bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Clinic-Based Measure of Everyday Planning Ability: The Overnight Trip Task
Authors: Brown Katelyn D , Schmitter-Edgecombe Maureen 
Published: July 2023

Abstract

Objective
Traditional measures of cognitive abilities most used by neuropsychologists are generally low in ecological validity and only capture a small proportion of the variance of a person’s true functional capacity. This study evaluates the association between clinic-based performance and parallel real-world completion of an everyday planning test, the Overnight Trip Task (OTT).

Method
A cross-sectional cohort of 65 community-dwelling older adults completed a battery of cognitive assessments and two formats of the OTT: the paper-and-pencil clinic OTT, which was completed remotely through video conferencing (Zoom), and the parallel real-world OTT (RW-OTT), which was completed at home between sessions. Both formats required participants to plan for what they would pack and prepare for a hypothetical overnight trip based on a provided story that included rules and embedded contingencies.

Results
The clinic OTT demonstrated a small-to-moderate relationship with the RW-OTT (r = 0.35) and no relationship with measures of learning, long delay recall, an executive function composite, and a measure of everyday planning. Hierarchical regressions indicated that the clinic OTT demonstrated incremental validity above an executive function composite measure and global cognition when predicting self-reported everyday functioning and RW-OTT performance.

Conclusions
The clinic OTT showed only modest association with the RW-OTT and discriminate but not convergent validity was demonstrated. The clinic OTT showed incremental validity when predicting self-reported everyday functioning and RW-OTT performance above more traditional measures. Before the clinic OTT could be considered a reliable and valid clinic-based measure for predicting real-world behavior, additional research would be needed.
Testing phylogenetic signal with categorical traits and tree uncertainty
Authors: Ribeiro Diogo , Borges Rui , Rocha Ana Paula , Antunes Agostinho 
Published: July 2023

Abstract

Summary
The phylogenetic signal, frequently used to identify signatures of adaptive evolution or important associations between genes and phenotypes, measures the tendency for recently diverged species to resemble each other more than distantly related species. An example of such a measure is the δ statistic, which uses Shannon entropy to measure the degree of phylogenetic signal between a categorical trait and a phylogeny. In this study, we refined this statistic to account for tree uncertainty, resulting in more accurate assessments of phylogenetic associations. In addition, we provided a more accessible and computationally efficient implementation of the δ statistic that will facilitate its use by the evolutionary community.

Availability and implementation
github.com/diogo-s-ribeiro/delta-statistic.
LegNet: a best-in-class deep learning model for short DNA regulatory regions
Authors: Penzar Dmitry , Nogina Daria , Noskova Elizaveta , Zinkevich Arsenii , Meshcheryakov Georgy , Lando Andrey , Rafi Abdul Muntakim , de Boer Carl , Kulakovskiy Ivan V 
Published: July 2023

Abstract

Motivation
The increasing volume of data from high-throughput experiments including parallel reporter assays facilitates the development of complex deep-learning approaches for modeling DNA regulatory grammar.

Results
Here, we introduce LegNet, an EfficientNetV2-inspired convolutional network for modeling short gene regulatory regions. By approaching the sequence-to-expression regression problem as a soft classification task, LegNet secured first place for the autosome.org team in the DREAM 2022 challenge of predicting gene expression from gigantic parallel reporter assays. Using published data, here, we demonstrate that LegNet outperforms existing models and accurately predicts gene expression per se as well as the effects of single-nucleotide variants. Furthermore, we show how LegNet can be used in a diffusion network manner for the rational design of promoter sequences yielding the desired expression level.

Availability and implementation
https://github.com/autosome-ru/LegNet. The GitHub repository includes Jupyter Notebook tutorials and Python scripts under the MIT license to reproduce the results presented in the study.
Exposing and exploiting host–parasite arms race clues in SARS-CoV-2: a principally new method for improved T cell immunogenicity prediction
Authors: Flegr Jaroslav , Králová Lesná Ivana , Zahradník Daniel 
Published: July 2023

Abstract
Computational prediction of T cell epitopes is a crucial component in the development of novel vaccines. T cells in a healthy vertebrate host can recognize as non-self only those peptides that are present in the parasite’s proteins but absent in the host’s proteins. This principle enables us to determine the current and past host specificity of a parasite and to predict peptides capable of eliciting a T cell response. Building upon the detailed mapping of T cell clone specificity for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) antigens, we employed Monte Carlo tests to determine that empirically confirmed T cell-stimulating peptides have a significantly increased proportion of pentapeptides, hexapeptides and heptapeptides not found in the human proteome (P &lt; 0.0001, Cohen’s d &gt; 4.9). We observed a lower density of potential pentapeptide targets for T cell recognition in the spike protein from the human-adapted SARS-CoV-2 ancestor compared to 10 other SARS-CoV-2 proteins originating from the horseshoe bat-adapted ancestor. Our novel method for predicting T cell immunogenicity of SARS-CoV-2 peptides is four times more effective than previous approaches. We recommend utilizing our theory-based method where efficient empirically based algorithms are unavailable, such as in the development of certain veterinary vaccines, and combining it with empirical methods in other cases for optimal results.
A temperature-dependent phenology model for Bemisia tabaci MEAM1 (Hemiptera: Aleyrodidae)
Authors: Sporleder Marc , Gamarra Heidy , Carhuapoma Pablo , Goicochea Luis , Kroschel Jürgen , Kreuze Jan 
Published: July 2023

Abstract
The sweetpotato whitefly, Bemisia tabaci (Gennadius) Middle East-Asia Minor 1 (MEAM1), is widespread across tropical and subtropical regions, affecting hundreds of cultivated and wild plant species. Because the species transmits a variety of viruses, the whitefly has become one of the most economically significant insect pests in the world. Determining a pest’s population growth potential as a function of temperature is critical for understanding a species population dynamics, predicting the potential range of the species and its associated diseases, and designing adaptive pest management strategies. The life history of B. tabaci MEAM1 was studied in life-table experiments at 7 constant temperatures ranging from 12 to 35 °C. Nonlinear equations were fitted to development, mortality, and reproduction data and compiled into an overall phenology rate-summation model using Insect Life Cycle Modeling (ILCYM) software, to simulate life-table parameters based on temperature. Life tables of B. tabaci MEAM1 observed at naturally variable temperature in La Molina, Lima, during different seasons, covering the entire temperature range of the species’ predicted performance curve, were used to validate the model. Simulations predicted population growth within temperature between 13.9 and 33.4 °C, revealing a maximum finite rate of population increase (λ = 1.163), with a generation time of 33.3 days at 26.4 °C. Predicted species performance agreed well when compared against observed life tables and published data. The process-based physiological model presented here for B. tabaci MEAM1 should prove useful to predict the potential spatial distribution of the species based on temperature and to adjust pest control measures taking different population growth potentials due to prevailing temperature regimes into account.
A guide to navigating administrative data linkage for research
Authors: Singh Gursharan K , Bowers Alison P 
Published: July 2023

Abstract
Data linkage brings together information from various sources, including routinely collected administrative data or data from different research studies, to create a new, richer dataset. It provides insights into complex relationships between health and outcomes and evidence pathways to good health. However, when considering data linkage, there are several processes and practicality aspects that need to be explored. Some of these include understanding the costs, complexity of linkage, data storage requirements, required applications, and time lags. Taking these practicalities into consideration will lead to a more efficient process for data linkage.
Freedom of Expression as a Rationale for IP Protection
Authors: Izyumenko Elena 
Published: July 2023

Abstract
This article revisits the discussion on the rationales for intellectual property (IP) protection by addressing a particular justificatory theory for IP that had come to the forefront of legal discussions in recent years – the theory based on freedom of expression and information. This modern vision of IP focuses on the communicative nature of IP subject-matter and of IP as a legal regime. Firstly, this article reviews the Kantian theory of copyright that lies at the origins of any modern discussions on the communicative nature of IP regulation with the aim of answering whether IP should be more properly conceived as the system for regulating communication. It then looks at the readings of this theory by contemporary copyright scholars and considers applicability of the communicative theory to other areas of IP such as trademarks and patents. The analysis then proceeds towards looking at the freedom of expression dimension of the ‘classic’ IP theories. Reflecting on this matter is important as the rationales for IP protection influence virtually all spheres of IP’s legal regulation, including – first and foremost – the reach of IP holders’ entitlements.
Deterrence through Inflicting Costs: Between Deterrence by Punishment and Deterrence by Denial
Authors: Lupovici Amir 
Published: July 2023

Abstract
The strategy of deterrence by denial is widely used by different actors. Despite its prominence, however, the scholarship on deterrence by denial stands to be developed further. It lags behind scholarship on deterrence by punishment on two points: in identifying the conditions under which the strategy works and in examining elements affecting its adoption. Deterrence by denial also carries some conceptual ambiguity since its employment takes many significantly different forms and also because it overlaps with deterrence by punishment. Despite the emphasis in current scholarship on “inflicting costs” as a defining element of deterrence by punishment, costs arguably also play a significant role in deterrence by denial. To address these challenges, I distinguish between deterrence strategies by focusing on two main elements: the means the deterrer actor threatens to use (offensive or non-offensive) and the timing of the threatened use of these means (before or after the unwanted activity). This offers a more nuanced distinction between deterrence strategies and better encompasses the role of inflicting costs in deterrence by denial. I suggest that this research offers a useful point of departure to further theorize about deterrence by denial, and it sets a promising research agenda that is pertinent given the growing interest in deterrence by denial, especially in its application to cyber deterrence.
Natural cordiaquinones as strategies to inhibit the growth and biofilm formation of methicillin-sensitive and methicillin-resistantStaphylococcusspp
Authors: de Oliveira Mariana Araújo , Barros Ayslan Batista , de Araújo Gisele Santos , de Araújo Alyne Rodrigues , José dos Santos Soares Maria , de Oliveira Daiane Fernandes , Lima Filipe Camargo Dalmatti Alves , Batagin-Neto Augusto , Leite José Roberto de Souza de Almeida , Cesário Hozana Patrícia Silva de Freitas , Pessoa Otília Deusdênia Loiola , Filho José Delano Barreto Marinho , Araújo Ana Jérsia 
Published: July 2023

AbstractAimsThe aim of this study was to investigate the antibacterial and antibiofilm potential of cordiaquinones B, E, L, N, and O against different Staphylococci strains, in addition to analyzing in silico the observed effect.Methods and resultsThe minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) were determined according to CLSI guidelines. The inhibition of biofilm formation was investigated at sub-MICs. Atomic force microscopy (AFM) and density functional theory method were performed. The tested strains of Staphylococcus spp. were susceptible to cordiaquinones B, E, and L, among which cordiaquinone B exerted a bactericidal effect, confirmed by a bacterial growth curve study, against Staphylococcus saprophyticus. Cordiaquinones B and E showed lowest MBC values against S. saprophyticus. AFM revealed that cordiaquinone L reduced the mean cell size of S. saprophyticus. Cordiaquinones B and E inhibited the biofilm formation ability of S. aureus by ∼90%. The in silico analysis suggested that the antimicrobial activity of cordiaquinones is driven by their electron donation capability.ConclusionsCordiaquinones inhibit the growth and biofilm formation (virulence factor) of both methicillin-sensitive and methicillin-resistant Staphylococci strains, indicating their antimicrobial potential.
Optimization of solid-state fermentation for enhanced production of pectinolytic complex by Aspergillus tubingensis FAT43 and its application in fruit juice processing
Authors: Pavlović Marija , Šokarda Slavić Marinela , Ristović Marina , Stojanović Sanja , Margetić Aleksandra , Momčilović Miloš , Vujčić Zoran 
Published: July 2023

Abstract
The main goal of this study was to examine the efficiency of a newly isolated fungus from quince, Aspergillus tubingensis FAT43, to produce the pectinolytic complex using agricultural and industrial waste as the substrate for solid state fermentation. Sugar beet pulp was the most effective substrate inducer of pectinolytic complex synthesis out of all the waste residues examined. For endo-pectinolytic and total pectinolytic activity, respectively, statistical optimization using Placked-Burman Design and Optimal (Custom) Design increased production by 2.22 and 2.15-fold, respectively. Liquification, clarification, and an increase in the amount of reducing sugar in fruit juices (apple, banana, apricot, orange, and quince) processed with pectinolytic complex were identified. Enzymatic pre-treatment considerably increases yield (14%–22%) and clarification (90%). After enzymatic treatment, the best liquefaction was observed in orange juice, whereas the best clarification was obtained in apricot juice. Additionally, the pectinolytic treatment of apricot juice resulted in the highest increase in reducing sugar concentration (11%) compared to all other enzymatically treated juices. Optimizing the production of a highly active pectinolytic complex and its efficient utilization in the processing of fruit juices, including the generation of an increasing amount of waste, are the significant outcomes of this research.
Day and night: habitability of tidally locked planets with sporadic rotation
Authors: Shakespeare Cody J , Steffen Jason H 
Published: July 2023

ABSTRACT
Tidally locked worlds provide a unique opportunity for constraining the probable climates of certain exoplanets. They are unique in that few exoplanet spin and obliquity states are known or will be determined in the near future: both of which are critical in modelling climate. A recent study shows the dynamical conditions present in the TRAPPIST-1 system make rotation and large librations of the substellar point possible for these planets, which are usually assumed to be tidally locked. We independently confirm the tendency for planets in TRAPPIST-1-like systems to sporadically transition from tidally locked libration to slow rotation using N-body simulations. We examine the nature and frequency of these spin states to best inform energy balance models which predict the temperature profile of the planet’s surface. Our findings show that tidally locked planets with sporadic rotation are able to be in both long-term persistent states and states with prolonged transient behaviour: where frequent transitions between behaviours occur. Quasi-stable spin regimes, where the planet exhibits one spin behaviour for up to hundreds of millennia, are likely able to form stable climate systems while the spin behaviour is constant. 1D energy balance models show that tidally locked planets with sporadic rotation around M-dwarfs will experience a relatively small change in substellar temperature due to the lower albedo of ice in an infrared dominant stellar spectrum. The exact effects of large changes in temperature profiles on these planets as they rotate require more robust climate models, like 3D global circulation models, to better examine.
Type Ia supernova observations combining data from the Euclid mission and the Vera C. Rubin Observatory
Authors: Bailey A C , Vincenzi M , Scolnic D , Cuillandre J-C , Rhodes J , Hook I , Peterson E R , Popovic B 
Published: July 2023

ABSTRACT
The Euclid mission will provide first-of-its-kind coverage in the near-infrared over deep (three fields, ∼10–20 square degrees each) and wide (∼10 000 square degrees) fields. While the survey is not designed to discover transients, the deep fields will have repeated observations over a two-week span, followed by a gap of roughly six months. In this analysis, we explore how useful the deep field observations will be for measuring properties of Type Ia supernovae (SNe Ia). Using simulations that include Euclid’s planned depth, area, and cadence in the deep fields, we calculate that more than 3700 SNe between 0.0 &lt; $z$ &lt; 1.5 will have at least five Euclid detections around peak with signal-to-noise ratio larger than 3. While on their own, Euclid light curves are not good enough to directly constrain distances, when combined with legacy survey of space and time (LSST) deep field observations, we find that uncertainties on SN distances are reduced by 20–30 per cent for $z$ &lt; 0.8 and by 40–50 per cent for $z$ &gt; 0.8. Furthermore, we predict how well additional Euclid mock data can be used to constrain a key systematic in SN Ia studies – the size of the luminosity ‘step’ found between SNe hosted in high-mass (&gt;1010 M⊙) and low-mass (&lt;1010 M⊙) galaxies. This measurement has unique information in the rest-frame near-infrared (NIR). We predict that if the step is caused by dust, we will be able to measure its reduction in the NIR compared to optical at the 4σ level. We highlight that the LSST and Euclid observing strategies used in this work are still provisional and some level of joint processing is required. Still, these first results are promising, and assuming that Euclid begins observations well before the Nancy Roman Space Telescope (Roman), we expect this data set to be extremely helpful for preparation for Roman itself.
Probing the soft state evolution of 4U 1543-47 during its 2021 outburst using AstroSat
Authors: Husain Nazma , Bhargava Yash , Garg Akash , Mudambi Sneha Prakash , Misra Ranjeev , Sen Somasri 
Published: July 2023

ABSTRACT
4U 1543-47 underwent its brightest outburst in 2021 after two decades of inactivity. During its decay phase, AstroSat conducted nine observations of the source spanning from 2021 July 1 to September 26. The first three observations were performed with an offset of 40 arcmin with AstroSat/LAXPC, while the remaining six were on-axis observations. In this report, we present a comprehensive spectral analysis of the source as it was in the High/Soft state during the entire observation period. The source exhibited a disc-dominated spectra with a weak high-energy tail (power-law index ≥2.5) and a high inner disc temperature (∼0.84 keV). Modelling the disc continuum with non-relativistic and relativistic models, we find inner radius to be significantly truncated at &gt;10 Rg. Alternatively, to model the spectral evolution with the assumption that the inner disc is at the innermost stable circular orbit, it is necessary to introduce variation in the spectral hardening in the range ∼1.5–1.9.
The quenched satellite population around Milky Way analogues
Authors: Karunakaran Ananthan , Sand David J , Jones Michael G , Spekkens Kristine , Bennet Paul , Crnojević Denija , Mutlu-Pakdı̇l Burçı̇n , Zaritsky Dennis 
Published: July 2023

ABSTRACT
We study the relative fractions of quenched and star-forming satellite galaxies in the Satellites Around Galactic Analogs (SAGA) survey and Exploration of Local VolumE Satellites (ELVES) program, two nearby and complementary samples of Milky Way-like galaxies that take different approaches to identify faint satellite galaxy populations. We cross-check and validate sample cuts and selection criteria, as well as explore the effects of different star-formation definitions when determining the quenched satellite fraction of Milky Way analogues. We find the mean ELVES quenched fraction (〈QF〉), derived using a specific star formation rate (sSFR) threshold, decreases from ∼50 per cent to ∼27 per cent after applying a cut in absolute magnitude to match that of the SAGA survey (〈QF〉SAGA ∼9 per cent). We show these results are consistent for alternative star-formation definitions. Furthermore, these quenched fractions remain virtually unchanged after applying an additional cut in surface brightness. Using a consistently derived sSFR and absolute magnitude limit for both samples, we show that the quenched fraction and the cumulative number of satellites in the ELVES and SAGA samples broadly agree. We briefly explore radial trends in the ELVES and SAGA samples, finding general agreement in the number of star-forming satellites per host as a function of radius. Despite the broad agreement between the ELVES and SAGA samples, some tension remains with these quenched fractions in comparison to the Local Group and simulations of Milky Way analogues.
APES: approximate posterior ensemble sampler
Authors: D P Vitenti Sandro , Barroso Eduardo J 
Published: July 2023

ABSTRACT
This paper proposes a novel approach to generate samples from target distributions that are difficult to sample from using Markov chain Monte Carlo (MCMC) methods. Traditional MCMC algorithms often face slow convergence due to the difficulty in finding proposals that suit the problem at hand. To address this issue, the paper introduces the approximate posterior ensemble sampler (APES) algorithm, which employs kernel density estimation and radial basis interpolation to create an adaptive proposal, leading to fast convergence of the chains. The APES algorithm’s scalability to higher dimensions makes it a practical solution for complex problems. The proposed method generates an approximate posterior probability that closely approximates the desired distribution and is easy to sample from, resulting in smaller autocorrelation times and a higher probability of acceptance by the chain. We compare the performance of the APES algorithm with the affine invariance ensemble sampler with the stretch move in various contexts, demonstrating the efficiency of the proposed method. For instance, on the Rosenbrock function, the APES presented an autocorrelation time 140 times smaller than the affine invariance ensemble sampler. The comparison showcases the effectiveness of the APES algorithm in generating samples from challenging distributions. This paper presents a practical solution to generating samples from complex distributions while addressing the challenge of finding suitable proposals. With new cosmological surveys set to deal with many new systematics, this method offers a practical solution for the upcoming era of cosmological analyses. The algorithms presented in this paper are available at https://github.com/NumCosmo/NumCosmo.