bluuebunny/crossref_metadata_2025_split huggingface dataset:
Convective modes reveal the incoherence of the Southern Polar Vortex
Authors: Blachut Chantelle , Balasuriya Sanjeeva 
Published: January 2024

AbstractThe Southern Polar Vortex (SPV) is prominent over Antarctica in the Austral winter, and typically associated with a region of low temperature, low ozone concentration, negative potential vorticity, and polar stratospheric clouds. Seasonal and unexpected changes in the SPV have a profound influence on global weather. A methodology which identifies the SPV’s coherence and breakup using only wind and pressure data is developed and validated against temperature, ozone and potential vorticity data. The process identifies “convective modes”, each with an assigned “coherence” value, which form building blocks for the observed spatial variation of the SPV. Analysis and interpretation are presented for 4 years with quite different known behavior of the SPV: 1999 (a relatively standard year), 2002 (when the SPV split into two), 2019 (an atmospheric warming year which led to an early dissipation in the SPV), and the most recent year 2022 (which was influenced by submarine volcano eruptions and a prolonged La Niña event). In decomposing convective effects into modes with quantifiable coherence, this study solidifies connections between wind velocities and atmospheric variables while providing new tools to study the evolution of coherent structures and signal the occurrence of atypical geophysical events.
Optimization of extracellular vesicles preparation from saliva of head and neck cancer patients
Authors: Tengler Luisa , Tiedtke Moritz , Schütz Julia , Bieback Karen , Uhlig Stefanie , Theodoraki Marie-Nicole , Nitschke Katja , Worst Thomas Stefan , Seiz Elena , Scherl Claudia , Rotter Nicole , Ludwig Sonja 
Published: January 2024

AbstractSmall extracellular vesicles from saliva (SEVs) have high potential as biomarkers in Head and Neck cancer (HNC). However, there is no common consensus on the ideal method for their isolation. This study compared different ultracentrifugation (UC) methods (durations and + /− additional purification) with size exclusion chromatography (SEC) and investigated the potential of SEVs as diagnostic biomarkers and their biological activity on NK and CD8+ T cells. SEVs from 19 HNC patients and 8 healthy donors (HDs) were thoroughly characterized. Transmission electron microscopy confirmed the isolation of vesicles by all methods. The average size determined via nanoparticle-tracking analysis was smaller for SEVs isolated by SEC than UC. The highest particle-to-protein yield was achieved by UC (3 h + 3 h) (UCopt) and SEC. However, SEC yielded considerably fewer SEVs. Comparing the surface marker cargo, SEVs isolated by UCopt from HNC patients carried more PD-L1, FasL, and TGF-β than SEVs from HDs. These levels correlated with tumor stage and HPV status. SEVs downregulated NKG2D expression on primary NK cells. HNC SEVs accelerated CD8+ T cell death compared to HD SEVs. This study suggests that UCopt is preferable when isolation of a high particle-to-protein load is required. Especially PD-L1 and FasL on SEVs hold substantial potential as diagnostic biomarkers.
Integrative analysis of single-cell and bulk RNA-sequencing data revealed T cell marker genes based molecular sub-types and a prognostic signature in lung adenocarcinoma
Authors: Peng Yueling , Dong Yafang , Sun Qihui , Zhang Yue , Zhou Xiangyang , Li Xiaoyang , Ma Yuehong , Liu Xingwei , Li Rongshan , Guo Fengjie , Guo Lili 
Published: January 2024

AbstractImmunotherapy has emerged as a promising modality for addressing advanced or conventionally drug-resistant malignancies. When it comes to lung adenocarcinoma (LUAD), T cells have demonstrated significant influence on both antitumor activity and the tumor microenvironment. However, their specific contributions remain largely unexplored. This investigation aimed to delineate molecular subtypes and prognostic indicators founded on T cell marker genes, thereby shedding light on the significance of T cells in LUAD prognosis and precision treatment. The cellular phenotypes were identified by scrutinizing the single-cell data obtained from the GEO repository. Subsequently, T cell marker genes derived from single-cell sequencing analyses were integrated with differentially expressed genes from the TCGA repository to pinpoint T cell-associated genes. Utilizing Cox analysis, molecular subtypes and prognostic signatures were established and subsequently verified using the GEO dataset. The ensuing molecular and immunological distinctions, along with therapy sensitivity between the two sub-cohorts, were examined via the ESTIMATE, CIBERSORT, and ssGSEA methodologies. Compartmentalization, somatic mutation, nomogram development, chemotherapy sensitivity prediction, and potential drug prediction analyses were also conducted according to the risk signature. Additionally, real-time qPCR and the HPA database corroborated the mRNA and protein expression patterns of signature genes in LUAD tissues. In summary, this research yielded an innovative T cell marker gene-based signature with remarkable potential to prognosis and anticipate immunotherapeutic outcomes in LUAD patients.
Optimal dilation duration of 10 mm diameter balloons after limited endoscopic sphincterotomy for common bile duct stones: a randomized controlled trial
Authors: Li Yuan-Yuan , Miao Yin-Shui , Wang Cai-Feng , Yan Jing , Zhou Xiao-Jiang , Chen You-Xiang , Li Guo-Hua , Zhu Liang 
Published: January 2024

AbstractLimited endoscopic sphincterotomy (EST) combined with endoscopic papillary balloon dilation (EPBD) is widely used. However, the optimal duration of small balloon dilation in choledocholithiasis remains controversial. We aimed to determine the optimal duration for 10 mm diameter balloon dilation after limited EST in choledocholithiasis. In this randomized controlled clinical trial, 320 patients were randomly assigned to receive small balloon dilation (10 mm in diameter) for 1 min (n = 160) or 3 min (n = 160) after deep bile duct cannulation. No significant difference in success rate of stone extraction between the two groups was observed. The incidence of post-ERCP pancreatitis (PEP) was higher in the 1 min group (10.6%) than in the 3 min group (4.4%) (P = 0.034). The logistic regression analysis showed that guidewire into the pancreatic duct, cannulation time > 5 min and 1 min balloon dilation were independent risk factors for PEP. There were no significant differences in other post-ERCP adverse events such as acute cholangitis, bleeding, perforation, etc. between the two groups. In conclusion, 3 min in duration was determined to be the optimal dilation condition for the removal of common bile duct stones.
Enhancing ReaxFF for molecular dynamics simulations of lithium-ion batteries: an interactive reparameterization protocol
Authors: De Angelis Paolo , Cappabianca Roberta , Fasano Matteo , Asinari Pietro , Chiavazzo Eliodoro 
Published: January 2024

AbstractLithium-ion batteries (LIBs) have become an essential technology for the green economy transition, as they are widely used in portable electronics, electric vehicles, and renewable energy systems. The solid-electrolyte interphase (SEI) is a key component for the correct operation, performance, and safety of LIBs. The SEI arises from the initial thermal metastability of the anode-electrolyte interface, and the resulting electrolyte reduction products stabilize the interface by forming an electrochemical buffer window. This article aims to make a first—but important—step towards enhancing the parametrization of a widely-used reactive force field (ReaxFF) for accurate molecular dynamics (MD) simulations of SEI components in LIBs. To this end, we focus on Lithium Fluoride (LiF), an inorganic salt of great interest due to its beneficial properties in the passivation layer. The protocol relies heavily on various Python libraries designed to work with atomistic simulations allowing robust automation of all the reparameterization steps. The proposed set of configurations, and the resulting dataset, allow the new ReaxFF to recover the solid nature of the inorganic salt and improve the mass transport properties prediction from MD simulation. The optimized ReaxFF surpasses the previously available force field by accurately adjusting the diffusivity of lithium in the solid lattice, resulting in a two-order-of-magnitude improvement in its prediction at room temperature. However, our comprehensive investigation of the simulation shows the strong sensitivity of the ReaxFF to the training set, making its ability to interpolate the potential energy surface challenging. Consequently, the current formulation of ReaxFF can be effectively employed to model specific and well-defined phenomena by utilizing the proposed interactive reparameterization protocol to construct the dataset. Overall, this work represents a significant initial step towards refining ReaxFF for precise reactive MD simulations, shedding light on the challenges and limitations of ReaxFF force field parametrization. The demonstrated limitations emphasize the potential for developing more versatile and advanced force fields to upscale ab initio simulation through our interactive reparameterization protocol, enabling more accurate and comprehensive MD simulations in the future.
Toxicity of ZnFe-SO4 layered double hydroxide in Tetradesmus obliquus and evaluation of some physiological responses of the microalgae for stress management
Authors: Torbati Samaneh , Yekan Motlagh Parisa , Khataee Alireza 
Published: January 2024

AbstractLayered double hydroxides (LDHs), regarding their physical and structural properties, have different and wide applications industry and their increasing use may raise ecological and human health concerns. However, the potential toxicity mechanisms of LDHs in different organisms are still unclear. In the present work, after synthesizing of ZnFe-SO4 LDH and studying of its characterization by XRD, FT-IR, SEM, EDX-mapping, TEM and Raman, its toxicity in Tetradesmus obliquus was evaluated. According to experimental results, the growth of the algae and content of photosynthetic pigments were significantly decreased after treatment with 100 mg/L of ZnFe-SO4 LDH. The high dose exposure to the LDH also inhibited the activity of SOD and POD enzymes, possibly due to the LDH- catalyzed reactive oxygen species production. In addition, lipid peroxidation and the content of phenolic compounds, as no-enzymatic antioxidants were increased by enhancement of the LDH concentration. The rise of phenol, flavonoids and MDA contents could be regarded as some manifestations and responses to the toxic effects of the contaminant in the algae cells. The results provided a better understanding of the undesirable effects and toxicity of LDHs in aquatic organisms.
A self-adaptive attraction and repulsion-based naked mole-rat algorithm for energy-efficient mobile wireless sensor networks
Authors: Singh Supreet , Singh Urvinder , Mittal Nitin , Gared Fikreselam 
Published: January 2024

AbstractNaked mole-rat algorithm (NMRA) is a swarm intelligence-based algorithm that draws inspiration from the mating behaviour of mole rats (workers and breeders). This approach, which is based on the ability of breeders to reproduce with the queen, has been utilized to tackle optimization problems. The algorithm, however, suffers from local optima stagnation problem and a slower rate of convergence in order to provide gobal optimal solution. This study suggests attraction and repulsion strategy based NMRA (ARNMRA) along with self-adaptive properties to avoid trapping of solution in local optima. This strategy is utilized to create new breeder rat solutions and mating factor$$(\lambda )$$(λ)is made self-adaptive using simulated annealing (sa) based mutation operator. ARNMRA is evaluated on CEC 2005 numerical benchmark problems and found to be superior to other algorithms, including well-known ones like selective operation based GWO (SOGWO), opposition based laplacian equilibrium optimizer (OB-L-EO), improved whale optimization algorithm (IWOA), success-history based adaptive DE (SHADE) and original NMRA. Further, according to experimental results, the performance of ARNMRA is likewise superior to the NMRA for the CEC 2019 and CEC 2020 numerical problems. Convergence profiles and statistical tests (rank-sum test and Friedman test) are employed further to validate the experimental results. Moreover, this article extends the application of ARNMRA to address the data gathering aspect in mobile wireless sensor networks (MWSNs) with the goal of prolonging network lifetime and enhancing energy efficiency. In this MWSN-based protocol, a sensor node is elected as a cluster head based on factors like mobility, residual energy, and connection time. The protocol aims to maximize the system lifetime by efficiently collecting data from all sensors and transmitting it to the base station. The study emphasizes the significance of considering dynamic node densities and speed when designing effective data-gathering protocols for MWSNs.
Effects of floral display size, local open raceme density, patch size, and distance between patches on pollinator behaviour in Salvia nipponica
Authors: Murakoshi Noriko , Itagaki Tomoyuki , Oguro Michio , Sakai Satoki 
Published: January 2024

AbstractFlowers cluster at various spatial scales, so pollinators use information from multiple scales when foraging in natural plant populations. Little is known about the effects of interactions between scales or their relative strength. We examined bumblebee foraging behaviour in a natural population of Salvia nipponica in 10 and 7 patches in 2019 and 2020, respectively. We recorded within-patch factors (display size of racemes and local open raceme densities) and patch-level factors (patch size and distance from the nearest patch) and analysed their relationships with pollinator behaviour. The numbers of visits per raceme and flower were mainly affected by the interaction of patch size and raceme density; they were higher in locations with lower raceme density in larger patches. The ratio of flowers visited to all open flowers in a raceme during a raceme visit, which relates to a bumblebee’s choice to leave a raceme, was mainly affected by the interaction of display size and local open raceme density; in 2019 it was higher in racemes with smaller display sizes, while in 2020 the strength and direction of the relationship depended on the open raceme density. These results suggest that pollinators relied on the sizes of flower clusters at different spatial scales when visiting and leaving racemes and adjusted their responses to the sizes of flower clusters depending on the distances between clusters. Therefore, it is important to evaluate factors at various spatial scales and their interactions to fully understand pollinator behaviour in natural plant populations.
Large-scale production of myco-fabricated ZnO/MnO nanocomposite using endophytic Colonstachys rosea with its antimicrobial efficacy against human pathogens
Authors: EL-Moslamy Shahira H. , Abd-Elhamid Ahmed Ibrahim , Fawal Gomaa El 
Published: January 2024

AbstractIn this study, a ZnO/MnO nanocomposite was myco-fabricated using the isolated endophytic Clonostachys rosea strain EG99 as the nano-factory. The extract of strain EG99, a reducing/capping agent, was successfully titrated with equal quantities of Zn(NO3)2·6H2O and Mn(NO3)2·6H2O (precursors) in a single step to fabricate the rod-shaped ZnO/MnO nanocomposite of size 6.22 nm. The ZnO/MnO nanocomposite was myco-fabricated in 20 min, and the results were validated at 350 and 400 nm using UV–Vis spectroscopy. In a 7-L bioreactor, an industrial biotechnological approach was used to scale up the biomass of this strain, EG99, and the yield of the myco-fabricated ZnO/MnO nanocomposite. A controlled fed-batch fermentation system with a specific nitrogen/carbon ratio and an identical feeding schedule was used in this production process. Higher yields were obtained by adopting a controlled fed-batch fermentation approach in a 7-L bioreactor with a regular feeding schedule using a nitrogen/carbon ratio of 1:200. Overall, the fed-batch produced 89.2 g/l of biomass at its maximum, 2.44 times more than the batch's 36.51 g/l output. Furthermore, the fed-batch's maximum ZnO/MnO nanocomposite yield was 79.81 g/l, a noteworthy 14.5-fold increase over the batch's yield of 5.52 g/l. Finally, we designed an innovative approach to manage the growth of the endophytic strain EG99 using a controlled fed-batch fermentation mode, supporting the rapid, cheap and eco-friendly myco-fabrication of ZnO/MnO nanocomposite. At a dose of 210 µg/ml, the tested myco-fabricated ZnO/MnO nanocomposite exhibited the maximum antibacterial activity against Staphylococcus aureus (98.31 ± 0.8%), Escherichia coli (96.70 ± 3.29%), and Candida albicans (95.72 ± 0.95%). At the same dose, Staphylococcus aureus biofilm was eradicated in 48 h; however, Escherichia coli and Candida albicans biofilms needed 72 and 96 h, respectively. Our myco-fabricated ZnO/MnO nanocomposite showed strong and highly selective antagonistic effects against a variety of multidrug-resistant human pathogens. Therefore, in upcoming generations of antibiotics, it might be employed as a nano-antibiotic.
Ablation alone is noninferior to radiotherapy plus ablation in the patients with early-stage hepatocellular carcinoma: a population-based study
Authors: Guo Yusheng , Chen Hebing , Wan Jiayu , Ren Yanqiao , Wu Feihong , Chen Lei , Sun Tao , Yang Lian , Zheng Chuansheng 
Published: January 2024

AbstractRecently, the efficacy of two low-invasive treatments, ablation, and radiotherapy, has been fully compared for the patients with the early-stage hepatocellular carcinoma (HCC). However, the comparison between radiotherapy plus ablation and ablation alone has been less frequently reported. Data from the Surveillance, Epidemiology, and End Results (SEER) database were searched for early-stage HCC patients treated with ablation plus radiotherapy or ablation alone. The outcome measures were overall survival (OS) and cancer-specific survival (CSS). The propensity score matching (PSM) was used to reduce selection bias. We included 240 and 6619 patients in the radiotherapy plus ablation group and ablation group before the PSM. After PSM, 240 pairs of patients were included. The median OS (mOS) and median CSS (mCSS) of patients receiving ablation alone were longer than that of receiving radiotherapy plus ablation (mOS: 47 vs. 34 months, P = 0.019; mCSS: 77 vs. 40 months, P = 0.018, after PSM) before and after PSM. The multivariate analysis indicated that radiotherapy plus ablation independent risk factor for OS and CSS before PSM, but the significance disappeared after PSM. The detailed subgroup analyses indicated ablation alone brought more benefit in very early-stage HCC and older patients. In addition, we found different types of radiotherapy might lead to different outcomes when combined with ablation. In conclusion, ablation alone is noninferior to radiotherapy plus ablation in patients with early-stage HCC. The additional radiation prior to ablation may bring survival benefits in the patients with higher tumor stage. However, due to the risk of selection bias in that study, the results should be interpreted cautiously.
Research on a new management model of distribution Internet of Things
Authors: Chen Chao , Gong Liwu , Luo Xin , Wang Fuwang 
Published: January 2024

AbstractBased on the characteristics of controllable intelligence of the Internet of Things (IoT) and the requirements of the new distribution Network for function and transmission delay, this study proposes a method of combining edge collaborative computing and distribution Network station area, and builds a distribution Network management structure model by combining the Packet Transport Network (PTN) Network structure. The multi-terminal node distribution model of distributed IoT is established. Finally, a distribution IoT management model is constructed based on the edge multi-node cooperative reasoning algorithm and collaborative computing architecture model. The purpose of this paper is to solve the problem of large reasoning delay caused by heavy computing tasks in distribution cloud servers. The final results show that the model reduces the inference delay of cloud computing when a large number of smart device terminals of distribution IoT are connected to the network.
Functionally coherent transcriptional responses of Jatropha curcas and Pseudomonas fragi for rhizosphere mediated degradation of pyrene
Authors: Singha L. Paikhomba , Singha K. Malabika , Pandey Piyush 
Published: January 2024

AbstractPyrene is an extremely hazardous, carcinogenic polycyclic aromatic hydrocarbon (PAH). The plant–microbe interaction between Pseudomonas fragi DBC and Jatropha curcas was employed for biodegradation of pyrene and their transcriptional responses were compared. The genome of P. fragi DBC had genes for PAH degrading enzymes i.e. dioxygenases and dehydrogenases, along with root colonization (trpD, trpG, trpE and trpF), chemotaxis (flhF and flgD), stress adaptation (gshA, nuoHBEKNMG), and detoxification (algU and yfc). The transcriptional expression of catA and yfc that respectively code for catabolic enzyme (catechol-1, 2-dioxygnase) and glutathione-s-transferase for detoxification functions were quantitatively measured by qPCR. The catA was expressed in presence of artificial root exudate with or without pyrene, and glucose confirming the non-selective approach of bacteria, as desired. Pyrene induced 100-fold increase of yfc expression than catA, while there was no expression of yfc in absence of pyrene. The transcriptome of plant roots, in presence of pyrene, with or without P. fragi DBC inoculation was analysed. The P. fragi DBC could upregulate the genes for plant growth, induced the systemic acquired resistance and also ameliorated the stress response in Jatropha roots.
Neuroactive steroid effects on autophagy in a human embryonic kidney 293 (HEK) cell model
Authors: Salvatore Sofia V. , Ilagan Ma. Xenia G. , Shu Hongjin , Lambert Peter M. , Benz Ann , Qian Mingxing , Covey Douglas F. , Zorumski Charles F. , Mennerick Steven 
Published: January 2024

AbstractNeuropsychiatric and neurodegenerative disorders are correlated with cellular stress. Macroautophagy (autophagy) may represent an important protective pathway to maintain cellular homeostasis and functionality, as it targets cytoplasmic components to lysosomes for degradation and recycling. Given recent evidence that some novel psychiatric treatments, such as the neuroactive steroid (NAS) allopregnanolone (AlloP, brexanolone), may induce autophagy, we stably transfected human embryonic kidney 293 (HEK) cells with a ratiometric fluorescent probe to assay NAS effects on autophagy. We hypothesized that NAS may modulate autophagy in part by the ability of uncharged NAS to readily permeate membranes. Microscopy revealed a weak effect of AlloP on autophagic flux compared with the positive control treatment of Torin1. In high-throughput microplate experiments, we found that autophagy induction was more robust in early passages of HEK cells. Despite limiting studies to early passages for maximum sensitivity, a range of NAS structures failed to reliably induce autophagy or interact with Torin1 or starvation effects. To probe NAS in a system where AlloP effects have been shown previously, we surveyed astrocytes and again saw minimal autophagy induction by AlloP. Combined with other published results, our results suggest that NAS may modulate autophagy in a cell-specific or context-specific manner. Although there is merit to cell lines as a screening tool, future studies may require assaying NAS in cells from brain regions involved in neuropsychiatric disorders.