bluuebunny/crossref_metadata_2025 huggingface dataset:
Topic Modeling LDA and SVM in Sentiment Analysis of Hotel Reviews
Authors: Erniyati Erniyati , Harsani Prihastuti , Mulyati Mulyati , Fahriza Lutfi Dani
Published: October 2023

The number of visitor comment review data that enters the TripAdvisor and Agoda sites continues to grow over time, this makes it difficult for the hotel to obtain overall information from all comment reviews. Therefore, the purpose of this study is to apply topic modeling and classifying in the analysis of hotel service sentiment.  The data for comment reviews were obtained from 3 five-star hotels, namely 1-HTL, 2-HTL and 3-HTL. The hotel has a five-star rating and has the most comments compared to other hotels in Jakarta. The topic modeling method using Latent Dirichlet Allocation (LDA) in this study succeeded in dividing the comments into several topics that were often discussed from Indonesian and English comments regarding the hotel services provided. By using Support Vector Machine (SVM) obtained the number of positive, negative and neutral comments.
Identification of Significant Proteins in Hypertension Using The Clustering Molecular Complex Detection (MCODE) Method
Authors: Setiani Lusi Agus , Kusuma Wisnu Ananta , Zulkarnaen Silvia Alviani
Published: October 2023

Hypertension is a condition where the systolic blood pressure value is more than 140 mmHg and the diastolic blood pressure value is more than 90 mmHg. A significant protein is a protein that has the greatest effect or is the center of protein regulation in all biochemical processes. The purpose of this study was to determine the significant protein that has the greatest ef- fect on hypertension by using the clustering Molecular Complex Detection (MCODE) method which will identify areas in the network with the highest density value locally and to determine the mechanism of action of the significant proteins obtained in the setting blood pressure using Gene Ontology and Kyoto Encyclopedia and Genome Analysis (KEGG) by looking at protein signaling pathways for hypertension. The results showed that the STAT3, MAPK3, AKT1, and EDN1 proteins were significant proteins involved in the mechanism of the response to leptin, the ERK1 and ERK2 cascades, the process of nitric oxide biosynthesis, and the cellular response to ROS.
Web Design for Stroke Early Detection Using Decision Tree C5.0
Authors: Purwanti Endah , Nor Reza Ummam Nor Ummam , Soelistyono Soegianto
Published: October 2023

Stroke is a disease that needs serious attention because it can cause disability and even death. According to World Health Organization (WHO) in 2022, stroke is the second leading cause of death and a leading cause of disability in the world. In Indonesia, stroke is the first leading of non-communicable disease proportion according to Riset Kesehatan Dasar in 2018. This study aims to design a web application that can help stroke early detection in a person so that people are more concerned about preventing a stroke. This study used Decision Tree (DT) C5.0 method by utilizing 10 stroke risk factors to analyze the risk of stroke in a person. Decision Tree method can break down complex datasets into several simple rules illustrated by a tree, hence the name Decision Tree. The DT C5.0 is one kind of Decision Tree method that has fast performance in classifying data compared to other methods. Therefore, this study observes how DT C5.0 works in detecting stroke risk. The output of this web application is a statement whether a person has a stroke risk or not. The secondary dataset used for model development totaled 5,109 data consisting of 249 stroke patient data and 4,860 non-stroke patient data. In this study, data balancing and cross validation were carried out so that the performance of the training results model was obtained, namely accuracy 83.54%, precision 78.67%, sensitivity 92.20%, and specificity 74.87%. Furthermore, the performance of the test results model is accuracy 84.42%, precision 79.26%, sensitivity 93.10%, and specificity 75.80%.
Building heat demand characteristics in a planned city district with low-temperature district heating supply
Authors: Israelsson Karin , Kayayan Vartan Ahrens , Johari Fatemeh , Gustafsson Mattias , Åberg Magnus
Published: October 2023

Due to desirable emission reductions and population growth, increasing energy demand is identified as a dire issue for energy systems. The introduction of low-energy building districts enables increased energy system efficiency. This study’s aim is twofold. Firstly, an extensive urban building energy model is used to simulate the hourly use and geographic distribution of the heat demand for residential and commercial buildings that are to be supplied by a low-temperature district heating system. The simulated buildings are a part of a planned city district, located in Gävle, Sweden. Two building energy performance cases are studied; one where all buildings are assumed to be of Passive House standard, and one where the building energy performance is in line with conventional new-building regulations in Sweden. Secondly, one specific building is modeled in detail and simulated in the building energy simulation software IDA ICE to investigate what building heating system is best suited for low-temperature heat supply. The temperature demands of floor heating and ventilation with heat recovery are investigated and compared to conventional water-based radiators. The building’s temperature demand results can be used when designing a lowtempered district heating system which will provide the supply temperature to identify a compatible heating system technique. Varying supply temperature demand will enable optimization for choosing building heating systems and consequently, possible cost reductions. The results could be used as an example for future city district planning as well as presenting relevant heating systems for low-temperature district heating.
Phase Fractions and Velocities in Multiphase Flow – Estimation using Sensor Data Fusion and Machine Learning
Authors: Rasmussen Andreas Lund , Fjalestad Kjetil , Yan Ru , Viumdal Håkon , Mylvaganam Saba , Johansen Tonni Franke
Published: October 2023

There is a strong interest in quantifying the amount of gas and its flow rate to facilitate better control of the processes involved in many industries. There are usually many sensors monitoring these processes, both intrusive and invasive, as well as non-invasive sensors which are usually clamped on to the process pipelines in which the multiphase flow occurs. In the multiphase flow rigs at Equinor and the University of South-Eastern Norway, experiments have been performed with different combinations and velocities of the phases and multiple sensors have been logged. The data from these sensors have been used to estimate volume fractions of the phases as well as their flow rates. This paper presents the estimated results of volume fractions and velocities of selected phases, obtained by fusing data from multiple sensors that monitor density, differential pressure, temperature, and acoustic emission using machine learning (ML) algorithms. These ML algorithms use neural networks with the non-linear input-output type with Levenberg-Marquardt training and provide estimates of volume fractions and phase velocities with RMSE values in the range of 4.6 to 16 m3/h, with the lowest RMSE for gas and the highest for multiphase flow. The total flow rate for the multiphase flow was in the range 30 to 120 m3/h. Results are compared with ML models using data from non-invasive sensors.
A Deep Learning Approach for Fault Diagnosis of Hydrogen Fueled Micro Gas Turbines
Authors: Hashmi Muhammad Baqir , Mansouri Mohammad , Fentaye Amare Desalegn , Ahsan Shazaib
Published: October 2023

Hydrogen fueled gas turbines are susceptible to rigorous health degradation in form of corrosion and erosion in the turbine section of a retrofitted gas turbine due to drastically different thermophysical properties of flue gas stemming from hydrogen combustion. In this context fault diagnosis of hydrogen fueled gas turbines becomes indispensable. To authors knowledge, there is a scarcity of fault diagnosis studies for retrofitted gas turbines considering hydrogen as a potential fuel. The present study, however, develops an artificial neural network (ANN) based fault diagnosis model using MATLAB environment. Prior to fault detection, isolation and identification modules, physics-based performance data of 100 kW micro gas turbine (MGT) was synthesized using GasTurb tool. ANN based classification algorithm showed a 99.4% classification accuracy of fault detection and isolation. Moreover, the feedforward neural network-based regression algorithm showed quite good training, testing and validation accuracies in terms of root mean square error (RMSE). The study revealed that presence of hydrogen induced corrosion fault (both as single corrosion fault or as simultaneous fouling and corrosion) led to false alarms thereby prompting other wrong faults during fault detection and isolation modules. Additionally, performance of fault identification module for hydrogen fuel scenario was found to be marginally lower than that of natural gas case due to assuming small magnitudes of faults arising from hydrogen induced corrosion.
Banks of Gaussian Process Sensor Models for Fault Detection in Wastewater Treatment Processes
Authors: Ivan Heidi Lynn , Ivan Jean-Paul André
Published: October 2023

The harsh operating environment in a wastewater treatment process (WWTP) makes sensor faults commonplace. Detecting these faults can be challenging due to the complex process dynamics, unknown inputs, and general noise in the process and measurements. Comparing sensor readings against predictions from a physics-based or data-driven model of the WWTP is a common strategy for detecting such faults. In this work sensor measurements are directly modelled using Gaussian process (GP) regression, a data-driven multivariate approach. These GP sensor models are, with a generalised product of experts, combined into a dedicated fault isolation scheme resembling traditional observer bank methods. The residuals are monitored with a multivariate exponentially weighted moving average chart which is used for fault detection and isolation. The method is evaluated using simulated data generated with the Benchmark Simulation Model No. 1 WWTP. Fault detection performance is reported using several standard metrics such as false alarms, missed detections, time to detection, and successful fault isolations, with emphasis on reporting across a wide range of sensors and faults to provide a point of comparison for future studies. The proposed approach performs well across these metrics. Given sufficient data representative of normal operation, this approach can easily be adapted across a wide variety of plant configurations and can be used to create operatorfriendly diagnostics resembling classical control charts.
Simulation of distribution system for low temperature district heating in future urban areas – Case study of a planned city district in Gävle
Authors: Olsson Oskar , Gustafsson Mattias , Åberg Magnus
Published: October 2023

In Europe, the prices of natural gas and electricity reached an all-time high in 2022. A way to mitigate high electricity costs is to expand district heating systems in urban areas, this will reduce electric load as well as increase the power generation possibilities in combined heat and power plants. District heating has been the dominant heat supply technology in urban areas in Sweden since the 1980s. However, as the energy efficiency in buildings increase, district heating distribution losses must be reduced to ensure a cost-efficient heat supply. This has led to the idea of the 4th generation district heating which is characterized by low distribution temperatures. In this study, low-temperature district heating distribution in a planned future city district is simulated using a Python-based tool. Two different low-temperature distribution systems are investigated: 1) 2-pipe low-temperature system, and 2) a cascading 3-pipe low-temperature system. The focus is on simulating the distribution losses, temperature drop, and mass flow in the pipe network. The scope of the analysis also includes an investigation of the effect of lower return temperatures on the central district heating network. The results indicate that the low-temperature distribution system with the 2-pipe system performs better than the cascading system when considering distribution losses and temperature drop. The mass flow depends on the temperature demand in the heating systems in the buildings and is considerably high for both low-temperature distribution systems investigated.
Retrofitting Biomass Combined Heat and Power Plant for Biofuel Production
Authors: Chen Hao , Mehmood Daheem , Dahlquist Erik , Kyprianidis Konstantinos
Published: October 2023

Thermochemical conversion processes of biomass, such as gasification and pyrolysis, can convert a wide range of feedstocks into liquid fuels, including forest residue, agricultural, food, and municipal solid waste. These more widely available and theoretically lower cost feedstocks make biofuel production through thermochemical pathway more cost-competitive. Furthermore, the thermochemical conversion pathway for biomass conversion could be relatively easy to integrate with the existing biomass combined heat and power plant, making it an attractive technology for the future commercialization of biofuel production through biomass. A detailed analysis was undertaken of a retrofitted biomass combined heat and power plant for biofuel production in this work. The biofuel production plant is designed to explore the polygeneration of hydrogen, biomethane, and biooil via the integration of gasification, pyrolysis, and renewable-powered electrolysis. The G-valve in the biomass circulating fluid bed plant, which is generally used for sand and char recycling, is retrofitted in the proposed system to fit the pyrolysis reaction for bio-oil production. Centering around the biomass circulating fluid bed gasifier, the system is also outfitted with a condensation and distillation process for bio-oil production, and a membrane reactor system for biomethane production. A mathematical model of the proposed biofuel production plant is established in Aspen Plus, followed by a performance investigation of the biofuel production plant under various design conditions. The limitations and opportunities of this retrofitted biomass combined heat and power plant for biofuel production are explored in this study.
Chi-square test for imprecise data in consistency table
Authors: Aslam Muhammad , Smarandache Florentin
Published: October 2023

In this paper, we propose the introduction of a neutrosophic chi-square-test for consistency, incorporating neutrosophic statistics. Our aim is to modify the existing chi-square -test for consistency in order to analyze imprecise data. We present a novel test statistic for the neutrosophic chi-square -test for consistency, which accounts for the uncertainties inherent in the data. To evaluate the performance of the proposed test, we compare it with the traditional chi-square -test for consistency based on classical statistics. By conducting a comparative analysis, we assess the efficiency and effectiveness of our proposed neutrosophic chi-square -test for consistency. Furthermore, we illustrate the application of the proposed test through a numerical example, demonstrating how it can be utilized in practical scenarios. Through this implementation, we aim to provide empirical evidence of the improved performance of our proposed test when compared to the traditional chi-square-test for consistency based on classical statistics. We anticipate that the proposed neutrosophic chi-square -test for consistency will outperform its classical counterpart, offering enhanced accuracy and reliability when dealing with imprecise data. This advancement has the potential to contribute significantly to the field of statistical analysis, particularly in situations where data uncertainty and imprecision are prevalent.
Systems and synthetic biology-driven engineering of live bacterial therapeutics
Authors: Kim Kangsan , Kang Minjeong , Cho Byung-Kwan
Published: October 2023

The past decade has seen growing interest in bacterial engineering for therapeutically relevant applications. While early efforts focused on repurposing genetically tractable model strains, such as Escherichia coli, engineering gut commensals is gaining traction owing to their innate capacity to survive and stably propagate in the intestine for an extended duration. Although limited genetic tractability has been a major roadblock, recent advances in systems and synthetic biology have unlocked our ability to effectively harness native gut commensals for therapeutic and diagnostic purposes, ranging from the rational design of synthetic microbial consortia to the construction of synthetic cells that execute “sense-and-respond” logic operations that allow real-time detection and therapeutic payload delivery in response to specific signals in the intestine. In this review, we outline the current progress and latest updates on microbial therapeutics, with particular emphasis on gut commensal engineering driven by synthetic biology and systems understanding of their molecular phenotypes. Finally, the challenges and prospects of engineering gut commensals for therapeutic applications are discussed.
Transcriptome analysis reveals genes associated with stem cell activation by physical exercise in the dentate gyrus of aged p16Ink4a knockout mice
Authors: Micheli Laura , D'Andrea Giorgio , Creanza Teresa Maria , Volpe Daniel , Ancona Nicola , Scardigli Raffaella , Tirone Felice
Published: October 2023

Throughout adulthood neural stem cells divide in neurogenic niches–the dentate gyrus of the hippocampus and the subventricular zone–producing progenitor cells and new neurons. Stem cells self-renew, thus preserving their pool. Furthermore, the number of stem/progenitor cells in the neurogenic niches decreases with age. We have previously demonstrated that the cyclin-dependent kinase inhibitor p16Ink4a maintains, in aged mice, the pool of dentate gyrus stem cells by preventing their activation after a neurogenic stimulus such as exercise (running). We showed that, although p16Ink4a ablation by itself does not activate stem/progenitor cells, exercise strongly induced stem cell proliferation in p16Ink4a knockout dentate gyrus, but not in wild-type. As p16Ink4a regulates stem cell self-renewal during aging, we sought to profile the dentate gyrus transcriptome from p16Ink4a wild-type and knockout aged mice, either sedentary or running for 12 days. By pairwise comparisons of differentially expressed genes and by correlative analyses through the DESeq2 software, we identified genes regulated by p16Ink4a deletion, either without stimulus (running) added, or following running. The p16Ink4a knockout basic gene signature, i.e., in sedentary mice, involves upregulation of apoptotic, neuroinflammation- and synaptic activity-associated genes, suggesting a reactive cellular state. Conversely, another set of 106 genes we identified, whose differential expression specifically reflects the pattern of proliferative response of p16 knockout stem cells to running, are involved in processes that regulate stem cell activation, such as synaptic function, neurotransmitter metabolism, stem cell proliferation control, and reactive oxygen species level regulation. Moreover, we analyzed the regulation of these stem cell-specific genes after a second running stimulus. Surprisingly, the second running neither activated stem cell proliferation in the p16Ink4a knockout dentate gyrus nor changed the expression of these genes, confirming that they are correlated to the stem cell reactivity to stimulus, a process where they may play a role regulating stem cell activation.
Electrokinetic properties of healthy and β-thalassemia erythrocyte membranes under in vitro exposure to static magnetic field
Authors: Doltchinkova Virjinia , Lozanova Siya , Rukova Blaga , Nikolov Rumin , Ivanova Elitsa , Roumenin Chavdar
Published: October 2023

Introduction: The current understanding of the biological impacts of a static magnetic field (SMF) is restricted to the direct interactions of the magnetic field with biological membranes. The electrokinetic (zeta) potential is an electrochemical property of erythrocyte surfaces which was negatively charged in physiological media after SMF exposure (0.1‒2.0 T).

Methods: The novel data about electrokinetic parameters of the erythrocytes is determined by microelectrophoresis after SMF-exposure in norm and heterozygous β-thalassemia. The methods of light scattering, lipid peroxidation, fluorescence microscopy are used.

Results: The electrokinetic potential of erythrocytes in norm is increased after SMF intensities due to enhanced negatively exposed charges on the outer surface of the membrane accompanied by an increase in light scattering where changes in cell morphology are observed. Conversely, a decrease in the zeta potential of β-thalassemia erythrocytes upon SMF-treatment was determined because of the reduction in the surface electrical charge of the membranes, where a significant decrease in light scattering at 1.5 T and 2.0 T was recorded. Exposure to SMF (0.5–2.0 T) was associated with an increase in the malondialdehyde content in erythrocytes. Biophysical studies regarding the influence of SMF on the electrostatic free energy of cells shows an increase in negative values in healthy erythrocytes, which corresponds to the implementation of a spontaneous process. This is also the process in β-thalassemia cells after SMF exposure with lower negative values of free electrostatic energy than erythrocytes in norm.

Discussion: The effect of static magnetic field (SMF 0.1–2.0 T) on the electrokinetic and morphological characteristics of erythrocytes in norm and β-thalassemia is determined and correlated with the increase/reduction in surface charge and shrinkage/swelling of the cells, respectively. Lipid peroxidation of healthy and β-thalassemia erythrocytes caused an enhancement of lipid peroxidation because of the higher concentrations of TBARS products in cellular suspension. SMF (0.1‒2.0 T) altered the spontaneous chemical processes with negative values of electrostatic free energy of erythrocytes in norm and β-thalassemia accompanied by a lower FITC-Concanavalin A binding affinity to membrane receptors (SMF 2.0 T). The electrokinetic properties of human erythrocytes in norm and β-thalassemia upon SMF treatment and their interrelationship with the structural-functional state of the membrane were reported. The presented work would have future fundamental applications in biomedicine.
Persistent ciprofloxacin exposure induced the transformation of Klebsiella pneumoniae small colony variant into mucous phenotype
Authors: Zou Hua , Li Qian , Su Yan , Zhang Lei , Zhang Xinyuan , Li Chunli
Published: October 2023

Introduction

Small colony variant (SCV) is a bacterial phenotype closely related to persistent and recurrent infections. SCVs are mutations that occur within bacterial populations, resulting in a change in bacterial morphology and the formation of small colonies. This morphological change may enhance bacterial resistance to antibiotics and contribute to persistent and recurrent infections.

Methods

We isolated Klebsiella pneumoniae (KPN) and its SCV from a child with recurrent respiratory tract infections. KPN and SCV were treated with subinhibitory concentrations of antibiotics. growth curves, serum resistance experiments, macrophage phagocytosis experiments and whole genome sequencing were used to characterize KPN and SCV.

Results

After treating KPN and SCV with subinhibitory concentrations of antibiotics, we found that ciprofloxacin induced the SCV transition to the mucoid phenotype. We found that the growth of mucoid Klebsiella pneumoniae was significantly slower than maternal strain and SCV though growth curves. Serum resistance experiments showed that mucoid strains had significantly higher serum resistance compared to maternal strain and SCV. Macrophage phagocytosis experiments revealed that SCV had significantly higher intracellular survival rates compared to maternal strain and mucoid strains. Differential gene analysis of three strains revealed that the mucoid strain contained DNA polymerase V subunit UmuC gene on the plasmid, while the SCV strain had an additional IcmK family IV secretion protein on its plasmid.

Discussion

Our study showed the SCV of KPN changed to a mucoid colony when exposed to subinhibitory concentrations of ciprofloxacin. The higher resistance of serum of mucoid colonies was possibly related to the UmuC gene, while the increased intracellular survival of SCV may be related to the IcmK family type IV secretion proteins.
Abnormal left ventricular systolic reserve function detected by treadmill exercise stress echocardiography in asymptomatic type 2 diabetes
Authors: Duan Yuyou , Ye Luwei , Shu Qinglan , Huang Yu , Zhang Hongmei , Zhang Qingfeng , Ding Geqi , Deng Yan , Li Chunmei , Yin Lixue , Wang Yi
Published: October 2023

Aims

Subclinical left ventricular (LV) dysfunction may occur in T2DM patients at the early asymptomatic stage, and LV reserve function is a sensitive index to detect subtle LV dysfunction. The purpose of our study is (1) to assess the LV reserve function using treadmill exercise stress echocardiography (ESE) in asymptomatic type 2 diabetes mellitus (T2DM) patients; (2) to explore the link of serum biological parameters and LV reserve function.

Methods

This study included 84 patients with asymptomatic T2DM from September 2021 to July 2022 and 41 sex- and age-matched healthy controls during the corresponding period. All subjects completed treadmill ESE, LV systolic function-related parameters such as global longitudinal strain (GLS) and systolic strain rate (SRs), as well as diastolic function-related parameters such as E wave (E), early diastolic velocity (e′), E/e′ ratio, early diastolic SR (SRe), and late diastolic SR (SRa) were compared at rest and immediately after exercise. The difference between LV functional parameters after treadmill exercise and its corresponding resting value was used to compute LV reserve function. In addition, the associations of LV reserve function and serum biological parameters were analyzed.

Results

Patients with T2DM did not significantly vary from the controls in terms of alterations in LV diastolic reserve measures, the changes of LVGLS and SRs (ΔGLS: 2.19 ± 2.72% vs. 4.13 ± 2.79%, P < 0.001 and ΔSRs:0.78 ± 0.33 s−1 vs. 1.02 ± 0.28 s−1, P < 0.001) in the T2DM group were both lower than those in the control group. Glycated hemoglobin (HbA1c), N-terminal pro-brain natriuretic peptide (NTproBNP), waist circumference, and high-sensitive C-reactive protein (hsCRP) were identified as independent predictors of LV systolic reserve by stepwise multiple linear regression analysis.

Conclusion

LV systolic reserve function, as measured by pre- and post-exercise differences in GLS and SRs were significantly impaired in patients with asymptomatic T2DM, whereas diastolic reserve remained normal during exercise and was comparable to that of the control group. This was different from previous findings. High levels of HbA1c, NTproBNP, hsCRP, and increasing waist circumference were independent predictors of LV systolic reserve.
Serial RV wall stress measurements: association with right ventricular function in repaired Tetralogy of Fallot patients
Authors: Minderhoud Savine C. S. , Hirsch Alexander , Marin Francesca , Kardys Isabella , Rodríguez-Matas José F. , Chiastra Claudio , Roos-Hesselink Jolien W. , Wentzel Jolanda J. , Helbing Willem A. , Akyildiz Ali C.
Published: October 2023

Background

Optimal timing of pulmonary valve replacement (PVR) in Tetralogy of Fallot (TOF) patients remains challenging. Ventricular wall stress is considered to be an early marker of right ventricular (RV) dysfunction.

Objectives

To investigate the association of RV wall stresses and their change over time with functional parameters in TOF patients.

Methods

Ten TOF patients after surgical repair with moderate/severe pulmonary regurgitation were included. At two timepoints (median follow-up time 7.2 years), patient-specific computational biventricular models for wall stress assessment were created using CMR short-axis cine images and echocardiography-based RV pressures. RV ejection fraction (RVEF), NT-proBNP and cardiopulmonary exercise tests were used as outcome measures reflecting RV function. Associations between regional RV diastolic wall stress and RV function were investigated using linear mixed models.

Results

Increased wall stress correlated with lower RV mass (rrm = −0.70, p = 0.017) and lower RV mass-to-volume (rrm = −0.80, p = 0.003) using repeated measures. Wall stress decreased significantly over time, especially in patients with a stable RVEF (p < 0.001). Higher wall stress was independently associated with lower RVEF, adjusted for left ventricular ejection fraction, RV end-diastolic volume and time since initial surgery (decrease of 1.27% RVEF per kPa increase in wall stress, p = 0.029) using repeated measurements. No association was found between wall stress, NT-proBNP, and exercise capacity.

Conclusions

Using a computational method to calculate wall stress locally in geometrically complex ventricles, we demonstrated that lower wall stress might be important to maintain ventricular function. RV wall stress assessment can be used in serial follow-up, and is potentially an early marker of impending RV dysfunction.
Analysis of immortal-time effect in post-infarction ventricular septal defect
Authors: González-Pacheco Héctor , Ortega-Hernandez Jorge Arturo , Meza-López Jesús Ángel , Soliz-Uriona Luis Alejandro , Manzur-Sandoval Daniel , Gopar-Nieto Rodrigo , Araiza-Garaygordobil Diego , Sierra-Lara Daniel , Arias-Sánchez Eduardo , Sandoval Juan Pablo , Altamirano-Castillo Alfredo , Mendoza-García Salvador , Arzate-Ramírez Arturo , Baranda-Tovar Francisco Martin , Martinez Humberto , Montañez-Orozco Álvaro , Baeza-Herrera Luis Augusto , Sierra-González De Cossio Alejandro , Arias-Mendoza Alexandra
Published: October 2023

Introduction

Time-fixed analyses have traditionally been utilized to examine outcomes in post-infarction ventricular septal defect (VSD). The aims of this study were to: (1) analyze the relationship between VSD closure/non-closure and mortality; (2) assess the presence of immortal-time bias.

Material and methods

In this retrospective cohort study, patients with ST-elevation myocardial infarction (STEMI) complicated by VSD. Time-fixed and time-dependent Cox regression methodologies were employed.

Results

The study included 80 patients: surgical closure (n = 26), transcatheter closure (n = 20), or conservative management alone (n = 34). At presentation, patients without VSD closure exhibited high-risk clinical characteristics, had the shortest median time intervals from STEMI onset to VSD development (4.0, 4.0, and 2.0 days, respectively; P = 0.03) and from STEMI symptom onset to hospital arrival (6.0, 5.0, and 0.8 days, respectively; P < 0.0001). The median time from STEMI onset to closure was 22.0 days (P = 0.14). In-hospital mortality rate was higher among patients who did not undergo defect closure (50%, 35%, and 88.2%, respectively; P < 0.0001). Closure of the defect using a fixed-time method was associated with lower in-hospital mortality (HR = 0.13, 95% CI 0.05–0.31, P < 0.0001, and HR 0.13, 95% CI 0.04–0.36, P < 0.0001, for surgery and transcatheter closure, respectively). However, when employing a time-varying method, this association was not observed (HR = 0.95, 95% CI 0.45–1.98, P = 0.90, and HR 0.88, 95% CI 0.41–1.87, P = 0.74, for surgery and transcatheter closure, respectively). These findings suggest the presence of an immortal-time bias.

Conclusions

This study highlights that using a fixed-time analytic approach in post-infarction VSD can result in immortal-time bias. Researchers should consider employing time-dependent methodologies.
How big is Big Data? A comprehensive survey of data production, storage, and streaming in science and industry
Authors: Clissa Luca , Lassnig Mario , Rinaldi Lorenzo
Published: October 2023

The contemporary surge in data production is fueled by diverse factors, with contributions from numerous stakeholders across various sectors. Comparing the volumes at play among different big data entities is challenging due to the scarcity of publicly available data. This survey aims to offer a comprehensive perspective on the orders of magnitude involved in yearly data generation by some public and private leading organizations, using an array of online sources for estimation. These estimates are based on meaningful, individual data production metrics and plausible per-unit sizes. The primary objective is to offer insights into the comparative scales of major big data players, their sources, and data production flows, rather than striving for precise measurements or incorporating the latest updates. The results are succinctly conveyed through a visual representation of the relative data generation volumes across these entities.
Humanizing STEM education: an ecological systems framework for educating the whole student
Authors: Yao Christina , Follmer Greenhoot Andrea , Mack Kelly , Myrick Chandra , Poolaw Johnny , Powell Linda , Yarger Lynette
Published: October 2023

STEM higher education in the U.S. has long been an uninviting space for minoritized individuals, particularly women, persons of color, and international students and scholars. In recent years, the contemporary realities of a global pandemic, sociopolitical divides, and heightened racial tensions, along with elevated levels of mental illness and emotional distress among college students, have intensified the need for an undergraduate STEM education culture and climate that recognizes and values the humanity of our students. The purpose of this article is to advance a more humanized undergraduate STEM education and to provide a framework to guide efforts toward achieving that vision. We argue that humanizing approaches recognize and value the complexity of individuals and the cultural capital that they bring to their education, and that this is particularly important for empowering minoritized students who are subordinated in status in STEM higher education. A STEM education that centers students’ humanity gives rise to equity and promotes human well-being and flourishing alongside knowledge acquisition and skill development. We then offer a guiding framework for conceptualizing the broader ecosystem in which undergraduate STEM students are embedded, and use it to outline the individual and collective roles that different stakeholders in the ecosystem can play in humanizing STEM education.
Measuring the classroom level of the Dynamic Model of Educational Effectiveness through teacher self-report: development and validation of a new instrument
Authors: Dierendonck Christophe
Published: October 2023

In the Dynamic Model of Educational Effectiveness, classroom-level effectiveness factors are assessed through observations or aggregated students’ ratings. The current study is aimed at developing and validating a complementary teacher self-report instrument of effective practices at classroom level (theDMEE-Class-T). The new instrument showed concurrent validity with theCSS-T. Dimensionality of both instruments was examined using the bifactor exploratory structural equation modeling (ESEM) framework, testing for alternative factorial representations of the data collected in a large-scale study conducted in all Luxembourgish elementary schools. For both instruments, the bifactor-ESEM and ESEM models showed excellent fitting indices and parameters, but the ESEM solution was retained as the best model for parsimony purpose. These results suggest that the eight types of practices assessed through theDMEE-Class-Tcould be considered as distinct facets of effective teaching practices while taking items cross-loadings into account. Implications for research and teachers’ professional development are discussed.
The molecular mechanism underlying dermatomyositis related interstitial lung disease: evidence from bioinformatic analysis and in vivo validation
Authors: Zeng Li , Tang Yiping , Zhang Yichen , Yue Li , Ma Gang , Ye Xumin , Yang Lijing , Chen Kai , Zhou Qiao
Published: October 2023

Background

Dermatomyositis (DM) is an autoimmune and inflammatory disease that can affect the lungs, causing interstitial lung diseases (ILD). However, the exact pathophysiological mechanisms underlying DM-ILD are unknown. Idiopathic pulmonary fibrosis (IPF) belongs to the broader spectrum of ILD and evidence shows that common pathologic pathways might lie between IPF and DM-ILD.

Methods

We retrieved gene expression profiles of DM and IPF from the Gene Expression Omnibus (GEO) and utilized weighted gene co-expression network analysis (WGCNA) to reveal their co-expression modules. We then performed a differentially expressed gene (DEG) analysis to identify common DEGs. Enrichment analyses were employed to uncover the hidden biological pathways. Additionally, we conducted protein-protein interaction (PPI) networks analysis, cluster analysis, and successfully found the hub genes, whose levels were further validated in DM-ILD patients. We also examined the relationship between hub genes and immune cell abundance in DM and IPF. Finally, we conducted a common transcription factors (TFs)-genes network by NetworkAnalyst.

Results

WGCNA revealed 258 intersecting genes, while DEG analysis identified 66 shared genes in DM and IPF. All of these genes were closely related to extracellular matrix and structure, cell-substrate adhesion, and collagen metabolism. Four hub genes (POSTN, THBS2, COL6A1, and LOXL1) were derived through intersecting the top 30 genes of the WGCNA and DEG sets. They were validated as active transcripts and showed diagnostic values for DM and IPF. However, ssGSEA revealed distinct infiltration patterns in DM and IPF. These four genes all showed a positive correlation with immune cells abundance in DM, but not in IPF. Finally, we identified one possible key transcription factor, MYC, that interact with all four hub genes.

Conclusion

Through bioinformatics analysis, we identified common hub genes and shared molecular pathways underlying DM and IPF, which provides valuable insights into the intricate mechanisms of these diseases and offers potential targets for diagnostic and therapeutic interventions.
Comparison of stress tolerance of hybrid and selfed offspring of two populations of Litopenaeus vannamei
Authors: Shi Miao , Jiang Song , Jiang Shigui , Yang Qibin , Li Yundong , Zhou Falin
Published: October 2023

In recent years, as the marine environment has been deteriorated, the aquaculture water environment has also been negatively affected to varying degrees. Negative environmental factors make extremely damaging to organisms, resulting in stress-induced diseases and high mortality rates of cultured shrimp. Therefore, stress resistance breeding of Litopenaeus vannamei and evaluating the stress tolerance of the breeding population are urgently needed now. Litopenaeus vannamei collected from Thailand (T) and the United States (M) were used as parents, while four progeny populations of TT, MM, TM, and MT were constructed by diallel cross, with a total of 20 families. The tolerance of young shrimp to high ammonia-N, high pH, and low salt was compared through a 96-h acute toxicity test; the heterosis of each mating combination was analyzed; and the tolerance of parents and offspring was evaluated. Here we show that under 96 h of high ammonia-N, high pH, and low salt stress, the mortality rates of each family were 19.52%–92.22%, 23.33%–92.22%, and 19.33%–80.00%, respectively. There were significant differences in the tolerance of different families to ammonia-N, pH, and salinity stress (P < 0.05). The population with a female parent from the United States had stronger tolerance to ammonia-N, pH, and low salt stress than the population with a female parent from Thailand. The population with a male parent from Thailand had weaker tolerance to pH and low salt stress than the population with a male parent from the United States, but it was superior to the population with a male parent from the United States under ammonia-N stress. The heterosis rates of the hybrid population TM in acute high ammonia-N, high pH and low salinity were 81.67%, 44.58% and −10.13%, respectively; However, the heterosis rates of the MT population were 14.89%, 38.89%, and −8.96%, respectively. The overall resistance of the four populations showed MM > MT > TT > TM. The population TM had obvious heterosis in high ammonia-N and high pH tolerance traits, and the family MM7 had a strong low salt tolerance, so it can be considered a candidate family for subsequent breeding work. Moreover, variability in stress resistance and heterosis of stress resistance of different populations obtained by family selection was discussed in this paper. The experimental results provide a basis for screening new strains of vannamei shrimp with strong stress resistance through family breeding.
Molecular and clinical characterization of ANG expression in gliomas and its association with tumor-related immune response
Authors: Wang Jin , Shan Aijun , Shi Fei , Zheng Qijun
Published: October 2023

Background

Angiogenin (ANG) has been widely reported as a crucial molecular regulator in multiple malignancies. However, its role in gliomagenesis remains unclear. This study aimed to investigate the molecular and clinical characterization of ANG expression at transcriptome level and the association with glioma-related immune response.

Methods

A total of 301 glioma samples with mRNA microarray data (CGGA301) was obtained from the official website of CGGA project for yielding preliminary results, followed by validation in two independent RNAseq datasets, including TCGA with 697 samples and CGGA325 with 325 patients. Moreover, CGGA single-cell RNAseq (scRNAseq) data were analyzed to identify differential and dynamic ANG expression in different cells. Immunohistochemistry was performed to evaluate ANG protein expression across different WHO grades in a tissue microarray (TMA). Figure generation and statistical analysis were conducted using R software.

Results

ANG expression was associated with clinical features, malignant phenotypes, and genomic alterations. Based on significantly correlated genes of ANG, subsequent gene ontology (GO) and gene set enrichment analysis (GSEA) concordantly pointed to the significant association of ANG in immune-related biological processes. Moreover, ANG showed robust correlations with canonical immune checkpoint molecules, including PD1 signaling, CTLA4, TIM3, and B7H3. Gene sets variation analysis (GSVA) found that ANG was particularly associated with activities of macrophages and antigen presentation cells (APCs) in both LGG and GBM across different datasets. Furthermore, the higher-ANG milieu seemed to recruit monocyte–macrophage lineage and dendritic cells into the glioma microenvironment. According to scRNAseq analysis, ANG was mainly expressed by neoplastic cells and tumor-associated macrophages (TAMs) and was correlated with the initiation and progression of tumor cells and the polarization of TAMs. Finally, Kaplan–Meier plots demonstrated that higher expression of ANG was significantly correlated with shorter survival in gliomas. Cox regression analysis further confirmed ANG as an independent predictor of prognosis for gliomas of all three datasets.

Conclusion

ANG is significantly correlated with a range of malignant and aggressive characteristics in gliomas and reveals considerable prognostic value for glioma patients. ANG seems to be primarily associated with immune activities of macrophages and APCs in gliomas. Furthermore, ANG is mainly expressed in neoplastic cells and TAMs and is involved in the initiation and progression of neoplastic cells as well as macrophage polarization.
Cardiovascular disease and thinning of retinal nerve fiber layer in a multi-ethnic Asian population: the Singapore epidemiology of eye diseases study
Authors: Majithia Shivani , Quek Debra Q. Y. , Chee Miao Li , Lim Zhi Wei , Nusinovici Simon , Soh Zhi-Da , Thakur Sahil , Rim Tyler Hyungtaek , Sabanayagam Charumathi , Cheng Ching-Yu , Tham Yih-Chung
Published: October 2023

Introduction

Our study aimed to examine the relationship between cardiovascular diseases (CVD) with peripapillary retinal fiber layer (RNFL) and macular ganglion cell-inner plexiform layer (GCIPL) thickness profiles in a large multi-ethnic Asian population study.

Methods

6,024 Asian subjects were analyzed in this study. All participants underwent standardized examinations, including spectral domain OCT imaging (Cirrus HD-OCT; Carl Zeiss Meditec). In total, 9,188 eyes were included for peripapillary RNFL analysis (2,417 Malays; 3,240 Indians; 3,531 Chinese), and 9,270 eyes (2,449 Malays, 3,271 Indians, 3,550 Chinese) for GCIPL analysis. History of CVD was defined as a self-reported clinical history of stroke, myocardial infarction, or angina. Multivariable linear regression models with generalized estimating equations were performed, adjusting for age, gender, ethnicity, diabetes, hypertension, hyperlipidaemia, chronic kidney disease, body mass index, current smoking status, and intraocular pressure.

Results

We observed a significant association between CVD history and thinner average RNFL (β = −1.63; 95% CI, −2.70 to −0.56; p = 0.003). This association was consistent for superior (β = −1.79, 95% CI, −3.48 to −0.10; p = 0.038) and inferior RNFL quadrant (β = −2.14, 95% CI, −3.96 to −0.32; p = 0.021). Of the CVD types, myocardial infarction particularly showed significant association with average (β = −1.75, 95% CI, −3.08 to −0.42; p = 0.010), superior (β = −2.22, 95% CI, −4.36 to −0.09; p = 0.041) and inferior (β = −2.42, 95% CI, −4.64 to −0.20; p = 0.033) RNFL thinning. Among ethnic groups, the association between CVD and average RNFL was particularly prominent in Indian eyes (β = −1.92, 95% CI, −3.52 to −0.33; p = 0.018). CVD was not significantly associated with average GCIPL thickness, albeit a consistent negative direction of association was observed (β = −0.22, 95% CI, −1.15 to 0.71; p = 0.641).

Discussion

In this large multi-ethnic Asian population study, we observed significant association between CVD history and RNFL thinning. This finding further validates the impact of impaired systemic circulation on RNFL thickness.