bluuebunny/crossref_metadata_2025_split huggingface dataset:
A spatially comprehensive, hydrometeorological data set for Mexico, the U.S., and Southern Canada 1950–2013
Authors: Livneh Ben , Bohn Theodore J. , Pierce David W. , Munoz-Arriola Francisco , Nijssen Bart , Vose Russell , Cayan Daniel R. , Brekke Levi 
Published: August 2015

AbstractA data set of observed daily precipitation, maximum and minimum temperature, gridded to a 1/16° (~6 km) resolution, is described that spans the entire country of Mexico, the conterminous U.S. (CONUS), and regions of Canada south of 53° N for the period 1950–2013. The dataset improves previous products in spatial extent, orographic precipitation adjustment over Mexico and parts of Canada, and reduction of transboundary discontinuities. The impacts of adjusting gridded precipitation for orographic effects are quantified by scaling precipitation to an elevation-aware 1981–2010 precipitation climatology in Mexico and Canada. Differences are evaluated in terms of total precipitation as well as by hydrologic quantities simulated with a land surface model. Overall, orographic correction impacts total precipitation by up to 50% in mountainous regions outside CONUS. Hydrologic fluxes show sensitivities of similar magnitude, with discharge more sensitive than evapotranspiration and soil moisture. Because of the consistent gridding methodology, the current product reduces transboundary discontinuities as compared with a commonly used reanalysis product, making it suitable for estimating large-scale hydrometeorologic phenomena.
A scenario for magnonic spin-wave traps
Authors: Busse Frederik , Mansurova Maria , Lenk Benjamin , von der Ehe Marvin , Münzenberg Markus 
Published: August 2015

AbstractSpatially resolved measurements of the magnetization dynamics on a thin CoFeB film induced by an intense laser pump-pulse reveal that the frequencies of resulting spin-wave modes depend strongly on the distance to the pump center. This can be attributed to a laser generated temperature profile. We determine a shift of 0.5 GHz in the spin-wave frequency due to the spatial thermal profile induced by the femtosecond pump pulse that persists for up to one nanosecond. Similar experiments are presented for a magnonic crystal composed of a CoFeB-film based antidot lattice with a Damon Eshbach mode at the Brillouin zone boundary and its consequences are discussed.
Junction formation and current transport mechanisms in hybrid n-Si/PEDOT:PSS solar cells
Authors: Jäckle Sara , Mattiza Matthias , Liebhaber Martin , Brönstrup Gerald , Rommel Mathias , Lips Klaus , Christiansen Silke 
Published: August 2015

AbstractWe investigated hybrid inorganic-organic solar cells combining monocrystalline n-type silicon (n-Si) and a highly conductive polymer poly(3,4-ethylenedioxythiophene)-poly(styrene sulfonate) (PEDOT:PSS). The build-in potential, photo- and dark saturation current at this hybrid interface are monitored for varying n-Si doping concentrations. We corroborate that a high build-in potential forms at the hybrid junction leading to strong inversion of the n-Si surface. By extracting work function and valence band edge of the polymer from ultraviolet photoelectron spectroscopy, a band diagram of the hybrid n-Si/PEDOT:PSS heterojunction is presented. The current-voltage characteristics were analyzed using Schottky and abrupt pn-junction models. The magnitude as well as the dependence of dark saturation current on n-Si doping concentration proves that the transport is governed by diffusion of minority charge carriers in the n-Si and not by thermionic emission of majorities over a Schottky barrier. This leads to a comprehensive explanation of the high observed open-circuit voltages of up to 634 mV connected to high conversion efficiency of almost 14%, even for simple planar device structures without antireflection coating or optimized contacts. The presented work clearly shows that PEDOT:PSS forms a hybrid heterojunction with n-Si behaving similar to a conventional pn-junction and not, like commonly assumed, a Schottky junction.
Experimental realization of spatially separated entanglement with continuous variables using laser pulse trains
Authors: Zhang Yun , Okubo Ryuhi , Hirano Mayumi , Eto Yujiro , Hirano Takuya 
Published: August 2015

AbstractSpatially separated entanglement is demonstrated by interfering two high-repetition squeezed pulse trains. The entanglement correlation of the quadrature amplitudes between individual pulses is interrogated. It is characterized in terms of the sufficient inseparability criterion with an optimum result of "Equation missing" in the frequency domain and "Equation missing" in the time domain. The quantum correlation is also observed when the two measurement stations are separated by a physical distance of 4.5 m, which is sufficiently large to demonstrate the space-like separation, after accounting for the measurement time.
Transcriptomic Analysis of the Regulation of Rhizome Formation in Temperate and Tropical Lotus (Nelumbo nucifera)
Authors: Yang Mei , Zhu Lingping , Pan Cheng , Xu Liming , Liu Yanling , Ke Weidong , Yang Pingfang 
Published: August 2015

AbstractRhizome is the storage organ of lotus derived from modified stems. The development of rhizome is a complex process and depends on the balanced expression of the genes that is controlled by environmental and endogenous factors. However, little is known about the mechanism that regulates rhizome girth enlargement. In this study, using RNA-seq, transcriptomic analyses were performed at three rhizome developmental stages—the stolon, middle swelling and later swelling stage —in the cultivars ‘ZO’ (temperate lotus with enlarged rhizome) and ‘RL’ (tropical lotus with stolon). About 348 million high-quality reads were generated and 88.5% of the data were mapped to the reference genome. Of 26783 genes identified, 24069 genes were previously predicted in the reference and 2714 genes were novel transcripts. Moreover, 8821 genes were differentially expressed between the cultivars at the three stages. Functional analysis identified that these genes were significantly enriched in pathways carbohydrate metabolism and plant hormone signal transduction. Twenty-two genes involved in photoperiod pathway, starch metabolism and hormone signal transduction were candidate genes inducing rhizome girth enlargement. Comparative transcriptomic analysis detected several differentially expressed genes and potential candidate genes required for rhizome girth enlargement, which lay a foundation for future studies on molecular mechanisms underlying rhizome formation.
Thermal-induced force release in oxyhemoglobin
Authors: Gevorkian S. G. , Allahverdyan A. E. , Gevorgyan D. S. , Hu Chin-Kun 
Published: August 2015

AbstractOxygen is released to living tissues via conformational changes of hemoglobin from R-state (oxyhemoglobin) to T-state (desoxyhemoglobin). The detailed mechanism of this process is not yet fully understood. We have carried out micromechanical experiments on oxyhemoglobin crystals to determine the behavior of the Young’s modulus and the internal friction for temperatures between 20 °C and 70 °C. We have found that around 49 °C oxyhemoglobin crystal samples undergo a sudden and strong increase of their Young’s modulus, accompanied by a sudden decrease of the internal friction. This sudden mechanical change (and the ensuing force release) takes place in a partially unfolded state and precedes the full denaturation transition at higher temperatures. After this transformation, the hemoglobin crystals have the same mechanical properties as their initial state at room temperatures. We conjecture that it can be relevant for explaining the oxygen-releasing function of native oxyhemoglobin when the temperature is increased, e.g. due to active sport. The effect is specific for the quaternary structure of hemoglobin and is absent for myoglobin with only one peptide sequence.
Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling
Authors: Kauko Otto , Laajala Teemu Daniel , Jumppanen Mikael , Hintsanen Petteri , Suni Veronika , Haapaniemi Pekka , Corthals Garry , Aittokallio Tero , Westermarck Jukka , Imanishi Susumu Y. 
Published: August 2015

AbstractHyperactivated RAS drives progression of many human malignancies. However, oncogenic activity of RAS is dependent on simultaneous inactivation of protein phosphatase 2A (PP2A) activity. Although PP2A is known to regulate some of the RAS effector pathways, it has not been systematically assessed how these proteins functionally interact. Here we have analyzed phosphoproteomes regulated by either RAS or PP2A, by phosphopeptide enrichment followed by mass-spectrometry-based label-free quantification. To allow data normalization in situations where depletion of RAS or PP2A inhibitor CIP2A causes a large uni-directional change in the phosphopeptide abundance, we developed a novel normalization strategy, named pairwise normalization. This normalization is based on adjusting phosphopeptide abundances measured before and after the enrichment. The superior performance of the pairwise normalization was verified by various independent methods. Additionally, we demonstrate how the selected normalization method influences the downstream analyses and interpretation of pathway activities. Consequently, bioinformatics analysis of RAS and CIP2A regulated phosphoproteomes revealed a significant overlap in their functional pathways. This is most likely biologically meaningful as we observed a synergistic survival effect between CIP2A and RAS expression as well as KRAS activating mutations in TCGA pan-cancer data set and synergistic relationship between CIP2A and KRAS depletion in colony growth assays.
Development of PD-1/PD-L1 Pathway in Tumor Immune Microenvironment and Treatment for Non-Small Cell Lung Cancer
Authors: He Jiabei , Hu Ying , Hu Mingming , Li Baolan 
Published: August 2015

AbstractLung cancer is currently the leading cause of cancer-related death in worldwide, non-small cell lung cancer (NSCLC) accounts for about 85% of all lung cancers. Surgery, platinum-based chemotherapy, molecular targeted agents and radiotherapy are the main treatment of NSCLC. With the strategies of treatment constantly improving, the prognosis of NSCLC patients is not as good as before, new sort of treatments are needed to be exploited. Programmed death 1 (PD-1) and its ligand PD-L1 play a key role in tumor immune escape and the formation of tumor microenvironment, closely related with tumor generation and development. Blockading the PD-1/PD-L1 pathway could reverse the tumor microenvironment and enhance the endogenous antitumor immune responses. Utilizing the PD-1 and/or PD-L1 inhibitors has shown benefits in clinical trials of NSCLC. In this review, we discuss the basic principle of PD-1/PD-L1 pathway and its role in the tumorigenesis and development of NSCLC. The clinical development of PD-1/PD-L1 pathway inhibitors and the main problems in the present studies and the research direction in the future will also be discussed.
Photodynamic activation as a molecular switch to promote osteoblast cell differentiation via AP-1 activation
Authors: Kushibiki Toshihiro , Tu Yupeng , Abu-Yousif Adnan O. , Hasan Tayyaba 
Published: August 2015

AbstractIn photodynamic therapy (PDT), cells are impregnated with a photosensitizing agent that is activated by light irradiation, thereby photochemically generating reactive oxygen species (ROS). The amounts of ROS produced depends on the PDT dose and the nature of the photosensitizer. Although high levels of ROS are cytotoxic, at physiological levels they play a key role as second messengers in cellular signaling pathways, pluripotency and differentiation of stem cells. To investigate further the use of photochemically triggered manipulation of such pathways, we exposed mouse osteoblast precursor cells and rat primary mesenchymal stromal cells to low-dose PDT. Our results demonstrate that low-dose PDT can promote osteoblast differentiation via the activation of activator protein-1 (AP-1). Although PDT has been used primarily as an anti-cancer therapy, the use of light as a photochemical “molecular switch” to promote differentiation should expand the utility of this method in basic research and clinical applications.
Seeing Central African forests through their largest trees
Authors: Bastin J.-F. , Barbier N. , Réjou-Méchain M. , Fayolle A. , Gourlet-Fleury S. , Maniatis D. , de Haulleville T. , Baya F. , Beeckman H. , Beina D. , Couteron P. , Chuyong G. , Dauby G. , Doucet J.-L. , Droissart V. , Dufrêne M. , Ewango C. , Gillet J.F. , Gonmadje C.H. , Hart T. , Kavali T. , Kenfack D. , Libalah M. , Malhi Y. , Makana J.-R. , Pélissier R. , Ploton P. , Serckx A. , Sonké B. , Stevart T. , Thomas D.W. , De Cannière C. , Bogaert J. 
Published: August 2015

AbstractLarge tropical trees and a few dominant species were recently identified as the main structuring elements of tropical forests. However, such result did not translate yet into quantitative approaches which are essential to understand, predict and monitor forest functions and composition over large, often poorly accessible territories. Here we show that the above-ground biomass (AGB) of the whole forest can be predicted from a few large trees and that the relationship is proved strikingly stable in 175 1-ha plots investigated across 8 sites spanning Central Africa. We designed a generic model predicting AGB with an error of 14% when based on only 5% of the stems, which points to universality in forest structural properties. For the first time in Africa, we identified some dominant species that disproportionally contribute to forest AGB with 1.5% of recorded species accounting for over 50% of the stock of AGB. Consequently, focusing on large trees and dominant species provides precise information on the whole forest stand. This offers new perspectives for understanding the functioning of tropical forests and opens new doors for the development of innovative monitoring strategies.
Facing the environment: onset and development of UV markings in young fish
Authors: Gagliano Monica , Depczynski Martial , Siebeck Ulrike E. 
Published: August 2015

AbstractMost colour patterns in animals represent an elegant compromise between conspicuousness to ensure effective communication with preferred receivers and camouflage to avoid attracting the attention of unwanted predators. Many species, including several coral reef fishes, overcome this conflict by using ultraviolet (UV) colouration and signalling, as these colours are visible only over short distances and are often invisible to their predators. Despite a great interest in their behavioural significance and ecological influence on survival, little is known about when these colours first develop on the bodies of free-living animals. Here we show for the first time that the UV facial patterns of a coral reef fish do not develop in captivity but only when juveniles experience the socio-behavioural conditions of their natural environment. Using field and laboratory experiments, we determined that the onset and early development of these UV facial markings did not occur at metamorphosis. Instead, juveniles developed the UV markings during their first two weeks on the reef. Exposure to different reef environments revealed significant plasticity in the development of these markings. The direct or indirect (through intraspecific interactions) exposure to predators is a likely candidate trigger for the plastic development of these UV markings in the wild.
In vivo micro-scale tomography of ciliary behavior in the mammalian oviduct
Authors: Wang Shang , Burton Jason C. , Behringer Richard R. , Larina Irina V. 
Published: August 2015

AbstractMotile cilia in the mammalian oviduct play a key role in reproduction, such as transporting fertilized oocytes to the uterus for implantation. Due to their small size (~5–10 μm in length and ~300 nm in diameter), live visualization of cilia and their activity in the lumen of the oviduct through tissue layers represents a major challenge not yet overcome. Here, we report a functional low-coherence optical imaging technique that allows in vivo depth-resolved mapping of the cilia location and cilia beat frequency (CBF) in the intact mouse oviduct with micro-scale spatial resolution. We validate our approach with widely-used microscopic imaging methods, present the first in vivo mapping of the oviduct CBF in its native context and demonstrate the ability of this approach to differentiate CBF in different locations of the oviduct at different post-conception stages. This technique opens a range of opportunities for live studies in reproductive medicine as well as other areas focused on cilia activity and related ciliopathies.
Functional Analysis and Characterization of Differential Coexpression Networks
Authors: Hsu Chia-Lang , Juan Hsueh-Fen , Huang Hsuan-Cheng 
Published: August 2015

AbstractDifferential coexpression analysis is emerging as a complement to conventional differential gene expression analysis. The identified differential coexpression links can be assembled into a differential coexpression network (DCEN) in response to environmental stresses or genetic changes. Differential coexpression analyses have been successfully used to identify condition-specific modules; however, the structural properties and biological significance of general DCENs have not been well investigated. Here, we analyzed two independent Saccharomyces cerevisiae DCENs constructed from large-scale time-course gene expression profiles in response to different situations. Topological analyses show that DCENs are tree-like networks possessing scale-free characteristics, but not small-world. Functional analyses indicate that differentially coexpressed gene pairs in DCEN tend to link different biological processes, achieving complementary or synergistic effects. Furthermore, the gene pairs lacking common transcription factors are sensitive to perturbation and hence lead to differential coexpression. Based on these observations, we integrated transcriptional regulatory information into DCEN and identified transcription factors that might cause differential coexpression by gain or loss of activation in response to different situations. Collectively, our results not only uncover the unique structural characteristics of DCEN but also provide new insights into interpretation of DCEN to reveal its biological significance and infer the underlying gene regulatory dynamics.
BDNF promoter methylation and genetic variation in late-life depression
Authors: Januar V , Ancelin M-L , Ritchie K , Saffery R , Ryan J 
Published: August 2015

AbstractThe regulation of the brain-derived neurotrophic factor (BDNF) is important for depression pathophysiology and epigenetic regulation of the BDNF gene may be involved. This study investigated whether BDNF methylation is a marker of depression. One thousand and twenty-four participants were recruited as part of a longitudinal study of psychiatric disorders in general population elderly (age⩾65). Clinical levels of depression were assessed using the Mini International Neuropsychiatric Interview for the diagnosis of major depressive disorder according to the Diagnostic and Statistical Manual of Mental Disorder IV criteria, and the Centre for Epidemiologic Studies Depression Scale (CES-D) for assessment of moderate to severe depressive symptoms. Buccal DNA methylation at the two most widely studied BDNF promoters, I and IV, was investigated using the Sequenom MassARRAY platform that allows high-throughput investigation of methylation at individual CpG sites within defined genomic regions. In multivariate linear regression analyses adjusted for a range of participant characteristics including antidepressant use, depression at baseline, as well as chronic late-life depression over the 12-year follow-up, were associated with overall higher BDNF methylation levels, with two sites showing significant associations (promoter I, Δ mean=0.4%, P=0.0002; promoter IV, Δ mean=5.4%, P=0.021). Three single-nucleotide polymorphisms (rs6265, rs7103411 and rs908867) were also found to modify the association between depression and promoter I methylation. As one of the largest epigenetic studies of depression, and the first investigating BDNF methylation in buccal tissue, our findings highlight the potential for buccal BDNF methylation to be a biomarker of depression.
The use of statins for the treatment of depression in patients with acute coronary syndrome
Authors: Kim S W , Bae K Y , Kim J M , Shin I S , Hong Y J , Ahn Y , Jeong M H , Berk M , Yoon J S 
Published: August 2015

AbstractThis study aimed to investigate the effect of statins for the treatment of depression in individuals with acute coronary syndrome (ACS). We used 1-year follow-up data of a 24-week double-blind, placebo-controlled trial of escitalopram and a naturalistic prospective observational cohort study. Of 446 participants with comorbid depressive disorders and ACS at baseline, 300 participated in a randomised escitalopram trial and the remaining 146 participated in a naturalistic observational study. The participants in the two studies were approached for a 1-year follow-up investigation. Treatment response rates, defined as a ⩾50% reduction in the Hamilton Depression Rating Scale (HAM-D) and Beck Depression Inventory (BDI) scores, were used as the outcome variables. In the escitalopram trial, both HAM-D and BDI response rates were highest in patients taking escitalopram and statins together and lowest in patients receiving neither medication. Logistic regression analyses revealed that statin use was significantly associated with higher response rates on both the HAM-D and BDI at 1 year, whereas no such associations were found for escitalopram. In the naturalistic observational study, the response rates at 1 year did not differ significantly by statin use. Instead, the HAM-D response rate was significantly higher in patients taking lipophilic statins than in those who did not. In conclusion, statins may be effective for the treatment of depression independent of medical status and escitalopram use, and they may potentiate the antidepressant action of serotonergic antidepressants in patients with ACS.
Akt activation increases cellular cholesterol by promoting the proteasomal degradation of Niemann–Pick C1
Authors: Du Ximing , Zhang Yuxi , Jo Sae Rom , Liu Xiaoyun , Qi Yanfei , Osborne Brenna , Byrne Frances L. , Smith Greg C. , Turner Nigel , Hoehn Kyle L. , Brown Andrew J. , Yang Hongyuan 
Published: August 2015

Null mutations of the Niemann–Pick type C1 (NPC1) gene cause NPC disease, a lysosomal storage disorder characterized by cholesterol accumulation in late endosomes (LE) and lysosomes (Ly). Nascent or mutated NPC1 is degraded through the ubiquitin–proteasome pathway, but how NPC1 degradation is regulated remains currently unknown. In the present study, we demonstrated a link between NPC1 degradation and the Akt (protein kinase B)/mTOR [mammalian (or mechanistic) target of rapamycin] signalling pathway in cervical cancer cell lines. We provided evidence that activated Akt/mTOR pathway increased NPC1 degradation by ∼50% in C33A cells when compared with SiHa or HeLa cells. NPC1 degradation in C33A cells was reversed when Akt/mTOR activation was blocked by specific inhibitors or when mTORC1 (mTOR complex 1) was disrupted by regulatory associated protein of mTOR (Raptor) knockdown. Importantly, inhibition of the Akt/mTOR pathway led to decreased NPC1 ubiquitination in C33A cells, pointing to a role of Akt/mTOR in the proteasomal degradation of NPC1. Moreover, we found that NPC1 depletion in several cancer cell lines inhibited cell proliferation and migration. Our results uncover Akt as a key regulator of NPC1 degradation and link NPC1 to cancer cell proliferation and migration.