bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Fe–O isotope correlation reveals magmatic origin of Kiruna-type apatite-iron-oxide ores
Authors: Troll Valentin R. , Weis Franz A. , Jonsson Erik , Andersson Ulf B. , Majidi Seyed Afshin , Högdahl Karin , Harris Chris , Millet Marc-Alban , Chinnasamy Sakthi Saravanan , Kooijman Ellen , Nilsson Katarina P. 
Published: April 2019

AbstractKiruna-type apatite-iron-oxide ores are key iron sources for modern industry, yet their origin remains controversial. Diverse ore-forming processes have been discussed, comprising low-temperature hydrothermal processes versus a high-temperature origin from magma or magmatic fluids. We present an extensive set of new and combined iron and oxygen isotope data from magnetite of Kiruna-type ores from Sweden, Chile and Iran, and compare them with new global reference data from layered intrusions, active volcanic provinces, and established low-temperature and hydrothermal iron ores. We show that approximately 80% of the magnetite from the investigated Kiruna-type ores exhibit δ56Fe and δ18O ratios that overlap with the volcanic and plutonic reference materials (> 800 °C), whereas ~20%, mainly vein-hosted and disseminated magnetite, match the low-temperature reference samples (≤400 °C). Thus, Kiruna-type ores are dominantly magmatic in origin, but may contain late-stage hydrothermal magnetite populations that can locally overprint primary high-temperature magmatic signatures.
Diel population and functional synchrony of microbial communities on coral reefs
Authors: Kelly Linda Wegley , Nelson Craig E. , Haas Andreas F. , Naliboff Douglas S. , Calhoun Sandi , Carlson Craig A. , Edwards Robert A. , Fox Michael D. , Hatay Mark , Johnson Maggie D. , Kelly Emily L. A. , Lim Yan Wei , Macherla Saichetana , Quinlan Zachary A. , Silva Genivaldo Gueiros Z. , Vermeij Mark J. A. , Zgliczynski Brian , Sandin Stuart A. , Smith Jennifer E. , Rohwer Forest 
Published: April 2019

AbstractOn coral reefs, microorganisms are essential for recycling nutrients to primary producers through the remineralization of benthic-derived organic matter. Diel investigations of reef processes are required to holistically understand the functional roles of microbial players in these ecosystems. Here we report a metagenomic analysis characterizing microbial communities in the water column overlying 16 remote forereef sites over a diel cycle. Our results show that microbial community composition is more dissimilar between day and night samples collected from the same site than between day or night samples collected across geographically distant reefs. Diel community differentiation is largely driven by the flux ofPsychrobactersp., which is two-orders of magnitude more abundant during the day. Nighttime communities are enriched with species ofRoseobacter,Halomonas, andAlteromonasencoding a greater variety of pathways for carbohydrate catabolism, further illustrating temporal patterns of energetic provisioning between different marine microbes. Dynamic diel fluctuations of microbial populations could also support the efficient trophic transfer of energy posited in coral reef food webs.
Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis
Authors: Yan Wenhao , Chen Dijun , Schumacher Julia , Durantini Diego , Engelhorn Julia , Chen Ming , Carles Cristel C. , Kaufmann Kerstin 
Published: April 2019

AbstractEnhancers are critical for developmental stage-specific gene expression, but their dynamic regulation in plants remains poorly understood. Here we compare genome-wide localization of H3K27ac, chromatin accessibility and transcriptomic changes during flower development in Arabidopsis. H3K27ac prevalently marks promoter-proximal regions, suggesting that H3K27ac is not a hallmark for enhancers in Arabidopsis. We provide computational and experimental evidence to confirm that distal DNase І hypersensitive sites are predictive of enhancers. The predicted enhancers are highly stage-specific across flower development, significantly associated with SNPs for flowering-related phenotypes, and conserved across crucifer species. Through the integration of genome-wide transcription factor (TF) binding datasets, we find that floral master regulators and stage-specific TFs are largely enriched at developmentally dynamic enhancers. Finally, we show that enhancer clusters and intronic enhancers significantly associate with stage-specific gene regulation by floral master TFs. Our study provides insights into the functional flexibility of enhancers during plant development, as well as hints to annotate plant enhancers.
Altered steady state and activity-dependent de novo protein expression in fragile X syndrome
Authors: Bowling Heather , Bhattacharya Aditi , Zhang Guoan , Alam Danyal , Lebowitz Joseph Z. , Bohm-Levine Nathaniel , Lin Derek , Singha Priyangvada , Mamcarz Maggie , Puckett Rosemary , Zhou Lili , Aryal Sameer , Sharp Kevin , Kirshenbaum Kent , Berry-Kravis Elizabeth , Neubert Thomas A. , Klann Eric 
Published: April 2019

AbstractWhether fragile X mental retardation protein (FMRP) target mRNAs and neuronal activity contributing to elevated basal neuronal protein synthesis in fragile X syndrome (FXS) is unclear. Our proteomic experiments reveal that the de novo translational profile in FXS model mice is altered at steady state and in response to metabotropic glutamate receptor (mGluR) stimulation, but the proteins expressed differ under these conditions. Several altered proteins, including Hexokinase 1 and Ras, also are expressed in the blood of FXS model mice and pharmacological treatments previously reported to ameliorate phenotypes modify their abundance in blood. In addition, plasma levels of Hexokinase 1 and Ras differ between FXS patients and healthy volunteers. Our data suggest that brain-based de novo proteomics in FXS model mice can be used to find altered expression of proteins in blood that could serve as disease-state biomarkers in individuals with FXS.
Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions
Authors: Kajitani Rei , Yoshimura Dai , Okuno Miki , Minakuchi Yohei , Kagoshima Hiroshi , Fujiyama Asao , Kubokawa Kaoru , Kohara Yuji , Toyoda Atsushi , Itoh Takehiko 
Published: April 2019

AbstractThe ultimate goal for diploid genome determination is to completely decode homologous chromosomes independently, and several phasing programs from consensus sequences have been developed. These methods work well for lowly heterozygous genomes, but the manifold species have high heterozygosity. Additionally, there are highly divergent regions (HDRs), where the haplotype sequences differ considerably. Because HDRs are likely to direct various interesting biological phenomena, many genomic analysis targets fall within these regions. However, they cannot be accessed by existing phasing methods, and we have to adopt costly traditional methods. Here, we develop a de novo haplotype assembler, Platanus-allee (http://platanus.bio.titech.ac.jp/platanus2), which initially constructs each haplotype sequence and then untangles the assembly graphs utilizing sequence links and synteny information. A comprehensive benchmark analysis reveals that Platanus-allee exhibits high recall and precision, particularly for HDRs. Using this approach, previously unknown HDRs are detected in the human genome, which may uncover novel aspects of genome variability.
Nanomechanical DNA resonators for sensing and structural analysis of DNA-ligand complexes
Authors: Stassi Stefano , Marini Monica , Allione Marco , Lopatin Sergei , Marson Domenico , Laurini Erik , Pricl Sabrina , Pirri Candido Fabrizio , Ricciardi Carlo , Di Fabrizio Enzo 
Published: April 2019

AbstractThe effect of direct or indirect binding of intercalant molecules on DNA structure is of fundamental importance in understanding the biological functioning of DNA. Here we report on self-suspended DNA nanobundles as ultrasensitive nanomechanical resonators for structural studies of DNA-ligand complexes. Such vibrating nanostructures represent the smallest mechanical resonator entirely composed of DNA. A correlative analysis between the mechanical and structural properties is exploited to study the intrinsic changes of double strand DNA, when interacting with different intercalant molecules (YOYO-1 and GelRed) and a chemotherapeutic drug (Cisplatin), at different concentrations. Possible implications of our findings are related to the study of interaction mechanism of a wide category of molecules with DNA, and to further applications in medicine, such as optimal titration of chemotherapeutic drugs and environmental studies for the detection of heavy metals in human serum.
Boosting oxygen evolution of single-atomic ruthenium through electronic coupling with cobalt-iron layered double hydroxides
Authors: Li Pengsong , Wang Maoyu , Duan Xinxuan , Zheng Lirong , Cheng Xiaopeng , Zhang Yuefei , Kuang Yun , Li Yaping , Ma Qing , Feng Zhenxing , Liu Wen , Sun Xiaoming 
Published: April 2019

AbstractSingle atom catalyst, which contains isolated metal atoms singly dispersed on supports, has great potential for achieving high activity and selectivity in hetero-catalysis and electrocatalysis. However, the activity and stability of single atoms and their interaction with support still remains a mystery. Here we show a stable single atomic ruthenium catalyst anchoring on the surface of cobalt iron layered double hydroxides, which possesses a strong electronic coupling between ruthenium and layered double hydroxides. With 0.45 wt.% ruthenium loading, the catalyst exhibits outstanding activity with overpotential 198 mV at the current density of 10 mA cm−2 and a small Tafel slope of 39 mV dec−1 for oxygen evolution reaction. By using operando X-ray absorption spectroscopy, it is disclosed that the isolated single atom ruthenium was kept under the oxidation states of 4+ even at high overpotential due to synergetic electron coupling, which endow exceptional electrocatalytic activity and stability simultaneously.
Plug-and-play metabolic transducers expand the chemical detection space of cell-free biosensors
Authors: Voyvodic Peter L. , Pandi Amir , Koch Mathilde , Conejero Ismael , Valjent Emmanuel , Courtet Philippe , Renard Eric , Faulon Jean-Loup , Bonnet Jerome 
Published: April 2019

AbstractCell-free transcription–translation systems have great potential for biosensing, yet the range of detectable chemicals is limited. Here we provide a workflow to expand the range of molecules detectable by cell-free biosensors through combining synthetic metabolic cascades with transcription factor-based networks. These hybrid cell-free biosensors have a fast response time, strong signal response, and a high dynamic range. In addition, they are capable of functioning in a variety of complex media, including commercial beverages and human urine, in which they can be used to detect clinically relevant concentrations of small molecules. This work provides a foundation to engineer modular cell-free biosensors tailored for many applications.
Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network
Authors: Maeda Kazuhiro , Westerhoff Hans V. , Kurata Hiroyuki , Boogerd Fred C. 
Published: April 2019

AbstractThe complex ammonium transport and assimilation network of E. coli involves the ammonium transporter AmtB, the regulatory proteins GlnK and GlnB, and the central N-assimilating enzymes together with their highly complex interactions. The engineering and modelling of such a complex network seem impossible because functioning depends critically on a gamut of data known at patchy accuracy. We developed a way out of this predicament, which employs: (i) a constrained optimization-based technology for the simultaneous fitting of models to heterogeneous experimental data sets gathered through diverse experimental set-ups, (ii) a ‘rubber band method’ to deal with different degrees of uncertainty, both in experimentally determined or estimated parameter values and in measured transient or steady-state variables (training data sets), (iii) integration of human expertise to decide on accuracies of both parameters and variables, (iv) massive computation employing a fast algorithm and a supercomputer, (v) an objective way of quantifying the plausibility of models, which makes it possible to decide which model is the best and how much better that model is than the others. We applied the new technology to the ammonium transport and assimilation network, integrating recent and older data of various accuracies, from different expert laboratories. The kinetic model objectively ranked best, has E. coli's AmtB as an active transporter of ammonia to be assimilated with GlnK minimizing the futile cycling that is an inevitable consequence of intracellular ammonium accumulation. It is 130 times better than a model with facilitated passive transport of ammonia.
Metric-guided regularisation parameter selection for statistical iterative reconstruction in computed tomography
Authors: Allner Sebastian , Gustschin Alex , Fehringer Andreas , Noël Peter B. , Pfeiffer Franz 
Published: April 2019

AbstractAs iterative reconstruction in Computed Tomography (CT) is an ill-posed problem, additional prior information has to be used to get a physically meaningful result (close to ground truth if available). However, the amount of influence of the regularisation prior is crucial to the outcome of the reconstruction. Therefore, we propose a scheme for tuning the strength of the prior via a certain image metric. In this work, the parameter is tuned for minimal histogram entropy in selected regions of the reconstruction as histogram entropy is a very basic approach to characterise the information content of data. We performed a sweep over different regularisation parameters showing that the histogram entropy is a suitable metric as it is well behaved over a wide range of parameters. The parameter determination is a feedback loop approach we applied to numerically simulated FORBILD phantom data and verified with an experimental measurement of a micro-CT device. The outcome is evaluated visually and quantitatively by means of root mean squared error (RMSE) and structural similarity (SSIM) for the simulation and visually for the measured sample (no ground truth available). The final reconstructed images exhibit noise-suppressed iterative reconstruction. For both datasets, the optimisation is robust where its initial value is concerned. The parameter tuning approach shows that the proposed metric-driven feedback loop is a promising tool for finding a suitable regularisation parameter in statistical iterative reconstruction.
Increased Plasma Levels of the TH2 chemokine CCL18 associated with low CD4+ T cell counts in HIV-1-infected Patients with a Suppressed Viral Load
Authors: Malhotra Prashant , Haslett Patrick , Sherry Barbara , Shepp David H. , Barber Paul , Abshier Jonathan , Roy Upal , Schmidtmayerova Helena 
Published: April 2019

AbstractThe chemokine (C-C motif) chemokine ligand 18 (CCL18) is a structural homolog of CCL3 primarily produced by monocyte-derived cells with an M2 phenotype. Elevated levels of CCL18 have been observed in several diseases associated with malignancies and chronic inflammation. The role of CCL18 in Human Immunodeficiency Virus (HIV-1) infection remains unknown. We analyzed expression levels of T helper cell-mediated (TH2) chemokines CCL18, CCL17, and CCL22 by ELISA in plasma collected from HIV-1-infected and healthy donors. In HIV-1-infected individuals, plasma viral loads were monitored by NucliSense HIV-1 QT assay and T cell counts and expression of the activation marker CD38 were determined by flow cytometry. Our data showed a significant increase in plasma levels of CCL18 in HIV-1-infected individuals compared to uninfected controls (p < 0.001) and a significant correlation between CCL18 levels and viral load in untreated patients. No significant difference of CCL18 levels was detected among the HIV-1-infected patients treated with combined antiretroviral therapy (cART) and HIV-1-untreated patients.CCL18 values are negatively correlated with CD4+CD38+ cell numbers and total CD4+ T cell counts in patients with a suppressed viral load. Notably, plasma levels of the TH2 chemokines CCL17 and CCL22 are also elevated during HIV-1 infection. However, no correlation of CCL17 and CCL22 production with CD4+ T cell counts was detected. Presented data shows that the chemokines, CCL17, CCL18, and CCL22 are increased during HIV-1 infection. However, only increased levels of CCL18, a marker of M2 macrophages, correlate with low CD4+ T cell counts in patients with suppressed viral load, raising the possibility that CCL18 and/or CCL18-producing cells may interfere with their reconstitution in HIV-1-infected patients on cART.
Predictive Big Data Analytics using the UK Biobank Data
Authors: Zhou Yiwang , Zhao Lu , Zhou Nina , Zhao Yi , Marino Simeone , Wang Tuo , Sun Hanbo , Toga Arthur W , Dinov Ivo D 
Published: April 2019

AbstractThe UK Biobank is a rich national health resource that provides enormous opportunities for international researchers to examine, model, and analyze census-like multisource healthcare data. The archive presents several challenges related to aggregation and harmonization of complex data elements, feature heterogeneity and salience, and health analytics. Using 7,614 imaging, clinical, and phenotypic features of 9,914 subjects we performed deep computed phenotyping using unsupervised clustering and derived two distinct sub-cohorts. Using parametric and nonparametric tests, we determined the top 20 most salient features contributing to the cluster separation. Our approach generated decision rules to predict the presence and progression of depression or other mental illnesses by jointly representing and modeling the significant clinical and demographic variables along with the derived salient neuroimaging features. We reported consistency and reliability measures of the derived computed phenotypes and the top salient imaging biomarkers that contributed to the unsupervised clustering. This clinical decision support system identified and utilized holistically the most critical biomarkers for predicting mental health, e.g., depression. External validation of this technique on different populations may lead to reducing healthcare expenses and improving the processes of diagnosis, forecasting, and tracking of normal and pathological aging.
Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4
Authors: Wright David W. , Wan Shunzhou , Meyer Christophe , van Vlijmen Herman , Tresadern Gary , Coveney Peter V. 
Published: April 2019

AbstractAs the application of computational methods in drug discovery pipelines becomes more widespread it is increasingly important to understand how reproducible their results are and how sensitive they are to choices made in simulation setup and analysis. Here we use ensemble simulation protocols, termed ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent), to investigate the sensitivity of the popular molecular mechanics Poisson-Boltzmann surface area (MMPBSA) methodology. Using the bromodomain-containing protein 4 (BRD4) system bound to a diverse set of ligands as our target, we show that robust rankings can be produced only through combining ensemble sampling with multiple trajectories and enhanced solvation via an explicit ligand hydration shell.
A Fundamental Micro Scale Study of the Roles of Associated Gas Content and Different Classes of Hydrocarbons on the Dominant Oil Recovery Mechanism by CWI
Authors: Seyyedi Mojtaba , Mahzari Pedram , Sohrabi Mehran 
Published: April 2019

AbstractVarious studies demonstrated new gaseous phase formation and oil swelling and viscosity reduction are the oil recovery mechanisms by carbonated water injection (CWI) with new gaseous phase formation being the major recovery mechanism for live oil systems. However, none of the previous studies investigated the influences of dissolved gas content of the oil and oil composition, on the new gaseous phase. This study attempts to provide insights on this area. Based on the results, during CWI as CO2 partitions into the oil the dissolved gas of the oil liberates, which leads to in-situ new gaseous phase formation. The dissolved gas content of the crude oil has a direct impact on the saturation and growth rate of the new gaseous phase. The new gaseous phase doesn’t form for oils that have an infinite capacity for dissolving CO2, such as light pure hydrocarbon components. Oils with limited capacity for dissolving CO2, such as heavy hydrocarbon components, are responsible for the formation of the new gaseous phase. Therefore for a live crude oil, the relatively heavier fractions of oil are responsible for triggering of the new gaseous phase and light to intermediate oil components control the further growth of the new gaseous phase.
Green barley mitigates cytotoxicity in human lymphocytes undergoing aggressive oxidative stress, via activation of both the Lyn/PI3K/Akt and MAPK/ERK pathways
Authors: Ruiz-Medina Blanca E. , Lerma Dennise , Hwang Michael , Ross Jeremy A. , Skouta Rachid , Aguilera Renato J. , Kirken Robert A. , Varela-Ramirez Armando , Robles-Escajeda Elisa 
Published: April 2019

AbstractOxidative stress plays a critical role in numerous diseases. Therefore, the pursuit of compounds with antioxidant activity remains critical. Green barley young leaves aqueous extract (GB) was tested for its capacity to ameliorate cellular oxidative stress, and its potential cytoprotective mechanism was partially elucidated. Through Folin-Ciocalteau and 1,1-diphenyl-2-picrylhydrazyl (DPPH) colorimetric assays, GB total phenolic content and free radical scavenging activity were found to be 59.91 ± 2.17 mg/L and 110.75 µg/ml (IC50), respectively. Using a live cell-based propidium iodide dye exclusion assay and flow cytometry, GB was found to display significant cytoprotection activity on three human lymphocytic cell lines exposed to an aggressive H2O2-induced oxidative stress. The molecular mechanism for GB cytoprotection activity was assessedviabead-based xMAP technology on the Luminex platform and western blot analysis. GB treatment resulted in activation of Lyn, Akt, and ERK1/2, suggesting that GB is able to mitigate the H2O2-induced oxidative stressviaactivation of both the Lyn/PI3K/Akt and ERK/MAPK pathways. Our findings support the notion that GB extract has the potential to be a valuable therapeutic agent and may serve to establish a strategy to discover potential compound(s) or biological extracts/mixtures to be incorporated as a treatment to prevent oxidative stress-related diseases.
The serial blocking effect: a testbed for the neural mechanisms of temporal-difference learning
Authors: Mahmud Ashraf , Petrov Petio , Esber Guillem R. , Iordanova Mihaela D. 
Published: April 2019

AbstractTemporal-difference (TD) learning models afford the neuroscientist a theory-driven roadmap in the quest for the neural mechanisms of reinforcement learning. The application of these models to understanding the role of phasic midbrain dopaminergic responses in reward prediction learning constitutes one of the greatest success stories in behavioural and cognitive neuroscience. Critically, the classic learning paradigms associated with TD are poorly suited to cast light on its neural implementation, thus hampering progress. Here, we present a serial blocking paradigm in rodents that overcomes these limitations and allows for the simultaneous investigation of two cardinal TD tenets; namely, that learning depends on the computation of a prediction error, and that reinforcing value, whether intrinsic or acquired, propagates back to the onset of the earliest reliable predictor. The implications of this paradigm for the neural exploration of TD mechanisms are highlighted.