bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression and characterization of recombinant Par j 1 and Par j 2 resembling the allergenic epitopes of Parietaria judaica pollen
Authors: Dorofeeva Yulia , Colombo Paolo , Blanca Miguel , Mari Adriano , Khanferyan Roman , Valenta Rudolf , Focke-Tejkl Margarete 
Published: October 2019

AbstractThe weed wall pellitory, Parietaria judaica, is one the most important pollen allergen sources in the Mediterranean area causing severe symptoms of hay fever and asthma in allergic patients. We report the expression of the major Parietaria allergens, Par j 1 and Par j 2 which belong to the family of lipid transfer proteins, in insect cells. According to circular dichroism analysis and gel filtration, the purified allergens represented folded and monomeric proteins. Insect cell-expressed, folded Par j 2 exhibited higher IgE binding capacity and more than 100-fold higher allergenic activity than unfolded Escherichia coli-expressed Par j 2 as demonstrated by IgE ELISA and basophil activation testing. IgE ELISA inhibition assays showed that Par j 1 and Par j 2, contain genuine and cross-reactive IgE epitopes. IgG antibodies induced by immunization with Par j 2 inhibited binding of allergic patients IgE to Par j 1 only partially. IgE inhibition experiments demonstrated that insect cell-expressed Par j 1 and Par j 2 together resembled the majority of allergenic epitopes of the Parietaria allergome and therefore both should be used for molecular diagnosis and the design of vaccines for allergen-specific immunotherapy of Parietaria allergy.
Human Adipose-derived Pericytes Display Steroidogenic Lineage Potential in Vitro and Influence Leydig Cell Regeneration in Vivo in Rats
Authors: Curley Michael , Gonzalez Zaniah N. , Milne Laura , Hadoke Patrick , Handel Ian , Péault Bruno , Smith Lee B. 
Published: October 2019

AbstractExogenous androgen replacement is used to treat symptoms associated with low testosterone in males. However, adverse cardiovascular risk and negative fertility impacts impel development of alternative approaches to restore/maintain Leydig cell (LC) androgen production. Stem Leydig cell (SLC) transplantation shows promise in this regard however, practicality of SLC isolation/transplantation impede clinical translation. Multipotent human adipose-derived perivascular stem cells (hAd-PSCs) represent an attractive extragonadal stem cell source for regenerative therapies in the testis but their therapeutic potential in this context is unexplored. We asked whether hAd-PSCs could be converted into Leydig-like cells and determined their capacity to promote regeneration in LC-ablated rat testes. Exposure of hAd-PSCs to differentiation-inducing factors in vitro upregulated steroidogenic genes but did not fully induce LC differentiation. In vivo, no difference in LC-regeneration was noted between Sham and hAd-PSC-transplanted rats. Interestingly, Cyp17a1 expression increased in hAd-PSC-transplanted testes compared to intact vehicle controls and the luteinising hormone/testosterone ratio returned to Vehicle control levels which was not the case in EDS + Sham animals. Notably, hAd-PSCs were undetectable one-month after transplantation suggesting this effect is likely mediated via paracrine mechanisms during the initial stages of regeneration; either directly by interacting with regenerating LCs, or through indirect interactions with trophic macrophages.
Coetaneous catalytic kinetic resolution of alkynes and azides through asymmetric triazole formation
Authors: Brittain William D. G. , Dalling Andrew G. , Sun Zhenquan , Duff Cécile S. Le , Male Louise , Buckley Benjamin R. , Fossey John S. 
Published: October 2019

AbstractA non-enzymatic simultaneous (coined coetaneous) kinetic resolution of a racemic alkyne and racemic azide, utilising an asymmetric CuAAC reaction is reported. The use of a CuCl (R,R)-Ph-Pybox catalyst system effects a simultaneous kinetic resolution of two racemic starting materials to give one major triazolic diastereoisomer in the ratio 74:12:4:10 (dr 84:16, 90% ee maj). The corresponding control reaction using an achiral copper catalyst gives the four possible diastereoisomers in a 23:27:23:27 ratio, demonstrating minimal inherent substrate control.
Large scale and information effects on cooperation in public good games
Authors: Pereda María , Tamarit Ignacio , Antonioni Alberto , Cuesta Jose A. , Hernández Penélope , Sánchez Angel 
Published: October 2019

AbstractThe problem of public good provision is central in economics and touches upon many challenging societal issues, ranging from climate change mitigation to vaccination schemes. However, results which are supposed to be applied to a societal scale have only been obtained with small groups of people, with a maximum group size of 100 being reported in the literature. This work takes this research to a new level by carrying out and analysing experiments on public good games with up to 1000 simultaneous players. The experiments are carried out via an online protocol involving daily decisions for extended periods. Our results show that within those limits, participants’ behaviour and collective outcomes in very large groups are qualitatively like those in smaller ones. On the other hand, large groups imply the difficulty of conveying information on others’ choices to the participants. We thus consider different information conditions and show that they have a drastic effect on subjects’ contributions. We also classify the individual decisions and find that they can be described by a moderate number of types. Our findings allow to extend the conclusions of smaller experiments to larger settings and are therefore a relevant step forward towards the understanding of human behaviour and the organisation of our society.
Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer
Authors: Flam Emily L. , Danilova Ludmila , Kelley Dylan Z. , Stavrovskaya Elena , Guo Theresa , Considine Michael , Qian Jiang , Califano Joseph A. , Favorov Alexander , Fertig Elana J. , Gaykalova Daria A. 
Published: October 2019

AbstractCurrent literature suggests that epigenetically regulated super-enhancers (SEs) are drivers of aberrant gene expression in cancers. Many tumor types are still missing chromatin data to define cancer-specific SEs and their role in carcinogenesis. In this work, we develop a simple pipeline, which can utilize chromatin data from etiologically similar tumors to discover tissue-specific SEs and their target genes using gene expression and DNA methylation data. As an example, we applied our pipeline to human papillomavirus-related oropharyngeal squamous cell carcinoma (HPV + OPSCC). This tumor type is characterized by abundant gene expression changes, which cannot be explained by genetic alterations alone. Chromatin data are still limited for this disease, so we used 3627 SE elements from public domain data for closely related tissues, including normal and tumor lung, and cervical cancer cell lines. We integrated the available DNA methylation and gene expression data for HPV + OPSCC samples to filter the candidate SEs to identify functional SEs and their affected targets, which are essential for cancer development. Overall, we found 159 differentially methylated SEs, including 87 SEs that actively regulate expression of 150 nearby genes (211 SE-gene pairs) in HPV + OPSCC. Of these, 132 SE-gene pairs were validated in a related TCGA cohort. Pathway analysis revealed that the SE-regulated genes were associated with pathways known to regulate nasopharyngeal, breast, melanoma, and bladder carcinogenesis and are regulated by the epigenetic landscape in those cancers. Thus, we propose that gene expression in HPV + OPSCC may be controlled by epigenetic alterations in SE elements, which are common between related tissues. Our pipeline can utilize a diversity of data inputs and can be further adapted to SE analysis of diseased and non-diseased tissues from different organisms.
Osmotically Driven and Detected DNA Translocations
Authors: McMullen Angus , Araujo George , Winter Michele , Stein Derek 
Published: October 2019

AbstractA salinity gradient propels a DNA molecule through a solid-state nanopore and generates an ionic current whose change allows for the detection of the translocation. Measurements and theoretical analyses reveal the role of diffusio-osmosis in driving these phenomena: After accounting for known salinity-dependent electrode effects, the measured current change caused by the presence of a DNA molecule inside the nanopore and the DNA translocation speed through it both increase with the magnitude of the applied salinity gradients. The effects are consistent with the theory of diffuisio-osmosis and strong enough to enable DNA translocations to overcome an applied retarding potential of tens of millivolts. This work illustrates how salinity gradients can be used to power and operate a nanopore sensor.
Marine heat wave and multiple stressors tip bull kelp forest to sea urchin barrens
Authors: Rogers-Bennett L. , Catton C. A. 
Published: October 2019

AbstractExtreme climatic events have recently impacted marine ecosystems around the world, including foundation species such as corals and kelps. Here, we describe the rapid climate-driven catastrophic shift in 2014 from a previously robust kelp forest to unproductive large scale urchin barrens in northern California. Bull kelp canopy was reduced by >90% along more than 350 km of coastline. Twenty years of kelp ecosystem surveys reveal the timing and magnitude of events, including mass mortalities of sea stars (2013-), intense ocean warming (2014–2017), and sea urchin barrens (2015-). Multiple stressors led to the unprecedented and long-lasting decline of the kelp forest. Kelp deforestation triggered mass (80%) abalone mortality (2017) resulting in the closure in 2018 of the recreational abalone fishery worth an estimated $44 M and the collapse of the north coast commercial red sea urchin fishery (2015-) worth $3 M. Key questions remain such as the relative roles of ocean warming and sea star disease in the massive purple sea urchin population increase. Science and policy will need to partner to better understand drivers, build climate-resilient fisheries and kelp forest recovery strategies in order to restore essential kelp forest ecosystem services.
Computational/experimental evaluation of liver metastasis post hepatic injury: interactions with macrophages and transitional ECM
Authors: Hudson Shanice V. , Miller Hunter A. , Mahlbacher Grace E. , Saforo Douglas , Beverly Levi J. , Arteel Gavin E. , Frieboes Hermann B. 
Published: October 2019

AbstractThe complex interactions between subclinical changes to hepatic extracellular matrix (ECM) in response to injury and tumor-associated macrophage microenvironmental cues facilitating metastatic cell seeding remain poorly understood. This study implements a combined computational modeling and experimental approach to evaluate tumor growth following hepatic injury, focusing on ECM remodeling and interactions with local macrophages. Experiments were performed to determine ECM density and macrophage-associated cytokine levels. Effects of ECM remodeling along with macrophage polarization on tumor growth were evaluated via computational modeling. For primary or metastatic cells in co-culture with macrophages, TNF-α levels were 5× higher with M1 vs. M2 macrophages. Metastatic cell co-culture exhibited 10× higher TNF-α induction than with primary tumor cells. Although TGFβ1 induction was similar between both co-cultures, levels were slightly higher with primary cells in the presence of M1. Simulated metastatic tumors exhibited decreased growth compared to primary tumors, due to high local M1-induced cytotoxicity, even in a highly vascularized microenvironment. Experimental analysis combined with computational modeling may provide insight into interactions between ECM remodeling, macrophage polarization, and liver tumor growth.
Mechanism of Common-mode Noise Generation in Multi-conductor Transmission Lines
Authors: Jinno Souma , Kitora Shuji , Toki Hiroshi , Abe Masayuki 
Published: October 2019

AbstractThe mechanism of common-mode noise generation in multi-conductor transmission lines is presented. Telegraphic equations, wave equations, and reflection coefficients in the normal and common modes are derived, which provide the mechanism of common-mode noise generation. In addition to coupling among transmission lines, the origin of the common-mode noise generation is elucidated by deriving the reflection coefficients in the normal and common modes.
NMR-based metabolomics in pediatric drug resistant epilepsy – preliminary results
Authors: Boguszewicz Łukasz , Jamroz Ewa , Ciszek Mateusz , Emich-Widera Ewa , Kijonka Marek , Banasik Tomasz , Skorupa Agnieszka , Sokół Maria 
Published: October 2019

AbstractEpilepsy in children is the most frequent, heterogeneous and difficult to classify chronic neurologic condition with the etiology found in 35–40% of patients. Our aim is to detect the metabolic differences between the epileptic children and the children with no neurological abnormalities in order to define the metabolic background for therapy monitoring. The studied group included 28 epilepsy patients (median age 12 months) examined with a diagnostic protocol including EEG, videoEEG, 24-hour-EEG, tests for inborn errors of metabolism, chromosomal analysis and molecular study. The reference group consisted of 20 patients (median age 20 months) with no neurological symptoms, no development delay nor chronic diseases. 1H-NMR serum spectra were acquired on 400 MHz spectrometer and analyzed using multivariate and univariate approach with the application of correction for age variation. The epilepsy group was characterized by increased levels of serum N-acetyl-glycoproteins, lactate, creatine, glycine and lipids, whereas the levels of citrate were decreased as compared to the reference group. Choline, lactate, formate and dimethylsulfone were significantly correlated with age. NMR-based metabolomics could provide information on the dynamic metabolic processes in drug-resistant epilepsy yielding not only disease-specific biomarkers but also profound insights into the disease course, treatment effects or drug toxicity.
The effect of anxiety on brain activation patterns in response to inspiratory occlusions: an fMRI study
Authors: Chan Pei-Ying S. , Wu Yu-Ting , Hsu Ai-Ling , Li Chia-Wei , Wu Changwei W. , von Leupoldt Andreas , Hsu Shih-Chieh 
Published: October 2019

AbstractRespiratory sensations such as breathlessness are prevalent in many diseases and are amplified by increased levels of anxiety. Cortical activation in response to inspiratory occlusions in high- and low-anxious individuals was found different in previous studies using the respiratory-related evoked potential method. However, specific brain areas showed different activation patterns remained unknown in these studies. Therefore, the purpose of this study was to compare cortical and subcortical neural substrates of respiratory sensation in response to inspiratory mechanical occlusion stimuli between high- and low-anxious individuals using functional magnetic resonance imaging (fMRI). In addition, associations between brain activation patterns and levels of anxiety, and breathlessness were examined. Thirty-four (17 high- and 17 low-anxious) healthy non-smoking adults with normal lung function completed questionnaires on anxiety (State Trait Anxiety Inventory - State), and participated in a transient inspiratory occlusion fMRI experiment. The participants breathed with a customized face-mask while respiration was repeatedly interrupted by a transient inspiratory occlusion of 150-msec, delivered every 2 to 4 breaths. Breathlessness was assessed by self-report. At least 32 occluded breaths were collected for data analysis. The results showed that compared to the low-anxious group, the high-anxious individuals demonstrated significantly greater neural activations in the hippocampus, insula, and middle cingulate gyrus in response to inspiratory occlusions. Moreover, a significant relationship was found between anxiety levels and activations of the right inferior parietal gyrus, and the right precuneus. Additionally, breathlessness levels were significantly associated with activations of the bilateral thalamus, bilateral insula and bilateral cingulate gyrus. The above evidences support stronger recruitment of emotion-related cortical and subcortical brain areas in higher anxious individuals, and thus these areas play an important role in respiratory mechanosensation mediated by anxiety.
Rigorous sampling of docking poses unveils binding hypothesis for the halogenated ligands of L-type Amino acid Transporter 1 (LAT1)
Authors: Singh Natesh , Villoutreix Bruno O. , Ecker Gerhard F. 
Published: October 2019

AbstractL-type Amino acid Transporter 1 (LAT1) plays a significant role in the growth and propagation of cancer cells by facilitating the cross-membrane transport of essential nutrients, and is an attractive drug target. Several halogen-containing L-phenylalanine-based ligands display high affinity and high selectivity for LAT1; nonetheless, their molecular mechanism of binding remains unclear. In this study, a combined in silico strategy consisting of homology modeling, molecular docking, and Quantum Mechanics-Molecular Mechanics (QM-MM) simulation was applied to elucidate the molecular basis of ligand binding in LAT1. First, a homology model of LAT1 based on the atomic structure of a prokaryotic homolog was constructed. Docking studies using a set of halogenated ligands allowed for deriving a binding hypothesis. Selected docking poses were subjected to QM-MM calculations to investigate the halogen interactions. Collectively, the results highlight the dual nature of the ligand-protein binding mode characterized by backbone hydrogen bond interactions of the amino acid moiety of the ligands and residues I63, S66, G67, F252, G255, as well as hydrophobic interactions of the ligand’s side chains with residues I139, I140, F252, G255, F402, W405. QM-MM optimizations indicated that the electrostatic interactions involving halogens contribute to the binding free energy. Importantly, our results are in good agreement with the recently unraveled cryo-Electron Microscopy structures of LAT1.
DNA methylation-based biological age, genome-wide average DNA methylation, and conventional breast cancer risk factors
Authors: Chen Minyuan , Wong Ee Ming , Nguyen Tuong L. , Dite Gillian S. , Stone Jennifer , Dugué Pierre-Antoine , Giles Graham G. , Southey Melissa C. , Milne Roger L. , Hopper John L. , Li Shuai 
Published: October 2019

AbstractDNA methylation-based biological age (DNAm age), as well as genome-wide average DNA methylation, have been reported to predict breast cancer risk. We aimed to investigate the associations between these DNA methylation-based risk factors and 18 conventional breast cancer risk factors for disease-free women. A sample of 479 individuals from the Australian Mammographic Density Twins and Sisters was used for discovery, a sample of 3354 individuals from the Melbourne Collaborative Cohort Study was used for replication, and meta-analyses pooling results from the two studies were conducted. DNAm age based on three epigenetic clocks (Hannum, Horvath and Levine) and genome-wide average DNA methylation were calculated using the HumanMethylation 450 K BeadChip assay data. The DNAm age measures were positively associated with body mass index (BMI), smoking, alcohol drinking and age at menarche (all nominal P < 0.05). Genome-wide average DNA methylation was negatively associated with smoking and number of live births, and positively associated with age at first live birth (all nominal P < 0.05). The association of DNAm age with BMI was also evident in within-twin-pair analyses that control for familial factors. This study suggests that some lifestyle and hormonal risk factors are associated with these DNA methylation-based breast cancer risk factors, and the observed associations are unlikely to be due to familial confounding but are likely causal. DNA methylation-based risk factors could interplay with conventional risk factors in modifying breast cancer risk.
Selection of suitable reference genes for gene expression studies in myxosporean (Myxozoa, Cnidaria) parasites
Authors: Kosakyan Anush , Alama-Bermejo Gema , Bartošová-Sojková Pavla , Born-Torrijos Ana , Šíma Radek , Nenarokova Anna , Eszterbauer Edit , Bartholomew Jerri , Holzer Astrid S. 
Published: October 2019

AbstractMyxozoans (Cnidaria: Myxozoa) are an extremely diversified group of endoparasites some of which are causative agents of serious diseases in fish. New methods involving gene expression studies have emerged over the last years to better understand and control myxozoan diseases. Quantitative RT-PCR is the most extensively used approach for gene expression studies. However, the accuracy of the results depends on the normalization of the data to reference genes. We studied the expression of eight commonly used reference genes, adenosylhomocysteinase (AHC1), beta actin (ACTB), eukaryotic translation elongation factor 2 (EF2), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), hypoxanthine-guanine phosphoribosyltransferase 1 (HPRT1), DNA-directed RNA polymerase II (RPB2), 18S ribosomal RNA (18S), 28S ribosomal RNA (28S) across different developmental stages of three myxozoan species, Sphaerospora molnari, Myxobolus cerebralis and Ceratonova shasta, representing the three major myxozoan linages from the largest class Myxosporea. The stable reference genes were identified using four algorithms: geNorm, NormFinder, Bestkeeper and ΔCq method. Additionally, we analyzed transcriptomic data from S. molnari proliferative and spore-forming stages to compare the relative amount of expressed transcripts with the most stable reference genes suggested by RT-qPCR. Our results revealed that GAPDH and EF2 are the most uniformly expressed genes across the different developmental stages of the studied myxozoan species.
Heart Rate Correction of the J-to-Tpeak Interval
Authors: Hnatkova Katerina , Vicente Jose , Johannesen Lars , Garnett Christine , Strauss David G. , Stockbridge Norman , Malik Marek 
Published: October 2019

AbstractDrug-induced changes of the J to T peak (JTp) and J to the median of area under the T wave (JT50) were reported to differentiate QT prolonging drugs that are predominant blockers of the delayed potassium rectifier current from those with multiple ion channel effects. Studies of drug-induced JTp/JT50 interval changes might therefore facilitate cardiac safety evaluation of new pharmaceuticals. It is not known whether formulas for QT heart rate correction are applicable to JTp and JT50 intervals. QT/RR, JTp/RR, and JT50/RR profiles were studied in 523 healthy subjects aged 33.5 ± 8.4 years (254 females). In individual subjects, 1,256 ± 220 electrocardiographic measurements of QT, JTp, and JT50 intervals were available including a 5-minute history of RR intervals preceding each measurement. Curvilinear, linear and log-linear regression models were used to characterize individual QT/RR, JTp/RR, and JT50/RR profiles both without and with correction for heart rate hysteresis. JTp/RR and JT50/RR hysteresis correction needs to be included but the generic universal correction for QT/RR hysteresis is also applicable to JTp/RR and JT50/RR profiles. Once this is incorporated, median regression coefficients of the investigated population suggest linear correction formulas JTpc = JTp + 0.150(1-RR) and JT50c = JT50 + 0.117(1-RR) where RR intervals of the underlying heart rate are hysteresis-corrected, and all measurements expressed in seconds. The established correction formulas can be proposed for future clinical pharmacology studies that show drug-induced heart rate changes of up to approximately 10 beats per minute.