bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of antiparasitic drug targets using a multi-omics workflow in the acanthocephalan model
Authors: Schmidt Hanno , Mauer Katharina , Glaser Manuel , Dezfuli Bahram Sayyaf , Hellmann Sören Lukas , Silva Gomes Ana Lúcia , Butter Falk , Wade Rebecca C. , Hankeln Thomas , Herlyn Holger 
Published: September 2022

AbstractBackgroundWith the expansion of animal production, parasitic helminths are gaining increasing economic importance. However, application of several established deworming agents can harm treated hosts and environment due to their low specificity. Furthermore, the number of parasite strains showing resistance is growing, while hardly any new anthelminthics are being developed. Here, we present a bioinformatics workflow designed to reduce the time and cost in the development of new strategies against parasites. The workflow includes quantitative transcriptomics and proteomics, 3D structure modeling, binding site prediction, and virtual ligand screening. Its use is demonstrated for Acanthocephala (thorny-headed worms) which are an emerging pest in fish aquaculture. We included three acanthocephalans (Pomphorhynchus laevis, Neoechinorhynchus agilis,Neoechinorhynchus buttnerae) from four fish species (common barbel, European eel, thinlip mullet, tambaqui).ResultsThe workflow led to eleven highly specific candidate targets in acanthocephalans. The candidate targets showed constant and elevated transcript abundances across definitive and accidental hosts, suggestive of constitutive expression and functional importance. Hence, the impairment of the corresponding proteins should enable specific and effective killing of acanthocephalans. Candidate targets were also highly abundant in the acanthocephalan body wall, through which these gutless parasites take up nutrients. Thus, the candidate targets are likely to be accessible to compounds that are orally administered to fish. Virtual ligand screening led to ten compounds, of which five appeared to be especially promising according to ADMET, GHS, and RO5 criteria: tadalafil, pranazepide, piketoprofen, heliomycin, and the nematicide derquantel.ConclusionsThe combination of genomics, transcriptomics, and proteomics led to a broadly applicable procedure for the cost- and time-saving identification of candidate target proteins in parasites. The ligands predicted to bind can now be further evaluated for their suitability in the control of acanthocephalans. The workflow has been deposited at the Galaxy workflow server under the URLtinyurl.com/yx72rda7.
Isolation and identification of a new biocontrol bacteria against Salvia miltiorrhiza root rot and optimization of culture conditions for antifungal substance production using response surface methodology
Authors: Sa Rongbo , He Song , Han Dongdong , Liu Mengjiao , Yu Yunxia , Shang Rongen , Song Meimei 
Published: September 2022

Abstract
Background
S. miltiorrhiza root rot is a soil-borne disease mainly caused by Fusarium solani and Fusarium oxysporum, which has spread rapidly in China in recent years. To reduce the amount of pesticides to control this plant fungal disease, biological control using endophytic bacteria is a promising method. Many endophytic bacteria show good biocontrol potential against various plant fungal diseases. The aims of this study were to isolate and identify endophytic bacteria with antifungal activity from Salvia miltiorrhiza plant tissue. In order to increase antifungal substances production, the culture conditions of the isolated DS-R5 strain were optimized through response surface methodology.

Results
Thirteen endophytic bacteria with antifungal activity against the target pathogenic fungus were successfully screened. The DS-R5 strain that had the strongest antifungal activity was identified based on morphological, physiological and biochemical characteristics, 16S rRNA and gyrB sequence analysis.The results of response surface methodology experiments showed that the optimal values of the three significant factors were as follows: medium volume, 51.0 ml; initial pH, 6.7; fermentation temperature, 33.1 °C. Under these optimal culture conditions, the titer of antifungal substances produced by the DS-R5 strain was 77.6% higher than that under the initial culture conditions.

Conclusions
The antifungal activity of endophytic bacteria from Salvia miltiorrhiza has been demonstrated for the first time, which may benefit future crop quality and production. In addition, response surface methodology can be well applied the optimization of culture conditions for antifungal substance, which lays the foundation for further research on strain DS-R5.
Choice of DNA extraction method affects detection of bacterial taxa from retail chicken breast
Authors: Flint Annika , Laidlaw Anna , Li Leo , Raitt Courtney , Rao Mary , Cooper Ashley , Weedmark Kelly , Carrillo Catherine , Tamber Sandeep 
Published: September 2022

Abstract
Background
Sequence-based methods for the detection of bacteria such as 16S rRNA amplicon sequencing and metagenomics can provide a comprehensive view of the bacterial microbiome of food. These methods rely on the detection of gene sequences to indicate the presence of viable bacteria. This indirect form of detection can be prone to experimental artefacts. Sample handling and processing are key sources of variation that require standard approaches. Extracting sufficient quantities of high quality DNA from food matrices is challenging because target bacterial species are usually minor components of the microbiota and foods contain an array of compounds that are inhibitory to downstream DNA applications. Here, three DNA extraction methods are compared for their ability to extract high quality bacterial DNA from retail chicken breast rinses, with or without enrichment. Method performance was assessed by comparing ease of use, DNA yield, DNA quality, PCR amplicon yield, and the detection of bacterial taxa by 16S rRNA amplicon sequencing.

Results
All three DNA extraction methods yielded DNA of sufficient quantity and quality to perform quantitative PCR and 16S rRNA amplicon sequencing. The extraction methods differed in ease of use, with the two commercial kits (PowerFood, PowerSoil) offering considerable time and cost savings over a hybrid method that used laboratory reagents for lysis and commercial column based kits for further purification. Bacterial richness as determined by 16S rRNA amplicon sequencing was similar across the three DNA extraction methods. However, differences were noted in the relative abundance of bacterial taxa, with significantly higher abundance of Gram-positive genera detected in the DNA samples prepared using the PowerFood DNA extraction kit.

Conclusion
The choice of DNA extraction method can affect the detection of bacterial taxa by 16S rRNA amplicon sequencing in chicken meat rinses. Investigators should be aware of this procedural bias and select methods that are fit for the purposes of their investigation.
Aspergillus flavus YRB2 from Thymelaea hirsuta (L.) Endl., a non-aflatoxigenic endophyte with ability to overexpress defense-related genes against Fusarium root rot of maize
Authors: Rashad Younes M. , Abdalla Sara A. , Shehata Ahmed S. 
Published: September 2022

AbstractFusarium root rot, caused by Fusarium solani (Mart.) Sacc., represents one of the most damaging diseases of maize affecting plant growth and yield. In this study, the antagonistic potential of a non-aflatoxigenic endophytic Aspergillus flavus YRB2, isolated from Thymelaea hirsuta (L.) Endl., was tested against F. solani in vitro. In addition, its biocontrol activity against Fusarium root rot of maize was evaluated under greenhouse conditions. Its impacts on plant molecular, pathological, physiological, and growth levels were also studied. Results obtained revealed a potent antagonistic behavior for A. flavus YRB2 against F. solani in vitro, recording 80% growth inhibition. Seventeen secondary metabolites were detected in the n-hexane extract of A. flavus YRB2 filtered culture broth using GC-MS analysis. Among them, various antifungal secondary metabolites were produced, namely palmitic acid, α-linolenic acid, stearic acid, 2, 4-di-tert-butylphenol, diisobutyl phthalate, and heneicosane. In contrast, HPLC analysis showed that no aflatoxins (B1, B2, G1, and G2) were detected. Under greenhouse conditions, colonization of maize plants with A. flavus YRB2 exhibited a potential biocontrol activity against Fusarium root rot, recording 73.4% reduction in the disease severity. Triggering of transcriptional expression level of the defense-related genes JERF3 (7.2-fold), CHI II (8-fold), and POD (9.1-fold) was reported, indicating the inducing effect on the plant immunity. In addition, an increment in the antioxidant enzymes POD and PPO, and the total phenolic content in maize roots was also observed in response to this treatment. Moreover, a growth-promoting effect was also observed for colonization of maize plants with A. flavus YRB2. Based on the obtained data, we can conclude that A. flavus YRB2 may represent a promising biocontrol and growth-promoting agent for maize plants against Fusarium root rot. Nevertheless, field evaluation is highly requested before the use recommendation.
Characteristics of auditory steady-state responses to different click frequencies in awake intact macaques
Authors: Nakamura Tomoya , Dinh Trong Ha , Asai Makoto , Nishimaru Hiroshi , Matsumoto Jumpei , Setogawa Tsuyoshi , Ichijo Hiroyuki , Honda Sokichi , Yamada Hiroshi , Mihara Takuma , Nishijo Hisao 
Published: September 2022

AbstractBackgroundAuditory steady-state responses (ASSRs) are periodic evoked responses to constant periodic auditory stimuli, such as click trains, and are suggested to be associated with higher cognitive functions in humans. Since ASSRs are disturbed in human psychiatric disorders, recording ASSRs from awake intact macaques would be beneficial to translational research as well as an understanding of human brain function and its pathology. However, ASSR has not been reported in awake macaques.ResultsElectroencephalograms (EEGs) were recorded from awake intact macaques, while click trains at 20–83.3 Hz were binaurally presented. EEGs were quantified based on event-related spectral perturbation (ERSP) and inter-trial coherence (ITC), and ASSRs were significantly demonstrated in terms of ERSP and ITC in awake intact macaques. A comparison of ASSRs among different click train frequencies indicated that ASSRs were maximal at 83.3 Hz. Furthermore, analyses of laterality indices of ASSRs showed that no laterality dominance of ASSRs was observed.ConclusionsThe present results demonstrated ASSRs, comparable to those in humans, in awake intact macaques. However, there were some differences in ASSRs between macaques and humans: macaques showed maximal ASSR responses to click frequencies higher than 40 Hz that has been reported to elicit maximal responses in humans, and showed no dominant laterality of ASSRs under the electrode montage in this study compared with humans with right hemisphere dominance. The future ASSR studies using awake intact macaques should be aware of these differences, and possible factors, to which these differences were ascribed, are discussed.
Non-invasive ventilation for preoxygenation before general anesthesia: a systematic review and meta-analysis of randomized controlled trials
Authors: Chiang Tsai-Lien , Tam Ka-Wai , Chen Jui-Tai , Wong Chung-Shun , Yeh Chun-Ting , Huang Ting-Yun , Ong Jiann-Ruey 
Published: September 2022

Abstract
Background and objectives
Preoxygenation is crucial for providing sufficient oxygen reservoir to a patient before intubation and enables the extension of the period between breathing termination and critical desaturation (safe apnoea time). Conventionally, face mask ventilation is used for preoxygenation. Non-invasive ventilation is a new preoxygenation method. The study objective was to compare the outcomes of non-invasive ventilation and face mask ventilation for preoxygenation.

Method
PubMed, Embase, Cochrane Library, and the ClinicalTrials.gov registry were searched for eligible studies published from database inception to September 2021. Individual effect sizes were standardized, and a meta-analysis was conducted using random effects models to calculate the pooled effect size. Inclusion criteria were randomised controlled trials of comparing the outcomes of non-invasive ventilation or face mask ventilation for preoxygenation in patients scheduled for surgeries. The primary outcome was safe apnea time, and the secondary outcomes were post-operative complications, number of patients who achieved the expired O2 fraction (FeO2) after 3 min of preoxygenation, minimal SpO2 during tracheal intubation, partial pressure of oxygen in the arterial blood (PaO2) and partial pressure of carbon dioxide (PaCO2) after preoxygenation, and PaO2 and PaCO2 after tracheal intubation.

Results
13 trials were eligible for inclusion in this study. Significant differences were observed in safe apnoea time, number of patients who achieved FeO2 90% after preoxygenation for 3 min, and PaO2 and PaCO2 after preoxygenation and tracheal intubation. Only in the non-obese subgroup, no significant difference was observed in safe apnoea time (mean difference: 125.38, 95% confidence interval: − 12.26 to 263.03).

Conclusion
Non-invasive ventilation appeared to be more effective than conventional methods for preoxygenation. We recommend non-invasive ventilation based on our results.
Post-cardiopulmonary bypass hypoxaemia in paediatric patients undergoing congenital heart disease surgery: risk factors, features, and postoperative pulmonary complications
Authors: Sun Yuan , Deng Xiao-Ming , Cai Ying , Shen Sai-E , Dong Li-Ya 
Published: September 2022

Abstract
Background
Hypoxemia after cardiopulmonary bypass (CPB) is the quantifiable manifestation of pulmonary dysfunction. This retrospective study was designed to investigate the risk factors for post-cardiopulmonary bypass hypoxaemia and the features of hypoxaemia and pulmonary complications in paediatric congenital heart disease surgery involving CPB.

Methods
Data including demographics, preoperative pulmonary or cardiac parameters, and intraoperative interventions were retrospectively collected from 318 paediatric patients who underwent radical surgery with CPB for congenital heart disease. Among them, the factors that were significant by univariate analysis were screened for multivariate Cox regression. The lowest ratio of arterial oxygen tension and the inspiratory oxygen fraction (PaO2/FiO2), hypoxaemia (PaO2/FiO2 ≤ 300) insult time, duration of hypoxaemia, extubation time, and pulmonary complications were also analysed postoperatively.

Results
The morbidity of post-cardiopulmonary bypass hypoxaemia was 48.4% (154/318). Months (6 < months ≤ 12, 12 < months ≤ 36 and 36 < months compared with 0 ≤ months ≤ 6: HR 0.582, 95% CI 0.388–0.873; HR 0.398, 95% CI 0.251–0.632; HR 0.336, 95% CI 0.197–0.574, respectively; p < 0.01), preoperative intracardiac right-to-left shunting (HR 1.729, 95% CI 1.200–2.493, p = 0.003) and intraoperative pleural cavity entry (HR 1.582, 95% CI 1.128–2.219, p = 0.008) were identified as independent risk factors for the development of post-cardiopulmonary bypass hypoxaemia. Most hypoxaemia cases (83.8%, 129/154) occurred within 2 h, and the rate of moderate hypoxaemia (100 < PaO2/FiO2 ≤ 200) was 60.4% (93/154).

Conclusion
The morbidity of post-cardiopulmonary bypass hypoxaemia in paediatric congenital heart disease surgery was considerably high. Most hypoxaemia cases were moderate and occurred in the early period after CPB. Scrupulous management should be employed for younger infants or children with preoperative intracardiac right-to-left shunting or intraoperative pleural cavity entry.
Fibroblast growth factor 21 is associated with widening QRS complex and prolonged corrected QT interval in patients with stable angina
Authors: Hung Wei-Chin , Yu Teng-Hung , Wang Chao-Ping , Hsu Chia-Chang , Lu Yung-Chuan , Wei Ching-Ting , Chung Fu-Mei , Lee Yau-Jiunn , Wu Cheng-Ching , Tang Wei-Hua 
Published: September 2022

Abstract
Background
Fibroblast growth factor 21 (FGF21) is produced by cardiac cells, may acts in an autocrine manner, and was suggested to has a cardioprotective role in atherosclerosis. Wide QRS complex and heart rate-corrected QT interval (QTc interval) prolongation are associated to dangerous ventricular arrhythmias and cardiovascular disease mortality. Yet, the role of FGF21 in cardiac arrhythmia has never been studied. The aim of the study was to investigate the relationship between plasma FGF21 and the QRS duration and QTc interval in patients with stable angina.

Methods
Three hundred twenty-one consecutive stable angina patients were investigated. Plasma FGF21 was measured through ELISA, and each subject underwent 12-lead electrocardiography.

Results
FGF21 plasma levels were positively associated with the QRS duration (β = 0.190, P = 0.001) and QTc interval (β = 0.277, P < 0.0001). With increasing FGF21 tertiles, the patients had higher frequencies of wide QRS complex and prolonged QTc interval. After adjusting for patients’ anthropometric parameters, the corresponding odd ratios (ORs) for wide QRS complex of the medium and high of FGF21 versus the low of FGF21 were 1.39 (95% CI 0.51–3.90) and 4.41 (95% CI 1.84–11.59), respectively, and p for trend was 0.001. Furthermore, multiple logistic regression analysis also showed the corresponding odd ratios (ORs) for prolonged QTc interval of the medium and high of FGF21 versus the low of FGF21 were 1.02 (95% CI 0.53–1.78) and 1.93 (95% CI 1.04–3.60) respectively with the p for trend of 0.037. In addition, age- and sex-adjusted FGF21 levels were positively associated with fasting glucose, HbA1c, creatinine, and adiponectin, but negatively associated with albumin, and the estimated glomerular filtration rate.

Conclusions
This study indicates that plasma FGF21 is associated with wide QRS complex and prolonged corrected QT interval in stable angina patients, further study is required to investigate the role of plasma FGF21 for the underlying pathogenesis.
Recurrent generalized seizures as the prominent manifestation in a patient with CADASIL: a case report and literature review
Authors: Pan Liuhua , Chen Yan , Zhao Shanshan 
Published: September 2022

Abstract
Background
Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is an inherited arteriopathy typically caused by mutations in the NOTCH-3 gene. Few detailed descriptions of recurrent generalized seizures in CADASIL has been reported.

Case presentation
This article details a case of recurrent generalized seizures, which eventually be diagnosed as CADASIL with a heterozygous variant, c.1630 C > T (p. Arg544Cys), in exon 11 of the Notch 3 gene. Here, we discussed the possible pathogenesis underlying the epilepsy associated with CADASIL through the brain magnetic resonance imaging changes and the captured epileptiform waves in the electroencephalography during the patient’s follow-up period. Related literatures were also reviewed to discuss the etiology of the epilepsy.

Conclusions
Recurrent generalized seizures may be a presenting neurological manifestation of CADASIL in the absence of other discernible causes. Clinicians should comprehensively seek the possible etiology of patients with recurrent generalized seizures, considering the possible diagnosis of CADASIL.
Tracing coalition changes in knowledge in and engagement with childhood obesity prevention to improve intervention implementation
Authors: Moore Travis R. , Pachucki Mark C. , Hennessy Erin , Economos Christina D. 
Published: September 2022

AbstractBackgroundWhile most coalition research focuses on studying the effects of peer relationship structure, this study examines the coevolution of coalition structure and behavior across three communities in the U.S. with the goal of identifying coalition dynamics that impact a childhood obesity prevention intervention. MethodsOver two years (2018–2020), three communities within the U.S. participated in a childhood obesity prevention intervention at different times. This intervention was guided by the Stakeholder-Driven Community Diffusion theory, which describes an empirically testable mechanism for promoting community change. Measures are part of the Stakeholder-driven Community Diffusion (SDCD) survey with demonstrated reliability, which include knowledge of and engagement with childhood obesity prevention and social networks. Data from three coalition-committees and their respective networks were used to build three different stochastic actor-oriented models. These models were used to examine the coevolution of coalition structure with coalition behavior (defined a priori as knowledge of and engagement with obesity prevention) among coalition-committee members and their nominated alters (Network A) and coalition-committee members only (Network B). ResultsOverall, coalitions decrease in size and their structure becomes less dense over time. Both Network A and B show a consistent preference to form and sustain ties with those who have more ties. In Network B, there was a trend for those who have higher knowledge scores to increase their number of ties over time. The same trend appeared in Network A but varied based on their peers’ knowledge in and engagement with childhood obesity prevention. Across models, engagement with childhood obesity prevention research was not a significant driver of changes in either coalition network structure or knowledge.ConclusionsThe trends in coalition Network A and B’s coevolution models may point to context-specific features (e.g., ties among stakeholders) that can be leveraged for better intervention implementation. To that end, examining tie density, average path length, network diameter, and the dynamics of each behavior outcome (i.e., knowledge in and engagement with childhood obesity prevention) may help tailor whole-of-community interventions. Future research should attend to additional behavioral variables (e.g., group efficacy) that can capture other aspects of coalition development and that influence implementation, and to testing the efficacy of network interventions after trends have been identified.