bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long non-coding RNA FAM83H-AS1 is regulated by human papillomavirus 16 E6 independently of p53 in cervical cancer cells
Authors: Barr Jamie A. , Hayes Karen E. , Brownmiller Tayvia , Harold Abby D. , Jagannathan Rajaganapathi , Lockman Paul R. , Khan Saleem , Martinez Ivan 
Published: March 2019

AbstractHigh-risk human papillomavirus (HPV) infection is one of the first events in the process of carcinogenesis in cervical and head and neck cancers. The expression of the viral oncoproteins E6 and E7 are essential in this process by inactivating the tumor suppressor proteins p53 and Rb, respectively, in addition to their interactions with other host proteins. Non-coding RNAs, such as long non-coding RNAs (lncRNAs) have been found to be dysregulated in several cancers, suggesting an important role in tumorigenesis. In order to identify host lncRNAs affected by HPV infection, we expressed the high-risk HPV-16 E6 oncoprotein in primary human keratinocytes and measured the global lncRNA expression profile by high-throughput sequencing (RNA-seq). We found several host lncRNAs differentially expressed by E6 including GAS5, H19, and FAM83H-AS1. Interestingly, FAM83H-AS1 was found overexpressed in HPV-16 positive cervical cancer cell lines in an HPV-16 E6-dependent manner but independently of p53 regulation. Furthermore, FAM83H-AS1 was found to be regulated through the E6-p300 pathway. Knockdown of FAM83H-AS1 by siRNAs decreased cellular proliferation, migration and increased apoptosis. FAM83H-AS1 was also found to be altered in human cervical cancer tissues and high expression of this lncRNA was associated with worse overall survival, suggesting an important role in cervical carcinogenesis.
Impact of laterality and mucinous histology on relapse-free and overall survival in a registry-based colon cancer series
Authors: Negri Francesca , De Giorgi Annamaria , Gilli Annalisa , Azzoni Cinzia , Bottarelli Lorena , Gnetti Letizia , Goldoni Matteo , Manotti Laura , Sgargi Paolo , Michiara Maria , Leonardi Francesco , Rindi Guido , Cascinu Stefano , Silini Enrico Maria 
Published: March 2019

AbstractRecent data suggest that tumor laterality and mucinous histology may be clinically relevant. We investigated how both variables impact on the prognosis and the response to therapies in a large population-based cohort of cancer patients. Incidence data, clinical and pathological features, and outcome were systematically collected from the Tumor Registry of Parma over the years 2004–2009. Survival data were modeled by multivariable analysis. 1358 patients affected by stage I–IV colon cancer were considered; 661 (49%) had right-sided and 697 (51%) left-sided tumors. 144 (11%) had mucinous (MAC) and 1214 (89%) non-mucinous (NMAC) histology. MACs and NMACs of the right colon showed no difference in stage distribution, whereas left colon MACs were more frequently in an advanced stage (stage IV) (p = 0.008). Stage IV right colon tumors had a poorer overall survival than stage IV left-sided colon cancers (75th percentile 20 vs 34 months, p < 0.001). At relapse, MACs were less responsive to systemic therapy and had worse survival compared with NMACs regardless of tumor side (7.1 vs 13.1 months, p = 0.018). Right-sided colon cancers had poorer survival compared to left-sided tumors; the effect was mainly attributable to NMACs. At relapse, MACs had unfavorable prognosis regardless of the primary tumor-side.
Activation of Peripheral Blood CD4+ T-Cells in IBS is not Associated with Gastrointestinal or Psychological Symptoms
Authors: Nasser Yasmin , Petes Carlene , Simmers Celine , Basso Lilian , Altier Christophe , Gee Katrina , Vanner Stephen J. 
Published: March 2019

AbstractImmune activation may underlie the pathogenesis of irritable bowel syndrome (IBS), but the evidence is conflicting. We examined whether peripheral CD4+ T-cells from IBS patients demonstrated immune activation and changes in cytokine production. To gain mechanistic insight, we examined whether immune activation correlated with psychological stress and changing symptoms over time. IBS patients (n = 29) and healthy volunteers (HV; n = 29) completed symptom and psychological questionnaires. IBS patients had a significant increase in CD4+ T-cells expressing the gut homing marker integrin β7 (p = 0.023) and lymphoid marker CD62L (p = 0.026) compared to HV. Furthermore, phytohaemagglutinin stimulated CD4+ T-cells from IBS-D patients demonstrated increased TNFα secretion when compared to HV (p = 0.044). Increased psychological scores in IBS did not correlate with TNFα production, while stress hormones inhibited cytokine secretion from CD4+ T-cells of HV in vitro. IBS symptoms, but not markers of immune activation, decreased over time. CD4+ T-cells from IBS-D patients exhibit immune activation, but this did not appear to correlate with psychological stress measurements or changing symptoms over time. This could suggest that immune activation is a surrogate of an initial trigger and/or ongoing parallel peripheral mechanisms.
A basic Helix-Loop-Helix (SlARANCIO), identified from a Solanum pennellii introgression line, affects carotenoid accumulation in tomato fruits
Authors: D’Amelia Vincenzo , Raiola Assunta , Carputo Domenico , Filippone Edgardo , Barone Amalia , Rigano Maria Manuela 
Published: March 2019

AbstractCarotenoid accumulation in tomato (Solanum lycopersicum) fruits is influenced by environmental stimuli and hormonal signals. However, information on the relative regulatory mechanisms are scanty since many molecular players of the carotenoid biosynthetic pathway are still unknown. Here, we reported a basic Helix-Loop-Helix transcription factor, named SlARANCIO (SlAR), whose silencing influences carotenoid accumulation in tomato fruits. The SlAR gene was found in the S. pennellii introgression line (IL) 12-4SL that holds the carotenoid QTL lyc12.1. We observed that the presence of the wild region in a cultivated genetic background led to a decrease in total carotenoid content of IL12-4SL fruits. To get insights into the function of SlAR, a quick reverse genetic approach was carried out. Virus-induced gene silencing of SlAR in S. lycopersicum M82 and MicroTom fruits reproduced the same phenotype observed in IL12-4SL, i.e. decreased content of lycopene and total carotenoids. Vice versa, the overexpression of SlAR in Nicotiana benthamiana leaves increased the content of total carotenoids and chlorophylls. Our results, combined with public transcriptomic data, highly suggest that SlAR acts indirectly on the carotenoid pathway and advances current knowledge on the molecular regulators controlling lyc12.1 and, potentially, precursors of carotenoid biosynthesis.
Genomic and metagenomic signatures of giant viruses are ubiquitous in water samples from sewage, inland lake, waste water treatment plant, and municipal water supply in Mumbai, India
Authors: Chatterjee Anirvan , Sicheritz-Pontén Thomas , Yadav Rajesh , Kondabagil Kiran 
Published: March 2019

AbstractWe report the detection of genomic signatures of giant viruses (GVs) in the metagenomes of three environment samples from Mumbai, India, namely, a pre-filter of a household water purifier, a sludge sample from wastewater treatment plant (WWTP), and a drying bed sample of the same WWTP. The de novo assembled contigs of each sample yielded 700 to 2000 maximum unique matches with the GV genomic database. In all three samples, the maximum number of reads aligned to Pandoraviridae, followed by Phycodnaviridae, Mimiviridae, Iridoviridae, and other Megaviruses. We also isolated GVs from every environmental sample (n = 20) we tested using co-culture of the sample with Acanthomoeba castellanii. From this, four randomly selected GVs were subjected to the genomic characterization that showed remarkable cladistic homology with the three GV families viz., Mimivirirdae (Mimivirus Bombay [MVB]), Megaviruses (Powai lake megavirus [PLMV] and Bandra megavius [BAV]), and Marseilleviridae (Kurlavirus [KV]). All 4 isolates exhibited remarkable genomic identity with respective GV families. Functionally, the genomes were indistinguishable from other previously reported GVs, encoding nearly all COGs across extant family members. Further, the uncanny genomic homogeneity exhibited by individual GV families across distant geographies indicate their yet to be ascertained ecological significance.
Minor allele of the factor V K858R variant protects from venous thrombosis only in non-carriers of factor V Leiden mutation
Authors: Ibrahim-Kosta M. , Suchon P. , Couturaud F. , Smadja D. , Olaso R. , Germain M. , Saut N. , Goumidi L. , Derbois C. , Thibord F. , Debette S. , Amouyel P. , Deleuze J. F. , van Doorn P. , Castoldi E. , Patin E. , Alessi M. C. , Trégouët D. A. , Morange P. E. 
Published: March 2019

AbstractFactor V serves an important role in the regulation of blood coagulation. The rs6025 (R534Q) and rs4524 (K858R) polymorphisms in the F5 gene, are known to influence the risk of venous thrombosis. While the rare Q534 (factor V Leiden) allele is associated with an increased risk of venous thrombosis, the minor R858 allele is associated with a lower risk of disease. However, no study has deeply examined the cumulative impact of these two variations on venous thrombosis risk. We study the association of these polymorphisms with the risk of venous thrombosis in 4 French case-control populations comprising 3719 patients and 4086 controls. We demonstrate that the Q534 allele has a dominant effect over R858. Besides, we show that in individuals not carrying the Q534 allele, the protective effect of the R858 allele acts in a dominant mode. Thrombin generation-based normalized activated protein C sensitivity ratio was lower in the 858R/R homozygotes than in the 858K/K homozygotes (1.92 ± 1.61 vs 2.81 ± 1.57, p = 0.025). We demonstrate that the R858 allele of the F5 rs4524 variant protects from venous thrombosis only in non-carriers of the Q534 allele of the F5 rs6025. Its protective effect is mediated by reduced factor VIII levels and reduced activated protein C resistance.
Efficient recycling of nutrients in modern and past hypersaline environments
Authors: Isaji Y. , Kawahata H. , Ogawa N. O. , Kuroda J. , Yoshimura T. , Jiménez-Espejo F. J. , Makabe A. , Shibuya T. , Lugli S. , Santulli A. , Manzi V. , Roveri M. , Ohkouchi N. 
Published: March 2019

AbstractThe biogeochemistry of hypersaline environments is strongly influenced by changes in biological processes and physicochemical parameters. Although massive evaporation events have occurred repeatedly throughout Earth history, their biogeochemical cycles and global impact remain poorly understood. Here, we provide the first nitrogen isotopic data for nutrients and chloropigments from modern shallow hypersaline environments (solar salterns, Trapani, Italy) and apply the obtained insights to δ15N signatures of the Messinian salinity crisis (MSC) in the late Miocene. Concentrations and δ15N of chlorophyll a, bacteriochlorophyll a, nitrate, and ammonium in benthic microbial mats indicate that inhibition of nitrification suppresses denitrification and anammox, resulting in efficient ammonium recycling within the mats and high primary productivity. We also suggest that the release of 15N-depleted NH3(gas) with increasing salinity enriches ammonium 15N in surface brine (≈34.0‰). Such elevated δ15N is also recorded in geoporphyrins isolated from sediments of the MSC peak (≈20‰), reflecting ammonium supply sufficient for sustaining phototrophic primary production. We propose that efficient nutrient supply combined with frequent bottom-water anoxia and capping of organic-rich sediments by evaporites of the Mediterranean MSC could have contributed to atmospheric CO2 reduction during the late Miocene.
Effect of ripasudil on diabetic macular edema
Authors: Minami Yoshiro , Song Young-seok , Ishibazawa Akihiro , Omae Tsuneaki , Ro-mase Tomoko , ishiko Satoshi , Yoshida Akitoshi 
Published: March 2019

AbstractThe current study aimed to address whether ripasudil, a Rho-associated coiled-coil containing protein kinase (ROCK) inhibitor developed to treat glaucoma and ocular hypertension (OH), improves diabetic macular edema (DME) since it is known that ROCK upregulates vascular endothelial growth factor. We retrospectively investigated the foveal thickness (FT) measured by spectral-domain optical coherence tomography, visual acuity (VA), and intraocular pressure (IOP) in 12 eyes with DME that received ripasudil treatment for primary open-angle glaucoma or OH and compared them with 14 eyes that received no treatment. One month after ripasudil therapy, the mean FT decreased significantly from 439 ± 72 µm to 395 ± 62 µm (P = 0.003); this change was significantly different from that in the controls, in which the mean FT increased by 1 ± 39 µm (P = 0.01). Ripasudil also caused a significant decrease in IOP from 17.3 ± 5.2 mmHg to 14.6 ± 4.0 mmHg (P = 0.02); this change was significantly greater than that in the controls, in which IOP changed by 0.0 ± 1.6 mmHg (P < 0.008). There was no significant difference in the VA changes between groups. Our results suggested that ripasudil may have positive effects on both IOP and DME.
Surveying of acid-tolerant thermophilic lignocellulolytic fungi in Vietnam reveals surprisingly high genetic diversity
Authors: Thanh Vu Nguyen , Thuy Nguyen Thanh , Huong Han Thi Thu , Hien Dinh Duc , Hang Dinh Thi My , Anh Dang Thi Kim , Hüttner Silvia , Larsbrink Johan , Olsson Lisbeth 
Published: March 2019

AbstractThermophilic fungi can represent a rich source of industrially relevant enzymes. Here, 105 fungal strains capable of growing at 50 °C and pH 2.0 were isolated from compost and decaying plant matter. Maximum growth temperatures of the strains were in the range 50 °C to 60 °C. Sequencing of the internal transcribed spacer (ITS) regions indicated that 78 fungi belonged to 12 species of Ascomycota and 3 species of Zygomycota, while no fungus of Basidiomycota was detected. The remaining 27 strains could not be reliably assigned to any known species. Phylogenetically, they belonged to the genusThielavia, but they represented 23 highly divergent genetic groups different from each other and from the closest known species by 12 to 152 nucleotides in the ITS region. Fungal secretomes of all 105 strains produced during growth on untreated rice straw were studied for lignocellulolytic activity at different pH and temperatures. The endoglucanase and xylanase activities differed substantially between the different species and strains, but in general, the enzymes produced by the novelThielaviaspp. strains exhibited both higher thermal stability and tolerance to acidic conditions. The study highlights the vast potential of an untapped diversity of thermophilic fungi in the tropics.
A trimetallic organometallic precursor for efficient water oxidation
Authors: Madadkhani Sepideh , Aghakhanpour Reza Babadi , Singh Jitendra Pal , Bagheri Robabeh , Chae Keun Hwa , Song Zhenlun , Najafpour Mohammad Mahdi 
Published: March 2019

AbstractHerein, we report an iron/nickel/zinc mixed oxide as a catalyst for the electrochemical water oxidation. This catalyst was synthesized by a straightforward method for the synthesis of an iron/nickel/zinc mixed oxide through the calcination of a Fe/Ni/Zn organometallic compound. The calcined product contains Fe and Ni as crucial ions for water oxidation, accompanied by the presence of Zn ions. The removal of Zn ions from the mixed oxide provides more active sites on the surface of the catalyst. The composition of the compound was characterized by some common methods and found to be an efficient water-oxidizing catalyst. The catalyst on FTO at pH = 13 yields a current density of 12 mA/cm2at 1.2 V (vs. Ag│AgCl). After 5 hours at 1.1 V, the electrode not only shows no decrease in performance, but also shows an increase from 4 to 7 mA/cm2in the water oxidation activity. Tafel plot, for the electrode at pH = 13 in KOH solution (0.1 M) showed linearity for the graph of lg j vs. V with both relatively low (220.4 mV per decade) and high overpotentials (903.7 mV per decade).
Deciphering host-parasitoid interactions and parasitism rates of crop pests using DNA metabarcoding
Authors: Sow Ahmadou , Brévault Thierry , Benoit Laure , Chapuis Marie-Pierre , Galan Maxime , Coeur d’acier Armelle , Delvare Gérard , Sembène Mbacké , Haran Julien 
Published: March 2019

AbstractAn accurate estimation of parasitism rates and diversity of parasitoids of crop insect pests is a prerequisite for exploring processes leading to efficient natural biocontrol. Traditional methods such as rearing have been often limited by taxonomic identification, insect mortality and intensive work, but the advent of high-throughput sequencing (HTS) techniques, such as DNA metabarcoding, is increasingly seen as a reliable and powerful alternative approach. Little has been done to explore the benefits of such an approach for estimating parasitism rates and parasitoid diversity in an agricultural context. In this study, we compared the composition of parasitoid species and parasitism rates between rearing and DNA metabarcoding of host eggs and larvae of the millet head miner, Heliocheilus albipunctella De Joannis (Lepidoptera, Noctuidae), collected from millet fields in Senegal. We first assessed the detection threshold for the main ten endoparasitoids, by sequencing PCR products obtained from artificial dilution gradients of the parasitoid DNAs in the host moth. We then assessed the potential of DNA metabarcoding for diagnosing parasitism rates in samples collected from the field. Under controlled conditions, our results showed that relatively small quantities of parasitoid DNA (0.07 ng) were successfully detected within an eight-fold larger quantity of host DNA. Parasitoid diversity and parasitism rate estimates were always higher for DNA metabarcoding than for host rearing. Furthermore, metabarcoding detected multi-parasitism, cryptic parasitoid species and differences in parasitism rates between two different sampling sites. Metabarcoding shows promise for gaining a clearer understanding of the importance and complexity of host-parasitoid interactions in agro-ecosystems, with a view to improving pest biocontrol strategies.
Chemically deposited palladium nanoparticles on graphene for hydrogen sensor applications
Authors: Tang Xiaohui , Haddad Pierre-Antoine , Mager Nathalie , Geng Xin , Reckinger Nicolas , Hermans Sophie , Debliquy Marc , Raskin Jean-Pierre 
Published: March 2019

AbstractGraphene decorated by palladium (Pd) nanoparticles has been investigated for hydrogen sensor applications. The density of Pd nanoparticles is critical for the sensor performance. We develop a new chemical method to deposit high-density, small-size and uniformly-distributed Pd nanoparticles on graphene. With this method, Pd precursors are connected to the graphene by π-π bonds without introducing additional defects in the hexagonal carbon lattice. Our method is simple, cheap, and compatible with complementary metal-oxide semiconductor (CMOS) technology. This method is used to fabricate hydrogen sensors on 3-inch silicon wafers. The sensors show high performance at room temperature. Particularly, the sensors present a shorter recovery time under light illumination. The sensing mechanism is explained and discussed. The proposed deposition method facilitates mass fabrication of the graphene sensors and allows integration with CMOS circuits for practical applications.
Metal-coated microsphere monolayers as surface plasmon resonance sensors operating in both transmission and reflection modes
Authors: Farcau Cosmin 
Published: March 2019

AbstractMetal-coated microsphere monolayers (MCM) are a class of plasmonic crystals consisting of noble metal films over arrays of self-assembled colloidal microspheres. Despite their ease of fabrication and tunable plasmonic response, their optical sensing potential has been scarcely explored. Here, silver coated polystyrene sphere monolayers are proposed as surface plasmon resonance sensors capable of functioning in both transmission (T) and reflection (R) readout modes. An original and key point is the use of ~200 nm colloids, smaller than in MCM studied before. It allowed us to reveal a previously unobserved, additional/secondary Enhanced Optical Transmission band, which can be exploited in sensing, with higher sensitivity than the better-known main transmission band. The reflection configuration however, is almost an order of magnitude more efficient for sensing than the transmission one. We also evidenced a strong impact of the adsorbate location on the metal surface on the sensing efficiency. Electric field distribution analysis is performed to explain these results. Proof-of-concept experiments on the detection of 11-MUA molecular monolayers, performed in both readout modes, confirm the behaviors observed through FDTD simulations. Results in this paper can serve as guidelines for designing optimized sensors based on metal-coated colloidal monolayers, and more generally for plasmonic sensors based on metal nanostructured films.
Temporal Dynamics of Visual Attention Allocation
Authors: Moon Jongmin , Choe Seonggyu , Lee Seul , Kwon Oh-Sang 
Published: March 2019

AbstractWe often temporally prepare our attention for an upcoming event such as a starter pistol. In such cases, our attention should be properly allocated around the expected moment of the event to process relevant sensory input efficiently. In this study, we examined the dynamic changes of attention levels near the expected moment by measuring contrast sensitivity to a target that was temporally cued by a five-second countdown. We found that the overall attention level decreased rapidly after the expected moment, while it stayed relatively constant before it. Results were not consistent with the predictions of existing explanations of temporal attention such as the hazard rate or the stimulus-driven oscillations. A control experiment ruled out the possibility that the observed pattern was due to biased time perception. In a further experiment with a wider range of cue-stimulus-intervals, we observed that attention level increased until the last 500 ms of the interval range, and thereafter, started to decrease. Based on the performances of a generative computational model, we suggest that our results reflect the nature of temporal attention that takes into account the subjectively estimated hazard rate and the probability of relevant events occurring in the near future.