bluuebunny/crossref_metadata_2025_split huggingface dataset:
Propagation of a precursory detachment front along a seismogenic plate interface in a rate–state friction model of earthquake cycles
Authors: Kato Naoyuki 
Published: August 2021

SUMMARYA numerical simulation of earthquake cycles at the subduction zone of a plate interface was conducted, using a rate- and state-dependent friction law, to examine aseismic sliding processes propagating into a locked plate interface. In the model, a reverse fault is assumed in a 2-D uniform elastic half-space, and relative plate motion is imposed with a constant velocity. Simulated earthquakes occur repeatedly at a shallower seismogenic plate interface with a velocity-weakening frictional property, while stable sliding occurs in the deeper part, in which a velocity-strengthening frictional property is assumed. During interseismic periods, deep stable sliding causes shear stress to concentrate at the deeper edge of the locked plate interface, and a partial drop in stress occurs, resulting in plate detachment. The resulting detachment front propagates upwards along the seismogenic plate interface until an earthquake occurs, causing aseismic sliding with a sliding velocity significantly lower than the imposed relative plate velocity. The propagation velocity of the detachment front is almost constant in each case, and it is proportional to the relative plate velocity and inversely proportional to the effective normal stress. Episodic events of increased slip velocity occur in the latter half of an interseismic period when the characteristic slip distance is small. Updip propagation of episodic slip is arrested by a low stress barrier, and episodic slips backpropagate downdip. During the final few years of the simulation cycle, the average sliding velocity is approximately inversely proportional to the time to occurrence for a large interplate earthquake.
Conditional and Relevant Common Information
Authors: Graczyk Robert , Lapidoth Amos , Wigger Michèle 
Published: August 2021

Abstract
Two variations on Wyner’s common information are proposed: conditional common information and relevant common information. These are shown to have operational meanings analogous to those of Wyner’s common information in appropriately defined distributed problems of compression, simulation and channel synthesis. For relevant common information, an additional operational meaning is identified: on a multiple-access channel with private and common messages, it is the minimal common-message rate that enables communication at the maximum sum-rate under a weak coordination constraint on the inputs and output. En route, the weak-coordination problem over a Gray-Wyner network is solved under the no-excess-rate constraint.
Optimal portfolio execution with a Markov chain approximation approach
Authors: Chen Jingnan , Feng Liming , Peng Jiming , Zhang Yu 
Published: August 2021

AbstractWe study the problem of executing a large multi-asset portfolio in a short time period where the objective is to find an optimal trading strategy that minimizes both the trading cost and the trading risk measured by quadratic variation. We contribute to the existing literature by considering a multi-dimensional geometric Brownian motion model for asset prices and proposing an efficient Markov chain approximation (MCA) approach to obtain the optimal trading trajectory. The MCA approach allows us not only to numerically compute the optimal strategy but also to theoretically analyse the influence of factors such as price impact, risk aversion and initial asset price on the optimal strategy, providing both quantitative and qualitative guidance on the trading behaviour. Numerical results verify the theoretical conclusions in the paper. They further illustrate the effects of cross impact and correlations on the optimal execution strategy in a multi-asset liquidation problem.
Row orientation affects the uniformity of light absorption, but hardly affects crop photosynthesis in hedgerow tomato crops
Authors: van der Meer Maarten , de Visser Pieter H B , Heuvelink Ep , Marcelis Leo F M 
Published: August 2021

Abstract
Light distribution within canopies is important for plant growth. We aimed to quantify the influence of row orientation on inter- and within-row variation of light absorption and photosynthesis in a hedgerow crop. An experiment with two row orientations of a tomato crop was conducted which was then used to calibrate a functional–structural plant model (FSPM). The FSPM was used to analyse light absorption and photosynthesis for each of the row facing directions in the double-row trellis system (e.g. north- and south-facing rows for the east–west row orientation). The measured leaf area decreased by 18 % and specific leaf area by 10 %, while fruit dry weight increased by 7 % for south-facing compared to north-facing rows, but total plant dry weight did not significantly differ. Model simulations showed a 7 % higher light absorption for the south-facing rows than north-facing rows, while net photosynthesis was surprisingly −4 % lower, due to local light saturation. When in the model leaf area was kept equal between the rows, light absorption for the south-facing rows was 19 % and net photosynthesis 8 % higher than for north-facing rows. We conclude that although south-facing rows would be expected to have a higher photosynthesis than north-facing rows, plants can adapt their morphology such that differences in light absorption and photosynthesis between north- and south-facing rows are minimal. Rows oriented north–south were more uniform in light absorption and photosynthesis than east–west rows, but the overall crop light absorption and photosynthesis were minimally affected (both 3 % lower compared to east–west orientation).
Detecting effective starting point of genomic selection by divergent trends from best linear unbiased prediction and single-step genomic best linear unbiased prediction in pigs, beef cattle, and broilers
Authors: Abdollahi-Arpanahi Rostam , Lourenco Daniela , Misztal Ignacy 
Published: August 2021

Abstract
Genomic selection has been adopted nationally and internationally in different livestock and plant species. However, understanding whether genomic selection has been effective or not is an essential question for both industry and academia. Once genomic evaluation started being used, estimation of breeding values with pedigree best linear unbiased prediction (BLUP) became biased because this method does not consider selection using genomic information. Hence, the effective starting point of genomic selection can be detected in two possible ways including the divergence of genetic trends and Realized Mendelian sampling (RMS) trends obtained with BLUP and single-step genomic BLUP (ssGBLUP). This study aimed to find the start date of genomic selection for a set of economically important traits in three livestock species by comparing trends obtained using BLUP and ssGBLUP. Three datasets were used for this purpose: 1) a pig dataset with 117k genotypes and 1.3M animals in pedigree, 2) an Angus cattle dataset consisted of ~842k genotypes and 11.5M animals in pedigree, and 3) a purebred broiler chicken dataset included ~154k genotypes and 1.3M birds in pedigree were used. The genetic trends for pigs diverged for the genotyped animals born in 2014 for average daily gain (ADG) and backfat (BF). In beef cattle, the trends started diverging in 2009 for weaning weight (WW) and in 2016 for postweaning gain (PWG), with little divergence for birth weight (BTW). In broiler chickens, the genetic trends estimated by ssGBLUP and BLUP diverged at breeding cycle 6 for two out of the three production traits. The RMS trends for the genotyped pigs diverged for animals born in 2014, more for ADG than for BF. In beef cattle, the RMS trends started diverging in 2009 for WW and in 2016 for PWG, with a trivial trend for BTW. In broiler chickens, the RMS trends from ssGBLUP and BLUP diverged strongly for two production traits at breeding cycle 6, with a slight divergence for another trait. Divergence of the genetic trends from ssGBLUP and BLUP indicates the onset of the genomic selection. The presence of trends for RMS indicates selective genotyping, with or without the genomic selection. The onset of genomic selection and genotyping strategies agrees with industry practices across the three species. In summary, the effective start of genomic selection can be detected by the divergence between genetic and RMS trends from BLUP and ssGBLUP.
Why are Jews Forbidden to Eat Meat and Milk Together? the Function of Eating Restrictions in Human Societies
Authors: Viezel Eran , Avieli Nir 
Published: August 2021

Abstract
The prohibition against eating meat and milk together is among the most widely known legal requirements in Judaism. This prohibition is not mentioned explicitly in the Bible (the Biblical commandment not to boil a kid in its mother’s milk does not necessarily imply its post-Biblical interpretation), and it apparently was not known even at the end of the Second Temple period. However, in the first centuries of the common era it was firmly established, and to this day it is a practice that distinguishes religiously observant Jews from the non-observant. Over the course of Jewish history, the prohibition against eating meat and milk together was at the centre of many lively discussions. The sages sought to justify and explain the prohibition in a variety of ways, and the considerations they raised show the complexity that arises from the encounter of daily eating practices with the dictates of faith. In this paper, we will examine the different explanations proposed, and we will propose a new solution to the question of the explanation for this restriction, along with other dietary restrictions recognized in world religions.
‘God has had Mercy on Me’: Theology and Soteriology in Philo of Alexandria’s de Sacrificiis Abelis et Caini
Authors: Mackie Scott D 
Published: August 2021

Abstract
Philo of Alexandria’s treatise De sacrificiis Abelis et Caini offers a rich example of his theology and soteriology. The majestic God of De sacrificiis is transcendent, omnipresent, and absolutely unique. Anthropomorphic and anthropopathic conceptions of God also are memorably discussed and dismissed. Standing in tension with these ontological characteristics are relational attributes of God, which often are expressed in redemptive acts. Thus, the merciful God of De sacrificiis ‘transcends his transcendence’, and compassionately reaches out to humans in need. A full array of soteriological themes populate the pages of the treatise, including the war against the passions, the allegory of the soul, transformative revelatory experiences, salvific worship, contemplative ascent, and the vision of God. Furthermore, the agential acts and roles played by God and humans are complexly intertwined, demonstrating a sophisticated, experientially informed soteriology. Though these important Philonic themes typically are interpreted thematically and systemically, thus ‘ironing out’ any idiosyncrasies, this essay closely attends to the particular thought of this treatise. As a consequence, unique elements and emphases emerge, which in addition to distinctive depictions of divine compassion and soteriological agency, include a Stoic emphasis on reason, the relative absence of mediatorial figures, and a rare portrayal of an unequivocal visio Dei.
Chlamydomonas proteases: classification, phylogeny, and molecular mechanisms
Authors: Zou Yong , Bozhkov Peter V 
Published: August 2021

Abstract
Proteases can regulate myriad biochemical pathways by digesting or processing target proteins. While up to 3% of eukaryotic genes encode proteases, only a tiny fraction of proteases are mechanistically understood. Furthermore, most of the current knowledge about proteases is derived from studies of a few model organisms, including Arabidopsis thaliana in the case of plants. Proteases in other plant model systems are largely unexplored territory, limiting our mechanistic comprehension of post-translational regulation in plants and hampering integrated understanding of how proteolysis evolved. We argue that the unicellular green alga Chlamydomonas reinhardtii has a number of technical and biological advantages for systematic studies of proteases, including reduced complexity of many protease families and ease of cell phenotyping. With this end in view, we share a genome-wide inventory of proteolytic enzymes in Chlamydomonas, compare the protease degradomes of Chlamydomonas and Arabidopsis, and consider the phylogenetic relatedness of Chlamydomonas proteases to major taxonomic groups. Finally, we summarize the current knowledge of the biochemical regulation and physiological roles of proteases in this algal model. We anticipate that our survey will promote and streamline future research on Chlamydomonas proteases, generating new insights into proteolytic mechanisms and the evolution of digestive and limited proteolysis.
Persistent homology of the cosmic web – I. Hierarchical topology in ΛCDM cosmologies
Authors: Wilding Georg , Nevenzeel Keimpe , van de Weygaert Rien , Vegter Gert , Pranav Pratyush , Jones Bernard J T , Efstathiou Konstantinos , Feldbrugge Job 
Published: August 2021

ABSTRACT
Using a set of Lambda cold dark matter simulations of cosmic structure formation, we study the evolving connectivity and changing topological structure of the cosmic web using state-of-the-art tools of multiscale topological data analysis (TDA). We follow the development of the cosmic web topology in terms of the evolution of Betti number curves and feature persistence diagrams of the three (topological) classes of structural features: matter concentrations, filaments and tunnels, and voids. The Betti curves specify the prominence of features as a function of density level, and their evolution with cosmic epoch reflects the changing network connections between these structural features. The persistence diagrams quantify the longevity and stability of topological features. In this study, we establish, for the first time, the link between persistence diagrams, the features they show, and the gravitationally driven cosmic structure formation process. By following the diagrams’ development over cosmic time, the link between the multiscale topology of the cosmic web and the hierarchical buildup of cosmic structure is established. The sharp apexes in the diagrams are intimately related to key transitions in the structure formation process. The apex in the matter concentration diagrams coincides with the density level at which, typically, they detach from the Hubble expansion and begin to collapse. At that level many individual islands merge to form the network of the cosmic web and a large number of filaments and tunnels emerge to establish its connecting bridges. The location trends of the apex possess a self-similar character that can be related to the cosmic web’s hierarchical buildup. We find that persistence diagrams provide a significantly higher and more profound level of information on the structure formation process than more global summary statistics like Euler characteristic or Betti numbers.
To “Fill Up, Completely, the Whole Capacity of the Mind”: Listening with Attention in Late Eighteenth-Century Scotland
Authors: Raz Carmel 
Published: August 2021

AbstractThis essay explores a hitherto unsuspected intellectual relationship among three important thinkers of the Scottish Enlightenment. The great philosopher and economist Adam Smith is known to have had a conception of instrumental music exceptional for his time in its foreshadowing of ideas generally associated with Eduard Hanslick. As I show here, Smith’s views were decisively influenced by the psychological theories of his countryman Thomas Reid in all likelihood by way of the extraordinary proto-cognitivist music theory of their contemporary John Holden, in particular the latter’s conceptualization of the faculty of attention. The innovative contributions of these writers constitute a compact and suggestive case study in the circulation of ideas about perception and listening between philosophy and music, and suggest that the Scottish Enlightenment attitude to psychology enabled a new kind of theorizing about the musical experience: one that foregrounded the importance of the faculty of attention in the process of perceiving music and sound.
Structural basis of l-tryptophan-dependent inhibition of release factor 2 by the TnaC arrest peptide
Authors: Su Ting , Kudva Renuka , Becker Thomas , Buschauer Robert , Komar Tobias , Berninghausen Otto , von Heijne Gunnar , Cheng Jingdong , Beckmann Roland 
Published: August 2021

Abstract
In Escherichia coli, elevated levels of free l-tryptophan (l-Trp) promote translational arrest of the TnaC peptide by inhibiting its termination. However, the mechanism by which translation-termination by the UGA-specific decoding release factor 2 (RF2) is inhibited at the UGA stop codon of stalled TnaC-ribosome-nascent chain complexes has so far been ambiguous. This study presents cryo-EM structures for ribosomes stalled by TnaC in the absence and presence of RF2 at average resolutions of 2.9 and 3.5 Å, respectively. Stalled TnaC assumes a distinct conformation composed of two small α-helices that act together with residues in the peptide exit tunnel (PET) to coordinate a single L-Trp molecule. In addition, while the peptidyl-transferase center (PTC) is locked in a conformation that allows RF2 to adopt its canonical position in the ribosome, it prevents the conserved and catalytically essential GGQ motif of RF2 from adopting its active conformation in the PTC. This explains how translation of the TnaC peptide effectively allows the ribosome to function as a L-Trp-specific small-molecule sensor that regulates the tnaCAB operon.
A novel view on an old drug, 5-fluorouracil: an unexpected RNA modifier with intriguing impact on cancer cell fate
Authors: Chalabi-Dchar Mounira , Fenouil Tanguy , Machon Christelle , Vincent Anne , Catez Frédéric , Marcel Virginie , Mertani Hichem C , Saurin Jean-Christophe , Bouvet Philippe , Guitton Jérôme , Venezia Nicole Dalla , Diaz Jean-Jacques 
Published: August 2021

Abstract5-Fluorouracil (5-FU) is a chemotherapeutic drug widely used to treat patients with solid tumours, such as colorectal and pancreatic cancers. Colorectal cancer (CRC) is the second leading cause of cancer-related death and half of patients experience tumour recurrence. Used for over 60 years, 5-FU was long thought to exert its cytotoxic effects by altering DNA metabolism. However, 5-FU mode of action is more complex than previously anticipated since 5-FU is an extrinsic source of RNA modifications through its ability to be incorporated into most classes of RNA. In particular, a recent report highlighted that, by its integration into the most abundant RNA, namely ribosomal RNA (rRNA), 5-FU creates fluorinated active ribosomes and induces translational reprogramming. Here, we review the historical knowledge of 5-FU mode of action and discuss progress in the field of 5-FU-induced RNA modifications. The case of rRNA, the essential component of ribosome and translational activity, and the plasticity of which was recently associated with cancer, is highlighted. We propose that translational reprogramming, induced by 5-FU integration in ribosomes, contributes to 5-FU-driven cell plasticity and ultimately to relapse.
Androgen signaling connects short isoform production to breakpoint formation at Ewing sarcoma breakpoint region 1
Authors: Nicholas Taylor R , Metcalf Stephanie A , Greulich Benjamin M , Hollenhorst Peter C 
Published: August 2021

Abstract
Ewing sarcoma breakpoint region 1 (EWSR1) encodes a multifunctional protein that can cooperate with the transcription factor ERG to promote prostate cancer. The EWSR1 gene is also commonly involved in oncogenic gene rearrangements in Ewing sarcoma. Despite the cancer relevance of EWSR1, its regulation is poorly understood. Here we find that in prostate cancer, androgen signaling upregulates a 5′ EWSR1 isoform by promoting usage of an intronic polyadenylation site. This isoform encodes a cytoplasmic protein that can strongly promote cell migration and clonogenic growth. Deletion of an Androgen Receptor (AR) binding site near the 5′ EWSR1 polyadenylation site abolished androgen-dependent upregulation. This polyadenylation site is also near the Ewing sarcoma breakpoint hotspot, and androgen signaling promoted R-loop and breakpoint formation. RNase H overexpression reduced breakage and 5′ EWSR1 isoform expression suggesting an R-loop dependent mechanism. These data suggest that androgen signaling can promote R-loops internal to the EWSR1 gene leading to either early transcription termination, or breakpoint formation.
Capitalism needs a new social contract
Authors: Shafik Minouche 
Published: August 2021

Abstract
Capitalism needs a new social contract to better manage the consequences of technology and an increasingly diverse and flexible workforce. That social contract should retain the benefits of flexibility but do a better job of providing security in the form of mandatory benefits, putting a floor on incomes, and investing far more in helping workers adapt to economic shocks and rising automation. It also means a new deal with business that would achieve a more level playing field in how capital and labour are taxed.
Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes
Authors: Pignon Charles P , Fernandes Samuel B , Valluru Ravi , Bandillo Nonoy , Lozano Roberto , Buckler Edward , Gore Michael A , Long Stephen P , Brown Patrick J , Leakey Andrew D B 
Published: August 2021

AbstractStomata allow CO2 uptake by leaves for photosynthetic assimilation at the cost of water vapor loss to the atmosphere. The opening and closing of stomata in response to fluctuations in light intensity regulate CO2 and water fluxes and are essential for maintaining water-use efficiency (WUE). However, a little is known about the genetic basis for natural variation in stomatal movement, especially in C4 crops. This is partly because the stomatal response to a change in light intensity is difficult to measure at the scale required for association studies. Here, we used high-throughput thermal imaging to bypass the phenotyping bottleneck and assess 10 traits describing stomatal conductance (gs) before, during and after a stepwise decrease in light intensity for a diversity panel of 659 sorghum (Sorghum bicolor) accessions. Results from thermal imaging significantly correlated with photosynthetic gas exchange measurements. gs traits varied substantially across the population and were moderately heritable (h2 up to 0.72). An integrated genome-wide and transcriptome-wide association study identified candidate genes putatively driving variation in stomatal conductance traits. Of the 239 unique candidate genes identified with the greatest confidence, 77 were putative orthologs of Arabidopsis (Arabidopsis thaliana) genes related to functions implicated in WUE, including stomatal opening/closing (24 genes), stomatal/epidermal cell development (35 genes), leaf/vasculature development (12 genes), or chlorophyll metabolism/photosynthesis (8 genes). These findings demonstrate an approach to finding genotype-to-phenotype relationships for a challenging trait as well as candidate genes for further investigation of the genetic basis of WUE in a model C4 grass for bioenergy, food, and forage production.