bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring the Mosaic-like Tissue Architecture of Kidney Diseases Using Relation Equivariant Graph Neural Networks on Spatially Resolved Transcriptomics
Authors: Raina Mauminah , Cheng Hao , Suryadevara Hari Naga Sai Kiran , Stransfield Treyden , Xu Dong , Ma Qin , Eadon Michael T. , Wang Juexin
Published: November 2023

Emerging spatially resolved transcriptomics (SRT) technologies provide unprecedented opportunities to discover the spatial patterns of gene expression at the cellular or tissue levels. Currently, most existing computational tools on SRT are designed and tested on the ribbon-like brain cortex. Their present expressive power often makes it challenging to identify highly heterogeneous mosaic-like tissue architectures, such as tissues from kidney diseases. This demands heightened precision in discerning the cellular and morphological changes within renal tubules and their interstitial niches. We present an empowered graph deep learning framework, REGNN (Relation Equivariant Graph Neural Networks), for SRT data analyses on heterogeneous tissue structures. To increase expressive power in the SRT lattice using graph modeling, the proposed REGNN integrates equivariance to handle the rotational and translational symmetries of the spatial space, and Positional Encoding (PE) to identify and strengthen the relative spatial relations of the nodes uniformly distributed in the lattice. Our study finds that REGNN outperforms existing computational tools in identifying inherent mosaic-like heterogenous tissue architectures in kidney samples sourced from different kidney diseases using the 10X Visium platform. In case studies on acute kidney injury and chronic kidney diseases, the results identified by REGNN are also validated by experienced nephrology physicians. This proposed framework explores the expression patterns of highly heterogeneous tissues with an enhanced graph deep learning model, and paves the way to pinpoint underlying pathological mechanisms that contribute to the progression of complex diseases. REGNN is publicly available athttps://github.com/Mraina99/REGNN.
SpatialCells: Automated Profiling of Tumor Microenvironments with Spatially Resolved Multiplexed Single-Cell Data
Authors: Wan Guihong , Maliga Zoltan , Yan Boshen , Vallius Tuulia , Shi Yingxiao , Khattab Sara , Chang Crystal , Nirmal Ajit J. , Yu Kun-Hsing , Liu David , Lian Christine G. , DeSimone Mia S. , Sorger Peter K. , Semenov Yevgeniy R.
Published: November 2023

Background

Cancer is a complex cellular ecosystem where malignant cells coexist and interact with immune, stromal, and other cells within the tumor microenvironment. Recent technological advancements in spatially resolved multiplexed imaging at single-cell resolution have led to the generation of large-scale and high-dimensional datasets from biological specimens. This underscores the necessity for automated methodologies that can effectively characterize the molecular, cellular, and spatial properties of tumor microenvironments for various malignancies.

Results

This study introduces SpatialCells, an open-source software package designed for region-based exploratory analysis and comprehensive characterization of tumor microenvironments using multiplexed single-cell data.

Conclusions

SpatialCells efficiently streamlines the automated extraction of features from multiplexed single-cell data and can process samples containing millions of cells. Thus, SpatialCells facilitates subsequent association analyses and machine learning predictions, making it an essential tool in advancing our understanding of tumor growth, invasion, and metastasis.

Availability of code and materials

https://github.com/SemenovLab/SpatialCells.
Sequential Image Classification of Human-Robot Walking Environments using Temporal Neural Networks
Authors: Ivanyuk-Skulskiy Bogdan , Kurbis Andrew Garrett , Mihailidis Alex , Laschowski Brokoslaw
Published: November 2023

Robotic prosthetic legs and exoskeletons require real-time and accurate estimation of the walking environment for smooth transitions between different locomotion mode controllers. However, previous studies have mainly been limited to static image classification, therein ignoring the temporal dynamics of human-robot locomotion. Motivated by these limitations, here we developed several state-of-the-art temporal convolutional neural networks (CNNs) to compare the performances between static vs. sequential image classification of real-world walking environments (i.e., level-ground terrain, incline stairs, and transitions to and from stairs). Using our large-scale image dataset, we trained a number of encoder networks such as VGG, MobileNetV2, ViT, and MobileViT, each coupled with a temporal long short-term memory (LSTM) backbone. We also trained MoViNet, a new video classification model designed for mobile and embedded devices, to further compare the performances between 2D and 3D temporal deep learning models. Our 3D network outperformed all the hybrid 2D encoders with LSTM backbones and the 2D CNN baseline model in terms of classification accuracy, suggesting that network architecture can play an important role in performance. However, although our 3D neural network achieved the highest classification accuracy, it had disproportionally higher computational and memory storage requirements, which can be disadvantageous for real-time control of robotic leg prostheses and exoskeletons with limited onboard resources.
Integration of metataxonomic datasets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables
Authors: Junker Romane , Valence Florence , Mistou Michel-Yves , Chaillou Stéphane , Chiapello Hélène
Published: November 2023

The management of food fermentation is still largely based on empirical knowledge, as the dynamics of microbial communities and the underlying metabolic networks that produce safe and nutritious products remain beyond our understanding. Although these closed ecosystems contain relatively few taxa, they have not yet been thoroughly characterized with respect to how their microbial communities interact and dynamically evolve. However, with the increased availability of metataxonomic datasets on different fermented vegetables, it is now possible to gain a comprehensive understanding of the microbial relationships that structure plant fermentation.

In this study, we present a bioinformatics approach that integrates public metataxonomic 16S datasets targeting fermented vegetables. Specifically, we developed a method for exploring, comparing, and combining public 16S datasets in order to perform meta-analyses of microbiota. The workflow includes steps for searching and selecting public time-series datasets and constructing association networks of amplicon sequence variants (ASVs) based on co-abundance metrics. Networks for individual datasets are then integrated into a core network of significant associations. Microbial communities are identified based on the comparison and clustering of ASV networks using the “stochastic block model” method. When we applied this method to 10 public datasets (including a total of 931 samples), we found that it was able to shed light on the dynamics of vegetable fermentation by characterizing the processes of community succession among different bacterial assemblages.

IMPORTANCE

Within the growing body of research on the bacterial communities involved in the fermentation of vegetables, there is particular interest in discovering the species or consortia that drive different fermentation steps. This integrative analysis demonstrates that the reuse and integration of public microbiome datasets can provide new insights into a little-known biotope. Our most important finding is the recurrent but transient appearance, at the beginning of vegetable fermentation, of ASVs belonging toEnterobacteralesand their associations with ASVs belonging toLactobacillales. These findings could be applied in the design of new fermented products.
Multiomic analysis reveals cellular, transcriptomic and epigenetic changes in intestinal pouches of ulcerative colitis patients
Authors: Zhao Yu , Zhou Ran , Xie Bingqing , Liu Cambrian Y , Kalski Martin , Cham Candace M , Jiang Zhiwei , Koval Jason , Weber Christopher R , Rubin David T , Sogin Mitch , Crosson Sean , Chen Mengjie , Huang Jun , Fiebig Aretha , Dalal Sushila , Chang Eugene B , Basu Anindita , Pott Sebastian
Published: November 2023

Total proctocolectomy with ileal pouch anal anastomosis is the standard of care for patients with severe ulcerative colitis. We generated a cell-type-resolved transcriptional and epigenetic atlas of ileal pouches using scRNA-seq and scATAC-seq data from paired biopsy samples of the ileal pouch and the ileal segment above the pouch (pre-pouch) from patients (male=4, female=2), and paired biopsies of the terminal ileum and ascending colon from healthy individuals (male=3, female=3) serving as reference. Our study finds previously uncharacterized populations of absorptive and secretory epithelial cells within the pouch but not the pre-pouch. These pouch- specific enterocytes express a subset of colon-specific genes, includingCEACAM5andCD24. However, compared to normal colonocytes, expression of these genes is lower, and these enterocytes also express inflammatory and secretory genes while maintaining expression of some ileal-specific genes. This cell-type-resolved transcriptomic and epigenetic atlas of the ileal pouch establishes a reference for investigating pouch physiology and pathology.
Correlation between umbilical cord torsion and Doppler parameters of umbilical artery: a single-center retrospective case-control study
Authors: Li Yuan , Zhang Dirong , Shi Yu
Published: November 2023

Objective

To explore the correlation between umbilical cord torsion and the changes of umbilical artery Doppler parameters, to provide valuable information for prenatal ultrasound screening of umbilical cord torsion, and to explore the possible mechanism of umbilical artery Doppler parameters changes during umbilical cord torsion. Method:The subjects were 962 pregnant women who were discharged from our hospital from January 2015 to November 2021 and were eligible for inclusion (415 in the case group and 547 in the control group). The measurement data of umbilical artery Doppler parameters (PSV, S/D, RI, PI) were collected from 21 to 40 weeks of gestation, and the differences among the above parameters were statistically analyzed.

Results

The peak systolic velocity (PSV) of umbilical artery is positively correlated with gestational age, while the Doppler resistance parameters (S/D, RI, PI) of umbilical artery are negatively correlated with gestational age. The mean values of umbilical artery Doppler parameters (PSV, S/D, RI, PI) in the case group were significantly lower than those in the control group of the same pregnancy age (P < 0.05).

Conclusion

The decrease of Doppler parameters of umbilical artery in late pregnancy is significantly related to umbilical cord torsion, which may be a clue for prenatal ultrasound screening of umbilical cord torsion. The Doppler parameters of umbilical artery during umbilical cord torsion are consistent with the basic principle of Doppler parameters change after vascular stenosis in other parts of the human body. It is necessary to conduct multicenter prospective study in the future.
Genomic Insights into the Shared and Distinct Genetic Architecture of Cognitive Function and Schizophrenia
Authors: Wootton Olivia , Shadrin Alexey A. , Bjella Thomas , Smeland Olav B. , van der Meer Dennis , Frei Oleksandr , O’Connell Kevin S , Ueland Torill , Andreassen Ole A. , Stein Dan J. , Dalvie Shareefa
Published: November 2023

Cognitive impairment is a major determinant of functional outcomes in schizophrenia, and efforts to understand the biological basis of cognitive dysfunction in the disorder are ongoing. Previous studies have suggested genetic overlap between global cognitive ability and schizophrenia, but further work is needed to delineate the shared genetic architecture. Here, we apply genomic structural equation modelling to identify latent cognitive factors capturing genetic liabilities to 12 cognitive traits measured in the UK Biobank (UKB). We explore the overlap between latent cognitive factors, schizophrenia, and schizophrenia symptom dimensions using a complementary set of statistical approaches, applied to data from the latest schizophrenia genome-wide association study (Ncase = 53,386, Ncontrol = 77,258) and the Thematically Organised Psychosis study (Ncase = 306, Ncontrol = 1060). We identified three broad factors (visuo-spatial, verbal analytic and decision/reaction time) that underly the genetic correlations between the UKB cognitive tests. Global genetic correlations showed a significant but moderate negative genetic correlation between each cognitive factor and schizophrenia. Local genetic correlations implicated unique genomic regions underlying the overlap between schizophrenia and each cognitive factor. We found evidence of substantial polygenic overlap between each cognitive factor and schizophrenia but show that most loci shared between the latent cognitive factors and schizophrenia have unique patterns of association with the cognitive factors. Biological annotation of the shared loci implicated gene-sets related to neurodevelopment and neuronal function. Lastly, we find that the common genetic determinants of the latent cognitive factors are not predictive of schizophrenia symptom dimensions. Overall, these findings inform our understanding of cognitive function in schizophrenia by demonstrating important differences in the shared genetic architecture of schizophrenia and cognitive abilities.
Spatial proteo-transcriptomic profiling reveals the molecular landscape of borderline ovarian tumors and their invasive progression
Authors: Schweizer Lisa , Krishnan Rahul , Shimizu Aasa , Metousis Andreas , Kenny Hilary , Mendoza Rachelle , Nordmann Thierry M. , Rauch Sarah , Kelliher Lucy , Heide Janna , Rosenberger Florian A. , Bilecz Agnes , Borrego Sanaa Nakad , Strauss Maximillian T. , Thielert Marvin , Rodriguez Edwin , Müller-Reif Johannes B. , Chen Mengjie , Yamada S. Diane , Mund Andreas , Lastra Ricardo R. , Mann Matthias , Lengyel Ernst
Published: November 2023

Serous borderline tumors (SBT) are epithelial neoplastic lesions of the ovaries that commonly have a good prognosis. In 10-15% of cases, however, SBT will recur as low-grade serous cancer (LGSC), which is deeply invasive and responds poorly to current standard chemotherapy1,2,3. While genetic alterations suggest a common origin, the transition from SBT to LGSC remains poorly understood4. Here, we integrate spatial proteomics5with spatial transcriptomics to elucidate the evolution from SBT to LGSC and its corresponding metastasis at the molecular level in both the stroma and the tumor. We show that the transition of SBT to LGSC occurs in the epithelial compartment through an intermediary stage with micropapillary features (SBT-MP), which involves a gradual increase in MAPK signaling. A distinct subset of proteins and transcripts was associated with the transition to invasive tumor growth, including the neuronal splicing factor NOVA2, which was limited to expression in LGSC and its corresponding metastasis. An integrative pathway analysis exposed aberrant molecular signaling of tumor cells supported by alterations in angiogenesis and inflammation in the tumor microenvironment. Integration of spatial transcriptomics and proteomics followed by knockdown of the most altered genes or pharmaceutical inhibition of the most relevant targets confirmed their functional significance in regulating key features of invasiveness. Combining cell-type resolved spatial proteomics and transcriptomics allowed us to elucidate the sequence of tumorigenesis from SBT to LGSC. The approach presented here is a blueprint to systematically elucidate mechanisms of tumorigenesis and find novel treatment strategies.
Integrating stimulus-organism-response model and theory of planned behavior to explore athletes’ intention to receive the COVID-19 vaccine booster—A moderated mediation model
Authors: Zhan Wenpeng , Deng Qianting , Nguyen Van Bac , Duc Anh Tran Phan , Na Phan Danh , Shia An-Shin , Ku Gordon Chih-Ming
Published: November 2023

This study aims to investigate the factors influencing athletes’ intention to receive the COVID-19 vaccine booster in Mainland China by integrating the stimulus-organization-response (SOR) model and theory of planned behavior (TPB) as the theoretical framework. Purposive sampling was used to select respondents from the National Games of the People’s Republic of China. Hard-copy questionnaires were utilized to collect data, resulting in 981 valid responses. Descriptive analysis and partial least squares structural equation modeling were used to analyze the data. The findings reveal that athletes’ subjective norm and knowledge significantly influence attitude, commitment, and perceived behavioral control. Attitude, commitment, and perceived behavioral control are verified as full mediators between subjective norm, knowledge, and intention to receive the COVID-19 vaccine booster. Knowledge to commitment is the most powerful path to predict athletes’ intention to receive the COVID-19 vaccine booster. Motivation moderates the relationships between knowledge, attitude, commitment, and perceived behavioral control. The integrating model’s explanatory power is 83.2%. Athletes’ knowledge is crucial in shaping a positive attitude, commitment, and perceived control, enhancing their intention to get the COVID-19 vaccine booster.
Atrial Fibrillation Catheter Ablation among Cancer Patients: Utilization Trends and In-Hospital Outcomes
Authors: Margolis Gilad , Goldhaber Ofir , Kazatsker Mark , Kobo Ofer , Roguin Ariel , Leshem Eran
Published: November 2023

BACKGROUND

Atrial fibrillation (AF) catheter ablation in cancer patients was evaluated in very few studies. We aimed to investigate trends of utilizations as well as in-hospital outcomes of AF catheter ablation procedures among cancer patients, in a large inpatient US registry.

METHODS AND RESULTS

Using the National Inpatient Sample (NIS) database, patients who underwent AF catheter ablations in the US between 2012 and 2019 were identified using ICD-9/10 codes. Sociodemographic, clinical data, in-hospital procedures and outcomes as well as in-hospital mortality and length-of-stay (LOS) were collected. Baseline characteristics and in-hospital outcomes were compared between patients with and without cancer. An estimated total of 67915 patients underwent AF catheter ablation between 2012-2019 in the US. Of them, 950 (1.4%) had cancer diagnosis. Compared with non-cancer patients, patients with cancer were older, had higher Charlson Comorbidity Index, as well as CHA2DS2-VASc and ATRIA bleeding indices scores.

Higher rate of total complications was observed in cancer patients (10.5% vs 7.9, p<0.001) driven mainly by more bleeding and infectious complications. LOS was also significantly longer in cancer patients (4.9 ± 5.8 vs. 2.7 ± 3.0 days, p<0.001). However, no significant differences in cardiac or neurological complications as well as in-hospital mortality rates were observed and were relatively low in both groups.

CONCLUSIONS

AF catheter ablation in cancer patients is associated with higher bleeding and infectious complication rates, but not with increased cardiac complications or in-hospital mortality rates in a nationwide, all-comer registry.
Human Brucellosis in Iraq: what does a spatiotemporal data analysis from 2007-2018 reveal?
Authors: Mustafa Ali Hazim , Khaleel Hanan Abdulghafoor , Al-Lami Faris
Published: November 2023

Background

Brucellosis is both endemic and enzootic in Iraq, resulting in long-term morbidity for humans as well as economic loss. No previous study of the spatial and temporal patterns of brucellosis in Iraq was done to identify potential clustering of cases.

Objectives

This study aims to detect the spatial and temporal distribution of human brucellosis in Iraq and identify any changes that occurred from 2007 to 2018.

Methods

A descriptive cross-sectional study using secondary data from the Communicable Diseases Control Center / Ministry of Health surveillance section. We used Moran’s I, local Getis-Ord’s Gi*, and the local indicators of spatial association (LISA) to detect the spatial distribution of the data. The data was analyzed using Excel software and the Quantum GIS (QGIS) version 2.18.20 (Steiniger and Hunter, 2013).

Results

50,621 human brucellosis cases were reported during the 12-year study period. Human brucellosis persisted annually in Iraq across the study period with no specific temporal clustering of cases. In contrast, spatial clustering was predominant in the Northern region of Iraq.

Conclusion

There were significant differences in the geographic distribution of brucellosis. The number of cases is highest in the north and northeast of the country, which has borders with nearby countries. In addition, people in these areas depend more on locally made dairy products, which can be inadequately pasteurized. Despite the lack of significant temporal clustering of cases, the highest number of cases were reported during Summer and Spring.

Recommendations

Considering these patterns when allocating resources to combat this disease, determining public health priorities, and planning prevention and control strategies is important.
Bacteriocin Distribution Patterns inEnterococcus faeciumandEnterococcus lactis:Bioinformatic Analysis Using a Tailored Genomics Framework
Authors: Tedim Ana P. , Almeida-Santos Ana C. , Lanza Val F. , Novais Carla , Coque Teresa M. , Freitas Ana R. , Peixe Luísa
Published: November 2023

Multidrug-resistantEnterococcus faeciumrepresent a major concern due to their ability to thrive in diverse environments and cause life-threatening infections. While antimicrobial resistance and virulence mechanisms have been extensively studied, the contribution of bacteriocins toE. faecium’s adaptability remains poorly explored.E. faecium, within the Bacillota phylum, is a prominent bacteriocin producer. Here, we developed a tailored database of 76 Bacillota bacteriocins (217 sequences, including 40 novel bacteriocins) and applied it to uncover bacteriocin distribution patterns in 997 quality-filteredE. faeciumandEnterococcus lactis(formerE. faeciumclade B) genomes. Curated using computational pipelines and literature mining, our database demonstrates superior precision versus leading public tools in identifying diverse bacteriocins. Distinct bacteriocin profiles emerged betweenE. faeciumandE. lactis, highlighting species-specific adaptations.E. faeciumstrains from hospitalized patients were significantly enriched for bacteriocins asentA,bac43,bacAS5 andbacAS11. These bacteriocins strongly associated with antibiotic resistance, particularly vancomycin and ampicillin, and Inc18rep2_pRE25-derivative plasmids, classically associated with vancomycin resistance transposons. Our integrated genomic and epidemiological analysis elucidates meaningful connections between bacteriocin determinants, antimicrobial resistance, mobile genetic elements, and ecological origins inE. faecium. This work significantly expands the knowledge on the understudied bacteriocin diversity in opportunistic enterococci, revealing their contribution to environmental adaptation. Further characterization of strain-level bacteriocin landscapes could inform strategies to combat high-risk clones. Overall, these insights provide a framework for unravelling bacteriocins’ therapeutic and biotechnological potential.
Fusion dynamics and size-dependent droplet microstructure in ssDNA mediated protein phase separation
Authors: Bian Yunqiang , Li Wenfei
Published: November 2023

Biomolecular cocondensation involving proteins and nucleic acids has been recognized to play crucial roles in genome organization and transcriptional regulation. However, the biophysical mechanisms underlying the fusion dynamics and microstructure evolution of the droplets during the early stage of liquid-liquid phase separation (LLPS) remain elusive. In this work, we study the phase separation of linker histone H1, which is among the most abundant chromatin proteins, in the presence of single-stranded DNA (ssDNA) capable of forming G-quadruplex structures by using residue-resolved molecular dynamics simulations. Firstly, we uncovered a kinetic bottleneck step in the droplet fusion. Productive fusion events are triggered by the formation of ssDNA mediated electrostatic bridge within the contacting zone of two droplets. Secondly, the simulations revealed a size-dependence of the droplet microstructure and stoichiometry. With droplet growth, its microstructure evolves as driven by the maximization of the electrostatic contacts between ssDNA and the highly charged segment of H1. Finally, we showed that the folding of ssDNA to G-quadruplex promotes LLPS by increasing the multivalency and strength of protein-DNA interactions. These findings provided new mechanistic insights into the microstructure and growth dynamics of the biomolecular droplets formed during the early stage of the ssDNA-protein cocondensation.
The AccelerAge framework: A new statistical approach to predict biological age based on time-to-event data
Authors: Sluiskes Marije , Goeman Jelle , Beekman Marian , Slagboom Eline , van den Akker Erik , Putter Hein , Rodríguez-Girondo Mar
Published: November 2023

Aging is a multifaceted and intricate physiological process characterized by a gradual decline in functional capacity, leading to increased susceptibility to diseases and mortality. While chronological age serves as a strong risk factor for age-related health conditions, considerable heterogeneity exists in the aging trajectories of individuals, suggesting that biological age may provide a more nuanced understanding of the aging process. However, the concept of biological age lacks a clear operationalization, leading to the development of various biological age predictors without a solid statistical foundation. This paper addresses these limitations by proposing a comprehensive operationalization of biological age, introducing the “AccelerAge” framework for predicting biological age, and introducing previously underutilized evaluation measures for assessing the performance of biological age predictors. The AccelerAge framework, based on Accelerated Failure Time (AFT) models, directly models the effect of candidate predictors of aging on an individual’s survival time, aligning with the prevalent metaphor of aging as a clock. We compare predictors based on the AccelerAge framework to a predictor based on the GrimAge predictor, which is considered one of the best-performing biological age predictors, using simulated data as well as data from the UK Biobank and the Leiden Longevity Study. Our approach seeks to establish a robust statistical foundation for biological age clocks, enabling a more accurate and interpretable assessment of an individual’s aging status.
Nonribosomal peptide synthetases require dynamic interaction between modular domains
Authors: Peng Ye-Jun , Zeng Xiaoli , Chen Yuxing , Zhou Cong-Zhao , Miao Wei , Jiang Yong-Liang , Zhang Cheng-Cai
Published: November 2023

Nonribosomal peptide synthetases (NRPSs) are large multidomain enzymes for the synthesis of a variety of bioactive peptides in a modular and pipelined fashion. Here, we investigated how the condensation (C) domain and the adenylation (A) domain cooperate with each other for the efficient catalytic activity in microcystin NRPS modules. We solved two crystal structures of the microcystin NRPS modules, representing two newly identified conformations in the NRPS catalytic cycle. Our data reveals that the dynamic interaction between the C and the A domains in these modules are mediated by the conserved “RXGR” motif, and this interaction is important for the adenylation activity. Furthermore, the “RXGR” motif-mediated dynamic interaction and its functional regulation is prevalent in different NRPSs modules possessing both the A and the C domains. This study provides new insight into the catalytic mechanism of NRPSs and should inspire novel ideas in NRPS enzyme engineering in synthetic biology.
Roles of linker region flanked by transmembrane and peptidoglycan binding region of PomB in energy conversion of theVibrioflagellar motor
Authors: Miyamura Yusuke , Nishikino Tatsuro , Koiwa Hiroaki , Homma Michio , Kojima Seiji
Published: November 2023

The energy converting complex of the sodium-driven flagellar motor in bacteria comprises two proteins, PomA and PomB, whose transmembrane regions form ion conducting channels and is called the stator complex. The transmembrane protein PomB is attached to the cell wall by its periplasmic region and has a plug segment following the transmembrane helix to prevent ion flux. PomB (Δ41-120), which lacks the periplasmic region from E41 to K120 immediately following its transmembrane region shows similar motility as that of wild-type PomB. In this study, three deletion mutants after the plug region, PomB (Δ61-120), PomB (Δ61-140), and PomB (Δ71-150), were generated and those deletion mutants were examined for their functionality. PomB (Δ61-120) conferred similar motility as that of the wild-type protein, whereas the other two mutants showed almost no motility in soft agar plate; however, we observed some swimming cells with speed similar to that of the wild-type cells. To observe dominance of wild-type proteins, we introduced the two PomB mutants into a wild-type strain, and its ability to swim was not affected by the mutants. Then, we purified the mutant PomAB complexes to confirm the stator formation. When we introduced the PomB mutations in the plug region, the reduced motility by the deletion was rescued, suggesting that the stator was activated. Our results indicate that the deletion prevents stator from transformation to an active form; however, the linker and plug regions from E41 to S150 are not essential for the motor function of PomB but are important for its regulation.

IMPORTANCE

The stator complex of flagella consists of PomA and PomB proteins and interacts with the rotor complex. PomB has a peptidoglycan binding (PGB) domain to fix the stator for generation of torque. PomB is attached to the cell wall only when the stator is activated by interaction between the cytoplasmic region of PomA and the rotor protein FliG. The flexible linker of PomB, which is a naturally unfolded region, is flanked by the peptidoglycan-binding (PGB) domain and transmembrane region. The plug region, which interacts with the periplasmic loops of PomA to prevent activation of the stator, is located next to its transmembrane region. In this study, we reveal the role of the flexible linker in activation of the stator complex.
An EWS::FLI1 monoclonal antibody with multimodal utility and specificity for FLI1
Authors: Selvanathan Saravana , Toretsky Jeffrey
Published: November 2023

Ewing sarcoma (ES) is a rare tumor that affects children, adolescents, and young adults. This tumor has a high morbidity in all patients and for those who present with metastatic disease a high mortality. A canonical chromosomal translocation, either t(11;22)(q24;p12) or t(21;22)(q22;q12) leads to the fusion oncoproteins EWS::FLI1 or EWS::ERG in 95% of ES patients. We recognized a critical need for a stably sourced high affinity antibody that recognizes EWS::FLI1 with maximal specificity. We created and validated a hybridoma that produces a mouse derived monoclonal antibody that recognizes EWS::FLI1 in multiple molecular biology applications.
The Dmc1 recombinase physically interacts with and promotes the meiotic crossover functions of the Mlh1-Mlh3 endonuclease
Authors: Pannafino Gianno , Chen Jun Jie , Mithani Viraj , Payero Lisette , Gioia Michael , Crickard J. Brooks , Alani Eric
Published: November 2023

The accurate segregation of homologous chromosomes during the Meiosis I reductional division in most sexually reproducing eukaryotes requires crossing over between homologs. In baker’s yeast approximately 80 percent of meiotic crossovers result from Mlh1-Mlh3 and Exo1 acting to resolve double-Holliday junction (dHJ) intermediates in a biased manner. Little is known about how Mlh1-Mlh3 is recruited to recombination intermediates and whether it interacts with other meiotic factors prior to its role in crossover resolution. We performed a haploinsufficiency screen in baker’s yeast to identify novel genetic interactors with Mlh1-Mlh3 using sensitizedmlh3alleles that disrupt the stability of the Mlh1-Mlh3 complex and confer defects in mismatch repair but do not disrupt meiotic crossing over. We identified several genetic interactions betweenMLH3andDMC1,the recombinase responsible for recombination between homologous chromosomes during meiosis. We then showed that Mlh3 physically interacts with Dmc1in vitroand at times in meiotic prophase when Dmc1 acts as a recombinase. Interestingly, restrictingMLH3expression to roughly the time of crossover resolution resulted in amlh3null-like phenotype for crossing over. Our data are consistent with a model in which Dmc1 nucleates a polymer of Mlh1-Mlh3 to promote crossing over.
tRNA modification enzyme-dependent redox homeostasis regulates synapse formation and memory
Authors: Madhwani Kimberly R. , Sayied Shanzeh , Ogata Carlson H. , Hogan Caley A. , Lentini Jenna M. , Mallik Moushami , Dumouchel Jennifer L. , Storkebaum Erik , Fu Dragony , O’Connor-Giles Kate M.
Published: November 2023

Post-transcriptional modification of RNA regulates gene expression at multiple levels. ALKBH8 is a tRNA modifying enzyme that methylates wobble uridines in specific tRNAs to modulate translation. Through methylation of tRNA-selenocysteine, ALKBH8 promotes selenoprotein synthesis and regulates redox homeostasis. Pathogenic variants in ALKBH8 have been linked to intellectual disability disorders in the human population, but the role of ALKBH8 in the nervous system is unknown. Throughin vivostudies inDrosophila, we show that ALKBH8 controls oxidative stress in the brain to restrain synaptic growth and support learning and memory.ALKBH8null animals lack wobble uridine methylation and exhibit a global reduction in protein synthesis, including a specific decrease in selenoprotein levels. Loss ofALKBH8or independent disruption of selenoprotein synthesis results in ectopic synapse formation. Genetic expression of antioxidant enzymes fully suppresses synaptic overgrowth inALKBH8null animals, confirming oxidative stress as the underlying cause of dysregulation.ALKBH8animals also exhibit associative learning and memory impairments that are reversed by pharmacological antioxidant treatment. Together, these findings demonstrate the critical role of tRNA modification in redox homeostasis in the nervous system and reveal antioxidants as a potential therapy for ALKBH8-associated intellectual disability.

Significance Statement

tRNA modifying enzymes are emerging as important regulators of nervous system development and function due to their growing links to neurological disorders. Yet, their roles in the nervous system remain largely elusive. Throughin vivostudies inDrosophila, we link tRNA methyltransferase-regulated selenoprotein synthesis to synapse development and associative memory. These findings demonstrate the key role of tRNA modifiers in redox homeostasis during nervous system development and highlight the potential therapeutic benefit of antioxidant-based therapies for cognitive disorders linked to dysregulation of tRNA modification.
[1,1′-Bicyclohexane]-1,1′-diol
Authors: Mtendeni Zukisani , Hosten Eric Cyriel , Betz Richard
Published: November 2023

The title compound, C12H22O2, is a symmetric diol derived from the pinacol coupling of cyclohexanone. The asymmetric unit contains three complete molecules. The cyclohexane moieties adopt chair conformations. Cooperative hydrogen bonding connects the individual molecules to infinite chains propagating along the crystallographic a-axis direction.
Reducing food waste by simply measuring it: insights from interventions to reduce household food waste
Authors: Ramos Gabriel Jäger , Borges João Augusto Rossi , Domingues Carla Heloisa de Faria , van Herpen Erica
Published: November 2023

Purpose

Overcooking and overbuying are two main causes of food waste in households. Therefore, this study tests whether two interventions, aimed at cooking planning versus purchasing planning, can reduce food waste in households by using self-report direct measurements. Because measuring household food waste can impact how much food is wasted, the effects of the mere measurement of household food waste over time were assessed as well.

Design/methodology/approach

A sample of 80 households was distributed into three groups (control, purchasing planning and cooking planning) and their household food waste was weighed over a period of 166 days. After the first 91 days, behavioral interventions were delivered to purchasing planning and cooking planning groups. Repeated measures ANOVA, linear regression and a two-level mixed model were used for data analysis.

Findings

Results showed that the interventions were not effective in influencing the participants to reduce household food waste beyond the reduction in the control group. However, there is evidence of a mere measurement effect that caused household food waste reduction over time.

Originality/value

This study's experimental period is longer than most of the studies that tested behavioral interventions for household food waste reduction. This enabled the authors to assess the effects of repeated measurement and discover that measurement alone can bring behavioral change.
Research on corporate financialization and green innovation: moderating role of CEO’s individual characteristics
Authors: Gu Yingqian , Zhang Wenqi , Sha Lin , Wang Lixia
Published: November 2023

Purpose

This paper aims to explore the impact of corporate financialization (CF) on green innovation (GI) and further disclose the moderating role of CEO’s individual characteristics in such relationship from the perspective of corporate governance.

Design/methodology/approach

This paper uses empirical research methods to study the impact of CF on GI based on the evidence from China capital market.

Findings

The findings indicate that: CF has a significant inhibiting effect on GI; female CEOs weaken the inhibiting effect of CF on GI compared to male CEOs; and CEO’s financial background positively moderates the inhibiting effect of CF on GI.

Originality/value

This paper, first, supplements the research literature on the economic consequences of CF and influencing factors of GI in non-financial firms. Then, it opens up the internal impact mechanism of CF on GI, which is moderated by the individual characteristics of corporate CEOs. Finally, it provides important reference for how to suppress CF of non-financial firms, cultivate CEOs that meet the needs of corporate development and promote GI development of enterprises through empirical evidence from China.
Refining the physical description of charge trapping and detrapping in a transport model for dielectrics using an optimization algorithm
Authors: Hallak Khaled , Baudoin Fulbert , Griseri Virginie , Bugarin Florian , Segonds Stephane , Le Roy Severine , Teyssedre Gilbert
Published: November 2023

Purpose

The purpose of this paper is to optimize and improve a bipolar charge transport (BCT) model used to simulate charge dynamics in insulating polymer materials, specifically low-density polyethylene (LDPE).

Design/methodology/approach

An optimization algorithm is applied to optimize the BCT model by comparing the model outputs with experimental data obtained using two kinds of measurements: space charge distribution using the pulsed electroacoustic (PEA) method and current measurements in nonstationary conditions.

Findings

The study provides an optimal set of parameters that offers a good correlation between model outputs and several experiments conducted under varying applied fields. The study evaluates the quantity of charges remaining inside the dielectric even after 24 h of short circuit. Moreover, the effects of increasing the electric field on charge trapping and detrapping rates are addressed.

Research limitations/implications

This study only examined experiments with different applied electric fields, and thus the obtained parameters may not suit the experimental outputs if the experimental temperature varies. Further improvement may be achieved by introducing additional experiments or another source of measurements.

Originality/value

This work provides a unique set of optimal parameters that best match both current and charge density measurements for a BCT model in LDPE and demonstrates the use of trust region reflective algorithm for parameter optimization. The study also attempts to evaluate the equations used to describe charge trapping and detrapping phenomena, providing a deeper understanding of the physics behind the model.
Mobile banking service quality and continuance intention: mediating role of satisfaction: a two-stage structural equation modeling-artificial neural network approach
Authors: Pokhrel Laxman , K.C. Anup
Published: November 2023

Purpose

The purpose of this paper is to investigate the mediating role of satisfaction (SAT) in relation to mobile banking service quality (MB-SQ) and continuance intention (CI) among Nepali mobile banking users.

Design/methodology/approach

The paper adopted a quantitative approach and cross-sectional survey research design. Data were collected with structured questionnaires from 326 mobile banking users. A partial least squares structural equation modeling (PLS-SEM) and artificial neuro network (ANN) approach were applied to examine hypotheses.

Findings

Results confirm a significant positive influence of MB-SQ on SAT and CI of mobile banking adoption. Moreover, MB-SQ partially mediates the relationship between SAT and CI of mobile banking adoption.

Research limitations/implications

Based on the findings of this research, theoretically, this paper attempted to investigate the mediating role of MB-SQ in the CI of mobile banking, and managerially, mobile banking service providers could have insights on designing mobile banking service marketing strategy.

Originality/value

This paper is among the earliest studies to investigate the role of MB-SQ as a higher-order reflective-reflective construct on CI. Moreover, the endogeneity issue has been tested, and ANN has been applied to investigate the predictive relevance of SAT and MB-SQ on CI of mobile banking users. Furthermore, the authors have delved into the ongoing discourse surrounding Generation Y and Generation Z, exploring their implications on CI within the realm of mobile service quality. It provides a critical juncture for understanding continuance intention in the mobile service quality context.
Impact valuation of droughts in soybean and maize production: the case of Argentina
Authors: Thomasz Esteban Otto , Vilker Ana Silvia , Pérez-Franco Ismael , García-García Agustin
Published: November 2023

Purpose

In Argentina, soy and maize represent 28% of the total country exports, affecting the balance of payments, international reserves accumulation and sovereign credit risk. In the past 10 years, three extreme and moderate droughts have affected the agricultural areas, causing significant losses in soybean and maize production. This study aims to estimate the economic impact generated by different drought levels for soy and maize production areas through a financial perspective that allows the estimation of the cash flow and income losses.

Design/methodology/approach

By analyzing the extreme deviations in yields during dry periods, the losses generated by droughts were valuated among 183 departments nationwide.

Findings

The aggregated results indicated a total loss of US$24.170m, representing 57.45% of the international reserves of the Argentinean Central Bank in 2021. This estimate shows the magnitude of the climate impact on the Argentinean economy, indicating that severe droughts have macroeconomic impacts, with the external sector as the main transmission channel in an economy with historic restrictions on the balance of payments, international reserve accumulation and sovereign credit risk.

Originality/value

This study analyses the macroeconomic impact of drought on Argentinean soybean and maize production.
Optimization of ultrasonic welding parameters for better seam performance
Authors: Raja Balasaraswathi S. , Bajpai Jonalee D.
Published: November 2023

Purpose

Ultrasonic welding is an emerging apparel manufacturing technique. However, the applications are widely explored in the field of technical textiles, with less exploration in the apparel endues. The purpose of this study is to explore the application of ultrasonic welding in apparel by analyzing the impacts of different parameters.

Design/methodology/approach

This study analyzed the influence of ultrasonic welding parameters, including pressure, welding speed and ultrasonic power on the seam performances (seam strength, seam bursting strength, seam thickness and seam stiffness). The parameters are optimized using Box–Behnken experimental design to achieve better seam performances.

Findings

The properties of ultrasonic seams are influenced by welding and fabric properties. Ultrasonically welded seams showed better performances in the case of comfort properties of seams, whereas the functional properties are lesser compared to conventional seams.

Originality/value

The findings of the research clearly outline the level of influence of different parameters on the performance of the ultrasonically welded seams in knitted fabrics, which can greatly help in applying ultrasonic welding manufacturing methods in apparel manufacturing.
A hybrid e-logistics service quality approach: modeling the evolution of B2C e-commerce
Authors: Uvet Hasan , Dickens John , Anderson Jason , Glassburner Aaron , Boone Christopher A.
Published: November 2023

Purpose

This research paper aims to examine two hybrid models of logistics service quality (LSQ) and its influence on satisfaction, loyalty and future purchase intention in a business-to-consumer (B2C) e-commerce context. This study extends the literature for LSQ by incorporating the second-order assurance quality construct, which comprises personnel contact quality, order discrepancy handling and order returns, into one of the hybrid models.

Design/methodology/approach

A survey-based approach is used to collect data. Participant responses to questions concerning multiple LSQ dimensions and behavioral perceptions from their most recent online shopping experience are measured using structural equation modeling.

Findings

Findings highlight the importance of including a second-order construct assurance quality as a more explanatory model. Results illustrate that online ordering procedures and assurance quality impact customer satisfaction more than other prominent LSQ dimensions. Furthermore, the findings revealed a customer loyalty is a partial mediator between customer satisfaction and future purchase intention. This underscores the significance of improved logistics services as a competitive edge for e-commerce retailers.

Research limitations/implications

Implications are limited to the e-commerce B2C domain.

Practical implications

The findings of this study underscore critical LSQ dimensions that garner greater satisfaction and retention in the online shopping experience. The results indicate that the effective and efficient handling of the initial order and any order problem significantly influences customer satisfaction and reaps the long-term benefits of customer retention.

Originality/value

The authors present and empirically test a hybrid model of LSQ in a B2C e-commerce domain that captures many of the important elements of the customer experience as espoused in the literature.