bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fine-scale genomic tracking of Ross River virus using nanopore sequencing
Authors: de Vries Ellen M. , Cogan Noel O. I. , Gubala Aneta J. , Rodoni Brendan C. , Lynch Stacey E. 
Published: June 2023

Abstract
Background
Ross River virus (RRV) is Australia’s most common and widespread mosquito-transmitted arbovirus and is of significant public health concern. With increasing anthropogenic impacts on wildlife and mosquito populations, it is important that we understand how RRV circulates in its endemic hotspots to determine where public health efforts should be directed. Current surveillance methods are effective in locating the virus but do not provide data on the circulation of the virus and its strains within the environment. This study examined the ability to identify single nucleotide polymorphisms (SNPs) within the variable E2/E3 region by generating full-length haplotypes from a range of mosquito trap-derived samples.

Methods
A novel tiled primer amplification workflow for amplifying RRV was developed with analysis using Oxford Nanopore Technology’s MinION and a custom ARTIC/InterARTIC bioinformatic protocol. By creating a range of amplicons across the whole genome, fine-scale SNP analysis was enabled by specifically targeting the variable region that was amplified as a single fragment and established haplotypes that informed spatial-temporal variation of RRV in the study site in Victoria.

Results
A bioinformatic and laboratory pipeline was successfully designed and implemented on mosquito whole trap homogenates. Resulting data showed that genotyping could be conducted in real time and that whole trap consensus of the viruses (with major SNPs) could be determined in a timely manner. Minor variants were successfully detected from the variable E2/E3 region of RRV, which allowed haplotype determination within complex mosquito homogenate samples.

Conclusions
The novel bioinformatic and wet laboratory methods developed here will enable fast detection and characterisation of RRV isolates. The concepts presented in this body of work are transferable to other viruses that exist as quasispecies in samples. The ability to detect minor SNPs, and thus haplotype strains, is critically important for understanding the epidemiology of viruses their natural environment.

Graphical Abstract
Examining the influence of pain neuroscience education followed by a Pilates exercises program in individuals with knee osteoarthritis: a pilot randomized controlled trial
Authors: Rabiei Pouya , Sheikhi Bahram , Letafatkar Amir 
Published: June 2023

Abstract
Background
Knee osteoarthritis (OA) is a multifactorial form of rheumatic condition contributing to physical and psychological factors. Treatments have been provided solely and often compared with each other. An alternative view is that combined treatments addressing physical and psychological factors may result in more benefits. This study aimed to investigate the effect of pain neuroscience education (PNE) followed by Pilates exercises (PEs) in participants with knee OA, compared to PE alone.

Methods
In this two-arm assessor-blind pilot randomized controlled trial, fifty-four community-dwelling adults with knee OA were randomly assigned to the PNE followed by PEs and PEs groups (27 in each group). The study was conducted between early July 2021 and early March 2022 at the university’s health center. Primary outcomes were Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) subscales of pain and physical limitation and secondary outcomes were Pain Catastrophizing Scale, Tampa Scale for Kinesiophobia, Pain Self-Efficacy Questionnaire, and Timed "Up & Go" test covering function. The primary and secondary outcomes were measured at baseline and eight weeks post-treatment. A general linear mixed model was used for between-group comparison with a statistical significance level of 0.05.

Results
Significant within-group differences were observed in all outcomes in both groups at post-treatment. There were no statistically between-group differences in pain (adjusted mean difference: -0.8; 95% CI -2.2 to 0.7; p = 0.288), physical limitation (adjusted mean difference: -0.4; 95% CI -4 to 3.1; p = 0.812) and function (adjusted mean difference: -0.8; 95% CI -1.8 to 0.1; p = 0.069) at eight weeks. For pain catastrophizing (adjusted mean difference: -3.9; 95% CI -7.2 to -0.6; p = 0.021), kinesiophobia (adjusted mean difference: -4.2; 95% CI -8.1 to -0.4; p = 0.032), and self-efficacy (adjusted mean difference: 6.1; 95% CI 0.7 to 11.5; p = 0.028) statistically between-group improvements were observed favoring PNE followed by PEs group after the treatment.

Conclusions
Combining PNE with PEs could have superior effects on psychological characteristics but not on pain, physical limitation, and function, compared to PEs alone. This pilot study emphasizes the need to investigate the combined effects of different interventions.

Trial registration
IRCT20210701051754N1.
Cefquinome shows a higher impact on the pig gut microbiome and resistome compared to ceftiofur
Authors: Rutjens Sofie , Vereecke Nick , Sauer Jannes , Croubels Siska , Devreese Mathias 
Published: June 2023

AbstractCephalosporins are licensed for treatment of severe bacterial infections in different species. However, the effect of these antimicrobials on the fecal microbiome and potential spread of resistance-associated genes causes great concern. This highlights the need to understand the impact of cephalosporins on the porcine fecal microbiome and resistome. A combination of long-read 16S rRNA gene and shotgun metagenomic sequencing was applied to investigate the effect of conventional treatment with either ceftiofur (3 mg.kg−1 intramuscular, 3 consecutive days) or cefquinome (2 mg.kg−1 intramuscular, 5 consecutive days) on the porcine microbiome and resistome. Fecal samples were collected from 17 pigs (6 ceftiofur treated, 6 cefquinome treated, 5 control pigs) at four different timepoints. Treatment with ceftiofur resulted in an increase in Proteobacteria members on microbiome level, while on resistome level selection in TetQ containing Bacteroides, CfxA6 containing Prevotella and blaTEM-1 containing Escherichia coli was observed. Cefquinome treatment resulted in a decline in overall species richness (α-diversity) and increase in Proteobacteria members. On genus level, administration of cefquinome significantly affected more genera than ceftiofur (18 vs 8). On resistome level, cefquinome resulted in a significant increase of six antimicrobial resistance genes, with no clear correlation with certain genera. For both antimicrobials, the resistome levels returned back to the control levels 21 days post-treatment. Overall, our study provides novel insights on the effect of specific cephalosporins on the porcine gut microbiome and resistome after conventional intramuscular treatment. These results might contribute to better tailoring of the most ideal treatment strategy for some bacterial infections.
Assessment of the relative benefits of monotherapy and combination therapy approaches to the treatment of hospital-acquired Stenotrophomonas maltophilia pneumonia: a multicenter, observational, real-world study
Authors: Chen Liang , Hua Jie , Hong Shujie , Yuan Chenyang , Jing Ruochen , Luo Xuanyu , Zhu Yihong , Le Le , Wang Ziqi , Sun Xiaoli , He Xiaopu 
Published: June 2023

Abstract
Purpose
Stenotrophomonas maltophilia is a Gram-negative pathogen that most commonly causes hospital-acquired infections that can be extremely challenging to treat, contributing to underrecognized mortality throughout the world. The relative benefits of monotherapy as compared to combination therapy in patients diagnosed with S. maltophilia pneumonia, however, have yet to be established.

Methods
Data from 307 patients diagnosed with S. maltophilia hospital-acquired pneumonia (HAP) across four Chinese teaching hospitals from 2016 to 2022 were retrospectively analyzed.

Results
Of the analyzed patients, 55.7% (171/307) were administered combination definitive therapy, with a 30-day all-cause mortality rate of 41.0% (126/307). A propensity score weighting analysis revealed that compared with monotherapy, combination definitive therapy was associated with a comparable 30-day mortality risk in the overall patient cohort (OR 1.124, 95% CI 0.707–1.786, P = 0.622), immunocompetent patients (OR 1.349, 95% CI 0.712–2.554, P = 0.359), and patients with APACHE II scores < 15 (OR 2.357, 95% CI 0.820–6.677, P = 0.111), whereas it was associated with a decreased risk of death in immunocompromised patients (OR 0.404, 95% CI .170–0.962, P = 0.041) and individuals with APACHE II scores ≥ 15 (OR 0.494, 95% CI 0.256–0.951, P = 0.035).

Conclusion
The present data suggest that when treating S. maltophilia-HAP, immunocompromised patients and individuals with APACHE II scores ≥ 15 may potentially benefit from combination therapy.
Mobile authentication of copy detection patterns
Authors: Taran Olga , Tutt Joakim , Holotyak Taras , Chaban Roman , Bonev Slavi , Voloshynovskiy Slava 
Published: June 2023

AbstractIn the recent years, the copy detection patterns (CDP) attracted a lot of attention as a link between the physical and digital worlds, which is of great interest for the internet of things and brand protection applications. However, the security of CDP in terms of their reproducibility by unauthorized parties or clonability remains largely unexplored. In this respect, this paper addresses a problem of anti-counterfeiting of physical objects and aims at investigating the authentication aspects and the resistances to illegal copying of the modern CDP from machine learning perspectives. A special attention is paid to a reliable authentication under the real-life verification conditions when the codes are printed on an industrial printer and enrolled via modern mobile phones under regular light conditions. The theoretical and empirical investigation of authentication aspects of CDP is performed with respect to four types of copy fakes from the point of view of (i) multi-class supervised classification as a baseline approach and (ii) one-class classification as a real-life application case. The obtained results show that the modern machine-learning approaches and the technical capacities of modern mobile phones allow to reliably authenticate CDP on end-user mobile phones under the considered classes of fakes.
Harnessing male germline epigenomics for the genetic improvement in cattle
Authors: Wang Xiao , Li Wenlong , Feng Xia , Li Jianbin , Liu George E. , Fang Lingzhao , Yu Ying 
Published: June 2023

AbstractSperm is essential for successful artificial insemination in dairy cattle, and its quality can be influenced by both epigenetic modification and epigenetic inheritance. The bovine germline differentiation is characterized by epigenetic reprogramming, while intergenerational and transgenerational epigenetic inheritance can influence the offspring’s development through the transmission of epigenetic features to the offspring via the germline. Therefore, the selection of bulls with superior sperm quality for the production and fertility traits requires a better understanding of the epigenetic mechanism and more accurate identifications of epigenetic biomarkers. We have comprehensively reviewed the current progress in the studies of bovine sperm epigenome in terms of both resources and biological discovery in order to provide perspectives on how to harness this valuable information for genetic improvement in the cattle breeding industry.
Emerging role of the RNA-editing enzyme ADAR1 in stem cell fate and function
Authors: Lu Di , Lu Jianxi , Liu Qiuli , Zhang Qi 
Published: June 2023

AbstractStem cells are critical for organism development and the maintenance of tissue homeostasis. Recent studies focusing on RNA editing have indicated how this mark controls stem cell fate and function in both normal and malignant states. RNA editing is mainly mediated by adenosine deaminase acting on RNA 1 (ADAR1). The RNA editing enzyme ADAR1 converts adenosine in a double-stranded RNA (dsRNA) substrate into inosine. ADAR1 is a multifunctional protein that regulate physiological processes including embryonic development, cell differentiation, and immune regulation, and even apply to the development of gene editing technologies. In this review, we summarize the structure and function of ADAR1 with a focus on how it can mediate distinct functions in stem cell self-renewal and differentiation. Targeting ADAR1 has emerged as a potential novel therapeutic strategy in both normal and dysregulated stem cell contexts.
Clustering analysis of acoustic emission signals in the monitoring of stone monuments: case of the freeze‒thaw deterioration of tuffs
Authors: Zhou Yishan , Li Li , Liu Yikun , Zhang Zhongjian , Matsui Toshiya 
Published: June 2023

Abstract
Acoustic emission (AE) technology is a promising technique for monitoring cultural monuments due to its characteristic ability to reflect status changes and perceive the development process of deterioration and damage even before their visual appearance. This study was established on the motivation of providing basic data and a methodology that can improve the signal processing, characteristics analysis and classification for the AE technique in the long-term in-situ monitoring of deterioration processes, starting from the freeze‒thaw deterioration of tuff monuments at the Chengde site. AE monitoring was carried out with an indoor freeze–thaw deterioration experiment. As a result, a set of procedures and related methodology is proposed based on the hit-based AE waveform parameters for denoising and classification of monitored AE signals by applying hierarchical cluster analysis, k-means clustering, distribution statistics, etc. The clustering results show that some signals may indicate deterioration and signals with certain characteristics are more likely to occur at a particular deterioration phase. Signals characterized by the significant absolute energy (ABE) are presumed to be related to the propagation of cracks to the outer layer. Signals characterized by a higher indirect parameter RA (Rise time divided by peak amplitude) value may connect with the opening/closing of microcracks in the earlier phase of deterioration prior to the exposure of visible surface cracks. The peak frequency (PF) is likely to decrease as the deterioration proceeds.
Polysaccharides from Dioscorea opposita Thunb.: isolation, structural characterization, and anti-inflammatory and anti-tumor effects against hepatocellular carcinoma
Authors: Ma Fanyi , Wang Ruijiao , Zhang Yun , Bai Jie , Fang Hao , Ma Wenjing , Liu Wei , Li Qian , Liu Xiuhua 
Published: June 2023

Abstract
Background
Dioscoreaopposita Thunb, as a dual-purpose edible plant with excellent nutritional and medical value, accumulates abundant bioactive compounds, including polysaccharides. Polysaccharides from D.opposita have been widely recognized and studied due to various biological activities, such as anti-inflammatory and anti-cancer, which are influenced by their complex structures. In recent years, numerous studies have investigated the structures and activities of D.opposita polysaccharides, and the relationships between them. However, the detailed structures remain different because the structures are susceptible to various species, producing areas, growth conditions (weather, soil, temperature, moisture, etc.), and extraction and separation methods. In this study, the structures of purified polysaccharides from D.opposita were determined and the biological activities were preliminarily investigated including anti-inflammatory and anti-tumor activities.

Results
The crude polysaccharides DOP1 and DOP2 were isolated and purified via DEAE-52 and Sephadex G-100 to obtain two purified polysaccharides fractions (DOP1-1 and DOP2-1), with the molecular weights of 15.63 kDa and 32.32 kDa, respectively. The structures of DOP1-1 and DOP2-1 were analyzed by HPLC, FT-IR, methylation, and 1D (1H, 13C) and 2D (HSQC, COSY, TOCSY, and ROESY) NMR spectra. The results indicated the presence of → 2)-β-Manp-(1 → 4)-α-Glcp-(1 → 2)-β-Manp-(1 → ,  → 1)-β-Manp-(2 → 1)-α-GalpA-(4 →, and  → 2)-β-Manp-(1 → 2)-β-Manp-(1 → in DOP1-1, and the ratio was 2:11:5. The bone structure of DOP2-1 was predicted as → 1)-β-d-Galp-(4 → , along with two main branching structures composed of arabinose of different degrees of polymerization. Preliminary anti-inflammatory and anti-tumor activities were investigated. DOP1-1 and DOP2-1 demonstrated inhibitory effects on macrophages cells (RAW264.7). DOP2-1 exhibited anti-tumor effects against hepatocellular carcinoma (SNU-739 and HepG2).

Conclusions
The structures and bioactivities of DOP1-1 and DOP2-1 were analyzed to provide a basis for the establishment of structure/function relationships. The polysaccharides derived from Dioscoreaopposita could be potentially employed in functional food, health care, and pharmaceutical industries.

Graphical Abstract
Households’ vulnerability assessment: empirical evidence from cyclone-prone area of Bangladesh
Authors: Rahman Md Mostafizur , Arif Md. Saidul Islam , Hossain Md. Tanvir , Almohamad Hussein , Al Dughairi Ahmed Abdullah , Al-Mutiry Motrih , Abdo Hazem Ghassan 
Published: June 2023

AbstractDespite Bangladesh being vulnerable to cyclones, there is a dearth of research on cyclone vulnerability assessment. Assessing a household's vulnerability is considered a crucial step in avoiding the adverse effects of catastrophe risks. This research was conducted in the cyclone-prone district of Barguna, Bangladesh. This study's purpose is to evaluate this region's vulnerability. A questionnaire survey was conducted using a convenience sample technique. A door-to-door survey of 388 households in two Unions of Patharghata Upazila, Barguna district, was conducted. Forty-three indicators were selected to assess cyclone vulnerability. The results were quantified using an index-based methodology with a standardized scoring method. Where applicable, descriptive statistics have been obtained. In terms of vulnerability indicators, we also utilized the chi-square test to compare Kalmegha and Patharghata Union. When appropriate, the non-parametric Mann–Whitney U test was employed to evaluate the relationship between the Vulnerability Index Score (VIS) and the union. According to the results, the environmental vulnerability (0.53 ± 0.17) and the composite vulnerability index (0.50 ± 0.08) were significantly greater in Kalmegha Union than in Patharghata Union. They faced inequity in government assistance (71%) and humanitarian aid (45%) from national and international organizations. However, 83% of them underwent evacuation practices. 39% were satisfied with the WASH conditions at the cyclone shelter, whereas around half were dissatisfied with the status of the medical facilities. Most of them (96%) rely only on surface water for drinking. National and international organizations should have a comprehensive plan for disaster risk reduction that encompasses all individuals, regardless of race, geography, or ethnicity.
The effect of a new developed synbiotic yogurt consumption on metabolic syndrome components, oxidative stress status, and some other cardiovascular disease risk factors in adults with metabolic syndrome: a study protocol for a randomized clinical trial
Authors: Zolghadrpour Mohammad-Amin , Karimpour Farzad , Jowshan Mohammad-Reza , Imani Hossein , Asghari Somayyeh 
Published: June 2023

AbstractBackgroundMetabolic syndrome is recognized as one of the most common global health issues, which may cause numerous side effects. Studies have shown the favorable effects of probiotic supplements on glycemic indices, lipid profiles, and oxidative stress status. However, the number of studies investigating the effects of food products containing probiotics and prebiotics on metabolic diseases is limited. Limited evidence also shows that products containing Lactobacillus plantarum could affect metabolic alterations in chronic diseases. No previous study evaluated the impact of synbiotic yogurt containing Lactobacillus plantarum on people with metabolic syndrome. Therefore, the current study aims to investigate the effect of the newly developed synbiotic yogurt containing Lactobacillus plantarum, Lactobacillus pentosus, and Chloromyces marcosianos yeast on the components of metabolic syndrome, oxidative stress status, and some other risk factors for cardiovascular diseases in adults with metabolic syndrome.MethodsIn this study, 44 patients with metabolic syndrome will be randomly assigned to intervention and control groups in a randomized, double-blind, controlled clinical trial. Participants in the intervention group will consume 300 g of synbiotic yogurt daily, while those in the control group will consume 300 g of regular yogurt daily for 12 weeks. Anthropometric measurements, blood pressure, and biochemical parameters will be evaluated before and after the intervention.DiscussionThe management of the metabolic syndrome presents significant clinical challenges. While probiotic supplementation for these individuals has been considered, the consumption of probiotic-rich foods has received considerably less attention.Trial registration numberIranian Registry of Clinical Trials (IRCT20220426054667N1) (2022–05-18).
The influence of temporal variation of some limnological parameters on finfish assemblage in Osun River, Nigeria.
Authors: Iyiola Adams , Jenyo-Oni Adetola 
Published: June 2023

AbstractBackgroundAnthropogenic activities is a major factor that determines the condition and sustainability of an environment. The nature and type of activities will determine the health, ecosystem services and general well-being of the environment. These activities have increased as a result of industrialization and urbanization, notwithstanding pressure on fish species for balanced nutrition and economic returns. The paucity of documented information about the limnological parameters and finfish assemblage in Osun River nessiciated this study.ResultsMean temperature (18.7 ± 2.69 °C) and dissolved oxygen (3.2 ± 0.54 mg/L) values were below the recommended limit for fish survival, pH (7.1 ± 0.25) and ammonia (1.2 ± 0.18 mg/L) were within and above the recommended limits. The river had a total of 4544 finfish belonging to 11 families and 19 species.Chrysichthys nigrodigitatus,sampling zone A and Cichlid family had the highest abundance in the river with 21.00%, 24.20% and 32.50% respectively.Fin fish abundance had a negative relationship between dissolved oxygen (r = − 0.032), ammonia (r = − 0.668), pH (r = − 0.819); temperature and DO with ammonia(r = − 0.668,r = − 0.590) and pH (r = − 0.043,r = − 0.011) respectively. Dissolved oxygen (b = − 137.1), ammonia (b = − 522) and pH (b = − 93.4) had a negative effect on finfish assemblage in the river. Significant correlated values (p < 0.05) were observed between fin fish and temperature (p = 0.008), ammonia (p = 0.017), pH (p = 0.001). dissolved oxygen (b = − 2.14), ammonia (b = − 2.72) and pH (b = − 1.97) had a negative association with fin fish abundance while significance (p < 0.05) were observed with dissolved oxygen (p = 0.048).ConclusionIt is worthy to note that human activities principally dictates the quality and quantity of limnological parameters which directly affect finfish assemblage; therefore proper environmental management is essential for sustenance of finfish in the river as elaborated by the United Nations Sustainable Development Goals.