bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using a sequential sampling algorithm to apply the niche-neutral model to species occurrence patterns
Authors: Kristensen Nadiah P. , Keita Sin Yong Chee , Lim Hyee Shynn , Rheindt Frank E. , Chisholm Ryan A. 
Published: November 2024

AbstractAimSpecies occurrence patterns are typically analysed using data-randomisation approaches, which reveal when observed patterns deviate from random expectation, but give little insight why. Mechanistic models, such as neutral models, have been proposed as an alternative null model, but they are computationally expensive. Here, we use an efficient method to simulate such models and to explore likely mechanisms governing the occurrence patterns of birds on islands.LocationRiau archipelago, Indonesia.TaxonBirds.MethodsWe used species richness and island area data to fit a niche–neutral model, where species obey neutral dynamics within non-overlapping discrete niches. We used a sequential sampling algorithm that can efficiently generate randomised presence– absence matrices under the niche-neutral model and used mismatches to identify which mechanisms were potentially important to occurrence patterns.ResultsBirds were more segregated and less nested than expected from both data randomisation and the niche–neutral model. The niche–neutral model reproduced the mean relationship between island size and species richness, but it could not produce sufficient variability to account for the richness data. The model was brought into closer agreement with the data by allowing niche diversity to vary across islands (increased segregation) and allowing the per-capita immigration rate to vary across islands (decreased nestedness).Main conclusionWhile the species-area relationship could be explained by a model with constant per-capita immigration rates and number of niches across islands, interisland heterogeneity was needed to explain higher-order metrics of nestedness and cooccurrence patterns. The sequential sampling algorithm allowed us to explore different scenarios efficiently, and our approach may be useful for identifying the mechanisms structuring occurrence patterns in other systems.
The paternally derived genome opposes seed dormancy induction by the mother plant in Arabidopsis
Authors: Barros-Galvão Thiago , Chen Xiaochao , Penfield Steven 
Published: November 2024

AbstractSeed dormancy in Arabidopsis is known to be mediated by the interaction of maternal and zygotic genomes during seed maturation. While studies have revealed the extensive influence of maternal processes on dormancy and germination, less is known about the influence of the father. Here we exploit differences in ploidy to explore the role of the paternal genome on progeny seed dormancy. We show that paternal genome acts to reduce seed dormancy regardless of maternal genome dose, resulting in lower dormancy in tetraploid Arabidopsis versus genetically identical diploids. We show that this paternal effect requires synthesis of RNA Polymerase IV-dependent RNAs in the male gametophyte which oppose the dormancy-inducing effects of maternal siRNAs on seed coat and endosperm development. We conclude that the paternal genome has evolved to subvert the dormancy-inducing role of the mother plant in progeny seeds.
Epstein-Barr Virus Latent Membrane Protein 1 Subverts IMPDH pathways to drive B-cell oncometabolism
Authors: Burton Eric M. , Liang Jin Hua , Mitra Bidisha , Asara John M. , Gewurz Benjamin E. 
Published: November 2024

AbstractEpstein-Barr virus (EBV) is associated with multiple types of cancers, many of which express the key viral oncoprotein Latent Membrane Protein 1 (LMP1). LMP1 is the only EBV-encoded protein whose expression is sufficient to transform both epithelial and B-cells. Although metabolism reprogramming is a cancer hallmark, much remains to be learned about how LMP1 alters lymphocyte oncometabolism. To gain insights into key B-cell metabolic pathways subverted by LMP1, we performed systematic metabolomic analyses on B cells with conditional LMP1 expression. This approach highlighted that LMP highly inducesde novopurine biosynthesis, with xanthosine-5-P (XMP) as one of the most highly LMP1-upregulated metabolites. Consequently, IMPDH inhibition by mycophenolic acid (MPA) triggered apoptosis of LMP1-expressing EBV-transformed lymphoblastoid cell lines (LCL), a key model for EBV-driven immunoblastic lymphomas. Whereas MPA instead caused growth arrest of Burkitt lymphoma cells with the EBV latency I program, conditional LMP1 expression triggered their apoptosis. Although both IMPDH isozymes are expressed in LCLs, only IMPDH2 was critical for LCL survival, whereas both contributed to proliferation of Burkitt cells with the EBV latency I program. Both LMP1 C-terminal cytoplasmic tail domains critical for primary human B-cell transformation were important for XMP production, and each contributed to LMP1-driven Burkitt cell sensitivity to MPA. MPA also de-repressed EBV lytic antigens including LMP1 in latency I Burkitt cells, highlighting crosstalk between the purine biosynthesis pathway and the EBV epigenome. These results suggest novel oncometabolism-based therapeutic approaches to LMP1-driven lymphomas.IMPORTANCEAltered metabolism is a hallmark of cancer, yet much remains to be learned about how EBV rewires host cell metabolism to support multiple malignancies. While the oncogene LMP1 is the only EBV-encoded gene that is sufficient to transform murine B-cells and rodent fibroblasts, knowledge has remained incomplete about how LMP1 alters host cell oncometabolism to aberrantly drive infected B-cell growth and survival. Likewise, it has remained unknown whether LMP1 expression creates metabolic vulnerabilities that can be targeted by small molecule approaches to trigger EBV-transformed B-cell programmed cell death. We therefore used metabolomic profiling to define how LMP1 signaling remodels the B-cell metabolome. We found that LMP1 upregulated purine nucleotide biosynthesis, likely to meet increased demand. Consequently, LMP1 expression sensitized Burkitt B-cells to growth arrest upon inosine monophosphate dehydrogenase blockade. Thus, while LMP1 itself may not be a therapeutic target, its signaling induces dependence on downstream druggable host cell nucleotide metabolism enzymes, suggesting rational therapeutic approaches.
Functional divergence of TBP homologs through distinct DNA binding dynamics
Authors: Cui Jieying H. , Kwan James Z.J. , Faghihi Armin , Nguyen Thomas F. , Teves Sheila S. 
Published: November 2024

AbstractThe TATA box-binding protein (TBP) is an evolutionarily conserved basal transcription factor common in the pre-initiation complex of all three eukaryotic RNA polymerases (RNA Pols). Despite their high conservation, homologous TBPs exhibit species- and tissue-specific functions that may contribute to the increasingly complex gene expression regulation across evolutionary time. To determine the molecular mechanisms of species- and tissue-specificity for homologous TBPs, we examined the ability of yeast TBP and murine TBP paralogs to replace the endogenous TBP in mouse embryonic stem cells. We show that, despite the high conservation in the DNA binding domain among the homologs, they cannot fully rescue the lethality of TBP depletion in mESCs, largely due to their inability to support RNA Pol III transcription. Furthermore, we show that the homologs differentially support stress-induced transcription reprogramming, with the divergent N-terminal domain playing a role in modulating changes in transcriptional response. Lastly, we show that the homologs have vastly different DNA binding dynamics, suggesting a potential mechanism for the distinct functional behavior observed among the homologs. Taken together, these data show a remarkable balance between flexibility and essentiality for the different functions of homologous TBP in eukaryotic transcription.
Identification and Characterization of Archaeal Pseudomurein Biosynthesis Genes through Pangenomics
Authors: Lupo Valérian , Roomans Célyne , Royen Edmée , Ongena Loïc , Jacquemin Olivier , Mullender Coralie , Kerff Frédéric , Baurain Denis 
Published: November 2024

AbstractThe peptidoglycan (PG; or murein) is a mesh-like structure, which is made of glycan polymers connected by short peptides and surrounds the cell membrane of nearly all bacterial species. In contrast, there is no PG counterpart that would be universally found in Archaea, but rather various polymers that are specific to some lineages. Methanopyrales and Methanobacteriales are two orders of Euryarchaeota that harbor pseudomurein (PM), a structural analogue of the bacterial PG. Owing to the differences between PG and PM biosynthesis, some have argued that the origin of both polymers is not connected. However, recents studies have revealed that the genomes of PM-containing Archaea encode homologues of the bacterial genes involved in PG biosynthesis, even though neither their specific functions nor the relationships within the corresponding inter-domain phylogenies have been investigated so far. In this work, we devised a pangenomic bioinformatic pipeline to identify proteins for PM biosynthesis in Archaea without prior genetic knowledge. The taxonomic distribution and evolutionary relationships of the candidate proteins were studied in detail in Archaea and Bacteria through HMM sequence mining and phylogenetic inference of the Mur domain-containing family, the ATP-grasp superfamily and the MraY-like family. Our results show that archaeal muramyl ligases are of bacterial origin, but diversified through a mixture of horizontal gene transfers and gene duplications. However, in the ATP-grasp and MraY-like families, the archaeal members were not found to originate from Bacteria. Our pangenomic approach further identified five new genes potentially involved in PM synthesis and that would deserve functional characterization.
Jasmonate Primes Plant Responses to Extracellular ATP through Purinoceptor P2K1
Authors: Jewell Jeremy B. , Carlton Ashleigh , Bartley Laura E. , Tanaka Kiwamu 
Published: November 2024

ABSTRACTExtracellular ATP (eATP) signaling inArabidopsis thalianais mediated by the purinoceptor P2K1. Previous studies have clarified that the downstream transcriptional responses to eATP involve jasmonate (JA)-based signaling components such as the JA receptor (COI1) and JA-responsive bHLH transcription factors (MYCs). However, the specific contributions of JA signaling itself on eATP signaling are unexplored. Here, we report that JA primes plant responses to eATP through P2K1. Our findings show that JA treatment significantly upregulates P2K1 transcription, corroborating our observation that JA facilitates eATP-induced cytosolic calcium elevation and transcriptional reprogramming in a JA signaling-dependent manner. Additionally, we find that salicylic acid represses eATP-induced plant response. These results suggest that JA accumulation during biotic or abiotic stresses may potentiate eATP signaling, enabling plants to better cope with subsequent stress events.
A Genetic Toggle Switch in Plants
Authors: Kassaw Tessema K. , Xu Wenlong , Zalewski Christopher S. , Kiwimagi Katherine , Weiss Ron , Antunes Mauricio S. , Prasad Ashok , Medford June I. 
Published: November 2024

AbstractIn synthetic biology, genetic components are assembled to make transcriptional units, and transcriptional units are assembled into circuits to perform specific and predictable functions of a genetic device. Genetic devices have been described in bacteria, mammalian cell cultures and small organoids, yet development of programmable genetic circuits for devices in plants has lagged. Programmable genetic devices require defining the component’s quantitative functions. Because plants have long life spans, studies often use transient analysis to define quantitative functions while verification in stably engineered plants is often neglected and largely unknown. This raises a question if unique attributes of plants such as environmental sensitivity, developmental plasticity, or alternation of generations, adversely impacts predictability of plant genetic circuits and devices. Alternatively, it is also possible that genetic elements to produce predictable genetic devices for plants require rigorous characterization with detailed mathematical modeling. Here we use plant genetic elements with quantitatively characterized transfer functions and developed in silico models to guide their assembly into a genetic device: a toggle switch or a mutually inhibitory gene-regulatory device. Our approach allows computational selection of plant genetic components and iterative refinement of the circuit if the desired genetic functions are not initially achieved. We show that our computationally selected genetic circuit functions as predicted in stably engineered plants including through tissue and organ differentiation. Developing abilities to produce predictable and programmable plant genetic devices opens the prospect of predictably engineering plant’s unique abilities in sustainable human and environmental systems.
p53 engagement is a hallmark of an unfolded protein response in the nucleus of mammalian cells
Authors: Park Joseph H , Wandless Thomas J 
Published: November 2024

AbstractExposure to exogenous and endogenous stress is associated with the intracellular accumulation of aberrant unfolded and misfolded proteins. In eukaryotic cells, protein homeostasis within membrane-bound organelles is regulated by specialized signaling pathways, with the unfolded protein response in the endoplasmic reticulum serving as a foundational example. Yet, it is unclear if a similar surveillance mechanism exists in the nucleus. Here we leveraged engineered proteins called destabilizing domains to acutely expose mammalian cells to nuclear- or cytosolic- localized unfolded protein. We show that the appearance of unfolded protein in either compartment engages a common transcriptional response associated with the transcription factors Nrf1 and Nrf2. Uniquely, only in the nucleus does unfolded protein activate a robust p53-driven transcriptional response and a transient p53-independent cell cycle delay. These studies highlight the distinct effects of localized protein folding stress and the unique protein quality control environment of the nucleus.
Polyhydroxybutyrate production in freshwater SAR11 (LD12)
Authors: Bennett Brittany D. , Meier David A.O. , Lanclos V. Celeste , Asrari Hasti , Coates John D. , Thrash J. Cameron 
Published: November 2024

AbstractSAR11 bacteria (orderPelagibacterales) are oligotrophs and often the most abundant bacterioplankton in aquatic environments. A subset of sequenced SAR11 genomes, predominantly in the brackish and freshwater SAR11 subclades, contain homologs ofphagenes, which in other organisms confer the ability to store carbon and energy via polyhydroxyalkanoate (PHA) polymers. Here, we investigated the relevance of PHA production to SAR11 biology. Phylogenetics showed that Pha proteins occurred on a long branch and provided evidence for origin at the common ancestor of the brackish IIIa and freshwater LD12 subclades, followed by horizontal transfer within SAR11. Using the LD12 representative “CandidatusFonsibacter ubiquis” strain LSUCC0530, we found that a large minority of LSUCC0530 cells contained a single Nile red-staining granule, confirmed that the cells produced polyhydroxybutyrate (PHB), and estimated the total PHB content in the cells. We heterologously expressed the LSUCC0530phaCABlocus inEscherichia coli, finding it to be functional and the likely origin of the PHB. We also determined that, irrespective of changes to carbon, nitrogen, and phosphorus concentrations, a similar fraction of LSUCC0530 cells generated PHB granules and expression of thephaCABlocus remained constant. We suggest that PHB synthesis in LSUCC0530 may be constitutively active due to the slow growth dynamics and minimal regulation that characterize SAR11 bacteria. This is the first characterization of polymer storage in SAR11, providing new insights into the likely fitness advantage for cells harboring this metabolism.
Superconductivity and strain-enhanced phase stability of Janus tungsten chalcogenide hydride monolayers
Authors: Seeyangnok Jakkapat , Pinsook Udomsilp , Ackland Graeme J. 
Published: November 2024

Janus transition metal-dichalcogenide materials have attracted a great deal of attention due to their remarkable physical properties arising from the two-dimensional geometry and the breakdown of the out-of-plane symmetry. Using first-principles density functional theory, we investigated the phase stability, strain-enhanced phase stability, and superconductivity of Janus WSeH and WSH. In addition, we investigated the contribution of the phonon linewidths from the phonon energy spectrum responsible for the superconductivity and the electron-phonon coupling as a function of phonon wave vectors and modes. Previous work has examined hexagonal 2H and tetragonal 1T structures, but we found that neither is a ground-state structure. The metastable 2H phase of WSeH is dynamically stable with Tc≈11.60K, similar to WSH. Compressive biaxial strain—the two-dimensional equivalent of pressure—can stabilize the 1T structures of WSeH and WSH with Tc≈9.23K and 10.52 K, respectively.

Published by the American Physical Society
2024
Multi-objective time-cost-safety risk trade-off optimization for the construction scheduling problem
Authors: Yılmaz Mehmet , Dede Tayfun 
Published: November 2024

PurposeThe purpose of this study is to enable the planning of construction projects with simultaneous consideration of time, cost and safety risks. It also aims to improve the decision-making process by evaluating the effectiveness of the Rao-2 algorithm in solving multi-objective time-cost-safety risk problems. In the end, this model is designed to support project managers in enhancing management approaches by addressing project challenges and constraints more efficiently.Design/methodology/approachIn this study, the Rao-2 algorithm, along with Grey Wolf Optimization (GWO) and Whale Optimization algorithm (WOA), were improved using the crowding distance-based non-dominated sorting method. Rao-2 was first compared to GWO and WOA. Subsequently, it was compared with well-established algorithms in the literature, including genetic algorithm (GA), particle swarm optimization (PSO) and differential evolution (DE). The C-metric, hypervolume and spread metrics were employed for performance measurement. The performance of the algorithms was evaluated on four case studies consisting of 11, 13, 18 and 25 activities.FindingsThe results revealed that Rao-2 performs better than other algorithms as the number of activities increases, when compared using the Hypervolume, Spread and C-metric measures. In terms of performance measures, the GWO algorithm outperformed Rao-2 in some evaluation metrics for the instance involving 11 activities. However, as the number of activities grew, the Rao-2 method consistently generated higher-quality Pareto fronts and outperformed GWO and WOA in all evaluation metrics. The solutions generated by Rao-2 were also superior to those obtained from GA, PSO and DE in all case studies, further demonstrating the capability of our framework to produce a wide range of optimal solutions with high diversity across different case studies.Originality/valueThis research demonstrates that Rao-2 not only improves solution quality when generating Pareto fronts but also achieves better results with fewer function evaluations compared to GA, PSO and DE. The algorithm's efficiency makes it particularly well-suited for optimizing time, cost and safety risks in large-scale construction projects, which in turn positions Rao-2 as a better choice for such projects by producing superior results compared to other algorithms. By providing high-quality solutions with reduced computational demands, Rao-2 offers a faster and more resource-efficient tool for decision-making, contributing to advancements in both the theory and practice of construction project management.
Impacts of effort recognition on nurses’ organizational commitment and turnover intention
Authors: Pham Thi Tuan Linh , Huang Tzu-Ling , Wong May-Kuen , Shyu Yea-Ing Lotus , Cheng T.C.E. , Chen Li-Tzu , Teng Ching-I 
Published: November 2024

PurposeOrganizational commitment could influence nurses’ turnover intention, but we know little about how effort recognition may enhance all three aspects of nurses’ organizational commitment and consequently reduce their turnover intention. This study adopts the self-affirmation theory to examine how the number of effort recognitions received by a nurse may impact the normative, continuance and affective aspects of their organizational commitment and their turnover intention.Design/methodology/approachWe collected two-wave data from the survey responses of 481 nurses in a large medical center in Taiwan between June and August, 2017 and between January and February, 2018 as well as counting the number of times their efforts were recognized as excellent by using patient/family performance appraisal forms in 2016. Bivariate correlation was used to test the hypotheses.FindingsWe found that effort recognition is positively associated with nurses’ normative organizational commitment but not with their continuance or affective commitment. The three aspects of organizational commitment are negatively associated with turnover intention.Practical implicationsNurse managers who hope to reduce nurses’ turnover intention could consider adequately recognizing nurses’ outstanding performance.Originality/valueThe present study is the first to employ the self-affirmation theory to examine the impact of effort recognition on the three aspects of organizational commitment and turnover intention.
Research on 3D humanoid robot pose estimation based on HRNet-Epipolar and CRF robot model by multiple view
Authors: Wang Kexin , Pei Yubin , Li Zhengxiao , Wang Xuanyin 
Published: November 2024

Purpose
This paper aims to present an unmarked method including entire two-dimensional (2D) and three-dimensional (3D) methods to recover absolute 3D humanoid robot poses from multiview images.

Design/methodology/approach
The method consists of two separate steps: estimating the 2D poses in multiview images and recovering the 3D poses from the multiview 2D heatmaps. The 2D one is conducted by High-Resolution Net with Epipolar (HRNet-Epipolar), and the Conditional Random Fields Humanoid Robot Pictorial Structure Model (CRF Robot Model) is proposed to recover 3D poses.

Findings
The performance of the algorithm is validated by experiments developed on data sets captured by four RGB cameras in Qualisys system. It illustrates that the algorithm has higher Mean Per Joint Position Error than Direct Linear Transformation and Recursive Pictorial Structure Model algorithms when estimating 14 joints of the humanoid robot.

Originality/value
A new unmarked method is proposed for 3D humanoid robot pose estimation. Experimental results show enhanced absolute accuracy, which holds important theoretical significance and application value for humanoid robot pose estimation and motion performance testing.