bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plastic responses to past environments shape adaptation to novel selection pressures
Authors: Coates Sarah E. R. , Comeault Aaron A. , Wood Daniel P. , Fay Michael F. , Creer Simon , Osborne Owen G. , Dunning Luke T , Papadopulos Alexander S. T. 
Published: May 2024

AbstractPhenotypic plasticity may pave the way for rapid adaptation to newly encountered environments. Although it is often contested, there is growing evidence that initial plastic responses of ancestral populations to new environmental cues may promote subsequent adaptation. However, we do not know whether plasticity to cues present in the ancestral habitat (past-cue plasticity) can facilitate adaptation to novel cues. Conceivably, this could occur if plastic responses are coincidentally optimal to both past and novel cues (i.e., are pre-adaptive) or if they are transferred to novel cues during adaptation. Past plastic phenotype values could also become fixed and genetically co-opted during adaptation to the new environment. To uncover the role of past-cue plasticity in adaptation, we tested gene expression plasticity responses of two parallel mine-waste adaptedSilene uniflorapopulations and their closest coastal relatives. Plants were exposed to the past and novel-cues of salt and zinc, which revealed that during adaptation to mine-waste plasticity to salt diminishes. Despite this, our results show that ancestral plasticity to salt has a substantial impact on subsequent adaptation to zinc. For a third of genes that have evolved zinc plasticity in mine populations, salt plasticity has been transferred to the zinc response. Furthermore, a quarter of fixed expression differences between mine and coastal populations were similar to ancestral salt responses. Alongside evidence that ancestral plasticity to novel cues can facilitate adaptation, our results provide a clear indication that ancestral past-cue plasticity can also play a key role in rapid, parallel adaptation to novel habitats.Significance StatementThe role of phenotypic plasticity in promoting adaptation is hotly debated, with conflicting evidence for the benefits of ancestral plasticity in newly encountered environments. Here, we present an alternative mode by which ancestral plasticity can promote adaptation. We investigated whether phenotypic plasticity towards environmental cues that are experienced only in ancestral habitats (past-cue plasticity) can significantly contribute towards rapid adaptation to completely distinct cues. We show that, in the maritime plant species,Silene uniflora, past-cue plasticity to salt has made a substantial contribution to rapid adaptation to heavy-metal pollution in newly encountered habitats. This phenomenon has broad implications for the capacity and predictability of species to persist in the face of anthropogenic environmental change.
Phasing millions of samples achieves near perfect accuracy, enabling parent-of-origin classification of variants
Authors: Williams Cole M. , O’Connell Jared , Freyman William A. ,   23andMe Research Team, Gignoux Christopher R. , Ramachandran Sohini , Williams Amy L. 
Published: May 2024

ABSTRACTHaplotype phasing, the process of determining which genetic variants are physically located on the same chromosome, is crucial for various genetic analyses. In this study, we first benchmark SHAPEIT and Beagle, two state-of-the-art phasing methods, on two large datasets: > 8 million diverse, research-consented 23andMe, Inc. customers and the UK Biobank (UKB). We find that both perform exceptionally well. Beagle’s median switch error rate (SER) (after excluding single SNP switches) in white British trios from UKB is 0.026% compared to 0.00% for European ancestry 23andMe research participants; 55.6% of European ancestry 23andMe research participants have zero non-single SNP switches, compared to 42.4% of white British trios. South Asian ancestry 23andMe research participants have the highest median SER amongst the 23andMe populations, but it is still remarkably low at 0.46%. We also investigate the relationship between identity-by-descent (IBD) and SER, finding that switch errors tend to occur in regions of little or no IBD segment coverage.SHAPEIT and Beagle excel at ‘intra-chromosomal’ phasing, but lack the ability to phase across chromosomes, motivating us to develop an inter-chromosomal phasing method, called HAPTIC (HAPlotypeTIling andClustering), that assigns paternal and maternal variants discretely genome-wide. Our approach uses identity-by-descent (IBD) segments to phase blocks of variants on different chromosomes. HAPTIC represents the segments a focal individual shares with their relatives as nodes in a signed graph and performs bipartite clustering on the signed graph using spectral clustering. We test HAPTIC on 1022 UKB trios, yielding a median phase error of 0.08% in regions covered by IBD segments (33.5% of sites). We also ran HAPTIC in the 23andMe database and found a median phase error rate (the rate of mismatching alleles between the inferred and true phase) of 0.92% in Europeans (93.8% of sites) and 0.09% in admixed Africans (92.7% of sites). HAPTIC’s precision depends heavily on data from relatives, so will increase as datasets grow larger and more diverse. HAPTIC enables analyses that require the parent-of-origin of variants, such as association studies and ancestry inference of untyped parents.
Intratumoral administration of mRNA-1273 vaccine delays melanoma growth in mice
Authors: Boehm Dylan T. , Landreth Kaitlyn M. , Kilic Emel Sen , Lee Katherine S. , Misra Bishal , Bobbala Sharan , Heath Damron F. , Liu Tracy W. 
Published: May 2024

AbstractBackgroundImmunotherapies are advantageous for treating cancers; however, their efficacy is limited in unresponsive hosts with “cold” tumor microenvironments. This limitation primarily stems from the lack of infiltrating CD8+T cells, which are major effectors of the anti-cancer immune response. Here, we demonstrate the effects of intratumoral (IT) injections of the COVID-19 mRNA vaccine on the impairment of tumor growth in mice.MethodsEstablished B16F10 subcutaneous tumor models in wild type mice were used to evaluate the tumor response from IT administration of mRNA-1273. We compared treatment outcomes, immune composition, and transcriptomic effects from mRNA-1273 using survival studies, intravital imaging, flow cytometry, single-cell RNA sequencing, and abscopal studies. The ability of mRNA-1273 to enhance immune checkpoint therapy response was also evaluated.ResultsTumor growth and survival studies following a single IT injection of the COVID-19 mRNA-1273 vaccine showed significant tumor suppression and prolonged survival in tumor-bearing mice. mRNA-1273 treatment resulted in a significant increase in CD8+T cell infiltration into the tumor microenvironment, as observed using intravital imaging and flow cytometry. Further tumor growth suppression was achieved using additional mRNA-1273 treatments. Combination administration of mRNA-1273 with immune checkpoint therapies demonstrated enhanced effects, further delaying tumor growth and improving the survival time of tumor-bearing mice.ConclusionIT injection of mRNA-1273 significantly reduced tumor growth and enhanced CD8+T cells in the tumor microenvironment. Tumor suppression was further enhanced following multiple injections of mRNA-1273 or when combined with immune checkpoint therapies. This study demonstrates that mRNA vaccines may be used as adjuvants for immunotherapies.What is already known on this topicMost cancer patients develop adequate antibody response to vaccination with mRNA-1273 and produce spike-specific T cell responses. However, it is unclear if the mRNA-1273 vaccine can be used to elicit anti-tumor T cell responses.What this study addsIntratumoral injection of mRNA-1273 significantly delayed melanoma growth.Treatment with mRNA-1273 significantly increased CD8+T cell infiltration into the tumor microenvironment.Enhanced effects of combination mRNA-1273 and immune checkpoint therapy in anti-tumor immunity.How this study might affect research, practice, or policymRNA vaccine may be an effective adjuvant with immune checkpoint therapy.
Triphasic Thrombosis Model: A Computational Study of Type B Aortic Dissection
Authors: Gupta Ishan , Schanz Martin , Ricken Tim 
Published: May 2024

AbstractThrombosis refers to the formation of a thrombus, or a blood clot, within the body, which can occur either partially or completely. It serves as a crucial indicator of the severity of a patient’s medical condition, with the location and characteristics of thrombosis dictating its clinical implications. Hence, accurate diagnosis and effective management of thrombosis are paramount.In our current investigation, we incorporate the porous attributes of a thrombus using the Theory of Porous Media. This involves dividing the aggregate into solid, liquid, and nutrient phases and utilising volume fractions to capture microstructural details. Fluid flow through the porous media is modelled using a modified Darcy-Brinkman type equation, with interaction terms within balance equations facilitating the modelling of the mass exchange and other phase interactions. The shorter time scales are neglected.We present a comprehensive framework of equations and assumptions governing the behaviour of a strongly coupled multiphasic porous medium problem. Additionally, we introduce scenarios involving type B Aortic Dissection and false lumen geometries, providing a detailed outline of the problem setup. Thereafter, we present the potential of the model for thrombi growth. The simulation results are compared with velocity plots aligning with Magnetic Resonance Imaging data for three distinct cases with varying entry and exit tear sizes. Consequently, our proposed model offers a promising and reasonable approach for numerically simulating thrombosis and gaining insights into the underlying growth mechanics.
Generating intermediate slices with U-nets in craniofacial CT images
Authors: Nishimoto Soh , Kawai Kenichiro , Nakajima Koyo , Ishise Hisako , Kakibuchi Masao 
Published: May 2024

AbstractAimThe Computer Tomography (CT) imaging equipment varies across facilities, leading to inconsistent image conditions. This poses challenges for deep learning analysis using collected CT images. To standardize the shape of the matrix, the creation of intermediate slice images with the same width is necessary. This study aimed to generate inter-slice images from two existing CT images.Materials and MethodsThe study utilized CT images from the Japanese Facial Bone Fracture CT Collection Project. The pixel values were converted to Hounsfield numbers and normalized. Three re-slice systems utilizing U-nets were developed: 1/3, 1/4, and 1/5. The datasets were divided into training and validation sets, and data augmentation techniques were applied. The U-net models were trained for 200 epochs. Validation was conducted using validation datasets. The generated images were compared to the corresponding original images using peak signal-to-noise ratio (PSNR), structural similarity (SSIM), and mean squared error (MSE) calculations. Results: Statistical analysis revealed significant differences between linear interpolation and U-net prediction in all indexes.ConclusionThe developed re-slice systems with U-net models showed practical value for making intermediate slice images from the existing images in the craniofacial area.
Executive Resources Shape the Effects of Language Predictability Across the Adult Lifespan
Authors: Schuckart Merle , Martin Sandra , Tune Sarah , Schmitt Lea-Maria , Hartwigsen Gesa , Obleser Jonas 
Published: May 2024

ABSTRACTHumans predict upcoming language effortlessly, but the cognitive costs of these predictions remain debated. In this study, we demonstrate that limiting executive resources through a concurrent task reduces the effect of language predictability on reading times. Participants (N=175, replication N=96) read short articles presented word-by-word while completing a secondary font colour n-back task, thus varying cognitive demand. Language predictability was indexed by word surprisal as derived from a generative pre-trained transformer model (GPT-2). Our results show that predictability effects increase with age (18–85 years), and across both samples, higher cognitive load consistently diminished the impact of word predictability on reading speed. These findings highlight the resource-dependent nature of predictive mechanisms in language comprehension across the lifespan. We conclude that linguistic predictions rely on executive resources, which helps resolve the debate about the cognitive cost of predictive language processing.
Spatial modulation of facial expression: enhanced recognition of faces behind the observer
Authors: Tamura Hideki , Kobayashi Yugo , Nakauchi Shigeki , Minami Tetsuto 
Published: May 2024

SummaryOur ability to recognize facial expressions is crucial for understanding others’ emotions1and facilitating smooth communication2. Numerous studies have explored how we perceive these cues, considering factors such as health3, social signals4and personality traits5. However, most of this research involves observers facing a monitor and assessing facial stimuli presented directly in front of them. Real-life scenarios offer more diverse spatial dynamics, such as conversing with someone at a table or glancing back at a passerby. Thus, faces behind the observer might trigger heightened recognition, akin to reacting swiftly to a perceived threat. Herein, we demonstrate that facial expression recognition is influenced by spatial relationships, i.e., faces in front of versus behind the observer. Participants judged the expressions of faces appearing in front of or behind them in virtual space. The findings of three experiments reveal an enhanced level of recognition for faces behind the participant. Interestingly, this effect varies with emotional valence; anger is amplified merely by the presence of a face behind the observer, while happiness requires actively turning to the rear for enhancement to occur. These findings suggest a biological instinct for perceiving threats behind us, potentially influencing subsequent actions. Hence, spatial relationships may modulate facial expression recognition.
Nothing but lies: improving the validity of neural predictors of deception
Authors: Lee Sangil , Niu Runxuan , Zhu Lusha , Kayser Andrew , Hsu Ming 
Published: May 2024

AbstractDeception is a universal human behavior. Yet longstanding skepticism about the validity of measures used to understand the biological mechanisms underlying deceptive behavior has relegated such studies to the scientific periphery. Here we address these fundamental questions by applying novel machine learning methods and functional neuroimaging to signaling games capturing motivated deception in human participants. First, we develop an approach to test for the presence of confounding processes and thereby validate past skepticism by showing that much of the predictive power of neural predictors trained on deception data comes from confounding processes. Second, we show that the presence of confounding signals need not be fatal, and we improve the validity of our neural predictor via a novel machine learning procedure that identifies and removes these confounding signals. Together, these findings point to a scientific approach for studying a neglected class of behavior, with important methodological and societal implications.
A mismatch between striatal cholinergic pauses and dopaminergic reward prediction errors
Authors: Duhne Mariana , Mohebi Ali , Kim Kyoungjun , Pelattini Lilian , Berke Joshua 
Published: May 2024

SummaryMovement, motivation and reward-related learning depend strongly on striatal dopamine and acetylcholine. These neuromodulators each regulate the other, and disturbances to their coordinated signals contribute to human disorders ranging from Parkinson’s Disease to depression and addiction. Pauses in the firing of cholinergic interneurons (CINs) are thought to coincide with pulses in dopamine release that encode reward prediction errors (RPEs), together shaping synaptic plasticity and thereby learning. However, such models are based upon recordings from unidentified neurons, and do not incorporate the distinct characteristics of striatal subregions. Here we compare the firing of identified, individual CINs to dopamine release as unrestrained rats performed a probabilistic decision-making task. The relationships between CIN spiking, dopamine release, and behavior varied strongly by subregion. In dorsal-lateral striatum aGo!cue evoked burst-pause CIN spiking, quickly followed by a very brief (~150ms) dopamine pulse that was unrelated to RPE. In dorsal-medial striatum the same cue evoked only a CIN pause; this pause was curtailed by a movement-selective rebound in firing. Finally in ventral striatum a reward cue evoked slower, RPE-coding increases in both dopamine and CIN firing, without any distinct pause. Our results demonstrate a spatial and temporal dissociation between CIN pauses and dopamine RPE signals, and will inform new models of striatal microcircuits and their contributions to behavior.
Effect of annealing treatment of hot-rolled AZ31 magnesium alloy on properties and stress corrosion resistance of MAO coatings
Authors: Zhou Feng , Lu S. S. , Jiang B. , Song R.G. 
Published: May 2024

Purpose
This study aims to study the formation mechanism of micro-arc oxidation (MAO) coating on AZ31 magnesium alloy and how the annealing process affects its corrosion resistance.

Design/methodology/approach
This study involved immersion experiments, electrochemical experiments and slow strain rate tensile experiments, along with scanning electron microscopy, optical microscopy observation and X-ray diffraction analysis.

Findings
The findings suggest that annealing treatment can refine the grain size of AZ31 magnesium alloy to an average of 6.9 µm at 300°C. The change in grain size leads to a change in conductivity, which affects the performance of MAO coatings. The MAO coating obtained by annealing the substrate at 300°C has smaller pores and porosity, resulting in better adhesion and wear resistance.

Originality/value
The coating acts as a barrier to prevent corrosive substances from entering the substrate. However, the smaller pores and porosity reduce the channels for the corrosive solution to pass through the coating. When the coating cracks or falls off, the corrosive medium and substrate come into direct contact. Smaller and uniform grains have better corrosion resistance.
Does social currency influence social media usage and brand experience: an empirical analysis
Authors: Mishra Yog , Singh Anurag 
Published: May 2024

PurposeLoading the work on social capital theory, we have tried to check the influence of social currency (SC) on social media usage (SMU) and its subsequent impact on the brand experience (BE). The study attempted to ascertain the mediation of loyalty (LT) between the SC and SMU as well as the moderation of perceived ease of use (PEU) in the SMU and BE relationship.Design/methodology/approachThe data were collected from 384 respondents employing snowball sampling technique by administering a questionnaire on seven-point Likert scale. The respondents were the active internet users, who devote the significant part of their daily routine to social media activities. Structural equation modelling was used to study the path of the considered variables.FindingsThe result of the study strengthened the findings of earlier studies on SC dimensions. This study elaborated about the positive impact of SC on SMU, SC on LT, LT on SMU, SMU on BE. The study also found the mediating effect of LT in the SC and BE relationship. The study did not identify a moderating role of PEU in the SMU and BE relationship.Research limitations/implicationsBy taking into account SC, SMU, LT, PEU and BE, the study adds the knowledge to the social capital theory.Practical implicationsThis study aids marketers in adjusting social media strategies for the effective use of SC aimed to deliver enhanced BE. Additionally, it demonstrates the value of customer LT in the context of SC and SMU by customers.Originality/valueThis study is among the few research on the SC of the Indian user and its impact on SMU and BE. Checking the mediation of LT and the moderation of PEU in the SC context makes this study novel and different from any study conducted earlier.
Governance dynamics and the human capital disclosure-engagement paradox: a Japanese perspective
Authors: Elamer Ahmed A. , Kato Misaki 
Published: May 2024

Purpose
This paper aims to delve into the nuanced relationship between corporate governance dynamics, human capital disclosure and their impact on the competitive positioning of Japanese listed companies. The study primarily examines how these factors influence employee engagement, a critical determinant of overall business competitiveness.

Design/methodology/approach
Panel data for Japanese listed companies for FY 2019 to FY 2021 were analysed using multiple regression analyses with two models.

Findings
The results indicate that the presence of independent and female board members has a positive impact on human capital disclosure. Surprisingly, employee engagement was found to be negatively related with human capital disclosure, signifying a potential trade-off between transparency and engagement.

Originality/value
Amidst the escalating emphasis on non-financial information and corporate social responsibility, this paper unveils a previously underexplored aspect of Japanese corporate competitiveness. Specifically, this study offers a fresh empirical perspective on the relationship between corporate governance, human capital disclosure and employee engagement in Japanese listed companies, a topic with limited academic research and no legal regulations in Japan. The findings have significant implications for companies seeking to enhance their human capital disclosure and employee engagement practices, especially in light of the growing focus on non-financial information and social responsibility.