bluuebunny/crossref_metadata_2025_split huggingface dataset:
Catalytic mechanism of graphene-nickel interface dipole layer for binder free electrochemical sensor applications
Authors: Zhang Chunfei , Lee Byong-June , Li Haiping , Samdani Jitendra , Kang Tong-Hyun , Yu Jong-Sung 
Published: December 2018

AbstractThe combination of graphene with metal nanoparticles can produce enhanced catalytic properties because of synergistic effects, and has been used to develop highly active catalysts for different applications. However, the mechanism of the synergistic effect between graphene and metal is poorly understood. Here we demonstrate that graphene-coated nickel foam shows a significant catalytic effect on electrodeless metal (gold, platinum, silver, and copper) deposition without any external reducing agent. This is attributed to the formation of an interface dipole layer, induced by the interaction between graphene and nickel. The interface dipole layer catalytic mechanism accelerates metal reduction reaction and explains the simultaneous formation of nickel hydroxide. The nickel hydroxide-wrapped silver hybrid self-assembly developed on the graphene-coated nickel foam serves as an efficient binder-free electrochemical sensor owing to its hierarchical structure.
Brilliant gamma-ray beam and electron–positron pair production by enhanced attosecond pulses
Authors: Gu Yan-Jun , Klimo Ondrej , Bulanov Sergei V. , Weber Stefan 
Published: December 2018

AbstractElectron–positron pair production via Breit–Wheeler process requires laser intensities approaching 1024 W cm−2 due to the small cross-section. Here, we propose a mechanism for brilliant γ-ray emission and dense GeV pairs creation accompanied with high-harmonic generation by using plasma mirror and an ultra short pulse with the intensity of 3 × 1023 W cm−2. The laser is reflected by the solid surface after propagating tens of microns in a near-critical density plasma and breaks into short wave packets. The intensity of the reflected high order harmonic field is enhanced by the focusing and compression effects from the deformed oscillating mirror. The radiation trapped electrons emit γ-photons while colliding with the reflected attosecond pulses. The peak intensity of the γ-ray reaches 0.74 PW with the brilliance of 2 × 1024 s−1 mm−2 mrad−2 (0.1%BW)−1 (at 58 MeV). A GeV positron beam is obtained with density of 4 × 1021 cm−3 and a particle number of 5.6 × 109.
Transcript- and protein-level analyses of the response of human eosinophils to glucocorticoids
Authors: Gadkari Manasi , Makiya Michelle A. , Legrand Fanny , Stokes Kindra , Brown Thomas , Howe Katherine , Khoury Paneez , Hu Zonghui , Klion Amy , Franco Luis M. 
Published: December 2018

AbstractGlucocorticoids are first-line agents for the treatment of many eosinophil-associated disorders; however, their effects on human eosinophils remain poorly understood. To gain an unbiased, genome-wide view of the early transcriptional effects of glucocorticoids on human eosinophils in vivo, RNA sequencing was performed on purified blood eosinophils obtained before and 30, 60, and 120 minutes after administration of a single dose of oral prednisone (1 mg/kg) to three unrelated healthy subjects with hypereosinophilia of unknown significance. The resulting dataset is of high quality and suitable for differential expression analysis. Flow cytometry and qPCR were then performed on three additional cohorts of human subjects, to validate the key findings at the transcript and protein levels. The resulting datasets provide a resource for understanding the response of circulating human eosinophils to glucocorticoid administration.
Unbalanced historical phenotypic data from seed regeneration of a barley ex situ collection
Authors: Gonzalez Maria Y. , Weise Stephan , Zhao Yusheng , Philipp Norman , Arend Daniel , Börner Andreas , Oppermann Markus , Graner Andreas , Reif Jochen C. , Schulthess Albert W. 
Published: December 2018

AbstractThe scarce knowledge on phenotypic characterization restricts the usage of genetic diversity of plant genetic resources in research and breeding. We describe original and ready-to-use processed data for approximately 60% of ~22,000 barley accessions hosted at the Federalex situGenebank for Agricultural and Horticultural Plant Species. The dataset gathers records for three traits with agronomic relevance: flowering time, plant height and thousand grain weight. This information was collected for seven decades for winter and spring barley during the seed regeneration routine. The curated data represent a source for research on genetics and genomics of adaptive and yield related traits in cereals due to the importance of barley as model organism. This data could be used to predict the performance of non-phenotyped individuals in other collections through genomic prediction. Moreover, the dataset empowers the utilization of phenotypic diversity of genetic resources for crop improvement.
An annotated test-retest collection of prostate multiparametric MRI
Authors: Fedorov Andriy , Schwier Michael , Clunie David , Herz Christian , Pieper Steve , Kikinis Ron , Tempany Clare , Fennessy Fiona 
Published: December 2018

AbstractMultiparametric Magnetic Resonance Imaging (mpMRI) is widely used for characterizing prostate cancer. Standard of care use of mpMRI in clinic relies on visual interpretation of the images by an expert. mpMRI is also increasingly used as a quantitative imaging biomarker of the disease. Little is known about repeatability of such quantitative measurements, and no test-retest datasets have been available publicly to support investigation of the technical characteristics of the MRI-based quantification in the prostate. Here we present an mpMRI dataset consisting of baseline and repeat prostate MRI exams for 15 subjects, manually annotated to define regions corresponding to lesions and anatomical structures, and accompanied by region-based measurements. This dataset aims to support further investigation of the repeatability of mpMRI-derived quantitative prostate measurements, study of the robustness and reliability of the automated analysis approaches, and to support development and validation of new image analysis techniques. The manuscript can also serve as an example of the use of DICOM for standardized encoding of the image annotation and quantification results.
Inherent auditory skills rather than formal music training shape the neural encoding of speech
Authors: Mankel Kelsey , Bidelman Gavin M. 
Published: December 2018

Significance
Musicianship is widely reported to enhance auditory brain processing related to speech–language function. Such benefits could reflect true experience-dependent plasticity, as often assumed, or innate, preexisting differences in auditory system function (i.e., nurture vs. nature). By recording speech-evoked electroencephalograms, we show that individuals who are naturally more adept in listening tasks but possess no formal music training (“musical sleepers”) have superior neural encoding of clear and noise-degraded speech, mirroring enhancements reported in trained musicians. Our findings provide clear evidence that certain individuals have musician-like auditory neurobiological function and temper assumptions that music-related neuroplasticity is solely experience-driven. These data reveal that formal music experience is neither necessary nor sufficient to enhance the brain’s neural encoding and perception of sound.
Resource extraction and infrastructure threaten forest cover and community rights
Authors: Bebbington Anthony J. , Humphreys Bebbington Denise , Sauls Laura Aileen , Rogan John , Agrawal Sumali , Gamboa César , Imhof Aviva , Johnson Kimberly , Rosa Herman , Royo Antoinette , Toumbourou Tessa , Verdum Ricardo 
Published: December 2018

Significance
While infrastructure expansion has been broadly investigated as a driver of deforestation, the impacts of extractive industry and its interactions with infrastructure investment on forest cover are less well studied. These challenges are urgent given growing pressure for infrastructure investment and resource extraction. We use geospatial and qualitative data from Amazonia, Indonesia, and Mesoamerica to explain how infrastructure and extractive industry lead directly and indirectly to deforestation, forest degradation, and increasingly precarious rights for forest peoples. By engaging in explicit analyses of community rights, the politics of development policy, and institutions for transparency, anticorruption, and the defense of human rights, Sustainability Science could be more effective in examining deforestation and related climate-change impacts and in contributing to policy innovation.
MRI demonstrates glutamine antagonist-mediated reversal of cerebral malaria pathology in mice
Authors: Riggle Brittany A. , Sinharay Sanhita , Schreiber-Stainthorp William , Munasinghe Jeeva P. , Maric Dragan , Prchalova Eva , Slusher Barbara S. , Powell Jonathan D. , Miller Louis H. , Pierce Susan K. , Hammoud Dima A. 
Published: December 2018

SignificanceCerebral malaria (CM) is the deadliest complication ofPlasmodium falciparuminfection, resulting in a 15 to 25% mortality rate in African children despite antimalarial chemotherapy. Tragically, nearly a fourth of pediatric CM survivors suffer long-term neurological sequelae. There is an urgent public health and humanitarian need for therapies for CM. In a mouse model of CM, we used magnetic resonance imaging (MRI) to monitor infected mice longitudinally as CM progressed and noninvasively demonstrate that the edema and blood–brain barrier dysfunction, which ultimately result in death, are rapidly reversed by treatment with the glutamine antagonist JHU-083. The similarities between CM MRI shown in mice and those reported in children and adults suggest that glutamine antagonists may be effective CM therapies.
Synergistic neuroprotection by coffee components eicosanoyl-5-hydroxytryptamide and caffeine in models of Parkinson's disease and DLB
Authors: Yan Run , Zhang Jie , Park Hye-Jin , Park Eun S. , Oh Stephanie , Zheng Haiyan , Junn Eunsung , Voronkov Michael , Stock Jeffry B. , Mouradian M. Maral 
Published: December 2018

Significance
Coffee consumption is linked with reduced risk of Parkinson’s disease (PD), and caffeine is generally believed to be the protective agent. However, several lines of evidence suggest the presence of additional compound(s) in coffee that can be protective as well. Here we show that eicosanoyl-5-hydroxytryptamide, which we purified from coffee as an agent that leads to enhanced enzymatic activity of the specific phosphatase PP2A that dephosphorylates the pathogenic protein α-synuclein, works in synergy with caffeine in protecting against mouse models of PD and Dementia with Lewy bodies. The mechanism of this synergy is also through enhancing PP2A, which is dysregulated in the brains of individuals with these α-synucleinopathies.
Basophils trigger emphysema development in a murine model of COPD through IL-4–mediated generation of MMP-12–producing macrophages
Authors: Shibata Sho , Miyake Kensuke , Tateishi Tomoya , Yoshikawa Soichiro , Yamanishi Yoshinori , Miyazaki Yasunari , Inase Naohiko , Karasuyama Hajime 
Published: December 2018

Significance
Chronic obstructive pulmonary disease has generally been considered a non-Th2-type lung disease, in contrast to allergic asthma. We identified unexpected roles for basophils, Th2 cytokine IL-4, and interstitial macrophages in triggering emphysema formation in spite of the fact that basophils account for less than 1% of cellular infiltrates in the lung. Our observations in a series of genetically engineered mice illustrated that basophil-derived IL-4 acts on lung-infiltrating monocytes to promote their differentiation into interstitial macrophages that in turn produce a pathogenic enzyme, matrix metalloproteinase-12 (MMP-12), resulting in the destruction of alveolar walls and leading to emphysema. Thus, the present study has identified a previously unappreciated role for the basophil-derived IL-4/monocyte–derived interstitial macrophage/MMP-12 axis at the initiation phase of emphysema development in mice.
Isolation and characterization of adrenocortical progenitors involved in the adaptation to stress
Authors: Steenblock Charlotte , Rubin de Celis Maria F. , Delgadillo Silva Luis F. , Pawolski Verena , Brennand Ana , Werdermann Martin , Berger Ilona , Santambrogio Alice , Peitzsch Mirko , Andoniadou Cynthia L. , Schally Andrew V. , Bornstein Stefan R. 
Published: December 2018

Significance
Humans are constantly confronted with multiple stressors, to which the bodily response and adaptation are essential. The adrenal gland plays a major role in the response to physiological challenges. Maintenance of the adrenal is partly accomplished by proliferation and differentiation of adult progenitors and stem cells in the cortex and medulla. In this study, we have isolated and characterized a subpopulation of adrenocortical progenitors, which are interconnected with adrenomedullary stress-dependent progenitors. Under stress, the adrenocortical progenitors are also activated and they mobilize, giving rise to steroidogenic cells. Our findings demonstrate the coordinated action of stress-inducible stem cells to ensure tissue remodeling and cellular and functional adaptation to stress.
Inosine, but none of the 8-oxo-purines, is a plausible component of a primordial version of RNA
Authors: Kim Seohyun Chris , O’Flaherty Derek K. , Zhou Lijun , Lelyveld Victor S. , Szostak Jack W. 
Published: December 2018

Significance
The RNA world hypothesis assumes the abiotic synthesis of nucleotides, as well as their participation in nonenzymatic RNA replication. Whereas prebiotic syntheses of the canonical purine nucleotides remain inefficient, a prebiotically plausible route to the 8-oxo-purines has been reported. Although these noncanonical purine nucleotides are known to engage in non-Watson–Crick pairing with their canonical purine counterparts, their behavior in nonenzymatic RNA copying has not been evaluated. Our study indicates that none of the 8-oxo-purines behaves as a suitable substrate for nonenzymatic RNA copying. However, inosine turns out to exhibit reasonable rates and fidelities in RNA copying reactions. We propose that inosine could have served as a surrogate for guanosine in the early emergence of life.
Dermal Advanced REACH Tool (dART)—Development of a Dermal Exposure Model for Low-Volatile Liquids
Authors: Goede Henk A , McNally Kevin , Gorce Jean-Philippe , Marquart Hans , Warren Nick D , Fransman Wouter , Tischer Martin , Schinkel Jody 
Published: December 2018

Abstract
This article describes the development of a mechanistic model for underpinning the dermal Advanced REACH Tool (dART), an extension of the existing ART model and its software platform. It was developed for hand exposure to low volatile liquids (vapour pressure ≤ 10 Pa at 20°C) including solids-in-liquid products. The model is based on an existing conceptual dermal source-receptor model that has been integrated into the ART framework. A structured taxonomy of workplace activities referred to as activity classes are adopted from ART.  Three key processes involved in mass transport associated with dermal exposure are applied, i.e. deposition, direct emission and contact, and transfer. For deposition, the model adopts all the relevant modifying factors (MFs) applied in ART. In terms of direct emission and contact (e.g. splashes) and transfer (e.g. hand-surface contacts), the model defines independent principal MFs, i.e. substance-related factors, activity-related factors, localized- and dispersion control and exposed surface area of the hands. To address event-based exposures as much as possible, the model includes crucial events during an activity (e.g. hand immersions) and translates objective information on tools and equipment (manual or automated) to probable events (e.g. splashes) and worker behaviours (e.g. surface contacts). Based on an extensive review of peer-reviewed literature and unpublished field studies, multipliers were assigned to each determinant and provide an approximated (dimensionless) numerical value. In the absence of (sufficient) evidence, multipliers were assigned to determinants based on assumptions made during discussions by experts in the consortium. A worked example is presented to illustrate the calculation of hand exposure for a specific scenario. The dART model is not yet implemented in the ART software platform, and a robust validation of the model is necessary to determine its predictive ability. With advancing knowledge on dermal exposure and its determinants, this model will require periodic updates and refinements, in addition to further expansion of the applicability domain of the model.
Use of Bone-Cartilaginous Unit in Revision Rhinoplasty
Authors: Sazgar Amir A , Teimouri Yeganeh , Sazgar Amir K 
Published: December 2018

Abstract

Background
Insufficient septal cartilage is a common finding when performing revision rhinoplasty. Such cases require costal or conchal cartilage to be harvested, which is time consuming and brings the risk of morbidity. A new technique involves the use of a septal bone-cartilage composite graft or a bone-cartilaginous (BC) unit as a rhinoplasty graft.

Objectives
The aim of this research was to evaluate the subjective and objective effects of using a BC unit graft in revision rhinoplasty.

Methods
In this clinical trial, we examined 40 patients with insufficient septal cartilage for grafting who were referred to a tertiary center and a private setting from January 2016 to March 2017 for revision septorhinoplasty. The patients had nasal deformity and nasal obstruction. Assessment of surgical outcome was based on anthropometric measurements and by measuring the width of the middle nasal third from photographs, and on 2 patient questionnaires: the Nasal Obstruction and Septoplasty Effectiveness (NOSE) and the Rhinoplasty Outcome Evaluation (ROE) questionnaires.

Results
Nasolabial angles and the middle nasal third improved significantly after surgery (P &lt; 0.005). Based on the NOSE questionnaire, 85% of patients had no or mild nasal obstruction, and the ROE questionnaire indicated that 62.5% were completely or very satisfied with the appearance of their nose.

Conclusions
The BC unit is an effective graft in revision rhinoplasty, and can be used in place of the rib graft. In skilled hands, harvesting of this graft results in no morbidity and is not time consuming.

Level of Evidence: 4
BaiHui: cross-species brain-specific network built with hundreds of hand-curated datasets
Authors: Li Hong-Dong , Bai Tianjian , Sandford Erin , Burmeister Margit , Guan Yuanfang 
Published: December 2018

Abstract

Motivation
Functional gene networks, representing how likely two genes work in the same biological process, are important models for studying gene interactions in complex tissues. However, a limitation of the current network-building scheme is the lack of leveraging evidence from multiple model organisms as well as the lack of expert curation and quality control of the input genomic data.

Results
Here, we present BaiHui, a brain-specific functional gene network built by probabilistically integrating expertly-hand-curated (by reading original publications) heterogeneous and multi-species genomic data in human, mouse and rat brains. To facilitate the use of this network, we deployed a web server through which users can query their genes of interest, visualize the network, gain functional insight from enrichment analysis and download network data. We also illustrated how this network could be used to generate testable hypotheses on disease gene prioritization of brain disorders.

Availability and implementation
BaiHui is freely available at: http://guanlab.ccmb.med.umich.edu/BaiHui/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Global Biobank Engine: enabling genotype-phenotype browsing for biobank summary statistics
Authors: McInnes Gregory , Tanigawa Yosuke , DeBoever Chris , Lavertu Adam , Olivieri Julia Eve , Aguirre Matthew , Rivas Manuel A 
Published: December 2018

Abstract

Summary
Large biobanks linking phenotype to genotype have led to an explosion of genetic association studies across a wide range of phenotypes. Sharing the knowledge generated by these resources with the scientific community remains a challenge due to patient privacy and the vast amount of data. Here, we present Global Biobank Engine (GBE), a web-based tool that enables exploration of the relationship between genotype and phenotype in biobank cohorts, such as the UK Biobank. GBE supports browsing for results from genome-wide association studies, phenome-wide association studies, gene-based tests and genetic correlation between phenotypes. We envision GBE as a platform that facilitates the dissemination of summary statistics from biobanks to the scientific and clinical communities.

Availability and implementation
GBE currently hosts data from the UK Biobank and can be found freely available at biobankengine.stanford.edu.
Temporal Metacognition as the Decoding of Self-Generated Brain Dynamics
Authors: Kononowicz Tadeusz W , Roger Clémence , van Wassenhove Virginie 
Published: December 2018

Abstract
Metacognition, the ability to know about one’s thought process, is self-referential. Here, we combined psychophysics and time-resolved neuroimaging to explore metacognitive inference on the accuracy of a self-generated behavior. Human participants generated a time interval and evaluated the signed magnitude of their temporal production. We show that both self-generation and self-evaluation relied on the power of beta oscillations (β; 15–40 Hz) with increases in early β power predictive of increases in duration. We characterized the dynamics of β power in a low-dimensional space (β state-space trajectories) as a function of timing and found that the more distinct trajectories, the more accurate metacognitive inferences were. These results suggest that β states instantiate an internal variable determining the fate of the timing network’s trajectory, possibly as release from inhibition. Altogether, our study describes oscillatory mechanisms for timing, suggesting that temporal metacognition relies on inferential processes of self-generated dynamics.