bluuebunny/crossref_metadata_2025 huggingface dataset:
BNIP3-mediated mitophagy boosts the competitive growth of Lenvatinib-resistant cells via energy metabolism reprogramming in HCC
Authors: Wang Sikai , Cheng Hongxia , Li Miaomiao , Gao Dongmei , Wu Haoran , Zhang Shanshan , Huang Yilan , Guo Kun
Published: July 2024

An increasing evidence supports that cell competition, a vital selection and quality control mechanism in multicellular organisms, is involved in tumorigenesis and development; however, the mechanistic contributions to the association between cell competition and tumor drug resistance remain ill-defined. In our study, based on a contructed lenvitinib-resistant hepatocellular carcinoma (HCC) cells display obvious competitive growth dominance over sensitive cells through reprogramming energy metabolism. Mechanistically, the hyperactivation of BCL2 interacting protein3 (BNIP3) -mediated mitophagy in lenvatinib-resistant HCC cells promotes glycolytic flux via shifting energy production from mitochondrial oxidative phosphorylation to glycolysis, by regulating AMP-activated protein kinase (AMPK) -enolase 2 (ENO2) signaling, which perpetually maintaining lenvatinib-resistant HCC cells’ competitive advantage over sensitive HCC cells. Of note, BNIP3 inhibition significantly sensitized the anti-tumor efficacy of lenvatinib in HCC. Our findings emphasize a vital role for BNIP3-AMPK-ENO2 signaling in maintaining the competitive outcome of lenvitinib-resistant HCC cells via regulating energy metabolism reprogramming; meanwhile, this work recognizes BNIP3 as a promising target to overcome HCC drug resistance.
Prospects of a thousand-ion Sn2+ Coulomb-crystal clock with sub-10−19 inaccuracy
Authors: Leibrandt David R. , Porsev Sergey G. , Cheung Charles , Safronova Marianna S.
Published: July 2024

Optical atomic clocks are the most accurate and precise measurement devices of any kind, enabling advances in international timekeeping, Earth science, fundamental physics, and more. However, there is a fundamental tradeoff between accuracy and precision, where higher precision is achieved by using more atoms, but this comes at the cost of larger interactions between the atoms that limit the accuracy. Here, we propose a many-ion optical atomic clock based on three-dimensional Coulomb crystals of order one thousand Sn2+ ions confined in a linear RF Paul trap with the potential to overcome this limitation. Sn2+ has a unique combination of features that is not available in previously considered ions: a 1S0 ↔  3P0 clock transition between two states with zero electronic and nuclear angular momentum (I = J = F = 0) making it immune to nonscalar perturbations, a negative differential polarizability making it possible to operate the trap in a manner such that the two dominant shifts for three-dimensional ion crystals cancel each other, and a laser-accessible transition suitable for direct laser cooling and state readout. We present calculations of the differential polarizability, other relevant atomic properties, and the motion of ions in large Coulomb crystals, in order to estimate the achievable accuracy and precision of Sn2+ Coulomb-crystal clocks.
2D/2D coupled MOF/Fe composite metamaterials enable robust ultra–broadband microwave absorption
Authors: Qu Ning , Sun Hanxu , Sun Yuyao , He Mukun , Xing Ruizhe , Gu Junwei , Kong Jie
Published: July 2024

The combination between macroscopic structure designs and microscopic material designs offers tremendous possibilities for the development of advanced electromagnetic wave (EMW) absorbers. Herein, we propose a metamaterial design to address persistent challenges in this field, including narrow bandwidth, low–frequency bottlenecks, and, particularly, the urgent issue of robustness (i.e., oblique, and polarized incidence). Our absorber features a semiconductive metal-organic framework/iron 2D/2D assembly (CuHT–FCIP) with abundant crystal/crystal heterojunctions and strong magneto-electric coupling networks. This design achieves remarkable EMW absorption across a broad range (2 to 40 GHz) at a thickness of just 9.3 mm. Notably, it maintains stable performance against oblique incidence (within 75°) and polarizations (both transverse electric and transverse magnetic). Furthermore, the absorber demonstrates high specific compressive strength (201.01 MPa·cm3·g−1) and low density (0.89 g·cm−3). This advancement holds promise for developing robust EMW absorbers with superior performance.
Stage-specific GATA3 induction promotes ILC2 development after lineage commitment
Authors: Furuya Hiroki , Toda Yosuke , Iwata Arifumi , Kanai Mizuki , Kato Kodai , Kumagai Takashi , Kageyama Takahiro , Tanaka Shigeru , Fujimura Lisa , Sakamoto Akemi , Hatano Masahiko , Suto Akira , Suzuki Kotaro , Nakajima Hiroshi
Published: July 2024

Group 2 innate lymphoid cells (ILC2s) are a subset of innate lymphocytes that produce type 2 cytokines, including IL-4, IL-5, and IL-13. GATA3 is a critical transcription factor for ILC2 development at multiple stages. However, when and how GATA3 is induced to the levels required for ILC2 development remains unclear. Herein, we identify ILC2-specific GATA3-related tandem super-enhancers (G3SE) that induce high GATA3 in ILC2-committed precursors. G3SE-deficient mice exhibit ILC2 deficiency in the bone marrow, lung, liver, and small intestine with minimal impact on other ILC lineages or Th2 cells. Single-cell RNA-sequencing and subsequent flow cytometry analysis show that GATA3 induction mechanism, which is required for entering the ILC2 stage, is lost in IL-17RB+PD-1− late ILC2-committed precursor stage in G3SE-deficient mice. Cnot6l, part of the CCR4-NOT deadenylase complex, is a possible GATA3 target during ILC2 development. Our findings implicate a stage-specific regulatory mechanism for GATA3 expression during ILC2 development.
Neuroimaging and fluid biomarkers in Parkinson’s disease in an era of targeted interventions
Authors: Zarkali Angeliki , Thomas George E. C. , Zetterberg Henrik , Weil Rimona S.
Published: July 2024

A major challenge in Parkinson’s disease is the variability in symptoms and rates of progression, underpinned by heterogeneity of pathological processes. Biomarkers are urgently needed for accurate diagnosis, patient stratification, monitoring disease progression and precise treatment. These were previously lacking, but recently, novel imaging and fluid biomarkers have been developed. Here, we consider new imaging approaches showing sensitivity to brain tissue composition, and examine novel fluid biomarkers showing specificity for pathological processes, including seed amplification assays and extracellular vesicles. We reflect on these biomarkers in the context of new biological staging systems, and on emerging techniques currently in development.
In situ copper photocatalysts triggering halide atom transfer of unactivated alkyl halides for general C(sp3)-N couplings
Authors: Luo Hang , Yang Yupeng , Fu Yukang , Yu Fangnian , Gao Lei , Ma Yunpeng , Li Yang , Wu Kaifeng , Lin Luqing
Published: July 2024

Direct reduction of unactivated alkyl halides for C(sp3)-N couplings under mild conditions presents a significant challenge in organic synthesis due to their low reduction potential. Herein, we introduce an in situ formed pyridyl-carbene-ligated copper (I) catalyst that is capable of abstracting halide atom and generating alkyl radicals for general C(sp3)-N couplings under visible light. Control experiments confirmed that the mono-pyridyl-carbene-ligated copper complex is the active species responsible for catalysis. Mechanistic investigations using transient absorption spectroscopy across multiple decades of timescales revealed ultrafast intersystem crossing (260 ps) of the photoexcited copper (I) complexes into their long-lived triplet excited states (>2 μs). The non-Stern-Volmer quenching dynamics of the triplets by unactivated alkyl halides suggests an association between copper (I) complexes and alkyl halides, thereby facilitating the abstraction of halide atoms via inner-sphere single electron transfer (SET), rather than outer-sphere SET, for the formation of alkyl radicals for subsequent cross couplings.
Genetically programmed synthetic cells for thermo-responsive protein synthesis and cargo release
Authors: Monck Carolina , Elani Yuval , Ceroni Francesca
Published: July 2024

Synthetic cells containing genetic programs and protein expression machinery are increasingly recognized as powerful counterparts to engineered living cells in the context of biotechnology, therapeutics and cellular modelling. So far, genetic regulation of synthetic cell activity has been largely confined to chemical stimuli; to unlock their potential in applied settings, engineering stimuli-responsive synthetic cells under genetic regulation is imperative. Here we report the development of temperature-sensitive synthetic cells that control protein production by exploiting heat-responsive mRNA elements. This is achieved by combining RNA thermometer technology, cell-free protein expression and vesicle-based synthetic cell design to create cell-sized capsules able to initiate synthesis of both soluble proteins and membrane proteins at defined temperatures. We show that the latter allows for temperature-controlled cargo release phenomena with potential implications for biomedicine. Platforms like the one presented here can pave the way for customizable, genetically programmed synthetic cells under thermal control to be used in biotechnology.
Climate data for building simulations with urban heat island effects and nature-based solutions
Authors: Lu Henry , Gaur Abhishek , Lacasse Michael
Published: July 2024

As cities face a changing climate, buildings will be subjected to increasing energy demand, heat stress, thermal comfort issues, and decreased service life. Therefore, evaluating building performance under climate change is essential for maintaining sustainable and resilient communities. To better prepare building simulation climate data with urban effects, a computationally efficient approach is used to generate “urbanized” data, where the city’s unique signature is obtained through the dynamic Weather Research and Forecasting model for the Ottawa, Canada region. We demonstrate this process using existing climate data and extend it to prepare projections for scenarios where nature-based solutions, such as increased greenery and albedo, were implemented. The data consists of several 31-year time series of climate variables such as temperature, humidity, wind speed and direction, pressure, cloud cover, and precipitation over different global warming thresholds. Such a dataset allows building practitioners to evaluate building performance under both historical and future climate conditions, as well as to evaluate the impacts of nature-based solutions to mitigate future climate change risks.
Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets
Authors: O’Leary Nuala A. , Cox Eric , Holmes J. Bradley , Anderson W. Ray , Falk Robert , Hem Vichet , Tsuchiya Mirian T. N. , Schuler Gregory D. , Zhang Xuan , Torcivia John , Ketter Anne , Breen Laurie , Cothran Jonathan , Bajwa Hena , Tinne Jovany , Meric Peter A. , Hlavina Wratko , Schneider Valerie A.
Published: July 2024

To explore complex biological questions, it is often necessary to access various data types from public data repositories. As the volume and complexity of biological sequence data grow, public repositories face significant challenges in ensuring that the data is easily discoverable and usable by the biological research community. To address these challenges, the National Center for Biotechnology Information (NCBI) has created NCBI Datasets. This resource provides straightforward, comprehensive, and scalable access to biological sequences, annotations, and metadata for a wide range of taxa. Following the FAIR (Findable, Accessible, Interoperable, and Reusable) data management principles, NCBI Datasets offers user-friendly web interfaces, command-line tools, and documented APIs, empowering researchers to access NCBI data seamlessly. The data is delivered as packages of sequences and metadata, thus facilitating improved data retrieval, sharing, and usability in research. Moreover, this data delivery method fosters effective data attribution and promotes its further reuse. This paper outlines the current scope of data accessible through NCBI Datasets and explains various options for exploring and downloading the data.
Correlation analysis of whole genome sequencing of a pathogenic Escherichia coli strain of Inner Mongolian origin
Authors: Jia Yan , Zhang Kai , Cao Jinshan , Mao Wei
Published: July 2024

Anal swabs of 1-month-old Holstein calves with diarrhea were collected from an intensive cattle farm, and a highly pathogenic Escherichia coli strain was obtained by isolation and purification. To study the virulence and resistance genes of pathogenic E.coli that cause diarrhea in calves, a strain of E. coli E12 isolated from calf diarrhea samples was used as experimental material in this experiment, and the virulence of the E12 strain were identified by the mouse infection test, and the whole genome map of the E12 strain were obtained by whole-genome sequencing and analyzed for genome characterization. The results showed that the lethality of strain E12 was 100%, the total length of E12-encoded genes was 4,294,530 bp, Cluster of Orthologous Groups of proteins (COG) annotated to 4,194 functional genes, and the virulence genes of sequenced strain E12 were compared with the virulence genes of sequenced strain E12 from the Virulence Factors of Pathogenic Bacteria (VFDB), which contained a total of 366 virulence genes in sequenced strain E12. The analysis of virulence genes of E12 revealed a total of 52 virulence genes in the iron transferrin system, 56 virulence genes in the secretory system, 41 virulence genes in bacterial toxins, and a total of 217 virulence genes in the Adhesin and Invasins group. The antibiotic resistance genes of sequenced strain E12 were identified through the Antibiotic Resistance Genes Database (ARDB) and Comprehensive Antibiotic Research Database, and it was found that its chromosome and plasmid included a total of 127 antibiotic resistance genes in four classes, and that E12 carried 71 genes related to the antibiotic efflux pumps, 36 genes related to antibiotic inactivation, and 14 antibiotic target alteration and reduced penetration into antibiotics, and 6 antibiotic resistance genes, and the resistance phenotypes were consistent with the genotypes. The pathogenic E. coli that causes diarrhea in calves on this ranch contains a large number of virulence and resistance genes. The results provide a theoretical basis for the prevention and treatment of diarrhea and other diseases caused by E. coli disease.
Adsorption characteristics and applications of andesite in removing some pollutants from wastewater
Authors: Khedr Abdalla M. , Elwakiel Nadia , Halawia Sameh E. , Mansour Ramadan Abdelghany
Published: July 2024

Andesite was employed to effectively extract mercury(II) in an aqueous solution. After evaluating its characteristics, andesite was characterized by applying modern techniques such as BET and TGA methods. The study employed SEM and TEM measurements to analyze the variation in the surface shape and crystallinity of the metal due to adsorption. Using the EDX process, the chemical composition, weight, and atomic percentage of each element of andesite were determined. FTIR techniques were also used to confirm the TEM–EDX findings. Zeta potential was estimated. Cycles of regeneration and desorption have been examined. 99.03% was the highest uptake percentage. Adsorbent quantity (0.0025–0.05) g/L, contact time (5–60) min, pH (2–10), temperature (25–60) °C, and dose (0.0027, 0.0044, 0.0125, 0.0155, and 0.0399) mg/L all affect the amount of removal that increases with the increase in contact time, pH, dose, and temperature but drops as the metal ion concentration rises. The ideal values for contact time, pH, metal ion concentration, dose, and temperature were found to be, respectively, 30 min, 0.0155 mg/l, 0.02 g/l, and 40 °C. The calculation of thermodynamic parameters, including ΔH, ΔG, and ΔS, was imperative in establishing that the mechanism of heavy metal adsorption on andesite was endothermic, exhibiting a physical nature that escalated with temperature rise. The Freundlich adsorption equation's linear form is matched by the adsorption of mercury(II) on andesite; constant n was 1.85, 1.06, 1.1, and 1.1, whereas the Langmuir constant qmwas found to be 1.85, 2.41, 3.54, and 2.28 mg/g at 25–60 °C. Furthermore, adsorption follows a pseudo-second-order rate constant of (3.08, 3.24, 3.24, and 13) g/mg/min under identical temperature conditions, as opposed to a first-order rate constant of 4, 3, 2.6, and 2. Hg2+, NH4+, Cl−, Br−, NO3−, SO42−, Na+, K+, H2S, and CH3SH were all extracted from wastewater by this application.
A retrospective study on the impact of radiotherapy on the survival outcomes of small cell lung cancer patients based on the SEER database
Authors: Chen Yao , Yao Ling , Chen Qingquan , Hu Yiming , Zhu Xi , Dai Rongrong , Chen Xiaoyang , Zeng Yifu , Zhu Yong , Song Duanhong , Zhang Yixiang
Published: July 2024

Small cell lung cancer (SCLC) patients exhibit significant heterogeneity in tumor burden, physical condition, and responses to initial treatment. This diversity in treatment responses can result in varying treatment outcomes. The primary objective of this study was to explore the patient demographics associated with improved survival outcomes through radiotherapy. Based on the SEER database, we identified 42,824 SCLC patients enrolled between 2004 and 2015. These patients were stratified into radiotherapy (n = 20,360) and non-radiotherapy groups (n = 22,464). We controlled for confounding factors using propensity score matching (PSM) analysis. Subsequently, Kaplan–Meier (KM) analysis was employed to evaluate the impact of radiotherapy on patients’ overall survival (OS) and cancer-specific survival (CSS). Cancer-specific mortality was further analyzed using competitive risk models. Cox analysis was also conducted to examine additional variables potentially affecting the survival of SCLC patients. We identified a total of 42,824 eligible patients, and following PSM, 13,329 patients were successfully matched in both the radiotherapy and non-radiotherapy groups. The KM analysis showed that the median OS was 9 months in the radiotherapy group and 6 months in the non-radiotherapy group. The median CSS was 10 months in the radiotherapy group and 7 months in the non-radiotherapy group. The 5-year OS and 10-year OS rates were 6.2% versus 1.6% in the radiotherapy group and 2.6% versus 0.8% in the non-radiotherapy group (P < 0.001). Competitive risk analysis showed that cancer-specific mortality was significantly higher in the non-radiotherapy group than in the radiotherapy group (P < 0.001). Multivariate Cox analysis showed that the radiotherapy group (relative non-radiotherapy group) showed a significant positive effect on survival outcomes (OS: HR 0.658 95% CI [0.642, 0.675] P < 0.001; CSS: HR 0.662 95% CI [0.645, 0.679], P < 0.001). In addition, age, gender, race, primary tumor site, T stage, N stage, M stage, chemotherapy, and surgery were also considered as important predictors of SCLC outcome. The results of the subgroup analysis showed that the radiotherapy group showed a significant survival advantage regardless of age, sex, race, primary tumor site, M stage, chemotherapy, and surgery (P < 0.001). Radiotherapy may improve both OS and CSS in SCLC patients. Patients with SCLC may benefit from radiotherapy regardless of age, sex, race, primary tumor site, M stage, chemotherapy, and surgery.
Exploring the ecological security evaluation of water resources in the Yangtze River Basin under the background of ecological sustainable development
Authors: Zhou Jie-Rong , Li Xiao-Qing , Yu Xin , Zhao Tian-Cheng , Ruan Wen-Xi
Published: July 2024

The Yangtze River (hereafter referred to as the YZR), the largest river in China, is of paramount importance for ensuring water resource security. The Yangtze River Basin (hereafter referred to as the YRB) is one of the most densely populated areas in China, and complex human activities have a significant impact on the ecological security of water resources. Therefore, this paper employs theories related to ecological population evolution and the Driving Force-Pressure-State-Impact-Response (DPSIR) model to construct an indicator system for the ecological security of water resources in the YRB. The report evaluates the ecological security status of water resources in each province of the YRB from 2010 to 2019, clarifies the development trend of its water resource ecological security, and proposes corresponding strategies for regional ecological security and coordinated economic development. According to the results of the ecological population evolution competition model, the overall indicator of the ecological security of water resources in the YRB continues to improve, with the safety level increasing annually. Maintaining sound management of water resources in the YRB is crucial for sustainable socioeconomic development. To further promote the ecological security of water resources in the YRB and the coordinated development of the regional economy, this paper proposes policy suggestions such as promoting the continuous advancement of sustainable development projects, actively adjusting industrial structure, continuously enhancing public environmental awareness, and actively participating in international ecological construction and seeking cooperation among multiple departments.
AI driven analysis of MRI to measure health and disease progression in FSHD
Authors: Riem Lara , DuCharme Olivia , Cousins Matthew , Feng Xue , Kenney Allison , Morris Jacob , Tapscott Stephen J. , Tawil Rabi , Statland Jeff , Shaw Dennis , Wang Leo , Walker Michaela , Lewis Leann , Jacobs Michael A. , Leung Doris G. , Friedman Seth D. , Blemker Silvia S.
Published: July 2024

Facioscapulohumeral muscular dystrophy (FSHD) affects roughly 1 in 7500 individuals. While at the population level there is a general pattern of affected muscles, there is substantial heterogeneity in muscle expression across- and within-patients. There can also be substantial variation in the pattern of fat and water signal intensity within a single muscle. While quantifying individual muscles across their full length using magnetic resonance imaging (MRI) represents the optimal approach to follow disease progression and evaluate therapeutic response, the ability to automate this process has been limited. The goal of this work was to develop and optimize an artificial intelligence-based image segmentation approach to comprehensively measure muscle volume, fat fraction, fat fraction distribution, and elevated short-tau inversion recovery signal in the musculature of patients with FSHD. Intra-rater, inter-rater, and scan-rescan analyses demonstrated that the developed methods are robust and precise. Representative cases and derived metrics of volume, cross-sectional area, and 3D pixel-maps demonstrate unique intramuscular patterns of disease. Future work focuses on leveraging these AI methods to include upper body output and aggregating individual muscle data across studies to determine best-fit models for characterizing progression and monitoring therapeutic modulation of MRI biomarkers.
Vaccination homophily in ego contact networks during the COVID-19 pandemic
Authors: Stefkovics Ádám , Albert Fruzsina , Ligeti Anna Sára , Dávid Beáta , Rudas Szilvia , Koltai Júlia
Published: July 2024

Vaccine hesitancy is an inevitable risk for societies as it contributes to outbreaks of diseases. Prior research suggests that vaccination decisions of individuals tend to spread within social networks, resulting in a tendency to vaccination homophily. The clustering of individuals resistant to vaccination can substantially make the threshold necessary to achieve herd immunity harder to reach. In this study, we examined the extent of vaccination homophily among social contacts and its association with vaccine uptake during the COVID-19 pandemic in Hungary using a contact diary approach in two cross-sectional surveys. The results indicate strong clustering among both vaccinated and unvaccinated groups. The most powerful predictor of vaccine uptake was the perceived vaccination rate within the egos’ social contact network. Vaccination homophily and the role of the interpersonal contact network in vaccine uptake were particularly pronounced in the networks of close relationships, including family, kinship, and strong social ties of the ego. Our findings have important implications for understanding COVID-19 spread dynamics by showing that the strong clustering of unvaccinated individuals posed a great risk in preventing the spread of the disease.
3D engineered scaffold for large-scale Vigil immunotherapy production
Authors: Kerneis Fabienne , Bognar Ernest , Stanbery Laura , Moon Seongjun , Kim Do Hoon , Deng Yuxuan , Hughes Elliot , Chun Tae-Hwa , Tharp Darron , Zupanc Heidi , Jay Chris , Walter Adam , Nemunaitis John , Lahann Joerg
Published: July 2024

Previously, we reported successful cellular expansion of a murine colorectal carcinoma cell line (CT-26) using a three-dimensional (3D) engineered extracellular matrix (EECM) fibrillar scaffold structure. CCL-247 were grown over a limited time period of 8 days on 3D EECM or tissue culture polystyrene (TCPS). Cells were then assayed for growth, electroporation efficiency and Vigil manufacturing release criteria. Using EECM scaffolds, we report an expansion of CCL-247 (HCT116), a colorectal carcinoma cell line, from a starting concentration of 2.45 × 105 cells to 1.9 × 106 cells per scaffold. Following expansion, 3D EECM-derived cells were assessed based on clinical release criteria of the Vigil manufacturing process utilized for Phase IIb trial operation with the FDA. 3D EECM-derived cells passed all Vigil manufacturing release criteria including cytokine expression. Here, we demonstrate successful Vigil product manufacture achieving the specifications necessary for the clinical trial product release of Vigil treatment. Our results confirm that 3D EECM can be utilized for the expansion of human cancer cell CCL-247, justifying further clinical development involving human tissue sample manufacturing including core needle biopsy and minimal ascites samples.
Probabilistic prediction and context tree identification in the Goalkeeper game
Authors: Hernández Noslen , Galves Antonio , García Jesús E. , Gubitoso Marcos D. , Vargas Claudia D.
Published: July 2024

In this article we address two related issues on the learning of probabilistic sequences of events. First, which features make the sequence of events generated by a stochastic chain more difficult to predict. Second, how to model the procedures employed by different learners to identify the structure of sequences of events. Playing the role of a goalkeeper in a video game, participants were told to predict step by step the successive directions—left, center or right—to which the penalty kicker would send the ball. The sequence of kicks was driven by a stochastic chain with memory of variable length. Results showed that at least three features play a role in the first issue: (1) the shape of the context tree summarizing the dependencies between present and past directions; (2) the entropy of the stochastic chain used to generate the sequences of events; (3) the existence or not of a deterministic periodic sequence underlying the sequences of events. Moreover, evidence suggests that best learners rely less on their own past choices to identify the structure of the sequences of events.
Nicotinamide N-methyltransferase inhibition mimics and boosts exercise-mediated improvements in muscle function in aged mice
Authors: Dimet-Wiley Andrea L. , Latham Christine M. , Brightwell Camille R. , Neelakantan Harshini , Keeble Alexander R. , Thomas Nicholas T. , Noehren Haley , Fry Christopher S. , Watowich Stanley J.
Published: July 2024

Human hallmarks of sarcopenia include muscle weakness and a blunted response to exercise. Nicotinamide N-methyltransferase inhibitors (NNMTis) increase strength and promote the regenerative capacity of aged muscle, thus offering a promising treatment for sarcopenia. Since human hallmarks of sarcopenia are recapitulated in aged (24-month-old) mice, we treated mice from 22 to 24 months of age with NNMTi, intensive exercise, or a combination of both, and compared skeletal muscle adaptations, including grip strength, longitudinal running capacity, plantarflexor peak torque, fatigue, and muscle mass, fiber type, cross-sectional area, and intramyocellular lipid (IMCL) content. Exhaustive proteome and metabolome analyses were completed to identify the molecular mechanisms underlying the measured changes in skeletal muscle pathophysiology. Remarkably, NNMTi-treated aged sedentary mice showed ~ 40% greater grip strength than sedentary controls, while aged exercised mice only showed a 20% increase relative to controls. Importantly, the grip strength improvements resulting from NNMTi treatment and exercise were additive, with NNMTi-treated exercised mice developing a 60% increase in grip strength relative to sedentary controls. NNMTi treatment also promoted quantifiable improvements in IMCL content and, in combination with exercise, significantly increased gastrocnemius fiber CSA. Detailed skeletal muscle proteome and metabolome analyses revealed unique molecular mechanisms associated with NNMTi treatment and distinct molecular mechanisms and cellular processes arising from a combination of NNMTi and exercise relative to those given a single intervention. These studies suggest that NNMTi-based drugs, either alone or combined with exercise, will be beneficial in treating sarcopenia and a wide range of age-related myopathies.
Prediction of optical properties of rare-earth doped phosphate glasses using gene expression programming
Authors: Ahmadi Fahimeh , El-Mallawany Raouf , Papanikolaou Stefanos , Asteris Panagiotis G.
Published: July 2024

The progression of optical materials and their associated applications necessitates a profound comprehension of their optical characteristics, with the Judd–Ofelt (JO) theory commonly employed for this purpose. However, the computation of JO parameters (Ω2, Ω4, Ω6) entails wide experimental and theoretical endeavors, rendering traditional calculations often impractical. To address these challenges, the correlations between JO parameters and the bulk matrix composition within a series of Rare-Earth ions doped sulfophosphate glass systems were explored in this research. In this regard, a novel soft computing technique named genetic expression programming (GEP) was employed to derive formulations for JO parameters and bulk matrix composition. The predictor variables integrated into the formulations consist of JO parameters. This investigation demonstrates the potential of GEP as a practical tool for defining functions and classifying important factors to predict JO parameters. Thus, precise characterization of such materials becomes crucial with minimal or no reliance on experimental work.
Reasoning with the inverse of 3D cardinal direction relations based on direction matrices
Authors: Wang Miao , Dong Xingxing , Gao Jixun , Fang Zhenxi , Tang Hao , Li Song
Published: July 2024

In order to improve the ability of intelligent reasoning and prediction of 3DR27 model which presented in our previous work, enhance the usability of this model, and better fulfill the demands of real applications for spatial database, we focused on the problem of reasoning with the inverse of 3D cardinal direction relations between spatial objects. In order to realize automated reasoning, an algorithm for computing the inverse of 3D cardinal direction relations based on matrices is proposed on the basis of the mapping between the 3D rectangular cardinal direction relations and 3D interval relation matrix. This algorithm improves the power of reasoning for this model by means of the excellent properties of matrix operations. Theorems are provided to prove formally that our algorithm is correct and complete. This study realized the automatic inference and calculation of the inverse of the 3D cardinal direction relations based on 3DR27 model and further improved the ability of spatial reasoning and spatial analysis of spatial database.
Microscopic evaluation of spin and orbital moment in ferromagnetic resonance
Authors: Ishii Yuta , Yamasaki Yuichi , Kozuka Yusuke , Lustikova Jana , Nii Yoichi , Onose Yoshinori , Yokoyama Yuichi , Mizumaki Masaichiro , Adachi Jun-ichi , Nakao Hironori , Arima Taka-hisa , Wakabayashi Yusuke
Published: July 2024

Time-resolved X-ray magnetic circular dichroism under the effects of ferromagnetic resonance (FMR), known as X-ray ferromagnetic resonance (XFMR) measurements, enables direct detection of precession dynamics of magnetic moment. Here we demonstrated XFMR measurements and Bayesian analyses as a quantitative probe for the precession of spin and orbital magnetic moments under the FMR effect. Magnetization precessions in two different Pt/Ni-Fe thin film samples were directly detected. Furthermore, the ratio of dynamical spin and orbital magnetic moments was evaluated quantitatively by Bayesian analyses for XFMR energy spectra around the Ni $$L_{2,3}$$

L

2
,
3

absorption edges. Our study paves the way for a microscopic investigation of the contribution of the orbital magnetic moment to magnetization dynamics.
Exposure to source-specific air pollution in residential areas and its association with dementia incidence: a cohort study in Northern Sweden
Authors: Oudin Anna , Raza Wasif , Flanagan Erin , Segersson David , Jalava Pasi , Kanninen Katja M. , Rönkkö Topi , Giugno Rosalba , Sandström Thomas , Muala Ala , Topinka Jan , Sommar Johan
Published: July 2024

The aim of this study was to investigate the relationship between source-specific ambient particulate air pollution concentrations and the incidence of dementia. The study encompassed 70,057 participants from the Västerbotten intervention program cohort in Northern Sweden with a median age of 40 years at baseline. High-resolution dispersion models were employed to estimate source-specific particulate matter (PM) concentrations, such as PM10 and PM2.5 from traffic, exhaust, and biomass (mainly wood) burning, at the residential addresses of each participant. Cox regression models, adjusted for potential confounding factors, were used for the assessment. Over 884,847 person-years of follow-up, 409 incident dementia cases, identified through national registers, were observed. The study population’s average exposure to annual mean total PM10 and PM2.5 lag 1–5 years was 9.50 µg/m3 and 5.61 µg/m3, respectively. Increased risks were identified for PM10-Traffic (35% [95% CI 0–82%]) and PM2.5-Exhaust (33% [95% CI − 2 to 79%]) in the second exposure tertile for lag 1–5 years, although no such risks were observed in the third tertile. Interestingly, a negative association was observed between PM2.5-Wood burning and the risk of dementia. In summary, this register-based study did not conclusively establish a strong association between air pollution exposure and the incidence of dementia. While some evidence indicated elevated risks for PM10-Traffic and PM2.5-Exhaust, and conversely, a negative association for PM2.5-Wood burning, no clear exposure–response relationships were evident.
Green spaces contribute to structural resilience of the gut microbiota in urban mammals
Authors: Łopucki Rafał , Sajnaga Ewa , Kalwasińska Agnieszka , Klich Daniel , Kitowski Ignacy , Stępień-Pyśniak Dagmara , Christensen Henrik
Published: July 2024

The gut microbiome of wild animals is subject to various environmental influences, including those associated with human-induced alterations to the environment. We investigated how the gut microbiota of a synurbic rodent species, the striped field mouse (Apodemus agrarius), change in cities of varying sizes, seeking the urban microbiota signature for this species. Fecal samples for analysis were collected from animals living in non-urbanized areas and green spaces of different-sized cities (Poland). Metagenomic 16S rRNA gene sequencing and further bioinformatics analyses were conducted. Significant differences in the composition of gut microbiomes among the studied populations were found. However, the observed changes were dependent on local habitat conditions, without strong evidence of a correlation with the size of the urbanized area. The results suggest that ecological detachment from a more natural, non-urban environment does not automatically lead to the development of an “urban microbiome” model in the studied rodent. The exposure to the natural environment in green spaces may serve as a catalyst for microbiome transformations, providing a previously underestimated contribution to the maintenance of native gut microbial communities in urban mammals.
Research on bearing fault diagnosis based on improved genetic algorithm and BP neural network
Authors: Chen Zenghua , Zhu Lingjian , Lu He , Chen Shichao , Zhu Fenghua , Liu Sheng , Han Yunjun , Xiong Gang
Published: July 2024

Health monitoring and fault diagnosis of rolling bearings are crucial for the continuous and effective operation of mechanical equipment. In order to improve the accuracy of BP neural network in fault diagnosis of rolling bearings, a feature model is established from the vibration signals of rolling bearings, and an improved genetic algorithm is used to optimize the initial weights, biases, and hyperparameters of the BP neural network. This overcomes the shortcomings of BP neural network, such as being prone to local minima, slow convergence speed, and sample dependence. The improved genetic algorithm fully considers the degree of concentration and dispersion of population fitness in genetic algorithms, and adaptively adjusts the crossover and mutation probabilities of genetic algorithms in a non-linear manner. At the same time, in order to accelerate the optimization efficiency of the selection operator, the elite retention strategy is combined with the hierarchical proportional selection operation. Using the rolling bearing dataset from Case Western Reserve University in the United States as experimental data, the proposed algorithm was used for simulation and prediction. The experimental results show that compared with the other seven models, the proposed IGA-BPNN exhibit superior performance in both convergence speed and predictive performance.
Investigating structural and optoelectronic properties of Cr-substituted ZnSe semiconductors
Authors: Iqbal Muhammad Aamir , Bakhsh Sunila , Maidin Siti Sarah , Morsy Kareem , Choi Jeong Ryeol , Alguno Arnold C.
Published: July 2024

The optoelectronic and structural characteristics of the Zn1−xCrxSe (0 ≤ x ≤ 1) semiconductor are reported by employing density functional theory (DFT) within the mBJ potential. The findings revealed that the lattice constant decreases with increasing Cr concentration, although the bulk modulus exhibits the opposite trend. ZnSe is a direct bandgap material; however, a change from direct to indirect electronic bandgap has been seen with Cr presence. This transition is caused by structural alterations by Cr and defects forming, which results in novel optical features, including electronic transitions. The electronic bandgap decreases from 2.769 to 0.216 eV, allowing phonons to participate and improving optical absorption. A higher concentration of Cr boosts infrared absorption and these Cr-based ZnSe (ZnCrSe) semiconductors also cover a wider spectrum in the visible range from red to blue light. Important optical parameters such as reflectance, optical conductivity, optical bandgap, extinction coefficient, refractive index, magnetization factor, and energy loss function are discussed, providing a theoretical understanding of the diverse applications of ZnCrSe semiconductors in photonic and optoelectronic devices.
UAV telephotography elucidates floristic variability and beta diversity of island cliffs under grazing interventions
Authors: Kim Seongjun , Lee Chang Woo , Park Hwan-Joon , Hwang Jung Eun , Park Hyeong Bin , Yoon Young-Jun , Kim Yeong-Joong
Published: July 2024

Cliffs contain one of the least known plant communities, which has been overlooked in biodiversity assessments due to the inherent inaccessibility. Our study adopted the unmanned aerial vehicle (UAV) with the telephoto camera to remotely clarify floristic variability across unreachable cliffs. Studied cliffs comprised 17 coastal and 13 inland cliffs in Gageodo of South Korea, among which 9 and 5 cliffs were grazed by the introduced cliff-dwelling goats. The UAV telephotography showed 154 and 166 plant species from coastal and inland cliffs, respectively. Inland cliffs contained more vascular plant species (P < 0.001), increased proportions of fern and woody species (P < 0.05), and decreased proportion of herbaceous species (P < 0.001) than coastal cliffs. It was also found that coastal and inland cliffs differed in the species composition (P < 0.001) rather than taxonomic beta diversity (P = 0.29). Furthermore, grazed coastal cliffs featured the elevated proportions of alien and annual herb species than ungrazed coastal cliffs (P < 0.05). This suggests that coastal cliffs might not be totally immune to grazing if the introduced herbivores are able to access cliff microhabitats; therefore, such anthropogenic introduction of cliff-dwelling herbivores should be excluded to conserve the native cliff plant communities.
Oral antidiabetic therapy versus early insulinization on glycemic control in newly diagnosed type 2 diabetes patients: a retrospective matched cohort study
Authors: Lee Yang-Ming , Lin Pei Ru , Sia Hon-Ke
Published: July 2024

Our study aims to compare the efficacy of oral antidiabetic therapy to early insulinization on glycemic control among newly diagnosed type 2 diabetes patients in real-world clinical practice. A retrospective cohort study conducted at a medical center in Taiwan analyzed 1256 eligible patients from January 2007 to December 2017. Propensity score matching resulted in well-balanced groups of 94 patients each in the oral antidiabetic drug (OAD) and early insulinization cohorts. Glycemic outcomes were assessed in both groups. Patients exclusively using OAD showed consistently lower glycated hemoglobin (HbA1c) levels at 3, 12, 24, and 36 months compared to insulin users. At later periods, 77.7% of OAD users achieved glycemic control versus 64.9% of insulin users, with a marginally significant difference. Subgroup analyses suggested a trend favoring well-controlled diabetes in the OAD group, though not statistically significant. Our study finds oral antidiabetic therapy is not inferior to early insulinization for glycemic control in newly diagnosed type 2 diabetes patients, irrespective of initial HbA1c levels. This supports oral therapy as a rational treatment option, even in cases with elevated HbA1c at diagnosis.
Evidence of membranolytic targeting and intracellular citrullination in neutrophils isolated from patients with rheumatoid arthritis
Authors: Moadab Fatemeh , Wang Xiaoxing , Le Ethan , Gazitt Tal , Najjar Rayan , Nelson J. Lee , Joshua Vijay , Malmström Vivianne , Elkon Keith , Grönwall Caroline , Mustelin Tomas
Published: July 2024

Anti-citrullinated protein autoantibodies (ACPA) are diagnostic for rheumatoid arthritis (RA). The antigens recognized by these autoantibodies are produced by protein arginine deiminases (PADs), particularly PAD4. However, it remains unknown why and how PAD4 causes this aberrant citrullination in RA. Here, we report that poly-perforin pores are present on freshly isolated neutrophils from RA patients, but not on healthy donor neutrophils. Neutrophils with perforin pores also contained intracellular citrullinated proteins in the region adjacent to the pores. This response was replicated in vitro by treating neutrophils with purified perforin, which generated intense dots of anti-perforin immunofluorescence, calcium influx, and intracellular citrullination. Extensive neutrophil killing in Felty’s syndrome, an aggressive form of RA, correlated with particularly high ACPA, and PAD4 autoantibodies. In contrast, other forms of death, including NETosis, apoptosis, and pyroptosis, produced minimal citrullination. We conclude that neutrophil targeting by perforin leading to intracellular citrullination takes place in patients with RA.
Using wet-bulb globe temperature meters to examine the effect of heat on various tennis court surfaces
Authors: Yamaguchi Hiroki , Mori Takaaki , Hanano Hiromi , Oishi Kan , Ikeue Kentaro , Yamamoto Yuiko , Ishii Kojiro
Published: July 2024

In this study, we evaluated the thermal environments of different tennis courts using wet-bulb globe temperature (WBGT) meters. WBGT meters were installed in an outdoor hard court, sand-filled artificial grass court, and clay court (a softball field), and measurements were taken hourly from 9:00 to 17:00 on weekdays from June 1 to September 21, 2022. The results were compared with data from different courts and the nearest Japan Meteorological Agency station (JMA WBGT) based on the Japan Sports Association’s guidelines for exercise to prevent heat stroke. The median WBGT on each court was significantly higher for hard courts at the “Warning” (25 ≤ JMA WBGT < 28) level or above, sand-filled artificial grass courts at the “Severe Warning” (28 ≤ JMA WBGT < 31) level or above, and clay courts at the “Danger” (31 ≤ JMA WBGT) level than the JMA WBGT. Compared with the JMA WBGT, hard and sand-filled artificial grass courts are played on under particularly hot conditions. The results of this study could indicate to tournament organizers and coaches the importance of measuring the WBGT on each court surface from an early stage to prevent heat-related incidents.
Imagined speech event detection from electrocorticography and its transfer between speech modes and subjects
Authors: de Borman Aurélie , Wittevrongel Benjamin , Dauwe Ine , Carrette Evelien , Meurs Alfred , Van Roost Dirk , Boon Paul , Van Hulle Marc M.
Published: July 2024

Speech brain-computer interfaces aim to support communication-impaired patients by translating neural signals into speech. While impressive progress was achieved in decoding performed, perceived and attempted speech, imagined speech remains elusive, mainly due to the absence of behavioral output. Nevertheless, imagined speech is advantageous since it does not depend on any articulator movements that might become impaired or even lost throughout the stages of a neurodegenerative disease. In this study, we analyzed electrocortigraphy data recorded from 16 participants in response to 3 speech modes: performed, perceived (listening), and imagined speech. We used a linear model to detect speech events and examined the contributions of each frequency band, from delta to high gamma, given the speech mode and electrode location. For imagined speech detection, we observed a strong contribution of gamma bands in the motor cortex, whereas lower frequencies were more prominent in the temporal lobe, in particular of the left hemisphere. Based on the similarities in frequency patterns, we were able to transfer models between speech modes and participants with similar electrode locations.