bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host genotype and time dependent antigen presentation of viral peptides: predictions from theory
Authors: Eccleston R. Charlotte , Coveney Peter V. , Dalchau Neil 
Published: October 2017

AbstractThe rate of progression of HIV infected individuals to AIDS is known to vary with the genotype of the host, and is linked to their allele of human leukocyte antigen (HLA) proteins, which present protein degradation products at the cell surface to circulating T-cells. HLA alleles are associated with Gag-specific T-cell responses that are protective against progression of the disease. While Pol is the most conserved HIV sequence, its association with immune control is not as strong. To gain a more thorough quantitative understanding of the factors that contribute to immunodominance, we have constructed a model of the recognition of HIV infection by the MHC class I pathway. Our model predicts surface presentation of HIV peptides over time, demonstrates the importance of viral protein kinetics, and provides evidence of the importance of Gag peptides in the long-term control of HIV infection. Furthermore, short-term dynamics are also predicted, with simulation of virion-derived peptides suggesting that efficient processing of Gag can lead to a 50% probability of presentation within 3 hours post-infection, as observed experimentally. In conjunction with epitope prediction algorithms, this modelling approach could be used to refine experimental targets for potential T-cell vaccines, both for HIV and other viruses.
Accurate and efficient band gap predictions of metal halide perovskites using the DFT-1/2 method: GW accuracy with DFT expense
Authors: Tao Shu Xia , Cao Xi , Bobbert Peter A. 
Published: October 2017

AbstractThe outstanding optoelectronics and photovoltaic properties of metal halide perovskites, including high carrier motilities, low carrier recombination rates, and the tunable spectral absorption range are attributed to the unique electronic properties of these materials. While DFT provides reliable structures and stabilities of perovskites, it performs poorly in electronic structure prediction. The relativistic GW approximation has been demonstrated to be able to capture electronic structure accurately, but at an extremely high computational cost. Here we report efficient and accurate band gap calculations of halide metal perovskites by using the approximate quasiparticle DFT-1/2 method. Using AMX3 (A = CH3NH3, CH2NHCH2, Cs; M = Pb, Sn, X = I, Br, Cl) as demonstration, the influence of the crystal structure (cubic, tetragonal or orthorhombic), variation of ions (different A, M and X) and relativistic effects on the electronic structure are systematically studied and compared with experimental results. Our results show that the DFT-1/2 method yields accurate band gaps with the precision of the GW method with no more computational cost than standard DFT. This opens the possibility of accurate electronic structure prediction of sophisticated halide perovskite structures and new materials design for lead-free materials.
Proton-solute coupling mechanism of the maltose transporter from Saccharomyces cerevisiae
Authors: Henderson Ryan , Poolman Bert 
Published: October 2017

AbstractMal11 catalyzes proton-coupled maltose transport across the plasma membrane of Saccharomyces cerevisiae. We used structure-based design of mutants and a kinetic analysis of maltose transport to determine the energy coupling mechanism of transport. We find that wildtype Mal11 is extremely well coupled and allows yeast to rapidly accumulate maltose to dangerous levels, resulting under some conditions in self-lysis. Three protonatable residues lining the central membrane-embedded cavity of Mal11 were identified as having potential roles in proton translocation. We probed the mechanistic basis for proton coupling with uphill and downhill transport assays and found that single mutants can still accumulate maltose but with a lower coupling efficiency than the wildtype. Next, we combined the individual mutations and created double and triple mutants. We found some redundancy in the functions of the acidic residues in proton coupling and that no single residue is most critical for proton coupling to maltose uptake, unlike what is usually observed in related transporters. Importantly, the triple mutants were completely uncoupled but still fully active in downhill efflux and equilibrium exchange. Together, these results depict a concerted mechanism of proton transport in Mal11 involving multiple charged residues.
New method for the identification of arbuscular mycorrhizal fungi by proteomic-based biotyping of spores using MALDI-TOF-MS
Authors: Crossay Thomas , Antheaume Cyril , Redecker Dirk , Bon Lucie , Chedri Nicolas , Richert Clément , Guentas Linda , Cavaloc Yvon , Amir Hamid 
Published: October 2017

AbstractArbuscular mycorrhizal fungi (AMF, Glomeromycota) are mutualistic symbionts associated with majority of land plants. These fungi play an important role in plant growth, but their taxonomic identification remains a challenge for academic research, culture collections and inoculum producers who need to certify their products. Identification of these fungi was traditionally performed based on their spore morphology. DNA sequence data have successfully been used to study the evolutionary relationships of AMF, develop molecular identification tools and assess their diversity in the environment. However, these methods require considerable expertise and are not well-adapted for “routine” quality control of culture collections and inoculum production. Here, we show that Matrix-Assisted Laser Desorption Ionisation Time of Flight Mass Spectrometry proteomic-based biotyping is a highly efficient approach for AMF identification. Nineteen isolates belonging to fourteen species, seven genera and five families were clearly differentiated by MALDI biotyping at the species level, and intraspecific differentiation was achieved for the majority. AMF identification by MALDI biotyping could be highly useful, not only for research but also in agricultural and environmental applications. Fast, accurate and inexpensive molecular mass determination and the possibility of automation make MALDI-TOF-MS a real alternative to conventional morphological and molecular methods for AMF identification.
An Effective Model of the Retinoic Acid Induced HL-60 Differentiation Program
Authors: Tasseff Ryan , Jensen Holly A. , Congleton Johanna , Dai David , Rogers Katharine V. , Sagar Adithya , Bunaciu Rodica P. , Yen Andrew , Varner Jeffrey D. 
Published: October 2017

AbstractIn this study, we present an effective model All-Trans Retinoic Acid (ATRA)-induced differentiation of HL-60 cells. The model describes reinforcing feedback between an ATRA-inducible signalsome complex involving many proteins including Vav1, a guanine nucleotide exchange factor, and the activation of the mitogen activated protein kinase (MAPK) cascade. We decomposed the effective model into three modules; a signal initiation module that sensed and transformed an ATRA signal into program activation signals; a signal integration module that controlled the expression of upstream transcription factors; and a phenotype module which encoded the expression of functional differentiation markers from the ATRA-inducible transcription factors. We identified an ensemble of effective model parameters using measurements taken from ATRA-induced HL-60 cells. Using these parameters, model analysis predicted that MAPK activation was bistable as a function of ATRA exposure. Conformational experiments supported ATRA-induced bistability. Additionally, the model captured intermediate and phenotypic gene expression data. Knockout analysis suggested Gfi-1 and PPARg were critical to the ATRAinduced differentiation program. These findings, combined with other literature evidence, suggested that reinforcing feedback is central to hyperactive signaling in a diversity of cell fate programs.
Hydrogen Bond Variations of Influenza A Viruses During Adaptation in Human
Authors: Luo Jiejian , Deng Lizong , Ding Xiao , Quan Lijun , Wu Aiping , Jiang Taijiao 
Published: October 2017

AbstractMany host specific mutations have been detected in influenza A viruses (IAVs). However, their effects on hydrogen bond (H-bond) variations have rarely been investigated. In this study, 60 host specific sites were identified in the internal proteins of avian and human IAVs, 27 of which contained mutations with effects on H-bonds. Besides, 30 group specific sites were detected in HA and NA. Twenty-six of 36 mutations existing at these group specific sites caused H-bond loss or formation in at least one subtype. The number of mutations in isolations of 2009 pandemic H1N1, human-infecting H5N1 and H7N9 varied. The combinations of mutations and H-bond changes in these three subtypes of IAVs were also different. In addition, the mutations in isolations of H5N1 distributed more scattered than those in 2009 pandemic H1N1 and H7N9. Eight wave specific mutations in isolations of the fifth H7N9 wave were also identified. Three of them, R140K in HA, Y170H in NA, and R340K in PB2, were capable of resulting in H-bond loss. As mentioned above, these host or group or wave specific H-bond variations provide us with a new field of vision for understanding the changes of structural features in the human adaptation of IAVs.
Rev-erb-α regulates atrophy-related genes to control skeletal muscle mass
Authors: Mayeuf-Louchart Alicia , Thorel Quentin , Delhaye Stéphane , Beauchamp Justine , Duhem Christian , Danckaert Anne , Lancel Steve , Pourcet Benoit , Woldt Estelle , Boulinguiez Alexis , Ferri Lise , Zecchin Mathilde , Staels Bart , Sebti Yasmine , Duez Hélène 
Published: October 2017

AbstractThe nuclear receptor Rev-erb-α modulates hepatic lipid and glucose metabolism, adipogenesis and thermogenesis. We have previously demonstrated that Rev-erb-α is also an important regulator of skeletal muscle mitochondrial biogenesis and function, and autophagy. As such, Rev-erb-α over-expression in skeletal muscle or its pharmacological activation improved mitochondrial respiration and enhanced exercise capacity. Here, in gain- and loss-of function studies, we show that Rev-erb-α also controls muscle mass. Rev-erb-α-deficiency in skeletal muscle leads to increased expression of the atrophy-related genes (atrogenes), associated with reduced muscle mass and decreased fiber size. By contrast,in vivoandin vitroRev-erb-α over-expression results in reduced atrogenes expression and increased fiber size. Finally, Rev-erb-α pharmacological activation blocks dexamethasone-induced upregulation of atrogenes and muscle atrophy. This study identifies Rev-erb-α as a promising pharmacological target to preserve muscle mass.
Factors influencing the success of aerial rabies vaccination of foxes
Authors: Henning J. , Giorgi E. , Soares Magalhães R. J. , Tizzani P. , Viviani P. , Pejovic N. , Hrapović M. , Potzsch C. 
Published: October 2017

AbstractSylvatic rabies has been eradicated from most of Central Europe, but cases still occur in the Balkans. Oral rabies vaccination of foxes is an effective method for controlling the disease. The aim of this study was to evaluate the success of aerial vaccination campaigns conducted in Montenegro by identifying ecological, environmental and climatic factors that influenced the prevalence of antibodies to the rabies vaccine. To monitor the bait uptake and the serological responses to vaccination, foxes were shot by hunters. Of 175 shot foxes, 142 foxes (81.1%) had consumed baits. Of these only a total of 81 (57.0%) tested positive for rabies vaccine antibodies, possibly, due to the delayed uptake of bait in which the rabies vaccine was already inactivated. We found that low vaccination responses were associated with high fox density and bait delivery in open areas. In high fox density habitat, bait uptake might be delayed as other food and prey options for foxes are abundant. Similarly, delayed bait uptake probably occurred in open areas as such areas are less frequently used by foxes. The findings of this study suggest that efficacy of oral rabies vaccination by aerial delivery is associated with landscape features.
Quantifying the Pathway and Predicting Spontaneous Emulsification during Material Exchange in a Two Phase Liquid System
Authors: Spooner Stephen , Rahnama Alireza , Warnett Jason M. , Williams Mark A. , Li Zushu , Sridhar Seetharaman 
Published: October 2017

AbstractKinetic restriction of a thermodynamically favourable equilibrium is a common theme in materials processing. The interfacial instability in systems where rate of material exchange is far greater than the mass transfer through respective bulk phases is of specific interest when tracking the transient interfacial area, a parameter integral to short processing times for productivity streamlining in all manufacturing where interfacial reaction occurs. This is even more pertinent in high-temperature systems for energy and cost savings. Here the quantified physical pathway of interfacial area change due to material exchange in liquid metal-molten oxide systems is presented. In addition the predicted growth regime and emulsification behaviour in relation to interfacial tension as modelled using phase-field methodology is shown. The observed in-situ emulsification behaviour links quantitatively the geometry of perturbations as a validation method for the development of simulating the phenomena. Thus a method is presented to both predict and engineer the formation of micro emulsions to a desired specification.
Angiotensin II-derived constrained peptides with antiplasmodial activity and suppressed vasoconstriction
Authors: Silva Adriana Farias , Torres Marcelo Der Torossian , Silva Leandro Souza , Alves Flavio Lopes , de Sá Pinheiro Ana Acácia , Miranda Antonio , Capurro Margareth Lara , de la Fuente-Nunez Cesar , Oliveira Vani Xavier 
Published: October 2017

AbstractAngiotensin II (Ang II) is a natural mammalian hormone that has been described to exhibit antiplasmodial activity therefore constituting a promising alternative for the treatment of malaria. Despite its promise, the development of Ang II as an antimalarial is limited by its potent induction of vasoconstriction and its rapid degradation within minutes. Here, we used peptide design to perform targeted chemical modifications to Ang II to generate conformationally restricted (disulfide-crosslinked) peptide derivatives with suppressed vasoconstrictor activity and increased stability. Designed constrained peptides were synthesized chemically and then tested for antiplasmodial activity. Two lead constrained peptides were identified (i.e., peptides 1 and 2), each composed of 10 amino acid residues. These peptides exhibited very promising activity in both our Plasmodium gallinaceum (>80%) and Plasmodium falciparum (>40%) models, an activity that was equivalent to that of Ang II, and led to complete suppression of vasoconstriction. In addition, peptide 5 exhibited selective activity towards the pre-erythrocytic stage (98% of activity against P. gallinaceum), thus suggesting that it may be possible to design peptides that target specific stages of the malaria life cycle. The Ang II derived stable scaffolds presented here may provide the basis for development of a new generation of peptide-based drugs for the treatment of malaria.
HBeAg-induced miR-106b promotes cell growth by targeting the retinoblastoma gene
Authors: Samal Jasmine , Kandpal Manish , Vivekanandan Perumal 
Published: October 2017

AbstractChronic HBV infection is a major cause of hepatocellular carcinoma (HCC). The association between hepatitis B “e” antigen (HBeAg) and HCC is well-established by epidemiological studies. Nonetheless, the biological role of HBeAg in HCC remains enigmatic. We investigate the role of HBeAg in HBV-related HCC. Our findings suggest that HBeAg enhances cell proliferation and accelerates progression from G0/G1 phase to the S phase of the cell cycle in Huh7 cells. Examination of host gene expression and miRNA expression profiles reveals a total of 21 host genes and 12 host miRNAs that were differentially regulated in cells expressing HBeAg. Importantly, HBeAg induced the expression of miR-106b, an oncogenic miRNA. Interestingly, HBeAg-expression results in a significant reduction in the expression of retinoblastoma (Rb) gene, an experimentally validated target of miR-106b. Inhibition of miR-106b significantly increased the expression of the Rb gene, resulting in reduced cell proliferation and slowing of cell cycle progression from the G0/G1 phase to S phase. These observations suggest that the up-regulation of miR-106b by HBeAg contributes to the pathogenesis of HBV-related HCC by down-regulating the Rb gene. Our results highlight a role for HBeAg in HCC and provide a novel perspective on the molecular mechanisms underlying HBV-related HCC.
Rare, Intense, Big fires dominate the global tropics under drier conditions
Authors: Hantson Stijn , Scheffer Marten , Pueyo Salvador , Xu Chi , Lasslop Gitta , van Nes Egbert H. , Holmgren Milena , Mendelsohn John 
Published: October 2017

AbstractWildfires burn large parts of the tropics every year, shaping ecosystem structure and functioning. Yet the complex interplay between climate, vegetation and human factors that drives fire dynamics is still poorly understood. Here we show that on all continents, except Australia, tropical fire regimes change drastically as mean annual precipitation falls below 550 mm. While the frequency of fires decreases below this threshold, the size and intensity of wildfires rise sharply. This transition to a regime of Rare-Intense-Big fires (RIB-fires) corresponds to the relative disappearance of trees from the landscape. Most dry regions on the globe are projected to become substantially drier under global warming. Our findings suggest a global zone where this drying may have important implications for fire risks to society and ecosystem functioning.
Highly Sensitive Plasmonic Detection of the Pancreatic Cancer Biomarker CA 19-9
Authors: Jawad Zaynab A. R. , Theodorou Ioannis G. , Jiao Long R. , Xie Fang 
Published: October 2017

AbstractPlasmonic gold (Au) nanotriangular arrays, functionalized with a near infrared (NIR) fluorophore-conjugated immunoassay to Carbohydrate Antigen 19-9 (CA 19-9), a pancreatic cancer biomarker, produce optically tunable substrates with two orders of magnitude fluorescence enhancement. Through nanoscale morphological control, the sensitivities of the plasmonic nanotriangular arrays are controllable, paving the way of such optical platforms for multiplexing. Here, we report a limit of detection (LOD) of 7.7 × 10−7 U.mL−1 for CA 19–9 by using such tunable Au nanotriangular arrays, a great improvement compared to commercially available CA 19–9 immunoassays. The linear dynamic range was from 1 × 10−6 U.mL−1 to 1 U.mL−1, i.e. up to six orders of magnitude. Moreover, high specificity was demonstrated, together with successful validation in serum samples. Their superior tunable sensitivity, along with efforts to combine CA 19–9 with other biomarkers for improved accuracy, open up the possibility for multiplexed NIR-fluorescence enhancement microarrays, for early cancer diagnosis and therapeutic monitoring.
CorMatrix Wrapped Around the Adventitia of the Arteriovenous Fistula Outflow Vein Attenuates Venous Neointimal Hyperplasia
Authors: Yang Binxia , Kilari Sreenivasulu , Brahmbhatt Akshaar , McCall Deborah L. , Torres Evelyn Nieves , Leof Edward B. , Mukhopadhyay Debabrata , Misra Sanjay 
Published: October 2017

AbstractVenous neointimal hyperplasia (VNH) at the outflow vein of hemodialysis AVF is a major factor contributing to failure. CorMatrix is an extracellular matrix that has been used in cardiovascular procedures primarily as scaffolding during surgery. In the present study, we sought to determine whether CorMatrix wrapped around the outflow vein of arteriovenous fistula (AVF) at the time of creation could reduce VNH. In mice, the carotid artery to the ipsilateral jugular vein was connected to create an AVF, and CorMatrix scaffold was wrapped around the outflow vein compared to control mice that received no scaffolding. Immunohistochemistry, Western blot, and qRT-PCR were performed on the outflow vein at 7 and 21 days after AVF creation. In outflow veins treated with CorMatrix, there was an increase in the mean lumen vessel area with a decrease in the ratio of neointima area/media + adventitia area (P < 0.05). Furthermore, there was a significant increase in apoptosis, with a reduction in cell density and proliferation in the outflow veins treated with CorMatrix compared to controls (P < 0.05). Immunohistochemical analysis revealed a significant reduction in fibroblasts, myofibroblasts, macrophages, and leukocytes with a reduction in Tnf-α gene expression (P < 0.05). In conclusion, outflow veins treated with CorMatrix have reduced VNH.
A platform for stereological quantitative analysis of the brain-wide distribution of type-specific neurons
Authors: Zhang Chen , Yan Cheng , Ren Miao , Li Anan , Quan Tingwei , Gong Hui , Yuan Jing 
Published: October 2017

AbstractQuantifying the distribution of specific neurons throughout the whole brain is crucial for understanding physiological actions, pathological alterations and pharmacological treatments. However, the precise cell number and density of specific neurons in the entire brain remain unknown because of a lack of suitable research tools. Here, we propose a pipeline to automatically acquire and analyse the brain-wide distribution of type-specific neurons in a mouse brain. We employed a Brain-wide Positioning System to collect high-throughput anatomical information with the co-localized cytoarchitecture of the whole brain at subcellular resolution and utilized the NeuroGPS algorithm to locate and count cells in the whole brain. We evaluated the data continuity of the 3D dataset and the accuracy of stereological cell counting in 3D. To apply this pipeline, we acquired and quantified the brain-wide distributions and somatic morphology of somatostatin-expressing neurons in transgenic mouse brains. The results indicated that this whole-brain cell counting pipeline has the potential to become a routine tool for cell type neuroscience studies.
Thermo-mechanical improvement of Inconel 718 using ex situ boron nitride-reinforced composites processed by laser powder bed fusion
Authors: Kim Sang Hoon , Shin Gi-Hun , Kim Byoung-Kee , Kim Kyung Tae , Yang Dong-Yeol , Aranas Clodualdo , Choi Joon-Phil , Yu Ji-Hun 
Published: October 2017

AbstractHexagonal boron nitride-reinforced Inconel 718 (h-BN/IN718) composites were fabricated using a laser powder bed fusion (LPBF) technique to treat a nanosheet-micropowder precursor mixture prepared in a mechanical blending process. Tailoring the BN in IN718 enhanced the thermal resistance of the composites, thereby dampening the sharpness of the melting temperature peak at 1364 °C. This is because the presence of the BN reinforcement, which has a low coefficient of thermal expansion (CTE), resulted in a heat-blocking effect within the matrix. Following this lead, we found that the BN (2.29 g/cm3) was uniformly distributed and strongly embedded in the IN718 (8.12 g/cm3), with the lowest alloy density value (7.03 g/cm3) being obtained after the addition of 12 vol% BN. Consequently, its specific hardness and compressive strength rose to 41.7 Hv0.5·cm3/g and 92.4 MPa·cm3/g, respectively, compared to the unreinforced IN718 alloy with 38.7 Hv0.5·cm3/g and 89.4 MPa·cm3/g, respectively. Most importantly, we discovered that the wear resistance of the composite improved compared to the unreinforced IN718, indicated by a decrease in the coefficient of friction (COF) from 0.43 to 0.31 at 2400 s. This is because the BN has an exfoliated surface and intrinsically high sliding and lubricating characteristics.