bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cholesterol-binding motifs in STING that control endoplasmic reticulum retention mediate anti-tumoral activity of cholesterol-lowering compounds
Authors: Zhang Bao-cun , Laursen Marlene F. , Hu Lili , Hazrati Hossein , Narita Ryo , Jensen Lea S. , Hansen Aida S. , Huang Jinrong , Zhang Yan , Ding Xiangning , Muyesier Maimaitili , Nilsson Emil , Banasik Agnieszka , Zeiler Christina , Mogensen Trine H. , Etzerodt Anders , Agger Ralf , Johannsen Mogens , Kofod-Olsen Emil , Paludan Søren R. , Jakobsen Martin R. 
Published: March 2024

AbstractThe cGAS-STING pathway plays a crucial role in anti-tumoral responses by activating inflammation and reprogramming the tumour microenvironment. Upon activation, STING traffics from the endoplasmic reticulum (ER) to Golgi, allowing signalling complex assembly and induction of interferon and inflammatory cytokines. Here we report that cGAMP stimulation leads to a transient decline in ER cholesterol levels, mediated by Sterol O-Acyltransferase 1-dependent cholesterol esterification. This facilitates ER membrane curvature and STING trafficking to Golgi. Notably, we identify two cholesterol-binding motifs in STING and confirm their contribution to ER-retention of STING. Consequently, depletion of intracellular cholesterol levels enhances STING pathway activation upon cGAMP stimulation. In a preclinical tumour model, intratumorally administered cholesterol depletion therapy potentiated STING-dependent anti-tumoral responses, which, in combination with anti-PD-1 antibodies, promoted tumour remission. Collectively, we demonstrate that ER cholesterol sets a threshold for STING signalling through cholesterol-binding motifs in STING and we propose that this could be exploited for cancer immunotherapy.
Machine-learning-assisted and real-time-feedback-controlled growth of InAs/GaAs quantum dots
Authors: Shen Chao , Zhan Wenkang , Xin Kaiyao , Li Manyang , Sun Zhenyu , Cong Hui , Xu Chi , Tang Jian , Wu Zhaofeng , Xu Bo , Wei Zhongming , Xue Chunlai , Zhao Chao , Wang Zhanguo 
Published: March 2024

AbstractThe applications of self-assembled InAs/GaAs quantum dots (QDs) for lasers and single photon sources strongly rely on their density and quality. Establishing the process parameters in molecular beam epitaxy (MBE) for a specific density of QDs is a multidimensional optimization challenge, usually addressed through time-consuming and iterative trial-and-error. Here, we report a real-time feedback control method to realize the growth of QDs with arbitrary density, which is fully automated and intelligent. We develop a machine learning (ML) model named 3D ResNet 50 trained using reflection high-energy electron diffraction (RHEED) videos as input instead of static images and providing real-time feedback on surface morphologies for process control. As a result, we demonstrate that ML from previous growth could predict the post-growth density of QDs, by successfully tuning the QD densities in near-real time from 1.5 × 1010 cm−2 down to 3.8 × 108 cm−2 or up to 1.4 × 1011 cm−2. Compared to traditional methods, our approach can dramatically expedite the optimization process and improve the reproducibility of MBE. The concepts and methodologies proved feasible in this work are promising to be applied to a variety of material growth processes, which will revolutionize semiconductor manufacturing for optoelectronic and microelectronic industries.
Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA
Authors: Shepherd Jack W. , Guilbaud Sebastien , Zhou Zhaokun , Howard Jamieson A. L. , Burman Matthew , Schaefer Charley , Kerrigan Adam , Steele-King Clare , Noy Agnes , Leake Mark C. 
Published: March 2024

AbstractBiopolymer topology is critical for determining interactions inside cell environments, exemplified by DNA where its response to mechanical perturbation is as important as biochemical properties to its cellular roles. The dynamic structures of chiral biopolymers exhibit complex dependence with extension and torsion, however the physical mechanisms underpinning the emergence of structural motifs upon physiological twisting and stretching are poorly understood due to technological limitations in correlating force, torque and spatial localization information. We present COMBI-Tweez (Combined Optical and Magnetic BIomolecule TWEEZers), a transformative tool that overcomes these challenges by integrating optical trapping, time-resolved electromagnetic tweezers, and fluorescence microscopy, demonstrated on single DNA molecules, that can controllably form and visualise higher order structural motifs including plectonemes. This technology combined with cutting-edge MD simulations provides quantitative insight into complex dynamic structures relevant to DNA cellular processes and can be adapted to study a range of filamentous biopolymers.
Subslab ultra low velocity anomaly uncovered by and facilitating the largest deep earthquake
Authors: Chen Weiwen , Wei Shengji , Wang Weitao 
Published: March 2024

AbstractIt is enigmatic that M8+ earthquakes can take place at depth greater than 600 km inside the slab, where the P-T conditions generally do not favor seismic slip rate (~m/s) on faults. Here we provide fresh insights to the initial rupture and mechanism of the Mw 8.3 Sea of Okhotsk earthquake by analyzing high-frequency (up to 0.8 Hz) teleseismic array data. We determine the relative location and timing of two early subevents, and the geometry and velocity perturbation of a nearby structure anomaly. We found a small-scale (~30 × 60 × 60 km) ultralow (−18 ± 2%) P-wave velocity anomaly located beneath the Pacific slab around the 660 km discontinuity. The volatile-bearing highly melted nature of the anomaly provides significant buoyancy, stressing the slab dramatically closer to the critical condition for thermal runaway weakening that allows the rupture to propagate beyond the metastable olivine wedge, forming M8+ events. Enormous velocity reduction urges for further mineral physics and geodynamic investigations.
Lactobacillus plantarum L168 improves hyperoxia-induced pulmonary inflammation and hypoalveolarization in a rat model of bronchopulmonary dysplasia
Authors: Shen Xian , Yang Zhaocong , Wang Qiang , Chen Xu , Zhu Qihui , Liu Zhi , Patel Nishant , Liu Xingyin , Mo Xuming 
Published: March 2024

AbstractAlteration of gut microbiota can affect chronic lung diseases, such as asthma and chronic obstructive pulmonary disease, through abnormal immune and inflammatory responses. Previous studies have shown a feasible connection between gut microbiota and bronchopulmonary dysplasia (BPD) in preterm infants. However, whether BPD can be ameliorated by restoring the gut microbiota remains unclear. In preterm infants with BPD, we found variance in the diversity and structure of gut microbiota. Similarly, BPD rats showed gut dysbiosis, characterized by a deficiency of Lactobacillus, which was abundant in normal rats. We therefore explored the effect and potential mechanism of action of a probiotic strain, Lactobacillus plantarum L168, in improving BPD. The BPD rats were treated with L. plantarum L168 by gavage for 2 weeks, and the effect was evaluated by lung histopathology, lung function, and serum inflammatory markers. Subsequently, we observed reduced lung injury and improved lung development in BPD rats exposed to L. plantarum L168. Further evaluation revealed that L. plantarum L168 improved intestinal permeability in BPD rats. Serum metabolomics showed altered inflammation-associated metabolites following L. plantarum L168 intervention, notably a marked increase in anti-inflammatory metabolites. In agreement with the metabolites analysis, RNA-seq analysis of the intestine and lung showed that inflammation and immune-related genes were down-regulated. Based on the information from RNA-seq, we validated that L. plantarum L168 might improve BPD relating to down-regulation of TLR4 /NF-κB /CCL4 pathway. Together, our findings suggest the potential of L. plantarum L168 to provide probiotic-based therapeutic strategies for BPD.
Effect of 60 days of head down tilt bed rest on amplitude and phase of rhythms in physiology and sleep in men
Authors: Bonmatí-Carrión María-Ángeles , Santhi Nayantara , Atzori Giuseppe , Mendis Jeewaka , Kaduk Sylwia , Dijk Derk-Jan , Archer Simon N. 
Published: March 2024

AbstractTwenty-four-hour rhythms in physiology and behaviour are shaped by circadian clocks, environmental rhythms, and feedback of behavioural rhythms onto physiology. In space, 24 h signals such as those associated with the light-dark cycle and changes in posture, are weaker, potentially reducing the robustness of rhythms. Head down tilt (HDT) bed rest is commonly used to simulate effects of microgravity but how HDT affects rhythms in physiology has not been extensively investigated. Here we report effects of −6° HDT during a 90-day protocol on 24 h rhythmicity in 20 men. During HDT, amplitude of light, motor activity, and wrist-temperature rhythms were reduced, evening melatonin was elevated, while cortisol was not affected during HDT, but was higher in the morning during recovery when compared to last session of HDT. During recovery from HDT, time in Slow-Wave Sleep increased. EEG activity in alpha and beta frequencies increased during NREM and REM sleep. These results highlight the profound effects of head-down-tilt-bed-rest on 24 h rhythmicity.
Quantifying in vitro B. anthracis growth and PA production and decay: a mathematical modelling approach
Authors: Williams Bevelynn , Paterson Jamie , Rawsthorne-Manning Helena J. , Jeffrey Polly-Anne , Gillard Joseph J. , Lythe Grant , Laws Thomas R. , López-García Martín 
Published: March 2024

AbstractProtective antigen (PA) is a protein produced by Bacillus anthracis. It forms part of the anthrax toxin and is a key immunogen in US and UK anthrax vaccines. In this study, we have conducted experiments to quantify PA in the supernatants of cultures of B. anthracis Sterne strain, which is the strain used in the manufacture of the UK anthrax vaccine. Then, for the first time, we quantify PA production and degradation via mathematical modelling and Bayesian statistical techniques, making use of this new experimental data as well as two other independent published data sets. We propose a single mathematical model, in terms of delay differential equations (DDEs), which can explain the in vitro dynamics of all three data sets. Since we did not heat activate the B. anthracis spores prior to inoculation, germination occurred much slower in our experiments, allowing us to calibrate two additional parameters with respect to the other data sets. Our model is able to distinguish between natural PA decay and that triggered by bacteria via proteases. There is promising consistency between the different independent data sets for most of the parameter estimates. The quantitative characterisation of B. anthracis PA production and degradation obtained here will contribute towards the ambition to include a realistic description of toxin dynamics, the host immune response, and anti-toxin treatments in future mechanistic models of anthrax infection.
A unified dataset for the city-scale traffic assignment model in 20 U.S. cities
Authors: Xu Xiaotong , Zheng Zhenjie , Hu Zijian , Feng Kairui , Ma Wei 
Published: March 2024

AbstractCity-scale traffic data, such as traffic flow, speed, and density on every road segment, are the foundation of modern urban research. However, accessing such data on a city scale is challenging due to the limited number of sensors and privacy concerns. Consequently, most of the existing traffic datasets are typically limited to small, specific urban areas with incomplete data types, hindering the research in urban studies, such as transportation, environment, and energy fields. It still lacks a city-scale traffic dataset with comprehensive data types and satisfactory quality that can be publicly available across cities. To address this issue, we propose a unified approach for producing city-scale traffic data using the classic traffic assignment model in transportation studies. Specifically, the inputs of our approach are sourced from open public databases, including road networks, traffic demand, and travel time. Then the approach outputs comprehensive and validated citywide traffic data on the entire road network. In this study, we apply the proposed approach to 20 cities in the United States, achieving an average correlation coefficient of 0.79 in average travel time and an average relative error of 5.16% and 10.47% in average travel speed when compared with the real-world data.
Effects of light perception on visual function recovery in patients with traumatic optic neuropathy
Authors: Wang Jiancun , Xue Qiang , Tan Xuewen , Huang Jie , Zhu Yibai , Li Wen 
Published: March 2024

AbstractThis study aimed to assess the impact of light perception presence or absence on visual function recovery in patients with traumatic optic neuropathy (TON). A retrospective analysis was conducted on the clinical data of 206 TON patients. Based on the presence or absence of light perception after injury, patients were categorized into a light perception group and a non-light perception group. A comparison was made between the two groups regarding visual acuity recovery before and after treatment. The non-light perception group comprised 63 patients, with a treatment effectiveness rate of 39.68%. The light perception group consisted of 143 patients, with a treatment effectiveness rate of 74.83%. The difference between the two groups was statistically significant (χ2 = 23.464, P < 0.01). Subgroup analysis indicated that surgical treatment appeared to be more effective than steroid hormone therapy for patients with light perception. Conversely, for patients without light perception, there was no significant difference in the effectiveness of the two methods. The total effectiveness rate of the light perception group was significantly higher than that of the non-light perception group, suggesting that patients with light perception before treatment experience better outcomes compared to those without light perception. Treatment choices should be individualized to ensure optimal results.
Risk factors for suboptimal glycemic control in pediatrics with type 1 diabetes mellitus: a cross-sectional study
Authors: Ghazaiean Mobin , Najafi Behnam , Zamanfar Daniel , Alipour Mohammad Javad 
Published: March 2024

AbstractThe objective of this research is to analyze the influence of various factors on glycemic control in pediatrics with type 1 diabetes mellitus (T1DM). The study, a cross-sectional analysis, involved 221 T1DM patients below 18 years old who visited our clinic between 2011 and 2020, predating the COVID-19 outbreak. Out of the initial pool, 204 participants were chosen based on specific criteria. By computing odds ratios and 95% confidence intervals, we determined the correlation between these factors and achieving optimal glycemic control (HbA1c < 7.5%). Of the 204 individuals, 55.9% (113 patients) were female. The average age at diagnosis was 6.93 ± 3.9 years. Mean HbA1c (A1C) level of optimal and suboptimal groups were 6.97, 95% CI 6.84 to 7.1 and 8.86, 95% CI 8.68 to 9.03, respectively (p-value < 0.001). Fifty patients had optimal glycemic control and 154 people experienced suboptimal glycemic control during the follow-up that the prevalence of each of them was 24.51, 95% CI 18.7 to 31 and 75.49, 95% CI 68.99 to 81.22, respectively. In the assessment of risk factors associated with suboptimal glycemic control, patients aged 10–14 years had the highest likelihood of experiencing suboptimal glycemic control (crude odds ratio [COR] 3.12, 95% CI 1.04 to 9.3), followed by duration of diabetes (COR 2.85, 95% CI 1.2 to 6.8), which both were significant. By utilizing multivariable logistic regression analysis, a noteworthy finding emerged. It was revealed that patients aged 10–14 years exhibited a significant association with suboptimal glycemic control, [adjusted odds ratio (AOR) 4.85, 95% CI 1.32 to 17.7]. Additionally, a statistically significant correlation was identified between individuals with a body mass index (BMI) falling within the ≥ 95th percentile category and suboptimal glycemic control, Cramer’s V = 0.21, p-value = 0.01. Our research has revealed a significant correlation between patients aged 10–14 years and obese individuals (BMI ≥ 95th) with suboptimal glycemic control. It is crucial to consider these factors as they can offer valuable insights during diagnosis, highlighting the increased risk of long-term suboptimal glycemic control.
Response of the metabolic activity and taxonomic composition of bacterial communities to mosaically varying soil salinity and alkalinity
Authors: Mucsi Márton , Borsodi Andrea K. , Megyes Melinda , Szili-Kovács Tibor 
Published: March 2024

AbstractSoil salinity and sodicity is a worldwide problem that affects the composition and activity of bacterial communities and results from elevated salt and sodium contents. Depending on the degree of environmental pressure and the combined effect of other factors, haloalkalitolerant and haloalkaliphilic bacterial communities will be selected. These bacteria play a potential role in the maintenance and restoration of salt-affected soils; however, until recently, only a limited number of studies have simultaneously studied the bacterial diversity and activity of saline–sodic soils. Soil samples were collected to analyse and compare the taxonomic composition and metabolic activity of bacteria from four distinct natural plant communities at three soil depths corresponding to a salinity‒sodicity gradient. Bacterial diversity was detected using 16S rRNA gene Illumina MiSeq amplicon sequencing. Community-level physiological profiles (CLPPs) were analysed using the MicroResp™ method. The genus-level bacterial composition and CLPPs differed significantly in soils with different alkaline vegetation. The surface soil samples also significantly differed from the intermediate and deep soil samples. The results showed that the pH, salt content, and Na+ content of the soils were the main edaphic factors influencing both bacterial diversity and activity. With salinity and pH, the proportion of the phylum Gemmatimonadota increased, while the proportions of Actinobacteriota and Acidobacteriota decreased.
Long-term cardiovascular outcome in women with preeclampsia in Korea: a large population-based cohort study and meta-analysis
Authors: Choi Eun-Saem , Jung Young Mi , Kim Dayoung , Cho Su Eun , Park Eun Sun , Park Chan-Wook , Park Joong Shin , Jun Jong Kwan , Lee Seung Mi 
Published: March 2024

AbstractRecent studies reported the long-term cardiovascular risk of preeclampsia. However, only a few studies have investigated the association between preeclampsia and long-term cardiovascular disease in Asian populations, although there could be racial/ethnic differences in the risk of cardiovascular diseases. Therefore, we aimed to evaluate the long-term effects of preeclampsia on cardiovascular disease in an Asian population. This study included 68,658 parous women in the Health Examinees Study (HEXA) cohort of South Korea and compared the risk of long-term cardiovascular disease, including ischemic heart disease and stroke, according to the history of preeclampsia. We also performed a meta-analysis combining current study data with data from existing literature in the Asian population. Among the study population, 3413 (5.23%) women had a history of preeclampsia, and 767 (1.12%) and 404 (0.59%) women developed ischemic heart disease and stroke for 22 years. Women with a history of preeclampsia were at a higher risk for both ischemic heart disease (adjusted hazard ratio 1.66 [1.19–2.04]) and stroke (adjusted hazard ratio 1.48 [1.02–2.16]) than those without. In the meta-analysis, the pooled hazard ratio of ischemic heart disease and stroke were also increased in women with a history of preeclampsia (ischemic heart disease 1.65 [1.51–1.82]; stroke 1.78 [1.52–2.10]).
Unveiling the antibacterial and antifungal potential of biosynthesized silver nanoparticles from Chromolaena odorata leaves
Authors: Bishoyi Ajit Kumar , Sahoo Chita Ranjan , Samal Priyanka , Mishra Nilima Priyadarsini , Jali Bigyan Ranjan , Khan Mohd Shahnawaz , Padhy Rabindra Nath 
Published: March 2024

AbstractThis research investigates the biogenic synthesis of silver nanoparticles (AgNPs) using the leaf extract of Chromolaena odorata (Asteraceae) and their potential as antibacterial and antifungal agents. Characterization techniques like ultraviolet–visible, Fourier transform infrared (FTIR), Dynamic light scattering and zeta potential (DLS), X-ray diffraction (XRD), transmission electron microscopy (TEM), and field emission scanning electron microscopy and energy-dispersive X-ray spectroscopy (FESEM-EDX) confirmed the formation of spherical (AgNPs). UV–vis spectroscopy reaffirms AgNP formation with a peak at 429 nm. DLS and zeta potential measurements revealed an average size of 30.77 nm and a negative surface charge (− 0.532 mV). Further, XRD analysis established the crystalline structure of the AgNPs. Moreover, the TEM descriptions indicate that the AgNPs are spherical shapes, and their sizes ranged from 9 to 22 nm with an average length of 15.27 nm. The X-ray photoelectron spectroscopy (XPS) analysis validated the formation of metallic silver and elucidated the surface state composition of AgNPs. Biologically, CO-AgNPs showed moderate antibacterial activity but excellent antifungal activity against Candida tropicalis (MCC 1559) and Trichophyton rubrum (MCC 1598). Low MIC values (0.195 and 0.390 mg/mL) respectively, suggest their potential as effective antifungal agents. This suggests potential applications in controlling fungal infections, which are often more challenging to treat than bacterial infections. Molecular docking results validated that bioactive compounds in C. odorata contribute to antifungal activity by interacting with its specific domain. Further research could pave the way for the development of novel and safe antifungal therapies based on biogenic nanoparticles.
Precise analysis of single small extracellular vesicles using flow cytometry
Authors: Kobayashi Hisano , Shiba Takayuki , Yoshida Takeshi , Bolidong Dilireba , Kato Koroku , Sato Yoshiki , Mochizuki Mao , Seto Takafumi , Kawashiri Shuichi , Hanayama Rikinari 
Published: March 2024

AbstractMethods that enable specific and sensitive quantification of small extracellular vesicles (sEVs) using flow cytometry are still under development. Aggregation or adsorption of antibodies causes sub-nano sized particles or non-specific binding and largely affects the results of flow cytometric analysis of single sEVs. Comparison of control IgG and target-specific IgG is inappropriate because they have different characters. Here, we evaluate four preparation methods for flow cytometry, including ultracentrifugation, density gradient centrifugation, size exclusion chromatography (SEC), and the TIM4-affinity method by using tetraspanin-deficient sEVs. The ultracentrifugation or density gradient centrifugation preparation method has large false-positive rates for tetraspanin staining. Conversely, preparation methods using SEC or the TIM4-affinity method show specific detection of single sEVs, which elucidate the roles of sEV biogenesis regulators in the generation of sEV subpopulations. The methods are also useful for the detection of rare disease-related markers, such as PD-L1. Flow cytometric analysis using SEC or the TIM4-affinity method could accelerate research into sEV biogenesis and the development of sEV-based diagnostics and therapies.