bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimated exposure to perfluoroalkyl substances during infancy and serum-adipokine concentrations in later childhood
Authors: Grandjean Philippe , Shih Yu-Hsuan , Jørgensen Louise Helskov , Nielsen Flemming , Weihe Pál , Budtz-Jørgensen Esben
Published: June 2023

Background

Perfluoroalkyl substances (PFASs) are transferred through human milk and may cause elevated exposure during infancy. Given the lack of early postnatal blood samples, PFAS concentrations can be estimated to serve as predictors of subsequent metabolic toxicity.

Methods

A total of 298 children from a prospective birth cohort were followed up through to age 9 years. Serum-PFAS was measured at birth and 18 months of age, while exposures during infancy were estimated by structural equations. Adiponectin, resistin, leptin, and the leptin receptor were measured in serum at age 9. Adjusted regression coefficients for estimated serum-PFAS concentrations were calculated, with additional consideration of the duration of breastfeeding and potential effect modification by sex.

Results

A doubling in estimated serum-PFAS concentrations, particularly at ages 6 and 12 months, was associated with a loss of about 10–15% in age 9 resistin concentrations, while other associations were much weaker. Sex dependence of the associations was not observed, and neither did the duration of breastfeeding affect outcomes at age 9.

Conclusion

Lowered serum-resistin concentrations at age 9 years were most strongly associated with early postnatal PFAS exposures. These findings suggest that infancy may represent a vulnerable time window for some aspects of metabolic programming that may be affected by PFAS exposure.

Impact

Serum-PFAS concentrations during infancy can be estimated in the absence of blood samples.

Adipokine concentrations were measured at age 9 years as metabolic biomarkers.

Resistin was significantly lower in children with elevated PFAS exposures in infancy.

The findings suggest that early postnatal PFAS exposures may affect subsequent metabolic health.

Assessment of infancy vulnerability to PFAS can be explored using estimated serum-PFAS concentrations.
Out with AI, in with the psychiatrist: a preference for human-derived clinical decision support in depression care
Authors: Maslej Marta M. , Kloiber Stefan , Ghassemi Marzyeh , Yu Joanna , Hill Sean L.
Published: June 2023

Advancements in artificial intelligence (AI) are enabling the development of clinical support tools (CSTs) in psychiatry to facilitate the review of patient data and inform clinical care. To promote their successful integration and prevent over-reliance, it is important to understand how psychiatrists will respond to information provided by AI-based CSTs, particularly if it is incorrect. We conducted an experiment to examine psychiatrists’ perceptions of AI-based CSTs for treating major depressive disorder (MDD) and to determine whether perceptions interacted with the quality of CST information. Eighty-three psychiatrists read clinical notes about a hypothetical patient with MDD and reviewed two CSTs embedded within a single dashboard: the note’s summary and a treatment recommendation. Psychiatrists were randomised to believe the source of CSTs was either AI or another psychiatrist, and across four notes, CSTs provided either correct or incorrect information. Psychiatrists rated the CSTs on various attributes. Ratings for note summaries were less favourable when psychiatrists believed the notes were generated with AI as compared to another psychiatrist, regardless of whether the notes provided correct or incorrect information. A smaller preference for psychiatrist-generated information emerged in ratings of attributes that reflected the summary’s accuracy or its inclusion of important information from the full clinical note. Ratings for treatment recommendations were also less favourable when their perceived source was AI, but only when recommendations were correct. There was little evidence that clinical expertise or familiarity with AI impacted results. These findings suggest that psychiatrists prefer human-derived CSTs. This preference was less pronounced for ratings that may have prompted a deeper review of CST information (i.e. a comparison with the full clinical note to evaluate the summary’s accuracy or completeness, assessing an incorrect treatment recommendation), suggesting a role of heuristics. Future work should explore other contributing factors and downstream implications for integrating AI into psychiatric care.
SMURF1 attenuates endoplasmic reticulum stress by promoting the degradation of KEAP1 to activate NRF2 antioxidant pathway
Authors: Dong Lei , Xu Mengchuan , Li Yang , Xu Wanting , Wu Chengwei , Zheng Hanfei , Xiao Zhenyu , Sun Guochen , Ding Lei , Li Xiaobo , Li Wenming , Zhou Liying , Xia Qin
Published: June 2023

Cancer cells consistently utilize the unfolded protein response (UPR) to encounter the abnormal endoplasmic reticulum (ER) stress induced by the accumulation of misfolded proteins. Extreme activation of the UPR could also provoke maladaptive cell death. Previous reports have shown that NRF2 antioxidant signaling is activated by UPR and serves as noncanonical pathway to defense and reduce excessive ROS levels during ER stress. However, the mechanisms of regulating NRF2 signaling upon ER stress in glioblastoma have not been fully elucidated. Here we identify that SMURF1 protects against ER stress and facilitates glioblastoma cell survival by rewiring KEAP1-NRF2 pathway. We show that ER stress induces SMURF1 degradation. Knockdown of SMURF1 upregulates IRE1 and PERK signaling in the UPR pathway and prevents ER-associated protein degradation (ERAD) activity, leading to cell apoptosis. Importantly, SMURF1 overexpression activates NRF2 signaling to reduce ROS levels and alleviate UPR-mediated cell death. Mechanistically, SMURF1 interacts with and ubiquitinates KEAP1 for its degradation (NRF2 negative regulator), resulting in NRF2 nuclear import. Moreover, SMURF1 loss reduces glioblastoma cell proliferation and growth in subcutaneously implanted nude mice xenografts. Taken together, SMURF1 rewires KEAP1-NRF2 pathway to confer resistance to ER stress inducers and protect glioblastoma cell survival. ER stress and SMURF1 modulation may provide promising therapeutic targets for the treatment of glioblastoma.
Quantum bath suppression in a superconducting circuit by immersion cooling
Authors: Lucas M. , Danilov A. V. , Levitin L. V. , Jayaraman A. , Casey A. J. , Faoro L. , Tzalenchuk A. Ya. , Kubatkin S. E. , Saunders J. , de Graaf S. E.
Published: June 2023

Quantum circuits interact with the environment via several temperature-dependent degrees of freedom. Multiple experiments to-date have shown that most properties of superconducting devices appear to plateau out at T ≈ 50 mK – far above the refrigerator base temperature. This is for example reflected in the thermal state population of qubits, in excess numbers of quasiparticles, and polarisation of surface spins – factors contributing to reduced coherence. We demonstrate how to remove this thermal constraint by operating a circuit immersed in liquid 3He. This allows to efficiently cool the decohering environment of a superconducting resonator, and we see a continuous change in measured physical quantities down to previously unexplored sub-mK temperatures. The 3He acts as a heat sink which increases the energy relaxation rate of the quantum bath coupled to the circuit a thousand times, yet the suppressed bath does not introduce additional circuit losses or noise. Such quantum bath suppression can reduce decoherence in quantum circuits and opens a route for both thermal and coherence management in quantum processors.
Genome expansion by a CRISPR trimmer-integrase
Authors: Wang Joy Y. , Tuck Owen T. , Skopintsev Petr , Soczek Katarzyna M. , Li Gary , Al-Shayeb Basem , Zhou Julia , Doudna Jennifer A.
Published: June 2023

CRISPR–Cas adaptive immune systems capture DNA fragments from invading mobile genetic elements and integrate them into the host genome to provide a template for RNA-guided immunity1. CRISPR systems maintain genome integrity and avoid autoimmunity by distinguishing between self and non-self, a process for which the CRISPR/Cas1–Cas2 integrase is necessary but not sufficient2–5. In some microorganisms, the Cas4 endonuclease assists CRISPR adaptation6,7, but many CRISPR–Cas systems lack Cas48. Here we show here that an elegant alternative pathway in a type I-E system uses an internal DnaQ-like exonuclease (DEDDh) to select and process DNA for integration using the protospacer adjacent motif (PAM). The natural Cas1–Cas2/exonuclease fusion (trimmer-integrase) catalyses coordinated DNA capture, trimming and integration. Five cryo-electron microscopy structures of the CRISPR trimmer-integrase, visualized both before and during DNA integration, show how asymmetric processing generates size-defined, PAM-containing substrates. Before genome integration, the PAM sequence is released by Cas1 and cleaved by the exonuclease, marking inserted DNA as self and preventing aberrant CRISPR targeting of the host. Together, these data support a model in which CRISPR systems lacking Cas4 use fused or recruited9,10 exonucleases for faithful acquisition of new CRISPR immune sequences.
A tripartite rheostat controls self-regulated host plant resistance to insects
Authors: Guo Jianping , Wang Huiying , Guan Wei , Guo Qin , Wang Jing , Yang Jing , Peng Yaxin , Shan Junhan , Gao Mingyang , Shi Shaojie , Shangguan Xinxin , Liu Bingfang , Jing Shengli , Zhang Jing , Xu Chunxue , Huang Jin , Rao Weiwei , Zheng Xiaohong , Wu Di , Zhou Cong , Du Bo , Chen Rongzhi , Zhu Lili , Zhu Yuxian , Walling Linda L. , Zhang Qifa , He Guangcun
Published: June 2023

Plants deploy receptor-like kinases and nucleotide-binding leucine-rich repeat receptors to confer host plant resistance (HPR) to herbivores1. These gene-for-gene interactions between insects and their hosts have been proposed for more than 50 years2. However, the molecular and cellular mechanisms that underlie HPR have been elusive, as the identity and sensing mechanisms of insect avirulence effectors have remained unknown. Here we identify an insect salivary protein perceived by a plant immune receptor. The BPH14-interacting salivary protein (BISP) from the brown planthopper (Nilaparvata lugens Stål) is secreted into rice (Oryza sativa) during feeding. In susceptible plants, BISP targets O. satvia RLCK185 (OsRLCK185; hereafter Os is used to denote O. satvia-related proteins or genes) to suppress basal defences. In resistant plants, the nucleotide-binding leucine-rich repeat receptor BPH14 directly binds BISP to activate HPR. Constitutive activation of Bph14-mediated immunity is detrimental to plant growth and productivity. The fine-tuning of Bph14-mediated HPR is achieved through direct binding of BISP and BPH14 to the selective autophagy cargo receptor OsNBR1, which delivers BISP to OsATG8 for degradation. Autophagy therefore controls BISP levels. In Bph14 plants, autophagy restores cellular homeostasis by downregulating HPR when feeding by brown planthoppers ceases. We identify an insect saliva protein sensed by a plant immune receptor and discover a three-way interaction system that offers opportunities for developing high-yield, insect-resistant crops.
A proposed FAIR approach for disseminating geospatial information system maps
Authors: Thompson P. Travis , Ojha Sweta , Powell Christian D. , Pennell Kelly G. , Moseley Hunter N. B.
Published: June 2023

We present a draft Minimum Information About Geospatial Information System (MIAGIS) standard for facilitating public deposition of geospatial information system (GIS) datasets that follows the FAIR (Findable, Accessible, Interoperable and Reusable) principles. The draft MIAGIS standard includes a deposition directory structure and a minimum javascript object notation (JSON) metadata formatted file that is designed to capture critical metadata describing GIS layers and maps as well as their sources of data and methods of generation. The associated miagis Python package facilitates the creation of this MIAGIS metadata file and directly supports metadata extraction from both Esri JSON and GEOJSON GIS data formats plus options for extraction from user-specified JSON formats. We also demonstrate their use in crafting two example depositions of ArcGIS generated maps. We hope this draft MIAGIS standard along with the supporting miagis Python package will assist in establishing a GIS standards group that will develop the draft into a full standard for the wider GIS community as well as a future public repository for GIS datasets.
Host nasopharyngeal transcriptome dataset of a SARS-CoV-2 positive Italian cohort
Authors: Salvati Annamaria , Ferravante Carlo , Lamberti Jessica , Rocco Teresa , Alexandrova Elena , D’Agostino Ylenia , Sorokin Maksim , Efimov Victor , Buzdin Anton , Strianese Oriana , Nassa Giovanni , Tarallo Roberta , Weisz Alessandro , Rizzo Francesca , Giurato Giorgio
Published: June 2023

The ongoing COVID-19 pandemic caused by SARS-CoV-2 has affected millions of people worldwide and has significant implications for public health. Host transcriptomics profiling provides comprehensive understanding of how the virus interacts with host cells and how the host responds to the virus. COVID-19 disease alters the host transcriptome, affecting cellular pathways and key molecular functions. To contribute to the global effort to understand the virus’s effect on host cell transcriptome, we have generated a dataset from nasopharyngeal swabs of 35 individuals infected with SARS-CoV-2 from the Campania region in Italy during the three outbreaks, with different clinical conditions. This dataset will help to elucidate the complex interactions among genes and can be useful in the development of effective therapeutic pathways.
A draft genome assembly of reef-building octocoral Heliopora coerulea
Authors: Ip Jack Chi-Ho , Ho Ming-Hay , Chan Benny K. K. , Qiu Jian-Wen
Published: June 2023

Coral reefs are under existential threat from climate change and anthropogenic impacts. Genomic studies have enhanced our knowledge of resilience and responses of some coral species to environmental stress, but reference genomes are lacking for many coral species. The blue coral Heliopora is the only reef-building octocoral genus and exhibits optimal growth at a temperature close to the bleaching threshold of scleractinian corals. Local and high-latitude expansions of Heliopora coerulea were reported in the last decade, but little is known about the molecular mechanisms underlying its thermal resistance. We generated a draft genome of H. coerulea with an assembled size of 429.9 Mb, scaffold N50 of 1.42 Mb and BUSCO completeness of 94.9%. The genome contains 239.1 Mb repetitive sequences, 27,108 protein coding genes, 6,225 lncRNAs, and 79 miRNAs. This reference genome provides a valuable resource for in-depth studies on the adaptive mechanisms of corals under climate change and the evolution of skeleton in cnidarian.
CD44 is a potential immunotherapeutic target and affects macrophage infiltration leading to poor prognosis
Authors: Liu Shuangqing , Liu Zehan , Shang Aichen , Xun Jing , Lv Zongjing , Zhou Siying , Liu Cui , Zhang Qi , Yang Yuming
Published: June 2023

CD44 plays a key role in the communication of CSCs with the microenvironment and the regulation of stem cell properties. UALCAN was used to analyze the expression of CD44 in bladder cancer (BLCA) and normal tissue. The UALCAN was utilized to analyze the prognostic value of CD44 in BLCA. The TIMER database was used to explore the relationship between CD44 and PD-L1; CD44 and tumor-infiltrating immune cells. The regulatory effect of CD44 on PD-L1 was verified by cell experiments in vitro. IHC confirmed the results of the bioinformatics analysis. GeneMania and Metascape were used to analyze protein–protein interaction (PPI) investigations and functional enrichment analysis. We found that BLCA patients with high CD44 expression had worse survival than those with low CD44 expression (P < 0.05). IHC and the TIMER database results showed that CD44 expression was positively correlated with PD-L1 expression (P < 0.05). At the cellular level, the expression of PD-L1 was significantly inhibited after CD44 expression was inhibited by siRNA. Immune infiltration analysis showed that CD44 expression levels in BLCA were significantly correlated with immune infiltration levels of different immune cells. IHC staining results further confirmed that the expression of CD44 in tumor cells was positively associated with the number of CD68+ macrophages and CD163+ macrophages (P < 0.05). Our results suggest that CD44 is a positive regulator of PD-L1 in BLCA and may be a key regulator of tumor macrophages infiltration and may be involved in M2 macrophage polarization. Our study provided new insights into the prognosis and immunotherapy of BLCA patients through macrophage infiltration and immune checkpoints.
ABCA1 deficiency contributes to podocyte pyroptosis priming via the APE1/IRF1 axis in diabetic kidney disease
Authors: Ito Marie , Ducasa Gloria Michelle , Molina Judith David , Santos Javier Varona , Mallela Shamroop Kumar , Kim Jin Ju , Ge Mengyuan , Mitrofanova Alla , Sloan Alexis , Merscher Sandra , Mimura Imari , Fornoni Alessia
Published: June 2023

Decreased ATP Binding Cassette Transporter A1 (ABCA1) expression and caspase-4-mediated noncanonical inflammasome contribution have been described in podocytes in diabetic kidney disease (DKD). To investigate a link between these pathways, we evaluated pyroptosis-related mediators in human podocytes with stable knockdown of ABCA1 (siABCA1) and found that mRNA levels of IRF1, caspase-4, GSDMD, caspase-1 and IL1β were significantly increased in siABCA1 compared to control podocytes and that protein levels of caspase-4, GSDMD and IL1β were equally increased. IRF1 knockdown in siABCA1 podocytes prevented increases in caspase-4, GSDMD and IL1β. Whereas TLR4 inhibition did not decrease mRNA levels of IRF1 and caspase-4, APE1 protein expression increased in siABCA1 podocytes and an APE1 redox inhibitor abrogated siABCA1-induced expression of IRF1 and caspase-4. RELA knockdown also offset the pyroptosis priming, but ChIP did not demonstrate increased binding of NFκB to IRF1 promoter in siABCA1 podocytes. Finally, the APE1/IRF1/Casp1 axis was investigated in vivo. APE1 IF staining and mRNA levels of IRF1 and caspase 11 were increased in glomeruli of BTBR ob/ob compared to wildtype. In conclusion, ABCA1 deficiency in podocytes caused APE1 accumulation, which reduces transcription factors to increase the expression of IRF1 and IRF1 target inflammasome-related genes, leading to pyroptosispriming.
Egg-mediated maternal effects in a cooperatively breeding cichlid fish
Authors: Reyes-Contreras Maria , de Vries Bonnie , van der Molen J. C. , Groothuis T. G. G. , Taborsky Barbara
Published: June 2023

Mothers can influence offspring phenotype through egg-mediated maternal effects, which can be influenced by cues mothers obtain from their environment during offspring production. Developing embryos use these components but have mechanisms to alter maternal signals. Here we aimed to understand the role of mothers and embryos in how maternal effects might shape offspring social phenotype. In the cooperatively breeding fish Neolamprologus pulcher different social phenotypes develop in large and small social groups differing in predation risk and social complexity. We manipulated the maternal social environment of N. pulcher females during egg laying by allocating them either to a small or a large social group. We compared egg mass and clutch size and the concentration of corticosteroid metabolites between social environments, and between fertilized and unfertilized eggs to investigate how embryos deal with maternal signalling. Mothers in small groups produced larger clutches but neither laid smaller eggs nor bestowed eggs differently with corticosteroids. Fertilized eggs scored lower on a principal component representing three corticosteroid metabolites, namely 11-deoxycortisol, cortisone, and 11-deoxycorticosterone. We did not detect egg-mediated maternal effects induced by the maternal social environment. We discuss that divergent social phenotypes induced by different group sizes may be triggered by own offspring experience.
Evaluation of the antiviral activity of ultraviolet light and zinc oxide nanoparticles on textile products exposed to Avian coronavirus
Authors: Asmat-Campos David , Rojas-Jaimes Jesús , Icochea-D’Arrigo Eliana , Castro-Sanguinetti Gina R. , More-Bayona Juan Anderson , Juárez-Cortijo Luisa , Delfín-Narciso Daniel , Montes de Oca-Vásquez Gabriela
Published: June 2023

This research has developed a piece of sanitizing locker-model equipment for textiles exposed to avian coronavirus, which has been put under the influence of UV light, UV + zinc oxide nanoparticles (phytosynthesized ZnONP), and water + UV, and, in turn, under the influence of the exposure time (60, 120, 180 s). The results linked to the phytosynthesis of ZnONP indicate a novel method of fabricating nanostructured material, nanoparticles with spherical morphology and an average size of 30 nm. The assays were made based on the viral viability of avian coronavirus according to the mortality of SPF embryonated eggs and a Real-Time PCR for viral load estimation. This was a model to evaluate the sanitizing effects against coronaviruses since they share a very similar structure and chemistry with SAR-CoV-2. The influence of the type of textile treatment evidenced the potential effect of the sanitizing UV light, which achieved 100% of embryo viability. The response of the ZnONP + UV nebulization showed a notorious influence of photoactivation according to the exposure time, and the 60-s treatment achieved a decrease of 88.9% in viral viability, compared to 77.8% and 55.6% corresponding to the 120 and 180-s treatments, respectively. Regarding the decrease in viral load between the types of treatments, UV 180 s reduced 98.42% and UV 60 s + ZnONP reduced 99.46%, respectively. The results show the combinatorial effect of UV light and zinc nanoparticles in decreasing the viral viability of avian coronavirus, as a model of other important coronaviruses in public health such as SARS-CoV-2.
Optimizing fluidity and tensile strength of magnetically driven epoxy-cement repair materials based on response surface
Authors: Qin Shifu , Liu Jie , Wang Xiaoping , Yu Fan , Li Zheng , Tan Delin , Yan Qiao , Wang Lehua
Published: June 2023

Underwater crack repair is challenging due to drainage and exhaust, slurry retention at fixed points, and other issues. Magnetically driven epoxy resin cement slurry was developed, which can perform directional movement and fixed-point retention of slurry under the effect of an applied magnetic field. This paper focuses on slurry fluidity and tensile properties. Firstly, in the preliminary pre-study, the main influencing factors of the ratios were determined. Then, the optimum range of each factor is determined by a single-factor experiment. Furthermore, the response surface method (RSM) is applied to obtain an optimal ratio. Finally, the slurry is characterized by micro. Results showed that the evaluation index F proposed in this paper can well evaluate the interaction between fluidity (X) and tensile strength (Y). The 2FI regression model and the quadratic regression model are developed with fluidity and tensile strength as the response values and Epoxy Resin (ER) content, water-cement ratio, Fe3O4 content and sulphoaluminate cement (SAC) content as the influencing factors, and have reasonable fit and reliability. The relationship between the degree of influence of the influencing factors on the response value X and the response value Y in ascending order was: ER content > water-cement ratio > SAC content > Fe3O4 content. The magnetically driven slurry made by the optimal ratio can reach a fluidity rate of 223.31 mm and a tensile strength of 2.47 MPa. This is with relative errors of 0.36% and 1.65% from the model predicted values. Microscopic analysis showed that the magnetically driven epoxy resin cement slurry had a favorable crystalline phase, surface morphology, and structural composition.
Synergistic influence of probiotic and florfenicol on embryonic viability, performance, and multidrug-resistant Salmonella Enteritidis in broiler chickens
Authors: Nabil Nehal M. , Tawakol Maram M. , Samir Abdelhafez , Hassan Heba M. , Yonis Ahlam E. , Reda Reem M. , Elsayed Mona M.
Published: June 2023

This study was conducted during the period of August 2021 to April 2022 and divided into two parts. The first part involved the isolation and characterization of Salmonella from 200 diseased broiler chickens collected from farms in Dakahlia Governorate, Egypt, with the detection of its antimicrobial susceptibility. The second experimental part involved in ovo inoculation of probiotics and florfenicol to evaluate their effects on hatchability, embryonic viability, growth performance traits and the control of multidrug-resistant Salmonella Enteritidis infections post hatching. The point prevalence of Salmonella in the internal organs of diseased chickens was 13% (26/200), including 6 serotypes: S. Enteritidis, S. Typhimurium, S. Santiago, S. Colindale, S. Takoradi and S. Daula. Multidrug resistance was found in 92% (24/26) of the isolated strains with a multiantibiotic resistance index of 0.33–0.88 and 24 antibiotic resistance patterns. The in ovo inoculation of probiotic with florfenicol showed significant improvement in the growth performance parameters compared with other groups and had the ability to prevent colonization of multidrug resistant S. Enteritidis in the majority of the experimental chicks, and the remaining chicks showed very low colonization, as detected by RT‒PCR. These findings suggested the application of in ovo inoculation techniques with both probiotics and florfenicol as a promising tool to control multidrug-resistant S. Enteritidis in poultry farms.
MHD mixed convection and heatlines approach of nanofluids in rectangular wavy enclosures with multiple solid fins
Authors: Azizul Fatin M. , Alsabery Ammar I. , Hashim Ishak , Roslan Rozaini , Saleh Habibis
Published: June 2023

Two dimensional wavy walls rectangular cavity with inclined magnetohydrodynamic has been examined in mixed convection configurations. Triple fins arranged in the upwards ladder were filled within alumina nanoliquid in the cavity. Vertical sinusoidal walls were heated, and the other side was kept cold while both horizontal walls were kept adiabatic. All walls were motionless except the top cavity that was driven to the right. The diversified range of control parameter in Richardson number, Hartmann number, number of undulations, length of the cavity has been performed in this study. The analysis was simulated using finite element method by employing the governing equation formula, and the results were delineated in the form of streamlines, isotherms, heatlines, and comparisons on several relationships between the local velocity in the y-axis line of 0.6, local and average Nusselt number along the heated surface and dimensionless average temperature. The findings revealed that high concentration nanofluids boost the rate of heat transfer without the need to apply any magnetic field. Results found that the best heat mechanisms are natural convection with significant-high Richardson number as well as constructing two waves on the vertical walls in the cavity.
The overexpression and clinical significance of TBX15 in human gliomas
Authors: Yan Dongming , Yu Yaping , Ni Qiongwei , Meng Qingwen , Wu Haolin , Ding Shun , Liu Xiaoqian , Tang Caiying , Liu Qibing , Yang Kun
Published: June 2023

T-box transcription factor 15 (TBX15) is upregulated in a variety of tumors and has been reported to promote uncontrolled proliferation of tumor cells and induce tumor cells to avoid apoptosis, thus accelerating the malignant transformation of malignant tumors. However, the prognostic value of TBX15 in glioma and its relationship with immune infiltration remain unknown. In this study, we intended to explore the prognostic value of TBX15 and its link to glioma immune infiltration and examine TBX15 expression in pan-cancer using RNAseq data in TPM format from TCGA and GTEx. TBX15 mRNA and protein expressions in glioma cells and adjacent normal tissue were detected and compared by RT-qPCR and Western blot. The effect of TBX15 on survival was assessed by Kaplan-Meier Method. The correlation between TBX15 upregulation and the clinicopathological characteristics of glioma patients was assessed by using TCGA databases, and the relationship between TBX15 and other genes in glioma was evaluated by using TCGA data. The top 300 genes most significantly associated with TBX15 were selected to establish a PPI network through the STRING database. The relationship between TBX15 mRNA expression and immune cell infiltration was explored by using ssGSEA and the TIMER Database. It was found that TBX15 mRNA expression in glioma tissues was significantly higher than that in the adjacent normal tissues, and this difference was most obvious in high-grade gliomas. TBX15 expression was increased in human gliomas and associated with worse clinicopathological characteristics and poorer survival prognosis in glioma patients. In addition, elevated TBX15 expression was linked to a collection of genes involved in immunosuppression. In conclusion, TBX15 played an important role in immune cell infiltration in glioma and may prove to be a predictor of the prognosis in glioma patients.
Panel of miR-150 and linc00673, regulators of CCR6/CCL20 may serve as non-invasive diagnostic marker of non-small cell lung cancer
Authors: Baran Kamila , Kordiak Jacek , Jabłoński Sławomir , Brzeziańska-Lasota Ewa
Published: June 2023

The C–C motif ligand 20 (CCL20) is a chemokine that specifically binds to the chemokine receptor 6 (CCR6) and the CCL20/CCR6 axis has been implicated in the non-small lung cancer (NSCLC) development and progression. Its expression is regulated by mutual interactions of non-coding RNAs (ncRNAs). This goals of presented study was to evaluate the expression level of CCR6/CCL20 mRNA in NSCLC tissue comparative to selected ncRNAs: miR-150, linc00673. The expression level of the studied ncRNAs was also assessed in serum extracellular vesicles (EVs). Thirty patients (n = 30) were enrolled as the study cohort. Total RNA was isolated from tumor tissue, adjacent macroscopically unchanged tissue and serum EVs. The expression level of studied genes and ncRNAs were estimated based on the qPCR method. Higher expression level of CCL20 mRNA but lower expression level of CCR6 mRNA were observed in tumor in comparison to control tissue. Relative to the smoking status, higher CCL20 (p < 0.05) and CCR6 mRNA (p > 0.05) expression levels were observed in current smokers than in never smokers. In serum EVs the expression level of miR-150 has a negative correlation with AJCC tumor staging, whereas the expression level of linc00673 positively correlated (p > 0.05). The lower expression level of miR-150 and higher expression level of linc00673 in serum EVs were observed in NSCLC patients with lymph nodes metastases (p > 0.05). Regarding the histopathological type, significantly lower expression level of miR-150 and higher expression level of linc00673 were observed in the serum EVs of patients with AC compared to patient with SCC. Our findings revealed that smoking significantly changed the expression level of CCL20 mRNA in NSCLC tissue. Changes in expression levels of miR-150 and linc00673 in the serum EVs of NSCLC patients in relation to presence of lymph node metastases and the stage of cancer development may serve as a non-invasive molecular biomarkers of tumor progression. Furthermore, expression levels of miR-150 and linc00673 may serve as non-intrusive diagnostic biomarkers differentiating adenocarcinoma from squamous cell carcinoma.
A reinforcement learning approach to airfoil shape optimization
Authors: Dussauge Thomas P. , Sung Woong Je , Pinon Fischer Olivia J. , Mavris Dimitri N.
Published: June 2023

Shape optimization is an indispensable step in any aerodynamic design. However, the inherent complexity and non-linearity associated with fluid mechanics as well as the high-dimensional design space intrinsic to such problems make airfoil shape optimization a challenging task. Current approaches relying on gradient-based or gradient-free optimizers are data-inefficient in that they do not leverage accumulated knowledge, and are computationally expensive when integrating Computational Fluid Dynamics (CFD) simulation tools. Supervised learning approaches have addressed these limitations but are constrained by user-provided data. Reinforcement learning (RL) provides a data-driven approach bearing generative capabilities. We formulate the airfoil design as a Markov decision process (MDP) and investigate a Deep Reinforcement Learning (DRL) approach to airfoil shape optimization. A custom RL environment is developed allowing the agent to successively modify the shape of an initially provided 2D airfoil and to observe the associated changes in aerodynamic metrics such as lift-to-drag (L/D), lift coefficient (Cl) and drag coefficient (Cd). The learning abilities of the DRL agent are demonstrated through various experiments in which the agent’s objective-maximizing L/D, maximizing Cl or minimizing Cd-as well as the initial airfoil shape are varied. Results show that the DRL agent is able to generate high performing airfoils within a limited number of learning iterations. The strong resemblance between the artificially produced shapes and those found in the literature highlights the rationality of the decision-making policy learned by the agent. Overall, the presented approach demonstrates the relevance of DRL to airfoil shape optimization and brings forward a successful application of DRL to a physics-based aerodynamics problem.
Advancing hyper-crosslinked materials with high efficiency and reusability for oil spill response
Authors: Karmelich Caleb , Wan Zhijian , Tian Wendy , Crooke Emma , Qi Xiubin , Carroll Ann , Konstas Kristina , Wood Colin
Published: June 2023

Developing materials with high efficiency for recovering oil to mitigate the environmental impact of oil spills has always been a challenging task. A commercial melamine formaldehyde sponge was coated with an optimised superhydrophobic/superoleophilic hyper-crosslinked polymer and applied to the removal of crude oil from oil-in-water emulsions for the improvement of oil spill clean-up processes. The high surface area, porosity, hydrophobicity, and selectivity of oil over water made the hyper-crosslinked polymer coated sponge (HPCS) an ideal sorbent for efficient oil/water separation. The system was able to strip crude oil from water emulsions of 1000 ppm to a negligible level of 2 ppm oil with minimal amounts of the HPCS material. More importantly, the HPCS material could be reused via a simple mechanical compression process, and the uptake capacity was retained over ten cycles. For five cycles of oil adsorption/mechanical compression the HPCS was able to provide water filtrate with oil concentrations of under 15 ppm. This is an effective and economical recovery system, removing the need for consistent solvent washing and drying processes. These results suggest that the HPCS is a promising material for oil/water separation and recovery under challenging conditions.
Normal human craniofacial growth and development from 0 to 4 years
Authors: Liang Ce , Profico Antonio , Buzi Costantino , Khonsari Roman H. , Johnson David , O’Higgins Paul , Moazen Mehran
Published: June 2023

Knowledge of human craniofacial growth (increase in size) and development (change in shape) is important in the clinical treatment of a range of conditions that affects it. This study uses an extensive collection of clinical CT scans to investigate craniofacial growth and development over the first 48 months of life, detail how the cranium changes in form (size and shape) in each sex and how these changes are associated with the growth and development of various soft tissues such as the brain, eyes and tongue and the expansion of the nasal cavity. This is achieved through multivariate analyses of cranial form based on 3D landmarks and semi-landmarks and by analyses of linear dimensions, and cranial volumes. The results highlight accelerations and decelerations in cranial form changes throughout early childhood. They show that from 0 to 12 months, the cranium undergoes greater changes in form than from 12 to 48 months. However, in terms of the development of overall cranial shape, there is no significant sexual dimorphism in the age range considered in this study. In consequence a single model of human craniofacial growth and development is presented for future studies to examine the physio-mechanical interactions of the craniofacial growth.
An antioxidant ameliorates allergic airway inflammation by inhibiting HDAC 1 via HIF-1α/VEGF axis suppression in mice
Authors: Islam Ramiya , Dash D. , Singh Rashmi
Published: June 2023

Histone deacetylase inhibitors (HDACi) are novel class of drugs as they are involved in post translational modification of several proteins involved in signaling pathways related to asthma. HDACi have been reported to elicit protective effects on asthma but the signaling pathways associated with it have not been investigated much. Recently, we have demonstrated that intranasal administrations of Pan-HDAC inhibitors, sodium butyrate and curcumin, which have effectively reduced asthma severity via HDAC1 inhibition in Ovalbumin induced mouse model. Present study aimed to investigate possible pathways by which curcumin and sodium butyrate may minimize asthma pathogenesis via HDAC 1 inhibition. Balb/c mice were exposed (sensitized and challenged) with Ovalbumin to establish allergic asthma model followed by pretreatment of curcumin (5 mg/kg) and sodium butyrate (50 mg/kg) through intranasal route. Effects of curcumin and sodium butyrate on HIF-1α/VEGF signaling through activation of PI3K/Akt axis has been investigated using protein expressions followed by chromatin immunoprecipitation of BCL2 and CCL2 against HDAC1. Molecular docking analysis was also performed to investigate effects of curcumin and butyrate on mucus hypersecretion, goblet cell hyperplasia and airway hyperresponsiveness. Augmented expressions of HDAC-1, HIF-1α, VEGF, p-Akt and p-PI3K were observed in asthmatic group which was suppressed in both the treatments. NRF-2 level was significantly restored by curcumin and butyrate treatments. Protein expressions of p-p38, IL-5 and mRNA expressions of GATA-3 were also reduced in curcumin and butyrate treatment groups. Our findings suggest that curcumin and sodium butyrate may attenuate airway inflammation via down regulation of p-Akt/p-PI3K/HIF-1α/VEGF axis.
Localization of the ventricular pacing site from BSPM and standard 12-lead ECG: a comparison study
Authors: Sedova Ksenia A. , van Dam Peter M. , Blahova Marie , Necasova Lucie , Kautzner Josef
Published: June 2023

Inverse ECG imaging methods typically require 32–250 leads to create body surface potential maps (BSPM), limiting their routine clinical use. This study evaluated the accuracy of PaceView inverse ECG method to localize the left or right ventricular (LV and RV, respectively) pacing leads using either a 99-lead BSPM or the 12-lead ECG. A 99-lead BSPM was recorded in patients with cardiac resynchronization therapy (CRT) during sinus rhythm and sequential LV/RV pacing. The non-contrast CT was performed to localize precisely both ECG electrodes and CRT leads. From a BSPM, nine signals were selected to obtain the 12-lead ECG. Both BSPM and 12-lead ECG were used to localize the RV and LV lead, and the localization error was calculated. Consecutive patients with dilated cardiomyopathy, previously implanted with a CRT device, were enrolled (n = 19). The localization error for the RV/LV lead was 9.0 [IQR 4.8–13.6] / 7.7 [IQR 0.0–10.3] mm using the 12-lead ECG and 9.1 [IQR 5.4–15.7] / 9.8 [IQR 8.6–13.1] mm for the BSPM. Thus, the noninvasive lead localization using the 12-lead ECG was accurate enough and comparable to 99-lead BSPM, potentially increasing the capability of 12-lead ECG for the optimization of the LV/RV pacing sites during CRT implant or for the most favorable programming.
A fast magnetic vector characterization method for quasi two-dimensional systems and heterostructures
Authors: Herguedas-Alonso A. E. , Aballe L. , Fullerton J. , Vélez M. , Martín J. I. , Sorrentino A. , Pereiro E. , Ferrer S. , Quirós C. , Hierro-Rodriguez A.
Published: June 2023

The use of magnetic vector tomography/laminography has opened a 3D experimental window to access the magnetization at the nanoscale. These methods exploit the dependence of the magnetic contrast in transmission to recover its 3D configuration. However, hundreds of different angular projections are required leading to large measurement times. Here we present a fast method to dramatically reduce the experiment time specific for quasi two-dimensional magnetic systems. The algorithm uses the Beer-Lambert equation in the framework of X-ray transmission microscopy to obtain the 3D magnetic configuration of the sample. It has been demonstrated in permalloy microstructures, reconstructing the magnetization vector field with a reduced number of angular projections obtaining quantitative results. The throughput of the methodology is × 10–× 100 times faster than conventional magnetic vector tomography, making this characterization method of general interest for the community.
Greenhouse gas emission potential of sewage treatment plants in Himachal Pradesh
Authors: Sharma Apurva , Bhardwaj Satish Kumar , Aggarwal R. K. , Sharma Ravinder , Agrawal Ghanshyam
Published: June 2023

In recent times, waste management has emerged as a significant environmental challenge, and sewage is among the major contributors due to the rapidly increasing population. Despite sewage treatment plants (STPs) being the solution for the treatment of sewage, they have been identified as sources of greenhouse gas (GHG) emissions. This study aimed to estimate the contribution of STPs to GHG emissions in the state. This was achieved by visiting the sites, filling scientifically designed questionnaires, sample collection as well as computational methods by Intergovernmental Panel on Climate Change. The assessment of direct and indirect emissions from the STPs revealed that emissions were caused by the activated sludge process, electricity consumption, transportation, and sludge storage. Electricity consumption by STPs was responsible for the highest emissions, accounting for 43% of the total emissions, equivalent to 20,823 tCO2 eq. The activated sludge process contributed 31% (14,934 tCO2 eq) of the emissions, while storage of sludge in landfills accounted for 24% (11,359 tCO2 eq). Additionally, transportation contributed 2% (1121 tCO2 eq) of the emissions. In total, the STPs in Himachal Pradesh had the potential to contribute 48,237 tCO2 eq GHG emissions annually. Thus, the study suggests process-level modifications in STPs of Himachal Pradesh to mitigate GHG emissions. This research provides insight into the GHG emissions from STPs and highlights the need for their management to reduce environmental impacts.
CXCL10 as a shared specific marker in rheumatoid arthritis and inflammatory bowel disease and a clue involved in the mechanism of intestinal flora in rheumatoid arthritis
Authors: Guan Yin , Zhang Yue , Zhu Yifan , Wang Yue
Published: June 2023

This study aimed to identify shared specific genes associated with rheumatoid arthritis (RA) and inflammatory bowel disease (IBD) through bioinformatic analysis and to examine the role of the gut microbiome in RA. The data were extracted from the 3 RA and 1 IBD gene expression datasets and 1 RA gut microbiome metagenomic dataset. Weighted correlation network analysis (WGCNA) and machine learnings was performed to identify candidate genes associated with RA and IBD. Differential analysis and two different machine learning algorithms were used to investigate RA’s gut microbiome characteristics. Subsequently, the shared specific genes related to the gut microbiome in RA were identified, and an interaction network was constructed utilizing the gutMGene, STITCH, and STRING databases. We identified 15 candidates shared genes through a joint analysis of the WGCNA for RA and IBD. The candidate geneCXCL10was identified as the shared hub gene by the interaction network analysis of the corresponding WGCNA module gene to each disease, andCXCL10was further identified as the shared specific gene by two machine learning algorithms. Additionally, we identified 3 RA-associated characteristic intestinal flora (Prevotella,Ruminococcus, andRuminococcus bromii) and built a network of interactions between the microbiomes, genes, and pathways. Finally, it was discovered that the geneCXCL10shared between IBD and RA was associated with the three gut microbiomes mentioned above. This study demonstrates the relationship between RA and IBD and provides a reference for research into the role of the gut microbiome in RA.
Lead induces mouse skin fibroblast apoptosis by disrupting intracellular homeostasis
Authors: Wang Hui , Wang Huinuan , Guan Jiawen , Guan Weijun , Liu Zheng
Published: June 2023

Lead (Pb) is a critical industrial and environmental contaminant that can cause pathophysiological changes in several cellular and organ systems and their processes, including cell proliferation, differentiation, apoptosis, and survival. The skin is readily exposed to and damaged by Pb, but the mechanisms through which Pb damages cells are not fully understood. We examined the apoptotic properties of Pb in mouse skin fibroblast (MSF) in vitro. Treatment of fibroblasts with 40, 80, and 160 μM Pb for 24 h revealed morphological alterations, DNA damage, enhanced caspase-3, -8, and -9 activities, and apoptotic cell population. Furthermore, apoptosis was dosage (0–160 μM) and time (12–48 h) dependent. Concentrations of intracellular calcium (Ca2+) and reactive oxygen species were increased, and the mitochondrial membrane potential was decreased in exposed cells. Cell cycle arrest was evident at the G0/G1 phase. The Bax, Fas, caspase-3 and -8, and p53 transcript levels were increased, whereas Bcl-2 gene expression was decreased. Based on our analysis, Pb triggers MSF apoptosis bydisrupting intracellular homeostasis. Our findings enrich the knowledge about the mechanistic function of Pb-induced cytotoxicity on human skin fibroblasts and could potentially guide future Pb health risk assessments.
Untargeted urinary metabolomics for bladder cancer biomarker screening with ultrahigh-resolution mass spectrometry
Authors: Nizioł Joanna , Ossoliński Krzysztof , Płaza-Altamer Aneta , Kołodziej Artur , Ossolińska Anna , Ossoliński Tadeusz , Nieczaj Anna , Ruman Tomasz
Published: June 2023

Bladder cancer (BC) is a common urological malignancy with a high probability of death and recurrence. Cystoscopy is used as a routine examination for diagnosis and following patient monitoring for recurrence. Repeated costly and intrusive treatments may discourage patients from having frequent follow-up screenings. Hence, exploring novel non-invasive ways to help identify recurrent and/or primary BC is critical. In this work, 200 human urine samples were profiled using ultra-high-performance liquid chromatography and ultra-high-resolution mass spectrometry (UHPLC-UHRMS) to uncover molecular markers differentiating BC from non-cancer controls (NCs). Univariate and multivariate statistical analyses with external validation identified metabolites that distinguish BC patients from NCs disease. More detailed divisions for the stage, grade, age, and gender are also discussed. Findings indicate that monitoring urine metabolites may provide a non-invasive and more straightforward diagnostic method for identifying BC and treating recurrent diseases.