bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Bilberry and Oat intake on lipids, inflammation and exercise capacity after Acute Myocardial Infarction (BIOAMI): study protocol for a randomized, double-blind, placebo-controlled trial
Authors: Bergh Cecilia , Landberg Rikard , Andersson Kristina , Heyman-Lindén Lovisa , Rascón Ana , Magnuson Anders , Khalili Payam , Kåregren Amra , Nilsson Johan , Pirazzi Carlo , Erlinge David , Fröbert Ole 
Published: May 2021

Abstract
Background
Bilberries from Sweden, rich in polyphenols, have shown cholesterol-lowering effects in small studies, and the cholesterol-lowering properties of oats, with abundant beta-glucans and potentially bioactive phytochemicals, are well established. Both may provide cardiometabolic benefits following acute myocardial infarction (AMI), but large studies of adequate statistical power and appropriate duration are needed to confirm clinically relevant treatment effects. No previous study has evaluated the potential additive or synergistic effects of bilberry combined with oats on cardiometabolic risk factors. Our primary objective is to assess cardioprotective effects of diet supplementation with dried bilberry or with bioprocessed oat bran, with a secondary explorative objective of assessing their combination, compared with a neutral isocaloric reference supplement, initiated within 5 days following percutaneous coronary intervention (PCI) for AMI.

Methods
The effects of Bilberry and Oat intake on lipids, inflammation and exercise capacity after Acute Myocardial Infarction (BIOAMI) trial is a double-blind, randomized, placebo-controlled clinical trial. A total of 900 patients will be randomized post-PCI to one of four dietary intervention arms. After randomization, subjects will receive beverages with bilberry powder (active), beverages with high-fiber bioprocessed oat bran (active), beverages with bilberry and oats combined (active), or reference beverages containing no active bilberry or active oats, for consumption twice daily during a 3-month intervention. The primary endpoint is the difference in LDL cholesterol change between the intervention groups after 3 months. The major secondary endpoint is exercise capacity at 3 months. Other secondary endpoints include plasma concentrations of biochemical markers of inflammation, metabolomics, and gut microbiota composition after 3 months.

Discussion
Controlling hyperlipidemia and inflammation is critical to preventing new cardiovascular events, but novel pharmacological treatments for these conditions are expensive and associated with negative side effects. If bilberry and/or oat, in addition to standard medical therapy, can lower LDL cholesterol and inflammation more than standard therapy alone, this could be a cost-effective and safe dietary strategy for secondary prevention after AMI.

Trial registration
ClinicalTrials.gov NCT03620266. Registered on August 8, 2018.
Synergistic mechanism of GH11 xylanases with different action modes from Aspergillus niger An76
Authors: Zhang Shu , Zhao Sha , Shang Weihao , Yan Zijuan , Wu Xiuyun , Li Yingjie , Chen Guanjun , Liu Xinli , Wang Lushan 
Published: May 2021

Abstract
Background
Xylan is the most abundant hemicellulose polysaccharide in nature, which can be converted into high value-added products. However, its recalcitrance to breakdown requires the synergistic action of multiple enzymes. Aspergillus niger, possessing numerous xylan degrading isozyme-encoding genes, are highly effective xylan degraders in xylan-rich habitats. Therefore, it is necessary to explore gene transcription, the mode of action and cooperation mechanism of different xylanase isozymes to further understand the efficient xylan-degradation by A. niger.

Results
Aspergillus niger An76 encoded a comprehensive set of xylan-degrading enzymes, including five endo-xylanases (one GH10 and four GH11). Quantitative transcriptional analysis showed that three xylanase genes (xynA, xynB and xynC) were up-regulated by xylan substrates, and the order and amount of enzyme secretion differed. Specifically, GH11 xylanases XynA and XynB were initially secreted successively, followed by GH10 xylanase XynC. Biochemical analyses displayed that three GH11 xylanases (XynA, XynB and XynD) showed differences in catalytic performance and product profiles, possibly because of intricate hydrogen bonding between substrates and functional residues in the active site architectures impacted their binding capacity. Among these, XynB had the best performance in the degradation of xylan and XynE had no catalytic activity. Furthermore, XynA and XynB showed synergistic effects during xylan degradation.

Conclusions
The sequential secretion and different action modes of GH11 xylanases were essential for the efficient xylan degradation by A. niger An76. The elucidation of the degradation mechanisms of these xylanase isozymes further improved our understanding of GH-encoding genes amplification in filamentous fungi and may guide the design of the optimal enzyme cocktails in industrial applications.
High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3
Authors: Söderhäll Cilla , Reinius Lovisa E. , Salmenperä Pertteli , Gentile Massimiliano , Acevedo Nathalie , Konradsen Jon R. , Nordlund Björn , Hedlin Gunilla , Scheynius Annika , Myllykangas Samuel , Kere Juha 
Published: May 2021

Abstract
Background
Methylation of DNA at CpG sites is an epigenetic modification and a potential modifier of disease risk, possibly mediating environmental effects. Currently, DNA methylation is commonly assessed using specific microarrays that sample methylation at a few % of all methylated sites.

Methods
To understand if significant information on methylation can be added by a more comprehensive analysis of methylation, we set up a quantitative method, bisulfite oligonucleotide-selective sequencing (Bs-OS-seq), and compared the data with microarray-derived methylation data. We assessed methylation at two asthma-associated genes, IL13 and ORMDL3, in blood samples collected from children with and without asthma and fractionated white blood cell types from healthy adult controls.

Results
Our results show that Bs-OS-seq can uncover vast amounts of methylation variation not detected by commonly used array methods. We found that high-density methylation information from even one gene can delineate the main white blood cell lineages.

Conclusions
We conclude that high-resolution methylation studies can yield clinically important information at selected specific loci missed by array-based methods, with potential implications for future studies of methylation-disease associations.
Early embryogenesis and organogenesis in the annelid Owenia fusiformis
Authors: Carrillo-Baltodano Allan Martín , Seudre Océane , Guynes Kero , Martín-Durán José María 
Published: May 2021

AbstractBackgroundAnnelids are a diverse group of segmented worms within Spiralia, whose embryos exhibit spiral cleavage and a variety of larval forms. While most modern embryological studies focus on species with unequal spiral cleavage nested in Pleistoannelida (Sedentaria + Errantia), a few recent studies looked intoOwenia fusiformis, a member of the sister group to all remaining annelids and thus a key lineage to understand annelid and spiralian evolution and development. However, the timing of early cleavage and detailed morphogenetic events leading to the formation of the idiosyncratic mitraria larva ofO. fusiformisremain largely unexplored.ResultsOwenia fusiformisundergoes equal spiral cleavage where the first quartet of animal micromeres are slightly larger than the vegetal macromeres. Cleavage results in a coeloblastula approximately 5 h post-fertilization (hpf) at 19 °C. Gastrulation occurs via invagination and completes 4 h later, with putative mesodermal precursors and the chaetoblasts appearing 10 hpf at the dorso-posterior side. Soon after, at 11 hpf, the apical tuft emerges, followed by the first neurons (as revealed by the expression ofelav1andsynaptotagmin-1) in the apical organ and the prototroch by 13 hpf. Muscles connecting the chaetal sac to various larval tissues develop around 18 hpf and by the time the mitraria is fully formed at 22 hpf, there are FMRFamide+neurons in the apical organ and prototroch, the latter forming a prototrochal ring. As the mitraria feeds, it grows in size and the prototroch expands through active proliferation. The larva becomes competent after ~ 3 weeks post-fertilization at 15 °C, when a conspicuous juvenile rudiment has formed ventrally.ConclusionsOwenia fusiformisembryogenesis is similar to that of other equal spiral cleaving annelids, supporting that equal cleavage is associated with the formation of a coeloblastula, gastrulation via invagination, and a feeding trochophore-like larva in Annelida. The nervous system of the mitraria larva forms earlier and is more elaborated than previously recognized and develops from anterior to posterior, which is likely an ancestral condition to Annelida. Altogether, our study identifies the major developmental events duringO. fusiformisontogeny, defining a conceptual framework for future investigations.
Sarcoidosis presenting with glazy mucoid sputum and dyspnea: a case report
Authors: Al-Kailany Wud , Timens Wim , Venmans Ben , de Jonge Gonda , van der Werf Tjip S. 
Published: May 2021

Abstract
Background
Patients with pulmonary sarcoidosis commonly present with a dry cough; a productive cough suggests a complicating airway infection or an alternative diagnosis such as tuberculosis or bronchiectasis.

Case presentation
A 36-year-old European (Frisian) woman recently diagnosed with pulmonary sarcoidosis presented with debilitating exertional dyspnea and cough productive of glazy mucoid sputum. Several different attempts including video-assisted thoracoscopic biopsies failed to reach a second or alternative diagnosis including an infectious, autoimmune or collagen-vascular condition. She responded to steroids but with poor tolerance to this treatment, which could not be tapered. After she was started on anti-tumor necrosis factor alpha (TNF-α) therapy with infliximab, 200 mg at three-monthly intervals, she has been fine for well over a decade.

Conclusions
In this patient with sarcoidosis who had a productive cough accompanied by fever, an extensive workup and prolonged follow-up, an alternative or second diagnosis could be ruled out; we therefore conclude that this highly unusual presentation is part of the clinical spectrum of sarcoidosis.
Effects of Bacillus subtilis iturin A on HepG2 cells in vitro and vivo
Authors: Zhao Haobin , Yan Lu , Guo Ling , Sun Hui , Huang Qingsheng , Shao Dongyan , Jiang Chunmei , Shi Junling 
Published: May 2021

AbstractIturin A with cyclic peptide and fatty acid chain isolated from Bacillus subtilis fermentation shows a variety of biological activities. Among them, the anticancer activity attracted much attention. However, the molecular mechanism of its inhibitory effect on hepatocellular carcinoma was still unclear. Thus its effect on hepatocellular carcinoma was tested in this research. It was found that iturin A could enter HepG2 cells immediately and cause reactive oxygen species burst, disrupt cell cycle and induce apoptosis, paraptosis and autophagy in vitro. The iturin A without fatty acid chain showed no antitumor activity. Amphiphilic is critical to the activity of iturin A. The anticancer activity of iturin A to hepatocellular carcinoma was also verified in mice models carrying xenograft tumors constructed by HepG2 cells. At a dosage of 3 mg/kg/day, iturin A significantly inhibited the further increase of the tumor weight by 58.55%, and reduced the expression of Ki67 in tumor. In the tumor treated with iturin A, lymphocyte infiltration was found, and the expressions of TGF-β1and PD-L1 were decreased, which indicated that the tumor immune microenvironment was improved. Besides, iturin A showed no significant harm on the health of mice except slight disturbance of liver function. These results suggested that iturin A had significant antitumor effect in vitro and vivo, and provide a basis for the application of iturin A as anticancer agent.
A probabilistic segmentation and entropy-rank correlation-based feature selection approach for the recognition of fruit diseases
Authors: Khan Muhammad Attique , Akram Tallha , Sharif Muhammad , Alhaisoni Majed , Saba Tanzila , Nawaz Nadia 
Published: May 2021

AbstractAgriculture plays a critical role in the economy of several countries, by providing the main sources of income, employment, and food to their rural population. However, in recent years, it has been observed that plants and fruits are widely damaged by different diseases which cause a huge loss to the farmers, although this loss can be minimized by detecting plants’ diseases at their earlier stages using pattern recognition (PR) and machine learning (ML) techniques. In this article, an automated system is proposed for the identification and recognition of fruit diseases. Our approach is distinctive in a way, it overcomes the challenges like convex edges, inconsistency between colors, irregularity, visibility, scale, and origin. The proposed approach incorporates five primary steps including preprocessing,Standard instruction requires city and country for affiliations. Hence, please check if the provided information for each affiliation with missing data is correct and amend if deemed necessary. disease identification through segmentation, feature extraction and fusion, feature selection, and classification. The infection regions are extracted using the proposed adaptive and quartile deviation-based segmentation approach and fused resultant binary images by employing the weighted coefficient of correlation (CoC). Then the most appropriate features are selected using a novel framework of entropy and rank-based correlation (EaRbC). Finally, selected features are classified using multi-class support vector machine (MC-SCM). A PlantVillage dataset is utilized for the evaluation of the proposed system to achieving an average segmentation and classification accuracy of 93.74% and 97.7%, respectively. From the set of statistical measure, we sincerely believe that our proposed method outperforms existing method with greater accuracy.
Co-designing strategies to support patient partners during a scoping review and reflections on the process: a commentary
Authors: McCarron Tamara L. , Clement Fiona , Rasiah Jananee , Moffat Karen , Wasylak Tracy , Santana Maria Jose 
Published: May 2021

AbstractBackgroundPatient partners can be described as individuals who assume roles as active members on research teams, indicative of individuals with greater involvement, increased sharing of power, and increased responsibility than traditionally described by patient participants who are primarily studied. A gap still remains in the understanding of how to engage patients. The objective of this commentary is to describe the involvement of four patient partners who worked with researchers during a scoping review.Main bodyWe describe approaches to meaningfully engage patient partners in conducting a scoping review. Patient partners were recruited through existing patient networks. Capacity development in the form of the training was provided to these four patient partners. Engagement strategies were co-designed with them to address potential barriers of involvement and acquiring the necessary skills for the successful completion of this scoping review.ConclusionInvolving patients partners early in the project established the foundational relationship so patient partners could contribute to their fullest. We witnessed the success of working alongside patient partners as members of the research team with a clear and mutually agreed upon purpose of the engagement in health research activities and how this seemed to contribute to an effective and rewarding experience for both researcher and patient partner.
Cross-sectional study of medical advertisements in a national general medical journal: evidence, cost, and safe use of advertised versus comparative drugs
Authors: Boesen Kim , Simonsen Anders Lykkemark , Jørgensen Karsten Juhl , Gøtzsche Peter C. 
Published: May 2021

Abstract
Background
Healthcare professionals are exposed to advertisements for prescription drugs in medical journals. Such advertisements may increase prescriptions of new drugs at the expense of older treatments even when they have no added benefits, are more harmful, and are more expensive. The publication of medical advertisements therefore raises ethical questions related to editorial integrity.

Methods
We conducted a descriptive cross-sectional study of all medical advertisements published in the Journal of the Danish Medical Association in 2015. Drugs advertised 6 times or more were compared with older comparators: (1) comparative evidence of added benefit; (2) Defined Daily Dose cost; (3) regulatory safety announcements; and (4) completed and ongoing post-marketing studies 3 years after advertising.

Results
We found 158 medical advertisements for 35 prescription drugs published in 24 issues during 2015, with a median of 7 advertisements per issue (range 0 to 11). Four drug groups and 5 single drugs were advertised 6 times or more, for a total of 10 indications, and we made 14 comparisons with older treatments. We found: (1) ‘no added benefit’ in 4 (29%) of 14 comparisons, ‘uncertain benefits’ in 7 (50%), and ‘no evidence’ in 3 (21%) comparisons. In no comparison did we find evidence of ‘substantial added benefit’ for the new drug; (2) advertised drugs were 2 to 196 times (median 6) more expensive per Defined Daily Dose; (3) 11 safety announcements for five advertised drugs were issued compared to one announcement for one comparator drug; (4) 20 post-marketing studies (7 completed, 13 ongoing) were requested for the advertised drugs versus 10 studies (4 completed, 6 ongoing) for the comparator drugs, and 7 studies (2 completed, 5 ongoing) assessed both an advertised and a comparator drug at 3 year follow-up.

Conclusions and relevance
In this cross-sectional study of medical advertisements published in the Journal of the Danish Medical Association during 2015, the most advertised drugs did not have documented substantial added benefits over older treatments, whereas they were substantially more expensive. From January 2021, the Journal of the Danish Medical Association no longer publishes medical advertisements.
2018 annual dialysis data report of the JSDT Renal Data Registry: patients with hepatitis
Authors:   on behalf of the Japanese Society for Dialysis Therapy Renal Data Registry Committee, Nitta Kosaku , Nakai Shigeru , Masakane Ikuto , Hanafusa Norio , Goto Shunsuke , Taniguchi Masatomo , Hasegawa Takeshi , Wada Atsushi , Hamano Takayuki , Hoshino Junichi , Joki Nobuhiko , Yamamoto Keichi , Miura Kenichiro , Abe Masanori , Nakamoto Hidetomo 
Published: May 2021

Abstract
According to the annual survey of the Japanese Society for Dialysis Therapy Renal Data Registry (JRDR) conducted at the end of 2018, a total of 339,841 patients were receiving dialysis (hereinafter, dialysis patients) in Japan. This survey included an investigation of individual test results for hepatitis B surface antigen (HBsAg), hepatitis C virus (HCV) antibody (HCV-Ab), HCV-RNA, and serum alanine aminotransferase (ALT) (glutamic pyruvic transaminase [GPT]). The survey revealed that among dialysis patients in Japan, the prevalence of HBsAg positivity was 1.38% and the prevalence of HCV-Ab positivity was 4.7% at the end of 2018, both of which were markedly lower than the corresponding rates documented in 2007 (9.8% and 4.7%, respectively). The proportion of HCV-RNA-positive patients among all HCV-Ab-positive patients was 37.5%, which was also markedly lower than the percentage recorded in 2007 (64.0%). The prevalence of HBsAg positivity tended to increase as the dialysis vintage increased. The prevalence of HCV-Ab positivity was also not correlated with the dialysis vintage during the first 30 years of dialysis; however, it tended to increase as the dialysis vintage increased beyond the 30th year.

Trial registration
University hospital Medical Information Network (UMIN) Clinical Trials Registry, UMIN000018641. The JRDR was approved by the ethics committee of the JSDT (approval number 1-3) and was registered on August 8, 2015 (accessed June 2, 2020).
Multidrug-resistant enteric pathogens in older children and adults with diarrhea in Bangladesh: epidemiology and risk factors
Authors: Garbern Stephanie C. , Chu Tzu-Chun , Gainey Monique , Kanekar Samika S. , Nasrin Sabiha , Qu Kexin , Barry Meagan A. , Nelson Eric J. , Leung Daniel T. , Schmid Christopher H. , Alam Nur H. , Levine Adam C. 
Published: May 2021

Abstract
Background
Antimicrobial resistance (AMR) is a global public health threat and is increasingly prevalent among enteric pathogens in low- and middle-income countries (LMICs). However, the burden of multidrug-resistant organisms (MDROs) in older children, adults, and elderly patients with acute diarrhea in LMICs is poorly understood. This study’s aim was to characterize the prevalence of MDR enteric pathogens isolated from patients with acute diarrhea in Dhaka, Bangladesh, and assess a wide range of risk factors associated with MDR.

Methods
This study was a secondary analysis of data collected from children over 5 years, adults, and elderly patients with acute diarrhea at the International Centre for Diarrhoeal Disease Research, Bangladesh Dhaka Hospital between March 2019 and March 2020. Clinical, historical, socio-environmental information, and a stool sample for culture and antimicrobial susceptibility testing were collected from each patient. Univariate statistics and multiple logistic regression were used to assess the prevalence of MDR among enteric pathogens and the association between independent variables and presence of MRDOs among culture-positive patients.

Results
A total of 1198 patients had pathogens isolated by stool culture with antimicrobial susceptibility results. Among culture-positive patients, the prevalence of MDR was 54.3%. The prevalence of MDR was highest in Aeromonas spp. (81.5%), followed by Campylobacter spp. (72.1%), Vibrio cholerae (28.1%), Shigella spp. (26.2%), and Salmonella spp. (5.2%). Factors associated with having MDRO in multiple logistic regression included longer transport time to hospital (>90 min), greater stool frequency, prior antibiotic use prior to hospital presentation, and non-flush toilet use. However, pseudo-R2 was low 0.086, indicating that other unmeasured variables need to be considered to build a more robust predictive model of MDR.

Conclusions
MDR enteric pathogens were common in this study population with clinical, historical, and socio-environmental risk factors associated with MDROs. These findings may help guide clinical decision-making regarding antibiotic use and selection in patients at greatest risk of complications due to MDROs. Further prospective research is urgently needed to determine what additional factors place patients at greatest risk of MDRO, and the best strategies to mitigate the spread of MDR in enteric pathogens.