bluuebunny/crossref_metadata_2025 huggingface dataset:
Implementation of Administration in MIN 1 Medan
Authors: Taher Jihan Fadhilah , Wijaya Candra
Published: August 2023

This study aims to (1) Describe how the implementation (implementation) of administration and (2) the constraints and solutions that exist in the implementation of administration in MIN 1 Medan. This research was conducted with a descriptive qualitative research approach. The informants of this study were madrasa heads, teachers, administrative staff and students. Data collection techniques used are interviews, observation, and documentation. Then the data were analyzed by interactive analysis which flowed with activities including data reduction, data display, and conclusion drawing/verification. Testing the validity of the data is done by triangulation of methods and sources. From the results of the study it can be concluded that: (1) The implementation of administration in MIN 1 Medan has been carried out properly and is organized as a function of the administration itself (2) Obstacles in the implementation of administration even if there are solutions can be found by first reflecting and evaluating.
Formulating Boarding School as a Leading School in the Era of ICT
Authors: Musyarif Musyarif , Ahdar Ahdar , Akbar Muhammad Irfan
Published: August 2023

Tujuan Penelitian ini untuk mengetahui Bagaimana Formulasi Boarding School (Pondok Pesantren) sebagai Sekolah Unggulan di Era Teknologi, Informasi dan Komunikasi (TIK).” Dengan sub masalah yakni, Bagaimana prototype boarding school era kontemporer, Bagaimana sistem sekolah unggulan yang relevan dengan era teknologi, informasi dan komunikasi dalam persfektif pendidikan Islam. Penelitian ini menggunakan beberapa metode. Diantaranya adalah metode pendekatan. Yaitu metode yang mengungkapkan pola piker yang dipergunakan untuk membahas objek penelitian. Pendekatan yang dimaksud ialah pendekatan sistem. Metode pelaksanaan, yaitu data yang dikumpulkan diolah kembali secara kualitatif yakni berupa keterangan-keterangan yang diperoleh dari sumber data, kemudian pengolahan data tersebut berupa ide-ide dan teori-teori yang tidak dapat disusun secara grafik. Hasil penelitian menunjukkan bahwa, Boarding school yang bercorak modern tidak lebih dari sikap akomodatif terhadap kemajuan zaman, menyesuaikan diri tanpa meninggalkan karakter budaya lokal, Panorama era kontemporer mendeskripsikan era teknolgi, informasi dan komunikasi (TIK), yakni fenomena ini mampu menembus sekat atau gap setiap bangsa sehingga dunia bagai global village, Boarding school yang relevan dengan tuntutan dan kebutuhan TIK apabila memilki sistem sekolah unggulan. Sekolah unggulan memilki sistem yang berbasis teknologi yang mengedepankan sikap terbuka, rasional, obyektif, ilmiah, progresif, profesional, dinamis, etos kerja yang tinggi, visioner dsb. Ketika karakter sekolah unggulan dikolaborasikan dengan sistem boarding school, maka boarding school akan mampu membangun peradaban yang sejajar dengan peradaban lain. Dengan demikian, boarding school yang berbasis TIK akan lebih efektif dalam mewujudkan misis profetik yaitu menjadikan Islam sebagai agama rahmatan lil alamin.
Evaluation Analysis of The Implementation of The Merdeka Belajar - Kampus Merdeka (MBKM) Program: A Literature Review
Authors: Nafisah Nisa'atun , Fikri Muhammad Afiq , Zuhriyah Indah Aminatuz
Published: August 2023

The purpose of the Merdeka Belajar - Kampus Merdeka (MBKM) program is to provide flexibility for students in choosing subjects, extracurricular activities, and skill development opportunities beyond those offered by the campus. The main objective of this program is to equip Indonesian students with the knowledge and abilities they need to succeed in the competitive world of work. The purpose of this literature review is to examine the past and current use of the MBKM Program in academic settings. A literature review of relevant papers, scientific journals, and other publications on the MBKM Program was conducted to learn more about the implementation, challenges, and benefits of the program. Several important conclusions can be drawn from the results of this literature review. First, the MBKM Program has not been fully implemented in higher education, and there are several obstacles that must be overcome. Second, problem solving will be more efficient if all interested parties work together. Evaluating the implementation of the MBKM Program is essential to make it more successful. By conducting a literature review, the university can learn about new problems, develop plans to address those problems, and improve the learning opportunities available to its students. By providing a greater understanding of the issues and challenges faced in implementing the MBKM Program in higher education, this literature review helps in improving the implementation of the program, overcoming barriers, and maximizing the benefits received by students.
Students' Perception on Public Speaking Lecture for Their Speaking Ability
Authors: Liani Sulis , Sari Heni Novita
Published: August 2023

The purpose of this study is to identify students’ perception on public speaking lecture for their speaking ability. The writer used a qualitative descriptive design to provide an overview of information obtained from the data. A sample of 10 students of fourth-semester students from the English Education Department in the Academic Year 2021/2022 who are studying Public Speaking Lectures will take part in this study. The interviews were the process of obtaining information for research by way of questions and answers while looking face to face respondents using an interview guide. An interactive model of analysis was used to analyze the data in this study. The results of student perceptions fou`1%nd that students stated that public speaking lecture is very influential on their speaking ability, the use of public speaking lecture can also make them more able to express their feelings, students can explore and increase their vocabulary, and influence people with their words.
Seawater irrigation on nests can increase male marine turtle production
Authors: Young LR , Booth DT , Smith CE , Madden Hof CA
Published: August 2023

Global warming is increasing marine turtle nesting beach sand temperatures throughout the world. All marine turtles have temperature-dependent sex determination, with female hatchlings produced at warmer incubation temperatures. These warmer sand temperatures are causing a scarcity of male hatchlings at many nesting beaches. A range of mitigation strategies including shading and freshwater irrigation are being trialled at marine turtle nesting beaches around the world to address this issue. Because seawater is always abundant at marine turtle nesting beaches, we trialled a number of intense, one-off seawater irrigation experiments (equivalent to 100 and 200 mm rainfall) to test if male green turtle Chelonia mydas hatchling production could be increased without decreasing overall hatching success at Heron Island, southern Great Barrier Reef, Australia. We found that different combinations of seawater volume and temperature could produce a short-term drop in nest temperature by 2°C. When applied during the middle of embryonic development, these irrigation treatments could increase the proportion of male hatchlings compared to non-irrigated control nests, with less than a 10% decrease in hatching success. Hence, seawater irrigation has the potential to be a viable management strategy to increase the proportion of male marine turtle hatchlings at beaches that produce all, or nearly all, female hatchlings.
Parvalbumin - Positive Neurons in the Neocortex: A Review
Authors: Druga R , Salaj M , Al-Redouan A
Published: August 2023

The calcium binding protein parvalbumin (PV) in the mammalian neocortex is expressed in a subpopulation of cortical GABAergic inhibitory interneurons. PV – producing interneurons represent the largest subpopulation of neocortical inhibitory cells, exhibit mutual chemical and electrical synaptic contacts and are well known to generate gamma oscillation. This review summarizes basic data of the distribution, afferent and efferent connections and physiological properties of parvalbumin expressing neurons in the neocortex. Basic data about participation of PV-positive neurons in cortical microcircuits are presented. Autaptic connections, metabolism and perineuronal nets (PNN) of PV positive neurons are also discussed.
Aki keres, az gyakran talál – a félrevezető recidív pulmonalis infiltrátumok
Authors: Czigány Diána Gréta , Sinkovicz András , Paraicz Gábor , Győri Zsófia , Szántó Árpád
Published: August 2023

Pulmonalis infiltrátumok számos betegségcsoportban megjelenhetnek, olyan esetekben, amikor az alveolusokat levegő helyett fehérvérsejtek, tumorsejtek, vér, genny, fehérje stb. tölti ki, azok légtelenségéhez vezetve. Ezen etiológiai tényezők közül a közösségben szerzett pneumonia a leggyakoribb, mely a mortalitás és morbiditás egyik vezető oka világszerte. Definíciója szerint az interstitiumot, alveolaris teret és a terminális légutakat érintő, élő kórokozók okozta infekció. Ugyanakkor diagnózisakor sokszor nem sikerül kimutatni a fertőzőágenst, melynek hátterében fennállhat az a lehetőség, hogy a képalkotókkal látott elváltozás, habár a klinikum is támogatja,mégsem pneumonia. Ebben a cikkben egy több alkalommal pneumonia diagnózisával kezelt 58 éves nő esete kerül bemutatásra, akit minden esetben antibiotikummal kezeltek, és habár állapota átmenetileg javult, a panaszai (fulladás, láz, gyengeség) rendszeresen vissza -tértek, CRP-szintje ismétlődően emelkedetté vált, a mellkas-CT-ken pedig kétoldali infiltráció ábrázolódott. Bronchoszkópos mintavételt követően a vett mintából tenyésztés és mélylégúti PCR készült, ezek, valamint a hemokultúra negativitása alapján a pneumonia ki zárásra került. További vizsgálatokkal, valamint immunológiai konzílium segítségével ANCA-asszociált granutomatosus polyangiitis igazolódott állapotromlásának hátterében. Ez az esetbemutatás felhívja a figyelmet, hogy a recidív, nem gyógyuló pneumoniás eseteket érdemes tüdőgyógyászhoz továbbküldeni, továbbá a mikrobiológiai mintavétel fontosságára, valamint a mélylégúti PCR szerepére a diagnosztikában.
Treatment of mixed leachate type I and type III by filtration and chemical oxidation
Authors:   Instituto Superior Tecnológico República Federal de Alemania, Pino Vallejo Marco Vinicio , Perugachi Cahueñas Nelly Patricia ,   Escuela Superior Politécnica de Chimborazo
Published: August 2023

In Riobamba city from Ecuador, for more than thirty years solid urban waste was placed in an open dump, without gas and leachate control. In 2016, the landfill was technically closed and an emerging cell with the characteristics of a sanitary landfill was built nearby. The Environmental Health and Hygiene Management Department of the Riobamba Municipal Decentralized Autonomous Government monitors leachate generation, recording 19.24 m3/day of young leachate (Type I) from the emerging cell and 5.78 m3/day of mature leachate (Type III) from the old landfill. The two types of leachates are mixed in the main collection pipe that reaches a storage pool that receives 25.02 m3/day. The results of the physical-chemical analysis determine that the values of the parameters are outside the permissible limits. Turbidity is >1000 NTU (Nephelometric Turbidity Unit), and the concentration of suspended solids is 1200 mg. L-1 and iron 135.85 mg. L-1. Calcium (1223 mg. L-1) and manganese (356.15 mg. L-1) were also evaluated, as these minerals are related to the 16,000 mg. L-1 of hardness. For the treatment of the mixed leachate, two phases are proposed: a) physical treatment by downward filtration in a granular bed to reduce the concentrations of suspended solids, and b) chemical treatment by oxidation using sodium hypochlorite. Laboratory results showed a 96.40% decrease in the concentration of suspended solids. Turbidity stabilized at 65 UTN. Iron, calcium, and manganese concentrations decreased by 95.60%, 96.28%, and 50.60%, respectively.
Modeling and analysis of the addiction of social media through fractional calculus
Authors: Shutaywi Meshal , Rehman Ziad Ur , Shah Zahir , Vrinceanu Narcisa , Jan Rashid , Deebani Wejdan , Dumitrascu Oana
Published: August 2023

Social media addiction (SMA) is the excessive use of social media platforms, resulting in negative consequences for individuals. It is characterized by an uncontrollable urge to use social media, leading to negative effects in human's life. This study aims to construct a mathematical model to conceptualize the transmission dynamics of SMA and explore the underlying mechanisms of this harmful addiction in the framework of fractional derivative. The fundamentals of fractional calculus are listed for examining the model. Equilibrium points are identified, and the reproduction parameter R0 is computed to understand the dynamics of SMA spread. Stability analysis of the equilibria is performed, and the impact of various input parameters is numerically investigated. The existence and uniqueness of the proposed SMA model are demonstrated through simulations, which also study the intricate dynamics with respect to different input factors. To develop effective control strategies, the system's dynamical behavior is examined, and the influence of fractional derivative order on fluctuations is explored. This research offers a range of suggestions aimed at reducing the occurrence of social media addiction.
Intraoperative sensor technology quantifies inter-prosthesis pressure for predicting lower limb alignment after Oxford unicompartmental knee arthroplasty
Authors: Ge Juncheng , Sun Xiaowei , Liu Changquan , Zhang Qidong , Wang Bailiang , Guo Wanshou
Published: August 2023

Purpose: The aim of this study is to quantify inter-prosthetic pressures at different knee angles in Oxford unicompartmental knee arthroplasty (OUKA) and its correlation with postoperative lower limb alignment.

Methods: This study included 101 patients (122 knees) who underwent OUKA from March 2022 to July 2022. The previously designed matrix flexible force sensor was used to measure the inter-prosthesis pressure of different knee joint angles during the UKA operation, and the force variation trend and gap balance difference were obtained. The correlation between inter-prosthesis pressure and postoperative lower limb alignment index including hip-knee-ankle angle (HKAA) and posterior tibial slope (PTS) was analyzed. The effect of PTS change (ΔPTS) on the inter-prosthesis pressure and the range of motion (ROM) of the knee joint was analyzed. Radiographic and short-term clinical outcomes of included patients were assessed.

Results: The inter-prosthesis pressure of the different knee joint angles during the operation was not consistent. The mean inter-prosthesis pressure and gap balance difference were 73.68.28 ± 41.65N and 36.48 ± 20.58N. The inter-prosthesis pressure at 0° and 20° was positively correlated with postoperative HKAA (p < 0.001). ΔPTS was positively correlated with the pressure at the end of knee extension and negatively correlated with the pressure at the end of knee flexion (p < 0.001). The HKAA, ROM, degree of fixed knee flexion deformity, and knee society score of the included patients were significantly improved compared with those before the operation (p < 0.001).

Conclusion: The inter-prosthesis pressure measured at the knee extension position can predict postoperative HKAA to some degree. Changes in PTS will affect the inter-prosthesis pressure at the end of flexion and end of knee extension, but this change is not related to the range of motion of the knee joint.
An update on the bridging factors connecting autophagy and Nrf2 antioxidant pathway
Authors: Ning Baike , Hang Shuqi , Zhang Wenhe , Mao Caiwen , Li Dan
Published: August 2023

Macroautophagy/autophagy is a lysosome-dependent catabolic pathway for the degradation of intracellular proteins and organelles. Autophagy dysfunction is related to many diseases, including lysosomal storage diseases, cancer, neurodegenerative diseases, cardiomyopathy, and chronic metabolic diseases, in which increased reactive oxygen species (ROS) levels are also observed. ROS can randomly oxidize proteins, lipids, and DNA, causing oxidative stress and damage. Cells have developed various antioxidant pathways to reduce excessive ROS and maintain redox homeostasis. Treatment targeting only one aspect of diseases with autophagy dysfunction and oxidative stress shows very limited effects. Herein, identifying the bridging factors that can regulate both autophagy and antioxidant pathways is beneficial for dual-target therapies. This review intends to provide insights into the current identified bridging factors that connect autophagy and Nrf2 antioxidant pathway, as well as their tight interconnection with each other. These factors could be potential dual-purpose targets for the treatment of diseases implicated in both autophagy dysfunction and oxidative stress.
Acute immune responses in zebrafish and evasive behavior of a parasite – who is winning?
Authors: Mathiessen Heidi , Kjeldgaard-Nintemann Sebastian , Gonzalez Carlota Marola Fernandez , Henard Cyril , Reimer Julie Algreen , Gelskov Sara Vebæk , Marana Moonika Haahr , Jørgensen Louise von Gersdorff
Published: August 2023

The protozoan parasite Ichthyophthirius multifiliis is an economically important parasite for the aquaculture- and ornamental fish industry. The parasite is abundant worldwide and infects the skin, gills and fins of freshwater fish species. For approximately the last fifty years the innate and protective immune mechanisms induced by I. multifiliis have been in focus in different fish hosts. By utilizing transgenic zebrafish, new tools to investigate this have emerged. The aim of this study was therefore to elucidate early immune responses in zebrafish larvae by using gene expression and in vivo imaging of neutrophil and macrophage behavior during infection. For the first time, zebrafish larvae were infected with the parasite and infection dynamics, parasite size and host-parasite interactions were investigated. Results showed that the larvae responded with mild inflammation and that the 12 compared to 5 days post fertilization larvae were significantly less susceptible. It was furthermore observed that neutrophils and macrophages were attracted to the parasites and that neutrophils reacted with neutrophil extracellular traps (NETs) when fighting the parasite. The parasite was rotating vigorously, presumably to impede the neutrophils and macrophages from attaching to it but on rare occasions, neutrophils and macrophages were able to kill the parasite. Based on these observations, we concluded that the parasite uses the rotation as an immune evasive strategy and that the zebrafish larvae respond with high activity from neutrophils and macrophages locally but systemically only with mild inflammation.
Case report: Transcatheter tricuspid valve intervention using K-Clip™ system after prior Kay’s annuloplasty
Authors: Wu Shengjun , Dai Xiaoyi , Liu Lingshan , Yuan Shuai , Teng Peng , Ni Yiming
Published: August 2023

The K-Clip™ system is emerging as an alternative to correct tricuspid regurgitation (TR) for patients with high surgical risk. However, patients with recurrent severe tricuspid regurgitation after prior Kay’s annuloplasty are not generally deemed to be candidates for K-Clip™ implantation. Herein, we report a case of a 63-year-old woman with recurrent symptomatic torrential tricuspid regurgitation 5 years after double valve replacement with Kay’s annuloplasty of the tricuspid valve. The K-Clip™ was successfully implanted, and the severity of tricuspid regurgitation and dimensions of tricuspid annulus achieved significant reduction. In conclusion, K-Clip™ can still be feasible and effective for patients with prior Kay’s annuloplasty. However, indications become more rigorous, and evaluation should be more comprehensive.
Identifying potential circulating miRNA biomarkers for the diagnosis and prediction of ovarian cancer using machine-learning approach: application of Boruta
Authors: Hamidi Farzaneh , Gilani Neda , Arabi Belaghi Reza , Yaghoobi Hanif , Babaei Esmaeil , Sarbakhsh Parvin , Malakouti Jamileh
Published: August 2023

Introduction

In gynecologic oncology, ovarian cancer is a great clinical challenge. Because of the lack of typical symptoms and effective biomarkers for noninvasive screening, most patients develop advanced-stage ovarian cancer by the time of diagnosis. MicroRNAs (miRNAs) are a type of non-coding RNA molecule that has been linked to human cancers. Specifying diagnostic biomarkers to determine non-cancer and cancer samples is difficult.

Methods

By using Boruta, a novel random forest-based feature selection in the machine-learning techniques, we aimed to identify biomarkers associated with ovarian cancer using cancerous and non-cancer samples from the Gene Expression Omnibus (GEO) database: GSE106817. In this study, we used two independent GEO data sets as external validation, including GSE113486 and GSE113740. We utilized five state-of-the-art machine-learning algorithms for classification: logistic regression, random forest, decision trees, artificial neural networks, and XGBoost.

Results

Four models discovered in GSE113486 had an AUC of 100%, three in GSE113740 with AUC of over 94%, and four in GSE113486 with AUC of over 94%. We identified 10 miRNAs to distinguish ovarian cancer cases from normal controls: hsa-miR-1290, hsa-miR-1233-5p, hsa-miR-1914-5p, hsa-miR-1469, hsa-miR-4675, hsa-miR-1228-5p, hsa-miR-3184-5p, hsa-miR-6784-5p, hsa-miR-6800-5p, and hsa-miR-5100. Our findings suggest that miRNAs could be used as possible biomarkers for ovarian cancer screening, for possible intervention.
WebNORM: a web application for calculating normative mineralogy
Authors: Buckle Tom , Williams Morgan , Nathwani Chetan L. , Hughes Hannah S. R.
Published: August 2023

Normative mineralogy is a valuable tool for interpreting the mineralogical composition of rocks based on their bulk rock geochemical data. Despite the development of various computational tools for normative mineralogy calculations, the accessibility and continued usage of many existing tools is limited by the use of older languages, licensing constraints, and restricted access to the source code. In this paper, we introduce a Python-based implementation of the normative mineralogy algorithm, which is accessible through a user-friendly web application webNORM, or as part of the pyrolite Python package. The algorithm uses major, minor, and trace element oxides as input and returns up to 31 normative minerals. It offers two methods for estimating the Fe2O3:FeO ratio. The web application offers a convenient interface for users without programming experience, while the pyrolite integration allows more advanced users to leverage the Python ecosystem for end-to-end geochemical data analysis. Comparison between our implementation of the normative calculation and previous implementations shows that our version is accurate and reliable. webNORM offers the geoscience community an accessible solution for calculating normative mineralogy. The algorithm and web application are open-source, and we encourage contributions and adaptations by the community for specific needs and improvements.
Systems thinking for general surveillance programs – practical insights and limiting factors to guide resourcing decisions
Authors: Kruger Heleen , Ticehurst Jenifer L. , Hester Susan M.
Published: August 2023

General surveillance programs promise cost-effective ways to contribute to various biosecurity outcomes, including early detection, understanding the spread of invasive species, and evidence of pest and disease freedom to support trade. These programs encourage people from all walks of life to monitor, detect, and report biosecurity threats. Because general surveillance programs make use of the general public and other people already operating in environments where pests may be present, it is often assumed that programs can occur at very low or even no cost. This article discusses lessons learnt about resourcing general surveillance programs from nine in-depth case studies in Australia and New Zealand across a range of biosecurity sectors. Lessons learnt are derived from qualitative analysis using systems thinking, in particular via the concept of limiting factors. It shows that funding is required for program establishment and coordination, adaptive management, and a range of other activities, and there are various sources of transaction cost. It outlines the strategies used to attract and maintain funding and in-kind contributions over time, including how programs navigated various funding challenges. It highlights the importance of using efficient tools and processes for reporting, species identification/disease diagnosis, and data management. The article provides insights that should prove useful for improving return on investment for general surveillance programs.
Indian Red Jungle fowl reveals a genetic relationship with South East Asian Red Jungle fowl and Indian native chicken breeds as evidenced through whole mitochondrial genome sequences
Authors: Kanakachari M. , Chatterjee R. N. , Reddy M. R. , Dange M. , Bhattacharya T. K.
Published: August 2023

Background: Native chickens are dispersed in a wide geographical range and have hereditary assets that are kept by farmers for various purposes. Mitochondrial DNA (mtDNA) is a widely utilized marker in molecular studies because of its quick advancement, matrilineal legacy, and simple molecular structure.

Method and Results: We performed NGS sequencing to investigate mitochondrial genomes and to evaluate the hereditary connections, diversity, and measure of gene stream estimation in Indian native chicken breeds and Red Jungle fowl. The chicken breeds were genotyped using the D-loop region and 23 haplotypes were identified. When compared to Indian native breeds, more haplotypes were identified in the NADH dehydrogenase subunits, Cytochrome c oxidase, Cytochrome b, ATP synthase subunit 6, and Ribosomal RNA genes. The phylogenetic examination indicated that the analyzed chicken breeds were divided into six significant clades, namely A, B, C, D, E, and F, of which the F clade indicated the domestication of chicken breeds in India. Additionally, our work affirmed that the Indian Red Jungle Fowl is the origin for both reference Red Jungle Fowl as well as all Indian breeds, which is reflected in the dendrogram as well as network analysis based on the whole mtDNA and D-loop region. Indian Red Jungle Fowl is distributed as an outgroup, suggesting that this ancestry was reciprocally monophyletic.

Conclusion: The mtDNA sequences of Indian native chickens provided novel insights into adaptation mechanisms and the significance of important mtDNA variations in understanding the maternal lineages of native birds.
Identifying immune cell infiltration and effective diagnostic biomarkers in Crohn’s disease by bioinformatics analysis
Authors: Huang Rong , Wang Wenjia , Chen Ziyi , Chai Jing , Qi Qin , Zheng Handan , Chen Bingli , Wu Huangan , Liu Huirong
Published: August 2023

Background

Crohn’s disease (CD) has an increasing incidence and prevalence worldwide. It is currently believed that both the onset and progression of the disease are closely related to immune system imbalance and the infiltration of immune cells. The aim of this study was to investigate the molecular immune mechanisms associated with CD and its fibrosis through bioinformatics analysis.

Methods

Three datasets from the Gene Expression Omnibus data base (GEO) were downloaded for data analysis and validation. Single sample gene enrichment analysis (ssGSEA) was used to evaluate the infiltration of immune cells in CD samples. Immune cell types with significant differences were identified by Wilcoxon test and Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis. Differentially expressed genes (DEGs) were screened and then subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional correlation analysis, as well as protein-protein interaction (PPI) network analysis. The cytoHubba program and the GSE75214 dataset were used to screen for hub genes and plot Receiver operating characteristic (ROC)curves to screen for possible biomarkers of CD based on diagnostic efficacy. The hub genes of CD were correlated with five significantly different immune cells. In addition, validation was performed by real time quantitative PCR (RT-qPCR) experiments in colonic tissue of CD intestinal fibrosis rats to further identify hub genes that are more related to CD intestinal fibrosis.

Results

The DEGs were analyzed separately by 10 algorithms and narrowed down to 9 DEGs after taking the intersection. 4 hub genes were further screened by the GSE75214 validation set, namely COL1A1, CXCL10, MMP2 and FGF2. COL1A1 has the highest specificity and sensitivity for the diagnosis of CD and is considered to have the potential to diagnose CD. Five immune cells with significant differences were screened between CD and health controls (HC). Through the correlation analysis between five kinds of immune cells and four biomarkers, it was found that CXCL10 was positively correlated with activated dendritic cells, effector memory CD8+ T cells. MMP2 was positively correlated with activated dendritic cells, gamma delta T cells (γδ T) and mast cells. MMP2 and COL1A1 were significantly increased in colon tissue of CD fibrosis rats.

Conclusion

MMP2, COL1A1, CXCL10 and FGF2 can be used as hub genes for CD. Among them, COL1A1 can be used as a biomarker for the diagnosis of CD. MMP2 and CXCL10 may be involved in the development and progression of CD by regulating activated dendritic cell, effector memory CD8+ T cell, γδ T cell and mast cell. In addition, MMP2 and COL1A1 may be more closely related to CD intestinal fibrosis.
Quantitative flow cytometric selection of tau conformational nanobodies specific for pathological aggregates
Authors: Zupancic Jennifer M. , Smith Matthew D. , Trzeciakiewicz Hanna , Skinner Mary E. , Ferris Sean P. , Makowski Emily K. , Lucas Michael J. , McArthur Nikki , Kane Ravi S. , Paulson Henry L. , Tessier Peter M.
Published: August 2023

Single-domain antibodies, also known as nanobodies, are broadly important for studying the structure and conformational states of several classes of proteins, including membrane proteins, enzymes, and amyloidogenic proteins. Conformational nanobodies specific for aggregated conformations of amyloidogenic proteins are particularly needed to better target and study aggregates associated with a growing class of associated diseases, especially neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. However, there are few reported nanobodies with both conformational and sequence specificity for amyloid aggregates, especially for large and complex proteins such as the tau protein associated with Alzheimer’s disease, due to difficulties in selecting nanobodies that bind to complex aggregated proteins. Here, we report the selection of conformational nanobodies that selectively recognize aggregated (fibrillar) tau relative to soluble (monomeric) tau. Notably, we demonstrate that these nanobodies can be directly isolated from immune libraries using quantitative flow cytometric sorting of yeast-displayed libraries against tau aggregates conjugated to quantum dots, and this process eliminates the need for secondary nanobody screening. The isolated nanobodies demonstrate conformational specificity for tau aggregates in brain samples from both a transgenic mouse model and human tauopathies. We expect that our facile approach will be broadly useful for isolating conformational nanobodies against diverse amyloid aggregates and other complex antigens.
Identification of cuproptosis and immune-related gene prognostic signature in lung adenocarcinoma
Authors: Zhang Wentao , Qu Haizeng , Ma Xiaoqing , Li Liang , Wei Yanjun , Wang Ye , Zeng Renya , Nie Yuanliu , Zhang Chenggui , Yin Ke , Zhou Fengge , Yang Zhe
Published: August 2023

Background

Cuproptosis is a novel form of programmed cell death that differs from other types such as pyroptosis, ferroptosis, and autophagy. It is a promising new target for cancer therapy. Additionally, immune-related genes play a crucial role in cancer progression and patient prognosis. Therefore, our study aimed to create a survival prediction model for lung adenocarcinoma patients based on cuproptosis and immune-related genes. This model can be utilized to enhance personalized treatment for patients.

Methods

RNA sequencing (RNA-seq) data of lung adenocarcinoma (LUAD) patients were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The levels of immune cell infiltration in the GSE68465 cohort were determined using gene set variation analysis (GSVA), and immune-related genes (IRGs) were identified using weighted gene coexpression network analysis (WGCNA). Additionally, cuproptosis-related genes (CRGs) were identified using unsupervised clustering. Univariate COX regression analysis and least absolute shrinkage selection operator (LASSO) regression analysis were performed to develop a risk prognostic model for cuproptosis and immune-related genes (CIRGs), which was subsequently validated. Various algorithms were utilized to explore the relationship between risk scores and immune infiltration levels, and model genes were analyzed based on single-cell sequencing. Finally, the expression of signature genes was confirmed through quantitative real-time PCR (qRT-PCR), immunohistochemistry (IHC), and Western blotting (WB).

Results

We have identified 5 Oncogenic Driver Genes namely CD79B, PEBP1, PTK2B, STXBP1, and ZNF671, and developed proportional hazards regression models. The results of the study indicate significantly reduced survival rates in both the training and validation sets among the high-risk group. Additionally, the high-risk group displayed lower levels of immune cell infiltration and expression of immune checkpoint compared to the low-risk group.
The role of neutrophil percentage to albumin ratio in predicting 1-year mortality in elderly patients with hip fracture and external validation
Authors: Jiao Songsong , Zhou Jiangfei , Feng Zhencheng , Huang Jian , Chen Lihong , Li Zhiwu , Meng Qingqi
Published: August 2023

Objectives

This study aimed to investigate the association between the neutrophil percentage to albumin ratio (NPAR) on the day of admission and mortality 1 year after surgery in elderly patients with hip fractures.

Methods

Clinical characteristics and blood markers of inflammation were retrospectively collected from October 2016 to January 2022 in elderly patients with hip fractures at two different regional tertiary medical centers. It is divided into a training set and an external validation set. Multivariate Nomogram models such as NPAR were constructed using the least absolute shrinkage and selection operator (LASSO) regression results and multi-factor logistic regression analysis. In addition, multivariate Cox regression analysis and Kaplan-Meier survival curves were used to explore the relationship between NPAR values and mortality within 1 year in elderly patients with hip fractures. The predictive performance of the Nomogram was evaluated using the concordance index (C Index) and receiver operating characteristic curve (ROC) and validated by Bootstrap, Hosmer-Lemesow goodness of fit test, calibration curve, decision curve, and clinical impact curve analysis.

Results

The study included data from 1179 (mean age, 80.34 ± 8.06 years; 61.4[52.1%] male) patients from the Guangzhou Red Cross Hospital affiliated with Jinan University and 476 (mean age, 81.18 ± 8.33 years; 233 [48.9%] male) patients from the Xiaogan Central Hospital affiliated with Wuhan University of Science and Technology. The results showed that NPAR has good sensitivity and specificity in assessing patients’ prognosis 1 year after surgery. Multivariate logistic regression models based on influencing factors such as NPAR have good discrimination and calibration ability (AUC=0.942, 95% CI:0.927-0.955; Hosmer-Lemeshow test: P >0.05). Kaplan-Meier survival curves for the training and validation sets showed that patients in the high NPAR group had a higher mortality rate at 1 year compared to the low NPAR group (P< 0.001). Multivariate Cox regression showed that high NPAR values were an independent risk factor for death within 1 year in elderly hip fracture patients (P< 0.001, HR =2.38,95%CI:1.84-3.08).

Conclusion

Our study showed that NPAR levels were significantly higher in patients who died within 1 year after surgery in both the training and validation sets. NPAR has good clinical value in assessing 1-year postoperative prognosis in elderly patients with hip fractures.
Negative association between ascaris lumbricoides seropositivity and Covid-19 severity: insights from a study in Benin
Authors: Adjobimey Tomabu , Meyer Julia , Hennenfent Anneka , Bara Anick J. , Lagnika Latifou , Kocou Bienvenu , Adjagba Marius , Laleye Anatole , Hoerauf Achim , Parcina Marijo
Published: August 2023

Introduction

The COVID-19 pandemic has had devastating effects worldwide, but the trajectory of the pandemic has been milder in Low-and-Middle-Income Countries (LMICs), including those in Africa. Co-infection with helminths, such as Ascaris lumbricoides, has been suggested as a possible factor contributing to the reduced severity observed in these regions.

Methods

The present study investigated the association between Ascaris-specific antibody levels and COVID-19 severity in 276 SARS-CoV-2-infected individuals in Benin. Participants were categorized into asymptomatic (n=100), mild (n=150), and severe (n=26) groups based on clinical disease severity. Sera were collected and analyzed using ELISA to measure Ascaris and SARS-CoV-2-specific antibodies, while Luminex was used to assess cytokines and SARS-CoV-2-specific neutralizing antibody expression.

Results and discussion

The results demonstrated that asymptomatic SARS-CoV-2 seropositive individuals expressed, on average, 1.7 and 2.2-times higher levels of Ascaris antibodies compared to individuals with mild and severe COVID-19, respectively. This finding suggests an inverse correlation between Ascaris antibody levels and COVID-19 severity. Notably, logistic regression analysis showed that Ascaris seropositivity was significantly associated with a reduced risk of severe COVID-19 (OR = 0.277, p = 0.021). Interestingly, COVID-19 patients with comorbidities such as type 2 diabetes and high blood pressure showed lower expression of Ascaris antibodies. Strikingly, no correlation was observed between Ascaris antibody levels and SARS-CoV-2-specific neutralizing antibodies. On the other hand, individuals seronegative for Ascaris displayed significantly higher levels of systemic pro-inflammatory markers compared to seropositive individuals. These findings suggest that higher expression of Ascaris antibodies is associated with asymptomatic SARS-CoV-2 infections and may contribute to the reduction of the risk to develop severe COVID-19. The beneficial effect of Ascaris seropositivity on COVID-19 outcomes in Benin may be attributed to a decrease in comorbidities and pro-inflammatory markers. These observations provide valuable insights into the milder COVID-19 trajectory observed in Africa and may have implications for future therapeutic strategies.
The temporal and spatial variation of chlorophyll a concentration in the China Seas and its impact on marine fisheries
Authors: Zhang Kunlong , Zhao Xunbo , Xue Jing , Mo Danqi , Zhang Dongyu , Xiao Zhongyong , Yang Wei , Wu Yingxu , Chen Yingfeng
Published: August 2023

Marine chlorophyll a is a key molecule for photosynthesis of marine plants and some plankton, which is important in marine ecosystems. This study utilized the chlorophyll a concentration data product observed by the MODIS sensor (MODerate resolution Imaging Spectroradiometer) to construct a long-term sequence of chlorophyll a concentration dataset by processing the raw data. Based on this, the multi-time-scale chlorophyll a concentration data was synthesized, and it was used to analyze the spatial and temporal variation characteristics of chlorophyll a concentration in China Seas. In addition, several oceanographic variables, including sea surface temperature, nutrients (phosphate, nitrate, silicate), partial pressure of seawater carbon dioxide, net primary productivity of the ocean, physical dynamics of seawater processes (mixed layer), were analyzed to ascertain their potential influence on chlorophyll a concentration. Finally, we analyzed the effects of changes in chlorophyll a concentration on marine fisheries. The result showed that: The average value of chlorophyll a concentration in China Seas from 2002 to 2022 was 0.874 mg/m3, with the highest concentration observed in the Bohai Sea area (4.547 mg/m3) and the lowest in the South China Sea area (0.288 mg/m3). The spatial variation of chlorophyll a concentration revealed an overall decrease of 0.0095 mg/m3 in China Seas from 2002 to 2022. From the perspective of time changes, the concentration of chlorophyll a in China’s Bohai Sea area showed a downward trend from 2002 to 2022, while the Yellow Sea area showed an upward trend. The concentration remained relatively stable in the East China Sea area, whereas a significant declining trend was observed in the South China Sea area. The relationship between temperature and chlorophyll a concentration was non-linear, and chlorophyll a concentration showed some fluctuation or threshold effect with the change of seawater temperature. The three nutrient salts studied have a promoting effect on chlorophyll a, among which phosphate has the most obvious promoting effect on chlorophyll a. Chlorophyll a was negatively correlated with pCO2 and positively correlated with ocean net primary productivity. Seasonal changes in the mixed layer had a significant effect on changes in the upper marine nutrients, which in turn affected changes in chlorophyll a concentration. Six of the eight types of algae studied show a trend toward deeper sea depths, which may have implications for the food availability of marine fish at different levels and pose new challenges for marine fisheries development.
Highly underexpanded rarefied jet flows
Authors: Bykov N. Y. , Gorbachev Yu. E. , Fyodorov S. A.
Published: August 2023

A highly underexpanded jet outflow into the background in transition and scattering regimes is studied computationally. The direct simulation Monte Carlo method and Navier–Stokes equations are used. The main parameters’ impact on the jet flow is analyzed. It is shown that a drastic flow structure transformation occurs in a relatively narrow Reynolds numbers’ range, 5 ≤ ReL≤ 30, featuring the jet–surrounding gas interaction. At ReL= 5, a shock wave structure that is typical for the underexpanded jet degenerates completely. The existing empirical expressions application for the estimation of the characteristic dimensions of the shock wave structure in the transition regime leads to significant inaccuracy. For the considered parameters’ range, the approaches based on the direct simulation Monte Carlo method and Navier–Stokes (NS) equations’ solution lead to similar results in the nozzle region, where the flow regime is hydrodynamic. Nevertheless, the NS approach employment for the assessment of flow parameters within rarefied shock layers is debatable.
Biological functions of endophytic bacteria in Robinia pseudoacacia ‘Hongsen’
Authors: Huang Minqing , Chen Lijing , Ma Jiasi , Mo Jingzhi , He Lu , Liang Qihua , Peng Guixiang , Tan Zhiyuan
Published: August 2023

Introduction

Endophytes and their host plants have co-evolved for a very long time. This relationship has led to the general recognition of endophytes as a particular class of microbial resources.R. pseudoacacia‘Hongsen’ is drought- and barren-resistant species that can be grown in both the north and south of China, efficiently addresses the ecological issues caused by China’s ‘southern eucalyptus and northern poplar. Up to date, cultured-dependent studies are available for theR. pseudoacacianitrogen-fixing and other endophytes. Therefore, the present research studied theR. pseudoacacia‘Hongsen,’ microbiome in detail by high-throughput sequencing and culture dependant.

Methods

This study examined microbial species and functional diversity inRobinia pseudoacacia‘Hongsen’ using culture-dependent (isolation) and culture-independent techniques.

Results

A total of 210 isolates were isolated fromR. pseudoacacia‘Hongsen.’ These isolates were clustered into 16 groups by the In Situ PCR (IS-PCR) fingerprinting patterns. 16S rRNA gene sequence analysis of the representative strain of each group revealed that these groups belonged to 16 species of 8 genera, demonstrating the diversity of endophytes inR. pseudoacacia‘Hongsen’. ’Bacillusis the most prevalent genus among all the endophytic bacteria. High-throughput sequencing of endophytic bacteria fromR. pseudoacacia‘Hongsen’ of the plant and the rhizosphere soil bacteria showed that the bacterial populations of soil near the root, leaf, and rhizosphere differed significantly. The microbial abundance decreased in the endophytes as compared to the rhizosphere. We observed a similar community structure of roots and leaves. With and without root nodules,Mesorhizobiumsp. was significantly different inR. pseudoacacia‘Hongsen’ plant.

Discussion

It was predicted thatR. pseudoacacia‘Hongsen’ plant endophytic bacteria would play a significant role in the metabolic process, such as carbohydrate metabolism, amino acid metabolism, membrane transport, and energy metabolism.
Ferroptosis and mitochondrial dysfunction in acute central nervous system injury
Authors: Dong Wenxue , Gong Fanghe , Zhao Yu , Bai Hongmin , Yang Ruixin
Published: August 2023

Acute central nervous system injuries (ACNSI), encompassing traumatic brain injury (TBI), non-traumatic brain injury like stroke and encephalomeningitis, as well as spinal cord injuries, are linked to significant rates of disability and mortality globally. Nevertheless, effective and feasible treatment plans are still to be formulated. There are primary and secondary injuries occurred after ACNSI. Most ACNSIs exhibit comparable secondary injuries, which offer numerous potential therapeutic targets for enhancing clinical outcomes. Ferroptosis, a newly discovered form of cell death, is characterized as a lipid peroxidation process that is dependent on iron and oxidative conditions, which is also indispensable to mitochondria. Ferroptosis play a vital role in many neuropathological pathways, and ACNSIs may induce mitochondrial dysfunction, thereby indicating the essentiality of the mitochondrial connection to ferroptosis in ACNSIs. Nevertheless, there remains a lack of clarity regarding the involvement of mitochondria in the occurrence of ferroptosis as a secondary injuries of ACNSIs. In recent studies, anti-ferroptosis agents such as the ferroptosis inhibitor Ferrostain-1 and iron chelation therapy have shown potential in ameliorating the deleterious effects of ferroptosis in cases of traumatic ACNSI. The importance of this evidence is extremely significant in relation to the research and control of ACNSIs. Therefore, our review aims to provide researchers focusing on enhancing the therapeutic outcomes of ACNSIs with valuable insights by summarizing the physiopathological mechanisms of ACNSIs and exploring the correlation between ferroptosis, mitochondrial dysfunction, and ACNSIs.