bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dehydration prompts increased activity and blood feeding by mosquitoes
Authors: Hagan Richard W. , Didion Elise M. , Rosselot Andrew E. , Holmes Christopher J. , Siler Samantha C. , Rosendale Andrew J. , Hendershot Jacob M. , Elliot Kiaira S. B. , Jennings Emily C. , Nine Gabriela A. , Perez Paula L. , Rizlallah Alexandre E. , Watanabe Miki , Romick-Rosendale Lindsey E. , Xiao Yanyu , Rasgon Jason L. , Benoit Joshua B. 
Published: April 2018

AbstractCurrent insights into the mosquito dehydration response rely on studies that examine specific responses but ultimately fail to provide an encompassing view of mosquito biology. Here, we examined underlying changes in the biology of mosquitoes associated with dehydration. Specifically, we show that dehydration increases blood feeding in the northern house mosquito, Culex pipiens, which was the result of both higher activity and a greater tendency to land on a host. Similar observations were noted for Aedes aegypti and Anopheles quadrimaculatus. RNA-seq and metabolome analyses in C. pipiens following dehydration revealed that factors associated with carbohydrate metabolism are altered, specifically the breakdown of trehalose. Suppression of trehalose breakdown in C. pipiens by RNA interference reduced phenotypes associated with lower hydration levels. Lastly, mesocosm studies for C. pipiens confirmed that dehydrated mosquitoes were more likely to host feed under ecologically relevant conditions. Disease modeling indicates dehydration bouts will likely enhance viral transmission. This dehydration-induced increase in blood feeding is therefore likely to occur regularly and intensify during periods when availability of water is low.
Effective in vivo treatment of acute lung injury with helical, amphipathic peptoid mimics of pulmonary surfactant proteins
Authors: Czyzewski Ann M. , McCaig Lynda M. , Dohm Michelle T. , Broering Lauren A. , Yao Li-Juan , Brown Nathan J. , Didwania Maruti K. , Lin Jennifer S. , Lewis Jim F. , Veldhuizen Ruud , Barron Annelise E. 
Published: April 2018

AbstractAcute lung injury (ALI) leads to progressive loss of breathing capacity and hypoxemia, as well as pulmonary surfactant dysfunction. ALI’s pathogenesis and management are complex, and it is a significant cause of morbidity and mortality worldwide. Exogenous surfactant therapy, even for research purposes, is impractical for adults because of the high cost of current surfactant preparations. Priorin vitrowork has shown that poly-N-substituted glycines (peptoids), in a biomimetic lipid mixture, emulate key biophysical activities of lung surfactant proteins B and C at the air-water interface. Here we report goodin vivoefficacy of a peptoid-based surfactant, compared with extracted animal surfactant and a synthetic lipid formulation, in a rat model of lavage-induced ALI. Adult rats were subjected to whole-lung lavage followed by administration of surfactant formulations and monitoring of outcomes. Treatment with a surfactant protein C mimic formulation improved blood oxygenation, blood pH, shunt fraction, and peak inspiratory pressure to a greater degree than surfactant protein B mimic or combined formulations. All peptoid-enhanced treatment groups showed improved outcomes compared to synthetic lipids alone, and some formulations improved outcomes to a similar extent as animal-derived surfactant. Robust biophysical mimics of natural surfactant proteins may enable new medical research in ALI treatment.
Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups
Authors: Stroehlein Andreas J. , Young Neil D. , Gasser Robin B. 
Published: April 2018

AbstractDespite the substantial amount of genomic and transcriptomic data available for a wide range of eukaryotic organisms, most genomes are still in a draft state and can have inaccurate gene predictions. To gain a sound understanding of the biology of an organism, it is crucial that inferred protein sequences are accurately identified and annotated. However, this can be challenging to achieve, particularly for organisms such as parasitic worms (helminths), as most gene prediction approaches do not account for substantial phylogenetic divergence from model organisms, such as Caenorhabditis elegans and Drosophila melanogaster, whose genomes are well-curated. In this paper, we describe a bioinformatic strategy for the curation of gene families and subsequent annotation of encoded proteins. This strategy relies on pairwise gene curation between at least two closely related species using genomic and transcriptomic data sets, and is built on recent work on kinase complements of parasitic worms. Here, we discuss salient technical aspects of this strategy and its implications for the curation of protein families more generally.
Comparative analyses of whole-genome protein sequences from multiple organisms
Authors: Yokono Makio , Satoh Soichirou , Tanaka Ayumi 
Published: April 2018

AbstractPhylogenies based on entire genomes are a powerful tool for reconstructing the Tree of Life. Several methods have been proposed, most of which employ an alignment-free strategy. Average sequence similarity methods are different than most other whole-genome methods, because they are based on local alignments. However, previous average similarity methods fail to reconstruct a correct phylogeny when compared against other whole-genome trees. In this study, we developed a novel average sequence similarity method. Our method correctly reconstructs the phylogenetic tree of in silico evolved E. coli proteomes. We applied the method to reconstruct a whole-proteome phylogeny of 1,087 species from all three domains of life, Bacteria, Archaea, and Eucarya. Our tree was automatically reconstructed without any human decisions, such as the selection of organisms. The tree exhibits a concentric circle-like structure, indicating that all the organisms have similar total branch lengths from their common ancestor. Branching patterns of the members of each phylum of Bacteria and Archaea are largely consistent with previous reports. The topologies are largely consistent with those reconstructed by other methods. These results strongly suggest that this approach has sufficient taxonomic resolution and reliability to infer phylogeny, from phylum to strain, of a wide range of organisms.
Weighted Multi-marker Genetic Risk Scores for Incident Coronary Heart Disease among Individuals of African, Latino and East-Asian Ancestry
Authors: Iribarren Carlos , Lu Meng , Jorgenson Eric , Martínez Manuel , Lluis-Ganella Carla , Subirana Isaac , Salas Eduardo , Elosua Roberto 
Published: April 2018

AbstractWe examined the clinical utility of two multi-locus genetic risk scores (GRSs) previously validated in Europeans among persons of African (AFR; n = 2,089), Latino (LAT; n = 4,349) and East-Asian (EA; n = 4,804) ancestry. We used data from the GERA cohort (30–79 years old, 68 to 73% female). We utilized two GRSs with 12 and 51 SNPs, respectively, and the Framingham Risk Score (FRS) to estimate 10-year CHD risk. After a median 8.7 years of follow-up, 450 incident CHD events were documented (95 in AFR, 316 in LAT and 39 EA, respectively). In a model adjusting for principal components and risk factors, tertile 3 vs. tertile 1 of GRS_12 was associated with 1.86 (95% CI, 1.15–3.01), 1.52 (95% CI, 1.02–2.25) and 1.19 (95% CI, 0.77–1.83) increased hazard of CHD in AFR, LAT and EA, respectively. Inclusion of the GRSs in models containing the FRS did not increase the C-statistic but resulted in net overall reclassification of 10% of AFR, 7% LAT and EA and in reclassification of 13% of AFR and EA as well as 10% LAT in the intermediate FRS risk subset. Our results support the usefulness of incorporating genetic information into risk assessment for primary prevention among minority subjects in the U.S.
Elevated expression of human bHLH factor ATOH7 accelerates cell cycle progression of progenitors and enhances production of avian retinal ganglion cells
Authors: Zhang Xiang-Mei , Hashimoto Takao , Tang Ronald , Yang Xian-Jie 
Published: April 2018

AbstractThe production of vertebrate retinal projection neurons, retinal ganglion cells (RGCs), is regulated by cell-intrinsic determinants and cell-to-cell signaling events. The basic-helix-loop-helix (bHLH) protein Atoh7 is a key neurogenic transcription factor required for RGC development. Here, we investigate whether manipulating human ATOH7 expression among uncommitted progenitors can promote RGC fate specification and thus be used as a strategy to enhance RGC genesis. Using the chicken retina as a model, we show that cell autonomous expression of ATOH7 is sufficient to induce precocious RGC formation and expansion of the neurogenic territory. ATOH7 overexpression among neurogenic progenitors significantly enhances RGC production at the expense of reducing the progenitor pool. Furthermore, forced expression of ATOH7 leads to a minor increase of cone photoreceptors. We provide evidence that elevating ATOH7 levels accelerates cell cycle progression from S to M phase and promotes cell cycle exit. We also show that ATOH7-induced ectopic RGCs often exhibit aberrant axonal projection patterns and are correlated with increased cell death during the period of retinotectal connections. These results demonstrate the high potency of human ATOH7 in promoting early retinogenesis and specifying the RGC differentiation program, thus providing insight for manipulating RGC production from stem cell-derived retinal organoids.
Children passively allow other’s rule violations in cooperative situations
Authors: Ikeda Ayaka , Okumura Yuko , Kobayashi Tessei , Itakura Shoji 
Published: April 2018

AbstractRecent studies in developmental psychology have revealed the developmental origins of cooperation. Although such studies regard cooperation as a pro-social behavior, studies on adults have found a negative aspect: cooperation sometimes promotes unethical behavior. Adults also exhibit altruistic cheating, even though their cheating might not actually benefit them. However, the development of negative aspects of cooperation remains unclear. Our study examined whether 7-year-old children engage in negative aspects of cooperation from two aspects using a peeking paradigm. Specifically, Experiment 1 examined children’s negative aspects of cooperation from the perspective of collaboration and Experiment 2 examined altruistic behavior. Results of Experiment 1 revealed that children kept the cheating of a collaborative partner secret even though they did not actively cheat themselves. In Experiment 2, children also kept the partner’s cheating secret even when violations did not provide any reward to themselves, if the predefined reward was high. In contrast, children did not keep the cheating secret if the predefined reward was low. Overall, our findings suggest that even 7-year-olds tend to act as if cooperating is more important than following rules that are compatible and exhibit negative aspects of cooperation.
Scandium doping brings speed improvement in Sb2Te alloy for phase change random access memory application
Authors: Chen Xin , Zheng Yonghui , Zhu Min , Ren Kun , Wang Yong , Li Tao , Liu Guangyu , Guo Tianqi , Wu Lei , Liu Xianqiang , Cheng Yan , Song Zhitang 
Published: April 2018

AbstractPhase change random access memory (PCRAM) has gained much attention as a candidate for nonvolatile memory application. To develop PCRAM materials with better properties, especially to draw closer to dynamic random access memory (DRAM), the key challenge is to research new high-speed phase change materials. Here, Scandium (Sc) has been found it is helpful to get high-speed and good stability after doping in Sb2Te alloy. Sc0.1Sb2Te based PCRAM cell can achieve reversible switching by applying even 6 ns voltage pulse experimentally. And, Sc doping not only promotes amorphous stability but also improves the endurance ability comparing with pure Sb2Te alloy. Moreover, according to DFT calculations, strong Sc-Te bonds lead to the rigidity of Sc centered octahedrons, which may act as crystallization precursors in recrystallization process to boost the set speed.
Accurate estimation of a phase diagram from a single STM image
Authors: Takeuchi Kazuhito , Yuge Koretaka , Tabata Shinya , Saito Hiroki , Kurokawa Shu , Sakai Akira 
Published: April 2018

AbstractWe propose a new approach to constructing a phase diagram using the effective Hamiltonian derived only from a single real-space image produced by scanning tunneling microscopy (STM). Currently, there have been two main methods to construct phase diagrams in material science: ab initio calculations and CALPHAD with thermodynamic information obtained by experiments and/or theoretical calculations. Although the two methods have successfully revealed a number of unsettled phase diagrams, their results sometimes contradicted when it is difficult to construct an appropriate Hamiltonian that captures the characteristics of materials, e.g., for a system consisting of multiple-scale objects whose interactions are essential to the system’s characteristics. Meanwhile, the advantage of our approach over existing methods is that it can directly and uniquely determine the effective Hamiltonian without any thermodynamic information. The validity of our approach is demonstrated through an Mg–Zn–Y long-period stacking-ordered structure, which is a challenging system for existing methods, leading to contradictory results. Our result successfully reproduces the ordering tendency seen in STM images that previous theoretical study failed to reproduce and clarifies its previously unknown phase diagram. Thus, our approach can be used to clear up contradictions shown by existing methods.
Transplantation of human microbiota into conventional mice durably reshapes the gut microbiota
Authors: Wrzosek Laura , Ciocan Dragos , Borentain Patrick , Spatz Madeleine , Puchois Virginie , Hugot Cindy , Ferrere Gladys , Mayeur Camille , Perlemuter Gabriel , Cassard Anne-Marie 
Published: April 2018

AbstractHuman microbiota-associated (HMA) mice are an important model to study the relationship between liver diseases and intestinal microbiota. We describe a new method to humanize conventional mice based on bowel cleansing with polyethylene glycol followed by fecal microbiota transplantation (FMT) from a human donor. Four successive bowel cleansings were sufficient to empty the intestine and decrease the microbiota by 90%. We then compared four different strategies based on the frequency of FMT over four weeks: (1) twice a week; (2) once a week; (3) two FMTs; (4) one FMT. We were able to transfer human bacteria to mice, irrespective of the strategy used. We detected human bacteria after four weeks, even if only one FMT was performed, but there was a shift of the microbiota over time. FMT twice a week for four weeks was too frequent and perturbed the stability of the newly formed ecosystem. FMT once a week appears to be the best compromise as it allowed engraftment of Faecalibacterium, and a higher diversity of bacteria belonging to the Bacteroidales order. Our easy to establish HMA mouse model could be used as an alternative to classical HMA mice to study the relationship between the liver and the microbiota.
Increased experimental conditions and marker densities identified more genetic loci associated with southern and northern leaf blight resistance in maize
Authors: Li Yong-xiang , Chen Lin , Li Chunhui , Bradbury Peter J. , Shi Yun-su , Song Yanchun , Zhang Dengfeng , Zhang Zhiwu , Buckler Edward S. , Li Yu , Wang Tianyu 
Published: April 2018

AbstractSouthern leaf blight (SLB) and northern leaf blight (NLB) are the two major foliar diseases limiting maize production worldwide. Upon previous study with the nested association mapping (NAM) population, which consist of 5,000 recombinant inbred lines from 25 parents crossed with B73, we expanded the phenotyping environments from the United States (US) to China, and increased the marker densities from 1106 to 7386 SNPs for linkage mapping, and from 1.6 to 28.5 million markers for association mapping. We identified 49 SLB and 48 NLB resistance-related unique QTLs in linkage mapping, and multiple loci in association mapping with candidate genes involved in known plant disease-resistance pathways. Furthermore, an independent natural population with 282 diversified inbred lines were sequenced for four candidate genes selected based on their biological functions. Three of them demonstrated significant associations with disease resistance. These findings provided valuable resources for further implementations to develop varieties with superior resistance for NLB and SLB.
Rest-related consolidation protects the fine detail of new memories
Authors: Craig Michael , Dewar Michaela 
Published: April 2018

AbstractNewly encoded memories are labile and consolidate over time. The importance of sleep in memory consolidation has been well known for almost a decade. However, recent research has shown that awake quiescence, too, can support consolidation: people remember more new memories if they quietly rest after encoding than if they engage in a task. It is not yet known how exactly this rest-related consolidation benefits new memories, and whether it affects the fine detail of new memories. Using a sensitive picture recognition task, we show that awake quiescence aids the fine detail of new memories. Young adults were significantly better at discriminating recently encoded target pictures from similar lure pictures when the initial encoding of target pictures had been followed immediately by 10 minutes of awake quiescence than an unrelated perceptual task. This novel finding indicates that, in addition to influencing how much we remember, our behavioural state during wakeful consolidation determines, at least in part, the level of fine detail of our new memories. Thus, our results suggest that rest-related consolidation protects the fine detail of new memories, allowing us to retain detailed memories.
Structural insights from lipid-bilayer nanodiscs link α-Synuclein membrane-binding modes to amyloid fibril formation
Authors: Viennet Thibault , Wördehoff Michael M. , Uluca Boran , Poojari Chetan , Shaykhalishahi Hamed , Willbold Dieter , Strodel Birgit , Heise Henrike , Buell Alexander K. , Hoyer Wolfgang , Etzkorn Manuel 
Published: April 2018

AbstractThe protein α-Synuclein (αS) is linked to Parkinson’s disease through its abnormal aggregation, which is thought to involve cytosolic and membrane-bound forms of αS. Following previous studies using micelles and vesicles, we present a comprehensive study of αS interaction with phospholipid bilayer nanodiscs. Using a combination of NMR-spectroscopic, biophysical, and computational methods, we structurally and kinetically characterize αS interaction with different membrane discs in a quantitative and site-resolved way. We obtain global and residue-specific αS membrane affinities, and determine modulations of αS membrane binding due to αS acetylation, membrane plasticity, lipid charge density, and accessible membrane surface area, as well as the consequences of the different binding modes for αS amyloid fibril formation. Our results establish a structural and kinetic link between the observed dissimilar binding modes and either aggregation-inhibiting properties, largely unperturbed aggregation, or accelerated aggregation due to membrane-assisted fibril nucleation.
DARPP-32 and t-DARPP promote non-small cell lung cancer growth through regulation of IKKα-dependent cell migration
Authors: Alam Sk. Kayum , Astone Matteo , Liu Ping , Hall Stephanie R. , Coyle Abbygail M. , Dankert Erin N. , Hoffman Dane K. , Zhang Wei , Kuang Rui , Roden Anja C. , Mansfield Aaron S. , Hoeppner Luke H. 
Published: April 2018

AbstractLung cancer is the leading cause of cancer-related death worldwide. Here we demonstrate that elevated expression of dopamine and cyclic adenosine monophosphate-regulated phosphoprotein, Mr 32000 (DARPP-32), and its truncated splice variant t-DARPP promote lung tumor growth, while abrogation of DARPP-32 expression in human non-small-cell lung cancer (NSCLC) cells reduces tumor growth in orthotopic mouse models. We observe a physical interaction between DARPP-32 and inhibitory kappa B kinase-α (IKKα) that promotes NSCLC cell migration through non-canonical nuclear factor kappa-light-chain-enhancer of activated B cells 2 (NF-κB2) signaling. Bioinformatics analysis of 513 lung adenocarcinoma patients reveals that elevated t-DARPP isoform expression is associated with poor overall survival. Histopathological investigation of 62 human lung adenocarcinoma tissues also shows that t-DARPP expression is elevated with increasing tumor (T) stage. Our data suggest that DARPP-32 isoforms serve as a negative prognostic marker associated with increasing stages of NSCLC and may represent a novel therapeutic target.
Comparison of the power-2 limb-darkening law from the STAGGER-grid to Kepler light curves of transiting exoplanets
Authors: Maxted P. F. L. 
Published: April 2018

Context. Inaccurate limb-darkening models can be a significant source of error in the analysis of the light curves for transiting exoplanet and eclipsing binary star systems, particularly for high-precision light curves at optical wavelengths. The power-2 limb-darkening law, Iλ(µ) = 1 − c(1−µα), has recently been proposed as a good compromise between complexity and precision in the treatment of limb-darkening.
Aims. My aim is to develop a practical implementation of the power-2 limb-darkening law and to quantify the accuracy of this implementation.
Methods. I have used synthetic spectra based on the 3D stellar atmosphere models from the STAGGER-grid to compute the limb-darkening for several passbands (UBVRI, CHEOPS, TESS, Kepler, etc.). The parameters of the power-2 limb-darkening laws are optimized using a least-squares fit to a simulated light curve computed directly from the tabulated Iλ(μ) values. I use the transformed parameters h1 = 1 − c(1 − 2−α) and h2 = c2−α to directly compare these optimized limb-darkening parameters to the limb darkening measured from Kepler light curves of 16 transiting exoplanet systems.
Results. The posterior probability distributions (PPDs) of the transformed parameters h1 and h2 resulting from the light curve analysis are found to be much less strongly correlated than the PPDs for c and α. The agreement between the computed and observed values of (h1, h2) is generally very good but there are significant differences between the observed and computed values for Kepler-17, the only star in the sample that shows significant variability between the eclipses due to magnetic activity (star spots).
Conclusions. The tabulation of h1 and h2 provided here can be used to accurately model the light curves of transiting exoplanets. I also provide estimates of the priors that should be applied to transformed parameters h1 and h2 based on my analysis of the Kepler light curves of 16 stars with transiting exoplanets.