bluuebunny/crossref_metadata_2025 huggingface dataset:
Soil viral and prokaryotic communities shifted significantly after wildfire in chaparral and woodland habitats
Authors: Geonczy Sara E. , ter Horst Anneliek M. , Emerson Joanne B.
Published: November 2024

Increased wildfire activity warrants more research into fire-driven biotic changes in soil, given that soil microbes contribute to biogeochemical processes by way of organic matter decomposition, nutrient cycling, and promoting plant growth. Viruses of prokaryotes apply pressure to microbial communities, making their responses to fire also important for understanding post-fire ecology. Leveraging viromes and 16S rRNA gene amplicon sequencing, here we studied viral and prokaryotic community responses to wildfire in woodland and chaparral soils at five timepoints over one year following the California LNU Complex wildfire.

We also compared post-fire samples to unburned controls at the final three timepoints, beginning five months after the fire. Viromic DNA yields were low-to-undetectable (indicative of low viral particle abundances), particularly for the first post-fire timepoint, and comparisons to controls suggest a return to baseline viral particle abundances within five months of the wildfire. Viral and prokaryotic community composition and soil chemistry differed significantly in burned samples compared to controls from both habitats. Compared to controls, a greater proportion of viral ‘species’ (vOTUs) from a burned conifer forest were detected in both burned habitats here, suggesting fire-associated habitat filtering. Published viromes collected from the same sites nine months pre-fire were more similar to controls than to post-fire viromes. Together, these results indicate significant changes in soil viral and prokaryotic communities due to wildfire.
Early exercise disrupts a pro-repair extracellular matrix program during zebrafish fin regeneration
Authors: Lewis Victor M. , Fernandez Rafael A. , Horst Samuel G. , Stankunas Kryn
Published: November 2024

Understanding how mechanical stimulation from exercise influences cellular responses during tissue repair could enhance therapeutic strategies. We explored zebrafish caudal fin regeneration to study exercise impacts on a robust model of tissue regeneration. We used a swim tunnel to determine that exercise initiated during but not after blastema establishment impaired fin regeneration, including of the bony ray skeleton. Long-term tracking of fluorescently labeled cell lineages showed exercise disrupted blastemal mesenchyme formation. Transcriptomic profiling and section staining indicated exercise reduced an extracellular matrix (ECM) gene expression program, including for hyaluronic acid (HA) synthesis. Like exercise, HA synthesis inhibition or blastemal HA depletion disrupted blastema formation. We considered if injury-upregulated HA establishes a pro-regenerative environment facilitating mechanotransduction. HA density across the blastema correlated with nuclear localization of the mechanotransducer Yes-associated protein (Yap). Further, exercise loading or reducing HA decreased nuclear Yap and cell proliferation. We conclude early exercise during fin regeneration disrupts expression of an HA-rich ECM supporting blastema expansion. These results highlight the interface between mechanotransduction and ECM as consideration for timing exercise interventions and developing regenerative therapies.

Significance Statement

Controlled exercise promotes healing and recovery from severe skeletal injuries. However, properly timed interventions are essential to promote recovery and prevent further damage. We use zebrafish caudal fin regeneration to mechanistically study exercise impacts on a naturally robust and experimentally accessible model of tissue repair. We link detrimental early exercise effects during fin regeneration to impaired ECM synthesis, mechanotransduction, and cell proliferation. These insights could explain the value of delaying the onset of physical therapy and suggest pursuing therapies that maintain ECM integrity for regenerative rehabilitation.
Dynamic programming algorithms for fast and accurate cell lineage tree reconstruction from CRISPR-based lineage tracing data
Authors: Dai Junyan , Molloy Erin K.
Published: November 2024

CRISPR-based lineage tracing, coupled with single-cell RNA sequencing, has emerged as a promising approach for studying cell transformations during development as well as disease progression. However, the high ratio of cells to CRISPR-induced mutations, combined with missing data from silencing or dropout, make cell lineage tree (CLT) reconstruction difficult. As a result, this computational problem has attracted significant attention in recent years, including the introduction of Star Homoplasy Parsimony (SHP) in 2023 to model the specific properties of CRISPR-induced mutations, along with the Startle family of methods based on integer linear programming (ILP) or heuristic search (NNI). Here, we present Star-CDP, the first dynamic programming algorithm for SHP. Star-CDP solves SHP within a constrained search space Σ defined by subsets of cells from which a solution CLT must draw its clades. When Σ is the power set, Star-CDP is an exact exponential algorithm with time complexityO(nm|Σ|2), wherenis the number of cells,mis the number of target sites, and |Σ |=O(2n). We show that it is possible to build clade constraints that are polynomially-sized and effective in practice. Motivated by the technological challenges in producing consistent phylogenetic signal across the tree during lineage tracing, we also present algorithms to efficiently count, sample, and build consensus trees from all solutions to the clade-constrained SHP problem. In simulations, Star-CDP’s strict consensus effectively reduced false positive branches while preserving many more true positives compared to the standard strict consensus implemented by PAUP*, a popular parsimony method from species phylogenetics. Likewise, Star-CDP’s strict consensus achieved the same or higher accuracy (f1-score) on all but one of the 15 model conditions tested, often outperforming leading the methods, Startle-ILP and Startle-NNI, while also scaling to larger data sets than Startle-ILP. Lastly, we analyzed lineage tracing data from the KP-Tracer mouse model of lung adenocarcinoma, finding that Star-CDP produced plausible CLTs, often lowering the number of migration and reseeding events needed to explain metastases compared to Startle. Our analysis also showed, for the first time, that strategies for preprocessing cells with missing data—specifically cell pruning and deduplicating techniques—can have a substantial impact on CLTs reconstructed with the same method, even changing relative performance across methods compared to previously published results. The same was true of postprocessing trees with LAML, a maximum likelihood method designed for mixed-type missing data. By exploring these different pipelines, we recovered the most plausible CLT for the largest KP-Tracer metastatic tumor, reducing the number of reseeding events from 42 to 10 without increasing the number of migrations. Star-CDP is available on Github:https://github.com/molloy-lab/Star-CDP.
Dynamic analysis of Q-fever transmission among cattle in the Tropical Savannah Grassland zone of Ghana
Authors: Otoo Dominic , Mensah Kennedy , Adjei Eugene , Danquah Baaba Abassawah , Adusei Hawa , Chuaya Razak G.
Published: November 2024

Livestock morbidity and death from Q-fever have been high, endangering local farmers’ livelihoods and affecting food security in Ghana. It is essential to understand the transmission dynamics of Q-fever to protect both the health of the animals and the main source of income for the community. A non-linear ordinary differential equation incorporating a vaccinated compartment was formulated and analyzed to gain insights into the spread of Q-fever. Routh Hurwitz criterion and Lyapunov function were used respectively to analyze the local and global stability of the disease-free equilibrium (Q0). We analyzed the behavior of the model compartments and discovered that many key factors significantly influence the persistence or eradication of Q-fever. Increased vaccination rates decrease the susceptible livestock while increasing the vaccinated livestock, potentially reducing the risk of outbreaks and limiting the spread of infections. A higher recovery rate leads to a quicker recovery, which aids in epidemic control by boosting population immunity and reducing the infectious time. The infection level rises whenR0>1, indicating a typical transcritical bifurcation behavior, but this growth stays steady and does not result in unbounded advancement.

Author summary

Q-fever presents considerable health hazards to livestock in Ghana’s Tropical Savannah Grassland, adversely affecting local farmers’ income and food security in regions such as North Tongu municipality. To elucidate the transmission dynamics of the disease and safeguard both animal health and the community’s principal economic resource, we proposed a mathematical model employing non-linear differential equations that incorporate a vaccine compartment. This model enables the evaluation of how parameters such as vaccination and recovery rates influence the transmission of Q-fever in livestock. Our findings indicate that increased vaccination rates may diminish the population of susceptible livestock, hence reducing the possibility of outbreaks. In addition, a rapid recovery rate not only diminishes the duration of infectiousness in livestock but also enhances herd immunity, assisting in the containment of possible epidemics. The proposed model indicates that asR0exceeds 1, the infection level rises, displaying transcritical bifurcation behavior. However, this rise stabilizes and prevents uncontrolled spread. These findings emphasize the value of vaccination and recovery techniques in controlling and possibly eliminating Q-fever in cattle, which would ultimately help Ghanaian farming communities remain sustainable.
Intramammary infection of bovine H5N1 influenza virus in ferrets leads to transmission and mortality in suckling neonates
Authors: Baker PH , Moyer M , Bai Y , Stafford LS , Kelvin AA , Lee C , Kenney SP , Langel SN
Published: November 2024

The spread of H5N1 clade 2.3.4.4b in dairy herds raises concerns about zoonotic transmission due to the high viral load in milk, a key point of contact between livestock and humans. H5N1 clade 2.3.4.4b exhibits tropism for the mammary gland, with milk from infected cows containing high levels of viral RNA and infectious virus. The virus’s ability to infect the mammary gland suggests potential risks of transmission to offspring through breastfeeding. Here, we show that mammary gland infection with bovine H5N1 influenza in lactating ferrets transmits virus and disease to suckling kits. Viral RNA titers significantly increased in milk over time and remained high in mammary gland tissue. Suckling kits had significantly increased viral RNA in the oral and nasal cavity, as well as in feces. However, viral detection in the dam nasal cavities was delayed, with only minimal virus present in the oral cavity. Lung viral RNA levels were low in dams but high in a sampled suckling kit. Additionally, we detected the expression of the H5N1 receptor, α2,3 sialic acid, in mammary tissue from both ferrets and humans. These data demonstrate that H5N1 clade 2.3.4.4b infection in lactating dams leads to mastitis-related disease and transmits to suckling pups, resulting in 100% mortality among the neonates.
Nucleosome condensate and linker DNA alter chromatin folding pathways and rates
Authors: Qiu Yunrui , Liu Shuming , Lin Xingcheng , Unarta Ilona Christy , Huang Xuhui , Zhang Bin
Published: November 2024

Chromatin organization is essential for DNA packaging and gene regulation in eukaryotic genomes. While significant progresses have been made, the exact atomistic arrangement of nucleosomes remains controversial. Using a well-calibrated residue-level coarse-grained model and advanced dynamics modeling techniques, particularly the non-Markovian dynamics model, we map the free energy landscape of tetra-nucleosome systems, identify both metastable conformations and intermediate states in folding pathways, and quantify the folding kinetics. Our findings show that chromatin with 10nbase pairs (bp) DNA linker lengths favor zigzag fibril structures. However, longer linker lengths destabilize this conformation. When the linker length is 10n+ 5 bp, chromatin loses unique conformations, favoring a dynamic ensemble of structures resembling folding intermediates. Embedding the tetra-nucleosome in a nucleosome condensate similarly shifts stability towards folding intermediates as a result of the competition of inter-nucleosomal contacts. These results suggest that chromatin organization observedin vivoarises from the unfolding of fibril structures due to nucleosome crowding and linker length variation. This perspective aids in unifying experimental studies to develop atomistic models for chromatin.

Significance

Atomic structures of chromatin have become increasingly accessible, largely through cryo-EM techniques. Nonetheless, these approaches often face limitations in addressing how intrinsicin vivofactors influence chromatin organization. We present a structural characterization of chromatin under the combined effects of nucleosome condensate crowding and linker DNA length variation—two criticalin vivofeatures that have remained challenging to capture experimentally. This work leverages a novel application of non-Markovian dynamical modeling, providing accurate mapping of chromatin folding kinetics and pathways. Our findings support a hypothesis thatin vivochromatin organization arises from folding intermediates advancing toward a stable fibril configuration, potentially resolving longstanding questions surrounding chromatin atomic structure.
Activation of hypothalamic-pontine-spinal pathway promotes locomotor initiation and functional recovery after spinal cord injury in mice
Authors: Ji Chengyue , Zhang Yunfan , Lin Zeyu , Zhao Ziqi , Jiao Zhuolei , Zheng Zhiyuan , Shi Xiaoxue , Wang Xiaofei , Li Ziyu , Yu Shuisheng , Qu Yun , Wei Yaxuan , Zheng Bowen , Shi Hanyu , Wang Qifang , Sandoval Alfredo , Chen Bo , Yu Xiao , Xu Xiaohong , Poo Mu-ming , Chen Juxiang , Cai Weihua , Li Yi
Published: November 2024

The hypothalamus is critical for regulating behaviors essential for survival and locomotion, but how it integrates internal needs and transmits locomotion commands to the spinal cord (SC) remains unclear. We found that glutamatergic neurons in lateral hypothalamic area (LHA) are essential for regulating motivated locomotor activity. Using single-neuron projectome analysis, trans-synaptic tracing, and optogenetic manipulation, we showed that LHA facilitates motivated locomotion during food seeking via pontine oral part (PnO) projection neurons, rather than direct SC projections or indirect stress signaling via medial septum and diagonal band. Activating PnO-SC projection neurons also initiated locomotion. Importantly, LHA-PnO projection neurons were crucial for regulating locomotor recovery following mouse spinal cord injury (SCI). Closed-loop deep brain stimulation (DBS) of LHA via gating by motor cortex signals markedly promoted long-term restoration of hindlimb motor functions after SCI. Thus, we have identified a hypothalamic-pontine- spinal pathway and the stimulation paradigm for potential therapeutic intervention after SCI.
Somatosensory high frequency oscillations across the human central nervous system
Authors: Bailey Emma , Nierula Birgit , Stephani Tilman , Nikulin Vadim , Eippert Falk
Published: November 2024

Sensory information processing in the central nervous system (CNS) requires both post-synaptic responses and spiking activity, with human electroencephalography (EEG) research largely focused on the former. However, EEG data also contain high-frequency oscillations (HFOs), which have been linked to cortical spike bursts in animal models, thus providing a non-invasive macroscopic marker of population spiking in humans. Here, we go beyond cortical processing and demonstrate that it is possible to simultaneously record HFOs to somatosensory stimulation across the entire human CNS – from spinal cord over subcortical to cortical processing stages. Using multivariate spatial filtering approaches in two independent datasets, we identify replicable and generalizable HFOs across the CNS and obtain a detailed characterization of these signals at each processing level. Finally, we provide evidence at the between- and within-individual level that low and high frequency electrophysiological responses represent at least partly independent information across the CNS. Taken together, our approach offers the first evidence that it is possible to detect and characterise HFOs simultaneously across the CNS, providing a unique non-invasive and multi-level window into human neurophysiology in health and disease.
Oropouche virus infects human placenta explants and trophoblast organoids
Authors: Megli Christina , Zack Rebecca K , McGaughey Jackson , Hoehl Ryan M , Snisky Taylor , Hartman Amy L , McMillen Cynthia
Published: November 2024

Clinical and epidemiologic evidence from the recent outbreak of Oropouche virus (OROV) has demonstrated increased severity in clinical disease and adverse pregnancy outcomes including miscarriage, stillbirth and neonatal demise. Serological evidence suggests vertical transmission of OROV may be responsible. OROV has not been studied in the context of pregnancy and has unknown ability to infect the relevant tissues of the maternal-fetal interface, which have anti-viral properties; therefore,the mechanisms of vertical transmission are unknown. We used polarized human trophoblast stem cell organoids and human placenta explants to demonstrate that OROV (BeAn19991) infects and replicates in human tissues of the maternal-fetal interface including chorionic villi and the microbial-resistant cell, syncytiotrophoblast. Viral replication is robust within the first 24 hours post infection, and tissues from earlier gestations may be more susceptible to infection. These data indicate tissues at the maternal-fetal interace are susceptible to OROV infection and may facilitate vertical transmission, leading to adverse pregnancy outcomes.
Modality-Specific and Amodal Language Processing by Single Neurons
Authors: Lakretz Yair , Friedmann Naama , King Jean-Rémi , Mankin Emily , Rangel Anthony , Tankus Ariel , Dehaene Stanislas , Fried Itzhak
Published: November 2024

According to psycholinguistic theories, during language processing, spoken and written words are first encoded along independent phonological and orthographic dimensions, then enter into modality-independent syntactic and semantic codes. Non-invasive brain imaging has isolated several cortical regions putatively associated with those processing stages, but lacks the resolution to identify the corresponding neural codes. Here, we describe the firing responses of over 1000 neurons, and mesoscale field potentials from over 1400 microwires and 1500 iEEG contacts in 21 awake neurosurgical patients with implanted electrodes during written and spoken sentence comprehension. Using forward modeling of temporal receptive fields, we determined which sensory or abstract dimensions are encoded. We observed a double dissociation between superior temporal neurons sensitive to phonemes and phonological features and previously unreported ventral occipito-temporal neurons sensitive to letters and orthographic features. We also discovered novel neurons, primarily located in middle temporal and inferior frontal areas, which are modality-independent and show responsiveness to higher linguistic features. Overall, these findings show how language processing can be linked to neural dynamics, across multiple brain regions at various resolutions and down to the level of single neurons.
Dynamic cytoplasmic fluidity during morphogenesis in a human fungal pathogen
Authors: Serrano A. , Puerner C. , Plumb E. , Chevalier L. , Elferich J. , Sinn L.R. , Grigorieff N. , Ralser M. , Delarue M. , Bassilana M. , Arkowitz R.A.
Published: November 2024

The molecular crowding of the cytoplasm impacts a range of cellular processes. Using a fluorescent microrheological probe (GEMs), we observed a striking decrease in molecular crowding during the yeast to filamentous growth transition in the human fungal pathogenCandida albicans. This decrease in crowding is due to a decrease in ribosome concentration that results in part from an inhibition of ribosome biogenesis, combined with an increase in cytoplasmic volume; leading to a dilution of the major cytoplasmic crowder. Moreover, our results suggest that inhibition of ribosome biogenesis is a trigger forC. albicansmorphogenesis.
Arv1 interacts with and regulates the first step of GPI biosynthesis inCandida albicans
Authors: Bharati Monika , Saini Harshita , Thakran Neha , Kumar Yatin , Yadav Usha , Shefali Shailja , Saun Sunyna , Anzar Aaisha , Komath Sneha Sudha
Published: November 2024

The ubiquitousARV1gene shows significant functional conservation across eukaryotes. In humans, it is implicated in early onset epileptic encephalopathy. Evidence suggests that the phenotypes manifested in affected patients are probably due to the deficiency in expression of cell surface GPI anchored proteins.S. cerevisiaeArv1 is proposed to be the elusive GPI flippase that delivers the GPI intermediate from the cytoplasmic face to the luminal side of the ER for further elaboration by the first mannosyltransferase of the pathway. Human and fungalARV1complementS. cerevisiae ARV1. Overexpressing some of the GPI-N-acetylglucosamine transferase (GPI-GnT) subunits rescues the null strain ofS. cerevisiae ARV1. In mammals and inT. bruceiArv1 co-immunoprecipitates with one or more subunits of the GPI-GnT. Based on these reports we hypothesized a cross-talk forARV1with the GPI biosynthetic pathway in the human pathogenic fungus,C. albicans. Using super resolution radial fluctuation (SRRF) analysis for co-localization, co-immunoprecipitation assays, and acceptor-photobleaching Förster resonance energy transfer (FRET) studies, we show thatC. albicansArv1 physically interacts with the GPI-GnT. It also transcriptionally regulates the expression of the GPI-GnT genes to control the GPI biosynthetic pathway via its very first step. Overexpression of one of the GPI-GnT subunits, CaGpi19, inC. albicans ARV1null strain rescues its cold-sensitive growth, azole sensitivity, cell wall phenotype and GPI-GnT activity. Thus, our results suggest extensive interactions between Arv1 and GPI biosynthesis inC. albicans.
Intraspecific Diversity ofStaphylococcus aureusPopulations Isolated from Cystic Fibrosis Respiratory Infections
Authors: Alexander Ashley M. , Loo Hui Qi , Askew Lauren , Raghuram Vishnu , Read Timothy D. , Goldberg Joanna B.
Published: November 2024

Chronic bacterial infections are often polymicrobial, comprising multiple bacterial species or variants of the same species. Because chronic infections may last for decades, they have the potential to generate high levels of intraspecific variation through within-host diversification over time, and the potential for superinfections to occur through the introduction of multiple pathogen populations to the ongoing infection. Traditional methods for identifying infective agents generally involve isolating one single colony from a given sample, usually after selecting for a specific pathogen or antibiotic resistance profile. Isolating a recognized virulent or difficult to treat pathogen is an important part of informing clinical treatment and correlative research; however, these reductive methods alone, do not provide researchers or healthcare providers with the potentially important perspective on the true pathogen population structure and dynamics over time. To begin to address this limitation, in this study, we compare findings onStaphylococcus aureussingle colonies versus and pools of colonies taken from fresh sputum samples from three patients with cystic fibrosis to isolates collected from the same sputum samples and processed by the clinical microbiology laboratory. Phenotypic and genotypic analysis of isolatedS. aureuspopulations revealed coexisting lineages in two of three sputum samples as well as population structures that were not reflected in the single colony isolates. Altogether, our observations presented here demonstrate that clinically relevant diversity can be missed with standard sampling methods when assessing chronic infections. More broadly, this work outlines the potential impact that comprehensive population-level sampling may have for both research efforts and more effective treatment practices.

Data Summary

The authors confirm all supporting data, code and protocols have been provided within the article.
Biocatalytic Tetrapeptide Macrocyclization by Cryptic Penicillin-binding Protein-type Thioesterases
Authors: Jeannette Paisley L. , Budimir Zachary L. , Johnson Lucas O. , Parkinson Elizabeth I.
Published: November 2024

Cyclic tetrapeptides (CTPs) are a diverse class of natural products with a broad range of biological activities. However, they are extremely challenging to synthesize due to the ring strain associated with their small ring size. While chemical methods have been developed to access CTPs, they generally require the presence of certain amino acids, limiting their substrate scopes. Herein, we report the first bioinformatics guided discovery of a thioesterase from a cryptic biosynthetic gene cluster for peptide cyclization. Specifically, we hypothesized that predicted Penicillin-binding type thioesterases (PBP-TEs) from cryptic nonribosomal peptide synthetase gene clusters containing four adenylation domains would catalyze tetrapeptide cyclization. We found that one of the predicted PBP-TEs, WP516, efficiently cyclizes a wide variety of tetrapeptide substrates. To date, it is only the second stand-alone enzyme capable of cyclizing tetrapeptides, and its substrate scope greatly surpasses that of the only other reported tetrapeptide cyclase Ulm16. AlphaFold modeling and covalent docking were used to rationalize the broad substrate scope of WP516 in comparison to other PBP-TEs. Overall, the bioinformatics guided workflow outlined in this paper, and the discovery of WP516, represent promising tools for the biocatalytic production of head-to-tail CTPs, as well as a more general strategy for discovery of enzymes for peptide cyclization.
Combining NeuroPainting with transcriptomics reveals cell-type-specific morphological and molecular signatures of the 22q11.2 deletion
Authors: Tegtmeyer Matthew , Liyanage Dhara , Han Yu , Hebert Kathryn B. , Pei Ruifan , Way Gregory P. , Ryder Pearl V. , Hawes Derek , Tromans-Coia Callum , Cimini Beth A. , Carpenter Anne E. , Singh Shantanu , Nehme Ralda
Published: November 2024

Neuropsychiatric conditions pose substantial challenges for therapeutic development due to their complex and poorly understood underlying mechanisms. High-throughput, unbiased phenotypic assays present a promising path for advancing therapeutic discovery, especially within disease-relevant neural tissues. Here, we introduce NeuroPainting, a novel adaptation of the Cell Painting assay, optimized for high-dimensional morphological phenotyping of neural cell types, including neurons, neuronal progenitor cells, and astrocytes derived from human stem cells. Using NeuroPainting, we quantified cell structure and organelle behavior across various brain cell types, creating a public dataset of over 4,000 cellular traits. This extensive dataset not only sets a new benchmark for phenotypic screening in neuropsychiatric research but also serves as a gold standard for the research community, enabling comparisons and validation of results. We then applied NeuroPainting to identify morphological signatures associated with the 22q11.2 deletion, a major genetic risk factor for schizophrenia. We observed profound cell-type-specific effects of the 22q11.2 deletion, with significant alterations in mitochondrial structure, endoplasmic reticulum organization, and cytoskeletal dynamics, particularly in astrocytes. Transcriptomic analysis revealed reduced expression of cell adhesion genes in 22q11.2 deletion astrocytes, consistent with recent post-mortem findings. Integrating the RNA sequencing data and morphological profiles uncovered a novel biological link between altered expression of specific cell adhesion molecules and observed changes in mitochondrial morphology in 22q11.2 deletion astrocytes. These findings underscore the power of combined phenomic and transcriptomic analyses to reveal mechanistic insights associated with human genetic variants of neuropsychiatric conditions.
Damped accumulation-based volatility multivariable grey prediction power model and its application
Authors: Li Ye , Wang Chengyun , Liu Junjuan
Published: November 2024

Purpose

In this paper, a new grey Cosine New Structured Grey Model (CNSGM(1,N)) prediction power model is constructed for the small-sample modeling and prediction problem with complex nonlinearity and insignificant volatility.

Design/methodology/approach

Firstly, the weight of some relevant factors is determined by the grey comprehensive correlation degree, and the data are preprocessed. Secondly, according to the principle of “new information priority” and the volatility characteristics of the sequence growth rate, the ideas of damping accumulation power index and trigonometric function are integrated into the New Structured Grey Model (NSGM(1,N)) model. Finally, the non-structural parameters are optimized by the genetic algorithm, and the structural parameters are calculated by the least squares method, so a new CNSGM(1,N) predictive power model is constructed.

Findings

Under the principle of “new information priority,” through the combination with the genetic algorithm, the traditional first-order accumulation generation is transformed into damping accumulation generation, and the trigonometric function with the idea of integer is introduced to further simulate the phenomenon that the volatility is not obvious in the real system. It is applied to the simulation and prediction of China’s carbon dioxide emissions, and compared with other comparison models; it is found that the model has a better simulation effect and excellent performance.

Originality/value

The main contribution of this paper is to propose a new grey CNSGM(1,N) prediction power model, which can not only be applied to complex nonlinear cases but also reflect the differences between the old and new data and can reflect the volatility characteristics of the characteristic behavior sequence of the system.
When patriarchy and individualism collide: experiences of women entrepreneurial leaders
Authors: Patterson Nicola , Mavin Sharon
Published: November 2024

Purpose

Through a feminist lens, the study explores women’s experiences of entrepreneurial leadership in the UK and how the women manage competing and contrary patriarchal and individualism discourses and associated discursive paradox.

Design/methodology/approach

This study follows social constructionism and Feminist Standpoint Research approach, providing space for women to voice and contextualise lived experiences from multiple standpoints. The study comprises five cases of women entrepreneurs in IT, law, construction, beauty and childcare, using a two-stage semi-structured interview process analysed through discourse analysis.

Findings

This study provides new insights into the entrenched patriarchal socio-cultural context for women entrepreneurial leaders in the UK. The competing discourses provoke a discursive paradox, which dominates and oppresses women. This is managed through a process of discursive blending, blurring and merging contrary discursive expectations. The women use the individualism discourse to obscure patriarchy’s domination and as a resource to resist patriarchal gender power relations. To blend the discourses, the women use particular tactics: engaging in patriarchal bargains, such as “dressing not to impress”; can sidestep and manoeuvre these bargains and can utilise “patriarchal advantages”, turning gender oppression into benefits by “working it positively”.

Originality/value

This study addresses the lack of research interrogating patriarchy in the Global North and the absence of understandings of how women entrepreneurial leaders manage the competing and contrary discourses of patriarchy and individualism, which actively shape their experiences. The study illuminates the significance and increasing requirement for feminism to disrupt the ever-increasing power of patriarchy in entrepreneurship.
Bank market power and its determinants: evidence from listed conventional commercial banks from Indonesia
Authors: Das Suman , Pati Ambika Prasad
Published: November 2024

Purpose

Over the past three decades, financial deregulation and various reforms have significantly transformed the competitive environment for banks in Indonesia. These changes have introduced new challenges for banks to retain their market power and ensure their survival. In light of this, the article aims to assess the current levels of market power held by Indonesian banks and explore the factors that influence it.

Design/methodology/approach

The paper measured the degree of market power and identified its impacting factors for 22 listed commercial banks using the Adjusted Lerner Index (ALI) and appropriate regression technique over a period of 2011–2023.

Findings

The empirical findings reveal that banks in Indonesia enjoy high market power, and factors such as capitalization, diversification, operational inefficiency, asset quality and GDP growth rate significantly impact banks’ market power. Additionally, the findings contradict the structure-conduct-performance paradigm, which advocates that a concentrated banking system impairs competition.

Research limitations/implications

The study suggests that regulatory authorities should closely monitor the market power levels and promote strategies to enhance competition within the banking sector. Additionally, banks should prioritize implementing measures to reduce operational costs and improve the quality of assets.

Originality/value

This research represents one of the early attempts to gauge the market power of publicly listed conventional commercial banks in Indonesia by employing the Adjusted Lerner Index. Additionally, it introduces “technology adoption” as a novel variable to the analysis alongside other established variables.
Residential student housing mobility and supportive design: a cross-sectional assessment of off-campus all-inclusive university student hostels in Ghana
Authors: Appau Miller Williams , Attakora-Amaniampong Elvis , Quansah Joseph Yaw Dwamena
Published: November 2024

Purpose

This study aims to examine the relationship between supportive design (SD) and residential mobility of students with disabilities (SWD) in off-campus student hostels in Ghana.

Design/methodology/approach

Quantitative research techniques were adopted. A sample of 243 SWD living in 190 University Student Housing were selected. Based on the SD indicators, the partial least square structural equation model was used to explore its effects on residential mobility in SWD living in university housing.

Findings

Findings indicate that a sense of control and positive distraction significantly influence residential mobility to a greater extent than social support design. While the sense of control emerged as a primary predictor of residential mobility, no direct relationships were observed between the sense of control, positive distraction and social support. Although social support did not exhibit significant direct effects, its potential relevance to residential mobility cannot be dismissed.

Practical implications

The enhancement and compliance of a sense of control and positive distraction SD in the common areas in student housing will reduce SWD residential mobility and increase investors’ profitability. Positive social support designs are critical to predicting percentage change in residential mobility in off-campus student housing in Ghana.

Originality/value

SD is a theory largely used in health-care buildings. The observation of no relationship between a sense of control and positive distraction, and social support aspects of SD in university housing in this study significantly differs from the inverse relationship that exists between SD in hospitals, especially in the developing world, is a theoretical contribution.
Compromised CD8+ T cell immunity in the aged brain increases severity of neurotropic coronavirus infection and postinfectious cognitive impairment
Authors: Reagin Katie L. , Lee Rae‐Ling , Williams Luke A. , Cocciolone Loren , Funk Kristen E.
Published: November 2024

Advanced age increases the risk of severe disease from SARS‐CoV‐2 infection, as well as incidence of long COVID and SARS‐CoV‐2 reinfection. We hypothesized that perturbations in the aged antiviral CD8+ T cell response predisposes elderly individuals to severe coronavirus infection, re‐infection, and postinfectious cognitive sequelae. Using MHV‐A59 as a murine model of respiratory coronavirus, we found that aging increased CNS infection and lethality to MHV infection. This was coupled with increased CD8+ T cells within the aged CNS but reduced antigen specificity. Aged animals also displayed a decreased proportion of CD103+ resident memory cells (TRM), which correlated with increased severity of secondary viral challenge. Using a reciprocal adoptive transfer paradigm, data show that not only were fewer aged CD8+ T cells retained within the adult brain post‐infection, but also that adult CD8+ cells expressed lower levels of TRM marker CD103 when in the aged microenvironment. Furthermore, aged animals demonstrated spatial learning impairment following MHV infection, which worsened in both aged and adult animals following secondary viral challenge. Spatial learning impairment was accompanied by increased TUNEL positivity in hippocampal neurons, suggestive of neuronal apoptosis. Additionally, primary cell coculture showed that activated CD8+ T cells induced TUNEL positivity in neurons, independent of antigen‐specificity. Altogether, these results show that non‐antigen specific CD8+ T cells are recruited to the aged brain and cause broad neuronal death without establishing a TRM phenotype that confers lasting protection against a secondary infection.
An endometrial thickness of <12 mm does not exclude malignancy or pre‐malignancy in cases of abnormal uterine bleeding: An observational study
Authors: Song Sae Jin , Miles Carina , Ponnampalam Sathana , Sowden Katherine , Shafique Asima , Oyston Charlotte
Published: November 2024

Background

It remains unclear if there is an endometrial thickness (ET) threshold below which malignancy can be excluded. Guidance on whether endometrial biopsy is needed based on ET varies among regions in New Zealand and there is a desire to standardise guidance nationwide. This study evaluates the potential impact of limiting endometrial biopsy in pre‐menopausal persons with abnormal uterine bleeding (AUB) to those with an ET of less than 12 mm.

Aims

To determine the number of pre‐menopausal patients with AUB with an ET of less than 12 mm undergoing endometrial sampling annually and assess the prevalence of pathology among these patients.

Materials and Methods

Endometrial samples from patients aged 18–50 years processed at a tertiary hospital between 15/06/2022 and 13/06/2023 were identified via a pathology lab search. Clinical, radiologic, and pathological data were obtained by case note review for those with AUB whose ET was less than 12 mm.

Results

Of 1271 endometrial samples, 355 patients met the eligibility criteria, and 2.2% of these were cancerous (three cases) or pre‐malignant (five cases).

Conclusions

If sampling thresholds would change to not perform biopsies in those with an ET of less than 12 mm, eight cases of treatable disease would be missed in pre‐menopausal people. This represents 13.6% of all endometrial cancers diagnosed in pre‐menopausal people in the same time period. There is no ET cut‐off to reliably exclude high‐risk pathology and endometrial sampling should be performed in all cases of AUB with risk factors.
Kinetics of the inhibition and recovery of spermatogenesis induced by treatment with WIN 18,446, a male contraceptive, in mice
Authors: Paik Jisun , Snyder Jessica M. , Kim Andy , Haenisch Michael , Fogassy Kevin , Amory John K.
Published: November 2024

Background

Retinoic acid (RA) is essential for spermatogenesis. Genetic deletion of the retinoic acid synthesizing enzymes, Aldh1a1/1a2, in the testes causes infertility in mice. An inhibitor of the ALDH1A1/1A2 enzymes, WIN 18,446 reversibly inhibit spermatogenesis and is a promising approach to male contraception. Previously we reported that a 4‐week treatment of WIN 18,446 inhibits spermatogenesis and 9‐week recovery from treatment normalized fertility of treated mice. However, the precise kinetics of this process has not been studied.

Objectives

To extend our knowledge of kinetics of ALDH1A inhibition, we studied the changes in the seminiferous epithelium and retinoic acid synthesis capacity of the testes during 4 weeks of WIN 18,446 treatment and during 9 weeks of recovery.

Materials and methods

Male mice were fed a diet containing WIN 18,446 for 4 weeks followed by a normal diet for up to 8 weeks. Frequently, during the treatment and recovery period, five mice were euthanized, and testes were analyzed for testicular histology and retinoic acid synthesis capacity and compared with controls.

Results

Testes weights progressively decreased, and the seminiferous epithelium deteriorated over the time with WIN 18,446 treatment and returned to normal after 8 weeks. Retinoic acid synthesis capacity was significantly inhibited 3 days after the WIN 18,446 treatment and recovered after 7 days of no treatment. After 4 weeks of treatment, complete blockage of spermatogenesis with only spermatogonia and Sertoli cells was observed. The RA biosynthetic capacity of the testes was significantly reduced before the disruption of spermatogenesis was observed and recovered prior to the reinitiation of spermatogonial differentiation.

Conclusions

Effects of ALDH1A inhibition on spermatogenesis are reversible. Our observation that strong inhibition of ALDH1A disrupts the seminiferous epithelium prior to the completion of a full cycle of spermatogenesis suggests that episodic inhibition of ALDH1A may function as a male contraceptive.
Primary resistance to nivolumab plus ipilimumab therapy affects second‐line treatment outcomes in patients with metastatic renal cell carcinoma
Authors: Mori Kanami , Numakura Kazuyuki , Matsushita Yuto , Kojima Takahiro , Osawa Takahiro , Sazuka Tomokazu , Hatakeyama Shingo , Goto Keisuke , Yamana Kazutoshi , Kandori Shuya , Kimura Takahiro , Nishiyama Naotaka , Bando Yukari , Fujita Kazutoshi , Ueda Kosuke , Tanaka Hajime , Tomida Ryotaro , Kurahashi Toshifumi , Kitamura Hiroshi , Miyake Hideaki , Habuchi Tomonori
Published: November 2024

Nivolumab plus ipilimumab (NIVO+IPI) has a long‐term response rate of 30% for patients with metastatic renal cell carcinoma (mRCC). However, 20% of patients develop primary resistant disease (PRD) to NIVO+IPI and show poor survival outcomes. In this study, we aimed to evaluate the effect of PRD as a second‐line treatment in patients with mRCC. The data used in this multi‐institutional, retrospective cohort were collected between August 2015 and January 2023. In total, 189 patients with mRCC were treated with NIVO+IPI and then with a vascular endothelial growth factor receptor‐tyrosine kinase inhibitor. Associations between PRD and progression‐free survival of second‐line treatment (PFS), progression‐free survival 2 (PFS2), and overall survival (OS) were analyzed. The median age at NIVO+IPI initiation was 67 years in the male‐dominant population (n = 140, 74.1%), and most patients had clear cell histology (n = 140, 74.1%). PRD was recorded in 42 (22.2%) of 189 patients during NIVO+IPI therapy. Patients who experienced PRD showed poor PFS (hazard ratio [HR], 1.788; 95% confidence interval [CI], 1.176–2.718; p = 0.007), PFS2 (HR, 4.127; 95% CI, 2.649–6.431; p < 0.001), and OS (HR, 3.330; 95% CI, 2.040–5.437; p < 0.001). Before starting second‐line therapy, patients with PRD tended to have a poor performance status compared with non‐PRD patients and a higher IMDC risk. Second‐line drug therapy was not associated with treatment outcomes in patients with PRD. PRD in patients with mRCC receiving NIVO+IPI as first‐line treatment was associated with poor clinical course, even with second‐line therapy.
The cumulative, timing‐specific, and enduring associations between student–teacher relationships and early elementary outcomes
Authors: Ansari Arya , Buckley M. Nicole , Woods S. Colby , Gottfried Michael
Published: November 2024

Using data from the Early Childhood Longitudinal Study—Kindergarten Class of 2011 (n = 14,370; 51% Male; 51% White; 14% Black; 25% Hispanic; 4% Asian; and 6% Other), this study examined the cumulative, timing‐specific, and enduring associations between student–teacher relationships in the United States and a broad range of student outcomes. Student–teacher conflict and closeness were consistently associated with outcomes between kindergarten and third grade, both contemporaneously and over time. The main exception was for student absenteeism, where there were less consistent associations with student–teacher conflict. Cumulative models underscore the significance of the overall experiences of high‐quality relationships over time. Despite little evidence of variability, girls fared less well socially due to more conflictual and less close relationships with their teachers than boys.
Procreative Prerogatives and Climate Change
Authors: Pinkert Felix , Sticker Martin
Published: November 2024

One of the most provocative claims in current climate ethics is that we ought to have fewer children, because procreation brings new people into existence and thereby causes large amounts of additional greenhouse gas emissions. The public debate about procreation and climate change is frequently framed in terms of the question of whether people may still have any children at all. Yet in the academic debate it is a common position that, despite the large carbon impact of procreation, it is still permissible to have one or two children per couple, if having children is needed for the parents' lives to go well. In this article, we propose a defence and a principled formulation of this procreative prerogative: agents are permitted to procreate if the goods that procreation provides are essential to their lives going well and cannot be replaced by other goods, nor be realized by lower‐emissions alternatives. This principle implies that procreative decisions require case‐by‐case assessment in which agents' self‐reflection, individual circumstances, and social context play a significant role.
First Record of Zygothrica Wiedemann, 1830 (Diptera: Drosophilidae) Species Infesting Shiitake Mushrooms (Lentinula edodes (Berk.) Pegler) on a Log Farm in the Atlantic Forest, Brazil
Authors: Mendes Mayara Ferreira , e Schühli Guilherme Schnell , Vieira Ricardo Luiz , Telles Marcos Henrique Frech , Gottschalk Marco Silva , Lamas Carlos José Einicker
Published: November 2024

We document the first observation of a severe shiitake mushroom infestation by several native Neotropical Zygothrica species (Drosophilidae, Diptera) under natural conditions. This infestation occurred in an agroforestry model, a medium‐scale, log‐based shiitake mushroom production culture. The mushroom farm is located in the Campo Largo municipality in the state of Paraná, Brazil, within the Atlantic Forest Biome. Adult flies, both males and females, were collected in December 2023. This study represents the first collection of Zygothrica parapoeyi Burla, 1956, Z. hypandriata Burla, 1956, Z. ptilialis Burla, 1956 and Z. paraptilialis Burla, 1956 from shiitake log culture. This record underscores the importance of field studies on macroscopic fungal infestations in Brazilian forests, particularly those within agroforestry systems, and their potential economic impacts. In this context, we also propose some preliminary preventive management actions.