bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural insights into the production of 3-hydroxypropionic acid by aldehyde dehydrogenase from Azospirillum brasilense
Authors: Son Hyeoncheol Francis , Park Sunghoon , Yoo Tae Hyeon , Jung Gyoo Yeol , Kim Kyung-Jin 
Published: April 2017

Abstract3-Hydroxypropionic acid (3-HP) is an important platform chemical to be converted to acrylic acid and acrylamide. Aldehyde dehydrogenase (ALDH), an enzyme that catalyzes the reaction of 3-hydroxypropionaldehyde (3-HPA) to 3-HP, determines 3-HP production rate during the conversion of glycerol to 3-HP. To elucidate molecular mechanism of 3-HP production, we determined the first crystal structure of a 3-HP producing ALDH, α-ketoglutarate-semialdehyde dehydrogenase from Azospirillum basilensis (AbKGSADH), in its apo-form and in complex with NAD+. Although showing an overall structure similar to other ALDHs, the AbKGSADH enzyme had an optimal substrate binding site for accepting 3-HPA as a substrate. Molecular docking simulation of 3-HPA into the AbKGSADH structure revealed that the residues Asn159, Gln160 and Arg163 stabilize the aldehyde- and the hydroxyl-groups of 3-HPA through hydrogen bonds, and several hydrophobic residues, such as Phe156, Val286, Ile288, and Phe450, provide the optimal size and shape for 3-HPA binding. We also compared AbKGSADH with other reported 3-HP producing ALDHs for the crucial amino acid residues for enzyme catalysis and substrate binding, which provides structural implications on how these enzymes utilize 3-HPA as a substrate.
A Short-Snouted, Middle Triassic Phytosaur and its Implications for the Morphological Evolution and Biogeography of Phytosauria
Authors: Stocker Michelle R. , Zhao Li-Jun , Nesbitt Sterling J. , Wu Xiao-Chun , Li Chun 
Published: April 2017

AbstractFollowing the end-Permian extinction, terrestrial vertebrate diversity recovered by the Middle Triassic, and that diversity was now dominated by reptiles. However, those reptilian clades, including archosaurs and their closest relatives, are not commonly found until ~30 million years post-extinction in Late Triassic deposits despite time-calibrated phylogenetic analyses predicting an Early Triassic divergence for those clades. One of these groups from the Late Triassic, Phytosauria, is well known from a near-Pangean distribution, and this easily recognized clade bears an elongated rostrum with posteriorly retracted nares and numerous postcranial synapomorphies that are unique compared with all other contemporary reptiles. Here, we recognize the exquisitely preserved, nearly complete skeleton of Diandongosuchus fuyuanensis from the Middle Triassic of China as the oldest and basalmost phytosaur. The Middle Triassic age and lack of the characteristically-elongated rostrum fill a critical morphological and temporal gap in phytosaur evolution, indicating that the characteristic elongated rostrum of phytosaurs appeared subsequent to cranial and postcranial modifications associated with enhanced prey capture, predating that general trend of morphological evolution observed within Crocodyliformes. Additionally, Diandongosuchus supports that the clade was present across Pangea, suggesting early ecosystem exploration for Archosauriformes through nearshore environments and leading to ease of dispersal across the Tethys.
Maxdenominator Reweighted Sparse Representation for Tumor Classification
Authors: Li Weibiao , Liao Bo , Zhu Wen , Chen Min , Peng Li , Wei Xiaohui , Gu Changlong , Li Keqin 
Published: April 2017

AbstractThe classification of tumors is crucial for the proper treatment of cancer. Sparse representation-based classifier (SRC) exhibits good classification performance and has been successfully used to classify tumors using gene expression profile data. In this study, we propose a three-step maxdenominator reweighted sparse representation classification (MRSRC) method to classify tumors. First, we extract a set of metagenes from the training samples. These metagenes can capture the structures inherent to the data and are more effective for classification than the original gene expression data. Second, we use a reweighted "Equation missing" regularization method to obtain the sparse representation coefficients. Reweighted "Equation missing" regularization can enhance sparsity and obtain better sparse representation coefficients. Third, we classify the data by utilizing a maxdenominator residual error function. Maxdenominator strategy can reduce the residual error and improve the accuracy of the final classification. Extensive experiments using publicly available gene expression profile data sets show that the performance of MRSRC is comparable with or better than many existing representative methods.
Allosteric inhibition of aminopeptidase N functions related to tumor growth and virus infection
Authors: Santiago César , Mudgal Gaurav , Reguera Juan , Recacha Rosario , Albrecht Sébastien , Enjuanes Luis , Casasnovas José M. 
Published: April 2017

AbstractCell surface aminopeptidase N (APN) is a membrane-bound ectoenzyme that hydrolyzes proteins and peptides and regulates numerous cell functions. APN participates in tumor cell expansion and motility, and is a target for cancer therapies. Small drugs that bind to the APN active site inhibit catalysis and suppress tumor growth. APN is also a major cell entry receptor for coronavirus, which binds to a region distant from the active site. Three crystal structures that we determined of human and pig APN ectodomains defined the dynamic conformation of the protein. These structures offered snapshots of closed, intermediate and open APN, which represent distinct functional states. Coronavirus envelope proteins specifically recognized the open APN form, prevented ectodomain progression to the closed form and substrate hydrolysis. In addition, drugs that bind the active site inhibited both coronavirus binding to cell surface APN and infection; the drugs probably hindered APN transition to the virus-specific open form. We conclude that allosteric inhibition of APN functions occurs by ligand suppression of ectodomain motions necessary for catalysis and virus cell entry, as validated by locking APN with disulfides. Blocking APN dynamics can thus be a valuable approach to development of drugs that target this ectoenzyme.
Dynamic representation of time in brain states
Authors: Bueno Fernanda Dantas , Morita Vanessa C. , de Camargo Raphael Y. , Reyes Marcelo B. , Caetano Marcelo S. , Cravo André M. 
Published: April 2017

AbstractThe ability to process time on the scale of milliseconds and seconds is essential for behaviour. A growing number of studies have started to focus on brain dynamics as a mechanism for temporal encoding. Although there is growing evidence in favour of this view from computational and in vitro studies, there is still a lack of results from experiments in humans. We show that high-dimensional brain states revealed by multivariate pattern analysis of human EEG are correlated to temporal judgements. First, we show that, as participants estimate temporal intervals, the spatiotemporal dynamics of their brain activity are consistent across trials. Second, we present evidence that these dynamics exhibit properties of temporal perception, such as scale invariance. Lastly, we show that it is possible to predict temporal judgements based on brain states. These results show how scalp recordings can reveal the spatiotemporal dynamics of human brain activity related to temporal processing.
Metabolomic characterisation of the effects of oncogenic PIK3CA transformation in a breast epithelial cell line
Authors: Lau Chung-Ho E. , Tredwell Gregory D. , Ellis James K. , Lam Eric W.-F. , Keun Hector C. 
Published: April 2017

AbstractSomatic mutations in PIK3CA are frequently found in a number of human cancers, including breast cancer, altering cellular physiology and tumour sensitivity to chemotherapy. This renders PIK3CA an attractive molecular target for early detection and personalised therapy. Using 1H Nuclear Magnetic Resonance spectroscopy (NMR) and Gas Chromatography – Mass Spectrometery (GC-MS) together with 13C stable isotope-labelled glucose and glutamine as metabolic tracers, we probed the phenotypic changes in metabolism following a single copy knock-in of mutant PIK3CA (H1047R) in the MCF10A cell line, an important cell model for studying oncogenic transformation in breast tissues. We observed effects in several metabolic pathways, including a decrease in glycerophosphocholine level together with increases in glutaminolysis, de novo fatty acid synthesis and pyruvate entry into the tricarboxylic acid cycle. Our findings highlight altered glyceroplipid metabolism and lipogenesis, as key metabolic phenotypes of mutant PIK3CA transformation that are recapitulated in the MCF10A cellular model.
Optimization of self-catalyzed InAs Nanowires on flexible graphite for photovoltaic infrared photodetectors
Authors: Anyebe Ezekiel A. , Sandall I. , Jin Z. M. , Sanchez Ana M. , Rajpalke Mohana K. , Veal Timothy D. , Cao Y. C. , Li H. D. , Harvey R. , Zhuang Q. D. 
Published: April 2017

AbstractThe recent discovery of flexible graphene monolayers has triggered extensive research interest for the development of III-V/graphene functional hybrid heterostructures. In order to fully exploit their enormous potential in device applications, it is essential to optimize epitaxial growth for the precise control of nanowire geometry and density. Herein, we present a comprehensive growth study of InAs nanowires on graphitic substrates by molecular beam epitaxy. Vertically well-aligned and thin InAs nanowires with high yield were obtained in a narrow growth temperature window of 420–450 °C within a restricted domain of growth rate and V/III flux ratio. The graphitic substrates enable high nanowire growth rates, which is favourable for cost-effective device fabrication. A relatively low density of defects was observed. We have also demonstrated InAs-NWs/graphite heterojunction devices exhibiting rectifying behaviour. Room temperature photovoltaic response with a cut-off wavelength of 3.4 μm was demonstrated. This elucidates a promising route towards the monolithic integration of InAs nanowires with graphite for flexible and functional hybrid devices.
A Strategy for Precise Treatment of Cardiac Malignant Neoplasms
Authors: Wang Wenshuo , Shen Jinqiang , Tao Hongyue , Zhao Yun , Nian Hui , Wei Lai , Ling Xiaoyuan , Yang Ye , Xia Limin 
Published: April 2017

AbstractThe prevalence of cardiac malignant neoplasms in the general population has been shown to be significant higher than what was previously estimated, yet their treatment has remained difficult and effective therapies are lacking. In the current study, we developed a novel thermotherapy in which PEG-functionalized carbon nanotubes were injected into the tumor regions to assist in the targeted delivery of infrared radiation energy with minimal hyperthermic damage to the surrounding normal tissues. In a mouse model of cardiac malignant neoplasms, the injected carbon nanotubes could rapidly induce coagulative necrosis of tumor tissues when exposed to infrared irradiation. In accordance, the treatment was also found to result in a restoration of heart functions and a concomitant increase of survival rate in mice. Taken together, our carbon nanotube-based thermotherapy successfully addressed the difficulty facing conventional laser ablation methods with regard to off-target thermal injury, and could pave the way for the development of more effective therapies against cardiac malignant neoplasms.
Baculovirus LEF-11 Hijack Host ATPase ATAD3A to Promote Virus Multiplication in Bombyx mori cells
Authors: Dong Zhan-Qi , Hu Nan , Dong Fei-Fan , Chen Ting-Ting , Jiang Ya-Ming , Chen Peng , Lu Cheng , Pan Min-Hui 
Published: April 2017

AbstractResearch on molecular mechanisms that viruses use to regulate the host apparatus is important in virus infection control and antiviral therapy exploration. Our previous research showed that the Bombyx mori nucleopolyhedrovirus (BmNPV) LEF-11 localized to dense regions of the cell nucleus and is required for viral DNA replication. Herein, we examined the mechanism of LEF-11 on BmNPV multiplication and demonstrated that baculovirus LEF-11 interacts with Bombyx mori ATAD3A and HSPD1 (HSP60) protein. Furthermore, we showed that LEF-11 has the ability to induce and up-regulate the expression of ATAD3A and HSPD1, phenomena that were both reversed upon knockdown of lef-11. Our findings showed that ATAD3A and HSPD1 were necessary and contributed to BmNPV multiplication in Bombyx mori cells. Moreover, ATAD3A was found to directly interact with HSPD1. Interestingly, ATAD3A was required for the expression of HSPD1, while the knockdown of HSPD1 had no obvious effect on the expression level of ATAD3A. Taken together, the data presented in the current study demonstrated that baculovirus LEF-11 hijacks the host ATPase family members, ATAD3A and HSPD1, efficiently promote the multiplication of the virus. This study furthers our understanding of how baculovirus modulates energy metabolism of the host and provides a new insight into the molecular mechanisms of antiviral research.
Increased Serum Hyaluronic Acid and Heparan Sulfate in Dengue Fever: Association with Plasma Leakage and Disease Severity
Authors: Tang Tommy Hing-Cheung , Alonso Sylvie , Ng Lisa Fong-Poh , Thein Tun-Linn , Pang Vincent Jun-Xiong , Leo Yee-Sin , Lye David Chien-Boon , Yeo Tsin-Wen 
Published: April 2017

AbstractPlasma leakage is a major pathogenic mechanism of severe dengue, but the etiology remains unclear. The association between endothelial glycocalyx integrity and vascular permeability in older adults with dengue has not been evaluated. A prospective cohort study of adults with undifferentiated fever screened for dengue by RT-PCR or NS1 antigen testing was performed. Patients were assessed daily while symptomatic and at convalescence. Serum hyaluronic acid (HA), heparan sulfate (HS) and selected cytokines (TNF-α, IL-6, IL-10) were measured on enrollment and convalescence. Patients were diagnosed as dengue fever (DF, n = 30), dengue hemorrhagic fever (DHF, n = 20) and non-dengue (ND) febrile illness (n = 11). Acute HA and HS levels were significantly higher in all dengue patients compared to ND (p = 0.0033 and p = 0.0441 respectively), but not different between DF and DHF (p = 0.3426 and p = 0.9180 respectively). Enrolment HA inversely correlated with serum albumin, protein and platelets in all dengue and DHF (p < 0.05). HA and HS in all dengue patients decreased significantly at convalescence. Serum IL-10 was significantly associated with HA in all dengue patients (p = 0.002). Serum HA and HS levels were increased in adult dengue and HA was associated with markers of disease severity. Endothelial glycocalyx damage may have a role in vascular leakage in dengue.
Response of the North Atlantic surface and intermediate ocean structure to climate warming of MIS 11
Authors: Kandiano Evgenia S. , van der Meer Marcel T. J. , Schouten Stefan , Fahl Kirsten , Sinninghe Damsté Jaap S. , Bauch Henning A. 
Published: April 2017

AbstractInvestigating past interglacial climates not only help to understand how the climate system operates in general, it also forms a vital basis for climate predictions. We reconstructed vertical stratification changes in temperature and salinity in the North Atlantic for a period some 400 ka ago (MIS11), an interglacial time analogue of a future climate. As inferred from a unique set of biogeochemical, geochemical, and faunal data, the internal upper ocean stratification across MIS 11 shows distinct depth-dependent dynamical changes related to vertical as well as lateral shifts in the upper Atlantic meridional circulation system. Importantly, transient cold events are recognized near the end of the long phase of postglacial warming at surface, subsurface, mid, and deeper water layers. These data demonstrate that MIS 11 coolings over the North Atlantic were initially triggered by freshwater input at the surface and expansion of cold polar waters into the Subpolar Gyre. The cooling signal was then transmitted downwards into mid-water depths. Since the cold events occurred after the main deglacial phase we suggest that their cause might be related to continuous melting of the Greenland ice sheet, a mechanism that might also be relevant for the present and upcoming climate.
Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection
Authors: Kommadath Arun , Bao Hua , Choi Igseo , Reecy James M. , Koltes James E. , Fritz-Waters Elyn , Eisley Chris J. , Grant Jason R. , Rowland Robert R. R. , Tuggle Christopher K. , Dekkers Jack C. M. , Lunney Joan K. , Guan Le Luo , Stothard Paul , Plastow Graham S. 
Published: April 2017

AbstractIt has been shown that inter-individual variation in host response to porcine reproductive and respiratory syndrome (PRRS) has a heritable component, yet little is known about the underlying genetic architecture of gene expression in response to PRRS virus (PRRSV) infection. Here, we integrated genome-wide genotype, gene expression, viremia level, and weight gain data to identify genetic polymorphisms that are associated with variation in inter-individual gene expression and response to PRRSV infection in pigs. RNA-seq analysis of peripheral blood samples collected just prior to experimental challenge (day 0) and at 4, 7, 11 and 14 days post infection from 44 pigs revealed 6,430 differentially expressed genes at one or more time points post infection compared to the day 0 baseline. We mapped genetic polymorphisms that were associated with inter-individual differences in expression at each day and found evidence ofcis-acting expression quantitative trait loci (cis-eQTL) for 869 expressed genes (qval < 0.05). Associations betweencis-eQTL markers and host response phenotypes using 383 pigs suggest that host genotype-dependent differences in expression ofGBP5, GBP6, CCHCR1 and CMPK2affect viremia levels or weight gain in response to PRRSV infection.
Giant caldera in the Arctic Ocean: Evidence of the catastrophic eruptive event
Authors: Piskarev Alexey , Elkina Daria 
Published: April 2017

AbstractA giant caldera located in the eastern segment of the Gakkel Ridge could be firstly seen on the bathymetric map of the Arctic Ocean published in 1999. In 2014, seismic and multibeam echosounding data were acquired at the location. The caldera is 80 km long, 40 km wide and 1.2 km deep. The total volume of ejected volcanic material is estimated as no less than 3000 km3 placing it into the same category with the largest Quaternary calderas (Yellowstone and Toba). Time of the eruption is estimated as ~1.1 Ma. Thin layers of the volcanic material related to the eruption had been identified in sedimentary cores located about 1000 km away from the Gakkel Ridge. The Gakkel Ridge Caldera is the single example of a supervolcano in the rift zone of the Mid-Oceanic Ridge System.
Nitrate application or P deficiency induce a decline in Medicago truncatula N2-fixation by similar changes in the nodule transcriptome
Authors: Liese Rebecca , Schulze Joachim , Cabeza Ricardo A. 
Published: April 2017

AbstractNitrogen fixation of Medicago truncatula is regulated by the nitrogen status of leaves through inducing a repeatedly occurring 24-h nodule activity rhythm that reduces per day nitrogen fixation. The hypotheses of the present study were that (1) long-term moderate whole-plant P deficiency in Medicago truncatula induces an according daily rhythm in nitrogenase activity comparable to that induced by nitrate application and (2), the changes in the nodule transcriptome that go along with a strong nitrogenase activity decline during the afternoon would be similar under P deficiency or after nitrate supply. The nodules of plants in a low P treatment developed a rhythmic pattern of activity that resembled the pattern following nitrate application. A comprehensive, RNAseq-based comparative transcriptome profiling of nodules during a repeated part of the rhythm revealed similarities between P deficiency versus nitrate supply. Under both treatments, the formation of nitrogenase was targeted by a reduction in the expression of genes for nodule-specific cysteine-rich peptides (NCR), and possibly also by a disturbance of the inner cell iron allocation. A strong reduction in the expression of leghemoglobin is likely to have restricted the supply of oxygen for respiration.
Demonstration of nanoimprinted hyperlens array for high-throughput sub-diffraction imaging
Authors: Byun Minseop , Lee Dasol , Kim Minkyung , Kim Yangdoo , Kim Kwan , Ok Jong G. , Rho Junsuk , Lee Heon 
Published: April 2017

AbstractOvercoming the resolution limit of conventional optics is regarded as the most important issue in optical imaging science and technology. Although hyperlenses, super-resolution imaging devices based on highly anisotropic dispersion relations that allow the access of high-wavevector components, have recently achieved far-field sub-diffraction imaging in real-time, the previously demonstrated devices have suffered from the extreme difficulties of both the fabrication process and the non-artificial objects placement. This results in restrictions on the practical applications of the hyperlens devices. While implementing large-scale hyperlens arrays in conventional microscopy is desirable to solve such issues, it has not been feasible to fabricate such large-scale hyperlens array with the previously used nanofabrication methods. Here, we suggest a scalable and reliable fabrication process of a large-scale hyperlens device based on direct pattern transfer techniques. We fabricate a 5 cm × 5 cm size hyperlenses array and experimentally demonstrate that it can resolve sub-diffraction features down to 160 nm under 410 nm wavelength visible light. The array-based hyperlens device will provide a simple solution for much more practical far-field and real-time super-resolution imaging which can be widely used in optics, biology, medical science, nanotechnology and other closely related interdisciplinary fields.
Resolvin D1 drives establishment of Leishmania amazonensis infection
Authors: Malta-Santos Hayna , Andrade Bruno B. , Zanette Dalila L. , Costa Jackson M. , Bozza Patrícia T. , Bandeira-Melo Christianne , Barral Aldina , França-Costa Jaqueline , Borges Valéria M. 
Published: April 2017

AbstractPrevious studies have indicated that the balance between different eicosanoids reflect the intensity of the inflammatory profile in patients with tegumentary leishmaniasis. More recently, pro-resolution lipid mediators have been shown to play critical roles in dampening pathological inflammatory processes to reestablish homeostasis in a diverse range of experimental settings. Among these lipid mediator, resolvins from D series have been described as potent anti-inflammatory and immunomodulatory mediators, and its activities include inhibition of leukocyte chemotaxis and blockage production of proinflammatory cytokines, while increasing the expression of regulatory mediators. Whether resolvins play significant roles in establishment and persistence ofLeishmaniainfection is currently unknown. We addressed this question in the current study by assessing circulating levels of D-series resolvins in tegumentary leishmaniasis patients presenting with localized or diffuse disease. We found heightened expression of resolvin D1 in diffuse cutaneous leishmaniasis which was correlated with expression profile of biomarkers associated with disease pathogenesis. Additionalin vitroexperiments using primary human macrophages indicated that resolvin D1 may promote intracellularLeishmania amazonensisreplication through a mechanism associated with induction of heme oxygenase-1. These results suggest that targeting resolvin D1 could serve as potential strategy for host directed therapy in diffuse cutaneous leishmaniasis.