bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new RANS-based added turbulence intensity model for wind-farm flow modelling.
Authors: Delvaux T , Van Der Laan M P , Terrapon V E 
Published: June 2024

Abstract
This work aims to alleviate the memory requirements of the recent wake engineering model described in Criado Risco et al. [1]. The original model relies on a RANS-based look-up table of three-dimensional velocity deficit and added turbulence intensity fields computed for a stand-alone turbine under a wide variety of conditions. The objective is to develop an alternative to the model of Criado Risco et al. [1], particularly in terms of added turbulence intensity, for which little research has been carried out to date. To achieve this, a one-dimensional analytical expression is fitted to the look-up table and generalized to higher dimensions. The turbulence intensity model is then coupled to a velocity deficit model and implemented in PyWake, an open-source wake engineering software. Overall, the new turbulence intensity model is found to provide a reliable description of the RANS look-up table data while reducing by half the memory requirements of the original model. This conclusion is extended to multiple wake situations, for which this work also establishes a direct link between the adequate superposition method and the definition chosen to describe the added turbulence intensity in the wake.
Near-wake measurements and simulations of a floating wind turbine using a four-beam nacelle-based lidar
Authors: Özinan Umut , Gräfe Moritz , Schulz Christian W. , Cheng Po Wen 
Published: June 2024

Abstract
Recent advances in lidar technology have expanded the possibilities for measuring full-scale wind turbine wakes within the atmospheric boundary layer. This study utilizes a four-beam pulsed lidar installed on the nacelle of a floating turbine to measure the near-wake. The wake measurement campaign was conducted on the Floatgen, with lidar measurements reaching up to 2.5 times the rotor diameter distance. These measurements are presented as 10-minute average radial wind speeds. The focus of this study is on the below rated wind speed of 7 m/s. Free flow conditions were assumed at the farthest measurement points, which are located ±0.9 times the rotor diameter from to the rotor center. The sensitivity of lidar measurements to turbulence intensity, vertical wind shear, and significant wave height was investigated. The environmental conditions were categorized into five cases, considering turbulence, vertical shear, and yaw misalignment as well as waves. Two simulation models with different fidelity levels are used to simulate these cases, and the beam-wise radial wind speed predictions are compared with the measurements. A maximum mean absolute error of 11.3% between the measurements and simulations is observed.
Wind Farm Wakes and Farm-to-Farm Interactions: Lidar and Wind Tunnel Tests
Authors: Ahmed W.U. , Moss C. , Roy S. , Shams Solari M. , Puccioni M. , Panthi K. , Moriarty P. , Iungo G.V. 
Published: June 2024

Abstract
Recent experimental and numerical evidence has shown that the cumulative wake generated from the overlapping of multiple wakes within a wind farm could reduce power performance and enhance fatigue loads of wind turbines installed in neighboring downstream wind farms and may also extend up to distances one order of magnitude larger than those typically considered for intra-farm wake interactions. Similar to individual wind turbine wakes, wind farm wakes have a velocity deficit and added turbulence intensity, both affected by the turbine rotor thrust forces and the incoming turbulence intensity. Therefore, the evolution of wind farm wakes will vary for different operational and atmospheric conditions. In this paper, lidar measurements collected during the American WAKE experimeNt (AWAKEN) and wind tunnel tests of wind farms reproduced by porous disks are leveraged to investigate wind farm wakes.
Exile, Incorporated
Authors: Liebermann Rosanne 
Published: June 2024

Abstract
The book of Ezekiel makes rhetorical use of the human body to construct an exile-centred Judean identity. This focus on the body is inextricable from Ezekiel’s setting in the sixth-century BCE Judean exile to Babylonia. In such a context of upheaval, all the displaced group reliably retains are their bodies. Even so, the material surroundings of those bodies change completely, calling previously accepted ways of being into question. The book of Ezekiel reveals acute awareness of this situation, evoking bodily practices and embodied experiences that serve to construct a Judean identity based on existence outside of the land of Judah. This identity excludes both non-Judeans and the Judeans who remained in Judah. The book of Ezekiel seeks to achieve this exclusion via descriptions of bodily practices—including circumcision, dress, and the observance of a cultic calendar—that distinguish its constructed in-group of exiled Judeans from outsiders. Ezekiel also evokes the embodied emotion of disgust regarding the bodies of those with “outsider” practices, which in turn encourages the practice of segregation and endogamy within the in-group. Focusing on the bodies in the book of Ezekiel also highlights how the text presents hierarchies within the exilic Judean group, which itself contains bodies differentiated by gender and priestly or nonpriestly descent. Reading the text in this way reveals how the book of Ezekiel constructs a model of a variegated community able to embody a Judean identity that not only survived but also was based on life outside of the land of Judah.
Exiled Bodies, Ezekiel’s Bodies
Authors: Liebermann Rosanne 
Published: June 2024

Abstract
The book of Ezekiel’s setting within the sixth-century BCE Judean displacement to Babylonia is largely consistent with what is known historically of this time period. While redactional and text-critical evidence indicates that the book was a work in progress until the second century BCE, its focus on the Judean community in diaspora is central to its outlook. The “material turn” in the studies of both religion and migration has revealed that bodily practices and embodied experiences are decisive for religious and other group identities, especially in contexts of upheaval, when other material identity markers become insecure. Via reference to practice theory, new materialism, and phenomenology (including the study of emotions, especially the emotion of disgust), the chapter argues that the book of Ezekiel makes rhetorical use of the body to construct an ethno-religious community limited to the Judeans who experienced displacement from their ancestral land.
Women’s Bodies
Authors: Liebermann Rosanne 
Published: June 2024

Abstract
The book of Ezekiel’s construction of an exclusive in-group identity relies on the participation of women, especially when it comes to marriage and reproduction. Therefore, the text has to account for feminine bodily practices, even though its idealized Judean identity is based on a masculine default. These feminine bodily practices come into focus in Ezekiel 16 and 23, which address behaviours related to marriage and reproduction at various stages of a metaphorical woman’s life, including birth, puberty, marriage (and infidelity), motherhood, and menopause. Via these descriptions, the book of Ezekiel communicates expectations concerning the behaviour of women in its constructed in-group, evoking the emotion of disgust regarding those who behave differently. Meanwhile, Ezekiel 13 condemns women who exercise what the book considers improper religious authority, using gendered language to undermine their bodily purity in contrast to that of those properly responsible for religious activities: the masculine priesthood.
Sublime Bodies
Authors: Liebermann Rosanne 
Published: June 2024

Abstract
The book of Ezekiel presents Yhwh as having a masculine, humanoid body that is so defined by its purity that it cannot remain in any unclean place. This is the reason for Yhwh abandoning the Jerusalem temple to destruction (Ezekiel 8–11), and it is the guiding principle behind Ezekiel’s description of an imagined, idealized new temple (Ezekiel 40–48). This new temple is constructed according to concentric circles of purity, whereby Yhwh occupies the purest, innermost part of the building, surrounded and protected by the Zadokite priesthood, whose bodies mirror his in their masculine gender and level of purity (achieved via special practices of dress, eating, drinking, mourning, and marriage). In the Babylonian exile, where such a temple and priesthood cannot be realized, the prophet Ezekiel is described as uniquely upholding a priestly level of purity to the extent possible, making him the appropriate mediator between Yhwh and his people.
Food Improvement Agents (Additives, Enzymes, Flavourings), and Use of Extraction Solvents
Authors: Schebesta Hanna , Purnhagen Kai 
Published: June 2024

Abstract
This chapter elaborates on the EU law frameworks on food improvement agents. It starts by introducing the so-called Food Improvement Agents Package (section 9.2) and explores in more detail the specific regulation of each agent, namely food additives (section 9.3), food enzymes (section 9.4), food flavourings (section 9.5), and processing aids (section 9.6). The common authorization procedure for these agents in Regulation 234/2011 (section 9.7) is discussed. This is followed by an exploration of the use of extraction solvents (section 9.8). The chapter concludes by analysing current and future trends about food improvement agents in EU food law (section 9.9).
The Meaning of Life and Transcendence
Authors: Cottingham John 
Published: June 2024

AbstractAtheism and naturalism have become the default positions in academic philosophy, and this is reflected in much of the contemporary work on meaning in life, which assumes what might be called an ‘immanentist’ perspective, according to which the sources of meaning must be sought entirely within the sphere of our purely human pursuits and activities. This chapter, by contrast, lays stress on the yearning for transcendence that seems an ineradicable part of our nature. It is argued that no human life can be fully meaningful if it denies or supresses that yearning, and that purely immanent goals cannot satisfy it. This in turn points to the need for humans to find a vehicle whereby they can enact their longing for an ultimate source of meaning and value, and seek to align themselves with the transcendent good for which they long.
Stakeholder perceptions of and attitudes towards problematic polypharmacy and prescribing cascades: a qualitative study
Authors: Jennings Aisling A , Doherty Ann Sinéad , Clyne Barbara , Boland Fiona , Moriarty Frank , Fahey Tom , Hally Larry , Kennelly Seán P , Wallace Emma 
Published: June 2024

Abstract

Introduction
Problematic polypharmacy is the prescribing of five or more medications potentially inappropriately. Unintentional prescribing cascades represent an under-researched aspect of problematic polypharmacy and occur when an adverse drug reaction (ADR) is misinterpreted as a new symptom resulting in the initiation of a new medication. The aim of this study was to elicit key stakeholders’ perceptions of and attitudes towards problematic polypharmacy, with a focus on prescribing cascades.

Methods
qualitative one-to-one semi-structured interviews were conducted with predefined key stakeholder groups. Inductive thematic analysis was employed.

Results
Thirty-one stakeholders were interviewed: six patients, two carers, seven general practitioners, eight pharmacists, four hospital doctors, two professional organisation representatives and two policymakers. Three main themes were identified: (i) ADRs and prescribing cascades—a necessary evil. Healthcare professionals (HCPs) expressed concern that experiencing an ADR would negatively impact patients’ confidence in their doctor. However, patients viewed ADRs pragmatically as an unpredictable risk. (ii) Balancing the risk/benefit tipping point. The complexity of prescribing decisions in the context of polypharmacy made balancing this tipping point challenging. Consequently, HCPs avoided medication changes. (iii) The minefield of medication reconciliation. Stakeholders, including patients and carers, viewed medication reconciliation as a perilous activity due to systemic communication deficits.

Conclusion
Stakeholders believed that at a certain depth of polypharmacy, the risk that a new symptom is being caused by an existing medication becomes incalculable. Therefore, in the absence of harm, medication changes were avoided. However, medication reconciliation post hospital discharge compelled prescribing decisions and was seen as a high-risk activity by stakeholders.
Population decline of the saguaro cactus throughout its distribution is associated with climate change
Authors: Félix-Burruel Ricardo E , Larios Eugenio , González Edgar J , Búrquez Alberto 
Published: June 2024

Abstract

Background and Aims
Climate change is a global phenomenon affecting species, which in arid regions will translate into more frequent and intense periods of drought. The Sonoran Desert is becoming hotter and drier, and many organisms are rapidly changing in abundance and distribution. These population attributes depend directly on the dynamics of the population, which in turn depends on the vital rates of its individuals; yet few studies have documented the effects of climate change on the population dynamics of keystone species such as the saguaro cactus (Carnegiea gigantea). Although saguaros have traits that enable them to withstand present environmental conditions, climate change could make them vulnerable if forced beyond their tolerance limits.

Methods
We evaluated the effect of climate change on 13 saguaro populations spanning most of the species’ distribution range. Using field data from 2014 to 2016, we built an integral projection model (IPM) describing the environmentally explicit dynamics of the populations. We used this IPM, along with projections of two climate change scenarios and one no-change scenario, to predict population sizes (N) and growth rates (λ) from 2017 to 2099 and compared these scenarios to demonstrate the effect of climate change on the future of saguaro cactuses.

Key Results
We found that all populations will decline, mainly due to future increases in drought, mostly hindering recruitment. However, the decline will be different across populations, since those located near the coast will be affected by harsher drought events than those located further inland.

Conclusions
Our study demonstrates that climate change and its associated increase in drought pose a significant threat to the saguaro cactus populations in the Sonoran Desert. Our findings indicate that the recruitment of saguaros, vital for establishing new individuals, is particularly vulnerable to intensifying drought conditions. Importantly, regional climate trends will have different impacts on saguaro populations across their distribution range.
sincFold: end-to-end learning of short- and long-range interactions in RNA secondary structure
Authors: Bugnon Leandro A , Di Persia Leandro , Gerard Matias , Raad Jonathan , Prochetto Santiago , Fenoy Emilio , Chorostecki Uciel , Ariel Federico , Stegmayer Georgina , Milone Diego H 
Published: June 2024

Abstract

Motivation
Coding and noncoding RNA molecules participate in many important biological processes. Noncoding RNAs fold into well-defined secondary structures to exert their functions. However, the computational prediction of the secondary structure from a raw RNA sequence is a long-standing unsolved problem, which after decades of almost unchanged performance has now re-emerged due to deep learning. Traditional RNA secondary structure prediction algorithms have been mostly based on thermodynamic models and dynamic programming for free energy minimization. More recently deep learning methods have shown competitive performance compared with the classical ones, but there is still a wide margin for improvement.

Results
In this work we present sincFold, an end-to-end deep learning approach, that predicts the nucleotides contact matrix using only the RNA sequence as input. The model is based on 1D and 2D residual neural networks that can learn short- and long-range interaction patterns. We show that structures can be accurately predicted with minimal physical assumptions. Extensive experiments were conducted on several benchmark datasets, considering sequence homology and cross-family validation. sincFold was compared with classical methods and recent deep learning models, showing that it can outperform the state-of-the-art methods.
Peptide-based drug discovery through artificial intelligence: towards an autonomous design of therapeutic peptides
Authors: Goles Montserrat , Daza Anamaría , Cabas-Mora Gabriel , Sarmiento-Varón Lindybeth , Sepúlveda-Yañez Julieta , Anvari-Kazemabad Hoda , Davari Mehdi D , Uribe-Paredes Roberto , Olivera-Nappa Álvaro , Navarrete Marcelo A , Medina-Ortiz David 
Published: June 2024

Abstract
With their diverse biological activities, peptides are promising candidates for therapeutic applications, showing antimicrobial, antitumour and hormonal signalling capabilities. Despite their advantages, therapeutic peptides face challenges such as short half-life, limited oral bioavailability and susceptibility to plasma degradation. The rise of computational tools and artificial intelligence (AI) in peptide research has spurred the development of advanced methodologies and databases that are pivotal in the exploration of these complex macromolecules. This perspective delves into integrating AI in peptide development, encompassing classifier methods, predictive systems and the avant-garde design facilitated by deep-generative models like generative adversarial networks and variational autoencoders. There are still challenges, such as the need for processing optimization and careful validation of predictive models. This work outlines traditional strategies for machine learning model construction and training techniques and proposes a comprehensive AI-assisted peptide design and validation pipeline. The evolving landscape of peptide design using AI is emphasized, showcasing the practicality of these methods in expediting the development and discovery of novel peptides within the context of peptide-based drug discovery.
Provision of choline chloride to the bovine preimplantation embryo alters postnatal body size and DNA methylation
Authors: Haimon McKenzie L J , Estrada-Cortés Eliab , Amaral Thiago F , Martin Hélène , Jeensuk Surawich , Block Jeremy , Heredia Daniella , Venturini M , Rojas Camila Santos , Gonella-Diaza Angela M , DiLorenzo Nicolas , Scheffler Tracy L , Dufour Pascal , Sirard Marc-André , de Melo Gabriela Dalmaso , Pohler Ky G , Hansen Peter J 
Published: June 2024

Abstract
Choline is a vital micronutrient. In this study, we aimed to confirm, and expand on previous findings, how choline impacts embryos from the first 7 days of development to affect postnatal phenotype. Bos indicus embryos were cultured in a choline-free medium (termed vehicle) or medium supplemented with 1.8 mM choline. Blastocyst-stage embryos were transferred into crossbred recipients. Once born, calves were evaluated at birth, 94 days, 178 days, and at weaning (average age = 239 days). Following weaning, all calves were enrolled into a feed efficiency trial before being separated by sex, with males being slaughtered at ~580 days of age. Results confirm that exposure of 1.8 mM choline chloride during the first 7 days of development alters postnatal characteristics of the resultant calves. Calves of both sexes from choline-treated embryos were consistently heavier through weaning and males had heavier testes at 3 months of age. There were sex-dependent alterations in DNA methylation in whole blood caused by choline treatment. After weaning, feed efficiency was affected by an interaction with sex, with choline calves being more efficient for females and less efficient for males. Calves from choline-treated embryos were heavier, or tended to be heavier, than calves from vehicle embryos at all observations after weaning. Carcass weight was heavier for choline calves and the cross-sectional area of the longissimus thoracis muscle was increased by choline.
Fast matrix completion in epigenetic methylation studies with informative covariates
Authors: Ribaud Mélina , Labbe Aurélie , Fouda Khaled , Oualkacha Karim 
Published: June 2024

Abstract
DNA methylation is an important epigenetic mark that modulates gene expression through the inhibition of transcriptional proteins binding to DNA. As in many other omics experiments, the issue of missing values is an important one, and appropriate imputation techniques are important in avoiding an unnecessary sample size reduction as well as to optimally leverage the information collected. We consider the case where relatively few samples are processed via an expensive high-density whole genome bisulfite sequencing (WGBS) strategy and a larger number of samples is processed using more affordable low-density, array-based technologies. In such cases, one can impute the low-coverage (array-based) methylation data using the high-density information provided by the WGBS samples. In this paper, we propose an efficient Linear Model of Coregionalisation with informative Covariates (LMCC) to predict missing values based on observed values and covariates. Our model assumes that at each site, the methylation vector of all samples is linked to the set of fixed factors (covariates) and a set of latent factors. Furthermore, we exploit the functional nature of the data and the spatial correlation across sites by assuming some Gaussian processes on the fixed and latent coefficient vectors, respectively. Our simulations show that the use of covariates can significantly improve the accuracy of imputed values, especially in cases where missing data contain some relevant information about the explanatory variable. We also showed that our proposed model is particularly efficient when the number of columns is much greater than the number of rows—which is usually the case in methylation data analysis. Finally, we apply and compare our proposed method with alternative approaches on two real methylation datasets, showing how covariates such as cell type, tissue type or age can enhance the accuracy of imputed values.
Disrupted cerebellar structural connectome in spinocerebellar ataxia type 3 and its association with transcriptional profiles
Authors: Dong Xinyi , Liu Bing , Huang Weijie , Chen Haojie , Zhang Yunhao , Yao Zeshan , Shmuel Amir , Yang Aocai , Dai Zhengjia , Ma Guolin , Shu Ni 
Published: June 2024

Abstract
Spinocerebellar ataxia type 3 (SCA3) is primarily characterized by progressive cerebellar degeneration, including gray matter atrophy and disrupted anatomical and functional connectivity. The alterations of cerebellar white matter structural network in SCA3 and the underlying neurobiological mechanism remain unknown. Using a cohort of 20 patients with SCA3 and 20 healthy controls, we constructed cerebellar structural networks from diffusion MRI and investigated alterations of topological organization. Then, we mapped the alterations with transcriptome data from the Allen Human Brain Atlas to identify possible biological mechanisms for regional selective vulnerability to white matter damage. Compared with healthy controls, SCA3 patients exhibited reduced global and nodal efficiency, along with a widespread decrease in edge strength, particularly affecting edges connected to hub regions. The strength of inter-module connections was lower in SCA3 group and negatively correlated with the Scale for the Assessment and Rating of Ataxia score, International Cooperative Ataxia Rating Scale score, and cytosine–adenine–guanine repeat number. Moreover, the transcriptome–connectome association study identified the expression of genes involved in synapse-related and metabolic biological processes. These findings suggest a mechanism of white matter vulnerability and a potential image biomarker for the disease severity, providing insights into neurodegeneration and pathogenesis in this disease.