bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shotgun metagenomic insights into secondary metabolite biosynthetic gene clusters reveal taxonomic and functional profiles of microbiomes in natural farmland soil
Authors: Kifle Bezayit Amare , Sime Amsale Melkamu , Gemeda Mesfin Tafesse , Woldesemayat Adugna Abdi 
Published: July 2024

AbstractAntibiotic resistance is a worldwide problem that imposes a devastating effect on developing countries and requires immediate interventions. Initially, most of the antibiotic drugs were identified by culturing soil microbes. However, this method is prone to discovering the same antibiotics repeatedly. The present study employed a shotgun metagenomics approach to investigate the taxonomic diversity, functional potential, and biosynthetic capacity of microbiomes from two natural agricultural farmlands located in Bekeka and Welmera Choke Kebelle in Ethiopia for the first time. Analysis of the small subunit rRNA revealed bacterial domain accounting for 83.33% and 87.24% in the two selected natural farmlands. Additionally, the analysis showed the dominance of Proteobacteria representing 27.27% and 28.79% followed by Actinobacteria making up 12.73% and 13.64% of the phyla composition. Furthermore, the analysis revealed the presence of unassigned bacteria in the studied samples. The metagenome functional analysis showed 176,961 and 104, 636 number of protein-coding sequences (pCDS) from the two samples found a match with 172,655 and 102, 275 numbers of InterPro entries, respectively. The Genome ontology annotation suggests the presence of 5517 and 3293 pCDS assigned to the “biosynthesis process”. Numerous Kyoto Encyclopedia of Genes and Genomes modules (KEGG modules) involved in the biosynthesis of terpenoids and polyketides were identified. Furthermore, both known and novel Biosynthetic gene clusters, responsible for the production of secondary metabolites, such as polyketide synthases, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptides (Ripp), and Terpene, were discovered. Generally, from the results it can be concluded that the microbiomes in the selected sampling sites have a hidden functional potential for the biosynthesis of secondary metabolites. Overall, this study can serve as a strong preliminary step in the long journey of bringing new antibiotics to the market.
Age-appropriate BMI cut-offs for malnutrition among older adults in India
Authors: Singh Akancha , Chattopadhyay Aparajita 
Published: July 2024

AbstractWith the increasing prevalence of obesity in India, body mass index (BMI) has garnered importance as a disease predictor. The current World Health Organization (WHO) body mass index (BMI) cut-offs may not accurately portray these health risks in older adults aged 60 years and above. This study aims to define age-appropriate cut-offs for older adults (60–74 years and 75 years and above) and compare the performance of these cut-offs with the WHO BMI cut-offs using cardio-metabolic conditions as outcomes. Using baseline data from the Longitudinal Ageing Study in India (LASI), classification and regression tree (CART) cross-sectional analysis was conducted to obtain age-appropriate BMI cut-offs based on cardio-metabolic conditions as outcomes. Logistic regression models were estimated to compare the association of the two sets of cut-offs with cardio-metabolic outcomes. The area under the receiver operating characteristic curve (AUC), sensitivity and specificity were estimated. Agreement with waist circumference, an alternate measure of adiposity, was conducted. For older adults aged 60–74 years and 75 years and above, the cut-off for underweight reduced from < 18.5 to < 17.4 and < 13.3 respectively. The thresholds for overweight and obese increased for older adults aged 60–74 years old from >  = 25 to > 28.8 and >  = 30 to > 33.7 respectively. For older adults aged 75 years and above, the thresholds decreased for both categories. The largest improvement in AUC was observed in older adults aged 75 years and above. The newly derived cut-offs also demonstrated higher sensitivity and specificity among all age-sex stratifications. There is a need to adopt greater rigidity in defining overweight/obesity among older adults aged 75 years and above, as opposed to older adults aged 60–74 years old among whom the thresholds need to be less conservative. Further stratification in the low risk category could also improve BMI classification among older adults. These age-specific thresholds may act as improved alternatives of the current WHO BMI thresholds and improve classification among older adults in India.
Construction of a novel prognostic scoring model for HBV-ACLF liver failure based on dynamic data
Authors: Cai Qun , Wang Hao , Zhu Mingyan , Xiao Yixin , Zhuo Tingting 
Published: July 2024

AbstractEarly prognostic assessment of patients with hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF) is important for guiding clinical management and reducing mortality. The aim of this study was to dynamically monitor the clinical characteristics of HBV-ACLF patients, thereby allowing the construction of a novel prognostic scoring model to predict the outcome of HBV-ACLF patients. Clinical data was prospectively collected for 518 patients with HBV-ACLF and randomly divided into training and validation sets. We constructed day-1, day-2, and day-(1 + 3) prognostic score models based on dynamic time points. The prognostic risk score constructed for day-3 was found to have the best predictive ability. The factors included in this scoring system, referred to as DSM-ACLF-D3, were age, hepatic encephalopathy, alkaline phosphatase, total bilirubin, triglycerides, very low-density lipoprotein, blood glucose, neutrophil count, fibrin, and INR. ROC analysis revealed the area under the curve predicted by DSM-ACLF-D3 for 28-day and 90-day mortality (0.901 and 0.889, respectively) was significantly better than those of five other scoring systems: COSSH-ACLF IIs (0.882 and 0.836), COSSH-ACLFs (0.863 and 0.832), CLIF-C ACLF (0.838 and 0.766), MELD (0.782 and 0.762) and MELD-Na (0.756 and 0.731). Dynamic monitoring of the changes in clinical factors can therefore significantly improve the accuracy of scoring models. Evaluation of the probability density function and risk stratification by DSM-ACLF-D3 also resulted in the best predictive values for mortality. The novel DSM-ACLF-D3 prognostic scoring model based on dynamic data can improve early warning, prediction and clinical management of HBV-ACLF patients.
Impact of baseline ECG characteristics on changes in cardiac biomarkers and echocardiographic metrices after acute myocardial infarction treated with Empagliflozin
Authors: Benedikt Martin , Aziz Faisal , Fröschl Thomas , Strohhofer Christoph , Kolesnik Ewald , Tripolt Norbert , Pferschy Peter , Wallner Markus , Bugger Heiko , Zirlik Andreas , Scherr Daniel , Sourij Harald , von Lewinski Dirk 
Published: July 2024

AbstractThe EMMY trial was a multicentre, investigator-initiated, placebo-controlled, double-blind trial, which enrolled 476 patients immediately following AMI and the first study demonstrating a significant reduction in NT-proBNP-levels as well as significant improvements in cardiac structure and function in patients after acute myocardial infarction treated with empagliflozin vs. placebo. However, hardly any data are available investigating the prognostic role of baseline electrocardiogram metrics in SGLT2-inhibitor-treated patients. This post-hoc analysis investigated the association of baseline ECG metrics collected in one centre of the trial (181 patients) with changes in structural and functional cardiac parameters as well as cardiac biomarkers in response to Empagliflozin treatment. A total of 181 patients (146 men; mean age 58 ± 14 years) were included. Median PQ-interval was 156 (IQR 144–174) milliseconds (ms), QRS width 92 (84–98) ms, QTc interval 453 (428–478) ms, Q-wave duration 45 (40–60) ms, Q-wave amplitude 0.40 (0.30–0.70) millivolt (mV), and heart rate was 71 (64–85) bpm. For functional cardiac parameters (LVEF and E/eʹ) of the entire cohort, a greater decrease of E/eʹ from baseline to week 26 was observed in shorter QRS width (P = 0.005).Structural cardiac endpoints were only found to have a significant positive correlation between LVEDD and Q wave duration (P = 0.037). Higher heart rate was significantly correlated with better response in LVEF (P = 0.001), E/eʹ (P = 0.021), and NT-proBNP (P = 0.005). Empagliflozin-treatment showed no interaction with the results. Baseline ECG characteristics post AMI are neither predictive for beneficial NTproBNP effects of Empagliflozin post AMI, nor for functional or structural changes within 26 weeks post AMI.
A streamlined approach for intelligent ship object detection using EL-YOLO algorithm
Authors: Yang Defu , Solihin Mahmud Iwan , Ardiyanto Igi , Zhao Yawen , Li Wei , Cai Bingyu , Chen Chaoran 
Published: July 2024

AbstractMaritime objects frequently exhibit low-quality and insufficient feature information, particularly in complex maritime environments characterized by challenges such as small objects, waves, and reflections. This situation poses significant challenges to the development of reliable object detection including the strategies of loss function and the feature understanding capabilities in common YOLOv8 (You Only Look Once) detectors. Furthermore, the widespread adoption and unmanned operation of intelligent ships have generated increasing demands on the computational efficiency and cost of object detection hardware, necessitating the development of more lightweight network architectures. This study proposes the EL-YOLO (Efficient Lightweight You Only Look Once) algorithm based on YOLOv8, designed specifically for intelligent ship object detection. EL-YOLO incorporates novel features, including adequate wise IoU (AWIoU) for improved bounding box regression, shortcut multi-fuse neck (SMFN) for a comprehensive analysis of features, and greedy-driven filter pruning (GDFP) to achieve a streamlined and lightweight network design. The findings of this study demonstrate notable advancements in both detection accuracy and lightweight characteristics across diverse maritime scenarios. EL-YOLO exhibits superior performance in intelligent ship object detection using RGB cameras, showcasing a significant improvement compared to standard YOLOv8 models.
Enhancement of endothelial function and attenuation of portal vein injury using mesenchymal stem cells carrying miRNA-25-3p
Authors: Nie Guole , Zhang Honglong , Luo Wei , Zhu Xingwang , Xie Danna , Yan Jun , Wang Haiping , Li Xun 
Published: July 2024

AbstractThe aims of this study were to determine whether human umbilical cord mesenchymal stem cells (hucMSCs) modified by miRNA-25-3p (miR-25-3p) overexpression could promote venous endothelial cell proliferation and attenuate portal endothelial cell injury. HucMSCs and human umbilical vein endothelial cells (HUVEC) were isolated and cultured from human umbilical cord and characterized. Lentiviral vectors expressing miRNA-25-3p were transfected into hucMSCs and confirmed by PCR. We verified the effect of miR-25-3p-modified hucMSCs on HUVEC by cell co-culture and cell supernatant experiments. Subsequently, exosomes of miR-25-3p-modified hucMSCs were isolated from cell culture supernatants and characterized by WB, NTA and TEM. We verified the effects of miR-25-3p-modified exosomes derived from hucMSCs on HUVEC proliferation, migration, and angiogenesis by in vitro cellular function experiments. Meanwhile, we further examined the downstream target genes and signaling pathways potentially affected by miR-25-3p-modified hucMSC-derived exosomes in HUVEC. Finally, we established a rat portal vein venous thrombosis model by injecting CM-DiR-labeled hucMSCs intravenously into rats and examining the homing of cells in the portal vein by fluorescence microscopy. Histological and immunohistochemical experiments were used to examine the effects of miRNA-25-3p-modified hucMSCs on the proliferation and damage of portal vein endothelial cells. Primary hucMSCs and HUVECs were successfully isolated, cultured and characterized. Primary hucMSCs were modified with a lentiviral vector carrying miR-25-3p at MOI 80. Co-culture and cell supernatant intervention experiments showed that overexpression of miRNA-25-3p in hucMSCs enhanced HUVEC proliferation, migration and tube formation in vitro. We successfully isolated and characterized exosomes of miR-25-3p-modified hucMSCs, and exosome intervention experiments demonstrated that miR-25-3p-modified exosomes derived from hucMSCs similarly enhanced the proliferation, migration, and angiogenesis of HUVECs. Subsequent PCR and WB analyses indicated PTEN/KLF4/AKT/ERK1/2 as potential pathways of action. Analysis in a rat portal vein thrombosis model showed that miR-25-3p-modified hucMSCs could homing to damaged portal veins. Subsequent histological and immunohistochemical examinations demonstrated that intervention with miR-25-3p overexpression-modified hucMSCs significantly reduced damage and attenuated thrombosis in rat portal veins. The above findings indicate suggest that hucMSCs based on miR-25-3p modification may be a promising therapeutic approach for use in venous thrombotic diseases.
P4HA2 promotes proliferation, invasion, and metastasis through regulation of the PI3K/AKT signaling pathway in oral squamous cell carcinoma
Authors: Chi Zengpeng , Wang Qimin , Wang Xin , Li Dagang , Tong Lei , Shi Yu , Yang Fang , Guo Qingyuan , Zheng Jiawei , Chen Zhenggang 
Published: July 2024

AbstractProline 4-hydroxylase 2 (P4HA2) is known for its hydroxylase activity, primarily involved in hydroxylating collagen precursors and promoting collagen cross-linking under physiological conditions. Although its overexpression influences a wide variety of malignant tumors' occurrence and development, its specific effects and mechanisms in oral squamous cell carcinoma (OSCC) remain unclear. This study focused on investigating the expression patterns, carcinogenic functions, and underlying mechanisms of P4HA2 in OSCC cells. Various databases, including TCGA, TIMER, UALCAN, GEPIA, and K-M plotter, along with paraffin-embedded samples, were used to ascertain P4HA2 expression in cancer and its correlation with clinicopathological features. P4HA2 knockdown and overexpression cell models were developed to assess its oncogenic roles and mechanisms. The results indicated that P4HA2 was overexpressed in OSCC and inversely correlated with patient survival. Knockdown of P4HA2 suppressed invasion, migration, and proliferation of OSCC cells both in vitro and in vivo, whereas overexpression of P4HA2 had the opposite effects. Mechanistically, the phosphorylation levels of the PI3K/AKT pathway were reduced following P4HA2 silencing. The study reveals that P4HA2 acts as a promising biomarker for predicting prognosis in OSCC and significantly affects metastasis, invasion, and proliferation of OSCC cells through the regulation of the PI3K/AKT signaling pathway.
A simple psychophysical procedure separates representational and noise components in impairments of speech prosody perception after right-hemisphere stroke
Authors: Adl Zarrabi Aynaz , Jeulin Mélissa , Bardet Pauline , Commère Pauline , Naccache Lionel , Aucouturier Jean-Julien , Ponsot Emmanuel , Villain Marie 
Published: July 2024

AbstractAfter a right hemisphere stroke, more than half of the patients are impaired in their capacity to produce or comprehend speech prosody. Yet, and despite its social-cognitive consequences for patients, aprosodia following stroke has received scant attention. In this report, we introduce a novel, simple psychophysical procedure which, by combining systematic digital manipulations of speech stimuli and reverse-correlation analysis, allows estimating the internal sensory representations that subtend how individual patients perceive speech prosody, and the level of internal noise that govern behavioral variability in how patients apply these representations. Tested on a sample of N = 22 right-hemisphere stroke survivors and N = 21 age-matched controls, the representation + noise model provides a promising alternative to the clinical gold standard for evaluating aprosodia (MEC): both parameters strongly associate with receptive, and not expressive, aprosodia measured by MEC within the patient group; they have better sensitivity than MEC for separating high-functioning patients from controls; and have good specificity with respect to non-prosody-related impairments of auditory attention and processing. Taken together, individual differences in either internal representation, internal noise, or both, paint a potent portrait of the variety of sensory/cognitive mechanisms that can explain impairments of prosody processing after stroke.
Evaluation of the optical and magnetic properties of novel Nd0.9Zn0.1FeO3 perovskite nanoparticles and their adsorption of Pb2+ ions from water
Authors: Arman M. M. 
Published: July 2024

AbstractNd0.9Zn0.1FeO3 was prepared in a single-phase with an average crystallite size of 25.82 nm using a citrate combustion technique. The energy dispersive X-ray assures the chemical formula of the sample. The elemental mapping of Zn-doped NdFeO3 illustrates the good homogeneous distribution of the elements in the sample. Nd0.9Zn0.1FeO3 has antiferromagnetic properties with weak ferromagnetic components and has good UV absorbance. The values of the band gap for the direct and indirect transitions are 1.473 eV and 1.250 eV, respectively. The adsorption of nickel(II), cobalt(II), chrome(VI), cadmium(II), and lead(II) ions has been studied at pH 7. The highest removal efficiency (η = 73.72%) was observed for the lead ions from water. The current study has examined the kinetics, recoveries, and mechanisms of utilizing Nd0.90Zn0.10FeO3 to remove Pb2+ ions from water. The optimum conditions for the absorbing Pb2+ are pH 7 and a contact time of 60 min. The Freundlich isotherm model is the best model for the absorption of Pb2+ ions. While, the pseudo-second-order kinetic model describes the kinetic adsorption data. The sample has a good efficiency for removing Pb2+ ions from water several times.
Speckled-speckle field as a resource for imaging techniques
Authors: Cassina Silvia , Cenedese Gabriele , Allevi Alessia , Bondani Maria 
Published: July 2024

AbstractCorrelated states of light, both classical and quantum, can find useful applications in the implementation of several imaging techniques. Among the employed sources, pseudo-thermal states, generated by the passage of a laser beam through a diffuser, represent the standard choice. To produce light with a higher level of correlation, in this work we consider and characterize the speckled-speckle field obtained with two diffusers using both a numerical simulation and an experimental implementation. In order to discuss the potential usefulness of super-thermal light in imaging protocols, we analyze the behavior of some figures of merit, namely the contrast, the signal-to-noise ratio and the image resolution. The obtained results clarify the possible advantages offered by this kind of light, and at the same time better emphasize the reasons why it does not outperform pseudo-thermal light.
Improved chaotic Bat algorithm for optimal coordinated tuning of power system stabilizers for multimachine power system
Authors: Tadj Mohammed , Chaib Lakhdar , Choucha Abdelghani , Alhazmi Mohannad , Alwabli Abdullah , Bajaj Mohit , Dost Mohammadi Shir Ahmad 
Published: July 2024

AbstractPower systems exhibit nonlinearity. causing dynamic instability and complex power oscillations. This research proposes an innovative strategy using the Novel Bat Algorithm (NBA) to achieve ideal Power System Stabilizers (PSSs) in a multimachine power system. The approach shifts electromechanical modes to specific areas in the s-plane. Enhancing the multi-machine power system and establishing stabilizer parameters for dynamic performance. The study examines the designed approach aptitude for standard lead-lag PSSs configurations. In order to elevate the global search problem and transfer some static operators for the optimum optimization process. the chaos mapping. also known as CNBA. is introduced into NBA. Four different forms of chaos maps are compared in experiments to resolve unconstrained mathematical issues in order to illustrate CNBA performance. In any other case. the challenge of designing PSS under a wide range of loading situations is transformed into an optimization challenge with the damping ratio of electromechanical modes with low damping as the target function. The optimal stabilizers’ gains are gotten by employing the CNBA algorithm. Second plan. an effective technique is astutely established to delineate the PSS location and quantity using CNBA and another side using participation factor. To examine the efficacy of the proposed CNBA-based PSS on a large system; it is tested on the interconnected of New-England/New-York (16 generators and 68 buses) power grid. and verified by comparative study with NBA through eigenvalue analysis and nonlinear simulation to provide evidence the algorithmic competence of CNBA. The CNBA approach yields a minimum damping ratio of 37%. which is consistent with the its eigenvalue. In contrast, the NBA approach achieves a minimum damping ratio of 31%. The simulation results reveal the fine performance of the proposed CNBA-PSS in a convincing manner and its capacity to provide an excellent damping for inter-area and local oscillations under diverse operating cases compared to NBA-PSS then in the case of PSS location.
Identifying Bayesian optimal experiments for uncertain biochemical pathway models
Authors: Isenberg Natalie M. , Mertins Susan D. , Yoon Byung-Jun , Reyes Kristofer G. , Urban Nathan M. 
Published: July 2024

AbstractPharmacodynamic (PD) models are mathematical models of cellular reaction networks that include drug mechanisms of action. These models are useful for studying predictive therapeutic outcomes of novel drug therapies in silico. However, PD models are known to possess significant uncertainty with respect to constituent parameter data, leading to uncertainty in the model predictions. Furthermore, experimental data to calibrate these models is often limited or unavailable for novel pathways. In this study, we present a Bayesian optimal experimental design approach for improving PD model prediction accuracy. We then apply our method using simulated experimental data to account for uncertainty in hypothetical laboratory measurements. This leads to a probabilistic prediction of drug performance and a quantitative measure of which prospective laboratory experiment will optimally reduce prediction uncertainty in the PD model. The methods proposed here provide a way forward for uncertainty quantification and guided experimental design for models of novel biological pathways.