bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Dawes Review 10: The impact of deep learning for the analysis of galaxy surveys
Authors: Huertas-Company M. , Lanusse F. 
Published: January 2023

AbstractThe amount and complexity of data delivered by modern galaxy surveys has been steadily increasing over the past years. New facilities will soon provide imaging and spectra of hundreds of millions of galaxies. Extracting coherent scientific information from these large and multi-modal data sets remains an open issue for the community and data-driven approaches such as deep learning have rapidly emerged as a potentially powerful solution to some long lasting challenges. This enthusiasm is reflected in an unprecedented exponential growth of publications using neural networks, which have gone from a handful of works in 2015 to an average of one paper per week in 2021 in the area of galaxy surveys. Half a decade after the first published work in astronomy mentioning deep learning, and shortly before new big data sets such as Euclid and LSST start becoming available, we believe it is timely to review what has been the real impact of this new technology in the field and its potential to solve key challenges raised by the size and complexity of the new datasets. The purpose of this review is thus two-fold. We first aim at summarising, in a common document, the main applications of deep learning for galaxy surveys that have emerged so far. We then extract the major achievements and lessons learned and highlight key open questions and limitations, which in our opinion, will require particular attention in the coming years. Overall, state-of-the-art deep learning methods are rapidly adopted by the astronomical community, reflecting a democratisation of these methods. This review shows that the majority of works using deep learning up to date are oriented to computer vision tasks (e.g. classification, segmentation). This is also the domain of application where deep learning has brought the most important breakthroughs so far. However, we also report that the applications are becoming more diverse and deep learning is used for estimating galaxy properties, identifying outliers or constraining the cosmological model. Most of these works remain at the exploratory level though which could partially explain the limited impact in terms of citations. Some common challenges will most likely need to be addressed before moving to the next phase of massive deployment of deep learning in the processing of future surveys; for example, uncertainty quantification, interpretability, data labelling and domain shift issues from training with simulations, which constitutes a common practice in astronomy.
Advancing Precision Medicine in Paediatrics: Past, present and future
Authors: Elzagallaai Abdelbaset , Barker Charlotte , Lewis Tamorah , Cohn Ronald , Rieder Michael 
Published: January 2023

Abstract
Precision Medicine is an approach to disease treatment and prevention taking into account individual genetic, environmental, therapeutic and lifestyle variability for each person. This holistic approach to therapeutics is intended to enhance drug efficacy and safety not only across healthcare systems but for individual patients. While weight and to some extent gestational age have been considered in determining drug dosing in children, historically other factors including genetic variability have not been factored into therapeutic decision making. As our knowledge of the role of ontogeny and genetics in determining drug efficacy and safety has expanded, these insights have provided new opportunities to apply principles of Precision Medicine to the care of infants, children and youth. These opportunities are most likely to be achieved first in select sub-groups of children. While there are many challenges to the successful implementation of Precision Medicine in children including the need to ensure that Precision Medicine enhances rather than reduces equity in children’s health care rather, there are many more opportunities. Research, advocacy, planning and teamwork are required to move Precision Medicine forward in children in pursuit of the common goal of safe and effective drug therapy.
CONTRACT AS PROPERTY: TRIANGLES AND TRAGIC CHOICES
Authors: Crawford Michael J.R. 
Published: January 2023

AbstractAccording to the “Inadequacy Thesis”, the law's refusal to extend the tort of conversion to interferences with contractual rights is evidence of systemic ossification and proof of its failure to protect the most valuable asset class in the modern economy. Whilst it is true that, like chattels, the benefit of contractual rights can be usurped by third parties, transforming such rights into objects of property is the wrong solution to the problem. This article departs from previous analyses by stressing that the analogue of acts of interference with contractual rights is not the conversion of a chattel but a “triangle dispute”. The problem raised by triangle disputes is not how to reach the primary wrongdoer, but how to allocate the loss between the innocent parties. Invoking the concept of “property” cannot solve this problem. Its efficient solution is to be found in better contracts, not more property.
A Theory of External Wars and European Parliaments
Authors: Kenkel Brenton , Paine Jack 
Published: January 2023

AbstractThe development of parliamentary constraints on the executive was critical in Western European political history. Previous scholarship identifies external wars as a key factor, but with varying effects. Sometimes, willing monarchs granted parliamentary rights in return for revenues to fight wars. Yet at other times, war threats empowered rulers over other elites or caused states to fragment. We analyze a formal model to understand how external wars can either stimulate or undermine prospects for a contractual relationship between a ruler and elite actors. We recover the standard intuition that war threats make the ruler more willing to grant parliamentary rights in return for revenue. Our key insight is that war threats also affect the bargaining position of elites. A previously unrecognized tension yields our new findings: stronger outsider threats increase pressure either on elites to fund the ruler or on the ruler to accept constraints—but not both simultaneously. Elites with immobile wealth depend on the ruler for security. War threats undercut their credibility to refuse funding for an unconstrained ruler. By contrast, war threats make elites with mobile wealth and a viable exit option unwilling to fund a hopeless war effort. Only under circumscribed conditions do war threats align three conditions needed for parliament to arise in equilibrium: ruler willingness, elite credibility, and elite willingness. We apply our theory to posit strategic foundations for waves and reversals of historical European parliaments.
Trinity or German idealism? Reconsidering the origins of Herman Bavinck's organic motif
Authors: Pass Bruce 
Published: January 2023

AbstractThis essay re-examines the origins of Herman Bavinck's organic motif. Contending with a central claim of the new interpretative paradigm in Bavinck studies, this article problematises the claim that Bavinck's organic motif does not draw on German idealism but derives solely from a classical western doctrine of the Trinity. This essay argues that the denial of Schelling's influence on Bavinck's organicism misconstrues the terms on which Bavinck forges his synthesis of orthodoxy and modernity, and cloaks the degree to which Bavinck allows philosophical constructs to determine the material content of his theology.
Reflection Machines: Supporting Effective Human Oversight Over Medical Decision Support Systems
Authors: Haselager Pim , Schraffenberger Hanna , Thill Serge , Fischer Simon , Lanillos Pablo , van de Groes Sebastiaan , van Hooff Miranda 
Published: January 2023

AbstractHuman decisions are increasingly supported by decision support systems (DSS). Humans are required to remain “on the loop,” by monitoring and approving/rejecting machine recommendations. However, use of DSS can lead to overreliance on machines, reducing human oversight. This paper proposes “reflection machines” (RM) to increase meaningful human control. An RM provides a medical expert not with suggestions for a decision, but with questions that stimulate reflection about decisions. It can refer to data points or suggest counterarguments that are less compatible with the planned decision. RMs think against the proposed decision in order to increase human resistance against automation complacency. Building on preliminary research, this paper will (1) make a case for deriving a set of design requirements for RMs from EU regulations, (2) suggest a way how RMs could support decision-making, (3) describe the possibility of how a prototype of an RM could apply to the medical domain of chronic low back pain, and (4) highlight the importance of exploring an RM’s functionality and the experiences of users working with it.
Rice tolerance to acetochlor with a fenclorim seed treatment
Authors: Avent Tristen H. , Norsworthy Jason K. , Butts Thomas R. , Roberts Trenton L. , Bateman Nicholas R. 
Published: January 2023

AbstractRice producers in the United States need effective herbicides to control problematic weeds. Previous research has demonstrated that acetochlor can provide in-season weed control in rice; however, undesirable injury is common. Thus, trials were initiated in 2020 and 2021 to evaluate 1) rice cultivar tolerance to microencapsulated (ME) acetochlor with the use of a fenclorim seed treatment at 2.5 g ai kg−1 of seed; 2) a dose-response of a fenclorim seed treatment with ME acetochlor; and 3) rice tolerance to fenclorim and ME acetochlor under cool, wet conditions. For all trials, acetochlor was applied delayed-preemergence (4 to 7 d after planting). In the dose-response trials and in the presence of acetochlor, the fenclorim seed treatment rate of 2.5 g ai kg−1 reduced rice injury and increased rice plant heights and shoot numbers relative to acetochlor without fenclorim, and plant heights and shoot numbers were comparable to those of the nontreated control in all evaluations. In the cultivar screening, 14 of 16 cultivars exhibited <20% injury with acetochlor at 1,260 g ai ha−1 and fenclorim at 2.5 g ai kg−1 2 wk after emergence (WAE) at the Pine Tree Research Station (PTRS). At the Rice Research and Extension Center (RREC) 2 and 4 WAE and at PTRS 4 WAE, all cultivars exhibited <20% injury with acetochlor and fenclorim. The fenclorim seed treatment in the presence of acetochlor provided comparable rice plant height, shoot numbers, groundcover, and rough rice yield to that of the nontreated control. Under cool, wet conditions, rice injury without fenclorim ranged from 15% to 60% with acetochlor at 1,050 g ai ha−1, whereas injury from acetochlor with the fenclorim seed treatment ranged from 0% to 20%. Based on the results of these experiments, the fenclorim seed treatment appears to safen an assortment of rice cultivars from injury caused by ME acetochlor.
Effects of Automatic Hyperparameter Tuning on the Performance of Multi‐Variate Deep Learning‐Based Rainfall Nowcasting
Authors: Amini Amirmasoud , Dolatshahi Mehri , Kerachian Reza 
Published: January 2023

AbstractRainfall nowcasting has become increasingly important as we move into an era where more and more storms are occurring in many countries as a result of climate change. Developing an accurate rainfall nowcasting model could provide insights into rainfall dynamics and ultimately could prevent significant damages. In this paper, deep neural networks (DNNs) and numerical weather predictions (NWPs) are applied for rainfall and runoff forecasting in an urban catchment with a complex drainage system. DNNs are among the most accurate models for rainfall nowcasting. However, the design and training of DNNs are usually complicated. This paper combines different convolutional, long short‐term memory (LSTM)‐based networks and NWPs using ensemble techniques (i.e., bagging, random forest, and adaboost methods) with automatic hyperparameter tuning for multi‐step rainfall nowcasting. The relative humidity, air temperature, and previous rainfall sequences are considered the inputs of the DNNs. We focus on applying two hyperparameter tuning methods (i.e., random search and tree structured Parzen estimator) to improve the performance of the proposed rainfall nowcasting models. The proposed framework was applied to the eastern drainage catchment (EDC) in Tehran city. The results illustrate that the utilization of automatic hyperparameter tuning along with multivariate DNNs, NWPs, and ensemble techniques could improve the nowcasting performance (10%–25%) compared to the traditional univariate models. Also, Adaboost is more accurate than other ensemble techniques in predicting both extreme and normal rainfall events with average RMSE of 0.765, and random forest obtain better results when predict sub normal rainfall events with overall RMSE of 0.315. The proposed framework is applicable to different climates and catchments.
Prematurity blunts protein synthesis in skeletal muscle independently of body weight in neonatal pigs
Authors: Rudar Marko , Naberhuis Jane K. , Suryawan Agus , Nguyen Hanh V. , Fiorotto Marta L. , Davis Teresa A. 
Published: January 2023

Abstract
Background
Postnatal growth failure in premature infants is associated with reduced lean mass accretion. Prematurity impairs the feeding-induced stimulation of translation initiation and protein synthesis in the skeletal muscle of neonatal pigs. The objective was to determine whether body weight independently contributes to the blunted postprandial protein synthesis.

Methods
Preterm and term pigs that were either fasted or fed were stratified into quartiles according to birth weight to yield preterm and term groups of similar body weight; first and second quartiles of preterm pigs and third and fourth quartiles of term pigs were compared (preterm-fasted, n = 23; preterm-fed, n = 25; term-fasted, n = 21; term-fed, n = 21). Protein synthesis rates and mechanistic target of rapamycin complex 1 (mTORC1) activation in skeletal muscle were determined.

Results
Relative body weight gain was lower in preterm compared to term pigs. Prematurity attenuated the feeding-induced increase in mTORC1 activation in longissimus dorsi and gastrocnemius muscles (P < 0.05). Protein synthesis in gastrocnemius (P < 0.01), but not in longissimus dorsi muscle, was blunted by preterm birth.

Conclusion
A lower capacity of skeletal muscle to respond adequately to feeding may contribute to reduced body weight gain and lean mass accretion in preterm infants.

Impact

This study has shown that the feeding-induced increase in protein synthesis of skeletal and cardiac muscle is blunted in neonatal pigs born preterm compared to pigs born at term independently of birth weight.

These findings support the notion that preterm birth, and not low birth weight, impairs the capacity of skeletal and cardiac muscle to upregulate mechanistic target of rapamycin-dependent anabolic signaling pathways and protein synthesis in response to the postprandial increase in insulin and amino acids.

These observations suggest that a blunted anabolic response to feeding contributes to reduced lean mass accretion and altered body composition in preterm infants.
SARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19
Authors: Stanevich Oksana V. , Alekseeva Evgeniia I. , Sergeeva Maria , Fadeev Artem V. , Komissarova Kseniya S. , Ivanova Anna A. , Simakova Tamara S. , Vasilyev Kirill A. , Shurygina Anna-Polina , Stukova Marina A. , Safina Ksenia R. , Nabieva Elena R. , Garushyants Sofya K. , Klink Galya V. , Bakin Evgeny A. , Zabutova Jullia V. , Kholodnaia Anastasia N. , Lukina Olga V. , Skorokhod Irina A. , Ryabchikova Viktoria V. , Medvedeva Nadezhda V. , Lioznov Dmitry A. , Danilenko Daria M. , Chudakov Dmitriy M. , Komissarov Andrey B. , Bazykin Georgii A. 
Published: January 2023

AbstractEvolution of SARS-CoV-2 in immunocompromised hosts may result in novel variants with changed properties. While escape from humoral immunity certainly contributes to intra-host evolution, escape from cellular immunity is poorly understood. Here, we report a case of long-term COVID-19 in an immunocompromised patient with non-Hodgkin’s lymphoma who received treatment with rituximab and lacked neutralizing antibodies. Over the 318 days of the disease, the SARS-CoV-2 genome gained a total of 40 changes, 34 of which were present by the end of the study period. Among the acquired mutations, 12 reduced or prevented the binding of known immunogenic SARS-CoV-2 HLA class I antigens. By experimentally assessing the effect of a subset of the escape mutations, we show that they resulted in a loss of as much as ~1% of effector CD8 T cell response. Our results indicate that CD8 T cell escape represents a major underappreciated contributor to SARS-CoV-2 evolution in humans.
Antiretroviral APOBEC3 cytidine deaminases alter HIV-1 provirus integration site profiles
Authors: Ajoge Hannah O. , Renner Tyler M. , Bélanger Kasandra , Greig Matthew , Dankar Samar , Kohio Hinissan P. , Coleman Macon D. , Ndashimye Emmanuel , Arts Eric J. , Langlois Marc-André , Barr Stephen D. 
Published: January 2023

AbstractAPOBEC3 (A3) proteins are host-encoded deoxycytidine deaminases that provide an innate immune barrier to retroviral infection, notably against HIV-1. Low levels of deamination are believed to contribute to the genetic evolution of HIV-1, while intense catalytic activity of these proteins can induce catastrophic hypermutation in proviral DNA leading to near-total HIV-1 restriction. So far, little is known about how A3 cytosine deaminases might impact HIV-1 proviral DNA integration sites in human chromosomal DNA. Using a deep sequencing approach, we analyze the influence of catalytic active and inactive APOBEC3F and APOBEC3G on HIV-1 integration site selections. Here we show that DNA editing is detected at the extremities of the long terminal repeat regions of the virus. Both catalytic active and non-catalytic A3 mutants decrease insertions into gene coding sequences and increase integration sites into SINE elements, oncogenes and transcription-silencing non-B DNA features. Our data implicates A3 as a host factor influencing HIV-1 integration site selection and also promotes what appears to be a more latent expression profile.
Additive-controlled asymmetric iodocyclization enables enantioselective access to both α- and β-nucleosides
Authors: Wang Qi , Mu Jiayi , Zeng Jie , Wan Linxi , Zhong Yangyang , Li Qiuhong , Li Yitong , Wang Huijing , Chen Fener 
Published: January 2023

Abstractβ-Nucleosides and their analogs are dominant clinically-used antiviral and antitumor drugs. α-Nucleosides, the anomers of β-nucleosides, exist in nature and have significant potential as drugs or drug carriers. Currently, the most widely used methods for synthesizing β- and α-nucleosides are via N-glycosylation and pentose aminooxazoline, respectively. However, the stereoselectivities of both methods highly depend on the assisting group at the C2’ position. Herein, we report an additive-controlled stereodivergent iodocyclization method for the selective synthesis of α- or β-nucleosides. The stereoselectivity at the anomeric carbon is controlled by the additive (NaI for β-nucleosides; PPh3S for α-nucleosides). A series of β- and α-nucleosides are prepared in high yields (up to 95%) and stereoselectivities (β:α up to 66:1, α:β up to 70:1). Notably, the introduced iodine at the C2’ position of the nucleoside is readily functionalized, leading to multiple structurally diverse nucleoside analogs, including stavudine, an FDA-approved anti-HIV agent, and molnupiravir, an FDA-approved anti-SARS-CoV-2 agent.
Resolving colistin resistance and heteroresistance in Enterobacter species
Authors: Doijad Swapnil Prakash , Gisch Nicolas , Frantz Renate , Kumbhar Bajarang Vasant , Falgenhauer Jane , Imirzalioglu Can , Falgenhauer Linda , Mischnik Alexander , Rupp Jan , Behnke Michael , Buhl Michael , Eisenbeis Simone , Gastmeier Petra , Gölz Hanna , Häcker Georg Alexander , Käding Nadja , Kern Winfried V. , Kola Axel , Kramme Evelyn , Peter Silke , Rohde Anna M. , Seifert Harald , Tacconelli Evelina , Vehreschild Maria J. G. T. , Walker Sarah V. , Zweigner Janine , Schwudke Dominik ,   DZIF R-Net Study Group, Diaz L. A. Peña , Pilarski G. , Thoma N. , Weber A. , Vavra M. , Schuster S. , Peyerl-Hoffmann G. , Hamprecht A. , Proske S. , Stelzer Y. , Wille J. , Lenke D. , Bader B. , Dinkelacker A. , Hölzl F. , Kunstle L. , Chakraborty Trinad 
Published: January 2023

AbstractSpecies within the Enterobacter cloacae complex (ECC) include globally important nosocomial pathogens. A three-year study of ECC in Germany identified Enterobacter xiangfangensis as the most common species (65.5%) detected, a result replicated by examining a global pool of 3246 isolates. Antibiotic resistance profiling revealed widespread resistance and heteroresistance to the antibiotic colistin and detected the mobile colistin resistance (mcr)−9 gene in 19.2% of all isolates. We show that resistance and heteroresistance properties depend on the chromosomal arnBCADTEF gene cassette whose products catalyze transfer of L-Ara4N to lipid A. Using comparative genomics, mutational analysis, and quantitative lipid A profiling we demonstrate that intrinsic lipid A modification levels are genospecies-dependent and governed by allelic variations in phoPQ and mgrB, that encode a two-component sensor-activator system and specific inhibitor peptide. By generating phoPQ chimeras and combining them with mgrB alleles, we show that interactions at the pH-sensing interface of the sensory histidine kinase phoQ dictate arnBCADTEF expression levels. To minimize therapeutic failures, we developed an assay that accurately detects colistin resistance levels for any ECC isolate.
Vascular smooth muscle-inspired architecture enables soft yet tough self-healing materials for durable capacitive strain-sensor
Authors: Sun FuYao , Liu LongFei , Liu Tong , Wang XueBin , Qi Qi , Hang ZuSheng , Chen Kai , Xu JianHua , Fu JiaJun 
Published: January 2023

AbstractCatastrophically mechanical failure of soft self-healing materials is unavoidable due to their inherently poor resistance to crack propagation. Here, with a model system, i.e., soft self-healing polyurea, we present a biomimetic strategy of surpassing trade-off between soft self-healing and high fracture toughness, enabling the conversion of soft and weak into soft yet tough self-healing material. Such an achievement is inspired by vascular smooth muscles, where core-shell structured Galinstan micro-droplets are introduced through molecularly interfacial metal-coordinated assembly, resulting in an increased crack-resistant strain and fracture toughness of 12.2 and 34.9 times without sacrificing softness. The obtained fracture toughness is up to 111.16 ± 8.76 kJ/m2, even higher than that of Al and Zn alloys. Moreover, the resultant composite delivers fast self-healing kinetics (1 min) upon local near-infrared irradiation, and possesses ultra-high dielectric constants (~14.57), thus being able to be fabricated into sensitive and self-healing capacitive strain-sensors tolerant towards cracks potentially evolved in service.