bluuebunny/crossref_metadata_2025 huggingface dataset:
Fast and reliable ancestral reconstruction on ancient genotype data with non-negative Least square and Principal Component Analysis
Authors: de Gennaro Luciana , Molinaro Ludovica , Raveane Alessandro , Santonastaso Federica , Saponetti Sandro Sublimi , Massi Michela Carlotta , Pagani Luca , Metspalu Mait , Hellenthal Garrett , Kivisild Toomas , Ventura Mario , Montinaro Francesco
Published: May 2024

The history of human populations has been strongly shaped by admixture events, contributing to the patterns of observed genetic diversity across populations. Given its significance for evolutionary and medical studies, many algorithms focusing on the inference of the genetic composition of admixed populations have been developed. In particular, the recent development of new ancestry estimation methods that consider the fragmentary nature of ancient genotype data, such as the f-statistics family and its derivations, have radically changed our understanding of the past. F-statistics capture similar genetic similarity information as Principal Component Analysis (PCA), which is widely used in population genetics to quantify genetic affinity between populations or individuals. In this study, we introduce ASAP (ASsessing ancestry proportions through Principal component Analysis) method that leverages PCA and Non-Negative Least Square (NNLS) to assess the ancestral compositions of admixed individuals given a large set of populations. We tested ASAP on different simulated models, incorporating high levels of missingness. Our results show its ability to reliably estimate ancestry across numerous scenarios, even those with a significant proportion of missing genotypes, in a fraction of the time required when using other tools. When harnessed on Eurasia’s genotype data, ASAP helped replicate and extend findings from previous studies proving to be a fast, efficient, and straightforward new ancestry estimation tool.
Episodic memory supports the acquisition of structured task representations
Authors: Lu Qihong , Hummos Ali , Norman Kenneth A.
Published: May 2024

Generalization to new tasks requires learning of task representations that accurately reflect the similarity structure of the task space. Here, we argue that episodic memory (EM) plays an essential role in this process by stabilizing task representations, thereby supporting the accumulation of structured knowledge. We demonstrate this using a neural network model that infers task representations that minimize the current task’s objective function; crucially, the model can retrieve previously encoded task representations from EM and use these to initialize the task inference process. With EM, the model succeeds in learning the underlying task structure; without EM, task representations drift and the network fails to learn the structure. We further show that EM errors can support structure learning by promoting the activation of similar task representations in tasks with similar sensory inputs. Overall, this model provides a novel account of how EM supports the acquisition of structured task representations.
AAV-DJ is Superior to AAV9 for Targeting Brain and Spinal Cord, and De-Targeting Liver Across Multiple Delivery Routes in Mice
Authors: Chauhan Monika , Daugherty Audrey L. , Khadir Fatemeh Ellie , Duzenli Ozgun F. , Hoffman Alexandra , Tinklenberg Jennifer A. , Kang Peter B. , Aslanidi George , Pacak Christina A.
Published: May 2024

Highly efficient adeno associated viruses (AAVs) targeting the central nervous system (CNS) are needed to deliver safe and effective therapies for inherited neurological disorders. The goal of this study was to compare the organ-specific transduction efficiencies of two AAV capsids across three different delivery routes. We compared AAV9-CBA-fLucYFP to AAV-DJ-CBA-fLucYFP using the following delivery routes in mice: intracerebroventricular (ICV) 1x1012 vg/kg, intrathecal (IT) 1x1012 vg/kg, and intravenous (IV) 1x1013 vg/kg body weight. Our evaluations revealed that following ICV and IT administrations, AAV-DJ demonstrated significantly increased vector genome (vg) uptake throughout the CNS as compared to AAV9. Through the IV route, AAV9 demonstrated significantly increased vg uptake in the CNS. However, significantly fewer vgs were detected in the off-target organs (kidney and liver) following administration of AAV-DJ using the IT and IV delivery routes as compared to AAV9. Distributions of vgs correlate well with transgene transcript levels, luciferase enzyme activities, and immunofluorescence detection of YFP. Overall, between the two vectors, AAV-DJ resulted in better targeting and expression in CNS tissues paired with de-targeting and reduced expression in liver and kidneys. Our findings support further examination of AAV-DJ as a gene therapy capsid for the treatment of neurological disorders.
Intraspecies warfare restricts strain coexistence in human skin microbiomes
Authors: Mancuso Christopher P. , Baker Jacob S. , Qu Evan , Tripp A. Delphine , Balogun Ishaq O. , Lieberman Tami D.
Published: May 2024

Determining why only a fraction of encountered or applied bacterial strains engraft in a given person’s microbiome is crucial for understanding and engineering these communities1. Previous work has established that metabolism can determine colonization successin vivo2–4, but relevance of bacterial warfare in preventing engraftment has been less explored. Here, we demonstrate that intraspecies warfare presents a significant barrier to strain transmission in the skin microbiome by profiling 14,884 pairwise interactions betweenStaphylococcus epidermidiscultured from eighteen human subjects from six families. We find that intraspecies antagonisms are abundant; these interactions are mechanistically diverse, independent of the relatedness between strains, and consistent with rapid evolution via horizontal gene transfer. Ability to antagonize more strains is associated with reaching a higher fraction of the on-personS. epidermidiscommunity. Moreover, antagonisms are significantly depleted among strains residing on the same person relative to random assemblages. Two notable exceptions, in which bacteria evolved to become sensitive to antimicrobials found on the same host, are explained by mutations that provide phage resistance, contextualizing the importance of warfare among other lethal selective pressures. Taken together, our results emphasize that accounting for intraspecies bacterial warfare is essential to the design of long-lasting probiotic therapeutics.
The visuomotor transformations underlying target-directed behavior
Authors: Zhao Peixiong , Tong Yuxin , Lazarte Ivan P. , Khan Biswadeep , Tian Guangnan , Chen Kenny K. Y. , Lam Thomas K. C. , Hu Yu , Semmelhack Julie L.
Published: May 2024

The visual system can process diverse stimuli and make the decision to execute appropriate behaviors, but it remains unclear where and how this transformation takes place. We imaged the zebrafish visual system while larvae responded with hunting, freezing, and escape behaviors, and systematically identified visually driven neurons and behaviorally correlated sensorimotor neurons. Our analyses indicate within the optic tectum, broadly tuned sensory neurons are functionally connected to sensorimotor neurons that respond specifically during one behavior, transforming visual information into motor output. We also identified sensorimotor neurons in four other areas downstream of the tectum, and these neurons are also specific for one behavior, indicating that once the decision to behave has been made, the segregation of the pathways continues in later areas. Our findings suggest that the tectum receives visual sensory information and is responsible for selecting a single behavioral outcome, which is then relayed to downstream areas.

Significance statement

Here, we developed a novel visually-evoked freezing paradigm in zebrafish, and combined this with escape and hunting behaviors to ask how visual stimuli are identified and converted into different behavioral outcomes. We found that the optic tectum contains neurons that detect all three stimuli, as well as sensorimotor neurons for the three behaviors, suggesting that it is a site of sensorimotor transformation, which was supported by our analysis of correlations between the populations. The sensorimotor neurons in the tectum are highly specific for one behavior, and this segregation is maintained in the three downstream areas where we also identified sensorimotor neurons, indicating that the tectum flexibly transforms visual information into a single behavioral output.
Mechanisms of RecA filament nucleation on ssDNA by the DprA protein
Authors: Bakhlanova Irina , Alekseev Aleksandr , Yakunina Maria , Morozova Natalia , Khodorkovskii Mikhail , Petukhov Michael , Baitin Dmitry
Published: May 2024

The DprA protein has been implicated in the protecton of incoming DNA. However, the presence of dprA gene family members, also known as smf, across diverse bacterial species suggests a broader functonality for their gene products. We eaamined the role of the Escherichia coli DprA/Smf homologue in conjugaton. Remarkably, Bacillus subtilis dprA/smf can complement an E. coli dprA mutant, indicatng interchangeability of dprA/smf genes between competent and non-competent species in conjugatonal processes. The DprA protein forms a complex with DNA, facilitatng the nucleaton of RecA protein flaments onto circular single-stranded DNA coated with SSB protein. To focus on RecA nucleaton, we employed short DNA oligonucleotdes that restrict RecA-DNA binding but allow for DprA-RecA-DNA binding. Analysis of dATPase actvity revealed that RecA-DNA complexes were readily formed only with olig50, while DprA-RecA-DNA complexes were also feasible with olig21. Combining eaperimental data with a full-atomic model of the RecA-DprA-ssDNA complex’s spatal structure, we proposed a molecular mechanism for DprA-mediated loading of RecA proteins onto ssDNA. Our fndings suggest that only one DprA-ssDNA interacton can occur sterically, occupying one strand of ssDNA in the complex.
Modulation of host signalling pathways reveal a major role for Wnt signalling in the maturation ofPlasmodium falciparumliver schizonts
Authors: Kanyal Abhishek , van Gemert Geert-Jan , Wu Haoyu , van der Starre Alex , de Wilt Johannes HW , Bousema Teun , Sauerwein Robert W. , Bartfai Richard , Yang Annie SP
Published: May 2024

After infection of the human host, the initial stage of thePlasmodium falciparum(Pf) lifecycle takes place in the liver. However, understanding of the host-parasite interaction has been limited by the rapid loss of functionality in cultured primary human hepatocytes (PHHs). Here, we link loss of hepatic functionality to drastic loss in Pf permissiveness, which we effectively prevent by using a novel medium containing serum-replacement and signal transduction inhibitors. Integrating transcriptomic analysis and phenotypic assessment of infection outcome, we identified several host signalling pathways that influence Pf liver stage development. Inhibition of the Wnt pathway in particular plays a major role in determining the size and maturity of Pf-liver schizonts, via retaining metabolic activity and epithelial nature of hepatocytes. Host signalling pathways determining Pf liver stage permissiveness provide insight into the complex host-parasite interaction and may accelerate development of novel therapeutic strategies for Pf-liver stages. (145)
Identification and Characterization of Novel Metagenome Assembled Uncultivated Virus Genomes from Human Gut
Authors: Bhardwaj Kanchan , Niharika  , Garg Anjali , Jain Aakriti , Kumar Manish , Datt Manish , Singh Vijay , Vrati Sudhanshu
Published: May 2024

Metagenomics has revealed an unprecedented viral diversity in human gut although, most of the sequence data remains to be characterized. In this study, we mined a collection of 1090 metagenome assembled “high quality” genomes of human gut viruses. Sequence analysis has revealed eight new species from seven genera of the class,Caudoviricetesand nineteen new species from fourteen genera of the ssDNA virus family,Microviridae.In addition, four “high quality” genomes were identified, which do not show similarity to sequences present in any of the four major viral databases, NCBI viral RefSeq, IMG-VR, Gut Phage Database (GPD) and Gut Virome Database (GVD). Further, annotation of the “high-quality” genomes and KEGG pathway analysis has identifiedantB,dnaB,DNMT1,DUT,xlyAB,xtmBandxtmAas the most widespread viral and Auxiliary Metabolic Genes (AMGs). Genes for virulence, host-takeover, drug resistance, tRNA, tmRNA and CRISPR elements were also found. Bacterial hosts are predicted for around 40% of the analyzed genomes. Overall, we report identification of new viral genomes and genome analyses of human gut viruses, which will be useful for biological characterization to establish their significance in physiology.

IMPORTANCE

Multiple studies have found that dysbiosis of gut virome is associated with conditions such as metabolic syndromes, autoimmune disorders and infectious diseases. In the interest of its therapeutic and diagnostic potential, intestinal virome warrants detailed investigation. However, limited ability to culture gut viruses becomes one of the challenges for their biological characterization and fully understanding their role in physiology. Sequence analysis and host prediction methods provide opportunities to understand gut viruses, their functional potential and devise ways for further characterization.
The impact of biophilic design in university study areas on students' productivity
Authors: Terblanche Rolien , Khumalo Dorcas
Published: May 2024

Purpose

The objective of this study is to determine how biophilic designs in study areas affect the productivity of students at the University of the Witwatersrand. The study also seeks to evaluate study areas at Wits in terms of biophilic design, determine whether biophilic design contributes to the preference of students and their study productivity.

Design/methodology/approach

This is a cross sectional study that used a mixed methodology. Five study areas were identified and evaluated in terms of biophilic design. At each study area, nine students participated in an open- and close-ended questionnaire regarding their perceptions on study areas and productivity.

Findings

The five study areas scored the following results according to the biophilic test: 29.09%, 34.55%, 36.36%, 80.00% and 85.45%, respectively. The students prefer to study in biophilic study areas as it prompts positive emotions and make them feel rejuvenated and energized. However, there are still students studying in the non-biophilic areas due to convenience or due to the biophilic areas that are noisy and lacks monitoring.

Research limitations/implications

With the small sample size, the generalizability of the findings are limited, but does create a foundation for further research.

Practical implications

Universities can learn from the findings and benefit greatly from many biophilic study areas. This could also encourage architects and interior designers to include biophilic design more so in general buildings/rooms.

Originality/value

Study areas at the University of the Witwatersrand was evaluated in terms of biophilic design, while determining whether biophilic design contributes to the preference of students and study productivity.
Determinants of perceived benefits: cultural recognition, traditions and cultural linkages
Authors: Zirena-Bejarano Patricia Pilar , Choquecahuana-Valverde Luis Guillermo
Published: May 2024

Purpose

The present study addresses the literature gap on cultural linkages, traditions, cultural recognition and the perceived benefits of consumers in the orange economy. The article focuses on analyzing the impact of traditions and cultural linkages on the relationship between cultural recognition and the perceived benefits of consumers.

Design/methodology/approach

The empirical study is conducted on a sample of 393 consumers from the city of Arequipa, Peru utilizing structural equation modeling (SEM) with Smart PLS software.

Findings

The research results demonstrate that traditions and cultural ties are important factors that entrepreneurs must consider in the production and marketing process to enhance the benefits perceived by consumers by providing cultural identity within the products.

Originality/value

The study provides theoretical implications that fill the existing gap in understanding the relationship between cultural recognition and perceived benefits. Additionally, it offers practical implications for the development of the cultural ecosystem, involving artisans, artists, cultural managers, entrepreneurs, businessmen, government authorities, non-governmental organizations and international organizations.
Resilience of ethical and nonethical stock during COVID-19 crisis: a case of Indonesia Stock Exchange
Authors: Qoyum Abdul , AlHashfi Rizqi Umar , Hanafi Mamduh Mahmadah , Mohd Thas Thaker Hassanudin , Effendi Jaenal
Published: May 2024

Purpose

This study aims to empirically investigates the effect of the COVID-19 pandemic on ethical and nonethical stocks in Indonesia. Ethical stocks which are characterized by moral-based companies’ activities and lower debt are expected to have better resilience during the COVID-19 crisis compared to nonethical stock.

Design/methodology/approach

This study observes 589 firms of ethical and nonethical stock during sample periods ranging from March 2, 2020 (first case announced) to June 30, 2021. Panel regression, with some control variables, was applied.

Findings

Testing firms in Indonesia revealed a significant difference in stock resilience, in which ethical stock has a better resilience compared to nonethical, with Islamic socially responsible investment (SRI) stock having the highest resilience, followed by Islamic stock and then SRI stock. This study documents a significant effect of some financial criteria on the stock resilience, namely, return market (RM), market capitalization (MCAP) and share turnover (TURN). Overall, after splitting the sample into different time horizons, this study consistently reveals that ethical firms have better resilience compared to nonethical stocks.

Research limitations/implications

This study makes several contributions to the literature on Islamic finance, especially concerning Islamic screening with SRI factors. In practical terms, this study supports the argument that focusing on integrating environmental, social and governance criteria in sharia screening will improve the quality of Islamic firms. The “Islamic” label is not only a marketing label but also a quality certification.

Originality/value

This study can be used as a reference for developing Islamic finance more focused on sustainability issues including socioeconomic and human development by improving the quality of screening of Islamic firms. Therefore, this study suggests that the establishment of Islamic SRI index is very crucial and significant to promote ethical-based investment.
Mindfulness and psychological capital: examining the role of intention from the person perspective in a multi-week mindfulness training program
Authors: Choi Ellen , Levallet Nadège , Bharti Mehak
Published: May 2024

Purpose

When evaluating the efficacy of mindfulness interventions, most studies take a linear approach to explore how an intervention impacts different outcomes for individuals, and rarely is the role of intention examined. This research takes a configural approach to consider how various elements of a participant’s training expectations and their experience in the training condition combine to predict increases in psychological capital.

Design/methodology/approach

Employees from hospital settings were randomized into three conditions (mindfulness training, active control (Pilates), and wait-list control group) and completed surveys at three time points (baseline, post-training and three months post-training). A qualitative comparative analysis was applied to see what combinations of motivational elements were associated with increases in psychological capital.

Findings

We find that all three conditions can boost their psychological capital based on different configurations involving efficacy beliefs, baseline states of well-being (psychological capital and perceived stress) and changes in levels of mindfulness and perceived stress.

Research limitations/implications

Individual characteristics, like motivation, expectancy and baseline needs, are an important consideration in addition to the training condition itself when determining whether a training is efficacious.

Practical implications

It is of increasing importance that organizations find ways to support employee well-being. Offering a variety of psychological and physical interventions can improve psychological capital. Applying needs assessments that clarify the desires, needs and expectations employees hold may help with intervention efficacy.

Originality/value

The current study offers an innovative methodology through which realist evaluation approaches can consider multiple factors to predict outcomes.
Consolidate? Diversify? Post‐M&A supply base structural changes and operational performance
Authors: Yang‐Sun Yang Sophie , Chae Sangho , Yan Tingting , Linderman Kevin
Published: May 2024

Firms increasingly engage in mergers and acquisitions (M&As) to improve their network positions and enhance performance. Yet, how the fundamental structure of the merged supply base changes after the M&A and how the structural changes affect the performance are largely unknown. Building upon the strategy‐structure‐performance framework, this study investigates dual roles of supply base structural changes in M&A events, namely, as an outcome and as a moderator to post‐M&A performance. In particular, we examine how the size and the country diversity of the merged supply base change after M&As, as well as how these structural changes affect the merged firm's operational performance. We conduct a difference‐in‐differences analysis by comparing firms that engaged in M&A events (treatment group) with those comparable firms that did not engage in any M&A events (control group). The results show that the merged firms tend to reduce the size of their supply bases after M&As. In addition, our results demonstrate that both supply base consolidation (i.e., reducing the number of suppliers) and country diversification (i.e., spreading suppliers across multiple countries) improve the merged firms’ post‐M&A operational performance, an effect that becomes stronger for horizontal M&As. We also explore how the type of M&As (i.e., horizontal vs. nonhorizontal), industry relatedness between the two merging firms, and the purposes of M&As affect the post‐M&A structural changes to the supply bases. This study helps inform supply managers the important roles of supply base in M&As to enhance post‐M&A operational performance or to limit the synergies when not properly done.
Chimera RNA transcribed from integrated HPV18 genome with adjacent host genomic region promotes oncogenic gene expression through condensate formation
Authors: Furugori Kazuki , Suzuki Hidefumi , Abe Ryota , Horiuchi Keiko , Akiyama Tomohiko , Hirose Tomonori , Toyoda Atsushi , Takahashi Hidehisa
Published: May 2024

Most cervical cancers are caused by human papillomavirus (HPV) infection. In HeLa cells, the HPV18 viral genome is integrated at chromosome 8q24.21 and activates transcription of the proto‐oncogene c‐Myc. However, the mechanism of how the integrated HPV genome and its transcribed RNAs exhibit transcription activation function has not been fully elucidated. In this study, we found that HPV18 transcripts contain an enhancer RNA‐like function to activate proximal genes including CCAT1‐5L and c‐Myc. We showed that the human genome‐integrated HPV18 genes are activated by transcription coregulators including BRD4 and Mediator. The transcribed HPV18 RNAs form a liquid‐like condensate at chromosome 8q24.21 locus, which in turn accumulates RNA polymerase II. Moreover, we focused on a relatively uncharacterized transcript from the upstream region of CCAT1, named URC. The URC RNA is transcribed as a chimera RNA with HPV18 and is composed of the 3′‐untranslated region of the HPV18 transcript. We experimentally showed that the URC contributes to stabilization of HPV18 RNAs by supplying a polyadenylation site for the HPV18 transcript. Our findings suggest that integrated HPV18 at 8q24.21 locus produces HPV18‐URC chimera RNA and promotes tumorigenesis through RNA‐based condensate formation.
How well does theatre translate into film: livestreaming clinical experiences to remotely located learners
Authors: Scott Ian
Published: May 2024

Drawing an analogy to the translation of stage productions to movie sets, Scott reflects on what is lost when education moves online.
Credible signaling to promote local compliance: Evidence from China's multiwave inspection of environmental protection
Authors: Zhu Xufeng , Wang Yue
Published: May 2024

Different from common knowledge on central–local information asymmetry, this study focuses on reverse information asymmetry, in which local governments may lack information on the intentions and resolve of the central government. Such information asymmetry can lead to a loss–loss scenario, wherein central‐government‐designed policies are eroded and local governments are punished. Arguably, with a multiwave inspection scheme, the central government can credibly signal its emphasis on certain policies and intentions to punish noncompliance, deterring yet‐to‐be‐inspected local governments. This argument is examined with China's Central Environmental Protection Inspection (CEPI) policy. Empirically, the CEPI policy can reduce pollution in the long run. Moreover, the credible signals generated by the previously completed inspection waves, which encourage local governments to rectify environmental regulations proactively, are essential. Furthermore, the strength of local compliance with central signaling largely depends on the hierarchical and geographical distances from the signaling source to the receiver.

Chinese Abstract

不同于对中央和地方政府间信息不对称的一般认识, 本研究关注中央和地方政府间的逆向信息不对称现象, 即地方政府可能缺乏对于中央政府意图和决心的了解。上述信息不对称的存在可能导致中央政府制定的政策无法得到有效落实, 同时地方政府由于未妥善履职而受到惩罚的双输局面。本研究指出, 通过分批次的督察机制, 中央政府可以就其对某些政策的重视程度和惩罚违规行为的决心发出可信的信号, 从而对尚未接受督察的地方政府形成有效威慑。本文以中国中央环境保护督察政策为例检验上述理论。实证结果表明, 长期来看中央环保督察政策可以有效控制污染。其核心机制在于, 已完成的督察批次所产生的可信信号, 可以激励其他地方政府主动改善环境规制, 形成对信号的有效响应。此外, 研究还发现地方政府对中央政府政策信号的响应强度取决于信号源的科层距离和地理距离。
Gender and Diversity in a Problem and Project Based Learning Environment: A Book Review
Authors: Ibrahim Mohamad Syahrul Nizam
Published: May 2024

"Gender and Diversity in a Problem and Project Based Learning Environment" by Xiangyun Du is a pioneering exploration of the intersection between pedagogical innovation and gender diversity in engineering education. This book expertly navigates the challenges of achieving gender inclusivity in male-dominated disciplines while showcasing the transformative potential of Problem-Based Learning (PBL) methodologies. Through insightful case studies, critical analyses, and a rich synthesis of research findings, Du presents a compelling argument for the effectiveness of PBL as a catalyst for fostering diversity and equity in engineering education. Her work not only informs but also inspires positive change, making it an indispensable resource for educators, researchers, and policymakers striving to create more inclusive and equitable engineering education.
Implementing Book-end Division Approach using ClassPoint to Energize Electrical and Electronics Engineering Student Engagement
Authors: Arshad Nurul Wahidah , Bakar Mohd. Shafie , Hasan Nurulfadzilah , Abdul Karim Rohana , Abdul Wahab Yasmin
Published: May 2024

TThis study investigates the efficacy of using ClassPoint in improving student engagement during class and its impact on academic performance among electrical and electronics engineering students by using student engagement framework that established by technology-enhanced learning (TEL) environment microsystem. To achieve this objective, five instructors teaching various courses incorporated ClassPoint into their classes. Then, quantitative data on student engagement and academic performance were collected via surveys. The student’s comments are extracted from university teaching evaluation survey (EPAT) for thematic analysis. The descriptive analysis revealed a significant increase in student engagement after ClassPoint was implemented. Furthermore, students appreciated the use of ClassPoint features such as slide-drawing, multiple choice questions, and word clouds during classes. Survey results also show students have greater attentiveness, active participation, and improved interactions with their peers and instructors. Likert scale responses indicate positive correlation between the use of ClassPoint and students’ enhanced performance in class discussions, idea integration, increased interest in learning, and improved classroom dynamics. Moreover, thematic analysis shows the empowering of five element in TEL microsystem with ClassPoint increase the student engagement. This study highlights ClassPoint's effectiveness in creating an inclusive and interactive learning environment, thus, transforming teaching methods for electrical and electronics engineering students.
Cell deformability drives fluid-to-fluid phase transition in active cell monolayers
Authors: Saito Nen , Ishihara Shuji
Published: May 2024

Cell deformability is an essential determinant for tissue-scale mechanical nature, such as fluidity and rigidity, and is thus crucial for tissue homeostasis and stable developmental processes. However, large-scale simulations of deformable cells have been restricted to those of polygonal-shaped cells, limiting our understanding of populations of arbitrarily deformable cells, such as mesenchymal, amoeboid cells, and nonconfluent epithelial cells. Here, we present an efficient approach for simulating large populations of nonpolygonally deformable cells with considerably higher computational efficiency than existing methods. Using the method, we demonstrate that the densely packed active cell population interacting via excluded volume interactions exhibits a fluid-to-fluid transition. An experimentally measurable index of topological defects, defined using the number of neighboring cells, is also proposed to characterize this transition. This study provides a flexible approach to tissue-scale cell population and a broader perspective on the biological fluid phases.
Supplemental Material: A sea of change: Tracing parasitic dynamics through the past millennia in the northern Adriatic, Italy
Authors: Fitzgerald Erin , Scarponi Daniele , Huntley John Warren , al. et
Published: May 2024

Supplemental data, methods, results, and R script. 
Surgery is better than nasal sprays for people with severely blocked airways caused by septal deviation
Authors: Saul Helen , Cassidy Samantha , Swaithes Laura , Carrie Sean
Published: May 2024

The study

Carrie S, O’Hara J, Fouweather T, et al. Clinical effectiveness of septoplasty versus medical management for nasal airways obstruction: multicentre, open label, randomised controlled trial.
BMJ
2023;383:e075445.

To read the full NIHR Alert, go to:
https://evidence.nihr.ac.uk/alert/surgery-is-better-than-nasal-sprays-for-people-with-severely-blocked-airways/
Barrow’s holographic dark energy model in axially symmetric spacetime
Authors: Goyal Neeru , Kumar Mukesh , Ghrera Aditya Sharma , Sharma Umesh Kumar , Yadav Anil Kumar , Srivastava Shikha
Published: May 2024

The Barrow’s Holographic Dark Energy (BHDE) Model is proposed in an axially symmetric anisotropic spacetime which is employing Hubble horizon as an infrared cutoff (IR cutoff). The transition of the universe from a matter dominated era to a dark energy dominated era is investigated in this model. Furthermore, the Equation of State (EoS) parameter explains how the universe evolves with non-extensive term or Barrow parameter [Formula: see text] for both phase (i) phantom era ([Formula: see text]) and (ii) quintessence era ([Formula: see text]). In order to reconcile the dark energy, the reconstruction of scalar field potential is considered. Some of the physical properties of the model are also described.
Implementation of cosmological bounce inflation with Nojiri–Odintsov generalized holographic dark fluid
Authors: Saha Sanghati , Chattopadhyay Surajit
Published: May 2024

This work reports a study on bounce cosmology with a highly generalized holographic dark fluid inspired by Nojiri and Odintsov [Eur. Phys. J. C 77 (2017) 1–8]. The holographic dark fluid that is mostly used for late-time acceleration has been implemented to reconstruct toward realization of cosmological bounce. We first used the most generalized Nojiri–Odintsov (NO) cutoff to implement the holographic dark fluid. Accordingly, we have reconstructed this dark fluid via some solutions of scale factors. With those solutions, we have explored the evolution of different cosmological parameters. We have examined the effects of each reconstructed parameter in the context of the realization of the cosmic bounce. Next, we use the analytical inferences of the scalar spectral index, tensor-to-scalar ratio, and slow-roll characteristics of the model to study a bounce inflationary scenario. Since inflation is usually associated with the existence of scalar fields, we looked at a possible relationship between NO generalized holographic dark energy and scalar field models. Plotting the evolution of the potential results from the scalar fields against time. Finally, we investigated the GSL of thermodynamics in the pre- and post-bounce scenarios.
Supplementary Data from Synergy of EGFR and AURKA Inhibitors in KRAS-mutated Non–small Cell Lung Cancers
Authors: Bagnyukova Tetyana , Egleston Brian L. , Pavlov Valerii A. , Serebriiskii Ilya G. , Golemis Erica A. , Borghaei Hossein
Published: May 2024

Additional information for Fig.1
Figure S3 from Synergy of EGFR and AURKA Inhibitors in KRAS-mutated Non–small Cell Lung Cancers
Authors: Bagnyukova Tetyana , Egleston Brian L. , Pavlov Valerii A. , Serebriiskii Ilya G. , Golemis Erica A. , Borghaei Hossein
Published: May 2024

Primary images for Fig.5C
FIGURE 4 from Synergy of EGFR and AURKA Inhibitors in KRAS-mutated Non–small Cell Lung Cancers
Authors: Bagnyukova Tetyana , Egleston Brian L. , Pavlov Valerii A. , Serebriiskii Ilya G. , Golemis Erica A. , Borghaei Hossein
Published: May 2024

Combination of erlotinib and alisertib enhances suppression of KRASmut NSCLC xenograft growth. A549 (A) and H358 (B) tumor xenografts, were treated with 10 mg/kg erlotinib, daily, and 10 mg/kg alisertib, twice daily, for 21 days. n = 5–8 for all groups. §, P < 0.001; #, additive effect; ##, synergistic effect (P = 0.011). Body weight of mice treated with erlotinib, alisertib or both for 21 days, from cohort shown in A (C) and B (D). Representative images and H-scores for Ki-67 (E, F) and cleaved caspase-3 (G, H) staining in A549 and H358 tumor xenografts treated with 10 mg/kg erlotinib, daily, 10 mg/kg alisertib, twice a day, or both for 21 days (mean ± SEM, n = 4–8). Scale bar, 100 µm. *, P < 0.05; **, P < 0.01; ***, P < 0.001, significantly different from comparison groups. Color of asterisks indicates comparison groups as follows: red, to control; orange, combination to erlotinib; green, combination to alisertib; purple, alisertib to erlotinib. C, vehicle; E, erlotinib; A, alisertib; EA, erlotinib + alisertib.
FIGURE 3 from Synergy of EGFR and AURKA Inhibitors in KRAS-mutated Non–small Cell Lung Cancers
Authors: Bagnyukova Tetyana , Egleston Brian L. , Pavlov Valerii A. , Serebriiskii Ilya G. , Golemis Erica A. , Borghaei Hossein
Published: May 2024

Signaling, cell cycle, and clonogenic analysis of combined erlotinib and alisertib in KRASmut NSCLC cells. A, Quantification of Western analysis of drug-treated cells using indicated antibodies, based on five to eight replicates. Cells were treated for 24 hours with concentrations reflecting the IC80 value of erlotinib and/or alisertib (9 µmol/L erlotinib: 13 µmol/L alisertib, in A549 cells, or 2.8 µmol/L erlotinib: 4.2 µmol/L alisertib in H358 cells). Primary Western blot data are shown in Supplementary Fig. S1. B, FACS analysis of cell cycle in H358 and A549 cells treated for 24 or 72 hours with drug concentrations 0.2 µmol/L erlotinib: 300 nmol/L alisertib, in A549 cells, or 1.2 µmol/L erlotinib: 1.8 µmol/L alisertib in H358 cells; three to four biological replicates, data shown represent averaged values. Representative data from clonogenic assays (C) and quantitation of images from three biological replicates (D), for the indicated cell lines treated with negative control, 75 nmol/L erlotinib, 25 nmol/L alisertib, or the combination for 10 days. Statistical comparisons are to control (red), combination to erlotinib (orange) or alisertib (green), alisertib to erlotinib (purple). *, P < 0.05; **, P < 0.01; ***, P < 0.001. C, vehicle; E, erlotinib; A, alisertib; EA, erlotinib + alisertib.
FIGURE 2 from Synergy of EGFR and AURKA Inhibitors in KRAS-mutated Non–small Cell Lung Cancers
Authors: Bagnyukova Tetyana , Egleston Brian L. , Pavlov Valerii A. , Serebriiskii Ilya G. , Golemis Erica A. , Borghaei Hossein
Published: May 2024

Sensitivity of NSCLC cell lines to erlotinib and alisertib. A, Western blot images and quantification of the protein levels of EGFR and AURKA in NSCLC cell lines and the human fibroblast cell line FC1010. Data for NSCLC cell lines are normalized to the levels in FC1010 cells. B, Determination of AURKA gene copy number in NSCLC cell lines, using the colorectal cancer cell lines HCT116 and SW420 as standards. Normalization to RNAseP, blue, or ALB, orange. The slopes of the standard curves were −3.64 (AURKA), −3,46 (RNAseP), −3.49 (ALB). Determination of sensitivity of the NSCLC cell lines and FC1010 control to erlotinib (C) and alisertib (D), with quantified IC50 values (E), based on CelltiterBlue analysis of viability after growth with indicated drugs for 72 hours. N/A, IC50s were not calculated because of low sensitivity to the drug. F, Combination indexes for erlotinib and alisertib over a range of molar ratios. Results shown reflect averages from four to five independent experiments, each done in quadruplicate, ± SEM and were calculated using CompuSyn software.
Aura e o esoterismo
Authors: Buoso Samara Fernanda
Published: May 2024

Inspirado pelas famosas Histórias do sr. Keuner, de Bertold Brecht, esse conjunto de três breves ficções traz uma mesma personagem, Aura, em um constante embate entre suas próprias questões e o esoterismo. Sem levar-se a sério, as narrativas buscam jogar com algumas questões caras ao gênero humano, convidando o leitor a também participar do jogo.
Naquela noite: uma história de feminicídio
Authors: Farias Adriana Merly
Published: May 2024

Criação literária de Adriana Merly Farias.
Lisianthus e astromélias
Authors: Carrijo Fabiana Rodrigues
Published: May 2024

Criação literária de Fabiana Rodrigues Carrijo.
Retratos de família: leitura de um ensaio de Antonio Candido
Authors: Ramassote Rodrigo
Published: May 2024

Este artigo tem como objetivo mais amplo evidenciar a centralidade e as ressonância de “The Brazilian family”, de autoria de Antonio Candido (1918-2017), no interior de parte significativa de sua obra, seja no campo da sociologia, seja no dos estudos literários. Para tal, apresento e discuto os principais argumentos do artigo à luz da sondagem dos condicionantes familiares e sociais de Candido, do exame das injunções profissionais e acadêmicas com as quais ele se defrontou e, por fim, da possível atualidade de seu conteúdo.
Prolegômenos a "A leitura crítica como ideologia" (anotações)
Authors: Bernardini Aurora
Published: May 2024

Texto escrito a partir de anotações de “A leitura crítica como ideologia”, título da última aula do curso “Leitura ideológica dos textos literários” ministrado por Antonio Candido em 1975 junto ao Programa de Pós-graduação em Teoria Literária e Literatura Comparada (PPG TLLC/FFLCH-USP).
The Soviet “Struggle for Peace,” the United Nations, and the Korean War
Authors: Dobrenko Vladimir
Published: May 2024

Before the Second World War the Soviet Union had been an isolated pariah state, but by the end of the war it had emerged as one of the world's two superpowers. Yet, the founding of the United Nations (UN) in October 1945 brought a new round of international isolation for the USSR, as a Western majority dominated the UN General Assembly during the first ten years of the organization's existence. This article focuses on the Soviet Union's attempt to overcome the Western-led majority during the Korean War, when the Soviet-backed World Peace Council became embroiled in an orchestrated propaganda campaign spreading false allegations that the United States had used biological weapons in Korea. Soviet officials used this campaign to try to discredit both the United States and Not until after the death of Joseph Stalin did Soviet policymakers curtail their support for the baseless allegations, though in public they refrained from acknowledging the falsity of the earlier claims.
China's Cultural Revolution and Mao's External Threat Inflation: Crushing Soviet-Style Capitalist Restoration, 1966–1969
Authors: He Yinan
Published: May 2024

Stoking fear and hatred of foreign countries to serve internal needs has been a recurring pattern in Communist China. This article examines Chinese discursive treatment of the Soviet Union in 1966–1969 in textual, visual, and audio outlets. During the height of the Cultural Revolution, radical followers of Mao Zedong deliberately choreographed anti-Soviet propaganda in accordance with their evolving political agenda at home. By emphasizing the need to forestall “capitalist restoration” in China, the propagandists alleged that capitalism had already been restored in the USSR. In the face of strong inner-party objection to the terror and destruction of the Cultural Revolution, Maoist polemicists discredited and attacked their domestic foes by accusing them of disloyalty and collaboration with Soviet “revisionists” to subvert China's Communist system. The radical Maoists sought to justify the chaotic violence of the Cultural Revolution by conjuring up the threat of a Soviet invasion, hoping to refocus domestic mass struggle on alleged sympathizers of the USSR. Yet Mao's invocation of this war scare triggered a dangerous security dilemma and turned the USSR into a strategic enemy, a striking example of a self-fulfilling prophecy in world politics.
The Lessons of the Cold War for 21st-Century Strategy
Authors: Larson Deborah Welch
Published: May 2024

This article assesses U.S. strategy during the Cold War and the lessons it holds for U.S. foreign policy in the 21st century, as laid out in a book recently published by Hal Brands of the Johns Hopkins University's School of Advanced International Studies. Although some points in the book are debatable, the exercise overall is valuable for what analysts nowadays refer to as a resurgence of “great-power competition.”
Fearsome Game, Popular Meat, Symbolic Wealth: Human-Pig Relations in Pre-Islamic Java
Authors: Hoogervorst Tom , Jákl Jiří
Published: May 2024

The Indonesian island of Java has been at the center of the world’s oldest interactions between humans and pigs. This article scrutinizes the complexities of human-pig relations through premodern texts. Philology remains uncommon in studying the past of nonhuman animals, yet its insights are highly relevant. Old Javanese poems and inscriptions differentiate two species: the Javan warty pig and the Eurasian wild pig. Both influenced human societies, including in the realm of religion, class, and gender. The textual record further reveals that pigs were regularly hunted and consumed by elites and commoners alike, and also played a role in rituals. Full domestication can be dated to the eleventh century and apparently coincided with urbanization and growing population density. By that time, pigs had come to symbolize wealth, as seen from Java’s unique piggybanks. Yet wild populations of pigs persisted and their aggression and fighting skills were both feared and respected.
On Munz’s Distinction between Explanation and Interpretation
Authors: Mion Giovanni
Published: May 2024

In this paper, I will explore Peter Munz’s philosophy of history and in particular, I will focus on Munz’s distinction between explanation and interpretation in history and the other social sciences. Among other things, I will attempt to show that its methodological implications have not been fully appreciated. Moreover, I will argue that Munz’s distinction offers a possible solution to some of the most outstanding problems in the social sciences, including the distinction between the natural and the social sciences (including history), and the role of causes vs. reasons in understanding agency.
Saharo-Sindian endemic flora of Egypt: critical checklist, floristic analysis, habitats, and phytogeographic distribution
Authors: ABO HATAB ASMAA S. , AL-SODANY YASSIN M. , SHALTOUT KAMAL H. , HAROUN SOLIMAN A. , EL-KHALAFY MOHAMED M.
Published: May 2024

The Saharo-Sindian region is characterized by savannas, semi-deserts, and hot deserts. This floristic region includes Morocco, Mauretania, Algeria, Libya, Egypt, Palestine, Kuwait, Saudi Arabia, Qatar, Bahrain, United Arab Emirates, Oman, Yemen, South of Jordan, Syria, Iraq, Afghanistan, Pakistan, in addition to the Sind region. The Sudano-Zambezian region, part of the Paleotropical Kingdom, and the Mediterranean and Irano-Turanian regions, included in the Holarctic Kingdom, share a significant portion of their flora with the studied region. This study initiates the examination of the Saharo-Sindian endemic plants occurring in Egypt. Its objectives include assessing the list of endemic plants within this floristic region, and studying various aspects such as: life forms, habitats, rarity forms, flowering times, dispersal types, and phytogeographical distribution. Twenty field trips were conducted from spring 2020 to September 2023, investigating different regions in Egypt. In addition, all the previous studies performed in the investigated area, scientific literature, and specimens from the region housed in different herbaria have been taken into consideration. The inventory of plants that are endemic to the Saharo-Sindian floristic region in Egypt comprises 126 plant taxa (109 species, 17 subspecies) distributed across 87 genera and 37 families. These endemics are found in 11 habitat types, with the most abundant occurrences observed in inland rocky areas (82 taxa) and temperate shrublands (57 taxa). Moreover, South Sinai stands out as the richest region for Saharo-Sindian endemics, hosting a remarkable 83 taxa, which constitute 65.9% of the total endemics. Among these, the chamaephytes group leads with 56 taxa, followed by the therophytes with 32 taxa. Pogonochores (45 taxa) are the most represented dispersal type. This study holds significant importance in evaluating a critical checklist of plants endemic to the Saharo-Sindian region in Egypt, contributing to our understanding of species diversity in regions facing severe anthropogenic disturbance. This list provides a foundational reference for future monitoring programs.
Echinoagave nievesiorum (Agavaceae, Asparagales): A new species from the Sierra Madre Occidental, Jalisco, Mexico
Authors: VÁZQUEZ-GARCÍA J. ANTONIO , NUÑO-RUBIO ANA T. , GARCÍA-MORALES LECCINUM JESÚS , LOMELÍ-HERNÁNDEZ JUAN LUIS , CHÁZARO-BASÁÑEZ MIGUEL. J. , PADILLA-LEPE JESÚS , CRISTÓBAL-GABRIEL SAÚL , HERNÁNDEZ-VERA GERARDO , MUÑIZ-CASTRO MIGUEL Á.
Published: May 2024

Echinoagave nievesiorum (Agavaceae, Asparagales), a new species endemic to the Sierra Wixárika (Huichola), part of the Sierra Madre Occidental, Jalisco, Mexico, is described. This species shares morphological characteristics with Echinoagave rzedowskiana but it differs from the latter by having narrower and striate leaves; leaf sheaths shorter, triangular and wider at the base; narrower ovary width; shorter tube length; tepal lobes at anthesis converging and tightening the filaments; larger filament length to flower length ratio; fruiting spikes thicker and denser with the peduncle covered by the capsules and the bracts usually deciduous; capsules broadly ellipsoid with dorsally blackish valves. A distribution map with biogeographic provinces is provided to place the species in an ecological and evolutionary context.