bluuebunny/crossref_metadata_2025 huggingface dataset:
Phenotypic Plasticity, Multiple Paternity, and Shell Shape Divergence Across Lake‐Stream Habitats in a Freshwater Mussel Brood (Pyganodon grandis)
Authors: Keogh Sean M. , Minerich Ben J. , Ohlman Lindsay M. , Pletta Madeline E. , Scheunemann Anna E. , Schroeder Zoe K. , Secrist Zebulin A. , Franzen Alex J. , Sietman Bernard E. , Simons Andrew M.
Published: December 2024

Hydrodynamic forces and their absence appear to exert differential selection pressure on aquatic biodiversity in lake and stream habitats, creating a tight fit between organismal phenotypes and their environments. Ecophenotypic variants may be the result of genetic differentiation or phenotypic plasticity, where a genotype can produce multiple phenotypes dependent on the environment. Freshwater mussels possess a wide degree of morphological variation that frequently covaries with the environment, making them a good system to understand the mechanisms of ecophenotypic variation across hydrological conditions.

We designed a two‐year experiment where individuals from the same Pyganodon grandis maternal brood (half and full siblings) were reared at a controlled site and four natural sites involving one lake and three streams. At the end of the experiment, shell shape was quantified for recaptured (N = 70), wild (N = 206), and zoo‐reared (N = 305) mussels. The maternal individual and 46 recaptured mussels were sequenced for genomic single nucleotide polymorphisms to test for multiple paternity and its effect on offspring morphology.

Analysis of covariance found significant differences in shell shape between rearing sites, particularly between stream and lake habitats, but no shape differences were detected across the three stream sites. At two of the four sites, the shell shape of recaptured individuals was not significantly different than that of wild populations. Genomic sequencing and parentage analysis identified 11–27 different fathers among recaptured individuals. Yet no genetic differences were present between stream and lake habitats, and there was no paternal effect on shell shape.

Taken together, phenotypic plasticity, over genetic differentiation, is identified as the primary mechanism of ecophenotypic variation. Plasticity is likely ubiquitous across freshwater mussels and may be a key adaptation given their high variance in habitat use. Multiple paternity may also play a role in the evolution of phenotypic plasticity, allowing more males from greater distances opportunities for fertilization, thus increasing genetic connectivity. Lastly, phenotypic plasticity and multiple paternity are convenient properties for freshwater mussel conservation and propagation. Multiple fathers increase the genetic variation of propagated broods, while plasticity may provide resilience to the release of stocked individuals across environmental heterogeneity.
Crises for Private Higher Education in Taiwan? A Conjunctural Analysis
Authors: Chan Sheng‐Ju
Published: December 2024

Private higher education (PHE) in Taiwan, similar to other East Asian systems, is a distinct sector that has played several significant roles. It experienced growth and prosperity during the massification of the entire higher education system. However, a multitude of emerging circumstances has ushered in dramatic changes and crises, impacting not only PHE but also the entire sector as a whole. These ongoing developments have the potential to fundamentally reshape the current components and structures of Taiwanese higher education. Therefore, we have adopted conjunctural analysis as a methodological approach to examine these forces and their effects on the evolving role of the private sector in the context of higher education system reconfigurations in Taiwan. Our findings reveal that PHE has faced a series of crises, encompassing demographic shifts, financial challenges, and legal complexities. The pursuit of greater “publicness” and the implementation of intervention measures through policy enactment and legal regulations have shifted the entire system toward a more “publicized” configuration. This new direction marks the onset of a new era in Taiwanese higher education.
Bacteraemia over 4 years in a Greater Western Sydney Metropolitan Local Health District: a retrospective descriptive study
Authors: Menon Vidthiya
Published: December 2024

Background

Bacteraemia is associated with significant morbidity and mortality. Understanding local patterns of bacteraemia including pathogen distribution, infection source, clinical speciality team burden, susceptibility data and mortality rates can inform empiric antibiotic choices, prevention approaches and education strategies.

Aims

To obtain descriptive data from positive blood cultures identified from Nepean Blue Mountains Local Health District in Greater Western Sydney.

Methods

A retrospective descriptive study was performed from August 2018 to March 2023 with data extracted from electronic medical records.

Results

A total of 6720 isolates were identified from positive blood cultures, of which 71.2% were clinically significant. The median age was 69 years. A total of 74.6% of clinically significant isolates were acquired in the community. The most commonly isolated pathogen was Escherichia coli (31.3%), followed by Staphylococcus aureus (14.3%), and 8.6% of patients with clinically significant positive blood cultures were neutropenic. Neutropenic patients were more likely to have Pseudomonas aeruginosa as the causative pathogen (11.4%) compared to the entire study population (3.9%). The most commonly identified source of infection was the urinary tract. The 30‐day all‐cause mortality rate for clinically significant positive blood cultures was 16.8%, with higher mortality rates seen with Candida species (and species previously known as Candida), P. aeruginosa and Enterococcus species. 94% of bacteraemia from Enterobacterales tested susceptible in vitro to ampicillin and/or gentamicin. The rate of methicillin resistance in S. aureus was 24%.

Conclusions

This study provides valuable insight into the local epidemiology of bacteraemia, which will allow for targeted prevention, management and educational strategies to improve outcomes.
Infants' Knowledge of Individual Words: Investigating Links Between Parent Report and Looking Time
Authors: López Pérez Melanie , Moore Charlotte , Sander‐Montant Andrea , Byers‐Heinlein Krista
Published: December 2024

Assessing early vocabulary development commonly involves parent report methods and behavioral tasks like looking‐while‐listening. While both yield reliable aggregate scores, findings are mixed regarding their reliability in measuring infants' knowledge of individual words. Using archival data from 126 monolingual and bilingual 14–31‐month‐olds, we further examined links across these methods at the word level, while controlling for potentially confounding child‐level factors. When data were averaged at the child level, performance on the looking‐while‐listening task correlated well with parent‐reported word production of the same words, as expected. However, mixed‐effects model comparisons suggested that at the word level, looking‐while‐listening performance was significantly predicted by age and total productive vocabulary, but not by parent‐reported knowledge of a word once these factors were controlled for. These findings invite careful consideration regarding the adequacy of these two popular methods for capturing children's idiosyncratic knowledge of individual words.
Climate Change Effects on the Only Western Palearctic Plethodontids: Range Changes and Possible Depletion of Intraspecific Genetic Diversity
Authors: Iannella Mattia , Cerasoli Francesco , Lunghi Enrico , Console Giulia , Biondi Maurizio , Sillero Neftalí
Published: December 2024

Aim

Amphibians are particularly sensitive to rapid climatic shifts, due to their eco‐physiology, life history traits and high frequency of narrowly distributed species. The genus Speleomantes encompasses the only extant Western Palearctic plethodontids, with three species occurring in peninsular Italy and the remaining five endemic to Sardinia Island.

Given the restricted ranges of Speleomantes species and their vulnerability to environmental change, we implemented Ecological Niche Models (ENMs) to estimate the likely impacts of various global warming scenarios on the extent and geographical location of climatically suitable areas.

Time Period

Current, with ENMs projected to 2030, 2050 and 2070 under alternative Shared Socioeconomic Pathways.

Location

Italian Peninsula and Sardinia Island.

Major Taxa Studied

Speleomantes Dubois 1984 (Caudata: Plethodontidae).

Methods

Ensembles of ENMs were fitted for each Speleomantes species, using the ‘biomod2’ modelling platform in R environment. Then, post‐modelling analyses were applied in GIS environment to highlight: (i) the primary geographic direction of predicted suitability shifts for each species and (ii) the proportion of stable, gained and lost suitable areas for each genetic lineage of the single species.

Results

We found a noticeable shrinking of suitable areas for all Speleomantes species, being particularly extensive under ‘business‐as‐usual’ scenarios for the Sardinian ones. Moreover, core suitable areas were predicted to shift for most species and suitability losses emerged to differently affect distinct genetic lineages, posing additional challenges for designing effective conservation measures.

Main Conclusions

The predicted shrinkage and shifting of climatically suitable areas for most Speleomantes species point to the urgency of evaluating in due time alternative conservation strategies for these endemic urodeles, to prevent losses of taxonomic and genetic diversity. Our modelling framework may be applied to other species with similar traits (e.g., low dispersal ability and narrow environmental niche breadth) to predict climate‐induced range contractions or shifts, using the gained information to optimise conservation outcomes.
Exclusive or partial breastfeeding and estimated protein intake in infancy: Associations with childhood growth and body composition at 7 years of age in the Odense Child Cohort
Authors: Honoré Karina Dyrvig , Bruun Signe , Michaelsen Kim F. , Möller Sören , Husby Steffen , Jacobsen Lotte Neergaard , Christesen Henrik Thybo , Andersen Marianne Skovsager , Zachariassen Gitte
Published: December 2024

Background

Protein intake in infancy influences infant growth, body composition, and possibly metabolic programming later in life. Our objectives were to investigate whether macronutrient content in mother's own milk (MOM) differed between exclusive (EBF) or partial breastfeeding (PBF), including an estimation of protein intake (ePI) during the first 6 months of life. Second, to investigate associations of feeding type and ePI with childhood growth and body composition at 7 years.

Methods

In a subset of 150 participants from the Odense Child Cohort, MOM was analysed for macronutrient content using midinfrared transmission spectroscopy. Information on breastfeeding duration was collected through weekly SMS questionnaires and used to calculate ePI. Outcomes were weight‐for‐age z‐scores (WAZ) and height‐for‐age z‐scores (HAZ) from birth to 7 years, and body composition in terms of dual X‐ray absorptiometry fat mass, fat‐free mass and calculated indexes at 7 years.

Results

The macronutrient content in MOM did not differ between EBF and PBF, but ePI was significantly higher in PBF infants than in EBF infants at 6 months. We found no difference in WAZ or HAZ until 7 years of age according to feeding type, but within the PBF group, ePI was positively associated with 7‐year WAZ (β = 0.001; 95% CI 0.000–0.003; p = 0.03) and HAZ (β = 0.002; 0.001–0.003;p = 0.007). ePI was not associated with body composition at 7 years.

Conclusion

Milk macronutrient content and childhood growth did not differ between EBF and PBF during infancy. Estimated protein intake in partially breastfed infants was positively associated with childhood growth, but not body composition, at 7 years of age.
Nucleated red blood cells for characterization of systemic inflammatory response syndrome in dogs
Authors: Cho ARom , Bae Hyeona , Kim Youngju , Jeon Yeseul , Jung Rankyung , Kim Minji , Kang Minjeong , Cha Sumin , Cho Kyu‐Woan , Jung Dong‐In , Park Jinho , Yu DoHyeon
Published: December 2024

Background

Nucleated red blood cells (nRBCs) are increased by disease processes and hematopoietic stress.

Objectives

To evaluate the utility of nRBCs as a marker of disease severity and prognosis in dogs with systemic inflammatory response syndrome (SIRS).

Animals

Sixty‐two client‐owned dogs met the criteria of SIRS without anemia.

Methods

nRBC‐positive (nRBCs: ≥5/500, n = 32) and nRBC‐negative (nRBCs: <5/500, n = 30) dogs were classified, and clinicopathological data, Acute Patient Physiologic and Laboratory Evaluation (APPLEfast) scores, cytokines, 2‐ and 4‐weeks survival were compared.

Results

The median WBC (17.63, interquartile range [IQR]: 11.72‐20.24 × 109/L), neutrophils (12.28, IQR: 7.17‐16.88 × 109/L), band neutrophils (1288.5, IQR: 252.5‐2575 cells/μL), serum IL‐6 (731.80, IQR: 299.79‐5522.05 pg/mL), and plasma C‐reactive protein (4.10, IQR: 1.00‐8.58 mg/L) were significantly higher in nRBC‐positive dogs than negative dogs (11.27, IQR: 7.63‐15.13 × 109/L; 7.57, IQR: 4.96‐11.71 × 109/L; 62.5, IQR: 0‐350.25 cells/μL; 232.30, IQR: 99.33‐447.01 pg/mL; 0.40, IQR: 0.10‐3.00 mg/L, respectively; P < .05). The median reticulocyte count (87.95, IQR: 52.45‐130.55 × 103/μL) and serum IL‐3 (40.94, IQR: 29.85‐53.52 ng/L) were also significantly greater in nRBC‐positive dogs than nRBC‐negative dogs (46.00, IQR: 26.43‐68.15 × 103/μL; 25.24, IQR: 21.65‐37.40 ng/L, respectively; P < .01). The presence of circulating nRBCs, but not the reticulocyte count, at admission was predictive of death in dogs with SIRS at 2 weeks (P = .01, AUC: 0.729) and 4 weeks (P = .002, AUC: 0.731). The overall survival time was shorter in nRBC‐positive dogs (95% CI, 47.35‐113.90) than nRBC‐negative dogs (95% CI, 90.92‐135.55; P = .03).

Conclusions and Clinical Importance

Measuring peripheral nRBCs in dogs with SIRS is rapid and clinically applicable, reflecting disease severity and associated prognosis.
Exosomal ETV4 Derived From M2 Macrophages Induces Growth, Glycolysis and Stemness in Hepatocellular Carcinoma by UpRegulating SULT2B1 Expression
Authors: Xu Qiaodong , Chen Xinyue , Ma Zhiyan , Zhong Haibin , Feng Gengren , Gu Songgang
Published: December 2024

Background

M2 macrophage‐derived exosomes have been identified to modulate hepatocellular carcinoma (HCC) progression. E‐twenty‐six (ETS) variant transcription factor 4 (ETV4) shows protumoral effects in HCC. Here, we aimed to probe whether ETV4 performed oncogenic effects on HCC by macrophage‐derived exosomes and its associated mechanism.

Methods

Exosomes were isolated from macrophages and co‐cultured with HCC cells. qRT‐PCR and western blotting were utilised for the detection of mRNA and protein. Cell survival was evaluated using EdU assay and flow cytometry. Glycolysis was determined by measuring the glucose uptake, lactate production, and ATP levels. Cell stemness was assessed by sphere formation and flow cytometry. The interaction between ETV4 and SULT2B1 (sulfotransferase family 2B member 1) was determined by a dual‐luciferase reporter and chromatin immunoprecipitation assays. In vivo assay was performed by establishing mouse xenograft models.

Results

ETV4 was highly expressed in the exosomes of M2 macrophages and could be internalised by HCC cells. ETV4 derived from M2 macrophage exosomes promoted HCC cell proliferation, glycolysis and stemness in vitro, and enhanced HCC growth in nude mice. Mechanistically, ETV4 interacted with SULT2B1 and promoted it transcription. SULT2B1 silencing suppressed HCC cell proliferation, glycolysis and stemness. In addition, exosomal ETV4 derived from M2 macrophage performed its effects by modulating SULT2B1.

Conclusion

ETV4 derived from M2 macrophage exosomes promoted HCC cell proliferation, glycolysis and stemness by interacting with SULT2B1, suggesting a novel insight into developing exosome‐based therapy for HCC.
Assessing the Clinical Value of 2‐h Versus 4‐h Gastric Emptying Scintigraphy in Pediatrics: A Systematic Review and Meta‐Analysis
Authors: Shargo Ryan , Luongo Michael , Mhaskar Rahul , Lu Peter L. , Wilsey Michael
Published: December 2024

Introduction

The gold‐standard diagnostic test for gastroparesis is gastric emptying scintigraphy (GES). Although a 4‐h GES is recommended in adult guidelines, no similar guidelines exist in the pediatric population, with many hospitals utilizing a 2‐h scan to reduce radiation exposure and save time.

Methods

We performed a systematic review and meta‐analysis to evaluate differences in the diagnosis of gastroparesis during 2‐h versus 4‐h GES. Four databases were systematically searched for articles reporting results of GES at both the 2‐ and 4‐h time points in a pediatric population. Outcomes included the proportion of patients with gastroparesis at 2‐ and 4‐h and the number of patients with differing transit status (normal or abnormal) from 2‐ to 4‐h. Meta‐analyses were conducted utilizing a random effects model. Heterogeneity among studies was assessed utilizing the I2 statistic.

Key Results

A total of 344 records were identified, of which 9 articles met inclusion criteria. Of these, six articles were included in the meta‐analysis. The pooled proportion of patients with alterations in gastric transit between 2 and 4 h was 0.2 (95% CI: 0.11 to 0.30). Overall, the extended 4‐h scan captured an additional 10% of patients with gastroparesis. There was significant heterogeneity among the studies (I2 = 91.8%, p < 0.001), likely due to differences in GES protocol and patient samples.

Conclusions and Inferences

The 4‐h GES offers a higher diagnostic yield in pediatric patients compared to a 2‐h study, despite heterogeneity in existing research. Further prospective studies are necessary to further quantify this advantage.
A Narrative Exploration of Family Members' Perspectives of Life Story Phases Following Transition of an Older Family Relative Into Long‐Term Care
Authors: Corbally Melissa , Ffrench Orla , Rodger Daragh , Ricci Rachele , Phelan Amanda
Published: December 2024

Background

The transition of an older person from a home environment into long‐term care is frequently unplanned and complex. Little is known about how relatives make sense of supporting the transition of their relatives to long‐term care.

Objective

This study explored family members' narratives of the process of supporting the transition of their older relative into long‐term care.

Method

Life stories of six relatives who supported transitioning their older family relatives into a nursing home were collected using open narrative questioning in accordance with the Biographical Narrative Interpretive Method. Data was analysed using a dialogic/performance analysis narrative analytic method.

Results

Four key life story phases were identified: before transition, crisis event, transition and after transition. These phases varied in time duration and involvement of healthcare providers. The longest phase was ‘before transition’ where a process of slow deterioration became more apparent to the participants retrospectively. This was followed by the shortest period ‘crisis event’ where the older person was admitted to tertiary care. Two permeating themes: family dynamics and knowledge/understanding underpinned all life story phases.

Conclusions

Relatives' knowledge, family dynamics and positioning of self‐informed the duration of the life story phases of participants as they navigated the transition. Understanding nuanced differences in relatives' life story phases highlights how timing of information provision can affect the emotional adjustment of relatives experiencing this challenging process.

Implications for Practice

Both community and gerontological nurses' offer real potential to provide tailored and effective responses to relatives depending on each life phase. Sequencing of information appropriate to the life phase could potentially ease the stress associated with transitioning to nursing home care, possibly preventing a crisis event from occurring. Anticipatory conversations also offer potential to alleviate relatives' concerns through life story phases.
Evaluating CNN Architectures for the Automated Detection and Grading of Modic Changes in MRI: A Comparative Study
Authors: Xing Li‐peng , Liu Gang , Zhang Hao‐chen , Wang Lei , Zhu Shan , Bao Man Du La Hua , Wang Yan‐ni , Chen Chao , Wang Zhi , Liu Xin‐yu , Zhang Shuai , Yang Qiang
Published: December 2024

Objective

Modic changes (MCs) classification system is the most widely used method in magnetic resonance imaging (MRI) for characterizing subchondral vertebral marrow changes. However, it shows a high degree of sensitivity to variations in MRI because of its semiquantitative nature. In 2021, the authors of this classification system further proposed a quantitative and reliable MC grading method. However, automated tools to grade MCs are lacking. This study developed and investigated the performance of convolutional neural network (CNN) in detecting and grading MCs based on their maximum vertical extent. In order to verify performance, we tested CNNs' generalization performance, the performance of CNN with that of junior doctors, and the consistency of junior doctors after AI assistance.

Methods

A retrospective analysis of 139 patients' MRIs with MCs was conducted and annotated by a spine surgeon. Of the 139 patients, MRIs from 109 patients were acquired using Philips scanners from June 2020 to June 2021, constituting Dataset 1. The remaining 30 patients had MRIs obtained from both Philips and United Imaging scanners from June 2022 to March 2023, forming Dataset 2. YOLOv8 and YOLOv5 were developed in PyCharm using the Python language and based on the PyTorch deep learning framework, data enhancement and transfer learning were applied to enhance model generalization. The model's performance was compared with precision, recall, F1 score, and mAP50. It also tested generalizability and compared it with the junior doctor's performance on the second data set (Dataset 2). Post hoc, the junior doctor graded Dataset 2 with CNN assistance. In addition, the region of interest was displayed using the class activation mapping heat map.

Results

On the unseen test set, the YOLOv8 and YOLOv5 models achieved precision of 81.60% and 61.59%, recall of 80.90% and 67.16%, mAP50 of 84.40% and 68.88%, and F1 of 0.81 and 0.60 respectively. On Dataset 2, YOLOv8 and junior doctor achieved precision of 95.1% and 72.5%, recall of 68.3% and 60.6%. In the AI‐assisted experiment, agreement between the junior doctor and the senior spine surgeon significantly improved from Cohen's kappa of 0.368–0.681.

Conclusions

YOLOv8 in detecting and grading MCs was significantly superior to that of YOLOv5. The performance of YOLOv8 is superior to that of junior doctors, and it can enhance the capabilities of junior doctors and improve the reliability of diagnoses.
Macrophage Polarization in the Osteoarthritis Pathogenesis and Treatment
Authors: Zou Xiongfei , Xu Hongjun , Qian Wenwei
Published: December 2024

Osteoarthritis (OA) is a prevalent degenerative disorder that severely impacts quality of life due to pain and disability. Although the pathophysiology of OA remains incompletely understood, recent research highlights the role of synovial inflammation in OA onset and progression, driven primarily by inflammatory infiltrates, especially macrophages, in the synovium. These macrophages respond to the local microenvironment, polarizing into either pro‐inflammatory (M1) or anti‐inflammatory (M2) subtypes. This review focuses on the role of macrophage polarization in OA pathogenesis and treatment, emphasizing how M1/M2 polarization is influenced by pathways such as STAT, NF‐κB, caspase, and MAPK. These pathways induce low‐grade inflammation within OA‐affected joints, altering chondrocyte metabolism, inhibiting cartilage repair, and impairing mesenchymal stem cell chondrogenesis, thereby contributing to OA progression. Additionally, this review discusses potential therapies targeting macrophage polarization, encompassing compounds, proteins, cells, and microRNAs, to offer insights into novel treatment strategies for OA.
Does lung function in preschoolers help to predict asthma in later life?
Authors: Owens Louisa , Le Souëf Peter N.
Published: December 2024

The earliest respiratory function assessments, within or close to the neonatal period, consistently show correlations with lung function and with the development of asthma into adulthood. Measurements of lung function in infancy reflect the in utero period of lung development, and if early enough, show little influence of postnatal environmental exposures. Later in the preschool and school age periods, influences of the environment are superimposed on initial levels. Fetal exposures before birth such as maternal smoking during pregnancy, lead to reduced lung function and an increased risk of asthma in females particularly those with certain glutathione S‐transferase genotypes. Lung function measurements later in the preschool period are also associated with development of asthma. Although lung function in preschoolers does help predict asthma in later life and these observations have increased our understanding of the physiology underlying asthma, the findings have not led to thewidespread use of lung function measurements being in preschoolers as clinical predictors of asthma due to the practicalities of testing in this age group.
CRISPR‐Cas9 Mediated Gene Editing Platform Through Callus‐to‐Plant Regeneration and Functional Analysis of DoALA4─DoALA6 in Dendrobium officinale
Authors: Li Ying , Yang Jiapeng , Zhang Qian , Zhang Ke , Xue Qingyun , Liu Wei , Ding Xiaoyu , Niu Zhitao
Published: December 2024

Dendrobium orchids are well known for their great horticultural and medicinal values; however, the CRISPR/Cas9 gene editing system for Dendrobium species still needs to be improved. Therefore, this study aims to establish a CRISPR/Cas9‐based functional validation system using Dendrobium officinale as a model species for the Dendrobium genus and to validate the DoALA4─DoALA6 genes, which may relate to growth and disease resistance. We first conducted a bioinformatics analysis of the P‐type ATPase gene family in D. officinale, revealing the evolutionary diversity of P‐type ATPase genes in orchids. Second, we inserted the GFP gene into the vector of CRISPR/Cas9 gene editing system to enhance the selection efficiency of genome‐edited plants. Comparative analysis showed that different explants exhibited varying transformation efficiencies, ranging from 5% to 46.2%. Considering the regeneration capability, survival rate and gene editing efficiency, we selected callus as the transformation explant. Third, we used this editing system to generate DoALA4─DoALA6 mutants. Phenotypic observations of the mutants and inoculation of D. officinale with Sclerotium rolfsii indicated that DoALA4─DoALA6 are crucial for the growth of D. officinale and its resistance to southern blight disease. This efficient and stable CRISPR/Cas9 platform offers a foundation for further gene studies and Dendrobium breeding.
Soft tissue tumor with BRAF and NRAS mutations sharing features with NTRK‐rearranged spindle cell neoplasm: A case report expanding the spectrum of spindle cell tumor with kinase gene alterations
Authors: Kakuda Yuko , Kato Ikuma , Kawata Takuya , Goto Keisuke , Ito Kan , Satake Ryo , Toki Shunichi , Murata Hideki , Wasa Junji , Katagiri Hirohisa , Takahashi Mitsuru , Nagashima Takeshi , Mori Taro , Oda Yoshinao , Sugino Takashi , Yamaguchi Ken
Published: December 2024

NTRK‐rearranged spindle cell neoplasm is a group of tumors characterized by NTRK1/2/3 gene fusion. Recently, tumors with other kinase fusion genes were reported to exhibit similar morphologies. Herein, we discuss an adult‐onset soft tissue tumor with similar histologic patterns as kinase gene fusion‐related tumors but with BRAF and NRAS mutations. A female in her 40s had a 40 mm tumor with an unclear border in the soft tissue of her foot joint. Short spindle‐shaped tumor cell proliferation with abundant capillaries and collagen fiber bundles were observed. The tumor infiltrated the subcutaneous adipose tissue, exhibiting a lipofibromatosis‐like pattern. Immunohistochemically, the tumor cells coexpressed CD34, S‐100, and BRAF V600E. Whole‐exome sequencing revealed BRAF p.V600E and NRAS p.Q61K mutations. Since BRAF activation occurs in BRAF fusion gene tumors and BRAF mutations, they could share a similar mechanism in tumorigenesis. This case suggests the further expansion of kinase‐related spindle cell tumors.
Numerical Approaches in Nonlinear Fourier Transform‐Based Signal Processing for Telecommunications
Authors: Sedov Egor , Chekhovskoy Igor , Fedoruk Mikhail , Turitsyn Sergey
Published: December 2024

We discuss applications of the inverse scattering transform, also known as the nonlinear Fourier transform (NFT) in telecommunications, both for nonlinear optical fiber communication channel equalization and time‐domain signal processing techniques. Our main focus is on the challenges and recent progress in the development of efficient numerical algorithms and approaches to NFT implementation.
Landscapes of state capitalism: Reconciling the vernacular, national development imaginaries, and green capital accumulation
Authors: Stokols Andrew
Published: December 2024

This article theorizes ‘state capitalist landscapes’ as a unique spatial form shaped by state‐owned developers that reconcile economic goals with national development imperatives and symbolic national imaginaries. State capitalist landscapes, I argue, integrate economically productive spaces with natural spaces to symbolize imaginaries of the nation. Through an inductive case study methodology, this article surveys three industrial zones developed and/or under development by state owned developers: Singapore's Jurong, China's Xiong’an New Area, and Thailand's Wangchan Valley. In each of these cases, natural landscapes are integrated into new economic zones in order to construct specific symbolic and/or political imaginaries of the nation: Singapore's ‘garden city’, China's ‘ecological civilization’, and in Thailand the ‘sufficiency economy’. By bringing together work on ‘infrastructural landscapes’ and ‘state capitalism’ this paper provides a concrete material perspective to contemporary discussions of state capitalism, while also bringing more grounded, political and institutional perspectives to landscape infrastructure studies, which has tended to set aside discussions of institutional forms or national political dynamics in a focus on form and materiality of infrastructure landscapes worldwide.
Externalist XAI?
Authors: Søgaard Anders
Published: December 2024

Developers of artificial intelligence (AI) often cannot explain the inferences their neural networks make, at least not in ways that satisfy user needs. XAI—explainable artificial intelligence—aims to develop techniques for providing such explanations. XAI researchers have adopted techniques that, to philosophers, seem representationalist–internalist, leading some philosophers to call for more externalist alternatives. But is explaining AI models through causally related external factors feasible? I suggest we compare the idea of externalist XAI to so‐called functionalist XAI. Two common arguments against functionalist XAI are the Epistemic Argument and the Trust Argument, respectively. I discuss whether these arguments can be met by externalists, as well as a new, previously unnoticed challenge from random initialization.
A conserved nuclear factor YC subunit, NF‐YC3, is essential for arbuscule development
Authors: Xie Kun , Ren Yuhan , Huang Yujuan , Wang Lingxiao , Li Lechuan , Ye Hanghang , Yang Congfan , Wang Shuangshuang , Xu Guohua , Chen Aiqun
Published: December 2024

Establishing reciprocal symbiosis with arbuscular mycorrhizal (AM) fungi is an important evolutionary strategy of most terrestrial plants to adapt to environmental stresses, especially phosphate (Pi) deficiencies. Identifying the key genes essential for AM symbiosis in plants and dissecting their functional mechanisms will be helpful for the breeding of new crop varieties with enhanced nutrient uptake efficiency. Here, we report a nuclear factor YC subunit‐encoding gene, OsNF‐YC3, whose expression is specifically induced in arbuscule‐containing cells, plays an essential role in AM symbiosis. Knockout of OsNF‐YC3 resulted in stunted arbuscule morphology and substantially decreased P accumulation, while overexpressing OsNF‐YC3 enhanced mycorrhization and Pi uptake efficiency. OsNF‐YC3 is directly regulated by OsPHRs, the major regulators of Pi starvation responses. Chromatin immunoprecipitation sequencing analysis uncovered multiple genes with crucial roles in arbuscule development as its potential downstream targets, including the AM‐specific Pi transporter gene OsPT11. OsNF‐YC3 can form a heterotrimer with the other two NF‐Y subunits, OsNF‐YA11 and OsNF‐YB11, in yeast. Loss of OsNF‐YA11 function also severely impaired arbuscule development in its mutants. Overall, our results highlight an essential role of OsNF‐YC3 and its potential interacting NF‐Y subunit, OsNF‐YA11, in regulating AM symbiosis and arbuscule development.
An independent biosynthetic route to frame a xanthanolide‐type sesquiterpene lactone in Asteraceae
Authors: Li Changfu , Li Yuanjun , Wang Jinxu , Lu Fengliu , Zheng Lifen , Yang Lu , Sun Wenwen , Ro Dae‐Kyun , Qu Xudong , Wu Yihan , Zhang Yansheng
Published: December 2024

Xanthanolides, also described as seco‐guaianolides, are unique sesquiterpene lactones (STLs) with diverse bioactivities. Most of xanthanolides are 12,8‐olides based on the position of their lactone ring. The biosynthetic pathway leading to xanthanolides has hitherto been elusive, especially how nature creates the xanthane skeleton is a long‐standing question. This study reports the elucidation of a complete biosynthetic pathway to the important 12,8‐xanthanolide 8‐epi‐xanthatin. The xanthane‐type backbone is directly derived from the central precursor germacrene‐type sesquiterpene, germacrene A acid, via oxidative rearrangement, catalyzed by an unusual cytochrome P450. Subsequently, a 12,8‐lactone ring is formed within this xanthane‐type backbone resulting in xanthanolides. The biosynthetic pathway for xanthanolides contrasts with the previously unified biosynthetic route for diverse 12,6‐guaianolides, in which a 12,6‐lactone ring formation precedes the transformation of a germacrene‐type skeleton into a guaiane‐type structure. The discovery of the full biosynthetic pathway of 8‐epi‐xanthantin opens new opportunities for producing xanthanolides in microbial organisms using synthetic biology strategies.
High Occurrence of ST131 Among Extraintestinal Pathogenic Escherichia coli in Humans and Dogs in Sri Lanka
Authors: Dewasmika W. A. Pamudi Maldam , Dissanayake D. R. Anuruddhika , Neelawala N. G. Dulanjalee Anuruddhika Kumari , Dissanayake B. G. Nilanthi , Prasada D. V. Pahan , Francis Veithehi Rajeevan , Octavia Sophie , Lan Ruiting
Published: December 2024

Aims

Extraintestinal pathogenic Escherichia coli (ExPEC) is an important human and animal pathogen. In particular, the ST131 of ExPEC is a widely distributed clone, resistant to extended‐spectrum cephalosporins and fluoroquinolones. We investigated the occurrence of ST131 among ExPEC from humans and dogs in Sri Lanka and determined its antimicrobial resistance.

Methods

A total of 215 ExPEC isolates were collected from humans (n = 179) and dogs (n = 36) from two different cities in Sri Lanka. Antimicrobial resistance was tested by the disk diffusion method, and the presence of resistance‐encoding genes (blaTEM, blaSHV and blaCTX‐M) and ST131 clades/subclades was tested by PCR.

Results

The majority of the isolates were (61.8%) ST131, with 55.8% in ST131‐clade C. Of the clade C isolates, 44.3%, 27.8%, 15.7% and 6.7% were in clades C2, C other, C1‐non‐M27 and C1‐M27, respectively. Approximately 11% of the ST131 isolates were carbapenem resistant. ExPEC from dogs showed comparable resistance rates to human isolates except for resistance to amoxicillin‐clavulanate and amikacin.

Conclusion

We observed a high occurrence of ST131 and its clade C, with more than 11% exhibiting resistance to carbapenems in Sri Lanka. Furthermore, ST131‐C1‐M27, with high resistance to both quinolones and extended‐spectrum cephalosporins, was also present. Our results emphasise the importance of the One Health approach in the monitoring of antimicrobial‐resistant E. coli in different regions of Sri Lanka to gain a better understanding of their prevalence over time, contributing to effective antimicrobial stewardship.
Transforming Governance: A Systematic Review of AI Applications in Policymaking
Authors: Badrul Hisham Amirah ‘Aisha , Mohamed Yusof Nor Ashikin , Salleh Siti Hasliah , Abas Hafiza
Published: December 2024

This systematic literature review examines the transformative applications of artificial intelligence (AI) in policymaking, exploring its potential to enhance decision-making, public engagement, and governance effectiveness. Employing a rigorous research methodology, this review analyzed scholarly articles from Scopus, Web of Science, and PubMed databases using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) framework, ensuring methodological transparency and reproducibility. The final dataset of 22 articles was synthesized into four key themes: (i) AI in policy development and implementation, which focuses on data-driven decision support in policy formulation; (ii) AI in public administration and governance, highlighting AI’s role in improving public sector efficiency and resilience; (iii) ethical and regulatory aspects of AI in policymaking, which addresses critical issues like transparency, privacy, and bias; and (iv) applications of AI in specific policy domains, encompassing areas such as public health, environmental sustainability, and education. Findings indicate that AI can support evidence-based policymaking by facilitating real-time data analysis, scenario modeling, and enhanced public participation. However, challenges persist, particularly concerning ethical considerations, algorithmic accountability, and regulatory frameworks that ensure AI is implemented responsibly and equitably. This review underscores the need for interdisciplinary collaboration, ethical standards, and robust governance frameworks to address these challenges and maximize AI’s benefits in policy development and implementation. The synthesis of insights from diverse policy contexts provides a foundation for future research, encouraging exploration of responsible AI integration in policymaking to advance public trust, accountability, and policy effectiveness).
A note on Stein fillability of circle bundles over symplectic manifolds
Authors: Oba Takahiro
Published: December 2024

We show that, given a closed integral symplectic manifold of dimension , for every integer , the Boothby–Wang bundle over carries no Stein fillable contact structure. This negatively answers a question raised by Eliashberg. A similar result holds for Boothby–Wang orbibundles. As an application, we prove the non‐smoothability of some isolated singularities.
Harder–Narasimhan filtrations of persistence modules
Authors: Fersztand Marc , Jacquard Emile , Nanda Vidit , Tillmann Ulrike
Published: December 2024

The Harder–Narasimhan (HN) type of a quiver representation is a discrete invariant parameterised by a real‐valued function (called a central charge) defined on the vertices of the quiver. In this paper, we investigate the strength and limitations of HN types for several families of quiver representations which arise in the study of persistence modules. We introduce the skyscraper invariant, which amalgamates the HN types along central charges supported at single vertices, and generalise the rank invariant from multiparameter persistence modules to arbitrary quiver representations. Our four main results are as follows: (1) We show that the skyscraper invariant is strictly finer than the rank invariant and incomparable to the generalised rank invariant; (2) we characterise the set of complete central charges for zigzag (and hence, ordinary) persistence modules; (3) we extend the preceding characterisation to rectangle‐decomposable multiparameter persistence modules of arbitrary dimension; and finally, (4) we show that although no single central charge is complete for interval‐decomposable ladder persistence modules, a finite set of central charges is complete.
Regularity and asymptotics of densities of inverse subordinators
Authors: Ascione Giacomo , Savov Mladen , Toaldo Bruno
Published: December 2024

In this article, densities (and their derivatives) of subordinators and inverse subordinators are considered. Under minor restrictions, generally milder than the existing in the literature, employing a useful modification of the saddle point method, we obtain the large asymptotic behaviour of these densities (and their derivatives) for a specific region of space and time and quantify how the ratio between time and space affects the explicit speed of convergence. The asymptotics is governed by an exponential term depending on the Laplace exponent of the subordinator and the region represents the behaviour of the subordinator when it is atypically small (the inverse one is larger than usual). As a result, a route to the derivation of novel general or particular fine estimates for densities with explicit constants in the speed of convergence in the region of the lower envelope/the law of iterated logarithm is available. Furthermore, under mild conditions, we provide a power series representation for densities (and their derivatives) of subordinators and inverse subordinators. This representation is explicit and based on the derivatives of the convolution of the tails of the corresponding Lévy measure, whose smoothness is also investigated. In this context, the methods adopted are based on Laplace inversion and strongly rely on the theory of Bernstein functions extended to the cut complex plane. As a result, smoothness properties of densities (and their derivatives) and their behaviour near zero immediately follow.
Looking Beyond Self-Reported Cognitive Load: Comparing Pupil Diameter Against Self-Reported Cognitive Load in Design Tasks
Authors: Cass Madison , Prabhu Rohan
Published: December 2024

As designers experience greater mental demands from the increased complexity of new design tools and methods, it is important to understand designers' cognitive load when performing design tasks. Several researchers have identified task- and designer-related factors that affect cognitive load, such as time or expected outcome. However, most of these design studies used self-report measures of cognitive load, which have been observed to be inaccurate and, to some extent, incomplete. In contrast, physiological measures (e.g., eye tracking) provide an objective assessment of mental workload. However, little research in engineering design has compared self-reported measures of cognitive load against physiological measures and our aim in this paper is to provide motivation and a starting point for such work. Specifically, we present a rich dataset comprising pupil diameter collected with ten student designers performing an hour-long loosely controlled design task using various design representations (e.g., computer-aided design and sketching). We also collected self-reported cognitive load using the NASA-TLX after the design task was completed. A preliminary analysis revealed that self-reported physical demand correlated with the minimum latent pupil diameter, whereas performance satisfaction correlated with the maximum latent pupil diameter. Furthermore, design representations vary in the range of cognitive load experienced by designers when utilizing them. These findings highlight the importance of statistical moments in the interpretation of physiological indicators such as pupil diameter. These findings also call for the use of a multi-modal approach for measuring cognitive load. Moreover, the accompanying dataset enables future research toward such studies.
Extracting Design Rationale in Technical Literature to Provide Inspirational Design Stimuli
Authors: Yue Gaofeng , Liu Jihong , Zhang Weijuan
Published: December 2024

Design rationale (DR) explains why the solution is designed the way it is, and can be used to stimulate creativity and facilitate the development of new solutions in the conceptual design phase. DR was mainly captured by recording the tacit knowledge of designers during the design process, which has hindered its application in conceptual design due to its interference with the design. This paper proposes a method for capturing DR from technical literature, providing an intuitively understandable textual stimulus for design ideation. A textual DR ontology, which includes literature, artifact, issue, intention, argument, and other entities along with their relationships, is used as a metamodel to construct the DR knowledge graph (DRKG). The DR vector space (DRVS) model and the DRVS-based method are used for the joint extraction of entities and relations. Sentences and terms extracted from the technical literature are then organized into a DRKG. A prototype design rationale management system was developed based on the methodology. Finally, we carried out experiments to construct the DRKG and apply it to the conceptual design of a police unmanned aerial vehicle for night patrols using patents and journal articles, and the results verified the feasibility of the method.
A Sustainable Response Surface Methodology and Analytic Hierarchy Process–Weighted Aggregated Sum Product Assessment Model to Evaluate Performance and Emissions Characteristics of Diesel Engine Using Clove Oil Biodiesel Blend
Authors: Singotia Pawan Kumar , Kumar Vijay , Choudhary Akhilesh Kumar , Jain Naveen
Published: December 2024

Replacing diesel with biodiesel generally results in a decrease in exhaust emissions like carbon monoxide, hydrocarbon, particulate matter, and carbon dioxide. However, nitrogen oxide emissions show increasing trends. On the other hand, a decrease in nitrogen oxide emissions has been found using various additives with diesel and biodiesel blends. In this work, the experiments are carried out on diesel, B30 (70% v/v diesel + 30% v/v biodiesel), and the B30CL1000 (70% v/v diesel + 30% v/v biodiesel + 1000 ppm clove oil) to evaluate the performance and emissions of diesel engine. The response surface methodology-based approach has been applied to evaluate the effect of different engine operating parameters on engine performance and emission while fueled with the B30CL1000 fuel blend. Further, the analytic hierarchy process–weighted aggregated sum product assessment method has been applied to identify the optimal setting of the parameters and rank the optimal engine operating range for the B30CL1000 blend. From the results, it was elicited that the accumulation of 1000 ppm of antioxidant (clove oil) additives in the B30 blend resulted in a reduction in the brake-specific fuel consumption by up to 11.5% at higher loads. Brake thermal efficiency increased by 16.3% at low load conditions for the B30CL1000 blend. Then the B30CL1000 blend showed a 2% drop in carbon monoxide emission at higher loads, and the decreased nitrogen oxide emission for the B30CL1000 blend has also been reported as 12% at low loads and 2% at higher loads, which follows a similar trend as exhaust gas temperature. The fifth experimental run having compression ratio (CR) of 17, exhaust gas recirculation (EGR) of 0%, and load of 12 kg has been ranked as 1.