bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutual dependence between membrane phase separation and bacterial division protein dynamics in synthetic cell models
Authors: Kanwa Nishu , Kohyama Shunshi , Fröhlich Leonard , Desai Amogh , Schwille Petra 
Published: September 2024

AbstractCell membranes in bacteria are laterally polarized to produce specific environments for membrane proteins, e.g., proteins involved in cell division which accumulate at mid-cell or the cell poles. An interesting result of such membrane-lipid interplay is the reorganization of lipid domains together with membrane-bound proteins at the onset of cell division, suggesting a functional significance of membrane compartments in the cell cycle. Here, by adopting the key bacterial division proteins MinCDE and FtsZ as an archetypal spatial patterning system, we present a simple vesicle-basedin vitromodel to explore the mutual dependence of protein pattern formation and membrane heterogeneity. Like many other peripheral membrane proteins, MinDE exhibit preferential binding and macro-scale pattern formation at Lddomains, which leads to altered oscillation mode selection in phase-separated membrane compartments (GUVs). Moreover, incorporating bacterial division proteins within phase-separated GUVs leads to blebbing-like membrane deformations followed by the reorganization of Lodomains aligning at the neck region of the bleb, which agrees well with the domain rearrangement in bacterial membranes immediately preceding the radial constriction process. Overall, the presentedin vitromodel system showcases a basic framework to better comprehend the cellular division mechanism in consideration of complex cellular lipid environments.
An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research
Authors: Standeven Francesca J. , Dahlquist-Axe Gwyn , Hendy Jessica , Fiddyment Sarah , Holst Malin , McGrath Krista , Collins Matthew , Mundorff Amy , Radini Anita , Wagner Josef , Meehan Conor J. , Tedder Andrew , Speller Camilla F. 
Published: September 2024

AbstractArchaeological dental calculus can provide detailed insights into the ancient human oral microbiome. We offer a multi-period, multi-site, ancient shotgun metagenomic dataset consisting of 174 samples obtained primarily from archaeological dental calculus derived from various skeletal collections in the United Kingdom. This article describes all the materials used including the skeletons’ historical period and burial location, biological sex, and age determination, data accessibility, and additional details associated with environmental and laboratory controls. In addition, this article describes the laboratory and bioinformatic methods associated with the dataset development and discusses the technical validity of the data following quality assessments, damage evaluations, and decontamination procedures. Our approach to collecting, making accessible, and evaluating bioarchaeological metadata in advance of metagenomic analysis aims to further enable the exploration of archaeological science topics such as diet, disease, and antimicrobial resistance (AMR).
Influence of formaldehyde on signaling pathways when used in mammalian cell culture
Authors: Ostmann Katharina , Kraegeloh Annette , Weber Wilfried 
Published: September 2024

AbstractFormaldehyde is the smallest existing aldehyde, a highly reactive color less gas at room temperature and ubiquitously present in our atmosphere. Because of its reactivity leading to the crosslinking of macromolecules like proteins, it is widely used in industrial applications, but also in cell biology in order to preserve cells and tissues for further analysis. In this work, we show that formaldehyde releasing solutions commonly used for fixation of cells, can diffuse via the gas phase to the neighboring well and influence signaling processes in the therein cultured cells. To analyze this effect, we utilized a stable reporter cell line for YAP signaling or a gene expression-based reporter for activation of the NF-κB pathway. Especially the stable reporter cell line can also be used as sensor for bioavailable formaldehyde. The observed impact of formaldehyde on cellular signaling underscores the need for careful planning of experimental protocols and emphasizes the importance of implementing proper controls when utilizing this reagent in cellular signaling analyses.
A modular system for programming multistep activation of endogenous genes in stem cells
Authors: Puppala Anupama K. , Nielsen Andrew C. , Regan Maureen R. , Mancinelli Georgina E. , De Pooter Renee F. , Arnovitz Stephen , Harding Caspian , McGregor Michaele , Balanis Nikolas G. , Clarke Ryan , Merrill Bradley J. 
Published: September 2024

AbstractAlthough genomes encode instructions for mammalian cell differentiation with rich syntactic relationships, existing methods for genetically programming cells have modest capabilities for stepwise regulation of genes. Here, we developed a sequential genetic system that enables transcriptional activation of endogenous genes in a preprogrammed, stepwise manner. The system relies on the removal of an RNA polymerase III termination signal to induce both the transcriptional activation and the DNA endonuclease activities of a Cas9-VPR protein to effect stepwise progression through cascades of gene activation events. The efficiency of the cascading system enables a new dimension for cellular programming by allowing the manipulation of the sequential order of gene activation for directing the differentiation of human stem cells.One-Sentence SummaryDevelopment of a synthetic biology system for preprogrammed, stepwise activation of endogenous genes.
Assessing Ebola Virus Circulation in the Tshuapa Province (Democratic Republic of the Congo): A One Health Investigation of Wildlife and Human Interactions
Authors: van Vredendaal Rianne , Joffrin Léa , Paviotti Antea , Mande Claude , Milolo Solange , Laurent Nicolas , Fourchault Léa , Adroabadrio Douglas , Baelo Pascal , Ngoy Steve , Ansobi Papy , Nebesse Casimir , Peeters Martine , Ayouba Ahidjo , Champagne Maeliss , Bouillin Julie , Těšíková Jana , Van Houtte Natalie , Gryseels Sophie , Salloum Maha , Bikioli Freddy , Thys Séverine , Mpato Jimmy , Ilonga Ruben , Kimina Henri , Larivière Ynke , Lemey Gwen , Van Damme Pierre , Van Geertruyden Jean-Pierre , Muhindo-Mavoko Hypolite , Mitashi Patrick , Leirs Herwig , Verheyen Erik , Gembu Guy-Crispin , Mariën Joachim 
Published: September 2024

AbstractThe wildlife reservoir and spillover mechanisms of the Ebola virus remain elusive despite extensive research efforts in endemic areas. This study employed a One Health approach to examine the virus’ circulation in wildlife and the associated human exposure risks in the Tshuapa province of the Democratic Republic of the Congo. In 2021, we collected 1015 samples from 888 animals, predominantly small mammals, and 380 inhabitants of Inkanamongo village, the site of an Ebola virus disease outbreak in 2014. These samples were screened for evidence of current (RNA) or past (IgG antibodies) Ebola virus infections. We also conducted interviews with 167 individuals in the surrounding districts to assess their interactions with wildlife. While no Ebola virus RNA was detected in the wildlife samples, anti-orthoebolavirus IgG antibodies were found in 13 bats and 38 rodents. Among the human participants, 120 individuals had IgG antibodies against at least one orthoebolavirus antigen, with 12 showing seropositivity for two antigens of the same orthoebolavirus, despite not having a prior Ebola disease diagnosis. Furthermore, over 50% of respondents reported frequent visits to the forest to hunt a variety of wild animals, particularly ungulates and rodents, which could account for occasional viral spillovers. The absence of active Ebola virus circulation in wildlife may reflect seasonal patterns in reservoir ecology, like those observed in bats. Similarly, seasonal human activities, like hunting and foraging, may result in periodic exposure risks. These findings highlight the importance of continuous, multidisciplinary surveillance to monitor changes in seasonal spillover risks.
Variant classification guidelines for animals to objectively evaluate genetic variant pathogenicity
Authors: Boeykens Fréderique , Abitbol Marie , Anderson Heidi , Casselman Iris , Dufaure de Citres Caroline , Hayward Jessica J. , Häggström Jens , Kittleson Mark D. , Lepri Elvio , Ljungvall Ingrid , Longeri Maria , Lyons Leslie A. , Ohlsson Åsa , Peelman Luc , Smets Pascale , Vezzosi Tommaso , van Steenbeek Frank G. , Broeckx Bart J.G. 
Published: September 2024

AbstractAssessing the pathogenicity of a disease-associated variant in animals accurately is vital, both on a population and individual scale. At the population level, breeding decisions based on invalid DNA tests can lead to the incorrect exclusion of animals and compromise the long- term health of a population, and at the level of the individual animal, lead to incorrect treatment and even life-ending decisions. Criteria to determine pathogenicity are not standardized, hence no guidelines for animal variants are available. Here, we developed and optimized the animal variant classification guidelines, based on those developed for humans by The American College of Medical Genetics and Genomics, and demonstrated a superior classification in animals. We described methods to develop datasets for benchmarking the criteria and identified the most optimal in silico variant effect predictor tools. As the reproducibility was high, we classified 72 known disease-associated variants in cats and 40 other disease-associated variants in eight additional species.
Cholesterol binding to VCAM-1 promotes vascular inflammation
Authors: Kennelly John P. , Xiao Xu , Gao Yajing , Kim Sumin , Hong Soon-Gook , Villanueva Miranda , Ferrari Alessandra , Vanharanta Lauri , Nguyen Alexander , Nagari Rohith T. , Burton Nikolas R. , Tol Marcus J. , Becker Andrew P. , Lee Min Jae , Ikonen Elina , Backus Keriann M. , Mack Julia J. , Tontonoz Peter 
Published: September 2024

AbstractHypercholesterolemia has long been implicated in endothelial cell (EC) dysfunction, but the mechanisms by which excess cholesterol causes vascular pathology are incompletely understood. Here we used a cholesterol-mimetic probe to map cholesterol-protein interactions in primary human ECs and discovered that cholesterol binds to and stabilizes the adhesion molecule VCAM-1. We show that accessible plasma membrane (PM) cholesterol in ECs is acutely responsive to inflammatory stimuli and that the nonvesicular cholesterol transporter Aster-A regulates VCAM-1 stability in activated ECs by controlling the size of this pool. Deletion of Aster-A in ECs increases VCAM-1 protein, promotes immune cell recruitment to vessels, and impairs pulmonary immune homeostasis. Conversely, depleting cholesterol from the endotheliumin vivodampens VCAM-1 induction in response to inflammatory stimuli. These findings identify cholesterol binding to VCAM-1 as a key step during EC activation and provide a biochemical explanation for the ability of excess membrane cholesterol to promote immune cell recruitment to the endothelium.
RNA Polymerase II coordinates histone deacetylation at active promoters
Authors: Hoffman Jackson A. , Trotter Kevin W. , Archer Trevor K. 
Published: September 2024

AbstractNucleosomes at actively transcribed promoters have specific histone post-transcriptional modifications and histone variants. These features are thought to contribute to the formation and maintenance of a permissive chromatin environment. Recent reports have drawn conflicting conclusions about whether these histone modifications depend on transcription. We used triptolide to inhibit transcription initiation and degrade RNA Polymerase II and interrogated the effect on histone modifications. Transcription initiation was dispensable forde novoand steady-state histone acetylation at transcription start sites (TSSs) and enhancers. However, at steady state, blocking transcription initiation increased the levels of histone acetylation and H2AZ incorporation at active TSSs. These results demonstrate that deposition of specific histone modifications at TSSs is not dependent on transcription and that transcription limits the maintenance of these marks.
Comparison of Explainable AI Models for MRI-based Alzheimer’s Disease Classification
Authors: Chattopadhyay Tamoghna , Joshy Neha Ann , Jagad Chirag , Gleave Emma J. , Thomopoulos Sophia I. , Feng Yixue , Villalón-Reina Julio E. , Laltoo Emily , Joshi Himanshu , Venkatasubramanian Ganesan , John John P. , Steeg Greg Ver , Ambite Jose Luis , Thompson Paul M. 
Published: September 2024

AbstractDeep learning models based on convolutional neural networks (CNNs) have been used to classify Alzheimer’s disease or infer dementia severity from 3D T1-weighted brain MRI scans. Here, we examine the value of adding occlusion sensitivity analysis (OSA) and gradient-weighted class activation mapping (Grad-CAM) to these models to make the results more interpretable. Much research in this area focuses on specific datasets such as the Alzheimer’s Disease Neuroimaging Initiative (ADNI) or National Alzheimer’s Coordinating Center (NACC), which assess people of North American, predominantly European ancestry, so we examine how well models trained on these data generalize to a new population dataset from India (NIMHANS cohort). We also evaluate the benefit of using a combined dataset to train the CNN models. Our experiments show feature localization consistent with knowledge of AD from other methods. OSA and Grad-CAM resolve features at different scales to help interpret diagnostic inferences made by CNNs.
Pseudoscalar heavy quarkonium production in heavy ion ultraperipheral collision
Authors: Jiang Jun , Li Shi-Yuan , Liang Xiao , Liu Yan-Rui , Qiao Cong-Feng , Si Zong-Guo , Yang Hao 
Published: September 2024

The inclusive production of pseudoscalar heavy quarkonia (ηc, ηb, and Bc) via photon-photon fusion in heavy ion ultraperipheral collision (UPC) are calculated to QCD next-to-leading order in the framework of nonrelativistic QCD (NRQCD). The total cross section of ηc produced in Pb-Pb UPC is 194  nb and 1275  nb at nucleon-nucleon c.m. energies SNN=5.52  TeV and 39.4 TeV, respectively. The cross sections for ηb and Bc mesons are more than two to three orders of magnitude smaller. We make a detailed phenomenological analysis on the ηc production; the uncertainties caused by the renormalization scale and the charm quark mass, the cross sections in other ultraperipheral nucleon-nucleon colliding systems, and the transverse momentum distribution are discussed. At the coming HL-LHC and future FCC, the heavy ion UPC opens another door of the study on the production of heavy quarkonium.

Published by the American Physical Society
2024
A dual opposition learning-based multi-objective Aquila Optimizer for trading-off time-cost-quality-CO2 emissions of generalized construction projects
Authors: Eirgash Mohammad Azim , Toğan Vedat 
Published: September 2024

PurposeMost of the existing time-cost-quality-environmental impact trade-off (TCQET) analysis models have focused on solving a simple project representation without taking typical activity and project characteristics into account. This study aims to present a novel approach called the “hybrid opposition learning-based Aquila Optimizer” (HOLAO) for optimizing TCQET decisions in generalized construction projects.Design/methodology/approachIn this paper, a HOLAO algorithm is designed, incorporating the quasi-opposition-based learning (QOBL) and quasi-reflection-based learning (QRBL) strategies in the initial population and generation jumping phases, respectively. The crowded distance rank (CDR) mechanism is utilized to rank the optimal Pareto-front solutions to assist decision-makers (DMs) in achieving a single compromise solution.FindingsThe efficacy of the proposed methodology is evaluated by examining TCQET problems, involving 69 and 290 activities, respectively. Results indicate that the HOLAO provides competitive solutions for TCQET problems in construction projects. It is observed that the algorithm surpasses multiple objective social group optimization (MOSGO), plain Aquila Optimization (AO), QRBL and QOBL algorithms in terms of both number of function evaluations (NFE) and hypervolume (HV) indicator.Originality/valueThis paper introduces a novel concept called hybrid opposition-based learning (HOL), which incorporates two opposition strategies: QOBL as an explorative opposition and QRBL as an exploitative opposition. Achieving an effective balance between exploration and exploitation is crucial for the success of any algorithm. To this end, QOBL and QRBL are developed to ensure a proper equilibrium between the exploration and exploitation phases of the basic AO algorithm. The third contribution is to provide TCQET resource utilizations (construction plans) to evaluate the impact of these resources on the construction project performance.
Dislocation-based finite element method for homogenized limit domain characterization of structured metamaterials
Authors: Zona Renato , Esposito Luca , Palladino Simone , Minutolo Vincenzo 
Published: September 2024

PurposeHeterogeneous and micro-structured materials have been the object of multiscale and homogenization techniques aimed at recognizing the elastic properties of the equivalent continuum. The proposed investigation deals with the mechanical characterization of the heterogeneous material structured metamaterials through analyzing the ultimate strength using the limit analysis of the Representative Volume Element (RVE). To get the desired material strength, a novel finite element formulation based on the derivation of self-equilibrated solutions through the finite elements devoted to calculating the lower bound theorem has been implemented together with the limit analysis in Melàn’s formulation.Design/methodology/approachThe finite element formulation is based on discrete mapping of Volterra dislocations in the structure using isoparametric representation. Using standard finite element techniques, the linear operator V, which relates the self-equilibrated internal solicitation to displacement-like nodal parameters, has been built through finite element discretization of displacement and strain.FindingsThe proposed work presented an elastic homogenization of the mechanical properties of an elementary cell with a geometry known in the literature, the isotropic truss. The matrix of elastic constants was calculated by subjecting the RVE to numerical load tests, simulated with a commercial FEM calculation code. This step showed the dependence of the isotropy properties, verified with Zener theory, on the density of the RVE. The isotropy condition of the material is only achieved for certain section ratios between body-centered cubic (BCC) and face-centered cubic (FCC), neglecting flexural effects at the nodes. The density that satisfies Zener’s conditions represents the isotropic geomatics of the isotropic truss.Originality/valueFor the isotropic case, the VFEM procedure was used to evaluate the isotropy of the limit domain and was compared with the Mises–Schleicher limit domain. The evaluation of residual ductility and dissipation energy allowed a measurement parameter for the limit anisotropy to be defined. The novelty of the proposal consisted in the formulation of both the linearized and the nonlinear limit locus of the material; hence, it furnished the starting point for further limit analysis of the structures whose elementary volume has been described through the proposed approach.
From lab to table: launching Thani Food Institute’s passion fruit-infused vinaigrette
Authors: Chirakranont Rangson , Racela Olimpia C. 
Published: September 2024

Learning outcomes
After reading and discussing this case study, students will be able to explain the concept of diffusion of innovation and predict how the passion fruit-infused vinaigrette (PFIV) might spread throughout the Thai market; analyze the market environment for condiments in Thailand and identify specific opportunities that Preedha Vinchit and her team should consider for the successful launch of the PFIV; interpret both qualitative and quantitative data gathered by the new product development (NPD) team and discuss its implications for the product’s market strategy and development; and critique the initial launch plan proposed by Krit Anon, suggest practical strategies and calculate the break-even point necessary to meet the project’s financial goals.

Case overview/synopsis
During July 2023, Vinchit, product marketer at the Thani Food Institute (TFI), faced a critical decision regarding the launch of the APFIV. Developed from TFI’s patented passion fruit peel powder, the PFIV offered functional benefits and addressed the sustainable use of passion fruit resources. As COVID-19 restrictions eased, TFI’s board of advisors anticipated a successful market entry for PFIV. Anon, culinologist and chef behind PFIV’s formulation, expressed keen interest in launching it independently with a startup investment of THB 500,000 (US$14,388). Vinchit, with market research and home-use test results indicating positive consumer reception in hand, contemplated whether to proceed with a launch plan of TFI’s design or endorse Anon’s entrepreneurial venture. Critical considerations included market viability, strategic partnerships, target demographics and marketing strategies encompassing pricing, distribution and promotional campaigns. The decision hinged on maximizing PFIV’s market potential amidst Thailand’s robust condiment consumption and growing health awareness.

Complexity academic level
This case study can be used in undergraduate and graduate courses in entrepreneurship, food product development, marketing strategy, market research and innovation on topics including NPD, opportunity identification, concept testing, consumer research analysis, marketing strategy formulation, business/financial analysis and launch strategies. This case study may be more useful in the middle or later parts of a course or module when an instructor is focusing on any or all stages of the NPD process and the strategic decisions, particularly for aspiring entrepreneurs with limited resources. Additionally, students should have developed at least some preliminary understanding of qualitative and quantitative research methods. This case study has been very effective in demonstrating various organizational processes and decision-making tools, which allow students to apply strategy frameworks and systematically evaluate several alternatives.

Supplementary materials
Teaching notes are available for educators only.

Subject code
CSS 3: Entrepreneurship.