bluuebunny/crossref_metadata_2025_split huggingface dataset:
Binding in visual working memory is task dependent
Authors: Cao Ruoyi , Deouell Leon Y. 
Published: November 2023

AbstractWorking memory is a neurocognitive system for maintaining and manipulating information online for a short period after the source of information disappears. The information held in working memory has been shown to flexibly match current functional goals. Considering this, we revisited the question of whether information is held in WM as separate features or as bound objects. We conjectured that rather than having a fixed answer, the format in which information is maintained in working memory is also task dependent. In two separate experiments, we investigated the binding between features when the location was not (Experiment 1, color and orientation binding) or was (Experiment 2, color and location binding) a task-relevant feature in a delayed (yes/no) recognition task by manipulating the relative relevance of conjunctions and separate features. Each experiment included two conditions, Binding dominant (BD), which emphasizes the retention of binding between features, and Feature dominant (FD), which emphasizes the retention of individual features. In both experiments, we found that memory for conjunctions was better in the BD condition and that memory for separate features was better in the FD condition. These patterns suggested that the formats of objects in VWM could be shaped by the tasks they serve. Additionally, we found that the memory of location was impaired when conjunction between location and color was task-irrelevant, while memory of color and orientation was relatively independent of each other. We conclude that the representation format of objects in working memory is influenced by task requirements.
Gene surgery as a potential treatment option for Nephropathic Cystinosisin vitro
Authors: Sendino Garví E. , Faria J. , Pou Casellas C. , Thijssen S. , Wubbolts E.J. , Jamalpoor A. , Harrison P. , Masereeuw R. , Janssen M.J. 
Published: November 2023

AbstractNephropathic cystinosis is a rare monogenetic kidney disease caused by mutations in the lysosomal transporter cystinosin (encoded byCTNS) that, to date, has no cure. The hallmark of this disease is lysosomal accumulation of cystine and decline in proximal tubular function leading to kidney failure early in life. In this project, we developed a novel gene repair strategy using CRISPR/Cas9 Homology-Independent Targeted Integration (HITI) to restoreCTNS. A novel, non-viral peptide-mediated approach was used to deliver the Cas9-guideRNA ribonucleoprotein (RNP) complex and repair templates to conditionally immortalized proximal tubule epithelial cell (ciPTEC) lines. The repair constructs contained either mCherry (1.7 kb), theCTNSSuperexon (1.7 Kb) or both (3.2 Kb). The results demonstrated that the smaller mCherry construct achieved a higher repair efficiency (63%) compared to theCTNS-mCherry construct (16%). Clonal expansion of repaired cells showed restoration of lysosomal cystine levels in 70-75% of the clones, which was accompanied by improved mitochondrial bioenergetics. In conclusion, CRISPR/Cas9 HITI can be used to precisely insert repair templates into the genome, resulting in a functional cystinosin restoration, and a reversal of the cystinotic disease phenotype.
1H-NMR metabolomics-guided DNA methylation mortality predictors
Authors: Bizzarri D. , Reinders M.J.T. , Kuiper L.M. , Beekman M. , Deelen J. , van Meurs J.B.J. , van Dongen J. , Pool R. , Boomsma D.I. , Ghanbari M. , Franke L. ,   BIOS Consortium,   BBMRI-NL Consortium, Slagboom P.E. , van den Akker E.B. 
Published: November 2023

Abstract1H-NMR metabolomics and DNA methylation in blood are widely known biomarkers predicting age-related physiological decline and mortality yet exert mutually independent mortality and frailty signals. Leveraging multi-omics data in four Dutch population studies (N=5238) we investigated whether the mortality signal captured by1H-NMR metabolomics could guide the construction of novel DNA methylation-based mortality predictors. Hence, we trained DNA methylation-based surrogates for 64 metabolomic analytes and found that analytes marking inflammation, fluid balance, or HDL/VLDL metabolism could be accurately reconstructed using DNA-methylation assays. Interestingly, a previously reported multi-analyte score indicating mortality risk (MetaboHealth) could also be accurately reconstructed. Sixteen of our derived surrogates, including the MetaboHealth surrogate, showed significant associations with mortality, independent of other relevant covariates. Finally, adding our novel surrogates to previously established DNA-methylation markers, such as GrimAge, showed significant improvement for predicting all-cause mortality, indicating that our metabolic analyte-derived surrogates potentially represent novel mortality signal.
TolRad: A model for predicting radiation tolerance using Pfam annotations identifies novel radiosensitive bacterial species from reference genomes and MAGs
Authors: Sweet Philip , Burroughs Matthew , Jang Sungyeon , Contreras Lydia 
Published: November 2023

AbstractThe trait of ionizing radiation (IR) tolerance is variable between bacterial species, with radiosensitive bacteria succumbing to acute doses around 100Gy and extremophiles able to survive doses exceeding 10,000Gy. While survival screens have identified multiple highly radioresistant bacteria, such systemic searches have not been conducted for radiosensitive bacteria. The taxonomy-level diversity of IR of intolerance across bacteria is poorly understood, as are genetic elements that influence IR sensitivity. Using the protein domain frequencies from 61 bacterial species with experimentally determined IR D10 values (the dose at which only 10% of the population survives) we trained TolRad, a random forest binary classifier, to distinguish between radiosensitive bacteria (D10 < 200Gy) and radiation tolerant bacteria (D10 > 200Gy). On the hidden species, TolRad had an accuracy of 0.900. We applied TolRad to 152 UniProt-hosted bacterial proteomes, including 37 strains from the ATCC Human Microbiome Collection, and classified 34 species as radiosensitive. Whereas IR intolerance (D10 < 200Gy) in the training dataset had been confined to the phylumProteobacterium, this initial TolRad screen identified radiosensitive bacteria in 2 additional phyla. We experimentally validated the predicted radiosensitivity of a key species of the human microbiome from theBacteroidotaphyla. To demonstrate that TolRad can be applied to Metagenome-Assembled Genome (MAGs), we tested the accuracy of TolRad on Egg-NOG assembled proteomes (0.965) and partial proteomes. Finally, three collections of MAGs were screened using TolRad, identifying further phylum with radiosensitive species and suggesting that environmental conditions influence the abundance of radiosensitive bacteria.ImportanceBacterial species have vast genetic diversity, allowing for life in extreme environments and the conduction of complex chemistry. The ability to harness the full potential of bacterial diversity is hampered by the lack of high-throughput experimental or bioinformatic methods for characterizing bacterial traits. Here, we present a computational model that usesde novogenerated genome annotations to classify a bacterium as tolerant of ionizing radiation (IR) or as radiosensitive. This model allows for rapid screening of bacterial communities for low-tolerance species that are of interest for both mechanistic studies into bacterial sensitivity to IR and biomarkers of IR exposure.
Transcriptomic responses of Mediterranean sponges upon encounter with seawater or symbiont microbial consortia
Authors: Marulanda-Gomez A. , Ribes M. , Franzenburg S. , Hentschel U. , Pita L. 
Published: November 2023

AbstractSponges (phylum Porifera) constantly interact with microbes from the water column while filter-feeding and with the symbiotic partners they harbor within their mesohyl. Despite early observations on differential uptake between symbiont and seawater bacteria, it is still poorly understood how sponges discriminate between different microbial consortia. Initial evidence of the diverse repertoire of sponge immune receptors suggests their involvement in specific microbial recognition, yet experimental data is still scarce. We characterized the transcriptomic response of two sponge species,Aplysina aerophobaandDysidea avara, upon incubation with two different microbial consortia, which were either enriched from ambient seawater or extracted fromA. aerophoba.The sponges were sampled after 1 h, 3 h, and 5 h for RNA-Seq differential gene expression analysis.D. avarashowed higher expression levels of genes related to immunity, ubiquitination, and signaling when incubated withA. aerophobasymbionts, than in incubations with seawater microbial consortia. Interestingly, the different bacteria consortia triggered changes in Nucleotide Oligomerization Domain (NOD)-Like Receptors (NLRs) gene expression inD. avara. We here provide the first experimental evidence for NLRs playing a role in distinguishing between different microbes in a sponge. In contrast, the response ofA. aerophobainvolved comparatively few genes and lacked genes encoding for immune receptors. This indicates thatA. aerophobais less responsive to microbial encounters thanD. avara. Our study further reveals different transcriptomic responses between the two sponge species to microbes. The study of sponge responses to microbes aids in understanding the evolution of immune specificity and animal-microbe interactions.Significant statementAnimals rely on components of the immune system to recognize specific microbes, whether they are pathogens, food, or beneficial symbionts. However, in marine invertebrates, the mechanisms of microbial discrimination and specificity are not well understood. Our work suggests that:(i) the transcriptomic response by the sponge can be scaled according to the type of exposure, (ii) the response to microbial encounters is species-specific and (iii) NLRs seem to have a prominent role in the differential response to microorganisms, whether symbionts or food bacteria.
Stereo-anomaly is found more frequently in tasks that require discrimination between depths
Authors: Baldwin Alex S , Min Seung Hyun , Carrillo Sara Alarcon , Wang Zili , Cheng Ziyun , Zhou Jiawei , Hess Robert F 
Published: November 2023

AbstractWithin the population of humans with otherwise normal vision, there exists some proportion whose ability to perceive depth from binocular disparity is poor or absent. The prevalence of this “stereoanomaly” has been investigated in previous studies, some finding the proportion to be as small as 2%, others finding it to be as great as 30%. In this study, we set out to investigate the possible reason for the wide range of results found in these studies. We used a digital stereoacuity measurement tool that could measure performance in tasks requiring either the detection of disparity or the discrimination of the sign of disparity. The stimulus design was otherwise similar between the two tasks. In a cohort of 228 participants, we found that 98% were able to consistently perform the detection task. In contrast, only 69% consistently performed the discrimination task. The 31% of participants who had difficulty with the discrimination task could further be divided into 17% who were consistently unable to perform the task (seeming to behave at chance), and 14% who showed some ability to perform the task. We propose that the greater prevalence of stereo-anomaly is revealed when tasks require the judgement of the direction of disparity.
TOPOVIBL function in meiotic DSB formation: new insights from its biochemical and structural characterization
Authors: Diagouraga Boubou , Tambones Izabella , Carivenc Coralie , Bechara Chérine , de Massy Bernard , le Maire Albane , Robert Thomas 
Published: November 2023

AbstractThe TOPOVIL complex catalyzes the formation of DNA double strand breaks (DSB) that initiate meiotic homologous recombination, an essential step for chromosome segregation and genetic diversity during gamete production. TOPOVIL is composed of two subunits (SPO11 and TOPOVIBL) and is evolutionarily related to the archaeal TopoVI topoisomerase complex. SPO11 is the TopoVIA subunit orthologue and carries the DSB formation catalytic activity. TOPOVIBL shares homology with the TopoVIB ATPase subunit. TOPOVIBL is essential for meiotic DSB formation, but its molecular function remains elusive, partly due to the lack of biochemical studies. Here, we purified TOPOVIBLΔC25 and characterized its structure and mode of actionin vitro. Our structural analysis revealed that TOPOVIBLΔC25 adopts a dynamic conformation in solution and our biochemical study showed that the protein remains monomeric upon incubation with ATP, which correlates with the absence of ATP binding. Moreover, TOPOVIBLΔC25 interacted with DNA, with a preference for some geometries, suggesting that TOPOVIBL senses specific DNA architectures. Altogether, our study identified specific TOPOVIBL features that might help to explain how TOPOVIL function evolved toward a DSB formation activity in meiosis.
Simplified post-assembly plasmid library amplification for increased transformation yields inE. coliandS. cerevisiae
Authors: Fryer Thomas , Wolff Darian S. , Overath Max D. , Schäfer Elena , Laustsen Andreas H. , Jenkins Timothy P. , Andersen Carsten 
Published: November 2023

AbstractMany biological disciplines rely upon the transformation of host cells with heterologous DNA, the limited efficiency of which can significantly hinder a researcher’s work. Directed evolution in particular typically requires the screening of large (thousand-billion member) libraries to identify sequences of interest, and the creation of these libraries at large enough scales to overcome transformation inefficiencies is a cost-and time-intensive process. We simplify this process by using Rolling Circle Amplification (RCA) to amplifyin vitroplasmid DNA assembly reactions, followed by facile resolution of the concatomeric products to monomers through treatment with specific endonucleases and subsequent efficient transformation of the linear DNA products into host cells forin vivocircularisation. We demonstrate that use of a nicking endonuclease to generate homologous single-stranded ends increases the efficiency ofE. colichemical transformation versus both linear DNA with double-stranded homologous ends, and circular golden-gate assembly products, whilst use of a restriction endonuclease to generate linear DNA with double-stranded homologous ends increases the efficiency of chemical and electrotransformation ofS. cerevisiae. Importantly, we also optimise the process such that both RCA and endonuclease treatment occur efficiently in the same buffer, streamlining the workflow and reducing product loss through purification steps. We expect our approach to have utility beyond directed evolution inE. coliandS. cerevisiae, to areas such as genome engineering and the manipulation of alternative organisms with even poorer transformation efficiencies.
Entropy generation minimization of hybrid nanofluid mixed convection flow in lid-driven square enclosure with heat-generating porous layer on inner walls
Authors: Çiçek Oktay , Baytaş A. Filiz , Baytaş A. Cihat 
Published: November 2023

Purpose
This study aims to numerically scrutinize the entropy generation minimization and mixed convective heat transfer of multi-walled carbon nanotubes–Fe3O4/water hybrid nanofluid flow in a lid-driven square enclosure with heat generation in the presence of a porous layer on inner surfaces, considering local thermal non-equilibrium (LTNE) approach and the non-Darcy flow model.

Design/methodology/approach
The dimensionless governing equations for hybrid nanofluid and solid phases are solved by applying the finite volume method and semi-implicit method for pressure-linked equations algorithm.

Findings
The roles of the internal heat generation in the porous layer, LTNE model and nanoparticles volume fraction on mixed convection phenomenon and entropy generation are introduced for lid-driven cavity hybrid nanofluid flow. Based on the investigation of entropy generation and heat transfer, the minimum total entropy generation and average Nusselt numbers are found at 1 ≤ Ri ≤ 10 where the effect of the forced and free convection flow directions being opposite each other is very significant. When considering various nanoparticle volume fractions, it becomes evident that the minimum entropy generation occurs in the case of φ = 0.1%. The outcomes of LTNE number reveal the operating parameters in which thermal equilibrium occurs between hybrid nanofluid and solid phases.

Originality/value
The analysis of entropy generation under various shear and buoyancy forces plays a significant role in the suitable thermal design and optimization of mixed convective heat transfer applications. This research significantly contributes to the optimization of design and the advancement of innovative solutions across diverse engineering disciplines, such as packed-bed thermal energy storage and thermal insulation.
A systematic review of analytical thinking skills in STEM education settings
Authors: Hidayat Riyan , Nugroho Irham , Zainuddin Zamzami , Ingai Tony Anak 
Published: November 2023

Purpose
In the realm of education, there has been an increasing emphasis on developing analytical thinking (AT) in the past few years. This systematic review focuses on an analysis of journal publications that have explored AT within the context of science, technology, engineering and mathematics (STEM) education. This analysis investigated four primary issues: (1) the operational definition that was used; (2) the types of theories that were used; (3) the interventions that were implemented to enhance AT skills; and (4) the research designs that were used.

Design/methodology/approach
To ensure a comprehensive and thorough review, we used the guidelines of preferred reporting items for systematic reviews and meta-analysis.

Findings
A comprehensive review of 28 pertinent scholarly articles reveals that scholars frequently rely on the concepts proposed by Anderson (2002), Marzano and Kendall (2008), Rodrangsee and Tuntiwongwanich (2021) and Suyatman et al. (2021) to establish a framework for delineating the competencies associated with analytical thinking (AT). Quasi-experimental designs were the most frequently used research designs in the studies analysed, followed by research and development approaches and then correlational designs. Most researchers have focused on investigating the effectiveness of problem-based learning as an intervention for improving AT skills. However, most research indicates that the theories or theoretical frameworks used to guide the research must be evident.

Originality/value
To the extent the authors know, this study represents the initial comprehensive examination of analytical thinking in STEM education. It presents a consolidated summary of the available evidence, assessing its quality and bringing it together in a single resource.
Effect of composite solid lubricant coatings on the tribological performance of thrust cylindrical roller bearings
Authors: Xu Xiao , Zhang Yimin 
Published: November 2023

Purpose
This study aims to form composite solid lubricant coatings on the surface of bearing steel, which can significantly improve the tribological properties of thrust cylindrical roller bearings (TCRBs). Phosphating films possess microscopic porosity that typically needs to be sealed with oil, grease or wax. Due to its unique crystal structure, the phosphating film itself also exhibits a certain degree of lubricity. In this study, solid lubricants are used to fill the pores of the phosphating film. By combining the phosphating film with solid lubricants, lubrication and wear reduction can be achieved.

Design/methodology/approach
In this study, the surfaces of the shaft washer (WS) and seat washer (GS) were treated with zinc-phosphating. Subsequently, a solid lubricant solution (polytetrafluoroethylene [PTFE], MoS2 and graphite) was sprayed onto the phosphated samples at concentrations of 1 , 2  and 3 g/L. The porous and adsorptive nature of the phosphating film was used to embed the solid lubricant particles into the film, thus forming a composite lubrication layer containing solid lubricants on the surface of the bearing steel.

Findings
The addition of solid lubricant materials has shown significant potential in reducing wear losses compared with phosphated samples without such additives. Increasing the amount of solid lubricant added can facilitate the formation of a transfer film, which further enhances the protective properties. However, it is important to note that excessive amounts of solid lubricant material can contribute to seizure, leading to increased wear losses of the cage and a higher average coefficient of friction (ACOF).By spraying a PTFE solution with a concentration of 2 g/L, the lowest ACOF and cage wear loss were achieved, resulting in reductions of 60.5% for the ACOF and 89.4% for the cage wear loss. Similarly, when spraying a graphite solution with a concentration of 3 g/L, the lowest wear losses for GS and WS were observed, with reductions of 51.7% for GS wear loss and 38.9% for WS wear loss.

Originality/value
The combination of the phosphating film and solid lubricants aims to achieve lubrication and wear reduction, providing a new approach to wear-resistant technology for TCRBs.

Peer review
The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-07-2023-0231/
An examination of comment letters on suggested Part 10: audits of groups' financial statements in the proposed ISA for less complex entities
Authors: Haapamäki Elina Elisabet , Mäki Juha 
Published: November 2023

PurposeThe purpose of this paper is to investigate the comment letters (CLs) in the standard-setting process of audits of less complex entities (LCEs). The objective is to gain insight into the overall picture of the CLs and to report on areas where comment providers agree or disagree with IAASB's Part 10.Design/methodology/approachA content analysis of 60 comment letter (CLs) was conducted to investigate the suggested additional Part 10 on audits of groups' financial statements in the proposed ISA for LCEs. Hence, this study examines three specific topics: (1) the views related to the use of the International Standard on Auditing (ISA) for LCEs for group audits in which component auditors are involved, (2) the proposed group-specific qualitative characteristics to describe the scope of group audits and, finally, (3) insights into the content of the proposed Part 10 and related conforming amendments. The Gioia method is used to provide a holistic approach to concept development of the arguments about the new Part 10.FindingsThe CLs stated that, while the proposed Part 10 has some weak points, it still provides a solid and practical structure within which to undertake an LCE group audit and a promising basis for further development. For instance, when discussing the improvements, the CLs stated that Part 10 should allow for more auditor judgment when determining when the involvement of component auditors renders a group audit complex. In addition, the CLs asserted that professional judgment should be engaged when considering the qualitative characteristics and the complexity of the group.Originality/valueThis study contributes to the very scarce research about the ISA for LCEs and the role of lobbying in shaping the audit standard-setting process.