bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can we replace computed tomography angiography by contrast-enhanced ultrasound in the surveillance of patients submitted to aortoiliac aneurysm repair?
Authors: Park Jong Hun , Filho Alvaro Razuk , Pires Ana Paula M , Telles Gustavo José P , Esteves Fernando P , Caffaro Roberto Augusto , Parrillo Eduardo F 
Published: June 2021

Objectives This study was designed for evaluation of CEUS (contrast-enhanced ultrasound) for the detection of endoleaks after EVAR (endovascular aortic aneurysms repair) as an alternative to CTA (computed tomography angiography), the gold standard in post-EVAR surveillance. Methods Post-EVAR surveillance of patients who underwent CEUS and CTA was retrospectively analyzed to compare the accuracy of CEUS compared to CTA. For that, the following parameters were analyzed: the largest aneurysm diameter, type of endoleaks, and the time elapsed after EVAR using both surveillance tests. Results The study involved 110 pairs of exams in patients with infrarenal aortoiliac or isolated iliac artery aneurysm, covering predominantly a male population (89%). The time elapsed after EVAR using CEUS or CTA exams were statistically similar, ranging from one to 58 months (mean 12.2) and one to 65 months (mean 9.7), respectively ( p = 0.124). CEUS sensitivity was 75.5%, specificity 96.7%, false positives were 24.5%, and false negatives were 3.3%. The accuracy between the two exams was 87.3%. A secondary analysis, comparing CTA with CEUS as a reference standard, revealed CEUS sensitivity of 24.5%, higher than CTA for detecting endoleaks, with a concordance rate of true positive results of 75.5%. Among the endoleaks detected solely by CEUS (12 cases), one case was type Ia and eleven were type II, while those detected only by CTA (2 cases), one was type Ia and one type II. Additionally, a type II endoleak associated with type Ib, identified by CEUS, was seen as type II for CTA only. There was no difference between the pre-EVAR and the post-EVAR diameters of aortoiliac aneurysm ( p = 0.058), both for CEUS and CTA. Computed tomography angiography, on the other hand, showed significant aneurysm diameter reduction compared to CEUS for isolated iliac artery aneurysms ( p < 0.001). Conclusion Contrast-enhanced ultrasound was more effective than CTA in identifying and characterizing endoleaks in patients undergoing EVAR, especially type II endoleaks. The advantages include efficacy and, particularly, safety, and must be considered in EVAR surveillance protocols so that its use becomes widespread. We understand that CEUS, as a surveillance exam, considerably reduces risks to patients compared to CTA.
Carotid intraplaque neovascularisation as a predictive factor for future vascular events in patients with mild and moderate carotid stenosis: an observational prospective study
Authors: Cui Liuping , Xing Yingqi , Zhou Yangyang , Wang Lijuan , Liu Kangding , Zhang Daofu , Chen Ying 
Published: June 2021

Background: Intraplaque neovascularisation (IPN) increases the vulnerability of plaques, which makes them more likely to rupture and increases the risk of vascular events. However, it is unclear whether IPN can predict future vascular events (stroke recurrence and cardiovascular events). Previous studies on IPN have focused on patients with severe stenosis but overlooked patients with mild and moderate stenosis. This study aimed to investigate whether IPN assessed by contrast-enhanced ultrasonography (CEUS) in patients with mild and moderate degrees of stenosis is associated with future vascular events. Methods: One hundred and twenty-one patients participated in this study. 76 patients who met the inclusion and exclusion criteria were included in the final dataset of the study. IPN was graded from 0 to 2 according to the extent of the microbubbles assessed using CEUS. The degree of carotid stenosis was graded as mild, moderate, or severe. We recorded future vascular events during the follow-up. Univariate and multivariate logistic regression analyses were used to evaluate risk factors for future vascular events. Results: After a follow-up period of 30 ± 6 months, 30 patients (39.5%) experienced subsequent vascular events. Compared with the ‘non-recurrent’ group, the ‘recurrent’ group showed a higher proportion of grade 2 neovascularisation ( p < 0.05), and it was an independent predictor of subsequent vascular events (odds ratio 6.066, 95% confidence interval 1.565–23.512, p < 0.05). Furthermore, in patients with mild and moderate stenosis, future vascular events occurred in an unexpectedly high proportion (up to 42.9%). In the ‘recurrent’ group, 55% of patients with mild and moderate stenosis had grade 2 neovascularisation. Conclusion: IPN by CEUS was an independent predictor of future vascular events in patients with recent ischemic stroke, and the high proportion of neovascularisation in patients with mild and moderate stenosis requires more attention.
Effect of Low Nutrition and T-2 Toxin on C28/I2 Chondrocytes Cell Line and Chondroitin Sulfate–Modifying Sulfotransferases
Authors: Deng Huan , Chilufya Mumba Mulutula , Liu Jiaxin , Qiao Lichun , Xiao Xiang , Zhao Yan , Guo Ziwei , Lv Yizhen , Wang Wenyue , Zhang Jiaheng , Han Jing 
Published: June 2021

Objective To investigate the effects of low nutrition and trichothecenes-2 toxin (T-2) on human chondrocytes cell line C28/I2 and the gene expression levels of some chondroitin sulfate (CS)–modifying sulfotransferases. Methods The chondrocytes were divided into 4 intervention groups: (a) control group (Dulbecco’s modified Eagle’s medium/Nutrient Mixture F-12 [DMEM/F-12] with fetal bovine serum [FBS]), (b) low-nutrition group (DMEM/F-12 without FBS), (c) T-2 group (DMEM/F-12 with FBS plus 20 ng/mL T-2), and (d) combined group (DMEM/F-12 without FBS plus 20 ng/mL T-2). Twenty-four hours postintervention, ultrastructural changes in the chondrocytes were observed by transmission electron microscopy (TEM). Live cell staining and methyl thiazolyl tetrazolium (MTT) assay were performed to observe cell viability. The expression of CS-modifying sulfotransferases, including carbohydrate sulfotransferase 3, 12, 13, 15 (CHST-3, CHST-12, CHST-13, and CHST-15, respectively), and uronyl 2-O-sulfotransferase (UST) were examined by quantitative real-time polymerase chain reaction (RT-qPCR) analysis. Results The cells in the T-2 group and combined group had significantly lower live cell counts and relative survival rates than the control group. TEM pictures revealed decreased electron density of mitochondria in the low-nutrition group. The T-2 group and combined group both caused mitochondrial swelling, damage, and reduction in mitochondrial number. RT-qPCR showed a trend of altered expression of CHST and increased expression of UST genes under low-nutrition, T-2 toxin and combined interventions. Conclusions These results show early-stage Kashin-Beck disease chondrocyte pathophysiology, consisting of chondrocyte cell damage and compensatory upregulation of CHST and UST genes.
Opioid dependence disorder and comorbid chronic pain: comparison of groups based on patient-attributed direction of the causal relationship between the two conditions
Authors: Higgins Cassie , Smith Blair H , Matthews Keith 
Published: June 2021

Background: Chronic pain is highly prevalent in treatment-seeking opioid-dependent patients; therefore, this comorbid presentation is an important clinical consideration for both addiction and pain specialists. The objectives of the present study were to examine whether the direction of causal attribution of opioid dependence disorder and chronic pain resulted in two distinct clinical populations, and, if so, to compare treatment received during the 5-year follow-up period. Methods: Participants comprised opioid-dependent patients with chronic pain who reported a perceived causal relationship, in either direction, between the development of these two conditions ( n = 252). A range of health- and addiction-related instruments were used at study inception. Treatment characteristics were obtained for the follow-up period from national health registers. Results: Those reporting that pain caused opioid dependence disorder ( n = 174; 69%) were characterised by poorer pain-related health, more illicit cannabinoid use ( p = 0.031), more frequent illicit use of opioid analgesics ( p = 0.025) and they were in receipt of higher doses of prescribed opioid analgesics. Those reporting that opioid dependence disorder caused pain ( n = 78; 31%) were characterised by poorer overall physical health ( p = 0.002), more severe psychiatric symptoms and more overall drug use ( p = 0.001). Conclusion: Two distinct clinical populations were identified, determined by how participants perceive the causal relationship between opioid dependence disorder and chronic pain. These two populations have differing clinical profiles and treatment requirements: those reporting that pain caused opioid dependence disorder were characterised by poorer pain-related health and more illicit use of drugs with analgesic properties; and those reporting that opioid dependence disorder caused pain were characterised by more overall use of substances, multiple substance use and more intravenous substance use and poorer general health. Identifying the causal direction, where such a relationship exists, could help addiction and pain services to develop more effective, individualised treatment strategies.
Fluid warming with parylene-coated enFlow cartridge: Bench and pilot animal study of aluminum extraction due to prolonged use
Authors: Waldmann Andreas D , Rose Edward A , Pedro Michael J 
Published: June 2021

Objectives: Intravenous fluid warming devices with surface heating systems transfer heat using aluminum blocks, which if uncoated elute toxic levels of aluminum into the infusate. This study examined extractable aluminum detected from prolonged use of the updated version of the enFlow® cartridge, which uses a parylene-coated aluminum heating block. Methods: In dynamic bench tests, we measured the concentration of aluminum that leached into three solutions (Sterofundin ISO, Plasma-Lyte 148, and whole blood) that were continuously pumped (0.2 and 5.5 mL min−1) and warmed to 40°C by the enFlow cartridge (parylene-coated) for 5 h. Prolonged quasi-static bench tests measured aluminum concentration in 16 solutions which were gently rocked within the enFlow cartridge (parylene-coated) for 72 h at 40°C. Aluminum concentrations were measured using inductively coupled mass spectroscopy and matrix blank corrected. Measured aluminum concentrations were compared to a Tolerable Exposure limit to calculate Margins of Safety based on the US Food and Drug Administration maximum recommended concentration in parenteral fluids (25 μg L−1). A parallel pilot in vivo animal study was performed using mice injected with fluids warmed for 72 h by the enFlow cartridge (parylene-coated). Results: The enFlow cartridge (parylene-coated) demonstrated low toxicological risks in all tests. Sterofundin ISO resulted in the highest aluminum concentration after simulated prolonged use of the enFlow cartridge (parylene-coated) (3.11 μg device−1), which represents a 99.2% decrease from the enFlow cartridge (uncoated) and Margin of Safety of 1.7. Dynamic tests at two different flow rates with three challenge solutions resulted in concentrations less than the method detection limits (20.6 or 41.2 μg L−1) of the analysis method. The animals in the in vivo study showed no evidence of toxicity. Conclusion: Observed toxicological risk levels associated with the enFlow cartridge (parylene-coated) intravenous fluid warmer were below those set by the Food and Drug Administration and suggest that the use of enFlow cartridge (parylene-coated) is safe with a variety of intravenous solution types and in different therapeutic scenarios.
Benthic community establishment on different concrete mixtures introduced to a German deep-water port
Authors: Becker Lydia R. , Kröncke Ingrid , Ehrenberg Andreas , Feldrappe Volkert , Bischof Kai 
Published: June 2021

AbstractConcrete is a widely used building material in coastal constructions worldwide. However, limited natural resources used in the production process, as well as high CO2-emission due to the calcination process of limestone and the thermal energy demand for Portland cement clinker production, raise the demand for alternative constituents. Alternative mixture types should be environmentally friendly and, at best, mimic natural hard substrates. Here five different concrete mixtures, containing different cements (Portland cement and blast furnace cements) and aggregates (sand, gravel, iron ore and metallurgical slags) were made. Three replicate cubes (15 × 15 × 15 cm) of each type were then deployed in a German deep-water Port, the JadeWeserPort, to study benthic community establishment after one year. Results are compared to a similar experiment conducted in a natural hard ground environment (Helgoland Island, Germany). Results indicate marked differences in settled communities in the Port site compared to natural environments. At the Port site community composition did not differ with the concrete mixtures. Surface orientation of the cubes (front/top/back) revealed significant differences in species abundances and compositions. Cubes hold more neobiota in the Port site than in natural hard ground environments. Implications for the usage of new concrete mixtures are discussed.
Caprine PRNP polymorphisms N146S and Q222K are associated with proteolytic cleavage of PrPC
Authors: Madsen-Bouterse Sally A. , Stewart Paula , Williamson Helen , Schneider David A. , Goldmann Wilfred 
Published: June 2021

AbstractExpression of the cellular prion protein (PrPC) is crucial for the development of prion diseases. Amino acid changes in PrPC or a reduced amount of PrPC may modulate disease resistance. The relative abundance of C1, a natural α-cleavage fragment of PrPC, was previously found to be associated with a resistant PRNP genotype in sheep. Goats are another small ruminant where classical scrapie susceptibility is under strong genetic control. In this study, we assessed PrPC in goats for the existence of similar associations between PrPC fragments and genotype. Brain tissue homogenates from scrapie-free goats with wild type PRNP or polymorphisms (I142M, H143R, N146S, or Q222K) were deglycosylated prior to immunoblot for assessment of the relative abundance of the C1 fragment of PrPC. The presence of K222 or S146 alleles demonstrated significantly different relative levels of C1 compared to that observed in wild type goats, which suggests that the genotype association with C1 is neither unique to sheep nor exclusive to the ovine Q171R dimorphism.
ORFik: a comprehensive R toolkit for the analysis of translation
Authors: Tjeldnes Håkon , Labun Kornel , Torres Cleuren Yamila , Chyżyńska Katarzyna , Świrski Michał , Valen Eivind 
Published: June 2021

Abstract
Background
With the rapid growth in the use of high-throughput methods for characterizing translation and the continued expansion of multi-omics, there is a need for back-end functions and streamlined tools for processing, analyzing, and characterizing data produced by these assays.

Results
Here, we introduce ORFik, a user-friendly R/Bioconductor API and toolbox for studying translation and its regulation. It extends GenomicRanges from the genome to the transcriptome and implements a framework that integrates data from several sources. ORFik streamlines the steps to process, analyze, and visualize the different steps of translation with a particular focus on initiation and elongation. It accepts high-throughput sequencing data from ribosome profiling to quantify ribosome elongation or RCP-seq/TCP-seq to also quantify ribosome scanning. In addition, ORFik can use CAGE data to accurately determine 5′UTRs and RNA-seq for determining translation relative to RNA abundance. ORFik supports and calculates over 30 different translation-related features and metrics from the literature and can annotate translated regions such as proteins or upstream open reading frames (uORFs). As a use-case, we demonstrate using ORFik to rapidly annotate the dynamics of 5′ UTRs across different tissues, detect their uORFs, and characterize their scanning and translation in the downstream protein-coding regions.

Conclusion
In summary, ORFik introduces hundreds of tested, documented and optimized methods. ORFik is designed to be easily customizable, enabling users to create complete workflows from raw data to publication-ready figures for several types of sequencing data. Finally, by improving speed and scope of many core Bioconductor functions, ORFik offers enhancement benefiting the entire Bioconductor environment.

Availability
http://bioconductor.org/packages/ORFik.
Genetic differentiation in an endangered and strongly philopatric, migrant shorebird
Authors: Rönkä Nelli , Pakanen Veli-Matti , Pauliny Angela , Thomson Robert L. , Nuotio Kimmo , Pehlak Hannes , Thorup Ole , Lehikoinen Petteri , Rönkä Antti , Blomqvist Donald , Koivula Kari , Kvist Laura 
Published: June 2021

AbstractBackgroundPopulations living in fragmented habitats may suffer from loss of genetic variation and reduced between-patch dispersal, which are processes that can result in genetic differentiation. This occurs frequently in species with reduced mobility, whereas genetic differentiation is less common among mobile species such as migratory birds. The high dispersal capacity in the latter species usually allows for gene flow even in fragmented landscapes. However, strongly philopatric behaviour can reinforce relative isolation and the degree of genetic differentiation. The Southern Dunlin (Calidris alpina schinzii) is a philopatric, long-distance migratory shorebird and shows reduced dispersal between isolated breeding patches. The endangered population of the Southern Dunlin breeding at the Baltic Sea has suffered from habitat deterioration and fragmentation of coastal meadows. We sampled DNA across the entire population and used 12 polymorphic microsatellite loci to examine whether the environmental changes have resulted in genetic structuring and loss of variation.ResultsWe found a pattern of isolation-by-distance across the whole Baltic population and genetic differentiation between local populations, even within the southern Baltic. Observed heterozygosity was lower than expected throughout the range and internal relatedness values were positive indicating inbreeding.ConclusionsOur results provide long-term, empirical evidence for the theoretically expected links between habitat fragmentation, population subdivision, and gene flow. They also demonstrate a rare case of genetic differentiation between populations of a long-distance migratory species. The Baltic Southern Dunlin differs from many related shorebird species that show near panmixia, reflecting its philopatric life history and the reduced connectivity of its breeding patches. The results have important implications as they suggest that reduced connectivity of breeding habitats can threaten even long-distance migrants if they show strong philopatry during breeding. The Baltic Southern Dunlin warrants urgent conservation efforts that increase functional connectivity and gene flow between breeding areas.
Functional prediction of de novo uni-genes from chicken transcriptomic data following infectious bursal disease virus at 3-days post-infection
Authors: Azli Bahiyah , Ravi Sharanya , Hair-Bejo Mohd , Omar Abdul Rahman , Ideris Aini , Mat Isa Nurulfiza 
Published: June 2021

Abstract
Background
Infectious bursal disease (IBD) is an economically very important issue to the poultry industry and it is one of the major threats to the nation’s food security. The pathogen, a highly pathogenic strain of a very virulent IBD virus causes high mortality and immunosuppression in chickens. The importance of understanding the underlying genes that could combat this disease is now of global interest in order to control future outbreaks. We had looked at identified novel genes that could elucidate the pathogenicity of the virus following infection and at possible disease resistance genes present in chickens.

Results
A set of sequences retrieved from IBD virus-infected chickens that did not map to the chicken reference genome were de novo assembled, clustered and analysed. From six inbred chicken lines, we managed to assemble 10,828 uni-transcripts and screened 618 uni-transcripts which were the most significant sequences to known genes, as determined by BLASTX searches. Based on the differentially expressed genes (DEGs) analysis, 12 commonly upregulated and 18 downregulated uni-genes present in all six inbred lines were identified with false discovery rate of q-value < 0.05. Yet, only 9 upregulated and 13 downregulated uni-genes had BLAST hits against the Non-redundant and Swiss-Prot databases. The genome ontology enrichment keywords of these DEGs were associated with immune response, cell signalling and apoptosis. Consequently, the Weighted Gene Correlation Network Analysis R tool was used to predict the functional annotation of the remaining unknown uni-genes with no significant BLAST hits. Interestingly, the functions of the three upregulated uni-genes were predicted to be related to innate immune response, while the five downregulated uni-genes were predicted to be related to cell surface functions. These results further elucidated and supported the current molecular knowledge regarding the pathophysiology of chicken’s bursal infected with IBDV.

Conclusion
Our data revealed the commonly up- and downregulated novel uni-genes identified to be immune- and extracellular binding-related, respectively. Besides, these novel findings are valuable contributions in improving the current existing integrative chicken transcriptomics annotation and may pave a path towards the control of viral particles especially towards the suppression of IBD and other infectious diseases in chickens.