bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping global development potential for renewable energy, fossil fuels, mining and agriculture sectors
Authors: Oakleaf James R. , Kennedy Christina M. , Baruch-Mordo Sharon , Gerber James S. , West Paul C. , Johnson Justin A. , Kiesecker Joseph 
Published: June 2019

AbstractMapping suitable land for development is essential to land use planning efforts that aim to model, anticipate, and manage trade-offs between economic development and the environment. Previous land suitability assessments have generally focused on a few development sectors or lack consistent methodologies, thereby limiting our ability to plan for cumulative development pressures across geographic regions. Here, we generated 1-km spatially-explicit global land suitability maps, referred to as “development potential indices” (DPIs), for 13 sectors related to renewable energy (concentrated solar power, photovoltaic solar, wind, hydropower), fossil fuels (coal, conventional and unconventional oil and gas), mining (metallic, non-metallic), and agriculture (crop, biofuels expansion). To do so, we applied spatial multi-criteria decision analysis techniques that accounted for both resource potential and development feasibility. For each DPI, we examined both uncertainty and sensitivity, and spatially validated the map using locations of planned development. We illustrate how these DPIs can be used to elucidate potential individual sector expansion and cumulative development patterns.
ZNF518B gene up-regulation promotes dissemination of tumour cells and is governed by epigenetic mechanisms in colorectal cancer
Authors: Gimeno-Valiente Francisco , Riffo-Campos Ángela L. , Vallet-Sánchez Azahara , Siscar-Lewin Sofía , Gambardella Valentina , Tarazona Noelia , Cervantes Andrés , Franco Luis , Castillo Josefa , López-Rodas Gerardo 
Published: June 2019

AbstractMost of colorectal cancer CRC-related death is due to metastasis and the finding of markers for prognosis of invasiveness, constitutes an appealing challenge. Here, after analysing cDNA array containing 43 tumour and 5 normal mucosa samples, we report that the expression of the ZNF518B gene as a whole and that of its two major splicing isoforms are significantly increased in tumours. The canonical isoform was also up-regulated in a patients’ cohort containing 70 tumour and 69 adjacent tissue samples. The effects of silencing ZNF518B on the phenotype of CRC cell lines were then studied. The gene does not affect cell proliferation, but plays a significant role in cell migration and invasiveness and induces changes in the epithelial-to-mesenchymal transition markers, suggesting that ZNF518B favours tumour cell dissemination. To study the regulation of the gene, transcription-related changes in nucleosomal organisation and epigenetic marks around the transcriptional start site were analysed. The positioning of a nucleosome over the transcription start site and the differential presence of the epigenetic marks H3K9ac, H3K27ac, H3K4me3 and H3K9me3 correlate with gene expression. Inhibition of histone deacetylases increases the transcription of ZNF518B, which may be a candidate for invasiveness prognosis in CRC and a target for epigenetic drugs.
PER3 variable number tandem repeat (VNTR) polymorphism modulates the circadian variation of the descending pain modulatory system in healthy subjects
Authors: Carvalho Fabiana , Pedrazzoli Mario , Gasparin Assunta , dos Santos Franciele , Zortea Maxciel , Souza Andressa , da Silva Lucena Torres Iraci , Fregni Felipe , Caumo Wolnei 
Published: June 2019

AbstractWe evaluated the circadian pattern of variation of the descending pain modulatory system (DPMS) using a conditioned pain modulation (CPM) paradigm according to the variable-number tandem-repeat (VNTR) of the clock gene PER3 polymorphism. We assessed the relationship between the genotypes PER34/4 and PER35/5 and the temporal pattern of variation across the day using the following measures: the heat pain threshold (HPT), the cold pressure test (CPT), and the serum levels of BDNF and S100-B protein. The ∆-values (from afternoon to morning) of these measures were used for the analysis. The circadian phenotype was according to the mid-point sleep time established by the Munich ChronoType Questionnaire (MCTQ). We included 18 healthy volunteers (15 women) ages 18 to 30. A Generalized Linear Model (GLM) revealed a significant difference in the ∆-CPM-task between Per34/4 and Per35/5 genotypes, with means (SDs) of −0.41 (0.78) vs. 0.67 (0.90) (χ2 = 7.256; df = 1′ P = 0.007), respectively. Both sleep deprivation of at least 2 h/day (B = −0.96, 95% confidence interval (CI) = −1.86 to −0.11)) and the ∆-S100-B protein (−0.03, 95% CI = −0.06 to −0.02) were negatively correlated with the ∆-CPM-task, while the ∆-BDNF was positively correlated with the ∆-CPM-task (0.015, 95% CI = 0.01 to 0.03). We observed a difference in the ∆-CPT between PER34/4 and PER35/5 (0.11 (4.51) vs. 4.00 (2.60), respectively) (χ2 = 22.251; df = 1 P = 0.001). These findings suggest that the polymorphism of PER35/5 is associated with a decrease in the inhibitory function of the DPMS over the course of the day. However, sleep deprivation is an independent factor that also reduces the inhibitory function of the DPMS, regardless of the PER3 VNTR polymorphism.
A proteomic analysis of the statocyst endolymph in common cuttlefish (Sepia officinalis): an assessment of acoustic trauma after exposure to sound
Authors: Solé M. , Monge M. , André M. , Quero C. 
Published: June 2019

AbstractRecent studies, both in laboratory and sea conditions, have demonstrated damage after sound exposure in the cephalopod statocyst sensory epithelium, which secretes endolymph protein. Here, the proteomic analysis of the endolymph was performed before and after sound exposure to assess the effects of exposure to low intensity, low frequency sounds on the statocyst endolymph of the Mediterranean common cuttlefish (Sepia officinalis), determining changes in the protein composition of the statocyst endolymph immediately and 24 h after sound exposure. Significant differences in protein expression were observed, especially 24 h after exposure. A total of 37 spots were significantly different in exposed specimens, 17 of which were mostly related to stress and cytoskeletal structure. Among the stress proteins eight spots corresponding to eight hemocyanin isoforms were under-expressed possible due to lower oxygen consumption. In addition, cytoskeletal proteins such as tubulin alpha chain and intermediate filament protein were also down-regulated after exposure. Thus, endolymph analysis in the context of acoustic stress allowed us to establish the effects at the proteome level and identify the proteins that are particularly sensitive to this type of trauma.
Coupling of Redox and Structural States in Cytochrome P450 Reductase Studied by Molecular Dynamics Simulation
Authors: Iijima Mikuru , Ohnuki Jun , Sato Takato , Sugishima Masakazu , Takano Mitsunori 
Published: June 2019

AbstractCytochrome P450 reductase (CPR) is the key protein that regulates the electron transfer from NADPH to various heme-containing monooxygenases. CPR has two flavin-containing domains: one with flavin adenine dinucleotide (FAD), called FAD domain, and the other with flavin mononucleotide (FMN), called FMN domain. It is considered that the electron transfer occurs via FAD and FMN (NADPH → FAD → FMN → monooxygenase) and is regulated by an interdomain open-close motion. It is generally thought that the structural state is coupled with the redox state, which, however, has not yet been firmly established. In this report, we studied the coupling of the redox and the structural states by full-scale molecular dynamics (MD) simulation of CPR (total 86.4 μs). Our MD result showed that while CPR predominantly adopts the closed state both in the oxidized and reduced states, it exhibits a tendency to open in the reduced state. We also found a correlation between the FAD-FMN distance and the predicted FMN-monooxygenase distance, which is embedded in the equilibrium thermal fluctuation of CPR. Based on these results, a physical mechanism for the electron transfer by CPR is discussed.
Enrichment of intestinal Lactobacillus by enhanced secretory IgA coating alters glucose homeostasis in P2rx7−/− mice
Authors: Perruzza Lisa , Strati Francesco , Gargari Giorgio , D’Erchia Anna Maria , Fosso Bruno , Pesole Graziano , Guglielmetti Simone , Grassi Fabio 
Published: June 2019

AbstractThe secretory immunoglobulin A (SIgA) in mammalian gut protects the organism from infections and contributes to host physiology by shaping microbiota composition. The mechanisms regulating the adaptive SIgA response towards gut microbes are poorly defined. Deletion of P2rx7, encoding for the ATP-gated ionotropic P2X7 receptor, leads to T follicular helper (Tfh) cells expansion in the Peyer’s patches (PPs) of the small intestine, enhanced germinal centre (GC) reaction and IgA secretion; the resulting alterations of the gut microbiota in turn affects host metabolism. Here, we define gut microbiota modifications that correlate with deregulated SIgA secretion and metabolic alterations in P2rx7−/− mice. In particular, Lactobacillus shows enhanced SIgA coating in P2rx7−/− with respect to wild-type (WT) mice. The abundance of SIgA-coated lactobacilli positively correlates with Tfh cells number and body weight, suggesting Lactobacillus-specific SIgA response conditions host metabolism. Accordingly, oral administration of intestinal Lactobacillus isolates from P2rx7−/− mice to WT animals results in altered glucose homeostasis and fat deposition. Thus, enhanced SIgA production by P2X7 insufficiency promotes Lactobacillus colonization that interferes with systemic metabolic homeostasis. These data indicate that P2X7 receptor-mediated regulation of commensals coating by SIgA is important in tuning the selection of bacterial taxa, which condition host metabolism.
Lineage tracing analysis of cone photoreceptor associated cis-regulatory elements in the developing chicken retina
Authors: Schick Estie , McCaffery Sean D. , Keblish Erin E. , Thakurdin Cassandra , Emerson Mark M. 
Published: June 2019

AbstractDuring vertebrate retinal development, transient populations of retinal progenitor cells with restricted cell fate choices are formed. One of these progenitor populations expresses the Thrb gene and can be identified by activity of the ThrbCRM1 cis-regulatory element. Short-term assays have concluded that these cells preferentially generate cone photoreceptors and horizontal cells, however developmental timing has precluded an extensive cell type characterization of their progeny. Here we describe the development and validation of a recombinase-based lineage tracing system for the chicken embryo to further characterize the lineage of these cells. The ThrbCRM1 element was found to preferentially form photoreceptors and horizontal cells, as well as a small number of retinal ganglion cells. The photoreceptor cell progeny are exclusively cone photoreceptors and not rod photoreceptors, confirming that ThrbCRM1 progenitor cells are restricted from the rod fate. In addition, specific subtypes of horizontal cells and retinal ganglion cells were overrepresented, suggesting that ThrbCRM1 progenitor cells are not only restricted for cell type, but for cell subtype as well.
Efficient Grafting of Cyclodextrin to Alginate and Performance of the Hydrogel for Release of Model Drug
Authors: Omtvedt Line Aa. , Dalheim Marianne Ø. , Nielsen Thorbjørn T. , Larsen Kim L. , Strand Berit L. , Aachmann Finn L. 
Published: June 2019

AbstractControlling the rate of release of molecules from a hydrogel is of high interest for various drug delivery systems and medical devices. A strategy to alter the release profiles of soluble and poorly soluble active ingredients from hydrogels can be to combine the hydrogel forming ability of alginate with the inclusion forming ability of cyclodextrins (CyD). Here, β-CyD was grafted to alginate in a three-step synthesis using periodate oxidation, reductive amination and copper(I)-catalyzed azide-alkyne cycloaddition. A grafting degree of 4.7% mol β-CyD/mol sugar residues was obtained. The grafting degree was controlled by varying the reaction parameters where the amount of linker used in reductive amination was especially influential. Ca-alginate gel beads grafted with β-CyD showed increased uptake of the model molecule methyl orange. Release experiments showed that the grafted material had a prolonged release of methyl orange and an increased total amount of released methyl orange. These results show that the β-CyD grafted alginate is still able to form a hydrogel while the grafted cyclodextrins retain their ability to form inclusion complex with methyl orange. Further testing should be done with this system to investigate capability for drug delivery applications.
Wnt signalling mediates miR-133a nuclear re-localization for the transcriptional control of Dnmt3b in cardiac cells
Authors: Di Mauro Vittoria , Crasto Silvia , Colombo Federico Simone , Di Pasquale Elisa , Catalucci Daniele 
Published: June 2019

AbstractMiR-133a is a muscle-enriched miRNA, which plays a key role for proper skeletal and cardiac muscle function via regulation of transduction cascades, including the Wnt signalling. MiR-133a modulates its targets via canonical mRNA repression, a process that has been largely demonstrated to occur within the cytoplasm. However, recent evidence has shown that miRNAs play additional roles in other sub-cellular compartments, such as nuclei. Here, we show that miR-133a translocates to the nucleus of cardiac cells following inactivation of the canonical Wnt pathway. The nuclear miR-133a/AGO2 complex binds to a complementary miR-133a target site within the promoter of the de novo DNA methyltransferase 3B (Dnmt3b) gene, leading to its transcriptional repression, which is mediated by DNMT3B itself. Altogether, these data show an unconventional role of miR-133a that upon its relocalization to the nucleus is responsible for epigenetic repression of its target gene Dnmt3b via a DNMT3B self-regulatory negative feedback loop.
Gene expression and functional comparison between multipotential stromal cells from lateral and medial condyles of knee osteoarthritis patients
Authors: Sanjurjo-Rodriguez Clara , Baboolal Thomas G. , Burska Agata N. , Ponchel Frederique , El-Jawhari Jehan J. , Pandit Hemant , McGonagle Dennis , Jones Elena 
Published: June 2019

AbstractOsteoarthritis (OA) is the most common degenerative joint disorder. Multipotential stromal cells (MSCs) have a crucial role in joint repair, but how OA severity affects their characteristics remains unknown. Knee OA provides a good model to study this, as osteochondral damage is commonly more severe in the medial weight-bearing compartment compared to lateral side of the joint. This study utilised in vitro functional assays, cell sorting, gene expression and immunohistochemistry to compare MSCs from medial and lateral OA femoral condyles. Despite greater cartilage loss and bone sclerosis in medial condyles, there was no significant differences in MSC numbers, growth rates or surface phenotype. Culture-expanded and freshly-purified medial-condyle MSCs expressed higher levels of several ossification-related genes. Using CD271-staining to identify MSCs, their presence and co-localisation with TRAP-positive chondroclasts was noted in the vascular channels breaching the osteochondral junction in lateral condyles. In medial condyles, MSCs were additionally found in small cavities within the sclerotic plate. These data indicate subchondral MSCs may be involved in OA progression by participating in cartilage destruction, calcification and sclerotic plate formation and that they remain abundant in severe disease. Biological or biomechanical modulation of these MSCs may be a new strategy towards cartilage and bone restoration in knee OA.
Interplay of Darwinian Selection, Lamarckian Induction and Microvesicle Transfer on Drug Resistance in Cancer
Authors: Álvarez-Arenas Arturo , Podolski-Renic Ana , Belmonte-Beitia Juan , Pesic Milica , Calvo Gabriel F. 
Published: June 2019

AbstractDevelopment of drug resistance in cancer has major implications for patients’ outcome. It is related to processes involved in the decrease of drug efficacy, which are strongly influenced by intratumor heterogeneity and changes in the microenvironment. Heterogeneity arises, to a large extent, from genetic mutations analogously to Darwinian evolution, when selection of tumor cells results from the adaptation to the microenvironment, but could also emerge as a consequence of epigenetic mutations driven by stochastic events. An important exogenous source of alterations is the action of chemotherapeutic agents, which not only affects the signalling pathways but also the interactions among cells. In this work we provide experimental evidence from in vitro assays and put forward a mathematical kinetic transport model to describe the dynamics displayed by a system of non-small-cell lung carcinoma cells (NCI-H460) which, depending on the effect of a chemotherapeutic agent (doxorubicin), exhibits a complex interplay between Darwinian selection, Lamarckian induction and the nonlocal transfer of extracellular microvesicles. The role played by all of these processes to multidrug resistance in cancer is elucidated and quantified.
Open‐loop transfer functions of buck–boost converter by circuit‐averaging technique
Authors: Saini Dalvir Kaur , Kazimierczuk Marian Kazimierz 
Published: June 2019

This study shows the derivation of the power‐stage transfer functions and input and output impedances of a buck–boost pulse width‐modulated (PWM) dc–dc converter operating in continuous‐conduction mode. The expressions are derived using the small‐signal model obtained by the circuit‐averaging technique. Using the small‐signal dynamic model, both transient and frequency domain characteristics are determined. An example buck–boost converter with the following specifications was considered: supply voltage 12 V, output voltage 5 V, switching frequency 200 kHz, and output power 10 W. The modification of the power‐stage transfer function to include the time delay between the MOSFET gate drive and the duty cycle is considered and is modelled by the first‐order Padè approximation. The theoretical predictions were verified by experiments and excellent agreement between the results was observed.
Three‐phase bi‐directional wireless EV charging system with high tolerance to pad misalignment
Authors: Song Yuan , Madawala Udaya K. , Thrimawithana Duleepa J. , Vilathgamuwa Mahinda 
Published: June 2019

Electric vehicles (EVs), which are becoming increasingly popular, can be charged by either wired or wireless means. The latter, based on wireless power transfer (WPT) technology, is convenient and safe, but pad misalignment is one of the major concerns as it causes a reduction in charging power level, prolonging the charging process. Therefore, wireless charging systems with high tolerance to pad misalignment are necessary. This study proposes a three‐phase bi‐directional wireless power transfer (BD‐WPT) system with a control scheme that offers high tolerance to pad misalignment in EV charging applications. The system uses simple coil designs for pads and utilises the magnetic coupling among pads to compensate for the power variation. A comprehensive mathematical model, incorporating all magnetic cross‐coupling effects, is presented to investigate the charging performance of the system under pad misalignment and different pad spacings. To demonstrate the validity of the proposed system, theoretical and simulated results are presented, benchmarking against a single phase WPT system, and in comparison to a prototype 1.3 kW three‐phase BD‐WPT system. Results are convincing and indicate that the proposed three‐phase BD‐WPT system with small pad spacing is more tolerant to wide pad misalignment in EV charging applications.
Biclustering‐based association rule mining approach for predicting cancer‐associated protein interactions
Authors: Dey Lopamudra , Mukhopadhyay Anirban 
Published: June 2019

Protein–protein interactions (PPIs) have been widely used to understand different biological processes and cellular functions associated with several diseases like cancer. Although some cancer‐related protein interaction databases are available, lack of experimental data and conflicting PPI data among different available databases have slowed down the cancer research. Therefore, in this study, the authors have focused on various proteins that are directly related to different types of cancer disease. They have prepared a PPI database between cancer‐associated proteins with the rest of the human proteins. They have also incorporated the annotation type and direction of each interaction. Subsequently, a biclustering‐based association rule mining algorithm is applied to predict new interactions with type and direction. This study shows the prediction power of association rule mining algorithm over the traditional classifier model without choosing a negative data set. The time complexity of the biclustering‐based association rule mining is also analysed and compared to traditional association rule mining. The authors are able to discover 38 new PPIs which are not present in the cancer database. The biological relevance of these newly predicted interactions is analysed by published literature. Recognition of such interactions may accelerate a way of developing new drugs to prevent different cancer‐related diseases.