bluuebunny/crossref_metadata_2025 huggingface dataset:
Impaired extinction of cocaine seeking in HIV-infected mice is accompanied by peripheral and central immune dysregulation
Authors: Barker Jacqueline , Buck Lauren , Xie Qiaowei , Willis Michelle , Side Christine , Giacometti Laura , Gaskill Peter , Park Kyewon , Shaheen Farida , Guo Lili , Gorantla Santhi
Published: September 2023

Substance use disorders (SUDs) are highly comorbid with HIV infection, necessitating an understanding of the interactive effects of drug exposure and HIV. The relationship between HIV infection and cocaine use disorder is likely bidirectional, with cocaine use directly impacting immune function while HIV infection alters addiction-related behavior. To better characterize the neurobehavioral and immune consequences of HIV infection and cocaine exposure, this study utilized a humanized mouse model to investigate the outcomes of HIV-1 infection on cocaine-related behaviors in a conditioned place preference (CPP) model, and the interactive effects of cocaine and HIV infection on peripheral and central nervous system inflammation. HIV infection selectively impaired cocaine CPP extinction without effecting reinstatement or cocaine seeking under conflict were observed. Behavioral alterations were accompanied by immune changes in HIV infected mice, including increased prefrontal cortex astrocyte immunoreactivity and brain-region specific effects on microglia number and reactivity. Peripheral immune system changes were observed in both mouse and human cytokines, including HIV-induced reductions in mouse IL-1α and G-CSF and human TNFα, and cocaine induced alterations in mouse GM-CSF. Together these data provide new insights into the unique neurobehavioral outcomes of HIV infection and cocaine exposure and how they interact to effect immune responses.
Mutational dissection of a hole hopping route that can be tuned to boost peroxygenase activity in LPMOs
Authors: Eijsink Vincent G.H. , Ayuso-Fernández Iván , Emrich-Mills Tom Z , Haak Julia , Golten Ole , Hall Kelsi R. , Schwaiger Lorenz , Moe Trond S. , Stepnov Anton A. , Ludwig Roland , III George Cutsail , Sørlie Morten , Røhr Åsmund Kjendseth
Published: September 2023

Oxidoreductases have evolved tyrosine/tryptophan pathways that channel highly oxidizing holes away from the active site to avoid damage. Here we dissect such a pathway in a bacterial lytic polysaccharide monooxygenase (LPMO), member of a widespread family of C-H bond activating enzymes with outstanding industrial potential. We show that a strictly conserved tryptophan is critical for radical formation and hole transference and that holes traverse the protein to reach a Tyr-His pair in the protein’s surface. Real-time monitoring of radical formation revealed a clear correlation between the efficiency of hole transference and enzyme performance under oxidative stress. Residues involved in this pathway vary considerably between natural LPMOs, which could reflect adaptation to different ecological niches. Importantly, we show that enzyme activity is increased in a mutant with slower radical transference, providing experimental evidence for a previously postulated trade-off between activity and redox robustness.
GeneXpert has perfect test agreement with WHO recommended TB lipoarabinomannan antigen test for the diagnosis of TB among under five children from urine sample in Tuberculosis endemic setting of Ethiopia
Authors: Derese Daniel , Teklu Takele , Kumalo Abere , Chinasho Tariku , Anjulo Temesgen
Published: September 2023

Background
Tuberculosis (TB) is one of the leading public health problems in children mainly due to difficulties in the diagnosis of disease in children. This study aimed to detect the diagnostic agreement between GeneXpert MTB/RIF and WHO recommended lipoarabinomannan (LAM) antigen test for the detection of TB in children using urine samples
Methods
Institutional based cross-sectional study was conducted on 337 children in Wolaita Sodo University comprehensive hospital. LAM antigen and GeneXpert methods were used to detect TB from urine sample. The agreement between two tests was assessed using Kappa statistics with the standard error (SE), concordance and disagreements statistics. Logistic regression was used to determine factors associated with TB and P-values less than 0.05 were considered as having a statistically significant association.
Results
M. tuberculosis was detected in 26 using TB LAM giving an overall prevalence of 7.7% and 29 (8.6%) using GeneXpert. The two tests had almost perfect agreement (Concordance of 99.1% and kappa value of 0.94 with standard error of 0.034) for the detection of TB in urine sample. Co-infections with other diseases [AOR = 4.00: 95% CI, 1.428, 11.203], cough for the previous two weeks [AOR = 3.700: 95% CI, 1.039, 13.183], night sweat [AOR = 4.255: 95% CI, 1.453, 12.463] and loss of appetite [AOR = 3.994: 95% CI, 1.444, 11.045] had significant associations with pulmonary TB among children in the study area.
Conclusion
Tuberculosis was still the public health concern among children of under five years old in the study area. The GeneXpert had almost perfect test agreement with WHO recommended TB LAM antigen test for the diagnosis TB among under five children, however, it needs further confirmation study with large sample size to use as diagnostic test.
Prognostic Value of Platelet Distribution Width to Lymphocyte Ratio in Patients with Hepatocellular Carcinoma Following Hepatectomy
Authors: Zhong Zhi-Han , Liang Lei , Fu Tian-Wei , Dai Mu-Gen , Cheng Jian , Liu Si-Yu , Ye Tai-Wei , Shen Guo-Liang , Zhang Cheng-Wu , Huang Dong-Sheng , Liu Jun-Wei
Published: September 2023

Background Platelet distribution width (PDW), but not platelet count, was found to more comprehensively reflect platelet activity. The present study, thus, aimed to evaluate the prognostic value of PDW to lymphocyte ratio (PDWLR)in patients with hepatocellular carcinoma (HCC) following hepatectomy.
MethodsPatients following hepatectomy were analyzed retrospectively. The Kaplan-Meier survival curves and Cox regression model were used to determine the prognostic value of PDWLR.
Results241 patients were analyzed eventually, and stratified into low and high PDWLR groups (≤ 9.66 vs. > 9.66). Results of comparing the baseline characteristics showed that high PDWLR was significantly associated with cirrhosis, and intraoperative blood loss (all P < 0.05). In multivariate COX regression analysis, PDWLR was demonstrated as an independent risk factor for OS (HR: 1.549, P = 0.041) and RFS (HR: 1.655, P = 0.005). Moreover, PDWLR demonstrated a superior capacity for predicting prognosis compared to other indicators.
Conclusion Preoperative PDWLR has a potential value in predicting the prognosis of HCC patients following hepatectomy, which may help in clinical decision-making for individual treatment.
DNA methylation profiles of cancer-related fatigue associated with markers of inflammation and immunometabolism
Authors: Xiao Canhua , Peng Gang , Conneely Karen , Zhao Hongyu , Felger Jennifer , Wommack Evanthia , Higgins Kristin , Shin Dong , Saba Nabil , Bruner Deborah , Miller Andrew
Published: September 2023

Cancer patients are commonly affected by fatigue. Herein, we sought to examine epigenetic modifications (i.e., DNA methylation) related to fatigue in peripheral blood among patients during and after treatment for head and neck cancer (HNC). Further, we determined whether these modifications were associated with gene expression and inflammatory protein markers, which we have previously linked to fatigue in HNC. This prospective, longitudinal study enrolled eligible patients with data collected at pre-radiotherapy, end of radiotherapy, and six months and one-year post-radiotherapy. Fatigue data were reported by patients using the Multidimensional Fatigue Inventory (MFI)-20. DNA methylation (Illumina MethylationEPIC) and gene expression (Applied Biosystems Clariom S) arrays and assays for seven inflammatory markers (R&D Systems multiplex) were performed. Mixed models and enrichment analyses were applied to establish the associations. A total of 386 methylation loci were associated with fatigue among 145 patients (FDR < 0.05). Enrichment analyses showed the involvement of genes related to immune and inflammatory responses, insulin and lipid metabolism, neuropsychological disorders, and tumors. We further identified 16 methylation-gene expression pairs (FDR < 0.05), which were linked to immune and inflammatory responses and lipid metabolism. Ninety-one percent (351) of the 386 methylation loci were also significantly associated with inflammatory markers (e.g., interleukin 6, c-reactive protein; FDR < 0.05), which further mediated the association between methylation and fatigue (FDR < 0.05). These data suggest that epigenetic modifications associated with inflammation and immunometabolism, in conjunction with relevant gene expression and protein markers, are potential targets for treating fatigue in HNC patients. The findings also merit future prospective studies in other cancer populations as well as interventional investigations.
The Mediating Effect of Chronic Pain on the Relationship between Falls and Frailty: A Cross-sectional Survey among Middle-aged and Older adults from Ethnic Minority Groups in Yunnan Province, China
Authors: Wen Xuan , Deng Rui , Wang Xinping , Deng Chunyan , Li Xiaoju , Zhang Yafang , Chen Ying , Huang Yuan
Published: September 2023

Background
Falls are associated with an increased risk of frailty in middle-aged and older adults; however, the mediating role between falls and frailty remains unclear. The primary objective of this study is to examine the relationship between falls and frailty in middle-aged and elderly individuals residing in Yunnan Province, China, with a specific emphasis on exploring the potential mediating effect of chronic pain across different ethnic groups.
Methods
Employing a cross-sectional design, data collection was conducted from July to December 2022 in five selected counties. Baron and Kenny’s causal steps method was used to explore the mediating effect of chronic pain on the relationship between falls and frailty. Spearman correlation analysis, multiple linear regression models, and bootstrap method were employed for data analysis.
Results
A total of 2,710 respondents participated in this study. The prevalence of falls among middle-aged and older individuals was 12.77%, while the prevalence of frailty in the same population was observed to be 21.62%. Spearman correlation analysis revealed significant positive association between chronic pain and both falls (r=0.135, P<0.05) as well as frailty (r=0.383, P<0.05). Frailty also exhibited a significant positive correlation with falls (r=0.162, P<0.05). After adjusting for all covariates, the total effect of falls on frailty was estimated to be 1.065 (95% bootstrap CI: 0.804~1.326), with a direct effect estimate of 0.797 (95% bootstrap CI: 0.511~1.083). The indirect effect of chronic pain on this association was found to be approximately one-quarter at 0.268 (95% bootstrap CI: 0.170~0.366). The subgroup analysis discovered differences in the mediating effects across different ethnic groups; specifically, the proportions mediated by chronic pain were found to be 28.2%, 18.4%, and 21.5% for Han majority group, Zhiguo ethnic minorities, and other ethnic minority groups, respectively.
Conclusion
This study provides valuable insights into the intricate association between frailty, falls, and chronic pain among middle-aged and older adults from diverse ethnic backgrounds in a western province of China. Effective management strategies targeting chronic pain and falls prevention could serve as crucial interventions to address frailty.
The radiation shielding parameters of a standard silica glass system
Authors: Kaky Kawa M. , Sayyed M. I.
Published: September 2023

We investigated the radiation shielding parameters for K2O-SiO2 glasses using Phy-X software. The results show that the glasses with a higher K2O concentration and lower SiO2 contents have higher mass attenuation coefficient (MAC) values at all energies. At 0.03 MeV, the MAC values of the tested glasses are varied between 0.873 and 1.907 cm2/g, while at 0.10 MeV they are in the range of 0.168–0.195 cm2/g. The linear attenuation coeffieicnet (LAC) shows a direct relation with the density, where the LAC for the glass with a density of 2.211 g/cm3 is 0.704 cm− 1 at 0.05 MeV and increases to1.351 cm− 1 for the glass with a density of 2.491 g/cm3. We reported the effective atomic number (Zeff) for the tested glasses and we found the glass with a composition of 40K2O-60SiO2 has the greatest Zeff at all energies. The Zeff values at 0.03 MeV are in order of 11.94–16.43, while at 4 MeV they are varied between 10.06 and 12.31. according to the half value layer results, 40K2O-60SiO2 glass has the lowest HVL, which means this glass has the best radiation shielding properties among the tested glasses.
Lycorine (Lycoris radiata)- A unique natural medicine on breast cancer
Authors: Xue Qinbing , Wang Bing , Feng Jie , Li Chaoyu , Yu Miao , Zhao Yan , Qi Zheng
Published: September 2023

Background: Breast cancer (BC) is one of the most common types of cancer among women worldwide. Lycorine (Lycoris radiata), a small molecule derived from the traditional Chinese herb Amaryllidaceae plants, has appeared potential effect on inhibiting the growth of cancer cells and inducing apoptosis in various types of cancer with minor side effects.
Methods: To discuss the therapeutic effects and molecular mechanisms of lycorine on BC established by lycorine-treated S180 tumor-bearing mice in vivo and MTT assay in vitro. The mitotic arrest and microtubule morphology was observed by flow cytometry and fluorescence microscopy. Furthermore, both the mitotic and microtubule assembly dynamics genes were performed by qPCR assays, and the protein expression associated with mitotic arrest was investigated by flow cytometry and western blot.
Results: Lycorine was demonstrated to reduce sarcoma growth of S180 tumor-bearing mice (50.6 % at 40 mg/kg·bw of lycorine) and inhibit the proliferation of MCF-7 cells in concentration-dependent manner. Likewise, lycorine appeared little effect on the thymus and spleen indexes. Moreover, lycorine induced M phase cell cycle arrest viainterfering with the mitotic apparatus regulated the expression of 20 genes and 15 proteins in cell cycle progression. Furthermore, this study confirmed that the potential effect of lycorine on BC might be mediated by cell cycle arrest in M phase for the first time.
Conclusion: These results would be the consequence of exploitation of lycorine as a potential drug for BC therapy, however further preclinical and clinical studies are still needed.
Excitation of noise-squeezed forward Brillouin lasers from intracavity backward Brillouin lasers in a multimode fiber microresonator
Authors: Nie Mingming , Jia Kunpeng , Zhu Shining , Xie Zhenda , Huang Shu-Wei
Published: September 2023

Stimulated Brillouin scattering (SBS) in low-power and compact microresonators has created a new field in cavity nonlinear photonics due to the marriage between acoustic and optical signal processing. Considering the fundamental differences between backward SBS and forward SBS processes, it is challenging to observe the coexistence of both processes in the same microresonator, as well as the photon noise suppression for the forward stimulated Brillouin laser (FSBL). Here, we demonstrate the first 20-dB-noise-squeezed FSBL generation excited by the coexisting backward SBL (BSBL) in an ultrahigh-quality-factor Fabry–Pérot (FP) microresonator based on multimode fiber (MMF). Multiple FSBLs and BSBLs are cascaded through multiple intermodal SBS processes in the multimode microresonator, where the cascaded process between backward SBS and forward SBS (pump-BSBL-FSBL) provides a route towards additional noise squeezing, rendering the FSBL phase noise to be -120 dBc/Hz at 1 MHz offset frequency. Furthermore, we demonstrate Brillouin-Kerr soliton from a high-order BSBL, which also coexists with FSBLs. Our experimental results show the potential of MMF FP microresonator as an ideal testbed for high-dimensional nonlinear cavity dynamics and laser source with ultrahigh coherence, benefitting critical applications such as acoustic and optical signal generation, processing, and sensing.
A validated restriction enzyme ddPCR cg05575921 (AHRR) assay to accurately assess smoking exposure
Authors: Fitzgerald Sandra , Bhat Basharat , Print Cristin , Jones Gregory
Published: September 2023

Background & Methods: In this study, a novel restriction enzyme (RE) digestion-based droplet digital polymerase chain reaction (ddPCR) assay was designed for cg005575921 within the AHRR gene body and compared with matching results obtained by bisulfite conversion (BIS) ddPCR and Illumina DNA methylation array.
Results: The RE ddPCR cg05575921 assay appeared concordant with BIS ddPCR (r2=0.94, P<0.0001) and when compared with the Illumina array, had significantly better smoking status classification performance for current versus never smoked (AUC 0.96 versus 0.93, P<0.04) and current versus ex-smoker (AUC 0.88 versus 0.83, P<0.04) comparisons.
Conclusions: The RE ddPCR cg05575921 assay accurately predicts smoking status and could be a useful component of ‘precision-medicine’ chronic disease risk screening tools.
Nitrogen Management for Optimum Potato Yields and Low Environmental Impact in Northwest China
Authors: Yang Haibo , Di Yunfei , Zhang Hailin , Li Fei
Published: September 2023

Understanding the changes in nitrate nitrogen (NO3−-N) content in the rooting zone is crucial for reducing nitrate leaching and improving nitrogen (N) use efficiency. The main objective of this study was to investigate the effects of N management strategies on NO3−-N dynamics in the main root zone (0–60 cm) at critical growth stages of drip-irrigated potatoes and to quantify the retention capacity of NO3−-N at harvest in an intensive potato cropping system. Three field experiments with no N application (CK), optimized management (OM) based on a realistic yield goal and soil mineral N content (Nmin) and farmer practice (FP) for three potato cultivars were conducted in Inner Mongolia of Northwest China from 2014 to 2016. A total of 52 farmers with over 3000 hectares of potato fields were also investigated at harvest. The results showed that OM treatment improved N use efficiency and reduced the environmental risk of N loss while ensuring potato yields. Overusing N fertilizer in farmer fields was common, but these N fertilizers only caused a temporary accumulation of NO3−-N during the growing season, then was reduced to the same level as the optimal treatment at harvest. The NO3−-N retention was about 70 kg ha− 1 at harvest in the drip-irrigated potatoes with higher yield and the data from farmers’ fields confirmed the universality of the NO3−-N retention content. Although retentional NO3−-N content in the main root zone at harvest was similar between FP and OM, over-application of N and additional leaching loss from FP were observed. The characteristics of soil NO3−-N accumulation in the root zone of drip-irrigated potatoes help to improve management strategies to maximize potato yield while minimizing environmental risks due to N fertilization.
Deep Learning based Automatic Image Annotation System for Image Retrieval with Arabic language
Authors: Al-Shammary Ali Abbas , Zaghden Nizar , Bouhlel Med Salim
Published: September 2023

Social media platforms like YouTube, Twitter, and Facebook have grown into new modalities of communication, allowing a great number of individuals to interact and learn. Furthermore, many social media users currently produce and share incorrect thoughts and images that are not accompanied by words. The automated generation of any text for raw photos is a difficult operation, particularly when working with Arabic and a limited amount of training samples. To tackle this challenge, smart technology and deep learning technology have been offered. The method employs a bi-level architecture, which allows for the use of self-supervision to produce rotation variants in order to increase the number of training samples. This, in turn, enhances the variability of the model representation and enables the investigation of high-level object information for more detailed picture production. GoogleNet model automatically overcomes the stability issues associated with parsing and synthesising any picture. The proposed technique makes use of deep learning technology to explain images received from the internet environment and gather information about the existence of identified items in order to create an optimal detection method that does not interfere with the deep learning process.
Impact of HER2-low status for patients with early-stage breast cancer and non-pCR after neoadjuvant chemotherapy: A National Cancer Database Analysis
Authors: Li Huiyue , Plichta Jennifer K. , Li Kan , Jin Yizi , Thomas Samantha M. , Ma Fei , Tang Li , Wei Qingyi , He You-Wen , Chen Qichen , Guo Yuanyuan , Liu Yueping , Zhang Jian , Luo Sheng
Published: September 2023

Purpose
To investigate potential differences in pathological complete response (pCR) rates and overall survival (OS) between HER2-low and HER2-zero patients with early-stage hormone receptor (HR)-positive and triple-negative breast cancer (TNBC), in the neoadjuvant chemotherapy setting.
Methods
We identified early-stage invasive HER2-negative BC patients who received neoadjuvant chemotherapy diagnosed between 2010 and 2018 in the National Cancer Database. HER2-low was defined by immunohistochemistry (IHC) 1 + or 2 + with negative in-situ hybridization, and HER2-zero by IHC0. All the methods were applied separately in the HR-positive and TNBC cohorts. Logistic regression was used to estimate the association of HER2 status with pCR (i.e., ypT0/Tis and ypN0). Kaplan-Meier method and Cox proportional hazards model were applied to estimate the association of HER2 status with OS. Inverse probability weighting and/or multivariable regression were applied to all analyses.
Results
For HR-positive patients, 70.9% (n = 17,934) were HER2-low, whereas 51.1% (n = 10,238) of TNBC patients were HER2-low. For both HR-positive and TNBC cohorts, HER2-low status was significantly associated with lower pCR rates [HR-positive: 5.0% vs. 6.7%; weighted odds ratio (OR) = 0.81 (95% CI: 0.72–0.91), P < 0.001; TNBC: 21.6% vs. 24.4%; weighted OR = 0.91 (95% CI: 0.85–0.98), P = 0.007] and improved OS [HR-positive: weighted hazard ratio = 0.85 (95% CI: 0.79–0.91), P < 0.001; TNBC: weighted hazard ratio = 0.91 (95% CI: 0.86–0.96), P < 0.001]. HER2-low status was associated with favorable OS among patients not achieving pCR [HR-positive: adjusted hazard ratio = 0.83 (95% CI: 0.77–0.89), P < 0.001; TNBC: adjusted hazard ratio = 0.88 (95% CI 0.83–0.94), P < 0.001], while no significant difference in OS was observed in patients who achieved pCR [HR-positive: adjusted hazard ratio = 1.00 (95% CI: 0.61–1.63), P > 0.99; TNBC: adjusted hazard ratio = 1.11 (95% CI: 0.85–1.45), P = 0.44].
Conclusion
In both early-stage HR-positive and TNBC patients, HER2-low status was associated with lower pCR rates. HER2-zero status might be considered an adverse prognostic factor for OS in patients not achieving pCR.
Safety Netting Advice for Acutely Ill Children Presenting to Ambulatory Care: Exploring Parents’ Opinions, Ideas, and Expectations Through Focus Group Interviews
Authors: Burvenich Ruben , Heytens Stefan , Bos David AG , Roy Kaatje Van , Struyf Thomas , Toelen Jaan , De Sutter An , Verbakel Jan Y
Published: September 2023

Background. Safety netting advice is an essential component of the management of acutely ill children, yet an international consensus definition is lacking. More research on parents’ ideas about safety netting advice is needed to develop a broadly supported definition. In this study we aimed to explore the perspectives of Belgian parents about safety netting advice for their acutely ill child(ren) presenting to ambulatory care.Methods . We conducted focus groups with Belgian parents of children 6 months to 12 years old who were recruited through maximum variation sampling. We transcribed the interviews verbatim. Using a combination of inductive and deductive ‘in vivo’ coding we distilled themes from the data. As per the Grounded Theory approach, we reiterated between data collection, coding, and analysis. After participant validation of provisional themes, we constructed the final thematic framework.Results. Through six focus groups with 30 parents, we identified five themes: (1) Relevant background information; (2) To know what to expect, what to look out for; (3) Instructions on child homecare and when to revisit a physician; (4) Physicians who consider parents’ perspectives and contexts; (5) A reliable source that provides safety netting advice only when necessary, possibly in a multimodal way.Conclusions. Our findings highlight the importance of clear and tailored background information and instructions from a reliable source on what to expect and what to look out for and what to do next when the child’s situation worsens. Our results can serve as an evidence base for further research into defining safety netting advice.
Investigation Diagnostic Gene Markers and Immune Infiltration in Idiopathic Pulmonary Fibrosis
Authors: sun shuang , Zhong diansheng
Published: September 2023

Objective: Idiopathic pulmonary fibrosis (IPF) is a difficult to cure and low survival lung disease, and the pathogenesis has not been elucidated clearly. This study is to explore the potential hub genes in IPF and explore their role in the progression of IPF with immune cell infiltration, providing evidence support for potential diagnostic markers and targets of IPF.
Method: Download the dataset GSE10667 from the GEO database to identify differentially expressed genes (DEG) between IPF patients and the normal population. Exploring hub genes related to IPF using differential expression analysis and Weighted correlation network analysis (WGCNA). Establish a Nomogram model and ROC (Receiver Operating Characteristic) curve to evaluate the diagnostic effectiveness of hub genes. Apply Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway-based enrichment analysis to explore the potential roles of these hub genes. Discover key networks of genes in protein level by Protein-Protein Interaction Networks (PPI) networks. And investigate the relationship between key gene MMP2(metallopeptidase 2) and immune infiltration. Finally, based on Genome-wide association study (GWAS), a Mendelian randomization study was conducted to determine the causal relationship between MMP2 and IPF.
Result:A total of 486 DEGs were identified in IPF patients. Gene co expression network was established by WGCNA to screen the highest correlation module. And The genes in it were mainly enriched in extracellular matrix （ECM ）formation, cell aging, endoplasmic reticulum stress, and metalloproteinase activation signaling pathways. Cross the genes in the DEG related modules with WGCNA traits to obtain the core hub genes. Then, key genes COL1A1, COL3A1, COL1A2, POSTN, MMP2 were found through the PPI. The nomogram was established to verify the risk of disease occurrence, and the ROC was applied to demonstrate the accuracy of the model and shows that five hub genes are potential biomarkers for IPF. Finally, we selected MMP2 and found a causal relationship with the occurrence and prognosis of IPF through Mendelian randomization (MR)studies, as well as immune cell infiltration in IPF.
Conclusion: We have identified the pivot gene MMP2 associated with IPF, which may play a key role in the progression of IPF. And may play an significant role in the pre symptom diagnosis of IPF, providing new therapeutic targets, and predicting prognosis.
Variable-length Differential Evolution for Numerical and Discrete Association Rule Mining
Authors: Mlakar Uroš , Fister Iztok , Fister Iztok
Published: September 2023

This paper proposes a variable-length Differential Evolution for Association Rule Mining. The proposed algorithm includes a novel representation of individuals, which can encode both numerical and discrete attributes in their original or absolute complement of the original intervals. The fitness function used is comprised of a weighted sum of Support and Confidence Association Rule Mining metrics. The proposed algorithm was tested on fourteen publicly available, and commonly used datasets from the UC Irvine Machine Learning Repository. It is also compared to the nature inspired algorithms taken from the NiaARM framework, providing superior results. The implementation of the proposed algorithm follows the principles of Green Artificial Intelligence, where a smaller computational load is required for obtaining promising results, and thus lowering the carbon footprint.
Evaluation of clustering-based differential expression analysis methods for RNA-seq data
Authors: Makino Manon , Shimizu Kentaro , Kadota Koji
Published: September 2023

Background
RNA-seq is a tool for measuring gene expression and is commonly used to identify differentially expressed genes (DEGs). Gene clustering has been widely used to classify DEGs with similar expression patterns, but rarely used to identify DEGs themselves. We recently reported that the clustering-based method (called MBCdeg) for identifying DEGs has great potential. However, a thorough investigation of its feasibility is still needed.
Results
We compared a total of six competing methods: three conventional R packages (edgeR, DESeq2, and TCC) and three versions of MBCdeg (denoted as MBCdeg1, 2, and 3) corresponding to three different normalization algorithms. Different scenarios of simulated data generated from three R packages (TCC, compcodeR, and PROPER) were mainly evaluated based on the area under the receiver operating characteristic curve (AUC) as a measure for both sensitivity and specificity. We found that the modified version of MBCdeg2 performed well for many scenarios on simulated data. However, MBCdeg showed very unstable results between trials for identical real data.
Conclusions
The current MBCdeg2 shows excellent performance in simulation analysis, but not at a practical level for real data. Since further improvements are needed for MBCdeg to reach a practical level, we cannot recommend the use of the current MBCdeg. Our report suggests not only the need for method developers to carefully describe their shortcomings, but also the need for the reader to critically decipher the conclusions reached under what conditions.
A Comparative Analysis of Using Ensemble Trees for Botnet Detection and Classification in IoT
Authors: Saied Mohamed , GUIRGUIS SHAWKAT , Madbouly Magda
Published: September 2023

Enhancing IoT security is a corner stone for building trust in its technology and driving its growth. Limited resources and diversified nature of IoT devices make them vulnerable to attacks. Botnet attacks compromise the IoT systems and can pose significant security challenges. Numerous investigations have utilized machine learning and deep learning techniques to identify botnet attacks in IoT. However, achieving high detection accuracy with reasonable computational requirements is still a challenging research considering the particularity of IoT. This paper aims to analytically study the performance of the tree based machine learning in detecting botnet attacks for IoT ecosystems. Through an empirical study performed on a public botnet dataset of IoT environment, basic decision tree algorithm in addition to ensemble learning of different bagging and boosting algorithms are compared. The comparison covers two perspectives: IoT botnet detection capability and computational performance. Results demonstrated that the significant potential for the tree based ML algorithms in detecting network intrusions in IoT environments. The RF algorithm achieved the best performance for multi-class classification with accuracy rates of 0.999991 respectively. It achieved also the highest results in all other measures.
Highly sensitive acetone gas sensor based on gold nanoparticles modified W18O49 porous polymeric spheres
Authors: Zhang Ke , Zhu Pengdang , Li Yunsheng , Wei Hang , Zhang Ruiyu
Published: September 2023

A two-step solvothermal approach was used to create porous polymeric spheres of W18O49 modified with gold nanoparticles. Various characterizations of the material were carried out by XRD, SEM, etc., and the results show that the material is highly crystalline and the surface has a porous nature, in addition, the addition of gold substantially improves the adsorbed oxygen content. The results of the gas sensitivity test showed that the gold nanoparticle-modified W18O49 porous polymeric spheres showed a significant improvement in performance compared to pure W18O49. The gold nanoparticle-modified W18O49 porous polymeric spheres demonstrated an increased reaction value to 100 ppm acetone at a lower temperature of 220 °C (S=66, 2.57 times that of the pure material), a quick response/recovery time (5s/12s), as well as strong selectivity and stability. W18O49 porous polymeric spheres enhanced with gold nanoparticles have good potential for acetone gas detection and are likely to be used in high-performance sensors.
The mRNA content of plasma extracellular vesicles provides a window into the brain during cerebral malaria disease progression
Authors: Abdi Abdirahman , Mwikali Kioko , Mwangi Shaban , Pance Alena , Ochola-Oyier Lynette , Kariuki Symon , Newton Charles , Bejon Philip , Rayner Julian
Published: September 2023

The impact of cerebral malaria on the transcriptional profiles of cerebral tissue is difficult to study using non-invasive approaches. We isolated plasma extracellular vesicles (EVs) from patients with cerebral malaria and community controls and sequenced their RNA content. Deconvolution of the tissue origins of the EV-RNA revealed that EVs from cerebral malaria patients are predominantly enriched in transcripts of brain origin. Next, we used manifold learning on the EV-RNAseq data to determine pseudotime against the community control samples as the baseline reference. We found that neuronal transcripts in plasma EVs decreased as pseudotime progressed, while transcripts of glial, endothelial, and immune cell origins increased over pseudotime. Pseudotime was associated with clinicopathological parameters of disease severity, including retinopathy, metabolic acidosis, respiratory rate, anaemia, malnutrition, depth of unconsciousness and death. Plasma EVs further provided evidence of platelet activation, TNF signalling, neurotrophin signalling, long-term potentiation and glutamatergic signalling during late disease stages of cerebral malaria. The transcriptional responses of cerebral tissue in cerebral malaria can be studied non-invasively using EVs circulating in peripheral blood.
How common is otogenic meningitis? A retrospective study in southern Sweden over 18 years
Authors: Bjar Nora , Hermansson Ann , Gisselsson-Solen Marie
Published: September 2023

Background
Bacterial meningitis is a rare, but life-threatening disease, which sometimes occurs as a complication to acute otitis media (AOM). The proportion of meningitis cases originating from AOM is not clear.
Purpose
The aim of this study was to investigate the proportion of meningitis cases caused by AOM, to compare risk factors, bacteriology and outcome between otogenic and non-otogenic meningitis, and to analyse the incidence of bacterial meningitis after the introduction of conjugate pneumococcal vaccines (PCV).
Methods
The medical charts of all patients admitted to hospitals in southern Sweden with bacterial meningitis between 2000 and 2017 were retrieved. Based on otoscopy and/or imaging, the proportion of otogenic meningitis cases was calculated, as were annual incidences.
Results
A total of 216 patients were identified, 25 of whom died. The proportion of otogenic meningitis was 31% but varied from 6% among teenagers to 40% among adults. Before PCV, 23% of meningitis cases were children < 2 years, compared to 1% post-PCV. The average incidence in the adult population, on the other hand, increased post-PCV, though there were large annual variations. S. pneumoniae was the most commonly identified pathogen in everyone but teenagers, in whom N. meningitidis was predominant.
Conclusion
AOM is an important cause of meningitis in children and adults. Though bacterial meningitis almost disappeared in children < 2 years after the introduction of PCV, the incidence of pneumococcal meningitis in adults seems to have increased.
Enhancing Wheat (Triticum aestivum L.) Crop Yield and Water Use Efficiency: A Study on Canopy Air Temperature Difference-Based Drip Irrigation Scheduling in a Semi-Arid Region of Western India
Authors: Patel R. J. , Rank P. H. , Vekariya P. B. , Rank H. D. , Vadar H. R. , Parmar H. V. , Tiwari M. K. , Marviya P. B. , Lunagaria M. M.
Published: September 2023

This study addresses efficient water usage in wheat cultivation in a semi-arid region of India with clay loam soil and an increasing water supply-demand gap. It focuses on optimizing drip irrigation (DI) scheduling, of wheat crops, based on canopy air temperature difference (CATD) using the crop water stress index (CWSI). The field experiments were conducted for two winter seasons, employing high-discharge drip irrigation (DI) on wheat crop (variety - GW 366) at Junagadh Agricultural University (JAU), Gujarat, India. The experiment had nine treatments, each replicated three times in randomized blocks. The DI treatments labeled as T1 to T6, were irrigated at CATD values of -4, -3, -2, -1, 0, and 1 °C, respectively.. While T7 were irrigated by border irrigation. In order to define upper and lower baselines of CWSI, well watered treatments (T8) and extreme dry treatment (T9) DI were considered. The drip irrigation system (DIS) had an application rate of 7.78 mm/h with a uniformity coefficient of 90.40%. Compared to surface irrigation, DI resulted in water savings ranging from 3.52% (T1) to 43.24% (T6). Using real-time CATD data, the theoretical CWSI (CWSITh) and the vapor pressure deficit (VPD) based semi-empirical CWSI (CWSIVPD) were calculated as 0.3351 and 0.3668, respectively. CATD values showed significant variation in CWSI across treatments. The CWSI demonstrated sensitivity to water stress during critical growth stages. The study identified an optimal CATD of -1 °C, yielding 36.48% higher crop yield (4744 kg/ha), 30.23% water savings (388.42 mm), and notable 95.67% more water use efficiency (12.21 kg/ha-mm,), surpassing the outcomes of border irrigation (3476 kg/ha, 556.74 mm and 6.24 kg/ha-mm). These findings hold significant implications for farmers and policymakers, effectively addressing food and water security concerns. The study underscores the efficiency of DI combined with CATD-based irrigation scheduling in optimizing wheat crop performance. In the context of critical water management, this research provides essential insights for sustainable agricultural practices.
Unpredictable, sudden-onset bleeding in deer mice (Peromyscus maniculatus bairdii) after oral exposure to a gut-sterilising antibiotic cocktail
Authors: Stoppel Heike , Harvey Brian , Minnaar Nico , Venter Kobus , Bester Cor , Wolmarans De Wet
Published: September 2023

Background: Animal models are valuable tools to investigate contributions of the gut microbiota to human disorders. Deer mice are studied for their expression of obsessive-compulsive-like behaviour, which has recently been associated with gut dysbiosis in this model. To this end, sterilisation of the gut microbiota by means of orally administered antibiotic cocktails, is a common procedure when studying the pathological role of dysbiosis.
Methods: In this case report, we refer to six unexpected mortalities after exposing 26 adult deer mice (Peromyscus maniculatus bairdii) of both sexes to a gut sterilising regimen that consisted of ampicillin, vancomycin, imipenem, gentamycin, and amphotericin B.
Results and conclusion: We recorded fatal bleeding episodes in four male and two female mice. While vancomycin is suspected to be the main agent of concern, future studies are needed to divulge the underlying mechanisms that resulted in the reported deaths.
Modular DNA origami compartments for the engineering of a protein unfolding and degradation pathway
Authors: Saccà Barbara , Huang Jing , Jaekel Andreas , Boom Johannes van den , Podlesainski David , Elnagar Manar , Heuer-Jungemann Amelie , Kaiser Markus , Meyer Hemmo
Published: September 2023

Within the cell, chemical reactions are often confined and organized through a modular architecture. This facilitates the targeted localization of molecular species and their efficient translocation to subsequent sites. Here, we present a cell-free nanoscale model that exploits this compartmentalization principle to carry out regulated protein unfolding and degradation. Our model is composed of two connected DNA origami nanocompartments, one containing the protein unfolding machine, p97, and the other housing the protease chymotrypsin. We achieve the unidirectional immobilization of p97, establishing a ‘gateway’ mechanism that controls compartment accessibility and directionality of substrate processing. Our data show that, whereas spatial confinement increases the reaction rate of each individual enzyme, their physical connection into a chimera further improves their performance, minimizing off-target proteolysis. We anticipate that our modular approach may serve as a blueprint for reshaping biocatalytic pathways and stimulating the creation of nanofactories with capabilities beyond those observed in natural systems.
Rapid proton diffusion in heavily Sc-doped soft perovskite oxides
Authors: Tsujikawa Kota , Hyodo Junji , Fujii Susumu , Takahashi Kazuki , Kasamatsu Shusuke , Yamazaki Yoshihiro
Published: September 2023

Advances in electrochemical devices have been primarily driven by the discovery and development of electrolyte materials. However, finding an electrolyte that exhibits both high ionic conductivity and chemical and electrochemical stability remains a significant challenge. Here, we developed such an electrolyte with heavily Sc-doped BaSn0.3Sc0.7O3H0.66. The resulting proton conductivities in BaSn0.3Sc0.7O3H0.66 and BaTi0.2Sc0.8O3H0.74 exceed 0.01 Scm−1 at 300°C. The former maintains chemical stability for over 360 h under 0.98 atm of humidified CO2 and electrochemical stability for over 100 h during fuel cell operation, with a theoretical overpotential of 1.194 V and proton conductivity of 0.01 Scm−1 at 300°C. Heavy Sc doping into perovskites reduces the activation energy for proton diffusion, probably due to reduced proton trapping. Screening for softer oxides with maximum Sc solubility is a promising strategy for developing fast and stable proton-conducting electrolytes capable of operating at 300°C.
Contrasting patterns of DNA damage in rural workers from central Brazil: what may account for the geographical variation in genotoxicity following occupational exposure to pesticides?
Authors: Nascimento Felipe de Araújo , Ramos Jheneffer Sonara Aguiar , Pedroso Thays Millena Alves , Godoy Fernanda Ribeiro , Souza Murilo Mendonça Oliveira , Parise Michelle Rocha , Silva Daniela Melo
Published: September 2023

In recent years, the use of pesticides has intensified worldwide, and many countries have tended to neglect the potential toxic effects associated with the indiscriminate use of these substances. Many diseases, such as Hodgkin’s lymphoma, lung and prostate cancer, and autoimmune disorders, have been linked to the use of pesticides. The present study compared the DNA damage observed in rural workers from five different areas of the central Brazilian state of Goiás. We attempted to identify the factors that influence the patterns of genotoxicity found in 367 rural workers from the municipalities of Goiânia, Rio Verde, Montividiu, Jatai, and Silvânia. The DNA damage was assessed using comet assays, and the results were compared with the data on epidemiological variables, behavioral parameters, and the types of pesticide used. Significant variation was found in the level of DNA damage in rural workers from different municipalities, although no clear differences were observed in demographic or behavioral parameters. All the different classes of pesticides were related to similar levels of DNA damage, which indicates that other factors may be influencing the differences observed among the populations. A positive correlation was found between the level of DNA damage and the number of pesticides used per individual, which suggests potential synergistic effects of pesticide mixtures, which may enhance the risk of DNA damage. Rural workers from Goiânia and Silvania presented the highest levels of DNA damage. In addition to the quantity of pesticides and the synergistic effects of mixtures, the results of the present study would appear to point to genetic polymorphisms in detoxification genes (e.g., OGG1 and XRCC), which may determine variation in the general susceptibility of the different populations to DNA damage. This emphasizes the need for further research on the possible variation in genetic factors in the different groups of rural workers.
The Effect of Fear of COVID-19 on Luxury Consumption Tendency and the Role of Materialism
Authors: Kurnaz Aysel
Published: September 2023

The purpose of this study is to assess the impact of COVID-19 fear on people’s luxury consumption tendencies and the role of materialism in mediating the effect of COVID-19 fear on people’s luxury consumption tendencies. The theory of psychological reactance (TPR) serves as the theoretical foundation for this work. TPR explains why people are so motivated to regain their freedom when their ability to perform a specific action is threatened or hampered. Panic behaviours triggered by anxiety, fear, and uncertainty were observed in almost every society at the start of the pandemic, and people tended to purchase food and hygiene products, particularly those required for survival. Consumers who gained the freedom to purchase goods or services from stores that opened as a result of the relaxation of restrictions immediately following the pandemic period turned to luxury goods in search of "compensation". When the pandemic rules are initially relaxed, consumers’ "luxury consuming" behaviour/freedom is restricted due to the COVID-19 pandemic, leading to "revenge buying". Based on the TPR, it is assumed that the COVID-19 fear of consumers following extraordinary processes such as pandemics may have a positive effect on their luxury consumption tendencies in this study. The online questionnaire technique was used in the study to collect data. Data were gathered from 845 adults aged 18 and up who volunteered to participate in the study in Turkey. Confirmatory factor analysis and structural equation modelling (SEM) were used to analyse the data for the measurement model and hypothesis testing in the study. The study’s findings show that COVID-19 fear has a significant and positive effect on the desire to consume luxury goods. Furthermore, materialism plays an important and positive mediating role in the influence of fear of COVID-19 on the tendency to consume luxury goods. While this study contains cultural relics of luxury consumption tendencies, it also provides critical insights into consumer luxury tendencies in the aftermath of COVID-19. It is critical to evaluate various elements that may influence luxury consumption tendencies to analyse the effects of comparable processes that may be experienced by future consumers.