bluuebunny/crossref_metadata_2025_split huggingface dataset:
Profiling of the plasma proteome across different stages of human heart failure
Authors: Egerstedt Anna , Berntsson John , Smith Maya Landenhed , Gidlöf Olof , Nilsson Roland , Benson Mark , Wells Quinn S. , Celik Selvi , Lejonberg Carl , Farrell Laurie , Sinha Sumita , Shen Dongxiao , Lundgren Jakob , Rådegran Göran , Ngo Debby , Engström Gunnar , Yang Qiong , Wang Thomas J. , Gerszten Robert E. , Smith J. Gustav 
Published: December 2019

AbstractHeart failure (HF) is a major public health problem characterized by inability of the heart to maintain sufficient output of blood. The systematic characterization of circulating proteins across different stages of HF may provide pathophysiological insights and identify therapeutic targets. Here we report application of aptamer-based proteomics to identify proteins associated with prospective HF incidence in a population-based cohort, implicating modulation of immunological, complement, coagulation, natriuretic and matrix remodeling pathways up to two decades prior to overt disease onset. We observe further divergence of these proteins from the general population in advanced HF, and regression after heart transplantation. By leveraging coronary sinus samples and transcriptomic tools, we describe likely cardiac and specific cellular origins for several of the proteins, including Nt-proBNP, thrombospondin-2, interleukin-18 receptor, gelsolin, and activated C5. Our findings provide a broad perspective on both cardiac and systemic factors associated with HF development.
Crystal scavenging from mush piles recorded by melt inclusions
Authors: Wieser Penny E. , Edmonds Marie , Maclennan John , Jenner Frances E. , Kunz Barbara E. 
Published: December 2019

AbstractOlivine-hosted melt inclusions are commonly used to determine pre-eruptive storage conditions. However, this approach relies on the assumption that co-erupted olivines have a simple association with their carrier melts. We show that primitive olivine crystal cargoes and their melt inclusions display a high degree of geochemical disequilibrium with their carrier melts at Kīlauea Volcano, Hawai’i. Within a given eruption, melt inclusions trapped in primitive olivine crystals exhibit compositional diversity exceeding that in erupted lava compositions since 1790 CE. This demonstrates that erupting liquids scavenge crystal cargoes from mush piles accumulating diverse melt inclusion populations over timescales of centuries or longer. Entrainment of hot primitive olivines into cooler, evolved carrier melts drives post-entrapment crystallization and sequestration of CO2 into vapour bubbles, producing spurious barometric estimates. While scavenged melt inclusion records may not be suitable for the investigation of eruption-specific processes, they record timescales of crystal storage and remobilization within magmatic mush piles.
Forty-five patient-derived xenografts capture the clinical and biological heterogeneity of Wilms tumor
Authors: Murphy Andrew J. , Chen Xiang , Pinto Emilia M. , Williams Justin S. , Clay Michael R. , Pounds Stanley B. , Cao Xueyuan , Shi Lei , Lin Tong , Neale Geoffrey , Morton Christopher L. , Woolard Mary A. , Mulder Heather L. , Gil Hyea Jin , Rehg Jerold E. , Billups Catherine A. , Harlow Matthew L. , Dome Jeffrey S. , Houghton Peter J. , Easton John , Zhang Jinghui , George Rani E. , Zambetti Gerard P. , Davidoff Andrew M. 
Published: December 2019

AbstractThe lack of model systems has limited the preclinical discovery and testing of therapies for Wilms tumor (WT) patients who have poor outcomes. Herein, we establish 45 heterotopic WT patient-derived xenografts (WTPDX) in CB17 scid-/- mice that capture the biological heterogeneity of Wilms tumor (WT). Among these 45 total WTPDX, 6 from patients with diffuse anaplastic tumors, 9 from patients who experienced disease relapse, and 13 from patients with bilateral disease are included. Early passage WTPDX show evidence of clonal selection, clonal evolution and enrichment of blastemal gene expression. Favorable histology WTPDX are sensitive, whereas unfavorable histology WTPDX are resistant to conventional chemotherapy with vincristine, actinomycin-D, and doxorubicin given singly or in combination. This WTPDX library is a unique scientific resource that retains the spectrum of biological heterogeneity present in WT and provides an essential tool to test targeted therapies for WT patient groups with poor outcomes.
Relationship between gut microbiota and circulating metabolites in population-based cohorts
Authors: Vojinovic Dina , Radjabzadeh Djawad , Kurilshikov Alexander , Amin Najaf , Wijmenga Cisca , Franke Lude , Ikram M. Arfan , Uitterlinden Andre G. , Zhernakova Alexandra , Fu Jingyuan , Kraaij Robert , van Duijn Cornelia M. 
Published: December 2019

AbstractGut microbiota has been implicated in major diseases affecting the human population and has also been linked to triglycerides and high-density lipoprotein levels in the circulation. Recent development in metabolomics allows classifying the lipoprotein particles into more details. Here, we examine the impact of gut microbiota on circulating metabolites measured by Nuclear Magnetic Resonance technology in 2309 individuals from the Rotterdam Study and the LifeLines-DEEP cohort. We assess the relationship between gut microbiota and metabolites by linear regression analysis while adjusting for age, sex, body-mass index, technical covariates, medication use, and multiple testing. We report an association of 32 microbial families and genera with very-low-density and high-density subfractions, serum lipid measures, glycolysis-related metabolites, ketone bodies, amino acids, and acute-phase reaction markers. These observations provide insights into the role of microbiota in host metabolism and support the potential of gut microbiota as a target for therapeutic and preventive interventions.
Perfect secrecy cryptography via mixing of chaotic waves in irreversible time-varying silicon chips
Authors: Di Falco A. , Mazzone V. , Cruz A. , Fratalocchi A. 
Published: December 2019

AbstractProtecting confidential data is a major worldwide challenge. Classical cryptography is fast and scalable, but is broken by quantum algorithms. Quantum cryptography is unclonable, but requires quantum installations that are more expensive, slower, and less scalable than classical optical networks. Here we show a perfect secrecy cryptography in classical optical channels. The system exploits correlated chaotic wavepackets, which are mixed in inexpensive and CMOS compatible silicon chips. The chips can generate 0.1 Tbit of different keys for every mm of length of the input channel, and require the transmission of an amount of data that can be as small as 1/1000 of the message’s length. We discuss the security of this protocol for an attacker with unlimited technological power, and who can access the system copying any of its part, including the chips. The second law of thermodynamics and the exponential sensitivity of chaos unconditionally protect this scheme against any possible attack.
A mitochondrial megachannel resides in monomeric F1FO ATP synthase
Authors: Mnatsakanyan Nelli , Llaguno Marc C. , Yang Youshan , Yan Yangyang , Weber Joachim , Sigworth Fred J. , Jonas Elizabeth A. 
Published: December 2019

AbstractPurified mitochondrial ATP synthase has been shown to form Ca2+-activated, large conductance channel activity similar to that of mitochondrial megachannel (MMC) or mitochondrial permeability transition pore (mPTP) but the oligomeric state required for channel formation is being debated. We reconstitute purified monomeric ATP synthase from porcine heart mitochondria into small unilamellar vesicles (SUVs) with the lipid composition of mitochondrial inner membrane and analyze its oligomeric state by electron cryomicroscopy. The cryo-EM density map reveals the presence of a single ATP synthase monomer with no density seen for a second molecule tilted at an 86o angle relative to the first. We show that this preparation of SUV-reconstituted ATP synthase monomers, when fused into giant unilamellar vesicles (GUVs), forms voltage-gated and Ca2+-activated channels with the key features of mPTP. Based on our findings we conclude that the ATP synthase monomer is sufficient, and dimer formation is not required, for mPTP activity.
An ultrathin ionomer interphase for high efficiency lithium anode in carbonate based electrolyte
Authors: Weng Yu-Ting , Liu Hao-Wen , Pei Allen , Shi FeiFei , Wang Hansen , Lin Chih-Yuan , Huang Sheng-Siang , Su Lin-Ya , Hsu Jyh-Ping , Fang Chia-Chen , Cui Yi , Wu Nae-Lih 
Published: December 2019

AbstractHigh coulombic efficiency and dendrite suppression in carbonate electrolytes remain challenges to the development of high-energy lithium ion batteries containing lithium metal anodes. Here we demonstrate an ultrathin (≤100 nm) lithium-ion ionomer membrane consisting of lithium-exchanged sulfonated polyether ether ketone embedded with polyhedral oligosilsesquioxane as a coating layer on copper or lithium for achieving efficient and stable lithium plating-stripping cycles in a carbonate-based electrolyte. Operando analyses and theoretical simulation reveal the remarkable ability of the ionomer coating to enable electric field homogenization over a considerably large lithium-plating surface. The membrane coating, serving as an artificial solid-electrolyte interphase filter in minimizing parasitic reactions at the electrolyte-electrode interface, enables dendrite-free lithium plating on copper with outstanding coulombic efficiencies at room and elevated (50 °C) temperatures. The membrane coated copper demonstrates itself as a promising current collector for manufacturing high-quality pre-plated lithium thin-film anode.
Ultrafast valence to non-valence excited state dynamics in a common anionic chromophore
Authors: Bull James N. , Anstöter Cate S. , Verlet Jan R. R. 
Published: December 2019

AbstractNon-valence states in neutral molecules (Rydberg states) have well-established roles and importance in photochemistry, however, considerably less is known about the role of non-valence states in photo-induced processes in anions. Here, femtosecond time-resolved photoelectron imaging is used to show that photoexcitation of the S1(ππ*) state of the methyl ester of deprotonated para-coumaric acid – a model chromophore for photoactive yellow protein (PYP) – leads to a bifurcation of the excited state wavepacket. One part remains on the S1(ππ*) state forming a twisted intermediate, whilst a second part leads to the formation of a non-valence (dipole-bound) state. Both populations eventually decay independently by vibrational autodetachment. Valence-to-non-valence internal conversion has hitherto not been observed in the intramolecular photophysics of an isolated anion, raising questions into how common such processes might be, given that many anionic chromophores have bright valence states near the detachment threshold.
The anticipation of events in time
Authors: Grabenhorst Matthias , Michalareas Georgios , Maloney Laurence T. , Poeppel David 
Published: December 2019

AbstractHumans anticipate events signaled by sensory cues. It is commonly assumed that two uncertainty parameters modulate the brain's capacity to predict: the hazard rate (HR) of event probability and the uncertainty in time estimation which increases with elapsed time. We investigate both assumptions by presenting event probability density functions (PDFs) in each of three sensory modalities. We show that perceptual systems use the reciprocal PDF and not the HR to model event probability density. We also demonstrate that temporal uncertainty does not necessarily grow with elapsed time but can also diminish, depending on the event PDF. Previous research identified neuronal activity related to event probability in multiple levels of the cortical hierarchy (sensory (V4), association (LIP), motor and other areas) proposing the HR as an elementary neuronal computation. Our results—consistent across vision, audition, and somatosensation—suggest that the neurobiological implementation of event anticipation is based on a different, simpler and more stable computation than HR: the reciprocal PDF of events in time.
Photorealistic modelling of metals from first principles
Authors: Prandini Gianluca , Rignanese Gian-Marco , Marzari Nicola 
Published: December 2019

AbstractThe colours of metals have attracted the attention of humanity since ancient times, and coloured metals, in particular gold compounds, have been employed for tools and objects symbolizing the aesthetics of power. In this work, we develop a comprehensive framework to obtain the reflectivity and colour of metals, and show that the trends in optical properties and the colours can be predicted by straightforward first-principles techniques based on standard approximations. We apply this to predict reflectivity and colour of several elemental metals and of different types of metallic compounds (intermetallics, solid solutions and heterogeneous alloys), considering mainly binary alloys based on noble metals. We validate the numerical approach through an extensive comparison with experimental data and the photorealistic rendering of known coloured metals.
Scalable repeater architectures for multi-party states
Authors: Kuzmin V. V. , Vasilyev D. V. , Sangouard N. , Dür W. , Muschik C. A. 
Published: December 2019

AbstractThe vision to develop quantum networks entails multi-user applications, which require the generation of long-distance multi-party entangled states. The current rapid experimental progress in building prototype-networks calls for new design concepts to guide future developments. Here we describe an experimentally feasible scheme implementing a two-dimensional repeater network for robust distribution of three-party entangled states of GHZ type in the presence of excitation losses and detector dark counts — the main sources of errors in real-world hardware. Our approach is based on atomic or solid state ensembles and employs built-in error filtering mechanisms peculiar to intrinsically two-dimensional networks. This allows us to overcome the performance limitation of conventional one-dimensional ensemble-based networks distributing multi-party entangled states and provides an efficient design for future experiments with a clear perspective in terms of scalability.
A longitudinal neuroimaging dataset on multisensory lexical processing in school-aged children
Authors: Lytle Marisa N. , McNorgan Chris , Booth James R. 
Published: December 2019

AbstractHere we describe the open access dataset entitled “Longitudinal Brain Correlates of Multisensory Lexical Processing in Children” hosted on OpenNeuro.org. This dataset examines reading development through a longitudinal multimodal neuroimaging and behavioral approach, including diffusion-weighted and T1-weighted structural magnetic resonance imaging (MRI), task based functional MRI, and a battery of psycho-educational assessments and parental questionnaires. Neuroimaging, psycho-educational testing, and functional task behavioral data were collected from 188 typically developing children when they were approximately 10.5 years old (session T1). Seventy children returned approximately 2.5 years later (session T2), of which all completed longitudinal follow-ups of psycho-educational testing, and 49 completed neuroimaging and functional tasks. At session T1 participants completed auditory, visual, and audio-visual word and pseudo-word rhyming judgment tasks in the scanner. At session T2 participants completed visual word and pseudo-word rhyming judgement tasks in the scanner.
Multi-Locus Genome Wide Association Mapping for Yield and Its Contributing Traits in Hexaploid Wheat under Different Water Regimes
Authors: Gahlaut Vijay , Jaiswal Vandana , Singh Sukhwinder , Balyan H. S. , Gupta P. K. 
Published: December 2019

AbstractMulti-locus genome wide association study was undertaken using a set of 320 diverse spring wheat accessions, which were each genotyped for 9,626 SNPs. The association panel was grown in replicated trials in four environments [two each in irrigated (IR) and rainfed (RF) environments], and phenotypic data were recorded for five traits including days to heading, days to maturity, plant height, thousand grain weight and grain yield. Forty-six significant marker-trait associations (MTAs) were identified for five traits. These included 20 MTAs in IR and 19 MTAs in RF environments; seven additional MTAs were common to both the environments. Five of these MTAs were co-localized with previously known QTL/MTAs and the remaining MTAs were novel and add to the existing knowledge. Three desirable haplotypes for agronomic traits, one for improvement in RF environment and two for improvement in IR environment were identified. Eighteen (18) promising candidate genes (CGs) involved in seven different biological activities were also identified. The expression profiles of four (Trehalose-6-Phosphate, APETALA2/Ethylene-responsive factor, DNA-binding One Zinc Finger and Gibberellin-dioxygenases) of the 18 genes showed that they were induced by drought stress in the wheat seedlings. The MTAs, haplotypes and CG-based markers may be used in marker-assisted breeding for drought tolerance in wheat.
Boson peak, elasticity, and glass transition temperature in polymer glasses: Effects of the rigidity of chain bending
Authors: Tomoshige Naoya , Mizuno Hideyuki , Mori Tatsuya , Kim Kang , Matubayasi Nobuyuki 
Published: December 2019

AbstractThe excess low-frequency vibrational spectrum, called boson peak, and non-affine elastic response are the most important particularities of glasses. Herein, the vibrational and mechanical properties of polymeric glasses are examined by using coarse-grained molecular dynamics simulations, with particular attention to the effects of the bending rigidity of the polymer chains. As the rigidity increases, the system undergoes a glass transition at a higher temperature (under a constant pressure), which decreases the density of the glass phase. The elastic moduli, which are controlled by the decrease of the density and the increase of the rigidity, show a non-monotonic dependence on the rigidity of the polymer chain that arises from the non-affine component. Moreover, a clear boson peak is observed in the vibrational density of states, which depends on the macroscopic shear modulusG. In particular, the boson peak frequency ωBPis proportional to$$\sqrt{G}$$G. These results provide a positive correlation between the boson peak, shear elasticity, and the glass transition temperature.
Data-mining Techniques for Image-based Plant Phenotypic Traits Identification and Classification
Authors: Rahaman Md. Matiur , Ahsan Md. Asif , Chen Ming 
Published: December 2019

AbstractStatistical data-mining (DM) and machine learning (ML) are promising tools to assist in the analysis of complex dataset. In recent decades, in the precision of agricultural development, plant phenomics study is crucial for high-throughput phenotyping of local crop cultivars. Therefore, integrated or a new analytical approach is needed to deal with these phenomics data. We proposed a statistical framework for the analysis of phenomics data by integrating DM and ML methods. The most popular supervised ML methods; Linear Discriminant Analysis (LDA), Random Forest (RF), Support Vector Machine with linear (SVM-l) and radial basis (SVM-r) kernel are used for classification/prediction plant status (stress/non-stress) to validate our proposed approach. Several simulated and real plant phenotype datasets were analyzed. The results described the significant contribution of the features (selected by our proposed approach) throughout the analysis. In this study, we showed that the proposed approach removed phenotype data analysis complexity, reduced computational time of ML algorithms, and increased prediction accuracy.
Signatures of Molecular Unification and Progressive Oxidation Unfold in Dissolved Organic Matter of the Ob-Irtysh River System along Its Path to the Arctic Ocean
Authors: Perminova I. V. , Shirshin E. A. , Zherebker A. , Pipko I. I. , Pugach S. P. , Dudarev O. V. , Nikolaev E. N. , Grigoryev A. S. , Shakhova N. , Semiletov I. P. 
Published: December 2019

AbstractThe Ob-Irtysh River system is the seventh-longest one in the world. Unlike the other Great Siberian rivers, it is only slightly impacted by the continuous permafrost in its low flow. Instead, it drains the Great Vasyugan mire, which is the world largest swamp, and receives huge load of the Irtysh waters which drain the populated lowlands of the East Siberian Plain. The central challenge of this paper is to understand the processes responsible for molecular transformations of natural organic matter (NOM) in the Ob-Irtysh river system along the South-North transect. For solving this task, the NOM was isolated from the water samples collected along the 3,000 km transect using solid-phase extraction. The NOM samples were further analyzed using high resolution mass spectrometry and optical spectroscopy. The obtained results have shown a distinct trend both in molecular composition and diversity of the NOM along the South-North transect: the largest diversity was observed in the Southern “swamp-wetland” stations. The samples were dominated with humic and lignin-like components, and enriched with aminosugars. After the Irtysh confluence, the molecular nature of NOM has changed drastically: it became much more oxidized and enriched with heterocyclic N-containing compounds. These molecular features are very different from the aliphatics-rich permafrost NOM. They witnesses much more conservative nature of the NOM discharged into the Arctic by the Ob-Irtysh river system. In general, drastic reduction in molecular diversity was observed in the northern stations located in the lower Ob flow.
Transcriptome-wide analysis associates ID2 expression with combined pre- and post-capillary pulmonary hypertension
Authors: Arwood Meghan J. , Vahabi Nasim , Lteif Christelle , Sharma Ravindra K. , Machado Roberto F. , Duarte Julio D. 
Published: December 2019

AbstractHeart failure with preserved ejection fraction (HFpEF) patients who develop pulmonary hypertension (PH) have an increased risk of death, with combined pre- and post-capillary PH (CpcPH) having the highest risk. However, the mechanism behind PH development in HFpEF is poorly understood. We aimed to identify transcriptomic associations with PH development in HFpEF. Blood was collected from 30 HFpEF patients: 10 without PH, 10 with isolated post-capillary PH, and 10 with CpcPH. Gene expression measurements were completed using transcriptome-wide RNA sequencing. Gene expression differences were compared using a quasi-likelihood method adjusting for age, sex, race, and smoking-status. Biological pathways were compared using global gene expression differences. A replication in 34 additional heart failure patients and a validation in lung tissue from a representative mouse model were completed using quantitative PCR. Six differentially expressed genes were identified when comparing transcriptomics between subjects with CpcPH and those without PH. When tested in additional subjects, only the association with ID2 replicated. Consistent with clinical findings, Id2 expression was also upregulated in mice with HFpEF and PH. Pathway analysis identified proliferative and mitochondrial pathways associated with CpcPH. Thus, these patients may possess systemic pathophysiological differences similar to those observed in pulmonary arterial hypertension patients.