bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generating constrained random data with uniform distribution
Authors: CLAESSEN KOEN , DUREGÅRD JONAS , PAŁKA MICHAŁ H. 
Published: July 2015

AbstractWe present a technique for automatically deriving test data generators from a given executable predicate representing the set of values we are interested in generating. The distribution of these generators is uniform over values of a given size. To make the generation efficient, we rely on laziness of the predicate, allowing us to prune the space of values quickly. In contrast, implementing test data generators by hand is labour intensive and error prone. Moreover, handwritten generators often have an unpredictable distribution of values, risking that some values are arbitrarily underrepresented. We also present a variation of the technique that has better performance, but where the distribution is skewed in a limited, albeit predictable way. Experimental evaluation of the techniques shows that the automatically derived generators are much easier to define than handwritten ones, and their performance, while lower, is adequate for some realistic applications.
Quantitative o perando visualization of the energy band depth profile in solar cells
Authors: Chen Qi , Mao Lin , Li Yaowen , Kong Tao , Wu Na , Ma Changqi , Bai Sai , Jin Yizheng , Wu Dan , Lu Wei , Wang Bing , Chen Liwei 
Published: July 2015

AbstractThe energy band alignment in solar cell devices is critically important because it largely governs elementary photovoltaic processes, such as the generation, separation, transport, recombination and collection of charge carriers. Despite the expenditure of considerable effort, the measurement of energy band depth profiles across multiple layers has been extremely challenging, especially for operando devices. Here we present direct visualization of the surface potential depth profile over the cross-sections of operando organic photovoltaic devices using scanning Kelvin probe microscopy. The convolution effect due to finite tip size and cantilever beam crosstalk has previously prohibited quantitative interpretation of scanning Kelvin probe microscopy-measured surface potential depth profiles. We develop a bias voltage-compensation method to address this critical problem and obtain quantitatively accurate measurements of the open-circuit voltage, built-in potential and electrode potential difference.
Subcycle-resolved probe retardation in strong-field pumped dielectrics
Authors: Pati Aseem Prakash , Wahyutama Imam Setiawan , Pfeiffer Adrian Nikolaus 
Published: July 2015

AbstractThe response of a bulk dielectric to an intense few-cycle laser pulse is not solely determined by the pulse envelope, but also by ultrafast processes occuring during each optical cycle. Here, a method is presented for measuring the retardation of a probe pulse in a strong-field pumped, bulk dielectric with subcycle resolution in the pump–probe delay. Comparisons to model calculations show that the measurement is sensitive to the timing of the electronic Kerr response. When conduction band states are transiently populated at the crests of the laser field, the measurement is also sensitive to the interband dephasing time.
Distinguishing between plasmon-induced and photoexcited carriers in a device geometry
Authors: Zheng Bob Y. , Zhao Hangqi , Manjavacas Alejandro , McClain Michael , Nordlander Peter , Halas Naomi J. 
Published: July 2015

AbstractThe use of surface plasmons, charge density oscillations of conduction electrons of metallic nanostructures, to boost the efficiency of light-harvesting devices through increased light-matter interactions could drastically alter how sunlight is converted into electricity or fuels. These excitations can decay directly into energetic electron–hole pairs, useful for photocurrent generation or photocatalysis. However, the mechanisms behind plasmonic carrier generation remain poorly understood. Here we use nanowire-based hot-carrier devices on a wide-bandgap semiconductor to show that plasmonic carrier generation is proportional to internal field-intensity enhancement and occurs independently of bulk absorption. We also show that plasmon-induced hot electrons have higher energies than carriers generated by direct excitation and that reducing the barrier height allows for the collection of carriers from plasmons and direct photoexcitation. Our results provide a route to increasing the efficiency of plasmonic hot-carrier devices, which could lead to more efficient devices for converting sunlight into usable energy.
Tumour Necrosis Factor-α Gene Polymorphism Is Associated with Metastasis in Patients with Triple Negative Breast Cancer
Authors: Li Hui-Hui , Zhu Hui , Liu Li-Sheng , Huang Yong , Guo Jun , Li Jie , Sun Xin-Ping , Chang Chun-Xiao , Wang Zhe-Hai , Zhai Kan 
Published: July 2015

AbstractTumour necrosis factor-α (TNF-α) is critical in the regulation of inflammation and tumour progression. TNF-α-308G > A is associated with constitutively elevated TNF-α expression. The purpose of this study was to assess the association between TNF-α-308G > A and breast cancer (BC) risk by subtype and the connection between genotypes and clinical features of BC. A total of 768 patients and 565 controls were enrolled in this study and genotypes were detected using the TaqMan assay. No effect on susceptibility for any BC subtype was found for the TNF-α-308 polymorphism in our study or in the pooled meta-analysis. This polymorphism was shown to be associated with age at menarche in all BC and in progesterone receptor-negative BC. Interestingly, triple negative breast cancer (TNBC) patients with TNF-α-308A had an increased risk of distant tumour metastasis (OR = 3.80, 95% CI: 1.31–11.02, P = 0.009). Multi-regression analysis showed that TNF-α-308A was also a risk factor for distant tumour metastasis after adjustment for tumour size and lymph node metastasis status (OR= 6.26, 95% CI: 1.88–20.87, P = 0.003). These findings indicate that TNF-α might play a distinct role in the progression of TNBC, especially in distant tumour metastasis of TNBC.
Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data
Authors: Forster Michael , Szymczak Silke , Ellinghaus David , Hemmrich Georg , Rühlemann Malte , Kraemer Lars , Mucha Sören , Wienbrandt Lars , Stanulla Martin ,   UFO Sequencing Consortium within the I-BFM Study Group, Franke Andre 
Published: July 2015

AbstractSeveral pathogenic viruses such as hepatitis B and human immunodeficiency viruses may integrate into the host genome. These virus/host integrations are detectable using paired-end next generation sequencing. However, the low number of expected true virus integrations may be difficult to distinguish from the noise of many false positive candidates. Here, we propose a novel filtering approach that increases specificity without compromising sensitivity for virus/host chimera detection. Our detection pipeline termed Vy-PER (Virus integration detection bY Paired End Reads) outperforms existing similar tools in speed and accuracy. We analysed whole genome data from childhood acute lymphoblastic leukemia (ALL), which is characterised by genomic rearrangements and usually associated with radiation exposure. This analysis was motivated by the recently reported virus integrations at genomic rearrangement sites and association with chromosomal instability in liver cancer. However, as expected, our analysis of 20 tumour and matched germline genomes from ALL patients finds no significant evidence for integrations by known viruses. Nevertheless, our method eliminates 12,800 false positives per genome (80× coverage) and only our method detects singleton human-phiX174-chimeras caused by optical errors of the Illumina HiSeq platform. This high accuracy is useful for detecting low virus integration levels as well as non-integrated viruses.
Disperse fine equiaxed alpha alumina nanoparticles with narrow size distribution synthesised by selective corrosion and coagulation separation
Authors: Pu Sanxu , Li Lu , Ma Ji , Lu Fuliang , Li Jiangong 
Published: July 2015

AbstractDisperse fine equiaxed α-Al2O3 nanoparticles with narrow size distribution are important materials in nanotechnology and nanomaterials, but syntheses of disperse fine equiaxed α-Al2O3 nanoparticles usually result in fine γ-Al2O3 nanoparticles or large α-Al2O3 nanoparticles larger than 15 nm. α-Al2O3 has a higher surface energy than γ-Al2O3 and becomes thermodynamically not stable with respect to γ-Al2O3 at specific surface areas larger than 100 m2/g (at sizes smaller than 15 nm for spherical particles) at room temperature. So disperse fine equiaxed α-Al2O3 nanoparticles smaller than 15 nm with narrow size distribution are extremely difficult to synthesise. Here we show the successful synthesis of disperse fine equiaxed α-Al2O3 nanoparticles with average sizes below 10 nm and narrow size distribution by selective corrosion and refined fractionated coagulation separation. An almost fully dense nanocrystalline α-Al2O3 ceramic with a relative density of 99.5% and an average grain size of 60 nm can be sintered from disperse fine equiaxed α-Al2O3 nanoparticles with narrow size distribution.
How warm is too warm for the life cycle of actinopterygian fishes?
Authors: Motani Ryosuke , Wainwright Peter C. 
Published: July 2015

AbstractWe investigated the highest constant temperature at which actinopterygian fishes can complete their lifecycles, based on an oxygen supply model for cleavage-stage eggs. This stage is one of the most heat-sensitive periods during the lifecycle, likely reflecting the exhaustion of maternally supplied heat shock proteins without new production. The model suggests that average eggs would not develop normally under a constant temperature of about 36 °C or higher. This estimate matches published empirical values derived from laboratory and field observations. Spermatogenesis is more heat sensitive than embryogenesis in fishes, so the threshold may indeed be lower, at about 35 °C, unless actinopterygian fishes evolve heat tolerance during spermatogenesis as in birds. Our model also predicts an inverse relationship between egg size and temperature and empirical data support this prediction. Therefore, the average egg size and hence hatching size, is expected to shrink in a greenhouse world but a feeding function prohibits the survival of very small hatchlings, posing a limit to the shrinkage. It was once suggested that a marine animal community may be sustained under temperatures up to about 38 °C and this value is being used, for example, in paleotemperature reconstruction. A revision of the value is overdue. (199/200)
Optimization of Parameter Selection for Partial Least Squares Model Development
Authors: Zhao Na , Wu Zhi-sheng , Zhang Qiao , Shi Xin-yuan , Ma Qun , Qiao Yan-jiang 
Published: July 2015

AbstractIn multivariate calibration using a spectral dataset, it is difficult to optimize nonsystematic parameters in a quantitative model, i.e., spectral pretreatment, latent factors and variable selection. In this study, we describe a novel and systematic approach that uses a processing trajectory to select three parameters including different spectral pretreatments, variable importance in the projection (VIP) for variable selection and latent factors in the Partial Least-Square (PLS) model. The root mean square errors of calibration (RMSEC), the root mean square errors of prediction (RMSEP), the ratio of standard error of prediction to standard deviation (RPD) and the determination coefficient of calibration (Rcal2) and validation (Rpre2) were simultaneously assessed to optimize the best modeling path. We used three different near-infrared (NIR) datasets, which illustrated that there was more than one modeling path to ensure good modeling. The PLS model optimizes modeling parameters step-by-step, but the robust model described here demonstrates better efficiency than other published papers.
Programmed Hydrolysis in Designing Paclitaxel Prodrug for Nanocarrier Assembly
Authors: Fu Q. , Wang Y. , Ma Y. , Zhang D. , Fallon J. K. , Yang X. , Liu D. , He Z. , Liu F. 
Published: July 2015

AbstractNanocarriers delivering prodrugs are a way of improving in vivo effectiveness and efficiency. For therapeutic efficacy, the prodrug must hydrolyze to its parent drug after administration. Based on the fact that the hydrolysis is impeded by steric hindrance and improved by sufficient polarity, in this study, we proposed the PTX-S-S-VE, the conjugation of paclitaxel (PTX) to vitamin E (VE) through a disulfide bridge. This conjugate possessed the following advantages: first, it can be encapsulated in the VE/VE2-PEG2000/water nanoemulsions because of favorable hydrophobic interactions; second, the nanoemulsions had a long blood circulation time; finally, the concentrated glutathione in the tumor microenvironment could cleave the disulfide bond to weaken the steric hindrance and increase the polarity, promoting the hydrolysis to PTX and increasing the anticancer activity. It was demonstrated in vitro that the hydrolysis of PTX-S-S-VE was enhanced and the cytotoxicity was increased. In addition, PTX-S-S-VE had greater anticancer activity against the KB-3-1 cell line tumor xenograft and the tumor size was smaller after the 4th injection. The present result suggests a new way, use of reduction, to improve the in vivo anticancer activity of a prodrug for nanocarrier delivery by unshielding the ester bond and taking off the steric block.
Enhancement of Charge Transfer and Quenching of Photoluminescence of Capped CdS Quantum Dots
Authors: Mehata Mohan Singh 
Published: July 2015

AbstractQuantum dots (Q-dots) of cadmium sulfide (CdS) with three different capping ligands, 1-butanethiol (BT), 2-mercaptoethanol (ME) and benzyl mercaptan (BM) have been investigated. An external electric field of variable strength of 0.2–1.0 MV cm−1 was applied to the sample of capped CdS Q-dots doped in a poly(methyl methacrylate) (PMMA) films. Field-induced changes in optical absorption of capped CdS Q-dots were observed in terms of purely the second-derivative of the absorption spectrum (the Stark shift), indicating an enhancement in electric dipole moment following transition to the first exciton state. The enhancement depends on the shape and size of the Q-dots prepared using different capping ligands. Field induced-change in photoluminescence (PL) reveals similar changes, an enhancement in charge-transfer (CT) character in exciton state. PL of capped CdS Q-dots is significantly quenched in presence of external electric field. The strong field-induced quenching occurs as a result of the increased charge separation resulting exciton dissociation. Thus, understanding the CT character and field-induced PL quenching of CdS Q-dots is important for photovoltaic, LEDs and biological applications.
Atmospheric benzenoid emissions from plants rival those from fossil fuels
Authors: Misztal P.K. , Hewitt C.N. , Wildt J. , Blande J.D. , Eller A.S.D. , Fares S. , Gentner D.R. , Gilman J.B. , Graus M. , Greenberg J. , Guenther A.B. , Hansel A. , Harley P. , Huang M. , Jardine K. , Karl T. , Kaser L. , Keutsch F.N. , Kiendler-Scharr A. , Kleist E. , Lerner B.M. , Li T. , Mak J. , Nölscher A.C. , Schnitzhofer R. , Sinha V. , Thornton B. , Warneke C. , Wegener F. , Werner C. , Williams J. , Worton D.R. , Yassaa N. , Goldstein A.H. 
Published: July 2015

AbstractDespite the known biochemical production of a range of aromatic compounds by plants and the presence of benzenoids in floral scents, the emissions of only a few benzenoid compounds have been reported from the biosphere to the atmosphere. Here, using evidence from measurements at aircraft, ecosystem, tree, branch and leaf scales, with complementary isotopic labeling experiments, we show that vegetation (leaves, flowers and phytoplankton) emits a wide variety of benzenoid compounds to the atmosphere at substantial rates. Controlled environment experiments show that plants are able to alter their metabolism to produce and release many benzenoids under stress conditions. The functions of these compounds remain unclear but may be related to chemical communication and protection against stress. We estimate the total global secondary organic aerosol potential from biogenic benzenoids to be similar to that from anthropogenic benzenoids (~10 Tg y−1), pointing to the importance of these natural emissions in atmospheric physics and chemistry.
Genetic variation in the TNF/TRAF2/ASK1/p38 kinase signaling pathway as markers for postoperative pulmonary complications in lung cancer patients
Authors: Hildebrandt Michelle A. T. , Roth Jack A. , Vaporciyan Ara A. , Pu Xia , Ye Yuanqing , Correa Arlene M. , Kim Jae Y. , Swisher Stephen G. , Wu Xifeng 
Published: July 2015

AbstractPost-operative pulmonary complications are the most common morbidity associated with lung resection in non-small cell lung cancer (NSCLC) patients. The TNF/TRAF2/ASK1/p38 kinase pathway is activated by stress stimuli and inflammatory signals. We hypothesized that genetic polymorphisms within this pathway may contribute to risk of complications. In this case-only study, we genotyped 173 germline genetic variants in a discovery population of 264 NSCLC patients who underwent a lobectomy followed by genotyping of the top variants in a replication population of 264 patients. Complications data was obtained from a prospective database at MD Anderson. MAP2K4:rs12452497 was significantly associated with a decreased risk in both phases, resulting in a 40% reduction in the pooled population (95% CI:0.43–0.83, P = 0.0018). In total, seven variants were significant for risk in the pooled analysis. Gene-based analysis supported the involvement of TRAF2, MAP2K4 and MAP3K5 as mediating complications risk and a highly significant trend was identified between the number of risk genotypes and complications risk (P = 1.63 × 10−8). An inverse relationship was observed between association with clinical outcomes and complications for two variants. These results implicate the TNF/TRAF2/ASK1/p38 kinase pathway in modulating risk of pulmonary complications following lobectomy and may be useful biomarkers to identify patients at high risk.
GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks
Authors: Law Brian , Bader Gary D. 
Published: July 2015

AbstractThe increasing ease and accuracy of protein-protein interaction detection has resulted in the ability to map the interactomes of multiple species. We now have an opportunity to compare species to better understand how interactomes evolve. As DNA and protein sequence alignment algorithms were required for comparative genomics, network alignment algorithms are required for comparative interactomics. A number of network alignment methods have been developed for protein-protein interaction networks, where proteins are represented as vertices linked by edges if they interact. Recently, protein interactions have been mapped at the level of amino acid positions, which can be represented as an interface-interaction network (IIN), where vertices represent binding sites, such as protein domains and short sequence motifs. However, current algorithms are not designed to align these networks and generally fail to do so in practice. We present a greedy algorithm, GreedyPlus, for IIN alignment, combining data from diverse sources, including network, protein and binding site properties, to identify putative orthologous relationships between interfaces in available worm and yeast data. GreedyPlus is fast and simple, allowing for easy customization of behaviour, yet still capable of generating biologically meaningful network alignments.
An anti-inflammatory role for C/EBPδ in human brain pericytes
Authors: Rustenhoven Justin , Scotter Emma L. , Jansson Deidre , Kho Dan T. , Oldfield Robyn L. , Bergin Peter S. , Mee Edward W. , Faull Richard L. M. , Curtis Maurice A. , Graham Scott E. , Park Thomas I-H. , Dragunow Mike 
Published: July 2015

AbstractNeuroinflammation contributes to the pathogenesis of several neurological disorders and pericytes are implicated in brain inflammatory processes. Cellular inflammatory responses are orchestrated by transcription factors but information on transcriptional control in pericytes is lacking. Because the transcription factor CCAAT/enhancer binding protein delta (C/EBPδ) is induced in a number of inflammatory brain disorders, we sought to investigate its role in regulating pericyte immune responses. Our results reveal that C/EBPδ is induced in a concentration- and time-dependent fashion in human brain pericytes by interleukin-1β (IL-1β). To investigate the function of the induced C/EBPδ in pericytes we used siRNA to knockdown IL-1β-induced C/EBPδ expression. C/EBPδ knockdown enhanced IL-1β-induced production of intracellular adhesion molecule-1 (ICAM-1), interleukin-8, monocyte chemoattractant protein-1 (MCP-1) and IL-1β, whilst attenuating cyclooxygenase-2 and superoxide dismutase-2 gene expression. Altered ICAM-1 and MCP-1 protein expression were confirmed by cytometric bead array and immunocytochemistry. Our results show that knock-down of C/EBPδ expression in pericytes following immune stimulation increased chemokine and adhesion molecule expression, thus modifying the human brain pericyte inflammatory response. The induction of C/EBPδ following immune stimulation may act to limit infiltration of peripheral immune cells, thereby preventing further inflammatory responses in the brain.
Spatial distribution and ecological niches of non-breeding planktivorous petrels
Authors: Navarro Joan , Cardador Laura , Brown Ruth , Phillips Richard A. 
Published: July 2015

AbstractAccording to niche theory, mechanisms exist that allow co-existence of organisms that would otherwise compete for the same prey and other resources. How seabirds cope with potential competition during the non-breeding period is poorly documented, particularly for small species. Here we investigate for the first time the potential role of spatial, environmental (habitat) and trophic (isotopic) segregation as niche-partitioning mechanisms during the non-breeding season for four species of highly abundant, zooplanktivorous seabird that breed sympatrically in the Southern Ocean. Spatial segregation was found to be the main partitioning mechanism; even for the two sibling species of diving petrel, which spent the non-breeding period in overlapping areas, there was evidence from distribution and stable isotope ratios for differences in habitat use and diving depth.