bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fine mapping of MHC region in lung cancer highlights independent susceptibility loci by ethnicity
Authors: Ferreiro-Iglesias Aida , Lesseur Corina , McKay James , Hung Rayjean J. , Han Younghun , Zong Xuchen , Christiani David , Johansson Mattias , Xiao Xiangjun , Li Yafang , Qian David C. , Ji Xuemei , Liu Geoffrey , Caporaso Neil , Scelo Ghislaine , Zaridze David , Mukeriya Anush , Kontic Milica , Ognjanovic Simona , Lissowska Jolanta , Szołkowska Małgorzata , Swiatkowska Beata , Janout Vladimir , Holcatova Ivana , Bolca Ciprian , Savic Milan , Ognjanovic Miodrag , Bojesen Stig Egil , Wu Xifeng , Albanes Demetrios , Aldrich Melinda C. , Tardon Adonina , Fernandez-Somoano Ana , Fernandez-Tardon Guillermo , Le Marchand Loic , Rennert Gadi , Chen Chu , Doherty Jennifer , Goodman Gary , Bickeböller Heike , Wichmann H-Erich , Risch Angela , Rosenberger Albert , Shen Hongbing , Dai Juncheng , Field John K. , Davies Michael , Woll Penella , Teare M. Dawn , Kiemeney Lambertus A. , van der Heijden Erik H. F. M. , Yuan Jian-Min , Hong Yun-Chul , Haugen Aage , Zienolddiny Shanbeh , Lam Stephen , Tsao Ming-Sound , Johansson Mikael , Grankvist Kjell , Schabath Matthew B. , Andrew Angeline , Duell Eric , Melander Olle , Brunnström Hans , Lazarus Philip , Arnold Susanne , Slone Stacey , Byun Jinyoung , Kamal Ahsan , Zhu Dakai , Landi Maria Teresa , Amos Christopher I. , Brennan Paul 
Published: September 2018

AbstractLung cancer has several genetic associations identified within the major histocompatibility complex (MHC); although the basis for these associations remains elusive. Here, we analyze MHC genetic variation among 26,044 lung cancer patients and 20,836 controls densely genotyped across the MHC, using the Illumina Illumina OncoArray or Illumina 660W SNP microarray. We impute sequence variation in classical HLA genes, fine-map MHC associations for lung cancer risk with major histologies and compare results between ethnicities. Independent and novel associations within HLA genes are identified in Europeans including amino acids in the HLA-B*0801 peptide binding groove and an independent HLA-DQB1*06 loci group. In Asians, associations are driven by two independent HLA allele sets that both increase risk in HLA-DQB1*0401 and HLA-DRB1*0701; the latter better represented by the amino acid Ala-104. These results implicate several HLA–tumor peptide interactions as the major MHC factor modulating lung cancer susceptibility.
Human hippocampal replay during rest prioritizes weakly learned information and predicts memory performance
Authors: Schapiro Anna C. , McDevitt Elizabeth A. , Rogers Timothy T. , Mednick Sara C. , Norman Kenneth A. 
Published: September 2018

AbstractThe hippocampus replays experiences during quiet rest periods, and this replay benefits subsequent memory. A critical open question is how memories are prioritized for this replay. We used functional magnetic resonance imaging (fMRI) pattern analysis to track item-level replay in the hippocampus during an awake rest period after participants studied 15 objects and completed a memory test. Objects that were remembered less well were replayed more during the subsequent rest period, suggesting a prioritization process in which weaker memories—memories most vulnerable to forgetting—are selected for replay. In a second session 12 hours later, more replay of an object during a rest period predicted better subsequent memory for that object. Replay predicted memory improvement across sessions only for participants who slept during that interval. Our results provide evidence that replay in the human hippocampus prioritizes weakly learned information, predicts subsequent memory performance, and relates to memory improvement across a delay with sleep.
Plasmodium co-infection protects against chikungunya virus-induced pathologies
Authors: Teo Teck-Hui , Lum Fok-Moon , Ghaffar Khairunnisa , Chan Yi-Hao , Amrun Siti Naqiah , Tan Jeslin J. L. , Lee Cheryl Y. P. , Chua Tze-Kwang , Carissimo Guillaume , Lee Wendy W. L. , Claser Carla , Rajarethinam Ravisankar , Rénia Laurent , Ng Lisa F. P. 
Published: September 2018

AbstractCo-infection withPlasmodiumand chikungunya virus (CHIKV) has been reported in humans, but the impact of co-infection on pathogenesis remains unclear. Here, we show that prior exposure toPlasmodiumsuppresses CHIKV-associated pathologies in mice. Mechanistically,Plasmodiuminfection induces IFNγ, which reduces viraemia of a subsequent CHIKV infection and suppresses tissue viral load and joint inflammation. Conversely, concomitant infection with both pathogens limits the peak of joint inflammation with no effect on CHIKV viraemia. Reduced peak joint inflammation is regulated by elevated apoptosis of CD4+T-cells in the lymph nodes and disrupted CXCR3-mediated CD4+T-cell migration that abolishes their infiltration into the joints. Virus clearance from tissues is delayed in both infection scenarios, and is associated with a disruption of B cell affinity-maturation in the spleen that reduces CHIKV-neutralizing antibody production.
Chirality amplification by desymmetrization of chiral ligand-capped nanoparticles to nanorods quantified in soft condensed matter
Authors: Nemati Ahlam , Shadpour Sasan , Querciagrossa Lara , Li Lin , Mori Taizo , Gao Min , Zannoni Claudio , Hegmann Torsten 
Published: September 2018

AbstractInduction, transmission, and manipulation of chirality in molecular systems are well known, widely applied concepts. However, our understanding of how chirality of nanoscale entities can be controlled, measured, and transmitted to the environment is considerably lacking behind. Future discoveries of dynamic assemblies engineered from chiral nanomaterials, with a specific focus on shape and size effects, require exact methods to assess transmission and amplification of nanoscale chirality through space. Here we present a remarkably powerful chirality amplification approach by desymmetrization of plasmonic nanoparticles to nanorods. When bound to gold nanorods, a one order of magnitude lower number of chiral molecules induces a tighter helical distortion in the surrounding liquid crystal–a remarkable amplification of chirality through space. The change in helical distortion is consistent with a quantification of the change in overall chirality of the chiral ligand decorated nanomaterials differing in shape and size as calculated from a suitable pseudoscalar chirality indicator.
Neonatally imprinted stromal cell subsets induce tolerogenic dendritic cells in mesenteric lymph nodes
Authors: Pezoldt Joern , Pasztoi Maria , Zou Mangge , Wiechers Carolin , Beckstette Michael , Thierry Guilhem R. , Vafadarnejad Ehsan , Floess Stefan , Arampatzi Panagiota , Buettner Manuela , Schweer Janina , Fleissner Diana , Vital Marius , Pieper Dietmar H. , Basic Marijana , Dersch Petra , Strowig Till , Hornef Mathias , Bleich André , Bode Ulrike , Pabst Oliver , Bajénoff Marc , Saliba Antoine-Emmanuel , Huehn Jochen 
Published: September 2018

AbstractGut-draining mesenteric lymph nodes (mLNs) are important for inducing peripheral tolerance towards food and commensal antigens by providing an optimal microenvironment for de novo generation of Foxp3+ regulatory T cells (Tregs). We previously identified microbiota-imprinted mLN stromal cells as a critical component in tolerance induction. Here we show that this imprinting process already takes place in the neonatal phase, and renders the mLN stromal cell compartment resistant to inflammatory perturbations later in life. LN transplantation and single-cell RNA-seq uncover stably imprinted expression signatures in mLN fibroblastic stromal cells. Subsetting common stromal cells across gut-draining mLNs and skin-draining LNs further refine their location-specific immunomodulatory functions, such as subset-specific expression of Aldh1a2/3. Finally, we demonstrate that mLN stromal cells shape resident dendritic cells to attain high Treg-inducing capacity in a Bmp2-dependent manner. Thus, crosstalk between mLN stromal and resident dendritic cells provides a robust regulatory mechanism for the maintenance of intestinal tolerance.
Sexual selection contributes to partial restoration of phenotypic robustness in a butterfly
Authors: Nieberding Caroline M. , San Martin Gilles , Saenko Suzanne , Allen Cerisse E. , Brakefield Paul M. , Visser Bertanne 
Published: September 2018

AbstractPhenotypic variation is the raw material for selection that is ubiquitous for most traits in natural populations, yet the processes underlying phenotypic evolution or stasis often remain unclear. Here, we report phenotypic evolution in a mutant line of the butterfly Bicyclus anynana after outcrossing with the genetically polymorphic wild type population. The comet mutation modifies two phenotypic traits known to be under sexual selection in this butterfly: the dorsal forewing eyespots and the pheromone-producing structures. The original comet mutant line was inbred and remained phenotypically stable for at least seven years, but when outcrossed to the wild type population the outcrossed comet line surprisingly recovered the wild type phenotype within 8 generations at high (27 °C), but not at low (20 °C), developmental temperatures. Male mating success experiments then revealed that outcrossed comet males with the typical comet phenotype suffered from lower mating success, while mating success of outcrossed comet males resembling wild types was partially restored. We document a fortuitous case where the addition of genetic polymorphism around a spontaneous mutation could have allowed partial restoration of phenotypic robustness. We further argue that sexual selection through mate choice is likely the driving force leading to phenotypic robustness in our system.
Observations of Deep Current at the Western Boundary of the Northern Philippine Basin
Authors: Zhou Chun , Zhao Wei , Tian Jiwei , Yang Qingxuan , Huang Xiaodong , Zhang Zhiwei , Qu Tangdong 
Published: September 2018

AbstractOne-year time series of current velocities and hydrographic parameters based on four deep moorings deployed east of the Luzon Strait are employed to study the deep current at the western boundary (DCWB) of the northern Philippine Basin. While the mean current is relatively weak, the DCWB is highly variable on an intraseasonal time scale, with dominant periods ranging between 30 and 80 days. During the period of observation (October 2011–October 2012), the DCWB reversed its direction at early April, and pointed southward (−2.4 cm/s) in summer/autumn and northward (1.7 cm/s) in winter/spring. This annual reversal of the DCWB is consistent with the water property distribution in the deep Philippine Basin, with relatively cold and fresh water to the north and relatively warm and salty water to the south. The moored time series also allow for discussion on the stratification of the deep Luzon Strait, which indicates the lower interface of Pacific deep water capable of furnishing the deepwater overflow in the Luzon Strait.
Effect of pentagonal-coordinated surface on crystal nucleation of an undercooled melt
Authors: Pasturel A. , Jakse N. 
Published: September 2018

AbstractBringing a liquid into contact with a solid is known to generally promote crystal nucleation at the freezing temperature. In contrast, it is much more difficult to conceive that a solid surface may hinder nucleation and favor large undercooling effects. Here we report on ab initio and classical molecular dynamic simulations to capture the underlying structural mechanism responsible for this striking effect. We find that the substrate/liquid interactions exert an important influence on in-plane ordering of the adjacent liquid layers in the undercooling regime. In particular, we identify that the presence of atomic arrangements with five-fold symmetry (FFS) on the substrate surface in the form of pentagonal atomic motifs allows the liquid to be undercooled well below its freezing temperature. Our findings clearly demonstrate that this pentagonal-coordinated surface enhances the presence of local arrangements with FFS in the adjacent liquid layers that prevents the crystal nucleation. Finally we suggest new technological developments to attain large undercooling effects.
The Smallest Diplodocid Skull Reveals Cranial Ontogeny and Growth-Related Dietary Changes in the Largest Dinosaurs
Authors: Woodruff D. Cary , Carr Thomas D. , Storrs Glenn W. , Waskow Katja , Scannella John B. , Nordén Klara K. , Wilson John P. 
Published: September 2018

AbstractSauropod dinosaurs were the largest terrestrial vertebrates; yet despite a robust global fossil record, the paucity of cranial remains complicates attempts to understand their paleobiology. An assemblage of small diplodocid sauropods from the Upper Jurassic Morrison Formation of Montana, USA, has produced the smallest diplodocid skull yet discovered. The ~24 cm long skull is referred to cf. Diplodocus based on the presence of several cranial and vertebral characters. This specimen enhances known features of early diplodocid ontogeny including a short snout with narrow-crowned teeth limited to the anterior portion of the jaws and more spatulate teeth posteriorly. The combination of size plus basal and derived character expression seen here further emphasizes caution when naming new taxa displaying the same, as these may be indicative of immaturity. This young diplodocid reveals that cranial modifications occurred throughout growth, providing evidence for ontogenetic dietary partitioning and recapitulation of ancestral morphologies.
Urine-derived cells provide a readily accessible cell type for feeder-free mRNA reprogramming
Authors: Gaignerie A. , Lefort N. , Rousselle M. , Forest-Choquet V. , Flippe L. , Francois–Campion V. , Girardeau A. , Caillaud A. , Chariau C. , Francheteau Q. , Derevier A. , Chaubron F. , Knöbel S. , Gaborit N. , Si-Tayeb K. , David L. 
Published: September 2018

AbstractOver a decade after their discovery, induced pluripotent stem cells (iPSCs) have become a major biological model. The iPSC technology allows generation of pluripotent stem cells from somatic cells bearing any genomic background. The challenge ahead of us is to translate human iPSCs (hiPSCs) protocols into clinical treatment. To do so, we need to improve the quality of hiPSCs produced. In this study we report the reprogramming of multiple patient urine-derived cell lines with mRNA reprogramming, which, to date, is one of the fastest and most faithful reprogramming method. We show that mRNA reprogramming efficiently generates hiPSCs from urine-derived cells. Moreover, we were able to generate feeder-free bulk hiPSCs lines that did not display genomic abnormalities. Altogether, this reprogramming method will contribute to accelerating the translation of hiPSCs to therapeutic applications.
The operational window of carbon nanotube electrical wires treated with strong acids and oxidants
Authors: Lepak-Kuc S. , Boncel S. , Szybowicz M. , Nowicka A. B. , Jozwik I. , Orlinski K. , Gizewski T. , Koziol K. , Jakubowska M. , Lekawa-Raus A. 
Published: September 2018

AbstractConventional metal wires suffer from a significant degradation or complete failure in their electrical performance, when subjected to harsh oxidizing environments, however wires constructed from Carbon Nanotubes (CNTs) have been found to actually improve in their electrical performance when subjected to these environments. These opposing reactions may provide new and interesting applications for CNT wires. Yet, before attempting to move to any real-world harsh environment applications, for the CNT wires, it is essential that this area of their operation be thoroughly examined. To investigate this, CNT wires were treated with multiple combinations of the strongest acids and halogens. The wires were then subjected to conductivity measurements, current carrying capacity tests, as well as Raman, microscopy and thermogravimetric analysis to enable the identification of both the limits of oxidative conductivity boosting and the onset of physical damage to the wires. These experiments have led to two main conclusions. Firstly, that CNT wires may operate effectively in harsh oxidizing environments where metal wires would easily fail and secondly, that the highest conductivity increase of the CNT wires can be achieved through a process of annealing, acetone and HCl purification followed by either H2O2 and HClO4 or Br2 treatment.
Insights into gold nanoparticles as a mucoadhesive system
Authors: Ouellette Mathieu , Masse Florence , Lefebvre-Demers Mathilde , Maestracci Quentin , Grenier Philippe , Millar Robert , Bertrand Nicolas , Prieto Manuel , Boisselier Élodie 
Published: September 2018

AbstractA large number of drugs are administered on different mucosal surfaces. However, due to the poor mucoadhesion of the current formulations, their bioavailability is often very low. The development of efficient mucoadhesive drug delivery systems is thus crucial for improving the performance of these drugs. The mucoadhesive properties of gold nanoparticles were investigated. First, two types of gold nanoparticles were synthesized: AuNP1 and AuNP2. AuNP1 only contain internal thiol groups on their metallic core, and AuNP2 contain both internal and peripheral thiol groups. Different protocols based on an adapted quantitative colorimetric method, UV-visible and fluorescence spectroscopies were then developed to gather information on their mucoadhesive properties. Moreover, a global correction factor for the inner filter effect in spectrofluorimetry was proposed, and the data obtained were compared to those commonly used in the literature. Mucins deeply interact with AuNP1, perturbing their core, whereas they remain at the periphery of AuNP2. The quantitative method suggests that a larger number of mucins interact with AuNP2. The establishment of this protocol could be applied to assess the mucoadhesive properties of other stable molecules. This mucoadhesive property of gold nanoparticles could be combined with their drug delivery ability in order to improve the medication administered on mucosa.
Comparison of spectral and spatial denoising techniques in the context of High Definition FT-IR imaging hyperspectral data
Authors: Koziol Paulina , Raczkowska Magda K. , Skibinska Justyna , Urbaniak-Wasik Sławka , Paluszkiewicz Czesława , Kwiatek Wojciech , Wrobel Tomasz P. 
Published: September 2018

AbstractThe recent emergence of High Definition (HD) FT-IR and Quantum Cascade Laser (QCL) Microscopes elevated the IR imaging field very close to clinical timescales. However, the speed of acquisition and data quality are still the critical factors in reaching the clinic. Denoising offers aide in both aspects if performed properly. However, there is a lack of a direct comparison of the efficiency of denoising techniques in IR imaging in general. To achieve such comparison within a rigorous framework and obtaining the critical information about signal loss, a simulated dataset strongly bound by experimental parameters was created. Using experimental structural and spectral information and experimental noise levels data as an input for the simulation, a direct comparison of spatial (Fourier transform, Mean Filter, Weighted Mean Filter, Gauss Filter, Median Filter, spatial Wavelets and Deep Neural Networks) and spectral (Savitzky-Golay, Fourier transform, Principal Component Analysis, Minimum Noise Fraction and spectral Wavelets) denoising schemes was enabled. All of these techniques were compared on the simulated dataset, taking into account SNR gain, signal distortion and sensitivity to tuning parameters as comparison metrics. Later, the best techniques were applied to experimental data for validation. The results presented here clearly show the benefit of using hyperspectral denoising schemes such as PCA and MNF which outperform other methods.
Synergetic effects of plastic mulching and nitrogen application rates on grain yield, nitrogen uptake and translocation of maize planted in the Loess Plateau of China
Authors: Wang Xiukang , Wang Ning , Xing Yingying , BEN El CAID Mohamed 
Published: September 2018

AbstractNitrogen (N) fertilization potentially affects the amount of N uptake and N translocation (NT) within plants, but the synergetic effects of plastic mulching and N application rates on the grain yield (GY), N uptake and NT of maize have not been studied. A fertilization experiment with six N application rates (0, 80, 160, 240, 350 and 450 kg ha−1) with or without mulch was conducted in 2015 and 2016 in the Loess Plateau of China. There were significant interactions between mulch and the N fertilizer rate on the GY. Under mulch treatments, the highest GY was observed at 450 kg ha−1, which was 53.9%, 36.4%, 20.2%, 1.6% and 0.3% higher than those obtained with N application rates of 0, 80, 160, 240 and 350 kg ha−1, respectively, in 2015. The ranking of NT to grain N accumulation was leaves > sheaths and stems > ear axis > bracts. The NT efficiency (NTE) levels averaged over the different N fertilization rates under the no-mulch treatment were 5.6% and 12.9% higher than those under the plastic mulch treatment in 2015 and 2016, respectively. We conclude that an N fertilizer application rate of 240 kg ha−1 with mulch can achieve a relatively higher NTE, GY, WUE and NUE.
Dust cleansing of star-forming gas
Authors: Gustafsson Bengt 
Published: September 2018

Aims. The possibility that the chemical composition of the solar atmosphere has been affected by radiative dust cleansing of late and weak accretion flows by the proto-sun itself is explored.
Methods. Estimates, using semi-analytical methods and numerical simulations of the motion of dust grains in a collapsing non-magnetic and non-rotating gas sphere with a central light source are made in order to model possible dust-cleansing effects.
Results. Our calculations indicate that the amount of cleansed material may well be consistent with the abundance differences observed for the Sun when compared with solar-like stars and with the relations found between these differences and the condensation temperature of the element.
Conclusions. It seems quite possible that the proposed mechanism produced the significant abundance effects observed for the Sun, provided that late and relatively weak accretion did occur. The effects of cleansing may, however, be affected by outflows from the Sun, the existence and dynamics of magnetic fields and of the accretion disk, and the possible presence and location of the early Sun in a rich stellar cluster.