bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pervasive role for biomass burning in tropical high ozone/low water structures
Authors: Anderson Daniel C. , Nicely Julie M. , Salawitch Ross J. , Canty Timothy P. , Dickerson Russell R. , Hanisco Thomas F. , Wolfe Glenn M. , Apel Eric C. , Atlas Elliot , Bannan Thomas , Bauguitte Stephane , Blake Nicola J. , Bresch James F. , Campos Teresa L. , Carpenter Lucy J. , Cohen Mark D. , Evans Mathew , Fernandez Rafael P. , Kahn Brian H. , Kinnison Douglas E. , Hall Samuel R. , Harris Neil R.P. , Hornbrook Rebecca S. , Lamarque Jean-Francois , Le Breton Michael , Lee James D. , Percival Carl , Pfister Leonhard , Pierce R. Bradley , Riemer Daniel D. , Saiz-Lopez Alfonso , Stunder Barbara J.B. , Thompson Anne M. , Ullmann Kirk , Vaughan Adam , Weinheimer Andrew J. 
Published: January 2016

AbstractAir parcels with mixing ratios of high O3 and low H2O (HOLW) are common features in the tropical western Pacific (TWP) mid-troposphere (300–700 hPa). Here, using data collected during aircraft sampling of the TWP in winter 2014, we find strong, positive correlations of O3 with multiple biomass burning tracers in these HOLW structures. Ozone levels in these structures are about a factor of three larger than background. Models, satellite data and aircraft observations are used to show fires in tropical Africa and Southeast Asia are the dominant source of high O3 and that low H2O results from large-scale descent within the tropical troposphere. Previous explanations that attribute HOLW structures to transport from the stratosphere or mid-latitude troposphere are inconsistent with our observations. This study suggest a larger role for biomass burning in the radiative forcing of climate in the remote TWP than is commonly appreciated.
Chromatin topology is coupled to Polycomb group protein subnuclear organization
Authors: Wani Ajazul H. , Boettiger Alistair N. , Schorderet Patrick , Ergun Ayla , Münger Christine , Sadreyev Ruslan I. , Zhuang Xiaowei , Kingston Robert E. , Francis Nicole J. 
Published: January 2016

AbstractThe genomes of metazoa are organized at multiple scales. Many proteins that regulate genome architecture, including Polycomb group (PcG) proteins, form subnuclear structures. Deciphering mechanistic links between protein organization and chromatin architecture requires precise description and mechanistic perturbations of both. Using super-resolution microscopy, here we show that PcG proteins are organized into hundreds of nanoscale protein clusters. We manipulated PcG clusters by disrupting the polymerization activity of the sterile alpha motif (SAM) of the PcG protein Polyhomeotic (Ph) or by increasing Ph levels. Ph with mutant SAM disrupts clustering of endogenous PcG complexes and chromatin interactions while elevating Ph level increases cluster number and chromatin interactions. These effects can be captured by molecular simulations based on a previously described chromatin polymer model. Both perturbations also alter gene expression. Organization of PcG proteins into small, abundant clusters on chromatin through Ph SAM polymerization activity may shape genome architecture through chromatin interactions.
Superlattice-based thin-film thermoelectric modules with high cooling fluxes
Authors: Bulman Gary , Barletta Phil , Lewis Jay , Baldasaro Nicholas , Manno Michael , Bar-Cohen Avram , Yang Bao 
Published: January 2016

AbstractIn present-day high-performance electronic components, the generated heat loads result in unacceptably high junction temperatures and reduced component lifetimes. Thermoelectric modules can, in principle, enhance heat removal and reduce the temperatures of such electronic devices. However, state-of-the-art bulk thermoelectric modules have a maximum cooling flux qmax of only about 10 W cm−2, while state-of-the art commercial thin-film modules have a qmax <100 W cm−2. Such flux values are insufficient for thermal management of modern high-power devices. Here we show that cooling fluxes of 258 W cm−2 can be achieved in thin-film Bi2Te3-based superlattice thermoelectric modules. These devices utilize a p-type Sb2Te3/Bi2Te3 superlattice and n-type δ-doped Bi2Te3−xSex, both of which are grown heteroepitaxially using metalorganic chemical vapour deposition. We anticipate that the demonstration of these high-cooling-flux modules will have far-reaching impacts in diverse applications, such as advanced computer processors, radio-frequency power devices, quantum cascade lasers and DNA micro-arrays.
Widely tunable two-colour seeded free-electron laser source for resonant-pump resonant-probe magnetic scattering
Authors: Ferrari Eugenio , Spezzani Carlo , Fortuna Franck , Delaunay Renaud , Vidal Franck , Nikolov Ivaylo , Cinquegrana Paolo , Diviacco Bruno , Gauthier David , Penco Giuseppe , Ribič Primož Rebernik , Roussel Eleonore , Trovò Marco , Moussy Jean-Baptiste , Pincelli Tommaso , Lounis Lounès , Manfredda Michele , Pedersoli Emanuele , Capotondi Flavio , Svetina Cristian , Mahne Nicola , Zangrando Marco , Raimondi Lorenzo , Demidovich Alexander , Giannessi Luca , De Ninno Giovanni , Danailov Miltcho Boyanov , Allaria Enrico , Sacchi Maurizio 
Published: January 2016

AbstractThe advent of free-electron laser (FEL) sources delivering two synchronized pulses of different wavelengths (or colours) has made available a whole range of novel pump–probe experiments. This communication describes a major step forward using a new configuration of the FERMI FEL-seeded source to deliver two pulses with different wavelengths, each tunable independently over a broad spectral range with adjustable time delay. The FEL scheme makes use of two seed laser beams of different wavelengths and of a split radiator section to generate two extreme ultraviolet pulses from distinct portions of the same electron bunch. The tunability range of this new two-colour source meets the requirements of double-resonant FEL pump/FEL probe time-resolved studies. We demonstrate its performance in a proof-of-principle magnetic scattering experiment in Fe–Ni compounds, by tuning the FEL wavelengths to the Fe and Ni 3p resonances.
Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68
Authors: Feracci Mikael , Foot Jaelle N. , Grellscheid Sushma N. , Danilenko Marina , Stehle Ralf , Gonchar Oksana , Kang Hyun-Seo , Dalgliesh Caroline , Meyer N. Helge , Liu Yilei , Lahat Albert , Sattler Michael , Eperon Ian C. , Elliott David J. , Dominguez Cyril 
Published: January 2016

AbstractSam68 and T-STAR are members of the STAR family of proteins that directly link signal transduction with post-transcriptional gene regulation. Sam68 controls the alternative splicing of many oncogenic proteins. T-STAR is a tissue-specific paralogue that regulates the alternative splicing of neuronal pre-mRNAs. STAR proteins differ from most splicing factors, in that they contain a single RNA-binding domain. Their specificity of RNA recognition is thought to arise from their property to homodimerize, but how dimerization influences their function remains unknown. Here, we establish at atomic resolution how T-STAR and Sam68 bind to RNA, revealing an unexpected mode of dimerization different from other members of the STAR family. We further demonstrate that this unique dimerization interface is crucial for their biological activity in splicing regulation, and suggest that the increased RNA affinity through dimer formation is a crucial parameter enabling these proteins to select their functional targets within the transcriptome.
Enhanced electronic properties in mesoporous TiO2 via lithium doping for high-efficiency perovskite solar cells
Authors: Giordano Fabrizio , Abate Antonio , Correa Baena Juan Pablo , Saliba Michael , Matsui Taisuke , Im Sang Hyuk , Zakeeruddin Shaik M. , Nazeeruddin Mohammad Khaja , Hagfeldt Anders , Graetzel Michael 
Published: January 2016

AbstractPerovskite solar cells are one of the most promising photovoltaic technologies with their extraordinary progress in efficiency and the simple processes required to produce them. However, the frequent presence of a pronounced hysteresis in the current voltage characteristic of these devices arises concerns on the intrinsic stability of organo-metal halides, challenging the reliability of technology itself. Here, we show that n-doping of mesoporous TiO2 is accomplished by facile post treatment of the films with lithium salts. We demonstrate that the Li-doped TiO2 electrodes exhibit superior electronic properties, by reducing electronic trap states enabling faster electron transport. Perovskite solar cells prepared using the Li-doped films as scaffold to host the CH3NH3PbI3 light harvester produce substantially higher performances compared with undoped electrodes, improving the power conversion efficiency from 17 to over 19% with negligible hysteretic behaviour (lower than 0.3%).
Precision medicine in heritable cancer: when somatic tumour testing and germline mutations meet
Authors: Ngeow Joanne , Eng Charis 
Published: January 2016

AbstractCancer is among the leading causes of death and disfigurement worldwide with an estimated global incidence of 14 million and ~8.2 million cancer-related deaths per annum. An estimated 5–10% of all cancers are hereditary, meaning a single gene mutation contributed to development of the cancer. In other words, inherited cancer has a worldwide incidence of ~1.4 million new cases per annum and a global prevalence of 300 million, and are often poorly recognised. The increase in genetic sequencing capability combined with the decrease in the cost of testing has altered both regulatory policy and clinical oncology practice Well-known examples of clinically important cancer susceptibility syndromes such as those caused by genetic mutations in highly penetrant genes such as BRCA1/2 hereditary breast-ovarian cancer syndrome genes have provided the framework for the practice of clinical cancer genetics. There is no question that these tests have provided clinical benefit to the patient and her/his family. However, with the expanding role of next generation sequencing in tumour profiling as well as in germline testing, clinicians are now faced with significant new challenges and potentially unexpected opportunities. Issues such as determining how best to deal with gene variants of uncertain clinical significance and the issue of incidental findings of hereditary cancer risk may be encountered during tumour genomic testing will require a concerted effort and dialogue on the part of the broad genomic community.
Constellation: a tool for rapid, automated phenotype assignment of a highly polymorphic pharmacogene, CYP2D6, from whole-genome sequences
Authors: Twist Greyson P , Gaedigk Andrea , Miller Neil A , Farrow Emily G , Willig Laurel K , Dinwiddie Darrell L , Petrikin Josh E , Soden Sarah E , Herd Suzanne , Gibson Margaret , Cakici Julie A , Riffel Amanda K , Leeder J Steven , Dinakarpandian Deendayal , Kingsmore Stephen F 
Published: January 2016

AbstractAn important component of precision medicine—the use of whole-genome sequencing (WGS) to guide lifelong healthcare—is electronic decision support to inform drug choice and dosing. To achieve this, automated identification of genetic variation in genes involved in drug absorption, distribution, metabolism, excretion and response (ADMER) is required. CYP2D6 is a major enzyme for drug bioactivation and elimination. CYP2D6 activity is predominantly governed by genetic variation; however, it is technically arduous to haplotype. Not only is the nucleotide sequence of CYP2D6 highly polymorphic, but the locus also features diverse structural variations, including gene deletion, duplication, multiplication events and rearrangements with the nonfunctional, neighbouring CYP2D7 and CYP2D8 genes. We developed Constellation, a probabilistic scoring system, enabling automated ascertainment of CYP2D6 activity scores from 2×100 paired-end WGS. The consensus reference method included TaqMan genotyping assays, quantitative copy-number variation determination and Sanger sequencing. When compared with the consensus reference Constellation had an analytic sensitivity of 97% (59 of 61 diplotypes) and analytic specificity of 95% (116 of 122 haplotypes). All extreme phenotypes, i.e., poor and ultrarapid metabolisers were accurately identified by Constellation. Constellation is anticipated to be extensible to functional variation in all ADMER genes, and to be performed at marginal incremental financial and computational costs in the setting of diagnostic WGS.
Hippocampal subfield atrophy in relation to cerebrospinal fluid biomarkers and cognition in early Parkinson’s disease: a cross-sectional study
Authors: Stav Ane Løvli , Johansen Krisztina Kunszt , Auning Eirik , Kalheim Lisa Flem , Selnes Per , Bjørnerud Atle , Hessen Erik , Aarsland Dag , Fladby Tormod 
Published: January 2016

AbstractCognition is often affected early in Parkinson’s disease (PD). Lewy body and amyloid β (Aβ) pathology and cortical atrophy may be involved. The aim of this study was to examine whether medial temporal lobe structural changes may be linked to cerebrospinal fluid (CSF) biomarker levels and cognition in early PD. PD patients had smaller volumes of total hippocampus, presubiculum, subiculum, CA2–3, CA4-DG, and hippocampal tail compared with normal controls (NCs). In the PD group, lower CSF Aβ38 and 42 were significant predictors for thinner perirhinal cortex. Lower Aβ42 and smaller presubiculum and subiculum predicted poorer verbal learning and delayed verbal recall. Smaller total hippocampus, presubiculum and subiculum predicted poorer visuospatial copying. Lower Aβ38 and 40 and thinner perirhinal cortex predicted poorer delayed visual reproduction. In conclusion, smaller volumes of hippocampal subfields and subhippocampal cortex thickness linked to lower CSF Aβ levels may contribute to cognitive impairment in early PD. Thirty-three early PD patients (13 without, 5 with subjective, and 15 with mild cognitive impairment) and NC had 3 T magnetic resonance imaging (MRI) scans. The MRI scans were post processed for volumes of hippocampal subfields and entorhinal and perirhinal cortical thickness. Lumbar puncture for CSF biomarkers Aβ38, 40, 42, total tau, phosphorylated tau (Innogenetics), and total α-synuclein (Meso Scale Diagnostics) were performed. Multiple regression analyses were used for between-group comparisons of the MRI measurements in the NC and PD groups and for assessment of CSF biomarkers and neuropsychological tests in relation to morphometry in the PD group.
Surface passivation of semiconducting oxides by self-assembled nanoparticles
Authors: Park Dae-Sung , Wang Haiyuan , Vasheghani Farahani Sepehr K. , Walker Marc , Bhatnagar Akash , Seghier Djelloul , Choi Chel-Jong , Kang Jie-Hun , McConville Chris F. 
Published: January 2016

AbstractPhysiochemical interactions which occur at the surfaces of oxide materials can significantly impair their performance in many device applications. As a result, surface passivation of oxide materials has been attempted via several deposition methods and with a number of different inert materials. Here, we demonstrate a novel approach to passivate the surface of a versatile semiconducting oxide, zinc oxide (ZnO), evoking a self-assembly methodology. This is achieved via thermodynamic phase transformation, to passivate the surface of ZnO thin films with BeO nanoparticles. Our unique approach involves the use of BexZn1-xO (BZO) alloy as a starting material that ultimately yields the required coverage of secondary phase BeO nanoparticles and prevents thermally-induced lattice dissociation and defect-mediated chemisorption, which are undesirable features observed at the surface of undoped ZnO. This approach to surface passivation will allow the use of semiconducting oxides in a variety of different electronic applications, while maintaining the inherent properties of the materials.
Electrical current through individual pairs of phosphorus donor atoms and silicon dangling bonds
Authors: Ambal K. , Rahe P. , Payne A. , Slinkman J. , Williams C. C. , Boehme C. 
Published: January 2016

AbstractNuclear spins of phosphorus [P] donor atoms in crystalline silicon are among the most coherent qubits found in nature. For their utilization in scalable quantum computers, distinct donor electron wavefunctions must be controlled and probed through electrical coupling by application of either highly localized electric fields or spin-selective currents. Due to the strong modulation of the P-donor wavefunction by the silicon lattice, such electrical coupling requires atomic spatial accuracy. Here, the spatially controlled application of electrical current through individual pairs of phosphorus donor electron states in crystalline silicon and silicon dangling bond states at the crystalline silicon (100) surface is demonstrated using a high‐resolution scanning probe microscope operated under ultra‐high vacuum and at a temperature of 4.3K. The observed pairs of electron states display qualitatively reproducible current-voltage characteristics with a monotonous increase and intermediate current plateaus.
Quantitative analysis of intrinsic and extrinsic factors in the aggregation mechanism of Alzheimer-associated Aβ-peptide
Authors: Meisl Georg , Yang Xiaoting , Frohm Birgitta , Knowles Tuomas P. J. , Linse Sara 
Published: January 2016

AbstractDisease related mutations and environmental factors are key determinants of the aggregation mechanism of the amyloid-β peptide implicated in Alzheimer's disease. Here we present an approach to investigate these factors through acquisition of highly reproducible data and global kinetic analysis to determine the mechanistic influence of intrinsic and extrinsic factors on the Aβ aggregation network. This allows us to translate the shift in macroscopic aggregation behaviour into effects on the individual underlying microscopic steps. We apply this work-flow to the disease-associated Aβ42-A2V variant and to a variation in pH as examples of an intrinsic and an extrinsic perturbation. In both cases, our data reveal a shift towards a mechanism in which a larger fraction of the reactive flux goes via a pathway that generates potentially toxic oligomeric species in a fibril-catalyzed reaction. This is in agreement with the finding that Aβ42-A2V leads to early-onset Alzheimer’s disease and enhances neurotoxicity.
Microbial community profiling shows dysbiosis in the lesional skin of Vitiligo subjects
Authors: Ganju Parul , Nagpal Sunil , Mohammed MH , Nishal Kumar P , Pandey Rajesh , Natarajan Vivek T , Mande Sharmila S. , Gokhale Rajesh S. 
Published: January 2016

AbstractHealthy human skin harbours a diverse array of microbes that comprise the skin microbiome. Commensal bacteria constitute an important component of resident microbiome and are intricately linked to skin health. Recent studies describe an association between altered skin microbial community and epidemiology of diseases, like psoriasis, atopic dermatitis etc. In this study, we compare the differences in bacterial community of lesional and non-lesional skin of vitiligo subjects. Our study reveals dysbiosis in the diversity of microbial community structure in lesional skin of vitiligo subjects. Although individual specific signature is dominant over the vitiligo-specific microbiota, a clear decrease in taxonomic richness and evenness can be noted in lesional patches. Investigation of community specific correlation networks reveals distinctive pattern of interactions between resident bacterial populations of the two sites (lesional and non-lesional). While Actinobacterial species constitute the central regulatory nodes (w.r.t. degree of interaction) in non-lesional skin, species belonging to Firmicutes dominate on lesional sites. We propose that the changes in taxonomic characteristics of vitiligo lesions, as revealed by our study, could play a crucial role in altering the maintenance and severity of disease. Future studies would elucidate mechanistic relevance of these microbial dynamics that can provide new avenues for therapeutic interventions.
PCNA appears in two populations of slow and fast diffusion with a constant ratio throughout S-phase in replicating mammalian cells
Authors: Zessin Patrick J. M. , Sporbert Anje , Heilemann Mike 
Published: January 2016

AbstractDNA replication is a fundamental cellular process that precedes cell division. Proliferating cell nuclear antigen (PCNA) is a central scaffold protein that orchestrates DNA replication by recruiting many factors essential for the replication machinery. We studied the mobility of PCNA in live mammalian cells using single-particle tracking in combination with photoactivated-localization microscopy (sptPALM) and found two populations. The first population which is only present in cells with active DNA replication, showed slow diffusion and was found to be located in replication foci. The second population showed fast diffusion and represents the nucleoplasmic pool of unbound PCNA not involved in DNA replication. The ratio of these two populations remained constant throughout different stages of S-phase. A fraction of molecules in both populations showed spatially constrained mobility. We determined an exploration radius of ~100 nm for 13% of the slow-diffusing PCNA molecules and of ~600 nm for 46% of the fast-diffusing PCNA molecules.
Direct molecular mimicry enables off-target cardiovascular toxicity by an enhanced affinity TCR designed for cancer immunotherapy
Authors: Raman Marine C C , Rizkallah Pierre J , Simmons Ruth , Donnellan Zoe , Dukes Joseph , Bossi Giovanna , Le Provost Gabrielle S , Todorov Penio , Baston Emma , Hickman Emma , Mahon Tara , Hassan Namir , Vuidepot Annelise , Sami Malkit , Cole David K , Jakobsen Bent K. 
Published: January 2016

AbstractNatural T-cell responses generally lack the potency to eradicate cancer. Enhanced affinity T-cell receptors (TCRs) provide an ideal approach to target cancer cells, with emerging clinical data showing significant promise. Nevertheless, the risk of off target reactivity remains a key concern, as exemplified in a recent clinical report describing fatal cardiac toxicity, following administration of MAGE-A3 specific TCR-engineered T-cells, mediated through cross-reactivity with an unrelated epitope from the Titin protein presented on cardiac tissue. Here, we investigated the structural mechanism enabling TCR cross-recognition of MAGE-A3 and Titin and applied the resulting data to rationally design mutants with improved antigen discrimination, providing a proof-of-concept strategy for altering the fine specificity of a TCR towards an intended target antigen. This study represents the first example of direct molecular mimicry leading to clinically relevant fatal toxicity, mediated by a modified enhanced affinity TCR designed for cancer immunotherapy. Furthermore, these data demonstrate that self-antigens that are expressed at high levels on healthy tissue should be treated with extreme caution when designing immuno-therapeutics.