pipeline is used to transfer knowledge for the case/control classification of the small population. In addition, we argue that this method can also be used in the realm of endangered species and personalized medicine. If the large population data is extensive compared to small population data, expect transfer learning results to improve significantly. We show that Transfer learning is capable to create powerful models for genotype-phenotype predictions in large, well-studied populations and fine-tune these models to populations were data is sparse.
Persistent memory as an effective alternative to random access memory in metagenome assembly
Authors: Sun Jingchao , Qiu Zhining , Egan Rob , Ho Harrison , Li Yue , Wang Zhong 
Published: November 2022

Abstract
Background
The assembly of metagenomes decomposes members of complex microbe communities and allows the characterization of these genomes without laborious cultivation or single-cell metagenomics. Metagenome assembly is a process that is memory intensive and time consuming. Multi-terabyte sequences can become too large to be assembled on a single computer node, and there is no reliable method to predict the memory requirement due to data-specific memory consumption pattern. Currently, out-of-memory (OOM) is one of the most prevalent factors that causes metagenome assembly failures.

Results
In this study, we explored the possibility of using Persistent Memory (PMem) as a less expensive substitute for dynamic random access memory (DRAM) to reduce OOM and increase the scalability of metagenome assemblers. We evaluated the execution time and memory usage of three popular metagenome assemblers (MetaSPAdes, MEGAHIT, and MetaHipMer2) in datasets up to one terabase. We found that PMem can enable metagenome assemblers on terabyte-sized datasets by partially or fully substituting DRAM. Depending on the configured DRAM/PMEM ratio, running metagenome assemblies with PMem can achieve a similar speed as DRAM, while in the worst case it showed a roughly two-fold slowdown. In addition, different assemblers displayed distinct memory/speed trade-offs in the same hardware/software environment.

Conclusions
We demonstrated that PMem is capable of expanding the capacity of DRAM to allow larger metagenome assembly with a potential tradeoff in speed. Because PMem can be used directly without any application-specific code modification, these findings are likely to be generalized to other memory-intensive bioinformatics applications.
ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization
Authors: Tamasco Gustavo , Kumar Manish , Zengler Karsten , Silva-Rocha Rafael , da Silva Ricardo Roberto 
Published: November 2022

Abstract
Background
Genome-scale metabolic reconstruction tools have been developed in the last decades. They have helped to reconstruct eukaryotic and prokaryotic metabolic models, which have contributed to fields, e.g., genetic engineering, drug discovery, prediction of phenotypes, and other model-driven discoveries. However, the use of these programs requires a high level of bioinformatic skills. Moreover, the functionalities required to build models are scattered throughout multiple tools, requiring knowledge and experience for utilizing several tools.

Results
Here we present ChiMera, which combines tools used for model reconstruction, prediction, and visualization. ChiMera uses CarveMe in the reconstruction module, generating a gap-filled draft reconstruction able to produce growth predictions using flux balance analysis for gram-positive and gram-negative bacteria. ChiMera also contains two modules for metabolic network visualization. The first module generates maps for the most important pathways, e.g., glycolysis, nucleotides and amino acids biosynthesis, fatty acid oxidation and biosynthesis and core-metabolism. The second module produces a genome-wide metabolic map, which can be used to retrieve KEGG pathway information for each compound in the model. A module to investigate gene essentiality and knockout is also present.

Conclusions
Overall, ChiMera uses automation algorithms to combine a variety of tools to automatically perform model creation, gap-filling, flux balance analysis (FBA), and metabolic network visualization. ChiMera models readily provide metabolic insights that can aid genetic engineering projects, prediction of phenotypes, and model-driven discoveries.
Mathematical model of the cell signaling pathway based on the extended Boolean network model with a stochastic process
Authors: Kim Minsoo , Kim Eunjung 
Published: November 2022

AbstractBackgroundIn cell signaling pathways, proteins interact with each other to determine cell fate in response to either cell-extrinsic (micro-environmental) or intrinsic cues. One of the well-studied pathways, the mitogen-activated protein kinase (MAPK) signaling pathway, regulates cell processes such as differentiation, proliferation, apoptosis, and survival in response to various micro-environmental stimuli in eukaryotes. Upon micro-environmental stimulus, receptors on the cell membrane become activated. Activated receptors initiate a cascade of protein activation in the MAPK pathway. This activation involves protein binding, creating scaffold proteins, which are known to facilitate effective MAPK signaling transduction.ResultsThis paper presents a novel mathematical model of a cell signaling pathway coordinated by protein scaffolding. The model is based on the extended Boolean network approach with stochastic processes. Protein production or decay in a cell was modeled considering the stochastic process, whereas the protein–protein interactions were modeled based on the extended Boolean network approach. Our model fills a gap in the binary set applied to previous models. The model simultaneously considers the stochastic process directly. Using the model, we simulated a simplified mitogen-activated protein kinase (MAPK) signaling pathway upon stimulation of both a single receptor at the initial time and multiple receptors at several time points. Our simulations showed that the signal is amplified as it travels down to the pathway from the receptor, generating substantially amplified downstream ERK activity. The noise generated by the stochastic process of protein self-activity in the model was also amplified as the signaling propagated through the pathway.ConclusionsThe signaling transduction in a simplified MAPK signaling pathway could be explained by a mathematical model based on the extended Boolean network model with a stochastic process. The model simulations demonstrated signaling amplifications when it travels downstream, which was already observed in experimental settings. We also highlight the importance of stochastic activity in regulating protein inactivation.
Gene expression profile for different susceptibilities to sound stimulation: a comparative study on brainstems between two inbred laboratory mouse strains
Authors: Zhu Lina , Chen Deng , Lin Xin , Liu Ling 
Published: November 2022

Abstract
Background
DBA/1 mice have a higher susceptibility to generalized audiogenic seizures (AGSz) and seizure-induced respiratory arrest (S-IRA) than C57/BL6 mice. The gene expression profile might be potentially related to this difference. This study aimed to investigate the susceptibility difference in AGSz and S-IRA between DBA/1 and C57BL/6 mice by profiling long noncoding RNAs (lncRNAs) and mRNA expression.

Methods
We compared lncRNAs and mRNAs from the brainstem of the two strains with Arraystar Mouse lncRNA Microarray V3.0 (Arraystar, Rockville, MD). Gene Ontology (GO) and pathway analyses were performed to determine the potentially related biological functions and pathways based on differentially expressed mRNAs. qRT–PCR was carried out to validate the results.

Results
A total of 897 lncRNAs and 438 mRNAs were differentially expressed (fold change ≥2, P < 0.05), of which 192 lncRNAs were upregulated and 705 lncRNAs were downregulated. A total of 138 mRNAs were upregulated, and 300 mRNAs were downregulated. In terms of specific mRNAs, Htr5b, Gabra2, Hspa1b and Gfra1 may be related to AGSz or S-IRA. Additionally, lncRNA Neat1 may participate in the difference in susceptibility. GO and pathway analyses suggested that TGF-β signaling, metabolic process and MHC protein complex could be involved in these differences. Coexpression analysis identified 9 differentially expressed antisense lncRNAs and 115 long intergenic noncoding RNAs (lincRNAs), and 2010012P19Rik and its adjacent RNA Tnfsf12-Tnfsf13 may have participated in S-IRA by regulating sympathetic neuron function. The results of the qRT–PCR of five selected lncRNAs (AK038711, Gm11762, 1500004A13Rik, AA388235 and Neat1) and four selected mRNAs (Hspa1b, Htr5b, Gabra2 and Gfra1) were consistent with those obtained by microarray.

Conclusion
We concluded that TGF-β signaling and metabolic process may contribute to the differential sensitivity to AGSz and S-IRA. Among mRNAs, Htr5b, Gabra2, Hspa1b and Gfra1 could potentially influence the susceptibility. LncRNA Neat1 and 2010012P19Rik may also contribute to the different response to sound stimulation. Further studies should be carried out to explore the underlying functions and mechanisms of differentially expressed RNAs.