bluuebunny/crossref_metadata_2025_split huggingface dataset:
MTGO: PPI Network Analysis Via Topological and Functional Module Identification
Authors: Vella Danila , Marini Simone , Vitali Francesca , Di Silvestre Dario , Mauri Giancarlo , Bellazzi Riccardo 
Published: March 2018

AbstractProtein-protein interaction (PPI) networks are viable tools to understand cell functions, disease machinery, and drug design/repositioning. Interpreting a PPI, however, it is a particularly challenging task because of network complexity. Several algorithms have been proposed for an automatic PPI interpretation, at first by solely considering the network topology, and later by integrating Gene Ontology (GO) terms as node similarity attributes. Here we present MTGO - Module detection via Topological information and GO knowledge, a novel functional module identification approach. MTGO let emerge the bimolecular machinery underpinning PPI networks by leveraging on both biological knowledge and topological properties. In particular, it directly exploits GO terms during the module assembling process, and labels each module with its best fit GO term, easing its functional interpretation. MTGO shows largely better results than other state of the art algorithms (including recent GO-based ones) when searching for small or sparse functional modules, while providing comparable or better results all other cases. MTGO correctly identifies molecular complexes and literature-consistent processes in an experimentally derived PPI network of Myocardial infarction. A software version of MTGO is available freely for non-commercial purposes at https://gitlab.com/d1vella/MTGO.
Gold Nanorods as Visual Sensing Platform for Chiral Recognition with Naked Eyes
Authors: Wang Yanwei , Zhou Xiaojuan , Xu Chunli , Jin Yan , Li Baoxin 
Published: March 2018

AbstractChirality plays a key role in modern science and technology. Here, we report a simple and effective sensing platform for visual chiral recognition of enantiomers. In this sensing platform, gold nanorods (AuNRs) prepared through a common synthesis route are used as colorimetric probes for visual recognition of glutamine (Gln) enantiomers. D-Gln could rapidly induce the aggregation of AuNRs, thereby resulting in appreciable blue-to-gray color change of AuNRs solution; however, L-Gln could not induce color change of AuNRs. This distinct color change can be easily distinguished by the naked eyes; as a result, a visual method of chiral recognition was suggested. The method was applied to determine the enantiometric excess of D-Gln through the whole range of −100% ~ 100%. The chiral assay can be performed with a simple UV-vis spectrometer or the naked eyes. Notably, the AuNRs do not need any chiral labeling or modification, and the chiral recognition is based on the inherent chirality of AuNRs. This chiral assay method is simple, sensitive, cheap and easy to operate. This study is the first example using AuNRs for direct visual recognition of enantiomers, and will open new opportunity to construct more chiral recognition methods for some important compounds.
Longitudinal outcomes of amyloid positive versus negative amnestic mild cognitive impairments: a three-year longitudinal study
Authors: Ye Byoung Seok , Kim Hee Jin , Kim Yeo Jin , Jung Na-Yeon , Lee Jin San , Lee Juyoun , Jang Young Kyoung , Yang Jin-ju , Lee Jong-Min , Vogel Jacob W. , Na Duk L. , Seo Sang Won 
Published: March 2018

AbstractWe aimed to compare the longitudinal outcome of amnestic mild cognitive impairment (aMCI) patients with significant Pittsburgh Compound B uptake [PiB(+) aMCI] and those without [PiB(−) aMCI]. Cerebral β-amyloid was measured in 47 patients with aMCI using PiB-positron emission tomography (PET) (31 PiB(+) aMCI and 16 PiB(−) aMCI). Clinical (N = 47) and neuropsychological follow-up (N = 37), and follow-up with brain magnetic resonance imaging (N = 38) and PiB-PET (N = 30) were performed for three years. PiB(+) aMCI had a higher risk of progression to dementia (hazard ratio = 3.74, 95% CI = 1.21–11.58) and faster rate of cortical thinning in the bilateral precuneus and right medial and lateral temporal cortices compared to PiB(−) aMCI. Among six PiB(−) aMCI patients who had regional PiB uptake ratio >1.5 in the posterior cingulate cortex (PCC), three (50.0%) progressed to dementia, and two of them had global PiB uptake ratio >1.5 at the follow-up PiB-PET. Our findings suggest that amyloid imaging is important for predicting the prognosis of aMCI patients, and that it is necessary to pay more attention to PiB(−) aMCI with increased regional PiB uptake in the PCC.
A role for the gibberellin pathway in biochar-mediated growth promotion
Authors: French Elizabeth , Iyer-Pascuzzi Anjali S. 
Published: March 2018

AbstractBiochar is a carbon negative soil amendment that can promote crop growth. However, the effects of biochar on different plant species and cultivars within a species are not well understood, nor is the underlying basis of biochar-mediated plant growth promotion. This knowledge is critical for optimal use of biochar and for breeding biochar-responsive plants. Here, we investigated the genotype-specific effects of biochar on two cultivars of Solanum lycopersicum (tomato), and two wild relatives of tomato, Solanum pimpinellifolium, and Solanum pennelli, in two types of biochar. Biochar promoted shoot growth in all genotypes independent of biochar type but had genotype-dependent effects on other plant traits. Germination tests, exogenous GA4 application and mutant analysis indicated a role for GA in biochar-mediated plant growth promotion. Together, our results suggest that biochar promotes growth partially through stimulation of the GA pathway.
Porphyrins inactivate Nosema spp. microsporidia
Authors: Ptaszyńska Aneta A. , Trytek Mariusz , Borsuk Grzegorz , Buczek Katarzyna , Rybicka-Jasińska Katarzyna , Gryko Dorota 
Published: March 2018

AbstractThe study of organic/inorganic molecules with activity against intracellular fungi of the phylum Microsporidia is of critical importance. Here, for the first time, the inactivation of these parasitic fungi by porphyrins is reported. The biological effects of porphyrins (10 µM and 100 µM) on the microsporidian Nosema ceranae was investigated in honeybee hosts using cage experiments. A significant reduction in the number of spores (from 2.6 to 5 fold) was observed in Nosema-infected honeybees with a sucrose-protoporphyrin amide [PP(Asp)2] syrup diet compared to the control honeybees. PP(Asp)2 and the other porphyrin examined in vitro, TMePyP, had a direct impact on the microsporidia. Notably, neither porphyrin requires light excitation to be active against microsporidia. Moreover, microsporidia preincubated with these porphyrins exhibited decreased ability to infect honeybees. In particular, PP(Asp)2, possessing amphiphilic characteristics, exhibited significant inactivation of microsporidia, preventing the development of the microsporidia and diminishing the mortality of infected honeybees. In addition, the porphyrin-treated spores examined by scanning electron microscopy (SEM) showed morphological changes in their exosporium layers, which were distinctly deformed. Thus, we postulate that the mechanism of action of porphyrins on microsporidia is not based on photodynamic inactivation but on the destruction of the cell walls of the spores.
Collaborative hierarchy maintains cooperation in asymmetric games
Authors: Antonioni Alberto , Pereda María , Cronin Katherine A. , Tomassini Marco , Sánchez Angel 
Published: March 2018

AbstractThe interplay of social structure and cooperative behavior is under much scrutiny lately as behavior in social contexts becomes increasingly relevant for everyday life. Earlier experimental work showed that the existence of a social hierarchy, earned through competition, was detrimental for the evolution of cooperative behaviors. Here, we study the case in which individuals are ranked in a hierarchical structure based on their performance in a collective effort by having them play a Public Goods Game. In the first treatment, participants are ranked according to group earnings while, in the second treatment, their rankings are based on individual earnings. Subsequently, participants play asymmetric Prisoner’s Dilemma games where higher-ranked players gain more than lower ones. Our experiments show that there are no detrimental effects of the hierarchy formed based on group performance, yet when ranking is assigned individually we observe a decrease in cooperation. Our results show that different levels of cooperation arise from the fact that subjects are interpreting rankings as a reputation which carries information about which subjects were cooperators in the previous phase. Our results demonstrate that noting the manner in which a hierarchy is established is essential for understanding its effects on cooperation.
InAs/AlGaAs quantum dots for single-photon emission in a red spectral range
Authors: Rakhlin M. V. , Belyaev K. G. , Klimko G. V. , Mukhin I. S. , Kirilenko D. A. , Shubina T. V. , Ivanov S. V. , Toropov A. A. 
Published: March 2018

AbstractWe report on comparative optical studies of InAs/Al0.44Ga0.56As quantum dots (QDs) grown by molecular beam epitaxy either with or without a thin GaAs interlayer inserted between the AlGaAs barrier and InAs QDs. Emission properties of individual QDs are investigated by micro-photoluminescence spectroscopy using 500-nm-size etched cylindric mesa structures. The single-photon statistics of the QDs of both types, emitting in the red spectral range between 636 and 750 nm, is confirmed by the measurements of the second-order correlation function. A negligibly small exciton fine structure splitting is detected in the majority of the QDs grown with the GaAs interlayer that implies the possibility of generating pairs of entangled photons with high entanglement fidelity.
A dynamic approach merging network theory and credit risk techniques to assess systemic risk in financial networks
Authors: Petrone Daniele , Latora Vito 
Published: March 2018

AbstractThe interconnectedness of financial institutions affects instability and credit crises. To quantify systemic risk we introduce here the PD model, a dynamic model that combines credit risk techniques with a contagion mechanism on the network of exposures among banks. A potential loss distribution is obtained through a multi-period Monte Carlo simulation that considers the probability of default (PD) of the banks and their tendency of defaulting in the same time interval. A contagion process increases the PD of banks exposed toward distressed counterparties. The systemic risk is measured by statistics of the loss distribution, while the contribution of each node is quantified by the new measures PDRank and PDImpact. We illustrate how the model works on the network of the European Global Systemically Important Banks. For a certain range of the banks’ capital and of their assets volatility, our results reveal the emergence of a strong contagion regime where lower default correlation between banks corresponds to higher losses. This is the opposite of the diversification benefits postulated by standard credit risk models used by banks and regulators who could therefore underestimate the capital needed to overcome a period of crisis, thereby contributing to the financial system instability.
Association of induced abortion with preterm birth risk in first-time mothers
Authors: Ke Li , Lin Weiyan , Liu Yangqi , Ou Weilin , Lin Zhifeng 
Published: March 2018

AbstractWomen who have previously had an induced abortion (IA) before their first birth have been associated with preterm birth (PTB). However, previous studies on the PTB are inconsistent. Therefore, the aim of this study was to clarify the association between IA and PTB and low birth weight (LBW) for first-time mothers. A total of 3,684 Southern Chinese women who gave birth for the first time to a live singleton infants were recruited between January 2015 and December 2015 in the province of Guangdong, China. Univariable and multivariable analyses were conducted to determine whether IA was associated with PTB and LBW. Previous IA was not associated with increased risks of PTB or LBW, adjusted odds ratios were 0.80 (95% CI = 0.53 to 1.20) and 0.86 (95% CI = 0.57 to 1.31), respectively. Additionally, no significant associations were observed for infants born at before 37, before 32, and before 28 gestational weeks. And no significant associations were also observed for LBW measuring lower than 2500 grams and also measuring lower than 1500 grams. Our study suggested that a previous IA, as compared with women who reported no previous IA, does not increase the risk of PTB or LBW in subsequent pregnancy for the first-time mothers among Southern Chinese women.
Quantifying extracellular matrix turnover in human lung scaffold cultures
Authors: Rosmark Oskar , Åhrman Emma , Müller Catharina , Elowsson Rendin Linda , Eriksson Leif , Malmström Anders , Hallgren Oskar , Larsson-Callerfelt Anna-Karin , Westergren-Thorsson Gunilla , Malmström Johan 
Published: March 2018

AbstractRemodelling of the extracellular matrix is accomplished by altering the balance between matrix macromolecule production and degradation. However, it is not well understood how cells balance production of new matrix molecules and degradation of existing ones during tissue remodelling and regeneration. In this study, we used decellularized lung scaffolds repopulated with allogenic lung fibroblasts cultured with stable isotope labelled amino acids to quantify the balance between matrix production and degradation at a proteome-wide scale. Specific temporal dynamics of different matrisome proteins were found to correspond to the proliferative activity of the repopulating cells and the degree of extracellular deposition. The remodeling of the scaffold was characterized by an initial phase with cell proliferation and high production of cell adhesion proteins such as emilin-1 and fibronectin. Extended culture time resulted in increased levels of core matrisome proteins. In a comparison with monolayer cultures on plastic, culture in lung scaffolds lead to a pronounced accumulation of proteoglycans, such as versican and decorin, resulting in regeneration of an extracellular matrix with greater resemblance to native lung tissue compared to standard monolayer cultures. Collectively, the study presents a promising technique for increasing the understanding of cell- extracellular matrix interactions under healthy and diseased conditions.
Vitamin C promotes apoptosis in breast cancer cells by increasing TRAIL expression
Authors: Sant David W. , Mustafi Sushmita , Gustafson Christopher B. , Chen Joshua , Slingerland Joyce M. , Wang Gaofeng 
Published: March 2018

AbstractGenomic loss of 5-hydroxymethylcytosine (5hmC) accompanies malignant cellular transformation in breast cancer. Vitamin C serves as a cofactor for TET methylcytosine dioxygenases to increase 5hmC generation. Here we show that the transcription of SVCT2, a major vitamin C transporter, was decreased in human breast cancers (113 cases) compared to normal breast tissues from the same patients. A decreased SVCT2 expression was also observed in breast cancer cell lines. Treatment with vitamin C (100 μM) increased the 5hmC content in MDA-MB-231 breast cancer cells and markedly altered the transcriptome. The vitamin C treatment induced apoptosis in MDA-MB-231 cells, which was verified in two additional breast cancer cell lines. This pro-apoptotic effect of vitamin C appeared to be mediated by TRAIL, a known apoptosis inducer. Vitamin C upregulated TRAIL transcripts (2.3-fold increase) and increased TRAIL protein levels. The upregulation of TRAIL by vitamin C was largely abolished by siRNAs targeting TETs and anti-TRAIL antibody abrogated the induction of apoptosis. Furthermore, the apoptosis promoted by vitamin C was associated with Bax and caspases activation, Bcl-xL sequestration, and cytochrome c release. Taken together, these results suggest a potential role of physiological doses of vitamin C in breast cancer prevention and treatment.
Response analysis of host Spodoptera exigua larvae to infection by Heliothis virescens ascovirus 3h (HvAV-3h) via transcriptome
Authors: Yu Huan , Li Zi-Qi , He Lei , Ou-Yang Yi-Yi , Li Ni , Huang Guo-Hua 
Published: March 2018

AbstractHeliothis virescens ascovirus 3 h (HvAV-3h), a dsDNA insect virus, belonging to the family Ascoviridae, can infect caterpillars of several Noctuidae species by ovipositing parasitoid wasps. In order to provide a comprehensive overview of the interactive responses of host larvae after infection by the ascovirus, a transcriptome analysis of Spodoptera exigua to HvAV-3h was conducted from 6 to 168 hours post infection (hpi). Approximately 101.64 Gb of RNA sequencing (RNA-seq) data obtained from infected and uninfected S. exigua larvae were used to perform a de novo transcriptome assembly, which generated approximately 62,258 S. exigua unigenes. Using differential gene expression analysis, it was determined that the majority of host transcripts were down-regulated beginning at 6 hpi and continuing throughout the infection period, although there was an increase in up-regulated unigene number during the 12 to 72 hpi stage. It is noteworthy that the most abundantly enriched pathways in KEGG annotation were Metabolism terms, indicating that the host larval metabolic mechanisms were highly influenced post HvAV-3h infection. In addition, the host cuticle protein encoding unigenes were highly down-regulated in most of the situations, suggesting that the host larval cuticle synthesis were inhibited by the viral infection.
Mechanism of translation control of the alternative Drosophila melanogaster Voltage Dependent Anion-selective Channel 1 mRNAs
Authors: Leggio L. , Guarino F. , Magrì A. , Accardi-Gheit R. , Reina S. , Specchia V. , Damiano F. , Tomasello M. F. , Tommasino M. , Messina A. 
Published: March 2018

AbstractThe eukaryotic porin, also called the Voltage Dependent Anion-selective Channel (VDAC), is the main pore-forming protein of the outer mitochondrial membrane. In Drosophila melanogaster, a cluster of genes evolutionarily linked to VDAC is present on chromosome 2L. The main VDAC isoform, called VDAC1 (Porin1), is expressed from the first gene of the cluster. The porin1 gene produces two splice variants, 1A-VDAC and 1B-VDAC, with the same coding sequence but different 5′ untranslated regions (UTRs). Here, we studied the influence of the two 5′ UTRs, 1A-5′ UTR and 1B-5′ UTR, on transcription and translation of VDAC1 mRNAs. In porin-less yeast cells, transformation with a construct carrying 1A-VDAC results in the expression of the corresponding protein and in complementation of a defective cell phenotype, whereas the 1B-VDAC sequence actively represses VDAC expression. Identical results were obtained using constructs containing the two 5′ UTRs upstream of the GFP reporter. A short region of 15 nucleotides in the 1B-5′ UTR should be able to pair with an exposed helix of 18S ribosomal RNA (rRNA), and this interaction could be involved in the translational repression. Our data suggest that contacts between the 5′ UTR and 18S rRNA sequences could modulate the translation of Drosophila 1B-VDAC mRNA. The evolutionary significance of this finding is discussed.
Recruitment kinetics of the homologous recombination pathway in procyclic forms of Trypanosoma brucei after ionizing radiation treatment
Authors: Marin Paula Andrea , da Silva Marcelo Santos , Pavani Raphael Souza , Machado Carlos Renato , Elias Maria Carolina 
Published: March 2018

AbstractOne of the most important mechanisms for repairing double-strand breaks (DSBs) in model eukaryotes is homologous recombination (HR). Although the genes involved in HR have been found in Trypanosoma brucei and studies have identified some of the proteins that participate in this HR pathway, the recruitment kinetics of the HR machinery onto DNA during DSB repair have not been clearly elucidated in this organism. Using immunofluorescence, protein DNA-bound assays, and DNA content analysis, we established the recruitment kinetics of the HR pathway in response to the DSBs generated by ionizing radiation (IR) in procyclic forms of T. brucei. These kinetics involved the phosphorylation of histone H2A and the sequential recruitment of the essential HR players Exo1, RPA, and Rad51. The process of DSB repair took approximately 5.5 hours. We found that DSBs led to a decline in the G2/M phase after IR treatment, concomitant with cell cycle arrest in the G1/S phase. This finding suggests that HR repairs DSBs faster than the other possible DSB repair processes that act during the G1/S transition. Taken together, these data suggest that the interplay between DNA damage detection and HR machinery recruitment is finely coordinated, allowing these parasites to repair DNA rapidly after DSBs during the late S/G2 proficient phases.
Acute metabolic actions of the major polyphenols in chamomile: an in vitro mechanistic study on their potential to attenuate postprandial hyperglycaemia
Authors: Villa-Rodriguez Jose A. , Kerimi Asimina , Abranko Laszlo , Tumova Sarka , Ford Lauren , Blackburn Richard S. , Rayner Christopher , Williamson Gary 
Published: March 2018

AbstractTransient hyperglycaemia is a risk factor for type 2 diabetes and endothelial dysfunction, especially in subjects with impaired glucose tolerance. Nutritional interventions and strategies for controlling postprandial overshoot of blood sugars are considered key in preventing progress to the disease state. We have identified apigenin-7-O-glucoside, apigenin, and (Z) and (E)−2-hydroxy-4-methoxycinnamic acid glucosides as the active (poly)phenols in Chamomile (Matricaria recutita) able to modulate carbohydrate digestion and absorption in vitro as assessed by inhibition of α-amylase and maltase activities. The latter two compounds previously mistakenly identified as ferulic acid hexosides were purified and characterised and studied for their contribution to the overall bioactivity of chamomile. Molecular docking studies revealed that apigenin and cinnamic acids present totally different poses in the active site of human α-amylase. In differentiated Caco-2/TC7 cell monolayers, apigenin-7-O-glucoside and apigenin strongly inhibited D-[U-14C]-glucose and D-[U-14C]-sucrose transport, and less effectively D-[U-14C]-fructose transport. Inhibition of D-[U-14C]-glucose transport by apigenin was stronger under Na+-depleted conditions, suggesting interaction with the GLUT2 transporter. Competitive binding studies with molecular probes indicate apigenin interacts primarily at the exofacial-binding site of GLUT2. Taken together, the individual components of Chamomile are promising agents for regulating carbohydrate digestion and sugar absorption at the site of the gastrointestinal tract.