bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epitaxial thin films of pyrochlore iridate Bi2+xIr2-yO7-δ: structure, defects and transport properties
Authors: Yang W. C. , Xie Y. T. , Zhu W. K. , Park K. , Chen A. P. , Losovyj Y. , Li Z. , Liu H. M. , Starr M. , Acosta J. A. , Tao C. G. , Li N. , Jia Q. X. , Heremans J. J. , Zhang S. X. 
Published: August 2017

AbstractWhile pyrochlore iridate thin films are theoretically predicted to possess a variety of emergent topological properties, experimental verification of these predictions can be obstructed by the challenge in thin film growth. Here we report on the pulsed laser deposition and characterization of thin films of a representative pyrochlore compound Bi2Ir2O7. The films were epitaxially grown on yttria-stabilized zirconia substrates and have lattice constants that are a few percent larger than that of the bulk single crystals. The film composition shows a strong dependence on the oxygen partial pressure. Density-functional-theory calculations indicate the existence of BiIr antisite defects, qualitatively consistent with the high Bi: Ir ratio found in the films. Both Ir and Bi have oxidation states that are lower than their nominal values, suggesting the existence of oxygen deficiency. The iridate thin films show a variety of intriguing transport characteristics, including multiple charge carriers, logarithmic dependence of resistance on temperature, antilocalization corrections to conductance due to spin-orbit interactions, and linear positive magnetoresistance.
Characterization of P. vivax blood stage transcriptomes from field isolates reveals similarities among infections and complex gene isoforms
Authors: Kim Adam , Popovici Jean , Vantaux Amélie , Samreth Reingsey , Bin Sophalai , Kim Saorin , Roesch Camille , Liang Li , Davies Huw , Felgner Philip , Herrera Sócrates , Arévalo-Herrera Myriam , Ménard Didier , Serre David 
Published: August 2017

AbstractOur understanding of the structure and regulation of Plasmodium vivax genes is limited by our inability to grow the parasites in long-term in vitro cultures. Most P. vivax studies must therefore rely on patient samples, which typically display a low proportion of parasites and asynchronous parasites. Here, we present stranded RNA-seq data generated directly from a small volume of blood from three Cambodian vivax malaria patients collected before treatment. Our analyses show surprising similarities of the parasite gene expression patterns across infections, despite extensive variations in parasite stage proportion. These similarities contrast with the unique gene expression patterns observed in sporozoites isolated from salivary glands of infected Colombian mosquitoes. Our analyses also indicate that more than 10% of P. vivax genes encode multiple, often undescribed, protein-coding sequences, potentially increasing the diversity of proteins synthesized by blood stage parasites. These data also greatly improve the annotations of P. vivax gene untranslated regions, providing an important resource for future studies of specific genes.
Cross-species transmission potential between wild pigs, livestock, poultry, wildlife, and humans: implications for disease risk management in North America
Authors: Miller Ryan S. , Sweeney Steven J. , Slootmaker Chris , Grear Daniel A. , Di Salvo Paul A. , Kiser Deborah , Shwiff Stephanie A. 
Published: August 2017

AbstractCross-species disease transmission between wildlife, domestic animals and humans is an increasing threat to public and veterinary health. Wild pigs are increasingly a potential veterinary and public health threat. Here we investigate 84 pathogens and the host species most at risk for transmission with wild pigs using a network approach. We assess the risk to agricultural and human health by evaluating the status of these pathogens and the co-occurrence of wild pigs, agriculture and humans. We identified 34 (87%) OIE listed swine pathogens that cause clinical disease in livestock, poultry, wildlife, and humans. On average 73% of bacterial, 39% of viral, and 63% of parasitic pathogens caused clinical disease in other species. Non-porcine livestock in the familyBovidaeshared the most pathogens with swine (82%). Only 49% of currently listed OIE domestic swine diseases had published wild pig surveillance studies. The co-occurrence of wild pigs and farms increased annually at a rate of 1.2% with as much as 57% of all farms and 77% of all agricultural animals co-occurring with wild pigs. The increasing co-occurrence of wild pigs with livestock and humans along with the large number of pathogens shared is a growing risk for cross-species transmission.
Enpp1 is an anti-aging factor that regulates Klotho under phosphate overload conditions
Authors: Watanabe Ryuichi , Fujita Nobuyuki , Sato Yuiko , Kobayashi Tami , Morita Mayu , Oike Takatsugu , Miyamoto Kana , Kuro-o Makoto , Michigami Toshimi , Fukumoto Seiji , Tsuji Takashi , Toyama Yoshiaki , Nakamura Masaya , Matsumoto Morio , Miyamoto Takeshi 
Published: August 2017

AbstractControl of phosphate metabolism is crucial to regulate aging in mammals. Klotho is a well-known anti-aging factor that regulates phosphate metabolism: mice mutant or deficient in Klotho exhibit phenotypes resembling human aging. Here we show that ectonucleotide pyrophosphatase/phosphodiesterase 1 (Enpp1) is required for Klotho expression under phosphate overload conditions. Loss-of-function Enpp1
ttw/ttw
mice under phosphate overload conditions exhibited phenotypes resembling human aging and Klotho mutants, such as short life span, arteriosclerosis and osteoporosis, with elevated serum 1,25(OH)2D3 levels. Enpp1
ttw/ttw
mice also exhibited significantly reduced renal Klotho expression under phosphate overload conditions, and aging phenotypes in these mice were rescued by Klotho overexpression, a low vitamin D diet or vitamin D receptor knockout. These findings indicate that Enpp1 plays a crucial role in regulating aging via Klotho expression under phosphate overload conditions.
Molecular identification of spiders preying on Empoasca vitis in a tea plantation
Authors: Yang Ting-bang , Liu Jie , Yuan Long-yu , Zhang Yang , Li Dai-qin , Agnarsson Ingi , Chen Jian 
Published: August 2017

AbstractBiological control using predators of key pest species is an attractive option in integrated pest management (IPM). Molecular gut analysis can provide an estimation of predator efficiency on a given prey. Here we use a combination of various experimental approaches, both in field and lab, to identify a potential biological control species of the common pest of commercially grown tea, Empoasca vitis (Göthe) (Hemiptera), in a Chinese plantation. We collected 2655 spiders from plantations and established relative abundances of spider species and their temporal overlap with the pest species in tea canopy. We analyzed DNA from 1363 individuals of the most common spider species using targeted RQ-PCR to quantify the potential efficiency of spiders as a predator on E. vitis. The results showed that, in the field, the jumping spider Evarcha albaria was the most abundant, had the closest temporal overlap with the pest, and frequently fed on it. Therefore, this spider may play a key role in pest suppression. The present study demonstrates the potential of our experimental approach to study predator-prey relationships in taxa that do not lend themselves to morphological identification of gut contents, such as spiders.
Water Circulation and Marine Environment in the Antarctic Traced by Speciation of 129I and 127I
Authors: Xing Shan , Hou Xiaolin , Aldahan Ala , Possnert Göran , Shi Keliang , Yi Peng , Zhou Weijian 
Published: August 2017

AbstractEmissions of anthropogenic 129I from human nuclear activities are now detected in the surface water of the Antarctic seas. Surface seawater samples from the Drake Passage, Bellingshausen, Amundsen, and Ross Seas were analyzed for total 129I and 127I, as well as for iodide and iodate of these two isotopes. The variability of 127I and 129I concentrations and their species (127I−/127IO3−, 129I−/129IO3−) suggest limited environmental impact where ((1.15–3.15) × 106 atoms/L for 129I concentration and (0.61–1.98) × 10−11 for 129I/127I atomic ratios are the lowest ones compared to the other oceans. The iodine distribution patterns provide useful information on surface water transport and mixing that are vital for better understanding of the Southern Oceans effects on the global climate change. The results indicate multiple spatial interactions between the Antarctic Circumpolar Current (ACC) and Antarctic Peninsula Coastal Current (APCC). These interactions happen in restricted circulation pathways that may partly relate to glacial melting and icebergs transport. Biological activity during the warm season should be one of the key factors controlling the reduction of iodate in the coastal water in the Antarctic.
Luciferase Expression Allows Bioluminescence Imaging But Imposes Limitations on the Orthotopic Mouse (4T1) Model of Breast Cancer
Authors: Baklaushev V. P. , Kilpeläinen A. , Petkov S. , Abakumov M. A. , Grinenko N. F. , Yusubalieva G. M. , Latanova A. A. , Gubskiy I. L. , Zabozlaev F. G. , Starodubova E. S. , Abakumova T. O. , Isaguliants M. G. , Chekhonin V. P. 
Published: August 2017

AbstractImplantation of reporter-labeled tumor cells in an immunocompetent host involves a risk of their immune elimination. We have studied this effect in a mouse model of breast cancer after the orthotopic implantation of mammary gland adenocarcinoma 4T1 cells genetically labelled with luciferase (Luc). Mice were implanted with 4T1 cells and two derivative Luc-expressing clones 4T1luc2 and 4T1luc2D6 exhibiting equalin vitrogrowth rates.In vivo, the daughter 4T1luc2 clone exhibited nearly the same, and 4T1luc2D6, a lower growth rate than the parental cells. The metastatic potential of 4T1 variants was assessed by magnetic resonance, bioluminescent imaging, micro-computed tomography, and densitometry which detected 100-μm metastases in multiple organs and bones at the early stage of their development. After 3–4 weeks, 4T1 generated 11.4 ± 2.1, 4T1luc2D6, 4.5 ± 0.6; and 4T1luc2, <1 metastases per mouse, locations restricted to lungs and regional lymph nodes. Mice bearing Luc-expressing tumors developed IFN-γ response to the dominant CTL epitope of Luc. Induced by intradermal DNA-immunization, such response protected mice from the establishment of 4T1luc2-tumors. Our data show that natural or induced cellular response against the reporter restricts growth and metastatic activity of the reporter-labelled tumor cells. Such cells represent a powerful instrument for improving immunization technique for cancer vaccine applications.
Role of water and protein dynamics in proton pumping by respiratory complex I
Authors: Haapanen Outi , Sharma Vivek 
Published: August 2017

AbstractMembrane bound respiratory complex I is the key enzyme in the respiratory chains of bacteria and mitochondria, and couples the reduction of quinone to the pumping of protons across the membrane. Recently solved crystal or electron microscopy structures of bacterial and mitochondrial complexes have provided significant insights into the electron and proton transfer pathways. However, due to large spatial separation between the electron and proton transfer routes, the molecular mechanism of coupling remains unclear. Here, based on atomistic molecular dynamics simulations performed on the entire structure of complex I from Thermus thermophilus, we studied the hydration of the quinone-binding site and the membrane-bound subunits. The data from simulations show rapid diffusion of water molecules in the protein interior, and formation of hydrated regions in the three antiporter-type subunits. An unexpected water-protein based connectivity between the middle of the Q-tunnel and the fourth proton channel is also observed. The protonation-state dependent dynamics of key acidic residues in the Nqo8 subunit suggest that the latter may be linked to redox-coupled proton pumping in complex I. We propose that in complex I the proton and electron transfer paths are not entirely separate, instead the nature of coupling may in part be ‘direct’.
CD71+ erythroid suppressor cells impair adaptive immunity against Bordetella pertussis
Authors: Namdar Afshin , Koleva Petya , Shahbaz Shima , Strom Stacy , Gerdts Volker , Elahi Shokrollah 
Published: August 2017

AbstractInfant’s immune system cannot control infection or respond to vaccination as efficiently as older individuals, a phenomenon that has been attributed to immunological immaturity. Recently, we challenged this notion and proposed the presence of actively immunosuppressive and physiologically enriched CD71+ erythroid cells in neonates. Here we utilized Bordetella pertussis, a common neonatal respiratory tract pathogen, as a proof of concept to investigate the role of these cells in adaptive immunity. We observed that CD71+ cells have distinctive immunosuppressive properties and prevent recruitment of immune cells to the mucosal site of infection. CD71+ cells ablation unleashed induction of B. pertussis-specific protective cytokines (IL-17 and IFN-γ) in the lungs and spleen upon re-infection or vaccination. We also found that CD71+ cells suppress systemic and mucosal B. pertussis-specific antibody responses. Enhanced antigen-specific adaptive immunity following CD71+ cells depletion increased resistance of mice to B. pertussis infection. Furthermore, we found that human cord blood CD71+ cells also suppress T and B cell functions in vitro. Collectively, these data provide important insight into the role of CD71+ erythroid cells in adaptive immunity. We anticipate our results will spark renewed investigation in modulating the function of these cells to enhance host defense to infections in newborns.
Epidemiology of tuberculosis in Chongqing, China: a secular trend from 1992 to 2015
Authors: Wu Bo , Yu Ya , Xie Weijia , Liu Ying , Zhang Yao , Hu Daiyu , Li Yafei 
Published: August 2017

AbstractChongqing is a southwest city of China with high tuberculosis (TB) burden. An observational retrospective study has been performed based on routine TB surveillance data in Chongqing from 1992 to 2015. The TB notification rate has declined to 70.8 cases per 100,000 population from the peak of 106 cases per 100,000 in 2005. The TB notification rate in population over-65 years has become the highest among all-ages population since 2010. The average proportion of farmers in all notified cases from 2008 to 2015 was 62.5%, and the notification rate of farmers has become the highest among all occupations since 2011. The TB notification showed a regional disparity in Chongqing. Despite the improvement achieved since 1992, the TB control efforts has been threatened by new challenges such as the demographic shift towards an aging population, the prevalence of MDR-TB and TB/HIV co-infection, and the regional disparity of TB notification. More effective interventions should be implemented. Our study can serve as a guidance for the future development of TB control in Chongqing, and we believe it has general relevance to TB control in other regions with similar situations.
Spatial disease dynamics of free-living pathogens under pathogen predation
Authors: Mononen Tommi , Ruokolainen Lasse 
Published: August 2017

AbstractThe epidemiological dynamics of potentially free-living pathogens are often studied with respect to a specific pathogen species (e.g., cholera) and most studies concentrate only on host-pathogen interactions. Here we show that metacommunity-level interactions can alter conventional spatial disease dynamics. We introduce a pathogen eating consumer species and investigate a deterministic epidemiological model of two habitat patches, where both patches can be occupied by hosts, pathogens, and consumers of free-living pathogens. An isolated habitat patch shows periodic disease outbreaks in the host population, arising from cyclic consumer-pathogen dynamics. On the other hand, consumer dispersal between the patches generate asymmetric disease prevalence, such that the host population in one patch stays disease-free, while disease outbreaks occur in the other patch. Such asymmetry can also arise with host dispersal, where infected hosts carry pathogens to the other patch. This indirect movement of pathogens causes also a counter-intuitive effect: decreasing morbidity in a focal patch under increasing pathogen immigration. Our results underline that community-level interactions influence disease dynamics and consistent spatial asymmetry can arise also in spatially homogeneous systems.
Quantitative response relationships between net nitrogen transformation rates and nitrogen functional genes during artificial vegetation restoration following agricultural abandonment
Authors: Wang Honglei , Deng Na , Wu Duoyang , Hu Shu 
Published: August 2017

AbstractA comprehensive understanding of how microbial associated with nitrogen (N) cycling respond to artificial vegetation restoration is still lacking, particularly in arid to semi-arid degraded ecosystems. We compared soil net N mineralization rates and the abundance of bacteria, archaea, and eleven N microbial genes on the northern Loess Plateau of China during the process of artificial vegetation restoration. The quantitative relationships between net N mineralization rates and N microbial genes were determined. We observed a significant difference of net transformation rates of NH4+-N (Ra), NO3−-N (Rd), and total mineralization (Rm), which rapidly decreased in 10-year soils and steadily increased in the 10–30-year soils. Different N functional microbial groups responded to artificial vegetation restoration distinctly and differentially, especially for denitrifying bacteria. Stepwise regression analysis suggested that Ra was collectively controlled by AOA-amoA and Archaea; Rd was jointly governed by narG, napA, nxrA, and bacreria; and Rm was jointly controlled by napA, narG, nirK, nirS, norB, nosZ, and nxrA.
Predictable Chronic Mild Stress during Adolescence Promotes Fear Memory Extinction in Adulthood
Authors: Deng Jia-Hui , Yan Wei , Han Ying , Chen Chen , Meng Shi-Qiu , Sun Cheng-Yu , Xu Ling-Zhi , Xue Yan-Xue , Gao Xue-Jiao , Chen Na , Zhang Fei-Long , Wang Yu-Mei , Shi Jie , Lu Lin 
Published: August 2017

AbstractEarly-life stress in adolescence has a long-lasting influence on brain function in adulthood, and it is mostly recognized as a predisposing factor for mental illnesses, such as anxiety and posttraumatic stress disorder. Previous studies also indicated that adolescent predictable chronic mild stress (PCMS) in early life promotes resilience to depression- and anxiety-like behaviors in adulthood. However, the role of PCMS in associated memory process is still unclear. In the present study, we found that adolescent PCMS facilitated extinction and inhibited fear response in reinstatement and spontaneous recovery tests in adult rats, and this effect was still present 1 week later. PCMS in adolescence increased the activity of brain-derived neurotrophic factor (BDNF)-extracellular signal-regulated kinase 1/2 (ERK1/2) signaling in infralimbic cortex (IL) but not prelimbic cortex in adulthood. Intra-IL infusion of BDNF antibody and the ERK1/2 inhibitor U0126 reversed PCMS-induced enhancement of fear extinction. Moreover, we found that PCMS decreased DNA methylation of the Bdnf gene at exons IV and VI and elevated the mRNA levels of Bdnf in the IL. Our findings indicate that adolescent PCMS exposure promotes fear memory extinction in adulthood, which reevaluates the traditional notion of adolescent stress.
Deep subwavelength ultrasonic imaging using optimized holey structured metamaterials
Authors: Amireddy Kiran Kumar , Balasubramaniam Krishnan , Rajagopal Prabhu 
Published: August 2017

AbstractThis paper reports the experimental demonstration of deep subwavelength ultrasonic imaging of defects in metallic samples with a feature size of λ/25 using holey-structured metamaterial lenses. Optimal dimensions of the metamaterial’s geometric parameters are determined using numerical simulation and the physics of wave propagation through holey lenses. The paper also shows how the extraordinary transmission capacity of holey structured metamaterials comes about by the coupling of higher frequencies in the incident ultrasonic wave field to resonant modes of the lens.
Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements
Authors: Bohórquez Hugo J. , Suárez Carlos F. , Patarroyo Manuel E. 
Published: August 2017

AbstractWhy is an amino acid replacement in a protein accepted during evolution? The answer given by bioinformatics relies on the frequency of change of each amino acid by another one and the propensity of each to remain unchanged. We propose that these replacement rules are recoverable from the secondary structural trends of amino acids. A distance measure between high-resolution Ramachandran distributions reveals that structurally similar residues coincide with those found in substitution matrices such as BLOSUM: Asn ↔ Asp, Phe ↔ Tyr, Lys ↔ Arg, Gln ↔ Glu, Ile ↔ Val, Met → Leu; with Ala, Cys, His, Gly, Ser, Pro, and Thr, as structurally idiosyncratic residues. We also found a high average correlation ($$\overline{R}$$

R

¯

= 0.85) between thirty amino acid mutability scales and the mutational inertia (I
X
), which measures the energetic cost weighted by the number of observations at the most probable amino acid conformation. These results indicate that amino acid substitutions follow two optimally-efficient principles: (a) amino acids interchangeability privileges their secondary structural similarity, and (b) the amino acid mutability depends directly on its biosynthetic energy cost, and inversely with its frequency. These two principles are the underlying rules governing the observed amino acid substitutions.
SNAP-25b-deficiency increases insulin secretion and changes spatiotemporal profile of Ca2+oscillations in β cell networks
Authors: Daraio Teresa , Bombek Lidija Križančić , Gosak Marko , Valladolid-Acebes Ismael , Klemen Maša Skelin , Refai Essam , Berggren Per-Olof , Brismar Kerstin , Rupnik Marjan Slak , Bark Christina 
Published: August 2017

AbstractSNAP-25 is a protein of the core SNARE complex mediating stimulus-dependent release of insulin from pancreatic β cells. The protein exists as two alternatively spliced isoforms, SNAP-25a and SNAP-25b, differing in 9 out of 206 amino acids, yet their specific roles in pancreatic β cells remain unclear. We explored the effect of SNAP-25b-deficiency on glucose-stimulated insulin release in islets and found increased secretion both in vivo and in vitro. However, slow photo-release of caged Ca2+ in β cells within pancreatic slices showed no significant differences in Ca2+-sensitivity, amplitude or rate of exocytosis between SNAP-25b-deficient and wild-type littermates. Therefore, we next investigated if Ca2+ handling was affected in glucose-stimulated β cells using intracellular Ca2+-imaging and found premature activation and delayed termination of [Ca2+]
i
elevations. These findings were accompanied by less synchronized Ca2+-oscillations and hence more segregated functional β cell networks in SNAP-25b-deficient mice. Islet gross morphology and architecture were maintained in mutant mice, although sex specific compensatory changes were observed. Thus, our study proposes that SNAP-25b in pancreatic β cells, except for participating in the core SNARE complex, is necessary for accurate regulation of Ca2+-dynamics.