bluuebunny/crossref_metadata_2025 huggingface dataset:
Creating microbiome-model harmony between metaproteomics data and the ADM1da for a two-step anaerobic digester
Authors: Hellwig Patrick , Seick Ingolf , Meinusch Nicole , Benndorf Dirk , Wiese Jürgen , Reichl Udo , Heyer Robert
Published: December 2024

The effective operation, planning, and optimization of renewable energy production in anaerobic digestion (AD) plants relies on advanced process models, such as the Anaerobic Digestion Model No. 1 (ADM1). This study applies an ADM1-based model (ADM1da) to simulate a two-step digester in an industrial setting. The data demonstrate that 2.6% of the methane is lost as a result of open hydrolysis. Conversely, the incorporation of a hydrolysis fermenter enhances methane production by an average of 2.5%. Although ADM1-like models are widely recognized for accurately representing anaerobic digestion processes, mechanistic insights into the microbiome involved have been limited by the absence of tools to analyze microbial composition and functionality at the time these models were developed.

To overcome this limitation, we utilized a metaproteomics approach to assess the abundance and biomass-correlated activity of microbial groups as defined by the model, aiming to bridge the gap between microbial ecology and bioprocess engineering in AD systems. We also developed and evaluated a series of rules for associating particular microbial species with functional groups of the model.

Our analysis demonstrates that while the model supports the presence of a stable microbiome composition in the main fermenter, it is difficult to capture the dynamic behavior observed in the hydrolysis fermenter. Furthermore, the actual AD microbiome displays a greater versatility than the model assumes, with microorganisms performing multiple functions rather than being restricted to single roles.

In conclusion, this study identifies options for improving AD models and integrating comprehensive biological knowledge to further optimize the performance of anaerobic digesters.

Highlights

Simulations revealed 2.6 % methane volume loss attributed to open hydrolysis

Implementation of a two-step process increased methane production by 2.5%

Identification of rules to map metaproteomics data to ADM1da

Simulations of ADM1da depict the dynamic in the main but not in the hydrolysis fermenter

Microbial species perform multiple functions not just one as assumed in the ADM1da
singIST: an integrative method for comparative single-cell trancriptomics between disease models and humans
Authors: Moruno-Cuenca Aitor , Picart-Armada Sergio , Perera-Lluna Alexandre , Fernandez-Albert Francesc
Published: December 2024

Motivation: Disease models serve as fundamental tools in drug discovery and early-stage drug development. However, these models are not a perfect reflection of human disease, and selecting a suitable model can be challenging. Existing computational approaches for molecular validation of pathophysiological resemblance to human conditions at single-cell resolution remain limited. Although quantitative computational methods exist to inform this selection, they are very limited at the single-cell resolution, which can be critical for model selection. Quantifying the resemblance of disease models to the human condition with single-cell technologies in an explainable, integrative, and generalizable manner remains a significant challenge. Results: We present singIST, a computational method for comparative single-cell transcriptomics analysis between disease models and human conditions. singIST provides explainable quantitative measures on disease model similarity to human condition at both pathway and cell type levels, highlighting the importance of each gene in the latter. These measures account for orthology, cell type presence in the disease model, cell type and gene importance in human condition, and gene changes in the disease model measured as fold change. This is achieved within a unifying framework that controls for the intrinsic complexities of single-cell data. We tested our method using three well-characterized murine models of moderate-to-severe Atopic Dermatitis, demonstrating its ability to recapitulate established biological knowledge while generating novel hypothesis through pathway-level analysis. Availability and implementation: Source code at https://github.com/amoruno/singIST-reproducibility
Development and early life stress sensitivity of the rat cortical microstructural similarity network
Authors: Smith Rachel L. , Sawiak Stephen J. , Dorfschmidt Lena , Dutcher Ethan G. , Jones Jolyon A. , Hahn Joel D. , Sporns Olaf , Swanson Larry W. , Taylor Paul A. , Glen Daniel R. , Dalley Jeffrey W. , McMahon Francis J. , Raznahan Armin , Vértes Petra E. , Bullmore Edward T.
Published: December 2024

The rat offers a uniquely valuable animal model in neuroscience, but we currently lack an individual-level understanding of the in vivo rat brain network. Here, leveraging longitudinal measures of cortical magnetization transfer ratio (MTR) from in vivo neuroimaging between postnatal days 20 (weanling) and 290 (mid-adulthood), we design and implement a computational pipeline that captures the network of structural similarity (MIND, morphometric inverse divergence) between each of 53 distinct cortical areas. We first characterized the normative development of the network in a cohort of rats undergoing typical development (N=47), and then contrasted these findings with a cohort exposed to early life stress (ELS, N=40). MIND as a metric of cortical similarity and connectivity was validated by cortical cytoarchitectonics and axonal tract-tracing data. The normative rat MIND network had high between-study reliability and complex topological properties including a rich club. Similarity changed during post-natal and adolescent development, including a phase of fronto-hippocampal convergence, or increasing inter-areal similarity. An inverse process of increasing fronto-hippocampal dissimilarity was seen with post-adult aging. Exposure to ELS in the form of maternal separation appeared to accelerate the normative trajectory of brain development – highlighting embedding of stress in the dynamic rat brain network. Our work provides novel tools for systems-level study of the rat brain that can now be used to understand network-based underpinnings of complex lifespan behaviors and experimental manipulations that this model organism allows.

Significance Statement

Network models derived from neuroimaging have revolutionized our understanding of human brain development but need translation into animal models to interrogate their underlying mechanisms. Rats provide a valuable model due to their complex behaviors and biological similarities to humans; however, in vivo models of individual-level brain networks remain underdeveloped. In this study, we present a novel computational pipeline to construct such networks from in vivo rat structural neuroimaging data. Our findings highlight the dynamic development and experiential sensitivity of fronto-hippocampal systems in rats, offering a reference for cross-species comparisons and mechanistic insights into brain architecture. To support broader research efforts, we include an open release of code and data for rat MIND similarity network analysis.
The farnesyl transferase inhibitor KO-2806 re-sensitizes relapsing tumors to RAS inhibition
Authors: Patel Hetika Vora , Smith Alison Elizabeth , Chan Stacia , Gasendo Jovylyn Gatchalian , Samantaray Tejas , Kessler Linda , Mitra Amitava , Zhu Xuefeng , Liu Yahu A. , Burrows Francis , Malik Shivani
Published: December 2024

Resistance remains a key issue limiting the clinical benefit from RAS-targeting therapeutic agents and necessitates combination approaches. We identify persistent mTORC1 activity in preclinicalKRAS-mutant NSCLC and CRC models as a frequent, nongenetic driver of inherent and adaptive resistance to RAS inhibition. This vulnerability is targetable with the farnesyl transferase inhibitor KO-2806, which blocks mTORC1 activation via RHEB while sparing mTORC2 and its associated toxicities. The addition of KO-2806 to NSCLC or CRC tumors progressing on mutant-selective RAS inhibitors led to rapid and durable tumor regression. In contrast, switching from mutant-selective to pan-RAS inhibitor monotherapy resulted in only stasis of NSCLC tumors and had no effect on CRC tumor progression. Further, the addition of KO-2806 rescued sensitivity of progressing tumors to the pan-RAS inhibitor RMC-6236. Our results establish mTORC1 as an important mediator of escape from RAS inhibition and highlight KO-2806 as a promising RAS companion inhibitor in patients with prior RAS inhibitor exposure.

Significance

Utilizingin vivomodels of tumor relapse, we define a subset of RAS inhibitor-resistant tumors in which vertical inhibition of MAPK is insufficient to restore sensitivity. By controlling parallel mTORC1 activity, KO-2806 may expand utility of RAS inhibitors in patients that have progressed on RAS-targeted therapy, regardless of inhibitor class.
An epigenetic clock forXenopus tropicalisreveals age-associated sites enriched in H4K20me3-marked heterochromatin
Authors: Bennett Ronan , Morselli Marco , Peshkin Leonid , Pellegrini Matteo
Published: December 2024

DNA methylation clocks have been widely used for accurate age prediction, but most studies have been carried out on mammals. Here we present a clock for the aquatic frogXenopus tropicalis, a widely used model organism in developmental biology and genomics. The clock, trained on targeted bisulfite sequencing data, achieved a cross-validation median absolute error of 0.70 years. To construct the clock, we collected DNA methylation data from 192 frogs at genomic regions containing CpG sites previously shown to have age-associated methylation inXenopus. We found that CpG sites with methylation levels significantly increasing or decreasing with age are enriched in heterochromatic regions marked with H4K20me3 and H3K9me3. CpG sites with positively age-associated methylation levels are enriched in bivalent chromatin and gene bodies with H3K36me3, and tend to be proximal to lowly expressed genes. These epigenetic features of aging are similar to those found in mammals, suggesting evolutionary conservation of epigenetic aging mechanisms. Our clock enables future aging biology experiments that leverage the unique properties of amphibians.
Spatiotemporal photocatalytic proximity labeling proteomics reveals ligand-activated extracellular and intracellular EGFR neighborhoods
Authors: Lin Zhi , Ngo Wayne , Chou Yu-Ting , Wu Harry , Susa Katherine J. , Jun Young-wook , Bivona Trever G. , Doudna Jennifer A. , Wells James A.
Published: December 2024

Photo-proximity labeling proteomics (PLP) methods have recently shown that the cell surface receptors can dynamically form lateral interactome networks. Here, we present a paired set of PLP workflows that simultaneously track neighborhood changes for oncogenic epidermal growth factor receptor (EGFR) with temporal resolution, both outside and inside of cells. We achieved this by augmenting the multiscale PLP workflow we call MultiMap, where three photo-probes with different labeling ranges were photo-activated by one photocatalyst, Eosin Y. By anchoring Eosin Y extracellularly and intracellularly on EGFR, we captured hundreds of proteins on both sides of the cell membrane that change in proximity to EGFR upon EGF activation. Neighbors engaged with EGFR within minutes to over an hour, reflecting dynamic interactomes during early, mid- and late-signaling including phosphorylation, internalization, degradation and transcriptional regulation. This rapid “photographic” labeling approach provides snapshots of signaling neighborhoods, revealing their dynamic nature, and potential for drug targeting.
Machine Learning Approaches to Predict Alcohol Consumption from Biomarkers in the UK Biobank
Authors: Hassan Mohammed F. , Gentry Amanda Elswick , Prom-Wormley Elizabeth C. , Peterson Roseann E. , Webb Bradley T.
Published: December 2024

Background

Measuring and estimating alcohol consumption (AC) is important for individual health, public health, and Societal benefits. While self-report and diagnostic interviews are commonly used, incorporating biological-based indices can offer a complementary approach.

Methods

We evaluate machine learning (ML) based predictions of AC using blood and urine-derived biomarkers. This research has been conducted using the UK Biobank (UKB) Resource. In addition to the prediction of the number of alcoholic Drinks Per Week (DPW), four other related phenotypes were predicted for performance comparison. Five ML models were assessed including LASSO, Ridge regression, Gradient Boosting Machines (GBM), Model Boosting (MBOOST), and Extreme Gradient Boosting (XGBOOST).

Results

All five ML methods achieved moderate prediction of DPW (r2=0.304-0.356) with biomarkers significantly increasing prediction above using only known covariates and liver enzymes (r2=0.105). XGBOOST achieved the best prediction performance (r2=0.356, MAE=5.214) at the expense of increasing model complexity and training resources compared to other ML methods. All ML models were able to accurately predict if subjects were heavy drinkers (DPW>8 for women and DPW>15 for men) and produced explainable models that highlighted the role of biomarkers in predicting DPW. While phenotype correlations were similar across methods, XGBOOST produced similar heritability estimates for observed (h2=0.064) and predicted (h2=0.077) DPW. The estimated genetic correlation between observed and predicted DPW was 0.877.

Conclusions

Predicting AC from ML-based biological measures provides an opportunity to identify individuals at increased risk of heavy AC, thereby offering complementary avenue for risk assessment beyond self-report, screening instruments, or structured interviews, which have some known biases. In addition, explainable AI tools identified a constellation of biomarkers associated with AC.
Angiotensin II elicits robust calcium oscillations coordinated within juxtaglomerular cell clusters to suppress renin secretion
Authors: Yamaguchi Hiroki , Guagliardo Nick A. , Smith Jason P. , Xu Fang , Yamaguchi Manako , Almeida Lucas F , Matsuoka Daisuke , Medrano Silvia , Gomez R. Ariel , Sequeira-Lopez Maria Luisa S.
Published: December 2024

BACKGROUND

Juxtaglomerular (JG) cells are sensors that control blood pressure and fluid-electrolyte homeostasis. In response to a decrease in perfusion pressure or changes in the composition and/or volume of the extracellular fluid, JG cells release renin, which initiates an enzymatic cascade that culminates in the production of angiotensin II (Ang II), a potent vasoconstrictor that restores blood pressure and fluid homeostasis. In turn, Ang II exerts a negative feedback on renin release, thus preventing excess circulating renin and the development of hypertension. How Ang II suppresses renin release from JG cells remains elusive. Ang II may inhibit renin release via increased systemic pressure sensed by JG cells, or through a direct effect on Ang II receptors in JG cells, which in turn mediate intracellular calcium (Ca2+) mobilization, a known suppressor of renin release. However, the intricate cellular events mediating Ca2+-induced renin inhibition by Ang II are not fully understood. Further, the unique structural organization of the juxtaglomerular apparatus (JGA), with JG cells clustered around afferent arterioles, suggests complex intercellular interactions, potentially facilitating coordinated Ca2+activity in response to Ang II. Here, we investigate the cellular processes that control Ca2+mobilization and the signaling mechanisms elicited when JG cells are stimulated with Ang II within the intact anatomical context of the JGA. By examining these processes, we aim to elucidate the role of cellular organization in Ca2+-mediated signaling and its impact on renin regulation within the JGA.

OBJECTIVE

To define intra- and inter-cellular Ca2+dynamics, identify the driving ion channels, and elucidate their functional role in Ang II-stimulated JG cells within the native kidney structure.

METHODS AND RESULTS

We generated mice expressing JG cell-specific GCaMP6f, a genetically encoded Ca2+indicator, under theRen1cpromoter.Ex vivoCa2+imaging in acutely prepared kidney slices revealed that JG cells within clusters exhibit coordinated, robust Ca2+oscillations in response to Ang II stimulation, contrary to previous observations in isolated cells. These oscillations showed dose-dependent increases in occurrence and correlated with suppressed renin secretion. Pharmacological inhibition identified key drivers of these oscillations: endoplasmic reticulum Ca2+storage and release, extracellular Ca2+uptake via ORAI channels, and intercellular communication through gap junctions. Blocking ORAI channels and gap junctions alleviated Ang II inhibition of renin secretion.

CONCLUSION

In intact kidney slices, Ang II elicits synchronized Ca2+oscillations in JG cells, driven by endoplasmic reticulum-derived Ca2+release, ORAI channels, and gap junctions, leading to suppressed renin secretion.
Cytosolic peroxiredoxin Tsa1 influences acetic acid metabolism and pH homeostasis in wine yeasts
Authors: Garrigós Víctor , Picazo Cecilia , Dengler Lisa , Ewald Jennifer C. , Matallana Emilia , Aranda Agustín
Published: December 2024

Acetic acid is a key metabolite in yeast fermentation, influencing wine quality through its role in volatile acidity. InSaccharomyces cerevisiae, acetic acid production involves aldehyde dehydrogenases, primarily Ald6 during fermentation and Ald4 under respiration. However, the regulatory mechanisms of these enzymes throughout fermentation and how they differ in commonly used strains remain partially unclear. This study explores the cytosolic peroxiredoxin Tsa1 as a novel regulator of acetic acid metabolism.TSA1gene deletion revealed strain-dependent effects on acetic acid metabolism and tolerance, showing reduced production and enhanced consumption in laboratory media. Under respiration, Ald4-driven acetic acid production, which raises extracellular pH, was mitigated by the absence of Tsa1. During wine fermentation,TSA1deletion decreased the initial acetic acid surge by downregulatingALD6transcription and enzymatic activity. These findings position Tsa1 as a metabolic regulator and a potential target for modulating acetic acid levels to manage volatile acidity and wine quality.
Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes
Authors: Andreani-Gerard Constanza M. , Jiménez Natalia E. , Palma Ricardo , Muller Coralie , Hamon-Giraud Pauline , Le Cunff Yann , Cambiazo Verónica , González Mauricio , Siegel Anne , Frioux Clémence , Maass Alejandro
Published: December 2024

Background

Soil microbiomes harbor complex communities and exhibit important ecological roles resulting from biochemical transformations and microbial interactions. Difficulties in characterizing the mechanisms and consequences of such interactions together with the multidimensionality of niches hinder our understanding of these ecosystems. The Atacama Desert is an extreme environment that includes unique combinations of stressful abiotic factors affecting microbial life. In particular, the Talabre Lejía transect has been proposed as a unique natural laboratory for understanding adaptation mechanisms.

Results

We propose a systems biology-based computational framework for the reconstruction and simulation of community-wide and genome-resolved metabolic models, in order to provide an overview of the metabolic potential as a proxy of how microbial communities are prepared to respond to the environment. Through a multifaceted approach that includes taxonomic and functional profiling of microbiomes, simulation of the metabolic potential, and multivariate analyses, we were able to identify key species and functions from six contrasting soil samples across the Talabre Lejía transect. We highlight the functional redundancy of whole metagenomes, which act as a gene reservoir from which site-specific functions emerge at the species level. We also link the physicochemistry from the puna and the lagoon samples to specific metabolic machineries that could be associated with their adaptation to the unique environmental conditions found there. We further provide an abstraction of community composition and structure for each site that allows to describe them as sensitive or resilient to environmental shifts through putative cooperation events.

Conclusion

Our results show that the study of community-wide and genome-resolved metabolic potential, together with targeted modeling, may help to elucidate the role of producible metabolites in the adaptation of microbial communities. Our framework was designed to handle non-model microorganisms, making it suitable for any (meta)genomic dataset that includes nucleotide sequence data and high-quality environmental metadata for different samples.
Confounder-aware foundation modeling for accurate phenotype profiling in cell imaging
Authors: Papanastasiou Giorgos , Sanchez Pedro P. , Christodoulidis Argyrios , Yang Guang , Pinaya Walter Hugo Lopez
Published: December 2024

Image-based profiling is rapidly transforming drug discovery, offering unprecedented insights into cellular responses. However, experimental variability hinders accurate identification of mechanisms of action (MoA) and compound targets. Existing methods commonly fail to generalize to novel compounds, limiting their utility in exploring uncharted chemical space. To address this, we present a confounder-aware foundation model integrating a causal mechanism within a latent diffusion model, enabling the generation of balanced synthetic datasets for robust biological effect estimation. Trained on over 13 million Cell Painting images and 107 thousand compounds, our model learns robust cellular phenotype representations, mitigating confounder impact. We achieve state-of-the-art MoA and target prediction for both seen (0.66 and 0.65 ROC-AUC) and unseen compounds (0.65 and 0.73 ROC-AUC), significantly surpassing real and batch-corrected data. This innovative framework advances drug discovery by delivering robust biological effect estimations for novel compounds, potentially accelerating hit expansion. Our model establishes a scalable and adaptable foundation for cell imaging, holding the potential to become a cornerstone in data-driven drug discovery.
Foveal action for the control of extrafoveal vision
Authors: Zhang Tong , Tian Xiaoguang , Malevich Tatiana , Baumann Matthias P. , Hafed Ziad M.
Published: December 2024

Microsaccades have been convincingly linked to extrafoveal covert attention shifts for more than two decades. However, the direction of causality between individual microsaccade generation and an alteration in both extrafoveal visual sensitivity and behavior remains debated: do microsaccades merely reflect, perhaps probabilistically, an altered extrafoveal sensitivity, or is the act of generating microsaccades sufficient to, on its own, modify such sensitivity? Using a novel exploitation of real-time retinal image stabilization, behavior, and neurophysiology in the superior colliculus, we show that exclusive experimental control over foveal oculomotor state is entirely sufficient to influence extrafoveal sensitivity. This happens for eccentricities as large as ∼50 times those associated with microsaccades, and it also takes place in the absence of any differential attentional demands. Most importantly, such influence is mediated through well-known, classic pre- and post-saccadic visual processing changes. Thus, seemingly-innocuous subliminal eye movements do constitute an integral component of cognitive processes like attention.
Habitat-specificity in SAR11 is associated with a handful of genes under high selection
Authors: Tucker Sarah J. , Freel Kelle C. , Eren A. Murat , Rappé Michael S.
Published: December 2024

The orderPelagibacterales(SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages likely play distinct roles in oceanic biogeochemical cycles. Yet, understanding the determinants of niche partitioning within SAR11 has been a formidable challenge due to the high genetic diversity within individual SAR11 sublineages and the limited availability of high-quality genomes from both cultivation and metagenomic reconstruction. Here, we take advantage of 71 new SAR11 genomes from strains we isolated from the tropical Pacific Ocean to evaluate the distribution of metabolic traits across thePelagibacteraceae,a recently classified family within the orderPelagibacteralesencompassing subgroups Ia and Ib. Our analyses of metagenomes generated from stations where the strains were isolated reveals distinct habitat preferences across SAR11 genera for coastal or offshore environments, and subtle but systematic differences in metabolic potential that support these observations. We also observe higher levels of selective forces acting on habitat-specific metabolic genes linked to SAR11 fitness and polyphyletic distributions of habitat preferences and metabolic traits across SAR11 genera, suggesting that contrasting lifestyles have emerged across multiple lineages independently. Together, these insights reveal niche-partitioning within sympatric and parapatric populations of SAR11 and demonstrate that the immense genomic diversity of SAR11 bacteria naturally segregates into ecologically and genetically cohesive units, or ecotypes, that vary in spatial distributions in the tropical Pacific.
Increased versatility and convenience: advances and strategy optimization of ReMOT-mediated genetic modification in insects
Authors: Liang Xia , Zhou Cao , Hong Junfeng , Jiang Yanping , Li Lingyi , Xie Xinyuan , Wang Siyi , Zou Qili , Yang Xiaolin , Xiang Kai , Ma Jin , Qiao Liang , Chen Bin , Sun Wei
Published: December 2024

Genetic modification via gene editing has become a widely adopted and demonstrably effective method in functional gene research within entomology. However, the optimal efficiency and simplicity of delivering exogenous guide RNA clustered regularly interspaced short palindromic repeats-associated protein 9 complexes into target tissues are crucial for successful gene editing. The Receptor Mediated Ovary Transduction of Cargo (ReMOT) strategy, which simplifies the delivery process, target site selection, technical requirements, and delivery cost compared with embryonic microinjection, enabling efficient editing at the germline level, is gaining increasing attention. Although the feasibility and advantages of this technique have been demonstrated in various insect species, further optimization of operational details and the overcoming of further bottlenecks are still required. This review focuses on advances in developing ReMOT as a valuable technology, exploring its applicability, rationale for selecting the ovary as a delivery target site, factors influencing its efficiency, and recommendations for improvement. The versatility and effectiveness of ReMOT make it a promising method for researchers looking to make precise genetic modifications with greater ease and efficiency.
Engineering an Exo70 integrated domain of a barley NLR for improved blast resistance
Authors: Saado Indira , Brabham Helen J. , Bennett Josh W. , Lam Anson Ho Ching , Hernández-Pinzón Inmaculada , Moscou Matthew J. , De la Concepcion Juan Carlos , Banfield Mark J.
Published: December 2024

Intracellular immune receptors protect plants from microbial invasion by detecting and responding to pathogen-derived effector molecules, often triggering cell death responses. However, pathogen effectors can evolve to avoid immune recognition, resulting in devastating diseases that threaten global agriculture. Here, we show that an integrated Exo70 domain from the barley NLR RGH2 can interact with both the rice blast pathogen effector AVR-Pii and a closely related wheat blast variant. We used structure-led engineering to develop RGH2+that shows increased binding affinity towards AVR-Pii variants and increased cell death responses on heterologous expression inNicotiana benthamiana. Infection assays in transgenic barley lines harbouring RGH2+(along with the paired NLR RGH3) show reduced virulence towards blast strains expressing AVR-Pii variants. These results demonstrate the potential of engineering NLR receptors as an effective strategy for improving resistance towards one of the most destructive diseases affecting cereal production.
NKX2.2 and KLF4 cooperate to regulate α-cell identity
Authors: Brooks Elliott P. , Casey McKenna R. , Wells Kristen L. , Liu Tsung-Yun , Van Orman Madeline , Sussel Lori
Published: December 2024

Transcription factors (TFs) are indispensable for maintaining cell identity through regulating cell-specific gene expression. Distinct cell identities derived from a common progenitor are frequently perpetuated by shared TFs, yet the mechanisms that enable these TFs to regulate cell-specific targets are poorly characterized. We report that the TF NKX2.2 is critical for the identity of pancreatic islet α cells by directly activating α-cell genes and repressing alternate islet cell fate genes. When compared with the known role of NKX2.2 in islet β cells, we demonstrate that NKX2.2 regulates α-cell genes, facilitated in part by α-cell-specific DNA binding at gene promoters. Furthermore, we have identified the reprogramming factor KLF4 as having enriched expression in α cells, where it co-occupies NKX2.2-bound α-cell promoters, is necessary for NKX2.2 promoter occupancy in α cells, and coregulates many NKX2.2 α-cell transcriptional targets. Overexpression ofKlf4in β cells is sufficient to manipulate chromatin accessibility, increase binding of NKX2.2 at α-cell-specific promoter sites, and alter expression of NKX2.2-regulated cell-specific targets. This study identifies KLF4 as a novel α-cell factor that cooperates with NKX2.2 to regulate α-cell identity.
Optical signatures of strain-induced ferromagnetism in a
LaCoO3
thin film
Authors: Abadizaman F. , Munzar D. , Kiaba M. , Dubroka A.
Published: December 2024

Using spectroscopic ellipsometry, we studied the optical conductivity of LaCoO3 with various degrees of strain. The optical response of the compressively strained LaCoO3 film is qualitatively similar to the one of the unstrained LaCoO3 polycrystalline sample and exhibits a redistribution of the spectral weight between ∼0.2 and 6 eV, which is most likely related to the thermal excitation of the high-spin (HS) states. The optical response of the ferromagnetic (FM) tensile strained film exhibits clear signatures of the FM state. Below the Curie temperature Tc=82 K, a spectral weight transfer sets on from high energies (between 3.3 and 5.6 eV) to low energies (between 0.2 and 3.3 eV). The temperature dependence of the low-energy spectral weight can be understood in the framework of the HS biexciton model of Sotnikov [] as corresponding to the increase of the concentration of the HS states that are stabilized below Tc. The magnitude of the redistribution of the spectral weight due to the formation of the FM state is sizable and corresponds to 0.009 e per Co ion. We discuss it in terms of the effective kinetic energy of Co 3d bands.

Published by the American Physical Society
2024
Summing large Pomeron loops in the saturation region: Amplitude and multiplicity distributions for dipole-dipole scattering
Authors: Levin Eugene
Published: December 2024

In this paper we found the parton densities at high energies. Their expressions stems from our attempts to reconcile the exact solution to the Balitsky-Kovchegov equation, which describes the rare fluctuation in the dipole-target scattering, with the fact that this equation sums the “fan” Pomeron diagrams. Using these densities we can calculate the contributions of large Pomeron loops to dipole-dipole scattering at high energies. We detected that the scattering matrix for this process has the same suppression as was predicted by Iancu and Mueller from their estimates of the “rare” fluctuation in QCD. Applying the Abramovsky, Gribov and Kancheli cutting rules we found that the produced gluons are distributed accordingly the Koba, Nielsen, and Olesen law that leads to the entropy SE=ln(xG(x,Q2)). xG has to be in the saturation region at high energies.

Published by the American Physical Society
2024
Evidence of
hb(2P)→ϒ(1S)η
Decay and Search for
hb(1P,2P)→ϒ(1S)π0
with the Belle Detector
Authors: Kovalenko E. , Adachi I. , Aihara H. , Asner D. M. , Aushev T. , Ayad R. , Babu V. , Banerjee Sw. , Belous K. , Bennett J. , Bessner M. , Bilka T. , Biswas D. , Bobrov A. , Bodrov D. , Bondar A. , Bozek A. , Bračko M. , Branchini P. , Browder T. E. , Budano A. , Campajola M. , Chang M.-C. , Cheon B. G. , Chilikin K. , Cho H. E. , Cho K. , Cho S.-J. , Choi S.-K. , Choi Y. , Choudhury S. , Dash N. , De Nardo G. , De Pietro G. , Dhamija R. , Di Capua F. , Doležal Z. , Dong T. V. , Dubey S. , Ecker P. , Epifanov D. , Ferlewicz D. , Fulsom B. G. , Garg R. , Gaur V. , Garmash A. , Giri A. , Goldenzweig P. , Graziani E. , Gu T. , Guan Y. , Gudkova K. , Hadjivasiliou C. , Hara T. , Hayasaka K. , Hazra S. , Hou W.-S. , Hsu C.-L. , Inami K. , Ipsita N. , Ishikawa A. , Itoh R. , Iwasaki M. , Jacobs W. W. , Jin Y. , Kawasaki T. , Kiesling C. , Kim C. H. , Kim D. Y. , Kim K.-H. , Kim Y.-K. , Kinoshita K. , Kodyš P. , Korobov A. , Korpar S. , Križan P. , Krokovny P. , Kuhr T. , Kumar R. , Kumara K. , Kuzmin A. , Kwon Y.-J. , Lai Y.-T. , Lam T. , Levit D. , Li L. K. , Li Gioi L. , Libby J. , Liventsev D. , Ma Y. , Martini A. , Masuda M. , Matsuda T. , Matvienko D. , Meier F. , Merola M. , Miyabayashi K. , Mizuk R. , Mohanty G. B. , Mussa R. , Nakamura I. , Nakao M. , Natkaniec Z. , Natochii A. , Nayak L. , Nayak M. , Niiyama M. , Nishida S. , Ogawa S. , Ono H. , Pakhlova G. , Pardi S. , Park J. , Park S.-H. , Passeri A. , Patra S. , Paul S. , Pedlar T. K. , Pestotnik R. , Piilonen L. E. , Podobnik T. , Prencipe E. , Prim M. T. , Purohit M. V. , Rout N. , Russo G. , Sandilya S. , Santelj L. , Savinov V. , Schnell G. , Schwanda C. , Seino Y. , Senyo K. , Sevior M. E. , Shan W. , Sharma C. , Shiu J.-G. , Shwartz B. , Sokolov A. , Solovieva E. , Starič M. , Sumihama M. , Takizawa M. , Tamponi U. , Tanida K. , Tenchini F. , Tiwary R. , Uchida M. , Unno Y. , Uno S. , Usov Y. , Vinokurova A. , Wang D. , Wang E. , Wang M.-Z. , Wang X. L. , Won E. , Yabsley B. D. , Yan W. , Yang S. B. , Yelton J. , Yin J. H. , Yook Y. , Yuan C. Z. , Zhang Z. P. , Zhilich V. ,   Belle Collaboration
Published: December 2024

We report the first evidence for the hb(2P)→ϒ(1S)η transition with a significance of 3.5 standard deviations. The decay branching fraction is measured to be B[hb(2P)→ϒ(1S)η]=(7.1−3.2+3.7±0.8)×10−3, which is noticeably smaller than expected. We also set upper limits on π0 transitions of B[hb(2P)→ϒ(1S)π0]<1.8×10−3, and B[hb(1P)→ϒ(1S)π0]<1.8×10−3, at the 90% confidence level. These results are obtained with a 131.4  fb−1 data sample collected near the ϒ(5S) resonance with the Belle detector at the KEKB asymmetric-energy e+e− collider.

Published by the American Physical Society
2024
Spiking Flip-Flop Memory in Resonant Tunneling Diode Neurons
Authors: Donati Giovanni , Owen-Newns Dafydd , Robertson Joshua , Malysheva Ekaterina , Adair Andrew , Figueiredo Jose , Romeira Bruno , Dolores-Calzadilla Victor , Hurtado Antonio
Published: December 2024

We report a spiking flip-flop memory mechanism that allows controllably switching between neural-like excitable spike-firing and quiescent dynamics in a resonant tunneling diode (RTD) neuron under low-amplitude (<150  mV pulses) and high-speed (ns rate) inputs pulses. We also show that the timing of the set-reset input pulses is critical to elicit switching responses between spiking and quiescent regimes in the system. The demonstrated flip-flop spiking memory, in which spiking regimes can be controllably excited, stored, and inhibited in RTD neurons via specific low-amplitude, high-speed signals (delivered at proper time instants) offers high promise for RTD-based spiking neural networks, with the potential to be extended further to optoelectronic implementations where RTD neurons and RTD memory elements are deployed alongside for fast and efficient photonic-electronic neuromorphic computing and artificial intelligence hardware.

Published by the American Physical Society
2024
Steady granular flow in a rotating drum: A theoretical nonlocal model for characterizing stress, velocity, and packing fraction profiles, encompassing grain shape effects from convex to highly concave
Authors: Wang Weiyi , Barés Jonathan , Renouf Mathieu , Azéma Emilien
Published: December 2024

In this work, we investigate the effect of particle shape, ranging from spherical to highly concave, on steady flows in a rotating drum, a system that facilitates a continuous transition from a jamming state at greater depths to an unjamming state at shallower regions. We develop an analytical model to elucidate granular behavior within the rotating drum: (i) First, by decomposing the shear stress, we reconcile the discrepancy between simulation data and theoretical predictions, establishing a relationship with the angle of repose. (ii) Second, we extend the generalized Bagnold scaling, coupled with a nonlocal fluidity relation based on packing fraction, providing a framework for a correlation between shear stress, shear rate, and packing fraction. Additionally, we introduce a characteristic length to quantify the influence of particle shape and drum speed. This analytical model offers explicit functional forms for physical quantity profiles, which are validated experimentally in a thin rotating drum and numerically in a two-dimensional rotating drum. Our results demonstrate that this model accurately describes the change in velocity from the bottom of the drum to the free surface. Moreover, for different shapes of particle and drum speeds, the characteristic length captures the interplay between shear stress, shear rate, and the variation of packing fraction.

Published by the American Physical Society
2024
A new hydrated crystalline form of N-[(E)-(4-hydroxyphenyl)methylidene]-1H-1,2,4-triazol-3-amine and its antifungal activity
Authors: Boutheina Boualia , Zakaria Bouhidel , Cherouana Aouatef , El-Eulmi Bendeif
Published: December 2024

The synthesis, crystal structure, Hirshfeld analysis, and antifungal assessment of a new monohydrated Schiff base with a triazole moiety are reported. The structural study revealed the presence of three significant hydrogen bonds (N—H...N, O—H...N, and O—H...O), which contribute to the cohesion of the crystal. These bonds generate two-dimensional layers parallel to the bc plane, built on the basis of rings with the graph-set motifs R
4
4(8) and R
4
4(24). The crystal structure is further consolidated by π–π interactions between similar rings. The antifungal activity of the Schiff base was evaluated against three fungi: Fusarium oxysporum, Botrytis cinerea, and Alternaria alternata, showing significant antifungal activity, particularly against Alternaria alternata.
Crystal structures of (±)-(1SR,5SR,6SR,7SR,10SR,11SR,13RS,14SR,15SR,16RS)-13-acetoxy-16-benzyloxy-15-hydroxy-7-methoxymethoxy-3-oxo-11,15,18,18-tetramethyl-2,4-dioxatetracyclo[12.3.1.01,5.06,11]octadecan-10-yl benzoate and its 13-epimer
Authors: Oishi Takeshi , Fukaya Keisuke , Sato Takaaki , Chida Noritaka
Published: December 2024

The title compounds, C38H48O11 (A and B), are tetracyclic benzoates composed of a taxane ring with a fused dioxolane ring as the core skeleton. In compound A, the five-membered dioxolane ring is essentially planar while the two cyclohexane rings and the cyclooctane ring adopt chair and chair–chair forms, respectively, and there are three intramolecular H...H short contacts. The corresponding ring conformations in B are similar; however, one intramolecular C—H...O interaction and two H...H short contacts are observed, and the benzoyl and methoxymethyl groups show orientational disorder. In the crystal of A, a pair of intermolecular O—H...O hydrogen bonds link two molecules into an inversion dimer, and weak intermolecular C—H...O interactions connect the dimers, forming a three-dimensional network. In the crystal of B, an inversion dimer is similarly generated by a pair of intermolecular O—H...O hydrogen bonds, and weak intermolecular C—H...O and C—H...π interactions connect the dimers into a three-dimensional architecture.
Poly[diaqua[μ2-1,4-bis(pyridin-3-ylmethyl)piperazine][μ2-4-(2-carboxylatoethyl)benzoato]cobalt(II)]
Authors: Ezenyilimba Frederick C. , LaDuca Robert L.
Published: December 2024

A layered cobalt coordination polymer containing both 4-(2-carboxylatoethyl)benzoate (ceb) and 1,4-bis(3-pyridylmethyl)piperazine (3-bpmp) ligands, [Co(C10H8O4)(C16H20N4)(H2O)2]
n
or [Co(ceb)(3-bpmp)(H2O)2]
n
, was isolated and structurally characterized by single-crystal X-ray diffraction. Chain-like [Co(ceb)(H2O)2]
n
units are oriented parallel to [101]. These are connected into (4,4)-grid coordination polymer layers by tethering 3-bpmp ligands. The layer motifs stack in an AAA pattern mediated by O—H...N hydrogen-bonding interactions between the aqua ligands in one layer and 3-bpmp piperazinyl N atoms in the abutting layer.
Research on the electrochemical dissolution behavior of Ni-based superalloys after different oxidation treatments in NaCl solution
Authors: Jiang Hairui , Guan Jianjun , Zhao Yan , Qu Jinglong , Yang Yanhong
Published: December 2024

Purpose

This study aims to investigate the corrosion resistance and electrochemical dissolution behavior of superalloys treated by different oxidation treatments.

Design/methodology/approach

Ni-based superalloys were subjected to oxidation treatment at 1000 °C for 10 h, 1150 °C for 10 h and 1200 °C for 20 h. The microstructure, electrochemical dissolution behavior, elemental distribution, as well as compactness and composition of the oxide layer, were studied.

Findings

The results show that both the thickness and the granular oxide size of the oxide layer on Ni-based superalloys increase with longer oxidation times and higher temperatures. The electrochemical dissolution efficiency of Ni-based superalloys decreases with increasing oxidation time and temperature. The reduced electrochemical dissolution efficiency observed in Ni-based superalloys oxidation-treated at 1200 °C for 20 h is primarily attributed to the thicker oxide layer, which contains the highest Cr oxide content.

Originality/value

The findings contribute to the advancement of recycling and utilization of Ni-based superalloy scrap.
Breaking down to build up: how deconstruction and carbon finance foster sustainable, resilient construction in the industry 5.0 era
Authors: Murali Drisya , Suresh M. , Raman Raghu
Published: December 2024

Purpose

This study aims to seek and identify key enablers influencing the integration of deconstruction and carbon finance to improve sustainable and resilient construction in the Industry 5.0 era and then examines how these enablers relate to one another and rank, classify and prioritize them appropriately.

Design/methodology/approach

This study adopts the Integrated Decision-Making Trial and Evaluation Laboratory-Interpretive Structural Modeling-Matrice d’impacts Croises Multiplication Appliquee a un Classment (DEMATEL-ISM-MICMAC) methodology.

Findings

The key enablers are the circular economy approach with closed-loop material flow, prioritizing material recovery and reuse, and structuring carbon credits for affordability.

Research limitations/implications

The construction industry can advance toward environmentally friendly, sustainable building techniques and help achieve the larger objectives of carbon neutrality and environmental preservation by adopting the study’s guiding principles.

Practical implications

This study implies switching to circular rather than linear economic methods. It is still unrealistic to achieve zero carbon emissions, which is why carbon finance is important because it allows companies to trade carbon credits and encourages negative carbon activities and to structure and trade carbon credits affordably so that businesses of all sizes can participate. To extend the lives of current materials and reduce waste, it is imperative to maximize their reuse and minimize their disposal.

Originality/value

The novelty of this research lies in introducing carbon trade finance concepts to the construction sector, particularly focusing on the deconstruction phase, to enhance sustainability and resilience in construction practices in the Industry 5.0 era.
Personal leadership resources used by principals during a period of contingency
Authors: del Arco Isabel , Ramos-Pla Anabel , Tintoré Mireia , Cabral Ilídia
Published: December 2024

Purpose

The objective of the present study is to compare the Personal Leadership Resources (PLR) of primary school principals in Spain and Portugal, before and during the COVID-19 pandemic.

Design/methodology/approach

A quantitative methodology was used to analyze the data obtained from a questionnaire that measured the PLR of a sample of 308 principals from both countries (Portugal and Spain).

Findings

The results showed that the education leaders utilized their PLR with less intensity in a health emergency. Also, it was shown that the PLR related to the need to know effective practices, the efficiency in problem-solving, and the management of one’s emotions were crucial in moments of crisis. It is essential to identify the PLR utilized in moments of crisis to influence the training of education leaders to manage future emergencies efficiently.

Originality/value

This is the first study comparing the PLR developed by school principals in Catalonia (Spain) and Portugal before and during the pandemic.
Exploring the role of ethical leadership and personality traits in shaping ethical behavior among Ugandan security officers
Authors: Kyambade Mahadih , Namatovu Afulah
Published: December 2024

Purpose

The study investigates the mediating role of ethical leadership on the association between personality traits and ethical behavior among police officers in Uganda. The primary aim is to understand how personality traits influence ethical behavior and the role ethical leadership plays in this dynamic.

Design/methodology/approach

Employing a quantitative, descriptive research design, data were collected through convenience sampling from 259 police officers across various stations. A self-administered questionnaire comprising closed-ended questions was utilized to assess the officers’ personality traits, ethical behavior and ethical leadership, with responses measured on a five-point Likert scale. The data were analyzed using structural equation modeling (SEM) with Smart PLS software, incorporating bootstrapping techniques to evaluate direct and indirect effects among the constructs.

Findings

The findings indicate a positive association between personality traits and ethical behavior, with ethical leadership significantly mediating this relationship.

Practical implications

Specifically, officers with favorable personality traits are more likely to engage in ethical behavior, facilitated by the presence of ethical leadership. These results emphasize the necessity of promoting ethical leadership to enhance the ethical conduct of police officers in Uganda.

Originality/value

This research contributes original insights into the interplay between personality traits, ethical leadership and ethical behavior within the Ugandan police context. The practical implications suggest that law enforcement agencies should prioritize ethical leadership development initiatives, as these can significantly enhance ethical standards among officers, thereby improving the overall integrity of the police force and fostering public trust.