bluuebunny/crossref_metadata_2025_split huggingface dataset:
Indoor Airborne Bacteria and Lung Health: Sex-Specific Associations
Authors: Amin Hesham , Cramer Christine , Drengenes Christine , Finster Kai , Real Francisco Gomez , Gislason Thorarinn , Holm Mathias , Janson Christer , Jögi Nils Oskar , Jogi Rain , Malinovschi Andrei , Modig Lars , Norbäck Dan , Shigdel Rajesh , Sigsgaard Torben , Svanes Cecilie , Thorarinsdottir Hulda , M.Wouters Inge , Šantl-Temkiv Tina , Schlünssen Vivi , J.Bertelsen Randi 
Published: June 2024

Abstract

Background
Sex is a significant epidemiological factor in the incidence of respiratory disease. However, the role of sex in indoor bacterial exposure remains largely unexplored.
Objective
Our objective was to investigate the association between indoor bacterial exposure and lung function and airway inflammation, focusing on sex-specific differences.
Methods
Airborne dust samples from the bedrooms of 463 men and 575 women in the European Community Respiratory Health Survey (ECRHS) III from five Nordic cities were subjected to 16S rRNA amplicon sequencing to characterize bacterial communities. Limulus amebocyte lysate (LAL) assay and qPCR were used to measure endotoxin and bacterial load, respectively. Sex stratified adjusted linear regression analysis were used to examine the association between bacterial profile and lung function and FeNO measurements.
Results
Higher indoor bacterial diversity were significantly associated with higher lung function (FVC and FEV1 Z-scores) in men only, and with higher FeNO levels in women only. Indoor endotoxin levels were significantly associated with higher FeNO levels in women only. No clear associations were found between endotoxin levels and lung function. Most bacterial genera associated with higher lung function were affiliated with the Actinobacteriota phylum. Higher relative abundance of Bacteroidia, and Patescibacteria were associated with lower lung function, and the same was seen for several bacterial genera considered to be part of the core oral microbiome, including Streptococcus and Veillonella. More bacterial genera were associated with high FeNO levels in women than in men, among them Campylobacter, Fusebactrium, and several Bacteroidia genera.
Conclusions
The results of our study indicate that there might be distinct sex-specific differences in how individuals respond to indoor bacterial community exposure and its impact on lung health. This underlines the importance of talking sex into consideration in future evaluations of health implications associated with various indoor microbial communities.
Circulating levels of interleukins and lung cancer and its subtypes: A Mendelian randomization study
Authors: Zhai Li , Wei Ying , Chen Meng , Zhang Aili , Luo Jianbo , Zheng Yating , Gao Lili , Wang Liangxiao , Zhang Xi 
Published: June 2024

Abstract

Background
Interleukins (ILs) are closely linked to the pathogenesis of lung cancer (LC). However, the precise causal relationship between them remains somewhat ambiguous. This study aimed to investigate the potential causal relationships between these ILs and LC based on the two-sample Mendelian randomization (TSMR) research framework.
Methods
We conducted TSMR analyses using summary dataset from large-scale genome-wide association studies (GWASs). Our primary method is random effects inverse variance weighted (RE-IVW) analysis, which was subsequently adjusted using the Bonferroni correction method. We established that results with p values less than 0.0022 (0.05/23) indicate a significant causal relationship, whereas results with p values between 0.0022 and 0.05 indicate a suggestive causal relationship. Additionally, sensitivity analyses were conducted to verify the robustness of the findings.
Results
Analysis revealed that IL-18 had a significantly protective effect on LC and shows a suggestive negative correlation with LUAD and LUSC. IL-20 and IL-8 were suggestive positive correlation with both LC and LUAD. Additionally, IL-24 showed had a significantly protective effect on LUSC, while IL-17A and IL-8 were suggestive positive correlation with LUSC.
Conclusions and Relevance:
Our study support IL-18 had protective effect on LC, and IL-24 showed had protective effect on LUSC, suggesting that these cytokines play a crucial role in disease pathogenesis. This finding underscores the need for further research into these associations to better understand their implications for LC development.
Multi-camera detection framework for lifelong broiler flock monitoring
Authors: Cardoen Thorsten , Leroux Sam , Simoens Pieter 
Published: June 2024

Abstract

In recent times, there has been an increased emphasis on chicken welfare within the poultry industry, leading to the adoption of camera-based solutions for continuous monitoring of broilers' activity and health parameters. Accurate detection and localization of broilers within the pen are crucial input for various welfare monitoring applications. However, current research has predominantly concentrated on single-camera setups, which are prone to occlusions caused by feeder or lighting equipment and struggle with scalability in larger pen sizes. To overcome these challenges, we propose a multi-camera setup that allows precise detection and localization of each broiler in a top-down view of the pen. Our approach ensures detection accuracy throughout the entire six-week lifespan of broilers, providing robust and consistent results despite the significant changes in the animals' visual appearance over time. We obtain a MODA score of 83.8% on real-world data and demonstrate its superior effectiveness compared to single-camera setups.
The nature of aerodynamic sound of turbulent temporal shear layers
Authors: Khujadze George , Gogichaishvili David , Chagelishvili George , Foyisi Holger , Tevzadze Alexander 
Published: June 2024

Abstract

This paper aims to establish the pivotal role of the linear non-modal dynamics of perturbations in the aerodynamic sound emission of turbulent temporal shear/mixing layers at the self-similar stage of evolution. This is achieved by comparing the results of direct numerical simulations (DNS) of the mixing layer to the linear non-modal analysis of the flow central/body part model – 3D homentropic, unbounded flow, U0(Ay, 0, 0), with shear rate, A. The non-modal analysis captures the only linear mechanism of acoustic wave generation – the linear vortex-wave mode coupling induced by the non-modal dynamics of perturbations in shear flows. The efficiency of this linear generation is uniquely determined by the mode-dependent Mach number,M= Aλx/cs, related to the convective Mach number viaM= Mcλx/πΔy. Here, λx, cs and Δy denote the streamwise wavelength, speed of sound and shear-layer width, respectively. DNS of compressible turbulent temporal mixing layers were performed for different convective Mach numbers (Mc = 0.3, 0.7, 1.4) and simulation boxes (Lx, Ly, Lz) for reliably identifying the essence of the origin of sound in the turbulent layer. The simulations clearly show the decisive role of the linear non-modal mechanism of sound generation in the flow. This novelty highlights the significance of M in the sound generation, thus ensuring maximum efficiency for harmonics with largest streamwise wavelength, λx = Lx. Accordingly, the aerodynamic sound efficiency is determined by McLx rather than Mc. Overall, our analysis points to the inadequacy of employing the modal approach to describe compressible dynamic processes in the turbulent flow.
Diaporthe atlantica improves tomato resistance against the vascular pathogen Fusarium oxysporum f. sp. lycopersici
Authors: Pereira Eric C. , de Aldana Beatriz R. Vázquez , Arellano Juan B. , Fernández Iván , Zabalgogeazcoa Iñigo 
Published: June 2024

Abstract

Background
Fungal pathogen attacks are a major threat to crop growth and productivity, with Fusarium oxysporum f. sp. lycopersici being particularly menacing to tomato plants by causing vascular wilt disease. Diaporthe atlantica is a main component of the root microbiome of Festuca rubra subsp. pruinosa, a grass that inhabits sea cliffs. This fungus can confer drought and salinity tolerance to some agricultural plant species. In this study, we evaluated the efficacy of Diaporthe atlantica in conferring resistance against Fusarium in tomato plants in a greenhouse experiment.
Results
A significant reduction in Fusarium wilt symptoms was observed in plants inoculated with Diaporthe atlantica. Furthermore, Diaporthe suppressed Fusarium colonisation, thereby mitigating vascular browning and improving plant growth, chlorophyll content and nutrient acquisition. In addition, the effect of Diaporthe atlantica on plant defence against Fusarium seems to not directly involve classical induced systemic resistance or systemic acquired resistance mechanisms.
Conclusion
These findings underscore the potential of Diaporthe as a biocontrol agent to enhance plant resistance against Fusarium wilt.
Identification of Novel Biomarkers for Breast Cancer through Multi-Chip Integration Analysis in GEO Database
Authors: Li Jia-Yi , Gao YaLi , Liu YaoBang , Bai ZhengYang , LI Ting , Ma Shuang , Zhang YangYang , Li JinPing 
Published: June 2024

Abstract

Background
Breast cancer is the most common cancer and the second leading cause of cancer death in women. In China, the incidence and mortality of breast cancer are both on the rise, and the prevention and treatment of breast cancer has become one of the most important cancer research hot-spots. Although great progress has been made in breast cancer research in recent years, there is still a lack of reliable and effective methods for early diagnosis. In this study, bioinformatics technology and multi-chip joint analysis methods are used to screen new biomarkers that can be adopted in the early diagnosis of breast cancer, aiming to improve the early diagnosis rate of breast cancer and reduce the rate of mortality.
Methods
the bioinformatics analysis of the chip data downloaded by GEO was carried out by R software to screen the differentially-expressed genes in breast cancer, and analyzing the data by GO and KEGG enrichment analysis after a multi-chip joint, constructing the interaction network of differentially-expressed gene protein and screen HUB gene through string website and cytoscape software, downloading the expression of TCGA breast cancer samples and clinical data, analyzing the survival and prognosis of the selected HUB genes, identifying the differential expressions of HUB genes of breast cancer with GEPIA database and verifying the differential expressions of mRNA and protein levels of breast cancer tissue samples and breast cancer cells by RT-qPCR and western-blot methods.
Results
A total of 9 HUB genes were screened by multi-chip combined bioinformatics analysis, which were EZH2, CD36, LPL, ADIPOQ, LIPE, PLIN1, CAV1, LEP and PPARG respectively. Combined with clinical prognostic data, 6 breast cancer HUB genes were selected again, which were EZH2, CD36, ADIPOQ, LIPE, LEP and PPARG; Both the clinical samples and cell experiments confirmed the high expression of EZH2 in breast cancer and the low expression of CD36, ADIPOQ, LIPE, LEP and PPARG in breast cancer.
Conclusion
the differentially-expressed genes EZH2, CD36, ADIPOQ, LIPE, LEP and PPARG obtained by breast cancer GEO microarray analysis may be molecular markers for early diagnosis of breast cancer.
Resting state EEG in young children with Tuberous Sclerosis Complex
Authors: Clements Caitlin C , Engelstad Anne-Michelle , Wilkinson Carol L. , Hyde Carly , Hartney Megan , Simmons Alexandra , Tager-Flusberg Helen , Jeste Shafali , Nelson Charles A 
Published: June 2024

Abstract

Background: Tuberous Sclerosis Complex (TSC) manifests behaviorally with features of autism, epilepsy, and intellectual disability. Resting state electroencephalography (EEG) offers a window into neural oscillatory activity and may serve as an intermediate biomarker between gene expression and behavioral manifestations. Such a biomarker could be useful in clinical trials as an endpoint or predictor of treatment response. However, seizures and antiepileptic medications also affect resting neural oscillatory activity and could undermine the utility of resting state EEG features as biomarkers in neurodevelopmental disorders such as TSC.
Methods: This paper compares resting state EEG features in a cross-sectional cohort of young children with TSC (n=49, ages 12-37 months) to 49 age- and sex-matched typically developing controls. Within children with TSC, associations were examined between resting state EEG features, seizure severity composite score, and use of GABA agonists.
Results: Compared to matched typically developing controls, children with TSC showed significantly greater alpha and beta power in permutation cluster analyses iterated across a broad frequency range (2-50Hz). Children with TSC also showed significantly greater aperiodic offset after power spectra were parameterized using SpecParam into aperiodic and periodic components. Within children with TSC, greater seizure severity was significantly related to increased periodic peak beta power. Use of GABA agonists was also independently and significantly associated with increased periodic peak beta power; the interaction between seizure severity and GABA agonist use had no significant effect on peak beta power.
Conclusions: The elevated peak beta power observed in children with TSC compared to matched typically developing controls may be driven by both seizures and GABA agonist use. It is recommended to collect seizure and mediation data alongside EEG data for clinical trials. These results highlight the challenge of using resting state EEG features as biomarkers in trials with neurodevelopmental disabilities when epilepsy and anti-epileptic medication are common.
The neuroprotective effect of hUC-MSCs-derived secretome against alpha-synuclein aggregates on the blood-brain barrier
Authors: Marzookian Kimia , Aliakbari Farhang , Hourfar Hamdam , Sabouni Farzaneh , Otzen Daniel E. , Morshedi Dina 
Published: June 2024

Abstract

The blood-brain barrier (BBB) is a specialized network in the central nervous system that maintains CNS homeostasis. Disruption of the BBB can lead to nerve damage and contribute to neurodegenerative diseases like Parkinson’s (PD), characterized by alpha-synuclein (αSN) aggregation causing intracellular inclusions. Mesenchymal stem cells (MSCs) have shown promise in alleviating the severity of neurological diseases through their active secretions. However, the impact of MSCs secretome on the BBB remains largely unclear. In this study, we investigated the impact of human umbilical cord-derived MSCs (hUC-MSCs) secretome on the BBB in the presence of toxic αSN-aggregates (αSN-AGs). Using in vitro BBB models established through mono- and co-culture systems of hCMEC/D3 cells, we assessed the influence of the secretome on the cytotoxicity and inflammatory responses induced by αSN-AGs. Our results demonstrate that the hUC-MSCs exerts protective effects by mitigating the toxic effects of αSN-AGs on the BBB. Particularly, this study showed a notable reduction in cytotoxicity and inflammation. Our findings highlight the potential of hUC-MSCs secretome as a promising candidate for innovative, cell-free therapies in PD treatment. Furthermore, we propose an optimized method for isolating MSCs from umbilical cord tissue, aimed to facilitating future research on the therapeutic applications of these cells.
Detecting Emotional Sentiments in Textual Data Using Various Machine Learning and Deep Learning Techniques
Authors: Sallam Amer A. , Saif Wedad Q. , Rassem Taha H. , Mohammed Badiea Abdulkarem 
Published: June 2024

Abstract

The digital age has led to a significant increase in text data, including social media updates, articles, and text messages. The ability to understand and extract emotions from this data is crucial in fields such as customer service analysis, psychological research, and social studies. It allows businesses and organizations to gain insight into customer opinions and emotions, leading to better decision-making and alignment with customer needs. However, accurately detecting emotions from text poses challenges due to linguistic structures, cultural nuances, and contextual differences. Although artificial intelligence and text analysis models have made progress in addressing these challenges, there is still a need for more sophisticated methodologies to understand textual content and explore emotions. This study aims to employ a range of machine learning and deep learning methods, including logistic regression, Extra tree classifier, voting classifier, SGD, linearSVC, BiLSTM, BERT, RoBERTa, and DistilBERT, to detect emotions in textual content. The objective is to analyze and compare the outcomes of these methods. This involves extracting features and semantic relationships using techniques such as Word2Vec and FastText, and integrating them with features derived from TF-IDF, Bag of Words (BoW), and N-grams. The findings demonstrate the effectiveness of various models. Specifically, the SGD model utilizing N-grams and FastText achieved an accuracy of 88.42\% on the AIT-2018 dataset, while LinearSVC using N-grams and Word2Vec achieved an accuracy of 88.23\% on the ISEAR dataset. It is worth noting that the BERT transformer model outperformed others, achieving an accuracy of 93.67\% on the AIT-2018 dataset and 89.49\% on the ISEAR dataset. These results align with previous studies, further supporting their reliability and coherence.
KDM6A facilitates Xist upregulation at the onset of X inactivation
Authors: Lin Josephine , Zhang Jinli , Ma Li , Fang He , Ma Rui , Groneck Camille , Filippova Galina N. , Deng Xinxian , Ma Wenxiu , Disteche Christine M. , Berletch Joel B. 
Published: June 2024

Abstract

Background: X chromosome inactivation (XCI) is a female-specific process in which one X chromosome is silenced to balance X-linked gene expression between the sexes. XCI is initiated in early development by upregulation of the lncRNA Xist on the future inactive X (Xi). A subset of X-linked genes escape silencing and thus have higher expression in females, suggesting female-specific functions. One of these genes is the highly conserved gene Kdm6a, which encodes a histone demethylase that removes methyl groups at H3K27 to facilitate gene expression. KDM6A mutations have been implicated in congenital disorders such as Kabuki Syndrome, as well as in sex differences in development and cancer.
Methods: Kdm6a was knocked out (KO) using CRISPR/Cas9 gene editing in hybrid female mouse embryonic stem cells derived from a 129 x Mus castaneus (cast) cross in which a transcriptional stop signal is inserted onto the 129 allele of Tsix, resulting in completely skewed silencing of the 129 X chromosome upon differentiation. Allelic RNA-seq was done to compare gene expression between wild-type and Kdm6aKO clones. The effects of Kdm6a KO on Xist expression during the onset of XCI and the resulting changes in XCI potency were investigated using allele-specific RNA-seq and RNA FISH. Changes in H3K27me3 enrichment on the Xi in KO cells were investigated by CUT&RUN followed by allelic analysis. KDM6A binding to the Xist gene during the onset of XCI in wild-type cells was characterized by CUT&RUN.
Results:We observed impaired upregulation of Xist during early stages of differentiation in hybrid mouse ES cells following CRISPR/Cas9 knockout of Kdm6a. This is associated with reduced Xist RNA coating of the Xi, suggesting diminished XCI potency. Indeed, Kdm6aknockout results in aberrant overexpression of genes from the Xi after differentiation. Consistent with a direct role in Xist regulation, KDM6A binds to the Xist promoter and knockout cells show an increase in H3K27me3 at Xist.
Conclusions:These results reveal a novel female-specific role for the X-linked histone demethylase, KDM6A in the initiation of XCI through histone demethylase-dependent activation of Xistduring early differentiation.
Large scale reorientation in cubic Rayleigh-Bénard convection using particle tracking velocimetry
Authors: Barta Robin , Wagner Claus 
Published: June 2024

Abstract

We measured the three-dimensional velocity field of a large-scale reorientation in turbulent Rayleigh-Bénard convection with a high Rayleigh number Ra = $2.5\cdot 10^9$ by long-term particle tracking velocimetry measurements over 30 hours in a water-filled cubic cell with a side length of $L=300$ mm. Reorientations are characterized by the large-scale circulation in the flow changing its orientation from one cell diagonal to the other, and they are rare events; one can expect about one reorientation per day in our measurement. No other three-dimensional velocity field measurements of such events are known in the literature. Dominant flow structures during the reorientation are extracted from the measurement data using POD. The convergence of the POD is supported by applying the symmetries of the cubic RB cell to our data set to make it equiprobalbe so that it mimics a long time series of reorientation events. The decomposition reveals degenerate mode pairs, i.e. modes that have the same energy and describe the same state, which is consistent with reorientation results found in the literature for DNS of turbulent RBC in cubic cells. The first six modes of the decomposition account for about 70\% of the total energy and contain the most important coherent structures in the system. Modes 1-3 reflect the orientation and dynamics of the large-scale circulation, i.e., the primary flow structure, and modes 4-6 provide the orientation and dynamics of corner circulations, i.e., the secondary flow structures. A pure $Y$ roll structure is observed in the middle of the reorientation event.
Primary ciliary dyskinesia as a rare cause of male infertility – case report and literature overview
Authors: Novák Jan , Horáková Lenka , Puchmajerová Alena , Vik Viktor , Krátká Zuzana , Thon Vojtěch 
Published: June 2024

Abstract

Background: Primary ciliary dyskinesia (PCD) is a heterogenous disease caused by mutations of miscellaneous genes which physiologically play an important role in proper structure and/or function of various cellular cilia including sperm flagella. Besides male infertility, the typical phenotypes, based on decreased mucociliary clearance, are lifelong respiratory issues, i.e., chronic bronchitis leading to bronchiectasis, chronic rhinosinusitis, and chronic otitis media. Moreover, since motile cilia are important during embryological development in the sense of direction of gut rotation, 50% of affected individuals develop situs inversus – so-called Kartagener’s syndrome.
Case presentation: We present two cases of PCD as a rare cause of male infertility.
Conclusions: Primary ciliary dyskinesia should be suspected in infertile males having (sub)normal sperm concentration values with persistent zero motility together with patient’s and/or family history of respiratory symptoms like bronchiectasis, chronic cough, rhinitis, recurrent sinusitis, and otitis media. Due to more than 50 identified mutations until now, the causal mechanism of male infertility is miscellaneous and not in all cases known in detail. Besides impaired sperm motility, other mechanisms significantly decreasing efficacy of assisted reproduction techniques play a pivotal role. Thus, proper diagnostic work-up including among other sperm DNA fragmentation is mandatory to avoid ineffective treatment burden.