bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tracking the polyclonal neutralizing antibody response to a dengue virus serotype 1 type-specific epitope across two populations in Asia and the Americas
Authors: Andrade Daniela V. , Warnes Colin , Young Ellen , Katzelnick Leah C. , Balmaseda Angel , de Silva Aravinda M. , Baric Ralph S. , Harris Eva 
Published: November 2019

AbstractThe four dengue virus serotypes (DENV1-4) cause major public health problems worldwide. Highly neutralizing type-specific human monoclonal antibodies (hmAbs) target conformation-dependent epitopes on the DENV envelope protein, including 1F4, a DENV1 type-specific hmAb. Using a recombinant DENV2 virus displaying the DENV1 1F4 epitope (rDENV2/1), we measured the proportion and kinetics of DENV1 neutralizing antibodies targeting the 1F4 epitope in individuals living in Asia and the Americas where different DENV1 genotypes were circulating. Samples from 20 individuals were analyzed 3 and 18 months post-primary DENV1 infection, alongside samples from 4 individuals collected annually for four years post-primary DENV1 infection, from two studies in Nicaragua. We also analyzed convalescent post-primary DENV1 plasma samples from Sri Lankan individuals. We found that neutralizing antibodies recognizing the 1F4 epitope vary in prevalence across both populations and were detected from 20 days to four years post-infection. Additionally, both populations displayed substantial variability, with a range of high to low proportions of DENV1 type-specific neutralizing antibodies recognizing the 1F4 epitope seen across individuals. Thus, the 1F4 epitope is a major but not exclusive target of type-specific neutralizing antibodies post-primary infection with different DENV1 genotypes in Asia and Latin America, and additional epitopes likely contribute to type-specific neutralization of DENV1.
Reward and punishment in climate change dilemmas
Authors: Góis António R. , Santos Fernando P. , Pacheco Jorge M. , Santos Francisco C. 
Published: November 2019

AbstractMitigating climate change effects involves strategic decisions by individuals that may choose to limit their emissions at a cost. Everyone shares the ensuing benefits and thereby individuals can free ride on the effort of others, which may lead to the tragedy of the commons. For this reason, climate action can be conveniently formulated in terms of Public Goods Dilemmas often assuming that a minimum collective effort is required to ensure any benefit, and that decision-making may be contingent on the risk associated with future losses. Here we investigate the impact of reward and punishment in this type of collective endeavors — coined as collective-risk dilemmas — by means of a dynamic, evolutionary approach. We show that rewards (positive incentives) are essential to initiate cooperation, mostly when the perception of risk is low. On the other hand, we find that sanctions (negative incentives) are instrumental to maintain cooperation. Altogether, our results are gratifying, given the a-priori limitations of effectively implementing sanctions in international agreements. Finally, we show that whenever collective action is most challenging to succeed, the best results are obtained when both rewards and sanctions are synergistically combined into a single policy.
Characterization and Identification of Lysine Succinylation Sites based on Deep Learning Method
Authors: Huang Kai-Yao , Hsu Justin Bo-Kai , Lee Tzong-Yi 
Published: November 2019

AbstractSuccinylation is a type of protein post-translational modification (PTM), which can play important roles in a variety of cellular processes. Due to an increasing number of site-specific succinylated peptides obtained from high-throughput mass spectrometry (MS), various tools have been developed for computationally identifying succinylated sites on proteins. However, most of these tools predict succinylation sites based on traditional machine learning methods. Hence, this work aimed to carry out the succinylation site prediction based on a deep learning model. The abundance of MS-verified succinylated peptides enabled the investigation of substrate site specificity of succinylation sites through sequence-based attributes, such as position-specific amino acid composition, the composition of k-spaced amino acid pairs (CKSAAP), and position-specific scoring matrix (PSSM). Additionally, the maximal dependence decomposition (MDD) was adopted to detect the substrate signatures of lysine succinylation sites by dividing all succinylated sequences into several groups with conserved substrate motifs. According to the results of ten-fold cross-validation, the deep learning model trained using PSSM and informative CKSAAP attributes can reach the best predictive performance and also perform better than traditional machine-learning methods. Moreover, an independent testing dataset that truly did not exist in the training dataset was used to compare the proposed method with six existing prediction tools. The testing dataset comprised of 218 positive and 2621 negative instances, and the proposed model could yield a promising performance with 84.40% sensitivity, 86.99% specificity, 86.79% accuracy, and an MCC value of 0.489. Finally, the proposed method has been implemented as a web-based prediction tool (CNN-SuccSite), which is now freely accessible at http://csb.cse.yzu.edu.tw/CNN-SuccSite/.
Characterization and diagnostic marker for TTG1 regulating tannin and anthocyanin biosynthesis in faba bean
Authors: Gutierrez Natalia , Torres Ana M. 
Published: November 2019

AbstractCondensed tannins, found in coloured-flowering varieties of faba bean (Vicia faba L) are, after vicine and convicine, one of the major anti-nutritional factors for monogastric animals. The development of tannin-free cultivars is a key goal in breeding to broaden the use of this legume in the animal feed industry. Two recessive genes, zt-1 and zt-2, control the zero-tannin content and promote white-flowered plants. Previous studies exploiting synteny with the model Medicago truncatula reported a mutation in TTG1, a gene encoding a WD40 transcription factor located in chromosome II, as the responsible for the zt-1 phenotypes. Here a comprehensive analysis of VfTTG1 (including phylogenetic relationships, gene structure and gene expression) has been conducted to confirm the identity of the gene and to reveal structural changes that may result in different functional alleles. The results confirmed the identity of the candidate and revealed the existence of two different alleles responsible for the phenotype: ttg1-a, probably due to a mutation in the promoter region, and ttg1-b caused by a deletion at the 5′end of VfTTG1. Based on the sequencing results, an allele-specific diagnostic marker was designed that differentiate zt-1 from wild and zt-2 genotypes and facilitates its deployment in faba bean breeding programs.
Kunitz type protease inhibitor from the canine tapeworm as a potential therapeutic for melanoma
Authors: Ranasinghe Shiwanthi L. , Rivera Vanessa , Boyle Glen M. , McManus Donald P. 
Published: November 2019

AbstractModulating the tumor microenvironment to promote an effective immune response is critical in managing any type of tumor. Melanoma is an aggressive skin cancer and the incidence rate is increasing worldwide. Potent protease inhibitors have recently been extensively researched as potential therapeutic agents against various cancers. EgKI-1 is a potent Kunitz type protease inhibitor identified from the canine tapeworm Echinococcus granulosus that has shown anti-cancer activities in vivo. In this study we show that EgKI-1 significantly reduced the growth of melanoma in the B16-F0 mouse model and was not toxic to normal surrounding tissue. Moreover, EgKI-1 treatment significantly reduced survivin expression levels and increased the CD8+ T cell population in draining axillary lymph nodes. Therefore, EgKI-1 potentially reduces tumor growth by inducing apoptosis and modulating the tumor microenvironment, and has potential for development as an intra-lesional treatment for melanoma.
Synergy of arbuscular mycorrhizal symbiosis and exogenous Ca2+ benefits peanut (Arachis hypogaea L.) growth through the shared hormone and flavonoid pathway
Authors: Cui Li , Guo Feng , Zhang Jialei , Yang Sha , Meng JingJing , Geng Yun , Li Xinguo , Wan Shubo 
Published: November 2019

AbstractPeanut yield is severely affected by exchangeable calcium ion (Ca2+) deficiency in the soil. Arbuscular mycorrhizal (AM) symbiosis increases the absorption of Ca2+ for host plants. Here, we analyzed the physiological and transcriptional changes in the roots of Arachis hypogaea L. colonized by Funneliformismosseae under Ca2+-deficient and -sufficient conditions. The results showed that exogenous Ca2+ application increased arbuscular mycorrhizal fungi (AMF) colonization, plant dry weight, and Ca content of AM plants. Simultaneously, transcriptome analysis showed that Ca2+ application further induced 74.5% of differentially expressed gene transcripts in roots of AM peanut seedlings. These genes are involved in AM symbiosis development, hormone biosynthesis and signal transduction, and carotenoid and flavonoid biosynthesis. The transcripts of AM-specific marker genes in AM plants with Ca2+ deprivation were further up-regulated by Ca2+ application. Gibberellic acid (GA3) and flavonoid contents were higher in roots of AM- and Ca2+-treated plants, but salicylic acid (SA) and carotenoid contents specifically increased in roots of the AM plants. Thus, these results suggest that the synergy of AM symbiosis and Ca2+ improves plant growth due to the shared GA- and flavonoid-mediated pathway, whereas SA and carotenoid biosynthesis in peanut roots are specific to AM symbiosis.
Direct, gabapentin-insensitive interaction of a soluble form of the calcium channel subunit α2δ-1 with thrombospondin-4
Authors: El-Awaad Ehab , Pryymachuk Galyna , Fried Cora , Matthes Jan , Isensee Jörg , Hucho Tim , Neiss Wolfram F. , Paulsson Mats , Herzig Stefan , Zaucke Frank , Pietsch Markus 
Published: November 2019

AbstractThe α2δ‐1 subunit of voltage-gated calcium channels binds to gabapentin and pregabalin, mediating the analgesic action of these drugs against neuropathic pain. Extracellular matrix proteins from the thrombospondin (TSP) family have been identified as ligands of α2δ‐1 in the CNS. This interaction was found to be crucial for excitatory synaptogenesis and neuronal sensitisation which in turn can be inhibited by gabapentin, suggesting a potential role in the pathogenesis of neuropathic pain. Here, we provide information on the biochemical properties of the direct TSP/α2δ-1 interaction using an ELISA-style ligand binding assay. Our data reveal that full-length pentameric TSP-4, but neither TSP-5/COMP of the pentamer-forming subgroup B nor TSP-2 of the trimer-forming subgroup A directly interact with a soluble variant of α2δ-1 (α2δ-1S). Interestingly, this interaction is not inhibited by gabapentin on a molecular level and is not detectable on the surface of HEK293-EBNA cells over-expressing α2δ‐1 protein. These results provide biochemical evidence that supports a specific role of TSP-4 among the TSPs in mediating the binding to neuronal α2δ‐1 and suggest that gabapentin does not directly target TSP/α2δ-1 interaction to alleviate neuropathic pain.
The beneficial effects of a muscarinic agonist on pancreatic β-cells
Authors: Ito Yuzuru , Kaji Mitsuyo , Sakamoto Eri , Terauchi Yasuo 
Published: November 2019

AbstractThe brain and nervous system play an important role in pancreatic β-cell function. This study investigated the role of muscarinic agonists or acetylcholine, which is the major neurotransmitter in the vagal nerve, in regulating pancreatic β-cell mass and glucose homeostasis. Administration of the muscarinic agonist bethanechol increased insulin secretion and improved glucose tolerance in insulin-receptor substrate 2 (IRS2)-knockout (IRS-2−/−) mice and diet-induced obesity mice. Oral administration of bethanechol increased β-cell mass and proliferation in wild-type mice, but not IRS-2−/− mice. The muscarinic agonist also increased the incorporation of 5-bromo-2′-deoxyuridine (BrdU) into islets isolated from wild-type mice and pancreatic β-cell line MIN6. The phosphorylation of protein kinase B (Akt) induced by oral administration of bethanechol was observed in wild-type mice, but not IRS-2−/− mice. The secretion of glucagon-like peptide-1 (GLP-1) was also stimulated by bethanechol in wild-type mice, and a GLP-1 antagonist partially inhibited the bethanechol-induced increase in β-cell mass. These results suggest that the muscarinic agonist exerted direct and indirect effects on β-cell proliferation that were dependent on the IRS-2/Akt pathway. The bethanechol-stimulated release of GLP-1 may be indirectly associated with β-cell proliferation.
Turbulence-Resistant FSO Communication Using a Few-Mode Pre-Amplified Receiver
Authors: Liu Huiyuan , Huang Bin , Zacarias Juan Carlos Alvarado , Wen He , Chen Haoshuo , Fontaine Nicolas K. , Ryf Roland , Antonio-Lopez Jose Enrique , Correa Rodrigo Amezcua , Li Guifang 
Published: November 2019

AbstractLeveraging recent advances in space-division multiplexing, we propose and demonstrate turbulence-resistant free-space optical communication using few-mode (FM) pre-amplified receivers. The rationale for this approach is that a distorted wavefront can be decomposed into a superposition of the fundamental Gaussian mode and high-order modes of a few-mode fiber. We present the noise statistics and the sensitivity of the FM pre-amplified receiver, followed by experimental and numerical comparisons between FM pre-amplified receivers and single-mode (SM) pre-amplified receivers with or without adaptive optics. FM pre-amplified receivers for FSO can achieve high sensitivity, simplicity and reliability.
ClpC affects the intracellular survival capacity of Staphylococcus aureus in non-professional phagocytic cells
Authors: Gunaratnam Gubesh , Tuchscherr Lorena , Elhawy Mohamed I. , Bertram Ralph , Eisenbeis Janina , Spengler Christian , Tschernig Thomas , Löffler Bettina , Somerville Greg A. , Jacobs Karin , Herrmann Mathias , Bischoff Markus 
Published: November 2019

AbstractInvasion and persistence of bacteria within host cells requires that they adapt to life in an intracellular environment. This adaptation induces bacterial stress through events such as phagocytosis and enhanced nutrient-restriction. During stress, bacteria synthesize a family of proteins known as heat shock proteins (HSPs) to facilitate adaptation and survival. Previously, we determined the Staphylococcus aureus HSP ClpC temporally alters bacterial metabolism and persistence. This led us to hypothesize that ClpC might alter intracellular survival. Inactivation of clpC in S. aureus strain DSM20231 significantly enhanced long-term intracellular survival in human epithelial (HaCaT) and endothelial (EA.hy926) cell lines, without markedly affecting adhesion or invasion. This phenotype was similar across a genetically diverse collection of S. aureus isolates, and was influenced by the toxin/antitoxin encoding locus mazEF. Importantly, MazEF alters mRNA synthesis and/or stability of S. aureus virulence determinants, indicating ClpC may act through the mRNA modulatory activity of MazEF. Transcriptional analyses of total RNAs isolated from intracellular DSM20231 and isogenic clpC mutant cells identified alterations in transcription of α-toxin (hla), protein A (spa), and RNAIII, consistent with the hypothesis that ClpC negatively affects the intracellular survival of S. aureus in non-professional phagocytic cells, via modulation of MazEF and Agr.
An Experimental Investigation on the Kinetics of Integrated Methane Recovery and CO2 Sequestration by Injection of Flue Gas into Permafrost Methane Hydrate Reservoirs
Authors: Hassanpouryouzband Aliakbar , Yang Jinhai , Okwananke Anthony , Burgass Rod , Tohidi Bahman , Chuvilin Evgeny , Istomin Vladimir , Bukhanov Boris 
Published: November 2019

AbstractLarge hydrate reservoirs in the Arctic regions could provide great potentials for recovery of methane and geological storage of CO2. In this study, injection of flue gas into permafrost gas hydrates reservoirs has been studied in order to evaluate its use in energy recovery and CO2 sequestration based on the premise that it could significantly lower costs relative to other technologies available today. We have carried out a series of real-time scale experiments under realistic conditions at temperatures between 261.2 and 284.2 K and at optimum pressures defined in our previous work, in order to characterize the kinetics of the process and evaluate efficiency. Results show that the kinetics of methane release from methane hydrate and CO2 extracted from flue gas strongly depend on hydrate reservoir temperatures. The experiment at 261.2 K yielded a capture of 81.9% CO2 present in the injected flue gas, and an increase in the CH4 concentration in the gas phase up to 60.7 mol%, 93.3 mol%, and 98.2 mol% at optimum pressures, after depressurizing the system to dissociate CH4 hydrate and after depressurizing the system to CO2 hydrate dissociation point, respectively. This is significantly better than the maximum efficiency reported in the literature for both CO2 sequestration and methane recovery using flue gas injection, demonstrating the economic feasibility of direct injection flue gas into hydrate reservoirs in permafrost for methane recovery and geological capture and storage of CO2. Finally, the thermal stability of stored CO2 was investigated by heating the system and it is concluded that presence of N2 in the injection gas provides another safety factor for the stored CO2 in case of temperature change.
Morphological MRI phenotypes of multiple sclerosis differ in resting-state brain function
Authors: Pinter Daniela , Beckmann Christian F. , Fazekas Franz , Khalil Michael , Pichler Alexander , Gattringer Thomas , Ropele Stefan , Fuchs Siegrid , Enzinger Christian 
Published: November 2019

AbstractWe aimed to assess differences in resting-state functional connectivity (FC) between distinct morphological MRI-phenotypes in multiple sclerosis (MS). Out of 180 MS patients, we identified those with high T2-hyperintense lesion load (T2-LL) and high normalized brain volume (NBV; a predominately white matter damage group, WMD; N = 37) and patients with low T2-LL and low NBV (N = 37; a predominately grey matter damage group; GMD). Independent component analysis of resting-state fMRI was used to test for differences in the sensorimotor network (SMN) between MS MRI-phenotypes and compared to 37 age-matched healthy controls (HC). The two MS groups did not differ regarding EDSS scores, disease duration and distribution of clinical phenotypes. WMD compared to GMD patients showed increased FC in all sub-units of the SMN (sex- and age-corrected). WMD patients had increased FC compared to HC and GMD patients in the central SMN (leg area). Only in the WMD group, higher EDSS scores and T2-LL correlated with decreased connectivity in SMN sub-units. MS patients with distinct morphological MRI-phenotypes also differ in brain function. The amount of focal white matter pathology but not global brain atrophy affects connectivity in the central SMN (leg area) of the SMN, consistent with the notion of a disconnection syndrome.
A New Chloroplast DNA Extraction Protocol Significantly Improves the Chloroplast Genome Sequence Quality of Foxtail Millet (Setaria italica (L.) P. Beauv.)
Authors: Liu Dan , Cui Yanjiao , Li Suying , Bai Guihua , Li Qiang , Zhao Zilong , Liang Dan , Wang Conglei , Wang Jianhe , Shi Xiaowei , Chen Chao , Feng Gang , Liu Zhengli 
Published: November 2019

AbstractThe complexity of the leaf constitution of foxtail millet (Setaria italica (L.) P. Beauv.) makes it difficult to obtain high-purity cpDNA. Here, we developed a protocol to isolate high-quality cpDNA from foxtail millet and other crops. The new protocol replaces previous tissue grinding and homogenization by enzyme digestion of tiny leaf strips to separate protoplasts from leaf tissue and protects chloroplasts from damage by undue grinding and homogenization and from contamination of cell debris and nuclear DNA. Using the new protocol, we successfully isolated high-quality cpDNAs for whole-genome sequencing from four foxtail millet cultivars, and comparative analysis revealed that they were approximately 27‰ longer than their reference genome. In addition, six cpDNAs of four other species with narrow and thin leaf blades, including wheat (Triticum aestivum L.), maize (Zea may L.), rice (Oryza sativa L.) and sorghum (Sorghum bicolor (L.) Moench), were also isolated by our new protocol, and they all exhibited high sequence identities to their corresponding reference genomes. A maximum-likelihood tree based on the chloroplast genomes we sequenced here was constructed, and the result was in agreement with previous reports, confirming that these cpDNA sequences were available for well-supported phylogenetic analysis and could provide valuable resources for future research.
Medical Geological assessment of fluoride contaminated groundwater in parts of Indo-Gangetic Alluvial plains
Authors: Kumar Suresh , Singh Rambabu , Venkatesh A. S. , Udayabhanu G. , Sahoo P. R. 
Published: November 2019

AbstractAs drinking water is considered as a major pathway of exposure to fluoride in the human body, an endeavor has been made for the assessment of the non-carcinogenic health risk by using hazard quotient (HQ) of fluoride for males, females, and children separately in fluoride affected ground water areas of Indo-Gangetic Alluvial Plains. The study suggests that children groups are more prone to the non-carcinogenic risk of fluoride in the area as HQ for fluoride is more than unitary in 44% (Pre-monsoon) and 38% (Post-monsoon) samples respectively. Field survey conducted in fluoride-affected villagers of the study area portrays cases of mottling of teeth and bone deformities depending on the duration and dosage of fluoride consumption. Petrographic observations of host rocks coupled with molar ratios of chemical species studies exemplify that weathered material developed over the granite-gneiss, mica-schist, amphibolite, granitic intrusive and pegmatite veins due to weathering and extensive water-rock interaction resulting higher concentration of fluoride in groundwater. Likewise, the base exchange index (r1) and meteoric genesis index (r2) advocates that most of the samples belong to Na+-HCO3− type and meteoric origin respectively, and substantiate longer residence time of water along with solute acquisition processes are responsible for elevated fluoride in groundwater. It is, therefore, solar energy-driven electrolytic de-fluoridation technology ought to be provided on a priority basis to the affected inhabitants besides the implementation of rainwater harvesting schemes for mitigation/ dilution of elevated fluoride concentration.