bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear spin-hyperpolarization generated in a flavoprotein under illumination: experimental field-dependence and theoretical level crossing analysis
Authors: Ding Yonghong , Kiryutin Alexey S. , Yurkovskaya Alexandra V. , Sosnovsky Denis V. , Sagdeev Renad Z. , Bannister Saskia , Kottke Tilman , Kar Rajiv K. , Schapiro Igor , Ivanov Konstantin L. , Matysik Jörg 
Published: December 2019

AbstractThe solid-state photo-chemically induced dynamic nuclear polarization (photo-CIDNP) effect generates non-equilibrium nuclear spin polarization in frozen electron-transfer proteins upon illumination and radical-pair formation. The effect can be observed in various natural photosynthetic reaction center proteins using magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy, and in a flavin-binding light-oxygen-voltage (LOV) domain of the blue-light receptor phototropin. In the latter system, a functionally instrumental cysteine has been mutated to interrupt the natural cysteine-involving photochemistry allowing for an electron transfer from a more distant tryptophan to the excited flavin mononucleotide chromophore. We explored the solid-state photo-CIDNP effect and its mechanisms in phototropin-LOV1-C57S from the green alga Chlamydomonas reinhardtii by using field-cycling solution NMR. We observed the 13C and, to our knowledge, for the first time, 15N photo-CIDNP signals from phototropin-LOV1-C57S. Additionally, the 1H photo-CIDNP signals of residual water in the deuterated buffer of the protein were detected. The relative strengths of the photo-CIDNP effect from the three types of nuclei, 1H, 13C and 15N were measured in dependence of the magnetic field, showing their maximum polarizations at different magnetic fields. Theoretical level crossing analysis demonstrates that anisotropic mechanisms play the dominant role at high magnetic fields.
Elevated CO2 regulates the Wnt signaling pathway in mammals, Drosophila melanogaster and Caenorhabditis elegans
Authors: Shigemura Masahiko , Lecuona Emilia , Angulo Martín , Dada Laura A. , Edwards Melanie B. , Welch Lynn C. , Casalino-Matsuda S. Marina , Sporn Peter H. S. , Vadász István , Helenius Iiro Taneli , Nader Gustavo A. , Gruenbaum Yosef , Sharabi Kfir , Cummins Eoin , Taylor Cormac , Bharat Ankit , Gottardi Cara J. , Beitel Greg J. , Kaminski Naftali , Budinger G. R. Scott , Berdnikovs Sergejs , Sznajder Jacob I. 
Published: December 2019

AbstractCarbon dioxide (CO2) is sensed by cells and can trigger signals to modify gene expression in different tissues leading to changes in organismal functions. Despite accumulating evidence that several pathways in various organisms are responsive to CO2 elevation (hypercapnia), it has yet to be elucidated how hypercapnia activates genes and signaling pathways, or whether they interact, are integrated, or are conserved across species. Here, we performed a large-scale transcriptomic study to explore the interaction/integration/conservation of hypercapnia-induced genomic responses in mammals (mice and humans) as well as invertebrates (Caenorhabditis elegans and Drosophila melanogaster). We found that hypercapnia activated genes that regulate Wnt signaling in mouse lungs and skeletal muscles in vivo and in several cell lines of different tissue origin. Hypercapnia-responsive Wnt pathway homologues were similarly observed in secondary analysis of available transcriptomic datasets of hypercapnia in a human bronchial cell line, flies and nematodes. Our data suggest the evolutionarily conserved role of high CO2 in regulating Wnt pathway genes.
Computing the statistical significance of optimized communities in networks
Authors: Palowitch John 
Published: December 2019

AbstractIn scientific problems involving systems that can be modeled as a network (or “graph”), it is often of interest to find network communities - strongly connected node subsets - for unsupervised learning, feature discovery, anomaly detection, or scientific study. The vast majority of community detection methods proceed via optimization of a quality function, which is possible even on random networks without communities. Therefore there is usually not an easy way to tell if a community is “significant”, in this context meaning more internally connected than would be expected under a random graph model without communities. This paper generalizes existing null models and statistical tests for this purpose to bipartite graphs, and introduces a new significance scoring algorithm called Fast Optimized Community Significance (FOCS) that is highly scalable and agnostic to the type of graph. Compared with existing methods on unipartite graphs, FOCS is more numerically stable and better balances the trade-off between detection power and false positives. On a large-scale bipartite graph derived from the Internet Movie Database (IMDB), the significance scores provided by FOCS correlate strongly with meaningful actor/director collaborations on serial cinematic projects.
Micromechanical Response of Crystalline Phases in Alternate Cementitious Materials using 3-Dimensional X-ray Techniques
Authors: Nair Sriramya D. , Nygren Kelly E. , Pagan Darren C. 
Published: December 2019

AbstractCementitious materials are complex composites that exhibit significant spatial heterogeneity in their chemical composition and micromechanical response. Modern 3-dimensional characterization techniques using X-rays from synchrotron light sources, such as micro-computed tomography (μCT) and far-field high-energy diffraction microscopy (ff-HEDM), are now capable of probing this micromechanical heterogeneity. In this work, the above mentioned techniques are used to understand the varying micromechanical response of crystalline phases (cubic iron oxide and α-quartz) inherently present within an alkali-activated fly ash (AAF) during in-situ confined compression. A subset of the crystals probed using ff-HEDM are registered with the tomographic reconstructions and tracked through the applied loads, highlighting the combination of μCT and ff-HEDM as a means to examine both elastic strain in the crystalline particles (and by extension local stress response) and plastic strain in the matrix. In this study, significant differences in the load carrying behaviors of the crystalline phases were observed wherein the cubic iron oxide crystals laterally expanded during the confined compression test, while the α-quartz particles laterally contracted and at the final load step, shed load likely due to failure in the surrounding matrix. Finally, the two characterization techniques are discussed in terms of both advantages and associated challenges for analysis of multi-phase cementitious materials.
Curcumin to Promote the Synthesis of Silver NPs and their Self-Assembly with a Thermoresponsive Polymer in Core-Shell Nanohybrids
Authors: Soto-Quintero Albanelly , Guarrotxena Nekane , García Olga , Quijada-Garrido Isabel 
Published: December 2019

AbstractThis work presents a simple one-pot protocol to achieve core-doped shell nanohybrids comprising silver nanoparticles, curcumin and thermoresponsive polymeric shell taking advantage of the reducing properties of phenolic curcumin substance and its ability to decorate metallic surfaces. Silver nanoparticles were synthesized, via sodium citrate and silver nitrate addition into a boiling aqueous solution of curcumin, monomers and surfactant. Curcumin and sodium citrate promoted silver nucleation, acting as reducing and stabilizing agents. These curcumin-capped AgNPs enabled, after adding the radical polymerization initiator, the assembling of the growing polymer chains around the hydrophobic AgNP surface. The resultant core-doped shell nanohybrids exhibit plasmonic, luminescent and volume thermoresponsive properties, with improved possibilities to be used as successful therapeutic platforms. In fact, the possibility to nanoconfine the synergistic antioxidant, antiviral, antibacterial features of silver and curcumin in one bioavailable hybrid paves the way to promising applications in the biomedical field.
Phenotypic and molecular assessment of genetic structure and diversity in a panel of winged yam (Dioscorea alata) clones and cultivars
Authors: Agre Paterne , Asibe Flora , Darkwa Kwabena , Edemodu Alex , Bauchet Guillaume , Asiedu Robert , Adebola Patrick , Asfaw Asrat 
Published: December 2019

AbstractA better understanding of the structure and extent of genetic variability in a breeding population of a crop is essential for translating genetic diversity to genetic gain. We assessed the nature and pattern of genetic variability and differentiation in a panel of 100 winged-yam (Dioscorea alata) accessions using 24 phenotypic traits and 6,918 single nucleotide polymorphism (SNP) markers. Multivariate analysis for phenotypic variability indicated that all phenotypic traits assessed were useful in discriminating the yam clones and cultivars. Cluster analysis based on phenotypic data distinguished two significant groups, while a corresponding analysis with SNP markers indicated three genetic groups. However, joint analysis for the phenotypic and genotypic data provided three clusters that could be useful for the identification of heterotic groups in the D. alata breeding program. Our analysis for phenotypic and molecular level diversity provided valuable information about overall diversity and variation in economically important traits useful for establishing crossing panels with contrasting traits of interest. The selection and hybridization of parental lines from the different heterotic groups identified would facilitate maximizing diversity and exploiting population heterosis in the D. alata breeding program.
Escherichia coli and Salmonella Enteritidis dual-species biofilms: interspecies interactions and antibiofilm efficacy of phages
Authors: Milho Catarina , Silva Maria Daniela , Alves Diana , Oliveira Hugo , Sousa Clara , Pastrana Lorenzo M. , Azeredo Joana , Sillankorva Sanna 
Published: December 2019

AbstractEscherichia coli and Salmonella Enteritidis are foodborne pathogens forming challenging biofilms that contribute to their virulence, antimicrobial resistance, and survival on surfaces. Interspecies interactions occur between species in mixed biofilms promoting different outcomes to each species. Here we describe the interactions between E. coli and S. Enteritidis strains, and their control using specific phages. Single-species biofilms presented more cells compared to dual-species biofilms. The spatial organization of strains, observed by confocal microscopy, revealed similar arrangements in both single- and dual-species biofilms. The EPS matrix composition, assessed by Fourier-transform infrared spectroscopy, disclosed that the spectra extracted from the different dual-species biofilms can either be a combination of both species EPS matrix components or that the EPS matrix of one species predominates. Phages damaged more the single-species biofilms than the mixed biofilms, showing also that the killing efficacy was greatly dependent on the phage growth characteristics, bacterial growth parameters, and bacterial spatial distribution in biofilms. This combination of methodologies provides new knowledge of species-species and phage-host interactions in biofilms of these two major foodborne pathogens.
Sodium valproate and 5-aza-2′-deoxycytidine differentially modulate DNA demethylation in G1 phase-arrested and proliferative HeLa cells
Authors: Rocha Marina Amorim , Veronezi Giovana Maria Breda , Felisbino Marina Barreto , Gatti Maria Silvia Viccari , Tamashiro Wirla M. S. C. , Mello Maria Luiza Silveira 
Published: December 2019

AbstractSodium valproate/valproic acid (VPA), a histone deacetylase inhibitor, and 5-aza-2-deoxycytidine (5-aza-CdR), a DNA methyltransferase 1 (DNMT1) inhibitor, induce DNA demethylation in several cell types. In HeLa cells, although VPA leads to decreased DNA 5-methylcytosine (5mC) levels, the demethylation pathway involved in this effect is not fully understood. We investigated this process using flow cytometry, ELISA, immunocytochemistry, Western blotting and RT-qPCR in G1 phase-arrested and proliferative HeLa cells compared to the presumably passive demethylation promoted by 5-aza-CdR. The results revealed that VPA acts predominantly on active DNA demethylation because it induced TET2 gene and protein overexpression, decreased 5mC abundance, and increased 5-hydroxy-methylcytosine (5hmC) abundance, in both G1-arrested and proliferative cells. However, because VPA caused decreased DNMT1 gene expression levels, it may also act on the passive demethylation pathway. 5-aza-CdR attenuated DNMT1 gene expression levels but increased TET2 and 5hmC abundance in replicating cells, although it did not affect the gene expression of TETs at any stage of the cell cycle. Therefore, 5-aza-CdR may also function in the active pathway. Because VPA reduces DNA methylation levels in non-replicating HeLa cells, it could be tested as a candidate for the therapeutic reversal of DNA methylation in cells in which cell division is arrested.
β-catenin activation down-regulates cell-cell junction-related genes and induces epithelial-to-mesenchymal transition in colorectal cancers
Authors: Kim Won Kyu , Kwon Yujin , Jang Mi , Park Minhee , Kim Jiyoon , Cho Suyeon , Jang Dong Geon , Lee Wook-Bin , Jung Sang Hoon , Choi Hye Jin , Min Byung Soh , Il Kim Tae , Hong Sung Pil , Paik Young-Ki , Kim Hoguen 
Published: December 2019

AbstractWNT signaling activation in colorectal cancers (CRCs) occurs through APC inactivation or β-catenin mutations. Both processes promote β-catenin nuclear accumulation, which up-regulates epithelial-to-mesenchymal transition (EMT). We investigated β-catenin localization, transcriptome, and phenotypic differences of HCT116 cells containing a wild-type (HCT116-WT) or mutant β-catenin allele (HCT116-MT), or parental cells with both WT and mutant alleles (HCT116-P). We then analyzed β-catenin expression and associated phenotypes in CRC tissues. Wild-type β-catenin showed membranous localization, whereas mutant showed nuclear localization; both nuclear and non-nuclear localization were observed in HCT116-P. Microarray analysis revealed down-regulation of Claudin-7 and E-cadherin in HCT116-MT vs. HCT116-WT. Claudin-7 was also down-regulated in HCT116-P vs. HCT116-WT without E-cadherin dysregulation. We found that ZEB1 is a critical EMT factor for mutant β-catenin-mediated loss of E-cadherin and Claudin-7 in HCT116-P and HCT116-MT cells. We also demonstrated that E-cadherin binds to both WT and mutant β-catenin, and loss of E-cadherin releases β-catenin from the cell membrane and leads to its degradation. Alteration of Claudin-7, as well as both Claudin-7 and E-cadherin respectively caused tight junction (TJ) impairment in HCT116-P, and dual loss of TJs and adherens junctions (AJs) in HCT116-MT. TJ loss increased cell motility, and subsequent AJ loss further up-regulated that. Immunohistochemistry analysis of 101 CRCs revealed high (14.9%), low (52.5%), and undetectable (32.6%) β-catenin nuclear expression, and high β-catenin nuclear expression was significantly correlated with overall survival of CRC patients (P = 0.009). Our findings suggest that β-catenin activation induces EMT progression by modifying cell-cell junctions, and thereby contributes to CRC aggressiveness.
α-Hydroxybutyrate dehydrogenase is associated with atherothrombotic events following infrainguinal angioplasty and stenting
Authors: Lee Silvia , Koppensteiner Renate , Kopp Christoph W. , Gremmel Thomas 
Published: December 2019

AbstractBesides clinical characteristics, easy-accessible laboratory markers could be of value to refine risk stratification in peripheral artery disease. In the current study, we investigated whether α-hydroxybutyrate dehydrogenase (HBDH) is associated with atherothrombotic events in 83 stable patients undergoing infrainguinal angioplasty and stenting. The primary endpoint was defined as the composite of the first occurrence of nonfatal myocardial infarction, nonfatal stroke or transient ischemic attack and cardiovascular death within 2 years after angioplasty and stenting, and occurred in 6 patients (7.2%). HBDH levels at baseline were significantly higher in patients who subsequently developed the primary endpoint (126 U/L [116–137 U/L] vs. 105 U/L [95–120 U/L]; p = 0.04). ROC curve analysis revealed that HBDH could distinguish between patients without and with future atherothrombotic events. A HBDH concentration ≥ 115 U/L was identified as the best threshold to predict the composite endpoint, providing a sensitivity of 83.3% and a specificity of 71.4%, and was therefore defined as high HBDH. High HBDH was seen in 28 patients (33.7%). Ischemic events occurred significantly more often in patients with high HBDH than in patients with lower HBDH levels (5 vs. 1 patients, p = 0.007). In conclusion, HBDH is associated with the occurrence of atherothrombotic events after infrainguinal angioplasty with stent implantation. Future trials are warranted to study the predictive role of HBDH for ischemic outcomes and to investigate underlying mechanisms.
The light-oxygen effect in biological cells enhanced by highly localized surface plasmon-polaritons
Authors: Khokhlova Anna , Zolotovskii Igor , Sokolovski Sergei , Saenko Yury , Rafailov Edik , Stoliarov Dmitrii , Pogodina Evgenia , Svetukhin Vyacheslav , Sibirny Vladimir , Fotiadi Andrei 
Published: December 2019

AbstractHere at the first time we suggested that the surface plasmon-polariton phenomenon which it is well described in metallic nanostructures could also be used for explanation of the unexpectedly strong oxidative effects of the low-intensity laser irradiation in living matters (cells, tissues, organism). We demonstrated that the narrow-band laser emitting at 1265 nm could generate significant amount of the reactive oxygen species (ROS) in both HCT116 and CHO-K1 cell cultures. Such cellular ROS effects could be explained through the generation of highly localized plasmon-polaritons on the surface of mitochondrial crista. Our experimental conditions, the low-intensity irradiation, the narrow spectrum band (<4 nm) of the laser and comparably small size bio-structures (~10 μm) were shown to be sufficient for the plasmon-polariton generation and strong laser field confinement enabling the oxidative stress observed.
Randomized Trial of Mindfulness-Based Stress Reduction in Cardiac Patients Eligible for Cardiac Rehabilitation
Authors: Nijjar Prabhjot S. , Connett John E. , Lindquist Ruth , Brown Roland , Burt Marsha , Pergolski Aaron , Wolfe Alexandra , Balaji Priya , Chandiramani Nitya , Yu Xiaohui , Kreitzer Mary Jo , Everson-Rose Susan A. 
Published: December 2019

AbstractCurrently, exercise-based cardiac rehabilitation (CR) is the only recommended secondary prevention strategy for cardiac patients that attempts to tackle stress and psychosocial wellbeing, but it is under-utilized and lacks a comprehensive curriculum for this purpose; hence there is a critical gap to address psychosocial needs of cardiac patients after an event. Mindfulness-based stress reduction (MBSR) has shown benefits in the general population but its role in cardiac patients is not clear. We conducted a pilot randomized controlled trial (RCT) of MBSR in CR-eligible cardiac patients during their initial year of recovery. Patients were allocated 2:1 (intervention:control) to an 8-week MBSR group intervention or usual care. Standard measures of depression, anxiety, perceived stress, health related quality of life (HRQOL), blood pressure, biomarkers (lipids, HbA1c, CRP) and 24-hour Holter monitoring were obtained at baseline, 3- and 9-months post-randomization. Sub-group analyses were performed for participants with at least mild depression (PHQ-9 ≥ 5). 47 patients [mean age 58.6 years; 38% female; 77% white] were enrolled in 2 cohorts. 87% of MBSR patients completed the intervention; study retention was >95% at each follow-up visit. At 3 months, compared to controls, MBSR patients showed improvements in depression [p = 0.01] and anxiety [p = 0.04] with a similar trend in HRQOL [p = 0.06]. The MBSR group showed greater improvement or less worsening of most CV risk factors, with an attenuation of treatment effects at 9 months. Participants with at PHQ-9 scores ≥5 at baseline showed greater improvement in psychosocial and CV outcomes, that persisted at 9 months. MBSR is a safe and well received secondary prevention strategy. This pilot RCT provides preliminary evidence of MBSR’s potential to improve short term psychosocial well-being in cardiac patients during their first year of recovery.
4,5-Disubstituted 1,2,3-triazoles: Effective Inhibition of Indoleamine 2,3-Dioxygenase 1 Enzyme Regulates T cell Activity and Mitigates Tumor Growth
Authors: Panda Subhankar , Pradhan Nirmalya , Chatterjee Soumya , Morla Sudhir , Saha Abhishek , Roy Ashalata , Kumar Sachin , Bhattacharyya Arindam , Manna Debasis 
Published: December 2019

AbstractThe improvement of body’s own immune system is considered one of the safest approaches to fight against cancer and several other diseases. Excessive catabolism of the essential amino acid, L-tryptophan (L-Trp) assists the cancer cells to escape normal immune obliteration. The formation of disproportionate kynurenine and other downstream metabolites suppress the T cell functions. Blocking of this immunosuppressive mechanism is considered as a promising approach against cancer, neurological disorders, autoimmunity, and other immune-mediated diseases. Overexpression of indoleamine 2,3-dioxygenase 1 (IDO1) enzyme is directly related to the induction of immunosuppressive mechanisms and represents an important therapeutic target. Several classes of small molecule-based IDO1 inhibitors have been already reported, but only few compounds are currently being evaluated in various stages of clinical trials as adjuvants or in combination with chemo- and radiotherapies. In the quest for novel structural class(s) of IDO1 inhibitors, we developed a series of 4,5-disubstituted 1,2,3-triazole derivatives. The optimization of 4,5-disubstituted 1,2,3-triazole scaffold and comprehensive biochemical and biophysical studies led to the identification of compounds, 3i, 4i, and 4k as potent and selective inhibitors of IDO1 enzyme with IC50 values at a low nanomolar level. These potent compounds also showed strong IDO1 inhibitory activities in MDA-MB-231 cells with no/negligible level of cytotoxicity. The T cell activity studies revealed that controlled regulation of IDO1 enzyme activity in the presence of these potent compounds could induce immune response against breast cancer cells. The compounds also showed excellent in vivo antitumor efficacy (of tumor growth inhibition = 79–96%) in the female Swiss albino mice. As a consequence, this study describes the first example of 4,5-disubstituted 1,2,3-triazole based IDO1 inhibitors with potential applications for immunotherapeutic studies.