bluuebunny/crossref_metadata_2025_split huggingface dataset:
Research Articles in Simplified HTML: a Web-first format for HTML-based scholarly articles
Authors: Peroni Silvio , Osborne Francesco , Di Iorio Angelo , Nuzzolese Andrea Giovanni , Poggi Francesco , Vitali Fabio , Motta Enrico 
Published: October 2017

PurposeThis paper introduces the Research Articles in Simplified HTML (or RASH), which is a Web-first format for writing HTML-based scholarly papers; it is accompanied by the RASH Framework, a set of tools for interacting with RASH-based articles. The paper also presents an evaluation that involved authors and reviewers of RASH articles submitted to the SAVE-SD 2015 and SAVE-SD 2016 workshops.DesignRASH has been developed aiming to: be easy to learn and use; share scholarly documents (and embedded semantic annotations) through the Web; support its adoption within the existing publishing workflow.FindingsThe evaluation study confirmed that RASH is ready to be adopted in workshops, conferences, and journals and can be quickly learnt by researchers who are familiar with HTML.Research LimitationsThe evaluation study also highlighted some issues in the adoption of RASH, and in general of HTML formats, especially by less technically savvy users. Moreover, additional tools are needed, e.g., for enabling additional conversions from/to existing formats such as OpenXML.Practical ImplicationsRASH (and its Framework) is another step towards enabling the definition of formal representations of the meaning of the content of an article, facilitating its automatic discovery, enabling its linking to semantically related articles, providing access to data within the article in actionable form, and allowing integration of data between papers.Social ImplicationsRASH addresses the intrinsic needs related to the various users of a scholarly article: researchers (focussing on its content), readers (experiencing new ways for browsing it), citizen scientists (reusing available data formally defined within it through semantic annotations), publishers (using the advantages of new technologies as envisioned by the Semantic Publishing movement).ValueRASH helps authors to focus on the organisation of their texts, supports them in the task of semantically enriching the content of articles, and leaves all the issues about validation, visualisation, conversion, and semantic data extraction to the various tools developed within its Framework.
Investigation of aerodynamic coefficients at Mach 6 over conical, hemispherical and flat-face spiked body
Authors: Kalimuthu R. , Mehta R. C. , Rathakrishnan E. 
Published: October 2017

ABSTRACTA forward spike attached to a blunt body significantly alters its flow field characteristics and influences aerodynamic characteristics at hypersonic flow due to formation of separated flow and re-circulation region around the spiked body. An experimental investigation was performed to measure aerodynamic forces for spikes blunt bodies with a conical, hemispherical and flat-face spike at Mach 6 and at an angle-of-attack range from 0° to 8° and length-to-diameterL/Dratio of spike varies from 0.5 to 2.0, whereLis the length of the spike andDis diameter of blunt body. The shape of the leading edge of the spiked blunt body reveals different types of flow field features in the formation of a shock wave, shear layer, flow separation, re-circulation region and re-attachment shock. They are analysed with the help of schlieren pictures. The shock distance ahead of the hemisphere and the flat-face spike is compared with the analytical solution and is showing satisfactory agreement with the schlieren pictures. The influence of geometrical parameters of the spike, the shape of the spike tip and angle-of-attack on the aerodynamic coefficients are investigated by measuring aerodynamic forces in a hypersonic wind tunnel. It is found that a maximum reduction of drag of about 77% was found for hemisphere spike ofL/D= 2.0 at zero angle-of-attack. Consideration for compensation of increased pitching moment is required to stabilise the aerodynamic forces.
Apical hypertrophic cardiomyopathy treated as ST-elevation myocardial infarction
Authors: Parr Christopher J. , Sharma Rajat , Garber Philip J. 
Published: October 2017

AbstractElectrocardiographic changes resulting from apical hypertrophic cardiomyopathy may mimic an acute coronary syndrome. A 67-year-old Sudanese male without cardiac risk factors presented to hospital with chest pain and electrocardiographic findings of septal ST-segment elevation, ST-segment depression in V4-V6, and diffuse T-wave inversion. He was treated as an acute ST-elevation myocardial infarction with thrombolytics. There was no cardiac biomarker rise and coronary angiography did not reveal evidence of significant coronary arterial disease. Ventriculography, transthoracic echocardiography, and cardiac magnetic resonance imaging were consistent with apical hypertrophic cardiomyopathy. The patient was discharged three days later with outpatient cardiology follow-up. We highlight the clinical and electrocardiographic findings of apical hypertrophic cardiomyopathy, with an emphasis on distinguishing this from acute myocardial infarction.
In vitro and in vivo antioxidant potential of milks, yoghurts, fermented milks and cheeses: a narrative review of evidence
Authors: Fardet Anthony , Rock Edmond 
Published: October 2017

AbstractThe antioxidant potential (AP) is an important nutritional property of foods, as increased oxidative stress is involved in most diet-related chronic diseases. In dairy products, the protein fraction contains antioxidant activity, especially casein. Other antioxidants include: antioxidant enzymes; lactoferrin; conjugated linoleic acid; coenzyme Q10; vitamins C, E, A and D3; equol; uric acid; carotenoids; and mineral activators of antioxidant enzymes. The AP of dairy products has been extensively studied in vitro, with few studies in animals and human subjects. Available in vivo studies greatly differ in their design and objectives. Overall, on a 100 g fresh weight-basis, AP of dairy products is close to that of grain-based foods and vegetable or fruit juices. Among dairy products, cheeses present the highest AP due to their higher protein content. AP of milk increases during digestion by up to 2·5 times because of released antioxidant peptides. AP of casein is linked to specific amino acids, whereas β-lactoglobulin thiol groups play a major role in the AP of whey. Thermal treatments such as ultra-high temperature processing have no clear effect on the AP of milk. Raw fat-rich milks have higher AP than less fat-rich milk, because of lipophilic antioxidants. Probiotic yoghurts and fermented milks have higher AP than conventional yoghurt and milk because proteolysis by probiotics releases antioxidant peptides. Among the probiotics, Lactobacillus casei/acidophilus leads to the highest AP. The data are insufficient for cheese, but fermentation-based changes appear to make a positive impact on AP. In conclusion, AP might participate in the reported dairy product-protective effects against some chronic diseases.
Effects of videoconference-embedded classrooms (VEC) on learners’ perceptions toward English as an international language (EIL)
Authors: Lee Ju Seong , Nakamura Yuji , Sadler Randall 
Published: October 2017

AbstractDespite the accumulated body of research on teaching English as an international language (EIL), few have offered a detailed overview of how to implement an EIL classroom, and still fewer empirical studies have been conducted. Twenty-one university students at a Japanese university participated in the study in the spring semester of 2015. The videoconference-embedded classroom (VEC) as an instructional intervention was implemented for 14 weeks: (1) pre-videoconference task (i.e. reading and presenting/discussing EIL issues) (11 weeks), (2) during-videoconference task (i.e. interacting online with EIL experts from three circle countries) (2 weeks), and (3) post-videoconference task (i.e. writing/presenting the final term paper on EIL issues) (1 week). Using a mixed research method consisting of a questionnaire, post-course class evaluations in spring 2014 (without VEC) and spring 2015 (with VEC), and in-class observations, VEC was found to have important pedagogical benefits as it created an interactive learning environment and deepened the understanding of the EIL content. Additionally, 81% of the participants had positive perceptions of EIL. Pedagogically, practitioners can implement EIL ideas using VEC pedagogy at the instructional level. Theoretically, it can also add new empirical findings to the field, which may help bridge a discrepancy between theory and practice.
The impact of reference isocentre position on set-up errors in head-and-neck image-guided radiotherapy
Authors: Lenko Helena , Peterlin Primož 
Published: October 2017

AbstractAimTo examine and quantify set-up errors in patient positioning in head-and-neck radiotherapy and to investigate the impact of the choice of reference isocentre—on the patient neck or patient skull—on the magnitude of set-up errors.Materials and methodsSet-up position corrections obtained using online kV 2D/2D matching were recorded automatically for every treatment fraction. 3,413 treatment records for 117 patients treated with volumetric modulated arc therapy during 2013 and 2014 on a single treatment machine in our clinic were analysed. In 79 treatment plans the reference isocentre was set to the patient skull, and in 47 to the neck.ResultsStandard deviation of group systematic error in the vertical, longitudinal and lateral direction and the couch rotation were found to be 2·5 mm, 2·1 mm, 1·9 mm and 0·43° (skull) and 2·5 mm, 1·8 mm, 1·7 mm and 0·49° (neck), respectively. Random error of the vertical, longitudinal, lateral and rotational position correction was 1·8 mm, 1·5 mm, 1·6 mm and 0·62° (skull) and 1·9 mm, 1·6 mm, 1·5 mm and 0·60° (neck), respectively. Positional shifts in different directions were found to be uncorrelated.ConclusionsNeither reference isocentre set-up shows a clear advantage over the other in terms of interfraction set-up error.
Nucleosome stability measured in situ by automated quantitative imaging
Authors: Imre László , Simándi Zoltán , Horváth Attila , Fenyőfalvi György , Nánási Péter , Niaki Erfaneh Firouzi , Hegedüs Éva , Bacsó Zsolt , Weyemi Urbain , Mauser Rebekka , Ausio Juan , Jeltsch Albert , Bonner William , Nagy László , Kimura Hiroshi , Szabó Gábor 
Published: October 2017

AbstractCurrent approaches have limitations in providing insight into the functional properties of particular nucleosomes in their native molecular environment. Here we describe a simple and powerful method involving elution of histones using intercalators or salt, to assess stability features dependent on DNA superhelicity and relying mainly on electrostatic interactions, respectively, and measurement of the fraction of histones remaining chromatin-bound in the individual nuclei using histone type- or posttranslational modification- (PTM-) specific antibodies and automated, quantitative imaging. The method has been validated in H3K4me3 ChIP-seq experiments, by the quantitative assessment of chromatin loop relaxation required for nucleosomal destabilization, and by comparative analyses of the intercalator and salt induced release from the nucleosomes of different histones. The accuracy of the assay allowed us to observe examples of strict association between nucleosome stability and PTMs across cell types, differentiation state and throughout the cell-cycle in close to native chromatin context, and resolve ambiguities regarding the destabilizing effect of H2A.X phosphorylation. The advantages of the in situ measuring scenario are demonstrated via the marked effect of DNA nicking on histone eviction that underscores the powerful potential of topological relaxation in the epigenetic regulation of DNA accessibility.
Bagging Nearest-Neighbor Prediction independence Test: an efficient method for nonlinear dependence of two continuous variables
Authors: Wang Yi , Li Yi , Liu Xiaoyu , Pu Weilin , Wang Xiaofeng , Wang Jiucun , Xiong Momiao , Yao Shugart Yin , Jin Li 
Published: October 2017

AbstractTesting dependence/correlation of two variables is one of the fundamental tasks in statistics. In this work, we proposed an efficient method for nonlinear dependence of two continuous variables (X and Y). We addressed this research question by using BNNPT (Bagging Nearest-Neighbor Prediction independence Test, software available at https://sourceforge.net/projects/bnnpt/). In the BNNPT framework, we first used the value of X to construct a bagging neighborhood structure. We then obtained the out of bag estimator of Y based on the bagging neighborhood structure. The square error was calculated to measure how well Y is predicted by X. Finally, a permutation test was applied to determine the significance of the observed square error. To evaluate the strength of BNNPT compared to seven other methods, we performed extensive simulations to explore the relationship between various methods and compared the false positive rates and statistical power using both simulated and real datasets (Rugao longevity cohort mitochondrial DNA haplogroups and kidney cancer RNA-seq datasets). We concluded that BNNPT is an efficient computational approach to test nonlinear correlation in real world applications.
Moiré Superstructure and Dimensional Crossover of 2D Electronic States on Nanoscale Lead Quantum Films
Authors: Kim Hyo Sung , Gye Gyeongcheol , Lee Sung-Hoon , Wang Lihai , Cheong Sang-Wook , Yeom Han Woong 
Published: October 2017

AbstractWe investigate using scanning tunneling microscopy and spectroscopy electronic aspects of Moiré superstructures in nanoscale Pb quantum films grown on IrTe2, which is a unique layered material with charge-order transitions into stripe phases. Pb ultrathin films exhibit a Moiré superstructure due to the lattice mismatch of Pb and IrTe2, which produces strong lateral electronic modulation of hexagonal symmetry and discreet subbands. Moreover, strongly anisotropic or 1D electronic states are formed in Pb films as modulated by the stripe charge order. Present results indicate the controllability of lateral electronic structures of various ultrathin films by extra interfacial potentials due not only to Moiré superstructures but also to novel electronic orderings of substrates.
Safety assessment of antibiotic and probiotic feed additives for Gallus gallus domesticus
Authors: Neveling D. P. , van Emmenes L. , Ahire J. J. , Pieterse E. , Smith C. , Dicks L. M. T. 
Published: October 2017

AbstractAntibiotics in feed select for resistant strains and is thus a threat to human health. In this study, the effect of a multi-strain probiotic and antibiotics on the growth and health of broilers was studied. Equal numbers of broilers received on a daily basis either a multi-strain probiotic or a combination of sulphadiazine, colistin and trimethoprim, whereas the control group received standard feed. The villi of immature broilers (19 days old) administered antibiotics had a larger surface area and their lymphocyte and basophil counts were higher compared to broilers from the probiotic and control groups. The cecal microbiomes of mature broilers (29 days old) that received probiotics had higher levels of Enterobacteriaceae, but lower numbers of Clostridiales, Brucellaceae, Synergistaceae, Erysipelotrichaceae and Coriobacteriaceae compared to the antibiotic-treated group. A decline in the bioluminescence of Listeria monocytogenes observed for broilers on probiotics suggested that the probiotic may be used to control bacterial infections. No significant differences in total red blood cell, haemoglobin and haematocrit content, and mean values for corpuscular volume, corpuscular haemoglobin and corpuscular haemoglobin numbers were recorded amongst broilers from the different treatment groups. This study provides valuable information on the health and performance of broilers when administered probiotics and antibiotics as additives.
Genetic variants affecting equivalent protein family positions reflect human diversity
Authors: Raimondi Francesco , Betts Matthew J. , Lu Qianhao , Inoue Asuka , Gutkind J. Silvio , Russell Robert B. 
Published: October 2017

AbstractMembers of diverse protein families often perform overlapping or redundant functions meaning that different variations within them could reflect differences between individual organisms. We investigated likely functional positions within aligned protein families that contained a significant enrichment of nonsynonymous variants in genomes of healthy individuals. We identified more than a thousand enriched positions across hundreds of family alignments with roles indicative of mammalian individuality, including sensory perception and the immune system. The most significant position is the Arginine from the Olfactory receptor “DRY” motif, which has more variants in healthy individuals than all other positions in the proteome. Odorant binding data suggests that these variants lead to receptor inactivity, and they are mostly mutually exclusive with other loss-of-function (stop/frameshift) variants. Some DRY Arginine variants correlate with smell preferences in sub-populations and all 2,504 humans studied contain a unique spectrum of active and inactive receptors. The many other variant enriched positions, across hundreds of other families might also provide insights into individual differences.
Reactive metabolites of acetaminophen activate and sensitize the capsaicin receptor TRPV1
Authors: Eberhardt Mirjam J. , Schillers Florian , Eberhardt Esther M. , Risser Linus , de la Roche Jeanne , Herzog Christine , Echtermeyer Frank , Leffler Andreas 
Published: October 2017

AbstractThe irritant receptor TRPA1 was suggested to mediate analgesic, antipyretic but also pro-inflammatory effects of the non-opioid analgesic acetaminophen, presumably due to channel activation by the reactive metabolites parabenzoquinone (pBQ) and N-acetyl-parabenzoquinonimine (NAPQI). Here we explored the effects of these metabolites on the capsaicin receptor TRPV1, another redox-sensitive ion channel expressed in sensory neurons. Both pBQ and NAPQI, but not acetaminophen irreversibly activated and sensitized recombinant human and rodent TRPV1 channels expressed in HEK 293 cells. The reducing agents dithiothreitol and N-acetylcysteine abolished these effects when co-applied with the metabolites, and both pBQ and NAPQI failed to gate TRPV1 following substitution of the intracellular cysteines 158, 391 and 767. NAPQI evoked a TRPV1-dependent increase in intracellular calcium and a potentiation of heat-evoked currents in mouse spinal sensory neurons. Although TRPV1 is expressed in mouse hepatocytes, inhibition of TRPV1 did not alleviate acetaminophen-induced hepatotoxicity. Finally, intracutaneously applied NAPQI evoked burning pain and neurogenic inflammation in human volunteers. Our data demonstrate that pBQ and NAQPI activate and sensitize TRPV1 by interacting with intracellular cysteines. While TRPV1 does not seem to mediate acetaminophen-induced hepatotoxicity, our data identify TRPV1 as a target of acetaminophen with a potential relevance for acetaminophen-induced analgesia, antipyresia and inflammation.
Enhancing robustness of interdependent network under recovery based on a two-layer-protection strategy
Authors: Gong Maoguo , Wang Yixing , Wang Shanfeng , Liu Wenfeng 
Published: October 2017

AbstractThe robustness of coupled networks has attracted great attention recently, because the spread of failures from one network to its coupled network makes the coupled networks more vulnerable. Most existing achievements mainly focused on the integrity properties of coupled networks. However, failures also exist when networks are being reconstructed. Moreover, existing node-protection methods which aim to enhance the robustness of coupled networks only protect the influential nodes in one layer. In this paper, firstly, a two-layer-protection strategy is proposed to enhance the robustness of coupled networks under their reconstruction. Secondly, we adopt five strategies based on different centralities to select influential nodes, and propose a two-layer vision for each of them. Lastly, experiments on three different coupled networks show that by applying the two-layer-protection strategy, the robustness of coupled networks can be enhanced more efficiently compared with other methods which only protect nodes in one layer.
Organs on chip approach: a tool to evaluate cancer -immune cells interactions
Authors: Biselli Elena , Agliari Elena , Barra Adriano , Bertani Francesca Romana , Gerardino Annamaria , De Ninno Adele , Mencattini Arianna , Di Giuseppe Davide , Mattei Fabrizio , Schiavoni Giovanna , Lucarini Valeria , Vacchelli Erika , Kroemer Guido , Di Natale Corrado , Martinelli Eugenio , Businaro Luca 
Published: October 2017

AbstractIn this paper we discuss the applicability of numerical descriptors and statistical physics concepts to characterize complex biological systems observed at microscopic level through organ on chip approach. To this end, we employ data collected on a microfluidic platform in which leukocytes can move through suitably built channels toward their target. Leukocyte behavior is recorded by standard time lapse imaging. In particular, we analyze three groups of human peripheral blood mononuclear cells (PBMC): heterozygous mutants (in which only one copy of the FPR1 gene is normal), homozygous mutants (in which both alleles encoding FPR1 are loss-of-function variants) and cells from ‘wild type’ donors (with normal expression of FPR1). We characterize the migration of these cells providing a quantitative confirmation of the essential role of FPR1 in cancer chemotherapy response. Indeed wild type PBMC perform biased random walks toward chemotherapy-treated cancer cells establishing persistent interactions with them. Conversely, heterozygous mutants present a weaker bias in their motion and homozygous mutants perform rather uncorrelated random walks, both failing to engage with their targets. We next focus on wild type cells and study the interactions of leukocytes with cancerous cells developing a novel heuristic procedure, inspired by Lyapunov stability in dynamical systems.
Circulating microRNAs: a novel potential biomarker for diagnosing acute aortic dissection
Authors: Dong Jian , Bao Junmin , Feng Rui , Zhao Zhiqing , Lu Qingsheng , Wang Guokun , Li Haiyan , Su Dingfeng , Zhou Jian , Jing Qing , Jing Zaiping 
Published: October 2017

AbstractAcute aortic dissection (AAD) is a catastrophic emergency with high mortality and misdiagnosis rate. We aimed to determine whether circulating microRNAs allow to distinguish AAD from healthy controls and chest pain patients without AAD (CP). Plasma microRNAs expression were determined in 103 participants, including 37 AAD patients, 26 chronic aortic dissection patients, 17 healthy volunteers, 23 patients without AAD. We selected 16 microRNAs from microarray screening as candidates for further testing via qRT-PCR. The results showed that plasma miR-15a in patients with AAD (n = 37) had significantly higher expression levels than it from control group (n = 40; P = 0.008). By receiver operating characteristic curve analysis, the sensitivity was 75.7%; the specificity was 82.5%; and the AUC was 0.761 for detection of AAD. Furthermore, 37 patients with AAD had significantly higher plasma expression levels of let-7b, miR-15a, miR-23a and hcmv-miR-US33-5p compared with 14 CP patients of 40 controls (P = 0.000, 0.000, 0.026 and 0.011, respectively). The corresponding sensitivity were 79.4%, 75.7%, 91.9% and 73.5%, respectively; the specificity were 92.9%, 100%, 85.7% and 85.7%, respectively; and the AUCs of these microRNAs were 0.887, 0.855, 0.925 and 0.815, respectively. These data indicate that plasma miR-15a and miR-23a have promising clinical value in diagnosing AAD.