bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asthma and elevation of anti-citrullinated protein antibodies prior to the onset of rheumatoid arthritis
Authors: Zaccardelli Alessandra , Liu Xinyi , Ford Julia A. , Cui Jing , Lu Bing , Chu Su H. , Schur Peter H. , Speyer Cameron B. , Costenbader Karen H. , Robinson William H. , Sokolove Jeremy , Karlson Elizabeth W. , Camargo Carlos A. , Sparks Jeffrey A. 
Published: November 2019

AbstractBackgroundAnti-citrullinated protein antibodies (ACPA) are central to rheumatoid arthritis (RA) pathogenesis and may develop at inflamed mucosa. We investigated whether asthma, a disease of airway mucosal inflammation, was associated with elevated ACPA before RA diagnosis.MethodsWe performed a nested case-control study among women in two prospective cohorts, the Nurses’ Health Study (NHS; 1976–2014) and NHSII (1989–2015). Blood was obtained on a subset (NHS: 1989–1990; NHSII: 1996–1999). Cases met 1987 ACR or 2010 ACR/EULAR RA criteria by medical record review and were classified as seropositive (ACPA+ or rheumatoid factor positivity) or seronegative by clinical laboratory testing at diagnosis. We identified RA cases with blood drawn before the date of RA diagnosis (index date), matching each to three controls by age, cohort, year, time from blood draw to index date, and menopause. Pre-RA ACPA elevation for cases was defined as >99th percentile of the control distribution on a research assay composed of autoantibodies targeting citrullinated protein epitopes or positivity on the second-generation commercial assay for cyclic citrullinated peptide. Asthma status and covariates were obtained through biennial questionnaires before blood draw. Conditional logistic regression estimated ORs and 95%CIs for RA by pre-RA ACPA and clinical serostatus, adjusted for matching factors, smoking pack-years, passive smoking, and body mass index (BMI).ResultsWe identified 284 incident RA cases and 849 matched controls; mean age at the index date was 61.2 years (SD 10.1). Blood was drawn 9.7 years (mean; SD 5.8) before the index date. We identified 96 (33.8%) RA cases with elevated pre-RA ACPA. At blood draw, 17.7% of pre-RA ACPA+ cases and 6.3% of matched controls (p = 0.0008) reported clinician-diagnosed asthma. After adjusting for matching factors, smoking pack-years, passive smoking, and BMI, asthma was significantly associated with pre-RA ACPA+ RA (OR 3.57, 95%CI 1.58,8.04). Asthma was not associated with overall RA (OR 1.45, 95%CI 0.91,2.31), but was significantly associated with seropositive RA (OR 1.79, 95%CI 1.01,3.18).ConclusionsAsthma was strongly associated with ACPA elevation in blood drawn prior to RA diagnosis, independent of smoking. Chronic mucosal airway inflammation may contribute to ACPA development and RA pathogenesis.
Searching for simple rules in Pseudomonas aeruginosa biofilm formation
Authors: Deveaux William , Selvarajoo Kumar 
Published: November 2019

Abstract
Objective
Living cells display complex and non-linear behaviors, especially when posed to environmental threats. Here, to understand the self-organizing cooperative behavior of a microorganism Pseudomonas aeruginosa, we developed a discrete spatiotemporal cellular automata model based on simple physical rules, similar to Conway’s game of life.

Results
The time evolution model simulations were experimentally verified for P. aeruginosa biofilm for both control and antibiotic azithromycin (AZM) treated condition. Our model suggests that AZM regulates the single cell motility, thereby resulting in delayed, but not abolished, biofilm formation. In addition, the model highlights the importance of reproduction by cell to cell interaction is key for biofilm formation. Overall, this work highlights another example where biological evolutionary complexity may be interpreted using rules taken from theoretical disciplines.
The factors present in regenerating muscles impact bone marrow-derived mesenchymal stromal/stem cell fusion with myoblasts
Authors: Kasprzycka Paulina , Archacka Karolina , Kowalski Kamil , Mierzejewski Bartosz , Zimowska Małgorzata , Grabowska Iwona , Piotrowski Mariusz , Rafałko Milena , Ryżko Agata , Irhashava Aliksandra , Senderowski Kamil , Gołąbek Magdalena , Stremińska Władysława , Jańczyk-Ilach Katarzyna , Koblowska Marta , Iwanicka-Nowicka Roksana , Fogtman Anna , Janowski Mirosław , Walczak Piotr , Ciemerych Maria A. , Brzoska Edyta 
Published: November 2019

AbstractBackgroundSatellite cells, a population of unipotent stem cells attached to muscle fibers, determine the excellent regenerative capability of injured skeletal muscles. Myogenic potential is also exhibited by other cell populations, which exist in the skeletal muscles or come from other niches. Mesenchymal stromal/stem cells inhabiting the bone marrow do not spontaneously differentiate into muscle cells, but there is some evidence that they are capable to follow the myogenic program and/or fuse with myoblasts.MethodsIn the present study we analyzed whether IGF-1, IL-4, IL-6, and SDF-1 could impact human and porcine bone marrow-derived mesenchymal stromal/stem cells (hBM-MSCs and pBM-MSCs) and induce expression of myogenic regulatory factors, skeletal muscle-specific structural, and adhesion proteins. Moreover, we investigated whether these factors could induce both types of BM-MSCs to fuse with myoblasts. IGF-1, IL-4, IL-6, and SDF-1 were selected on the basis of their role in embryonic myogenesis as well as skeletal muscle regeneration.ResultsWe found that hBM-MSCs and pBM-MSCs cultured in vitro in the presence of IGF-1, IL-4, IL-6, or SDF-1 did not upregulate myogenic regulatory factors. Consequently, we confirmed the lack of their naïve myogenic potential. However, we noticed that IL-4 and IL-6 impacted proliferation and IL-4, IL-6, and SDF-1 improved migration of hBM-MSCs. IL-4 treatment resulted in the significant increase in the level of mRNA encoding CD9, NCAM, VCAM, and m-cadherin, i.e., proteins engaged in cell fusion during myotube formation. Additionally, the CD9 expression level was also driven by IGF-1 treatment. Furthermore, the pre-treatment of hBM-MSCs either with IGF-1, IL-4, or SDF-1 and treatment of pBM-MSCs either with IGF-1 or IL-4 increased the efficacy of hybrid myotube formation between these cells and C2C12 myoblasts.ConclusionsTo conclude, our study revealed that treatment with IGF-1, IL-4, IL-6, or SDF-1 affects BM-MSC interaction with myoblasts; however, it does not directly promote myogenic differentiation of these cells.
Randomized SMILES strings improve the quality of molecular generative models
Authors: Arús-Pous Josep , Johansson Simon Viet , Prykhodko Oleksii , Bjerrum Esben Jannik , Tyrchan Christian , Reymond Jean-Louis , Chen Hongming , Engkvist Ola 
Published: November 2019

AbstractRecurrent Neural Networks (RNNs) trained with a set of molecules represented as unique (canonical) SMILES strings, have shown the capacity to create large chemical spaces of valid and meaningful structures. Herein we perform an extensive benchmark on models trained with subsets of GDB-13 of different sizes (1 million, 10,000 and 1000), with different SMILES variants (canonical, randomized and DeepSMILES), with two different recurrent cell types (LSTM and GRU) and with different hyperparameter combinations. To guide the benchmarks new metrics were developed that define how well a model has generalized the training set. The generated chemical space is evaluated with respect to its uniformity, closedness and completeness. Results show that models that use LSTM cells trained with 1 million randomized SMILES, a non-unique molecular string representation, are able to generalize to larger chemical spaces than the other approaches and they represent more accurately the target chemical space. Specifically, a model was trained with randomized SMILES that was able to generate almost all molecules from GDB-13 with a quasi-uniform probability. Models trained with smaller samples show an even bigger improvement when trained with randomized SMILES models. Additionally, models were trained on molecules obtained from ChEMBL and illustrate again that training with randomized SMILES lead to models having a better representation of the drug-like chemical space. Namely, the model trained with randomized SMILES was able to generate at least double the amount of unique molecules with the same distribution of properties comparing to one trained with canonical SMILES.
Antibacterial activity of Bacillus species-derived surfactin on Brachyspira hyodysenteriae and Clostridium perfringens
Authors: Horng Yi-Bing , Yu Yu-Hsiang , Dybus Andrzej , Hsiao Felix Shih-Hsiang , Cheng Yeong-Hsiang 
Published: November 2019

AbstractSwine dysentery and necrotic enteritis are a bane to animal husbandry worldwide. Some countries have already banned the use of antibiotics as growth promoters in animal production. Surfactin is a potential alternative to antibiotics and antibacterial agents. However, the antibacterial activity of Bacillus species-derived surfactin on Brachyspira hyodysenteriae and Clostridium perfringens are still poorly understood. In the current study, the antibacterial effects of surfactin produced from Bacillus subtilis and Bacillus licheniformis on B. hyodysenteriae and C. perfringens were evaluated. Results showed that multiple surfactin isoforms were detected in B. subtilis, while only one surfactin isoform was detected in B. licheniformis fermented products. The surfactin produced from B. subtilis exhibited significant antibacterial activity against B. hyodysenteriae compared with surfactin produced from B. licheniformis. B. subtilis-derived surfactin could inhibit bacterial growth and disrupt the morphology of B. hyodysenteriae. Furthermore, the surfactin produced from B. subtilis have the highest activity against C. perfringens growth. In contrast, B. licheniformis fermented product-derived surfactin had a strong bacterial killing activity against C. perfringens compared with surfactin produced from B. subtilis. These results together suggest that Bacillus species-derived surfactin have potential for development as feed additives and use as a possible substitute for antibiotics to prevent B. hyodysenteriae and C. perfringens-associated disease in the animal industry.
Soil microbial communities of Japanese apricot (Prunus mume) orchard under organic and conventional management
Authors: Cho Hyeon Ji , Lee Young Han , Choi Si-Lim , Seo Dong Cheol , Min Sung Ran , Heo Jae-Young 
Published: November 2019

AbstractOrganic farming has positive effects on soil microbial population, process, and activity. To examine effects of two different management methods (organic farming vs. conventional farming) on the cultivation of Japanese apricot, contents of fatty acid methyl ester (FAME), total glomalin, and soil chemical properties were analyzed and compared. The organic farming practice resulted in significantly higher contents of organic matter, total FAME, total bacteria, Gram-negative bacteria, arbuscular mycorrhizal fungi, and total glomalin than the conventional farming practice. Soil organic matter showed positive correlation with contents of soil microbial biomass, total bacteria, total glomalin, Gram-positive bacteria, Gram-negative bacteria, actinomycetes, and arbuscular mycorrhizal fungi. In 2018, the organic farming practice resulted in lower ratios of cy17:0 and 16:1ω7c than the conventional farming practice, indicating that microbial stress was reduced by the input of organic fertilizer into soil. Based on principal component analyses (PCA) of soil microbial communities, ratios of cy17:0 to 16:1ω7c in orchid soil can be used as microbial indicators to distinguish organically farmed orchard soil from conventionally farmed orchard soil.
Comparison of the adhesive joints’ strength of the similar and dissimilar systems of metal alloy/polymer composite
Authors: Rudawska Anna 
Published: November 2019

AbstractThe aim of the present article is to compare the strength of the adhesive lap joints of the selected materials used in aviation. The joints were made in the similar and dissimilar systems with the use of three epoxy adhesives. Three different adherends were used: the EN AW-7075 aluminium alloy, the aramid-epoxy composite and the carbon-epoxy composite. Three adhesive compounds based on the Epidian 53 epoxy resin and three types of curing agents: two amine curing agents—Z1 (triethylenetetramine curing agent) and IDA, and one polyamide curing agent—PAC (polyaminoamide C) were used to make the adhesive joints. Three variants of similar joints and two variants of dissimilar joints were prepared for the tests. The shear strength was defined according to the ISO 4587 standard, with the use of Zwick/Roell 150 testing machine. In addition, the joined materials’ surface roughness was measured. Based on the strength test’s results, it was observed that the highest strength was obtained by the adhesive joints made with the Epidian 53/PAC/100:80 adhesive compound and that, in the majority of cases; similar joints show higher strength.
An investigation of solar flare effects on equatorial ionosphere and thermosphere using co-ordinated measurements
Authors: Sumod S. G. , Pant Tarun Kumar 
Published: November 2019

AbstractThe response of equatorial ionosphere–thermosphere system to the X3.8 solar flare of January 17, 2005 has been studied using the coordinated measurements of GPS-derived Total Electron Content (TEC), OI 630.0 nm dayglow and magnetic field measurements over a dip equatorial station Trivandrum (8.5° N, 77° E, dip 0.5° N), in India. It has been observed that Equatorial Electrojet (EEJ) as inferred using the ground-based magnetometers and GPS-derived TEC measurements show prompt enhancements during the peak flare, as expected. Interestingly, the temporal evolution of TEC at different latitudes revealed that the X3.8 class flare produced significant weakening of the plasma fountain and hence in the Equatorial Ionization Anomaly (EIA). Furthermore, the response of OI 630.0 nm dayglow during the flare is found to be strongly affected by the prevailing electrodynamics. The plausible physical mechanism for these effects is discussed in context of the current understanding of the neutral and electrodynamical coupling processes.
Measuring energy, macro and micronutrient intake in UK children and adolescents: a comparison of validated dietary assessment tools
Authors: Bush Linda A. , Hutchinson Jayne , Hooson Jozef , Warthon-Medina Marisol , Hancock Neil , Greathead Katharine , Knowles Bethany , Vargas-Garcia Elisa J. , Gibson Lauren E. , Margetts Barrie , Robinson Sian , Ness Andy , Alwan Nisreen A. , Wark Petra A. , Roe Mark , Finglas Paul , Steer Toni , Page Polly , Johnson Laura , Roberts Katharine , Amoutzopoulos Birdem , Greenwood Darren C. , Cade Janet E. 
Published: November 2019

Abstract
Background
Measuring dietary intake in children and adolescents can be challenging due to misreporting, difficulties in establishing portion size and reliance on recording dietary data via proxy reporters. The aim of this review was to present results from a recent systematic review of reviews reporting and comparing validated dietary assessment tools used in younger populations in the UK.

Methods
Validation data for dietary assessment tools used in younger populations (≤18 years) were extracted and summarised using results from a systematic review of reviews of validated dietary assessment tools. Mean differences and Bland-Altman limits of agreement (LOA) between the test and reference tool were extracted or calculated and compared for energy, macronutrients and micronutrients.

Results
Seventeen studies which reported validation of 14 dietary assessment tools (DATs) were identified with relevant nutrition information. The most commonly validated nutrients were energy, carbohydrate, protein, fat, calcium, iron, folate and vitamin C. There were no validated DATs reporting assessment of zinc, iodine or selenium intake. The most frequently used reference method was the weighed food diary, followed by doubly labelled water and 24 h recall. Summary plots were created to facilitate comparison between tools. On average, the test tools reported higher mean intakes than the reference methods with some studies consistently reporting wide LOA. Out of the 14 DATs, absolute values for LOA and mean difference were obtained for 11 DATs for EI. From the 24 validation results assessing EI, 16 (67%) reported higher mean intakes than the reference. Of the seven (29%) validation studies using doubly labelled water (DLW) as the reference, results for the test DATs were not substantially better or worse than those using other reference measures. Further information on the studies from this review is available on the www.nutritools.org website.

Conclusions
Validated dietary assessment tools for use with children and adolescents in the UK have been identified and compared. Whilst tools are generally validated for macronutrient intakes, micronutrients are poorly evaluated. Validation studies that include estimates of zinc, selenium, dietary fibre, sugars and sodium are needed.
Developing a competency taxonomy for teacher design knowledge in technology-enhanced learning environments: a literature review
Authors: Kim Mi Song 
Published: November 2019

AbstractRecent research in technology-enhanced learning environments has indicated the need to redefine the role of teachers as designers. This supports successful learners better able to adapt to twenty-first century education, in particular STEM education. However, such a repositioning of teaching as a design science challenges teachers to reconceptualize educational practice as an act of design, not in the artistic meaning of the word. Our recent research finding also indicated that teacher design knowledge (TDK) processes are often invisible to both the teacher educators and the teachers. To respond to these challenges, this paper will define TDK for STEM teachers by making TDK visible in the form of a TDK competency taxonomy. A systematic literature review was conducted to identify the characteristics of teaching practices in technology-enhanced learning environments. This TDK competency taxonomy consists of four main categories drawing on existing literature on teacher design work and teacher instructional design: data practice, design practice, knowledge creation practice, and professional teaching practice. The implications of these findings were discussed.
Individualised prediction of psychosis in individuals meeting at-risk mental state (ARMS) criteria: protocol for a systematic review of clinical prediction models
Authors: Bonnett Laura J. , Varese Filippo , Smith Catrin Tudur , Flores Allan , Yung Alison R. 
Published: November 2019

Abstract
Background
Psychotic disorders affect about 3% of the population worldwide and are associated with high personal, social and economic costs. They tend to have their first onset in adolescence. Increasing emphasis has been placed on early intervention to detect illness and minimise disability. In the late 1990s, criteria were developed to identify individuals at high risk for psychotic disorder. These are known as the at-risk mental state (ARMS) criteria. While ARMS individuals have a risk of psychosis much greater than the general population, most individuals meeting the ARMS criteria will not develop psychosis. Despite this, the National Institute for Health and Care Excellence recommends cognitive behavioural therapy (CBT) for all ARMS people.
Clinical prediction models that combine multiple patient characteristics to predict individual outcome risk may facilitate identification of patients who would benefit from CBT and conversely those that would benefit from less costly and less intensive regular mental state monitoring. The study will systematically review the evidence on clinical prediction models aimed at making individualised predictions for the transition to psychosis.

Methods
Database searches will be conducted on PsycINFO, Medline, EMBASE and CINAHL. Reference lists and subject experts will be utilised. No language restrictions will be placed on publications, but searches will be restricted to 1994 onwards, the initial year of the first prospective study using ARMS criteria. Studies of any design will be included if they examined, in ARMS patients, whether more than one factor in combination is associated with the risk of transition to psychosis. Study quality will be assessed using the prediction model risk of bias assessment tool (PROBAST). Clinical prediction models will be summarised qualitatively, and if tested in multiple validation studies, their predictive performance will be summarised using a random-effects meta-analysis model.

Discussion
The results of the review will identify prediction models for the risk of transition to psychosis. These will be informative for clinicians currently treating ARMS patients and considering potential preventive interventions. The conclusions of the review will also inform the possible update and external validation of prediction models and clinical prediction rules to identify those at high or low risk of transition to psychosis.

Trial registration
The review has been registered with PROSPERO (CRD42018108488).
Business ecosystem modeling- the hybrid of system modeling and ecological modeling: an application of the smart grid
Authors: Ma Zheng 
Published: November 2019

AbstractBusiness ecosystem is popularly used to investigate a complex social system with the business perspective, and particularly contributes to the understanding of actors and their relations in the innovation research. However, the aspect of business ecosystem modeling is limited discussed in the literature, although the importance has emerged significantly in recent years due to the emphasis on cross-disciplinary research and digitalization with artificial intelligence. Therefore, this paper proposes a framework for business ecosystem modeling with the discussion of system engineering and ecological modeling. The domain of smart grid is selected to demonstrate how system engineering, especially standards and ontologies contribute to the business ecosystem modeling. The proposed framework of the business ecosystem modeling includes three parts and nine stages that combines theories from system engineering, ecology, and business ecosystem. Part I-Business ecosystem architecture development includes four stages which aims to identify a target business ecosystem and its elements (actors, roles, and interactions). Part II-Factor analysis includes two stages to identify potential changes (and the dimensions of the changes) in the ecosystem. Part III- Ecosystem simulation and reconfiguration aims to use simulations to investigate the transition of an ecosystem and the re-configurated ecosystem. The framework not only provides a systematic approach for modeling a business ecosystem but also provides a methodological foundation for research on the aspect of complex systems in the business ecosystem field.