bluuebunny/crossref_metadata_2025_split huggingface dataset:
Baseline gene signatures of reactogenicity to Ebola vaccination: a machine learning approach across multiple cohorts
Authors: Gonzalez Dias Carvalho Patrícia Conceição , Dominguez Crespo Hirata Thiago , Mano Alves Leandro Yukio , Moscardini Isabelle Franco , do Nascimento Ana Paula Barbosa , Costa-Martins André G. , Sorgi Sara , Harandi Ali M. , Ferreira Daniela M. , Vianello Eleonora , Haks Mariëlle C. , Ottenhoff Tom H. M. , Santoro Francesco , Martinez-Murillo Paola , Huttner Angela , Siegrist Claire-Anne , Medaglini Donata , Nakaya Helder I. 
Published: November 2023

IntroductionThe rVSVDG-ZEBOV-GP (Ervebo®) vaccine is both immunogenic and protective against Ebola. However, the vaccine can cause a broad range of transient adverse reactions, from headache to arthritis. Identifying baseline reactogenicity signatures can advance personalized vaccinology and increase our understanding of the molecular factors associated with such adverse events.MethodsIn this study, we developed a machine learning approach to integrate prevaccination gene expression data with adverse events that occurred within 14 days post-vaccination.Results and DiscussionWe analyzed the expression of 144 genes across 343 blood samples collected from participants of 4 phase I clinical trial cohorts: Switzerland, USA, Gabon, and Kenya. Our machine learning approach revealed 22 key genes associated with adverse events such as local reactions, fatigue, headache, myalgia, fever, chills, arthralgia, nausea, and arthritis, providing insights into potential biological mechanisms linked to vaccine reactogenicity.
No causal effect of genetically determined circulating homocysteine levels on psoriasis in the European population: evidence from a Mendelian randomization study
Authors: Chen Chaojian , Liu Shuo , Liu Junhao , Zheng Ziqi , Zheng Yixi , Lin Zhongliang , Liu Yuchun 
Published: November 2023

BackgroundAlthough numerous studies demonstrated a link between plasma homocysteine (Hcy) levels and psoriasis, there still exists a certain level of controversy. Therefore, we conducted a Mendelian randomization study to investigate whether homocysteine plays a causative role in the development or exacerbation of psoriasis.MethodsA two-sample Mendelian randomization (MR) analysis was conducted. Summary-level data for psoriasis were acquired from the latest R9 release results from the FinnGen consortium (9,267 cases and 364,071 controls). Single nucleotide polymorphisms (SNPs) robustly linked with plasma Hcy levels at the genome-wide significance threshold (p &lt; 5 × 10−8) (18 SNPs) were recognized from the genome-wide meta-analysis on total Hcy concentrations (n = 44,147 participants) in individuals of European ancestry. MR analyses were performed utilizing the random-effect inverse variance-weighted (IVW), weighted median, and MR-Egger regression methods to estimate the associations between the ultimately filtrated SNPs and psoriasis. Sensitivity analyses were conducted to evaluate heterogeneity and pleiotropy.ResultsMR analyses revealed no causal effects of plasma Hcy levels on psoriasis [IVW: odds ratio (OR) = 0.995 (0.863–1.146), p = 0.941; weighed median method: OR = 0.985 (0.834–1.164), p = 0.862; MR-Egger regression method: OR = 0.959 (0.704–1.305), p = 0.795]. The sensitivity analyses displayed no evidence of heterogeneity and directional pleiotropy, and the causal estimates of Hcy levels were not influenced by any individual SNP.ConclusionOur study findings did not demonstrate a causal effect of genetically determined circulating Hcy levels on psoriasis.
Diagnostic and prognostic values of conjunctival and oral biopsies analyzed by direct immunofluorescence in patients with mucous membrane pemphigoid
Authors: Jakubowska Beata , Pietrzyk Ewelina , Maciejewicz Piotr , Kowalewski Cezary , Wozniak Katarzyna 
Published: November 2023

IntroductionMucous membrane pemphigoid (MMP) is diagnosed on the basis of a characteristic clinical picture (a predilection for mucosal involvement and scarring in the affected tissues) and a positive direct immunofluorescence (DIF) result.MethodsIn this study, we compare the diagnostic and prognostic values of conjunctival and oral biopsies analyzed by DIF in patients with MMP. Sixteen patients with MMP and mucosal involvement as a predominant symptom were classified into three groups based on the clinical picture. Oral and conjunctival DIF were performed on all patients.ResultsOur study showed that patients with simultaneous oral and conjunctival involvement had a positive oral DIF in 83% and a positive ocular DIF in 100% of the examined cases, respectively. Patients with isolated ocular MMP had a positive oral DIF in 50% and a positive ocular DIF in 66% of the examined cases, respectively. Patients with only oral involvement with MMP had a positive oral DIF in 100% and a positive ocular DIF in 50% of the examined cases, respectively.DiscussionOral biopsy should be performed first and is usually sufficient for the diagnosis, even in patients with exclusively ocular MMP, whereas in patients without clinical ocular involvement, ocular DIF is positive in half of the cases and may be a predictive factor for ocular lesions in the future.
Willow (Salix spp.) bark hot water extracts inhibit both enveloped and non-enveloped viruses: study on its anti-coronavirus and anti-enterovirus activities
Authors: Reshamwala Dhanik , Shroff Sailee , Liimatainen Jaana , Tienaho Jenni , Laajala Mira , Kilpeläinen Petri , Viherä-Aarnio Anneli , Karonen Maarit , Jyske Tuula , Marjomäki Varpu 
Published: November 2023

IntroductionRecurring viral outbreaks have a significant negative impact on society. This creates a need to develop novel strategies to complement the existing antiviral approaches. There is a need for safe and sustainable antiviral solutions derived from nature.ObjectiveThis study aimed to investigate the antiviral potential of willow (Salix spp.) bark hot water extracts against coronaviruses and enteroviruses. Willow bark has long been recognized for its medicinal properties and has been used in traditional medicines. However, its potential as a broad-spectrum antiviral agent remains relatively unexplored.MethodsCytopathic effect inhibition assay and virucidal and qPCR-based assays were used to evaluate the antiviral potential of the bark extracts. The mechanism of action was investigated using time-of-addition assay, confocal microscopy, TEM, thermal, and binding assays. Extracts were fractionated and screened for their chemical composition using high-resolution LC-MS.ResultsThe native Salix samples demonstrated their excellent antiviral potential against the non-enveloped enteroviruses even at room temperature and after 45 s. They were equally effective against the seasonal and pandemic coronaviruses. Confocal microscopy verified the loss of infection capacity by negligible staining of the newly synthesized capsid or spike proteins. Time-of-addition studies demonstrated that Salix bark extract had a direct effect on the virus particles but not through cellular targets. Negative stain TEM and thermal assay showed that antiviral action on enteroviruses was based on the added stability of the virions. In contrast, Salix bark extract caused visible changes in the coronavirus structure, which was demonstrated by the negative stain TEM. However, the binding to the cells was not affected, as verified by the qPCR study. Furthermore, coronavirus accumulated in the cellular endosomes and did not proceed after this stage, based on the confocal studies. None of the tested commercial reference samples, such as salicin, salicylic acid, picein, and triandrin, had any antiviral activity. Fractionation of the extract and subsequent MS analysis revealed that most of the separated fractions were very effective against enteroviruses and contained several different chemical groups such as hydroxycinnamic acid derivatives, flavonoids, and procyanidins.ConclusionSalix spp. bark extracts contain several virucidal agents that are likely to act synergistically and directly on the viruses.
Redox imbalance in patients with heart failure and ICD/CRT-D intervention. Can it be an underappreciated and overlooked arrhythmogenic factor? A first preliminary clinical study
Authors: Szyller Jakub , Antoniak Radosław , Wadowska Katarzyna , Bil-Lula Iwona , Hrymniak Bruno , Banasiak Waldemar , Jagielski Dariusz 
Published: November 2023

Introduction: Redox imbalance and oxidative stress are involved in the pathogenesis of arrhythmias. They also play a significant role in pathogenesis of heart failure (HF). In patients with HFand implanted cardioverter-defibrillator (ICD) or cardiac resynchronization therapy defibrillator (CRT-D), the direct current shocks may be responsible for additional redox disturbances and additionally increase arrhythmia risk. However, the precise role of oxidative stress in potentially fatal arrhythmias and shock induction remains unclear.Methods: 36 patients with diagnosed HF and implanted ICD/CRT-D were included in this study. Patients were qualified to the study group in case of registered ventricular arrhythmia and adequate ICD/CRT-D intervention. The control group consisted of patients without arrhythmia with elective replacement indicator (ERI) status. Activity of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), glutathione (GSH) in erythrocyte (RBC), SOD, GPx activity and reactive oxygen/nitrogen species (ROS/RNS) concentration in plasma were determined. The values were correlated with glucose, TSH, uric acid, Mg and ion concentrations.Results: In the perishock period, we found a significant decrease in RBC and extracellular (EC) SOD and RBC CAT activity (p = 0.0110, p = 0.0055 and p = 0.0002, respectively). EC GPx activity was also lower (p = 0.0313). In all patients, a decrease in the concentration of all forms of glutathione was observed compared to the ERI group. Important association between ROS/RNS and GSH, Mg, TSH and uric acid was shown. A relationship between the activity of GSH and antioxidant enzymes was found. Furthermore, an association between oxidative stress and ionic imbalance has also been demonstrated. The patients had an unchanged de Haan antioxidant ratio and glutathione redox potential.Conclusion: Here we show significant redox disturbances in patients with HF and ICD/CRT-D interventions. Oxidative stress may be an additional risk factor for the development of arrhythmia in patients with HF. The detailed role of oxidative stress in ventricular arrhythmias requires further research already undertaken by our team.
Mining the Utricularia gibba genome for insulator-like elements for genetic engineering
Authors: Laspisa Daniel , Illa-Berenguer Eudald , Bang Sohyun , Schmitz Robert J. , Parrott Wayne , Wallace Jason 
Published: November 2023

IntroductionGene expression is often controlled via cis-regulatory elements (CREs) that modulate the production of transcripts. For multi-gene genetic engineering and synthetic biology, precise control of transcription is crucial, both to insulate the transgenes from unwanted native regulation and to prevent readthrough or cross-regulation of transgenes within a multi-gene cassette. To prevent this activity, insulator-like elements, more properly referred to as transcriptional blockers, could be inserted to separate the transgenes so that they are independently regulated. However, only a few validated insulator-like elements are available for plants, and they tend to be larger than ideal.MethodsTo identify additional potential insulator-like sequences, we conducted a genome-wide analysis of Utricularia gibba (humped bladderwort), one of the smallest known plant genomes, with genes that are naturally close together. The 10 best insulator-like candidates were evaluated in vivo for insulator-like activity.ResultsWe identified a total of 4,656 intergenic regions with expression profiles suggesting insulator-like activity. Comparisons of these regions across 45 other plant species (representing Monocots, Asterids, and Rosids) show low levels of syntenic conservation of these regions. Genome-wide analysis of unmethylated regions (UMRs) indicates ~87% of the targeted regions are unmethylated; however, interpretation of this is complicated because U. gibba has remarkably low levels of methylation across the genome, so that large UMRs frequently extend over multiple genes and intergenic spaces. We also could not identify any conserved motifs among our selected intergenic regions or shared with existing insulator-like elements for plants. Despite this lack of conservation, however, testing of 10 selected intergenic regions for insulator-like activity found two elements on par with a previously published element (EXOB) while being significantly smaller.DiscussionGiven the small number of insulator-like elements currently available for plants, our results make a significant addition to available tools. The high hit rate (2 out of 10) also implies that more useful sequences are likely present in our selected intergenic regions; additional validation work will be required to identify which will be most useful for plant genetic engineering.
Risk perception and usage of non-occupational post-exposure prophylaxis among fisherfolk in Ggulwe parish on the shores of Lake Victoria in central Uganda
Authors: Bahikire Daraus , Nanyingi Miisa , Atuhairwe Christine , Matama Catherine , Ninsiima Lesley Rose , Bbuye Mudarshiru 
Published: November 2023

BackgroundThe use of non-occupational post-exposure prophylaxis (nPEP) to prevent HIV acquisition among those exposed as an approach to HIV prevention has expanded in Uganda. Although there are increased efforts to avail nPEP services among most at-risk populations, the usage of nPEP medicines remains low. Therefore, this study examined the risk perception and usage of non-occupational post-exposure prophylaxis (nPEP) among fisherfolk in the Ggulwe fishing parish, Bussi sub-county, Wakiso district.MethodsA cross-sectional study among adults was carried out from October 2020 to January 2021 in Ggulwe parish, Bussi sub-county, Wakiso district, to examine the usage of nPEP and factors influencing the usage. Data were collected using semi-structured questionnaires, and key informants' interviews were conducted among healthcare providers and the local leadership. The quantitative data were summarized using bivariate and multivariate logistic regression, while the qualitative data were analyzed thematically to enrich the quantitative results.ResultsOverall, 248 fisherfolk encountered an event that required the use of nPEP, and of these, 55/248 (22.2%) were able to use nPEP to prevent them from acquiring HIV. The usage of nPEP among adults in the Bussi sub-county, Wakiso district, was associated with not knowing that HIV can be prevented using nPEP medicines (AOR:0.1, 95% CI 0.03–0.36, p &lt; 0.001), lack of knowledge of the existence of nPEP (AOR: 0.3, 95% CI 0.13–0.76, p = 0.01), the perception that nPEP can effectively prevent HIV infection after exposure (AOR 0.0586, 95% CI: 0.0177–0.1944, p &lt; 0.001), and the community's opinion affecting the willingness to take nPEP (AOR 0.1924, 95% CI: 0.0380–0.9727, p = 0.0462).ConclusionThe usage of nPEP among fisherfolk was low (22.2%). The low usage of nPEP was associated with a lack of knowledge and awareness about nPEP. This effort to improve the usage of nPEP should include community sensitization and HIV infection prevention using nPEP to raise awareness about HIV infection exposures and the risk of HIV infection during non-occupational exposures.
Regional and epidemiological characteristics of tuberculosis and treatment outcomes in West China
Authors: Wang Qiaolan , Zhu Jiangchuan , Zhang Luoning , Xie Linshen 
Published: November 2023

ObjectiveTo understand the prevalence and treatment outcome of tuberculosis in a typically regional County from 2016 to 2021, so as to provide reference and basis for the prevention and treatment of tuberculosis in this area.MethodsDescriptive epidemiological methods were used to analyze the population, time and location distribution of pulmonary tuberculosis in Dazhu County from 2016 to 2021. The incidence rates were compared by Chi-square test and trend test, time distribution combined with seasonal index analysis, and the test level was α = 0.05.ResultsA total of 2,899 cases of pulmonary tuberculosis were reported in Dazhu County from 2016 to 2021, with an average annual incidence rate of 44.29/100,000 and standardized reported incidence rate was 36.77/100,000, showing a downward trend year by year (χ2 trend = 124.629, p &lt; 0.001). A total of 955 cases of pathogen positive were reported, showing an increasing trend year by year (χ2 trend = 59.773, p &lt; 0.001). In terms of time distribution, the incidence rate was high in autumn and winter, and September and December were the peak of the disease in the whole year, and the overall trend increased first, then decreased and once again increased (F = 5.861, p &lt; 0.05). In regional distribution, the highest annual average reported incidence rate was in concentrated population. The incidence rate of male was higher than female in population distribution. After standardization, the overall incidence rate increased from 34 to 45 years old (χ2 trend = 6963.101, p &lt; 0.001), and decreased after 45 years old (χ2 trend = 1104.393, p &lt; 0.001). The occupation distribution is mainly farmers (82.75%). The overall arrival rate and cure rate of patients showed an upward trend year by year (χ2 trend = 4.306, χ2 trend = 5.772, p &lt; 0.001).ConclusionThe incidence rate of pulmonary tuberculosis in this regional county is decreasing year by year. Male patients are higher than female patients and have certain seasonal characteristics. Attention should be paid to male, older adult, farmers and other groups, and corresponding measures should be taken to strengthen the prevention and treatment of tuberculosis in high incidence areas.
Governance of the business environment based on food safety disputes: empirical analysis based on the case of “Cordyceps sinensis”
Authors: Sun Jiangjie , Li Limin , Li Hui , Liu Tong , Deng Jianyi , Zhang Tingting , Li Junhao , You Jinliang , Zhang Liping 
Published: November 2023

IntroductionThe use of the fungus Cordyceps sinensis (CS), which has a long history of use in China for its tonic properties, has sparked controversy based on the risk from high arsenic levels in CS.MethodsThis study collected all 24 online dispute cases related to CS from the China Legal Documents Network. Excel software was applied to fit the distribution of the sample data and analyze the trend of trial results of CS disputes and the tendency of professional claims trials. The analysis covers the trend of trial results of contract dispute cases involving CS products (CDCCS), and the tendency of the results of CDCCS, using correlation to analyze the factors influencing the results. We analyzed trial tendencies in CDCCS by the methods of complex network analysis (Gephi software) to explore each factor’s effect on the trial outcome of in these claims cases and to predict the trial outcomes of new cases. Simultaneously use KNN to train and predict CS cases.ResultsThe peak number of trial cases was in 2018, and there has been a gradual increase in the rate of losing claims on the claimant. Correlation analysis was used to obtain that the likelihood of the defendant winning a claim is positively correlated with DR, FSS, IDP, and KSP, and negatively correlated with the adoption of JIFDD (3), JIFDD (15), and APL. Gephi software was used to conduct a complex network analysis of the factors influencing the tendency of trial results in CS disputes, showing that noncompliance with FSS, existence of KSP, and submission of IDP evidence by the buyer are the direct factors influencing the seller’s defeat. The seller’s “failure to perform DR” is the key factor in the seller’s defeat in cases. On this basis a probability function is developed to predict a trial win rate of 0.7803 for freshman cases, classifier to predict the remaining four samples and new cases, and get the prediction accuracy is 0.8, 95% CI: (0.2836, 0.9949), and the latter was higher than the former.DiscussionIt is concluded that the attribute of CS products is a scientific issue, the jurisdiction of CS disputes is confusing and needs to be clarified, and the application of the provisions in judicial trials is cannot adapt to the current environment and needs to be resolved. This study advocates that the government design policy from the top and establish a study on the boundary between administrative and judicial functions to provide a theoretical guarantee to circumvent lazy administration and unscientific law enforcement. The government can provide a legal and regulatory system to improve food quality and regulate management.
Peak-to-Peak Stabilization of Sampled-Data Systems Subject to Actuator Saturation and Its Practical Application to an Inverted Pendulum
Authors: Nguyen Khanh Hieu , Kim Sung Hyun 
Published: November 2023

This paper investigates the local stability and stabilization criteria of sampled-data control systems, taking into account actuator saturation and peak-bounded exogenous disturbances. Specifically, this study introduces two innovations to extend the maximum upper bound of the sampling interval: two novel time integrals of the weighted state derivative are introduced to formulate an improved looped-functional; second, the introduction of two supplementary zero-equalities to improve the relationship among the components of the augmented state. Building on this, a set of linear matrix inequality-based stabilization conditions is derived. These conditions ensure that a closed-loop sampled-data system can become exponentially stable and achieve a guaranteed peak-to-peak performance in the domain of attraction. Finally, the efficacy of the proposed methodology is substantiated through both simulation and experimental results, focusing on the sampled-data control of an inverted pendulum system.
Characterization and Identification of Drought-Responsive ABA-Aldehyde Oxidase (AAO) Genes in Potato (Solanum tuberosum L.)
Authors: Yao Panfeng , Zhang Chunli , Zhang Dan , Qin Tianyuan , Xie Xiaofei , Liu Yuhui , Liu Zhen , Bai Jiangping , Bi Zhenzhen , Cui Junmei , Liang Jingwen , Sun Chao 
Published: November 2023

Abscisic acid (ABA) is an important stress hormone that affects plants’ tolerance to stress. Changes in the content of abscisic can have an impact on plant responses to abiotic stress. The abscisic acid aldehyde oxidase (AAO) plays a crucial role in the final step in the synthesis of abscisic acid; therefore, understanding the function of the AAO gene family is of great significance for insight into plants’ response to abiotic stresses. In this study, Solanum tuberosum AAO (StAAO) members were exhaustively explored using genome databases, and nine StAAOs were identified. Chromosomal location analysis indicated that StAAO genes mapped to 4 of the 14 potato chromosomes. Further analyses of gene structure and motif composition showed that members of the specific StAAO subfamily showed relatively conserved characteristics. Phylogenetic relationship analysis indicated that StAAOs proteins were divided into three major clades. Promoter analysis showed that most StAAO promoters contained cis-elements related to abiotic stress response and plant hormones. The results of tissue-specific expression analysis indicated that StAAO4 was predominantly expressed in the roots. Analysis of transcriptome data revealed that StAAO2/4/6 genes responded significantly to drought treatments. Moreover, further qRT-PCR analysis results indicated that StAAO2/4/6 not only significantly responded to drought stress but also to various phytohormone (ABA, SA, and MeJA) and abiotic stresses (salt and low temperature), albeit with different expression patterns. In summary, our study provides comprehensive insights into the sequence characteristics, structural properties, evolutionary relationships, and expression patterns of the StAAO gene family. These findings lay the foundation for a deeper understanding of the StAAO gene family and offer a potential genetic resource for breeding drought-resistant potato varieties.