bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid RNA–ligand interaction analysis through high-information content conformational and stability landscapes
Authors: Baird Nathan J. , Inglese James , Ferré-D’Amaré Adrian R. 
Published: December 2015

AbstractThe structure and biological properties of RNAs are a function of changing cellular conditions, but comprehensive, simultaneous investigation of the effect of multiple interacting environmental variables is not easily achieved. We have developed an efficient, high-throughput method to characterize RNA structure and thermodynamic stability as a function of multiplexed solution conditions using Förster resonance energy transfer (FRET). In a single FRET experiment using conventional quantitative PCR instrumentation, 19,400 conditions of MgCl2, ligand and temperature are analysed to generate detailed empirical conformational and stability landscapes of the cyclic diguanylate (c-di-GMP) riboswitch. The method allows rapid comparison of RNA structure modulation by cognate and non-cognate ligands. Landscape analysis reveals that kanamycin B stabilizes a non-native, idiosyncratic conformation of the riboswitch that inhibits c-di-GMP binding. This demonstrates that allosteric control of folding, rather than direct competition with cognate effectors, is a viable approach for pharmacologically targeting riboswitches and other structured RNA molecules.
Room-temperature in situ nuclear spin hyperpolarization from optically pumped nitrogen vacancy centres in diamond
Authors: King Jonathan P. , Jeong Keunhong , Vassiliou Christophoros C. , Shin Chang S. , Page Ralph H. , Avalos Claudia E. , Wang Hai-Jing , Pines Alexander 
Published: December 2015

AbstractLow detection sensitivity stemming from the weak polarization of nuclear spins is a primary limitation of magnetic resonance spectroscopy and imaging. Methods have been developed to enhance nuclear spin polarization but they typically require high magnetic fields, cryogenic temperatures or sample transfer between magnets. Here we report bulk, room-temperature hyperpolarization of 13C nuclear spins observed via high-field magnetic resonance. The technique harnesses the high optically induced spin polarization of diamond nitrogen vacancy centres at room temperature in combination with dynamic nuclear polarization. We observe bulk nuclear spin polarization of 6%, an enhancement of ∼170,000 over thermal equilibrium. The signal of the hyperpolarized spins was detected in situ with a standard nuclear magnetic resonance probe without the need for sample shuttling or precise crystal orientation. Hyperpolarization via optical pumping/dynamic nuclear polarization should function at arbitrary magnetic fields enabling orders of magnitude sensitivity enhancement for nuclear magnetic resonance of solids and liquids under ambient conditions.
The climate hazards infrared precipitation with stations—a new environmental record for monitoring extremes
Authors: Funk Chris , Peterson Pete , Landsfeld Martin , Pedreros Diego , Verdin James , Shukla Shraddhanand , Husak Gregory , Rowland James , Harrison Laura , Hoell Andrew , Michaelsen Joel 
Published: December 2015

AbstractThe Climate Hazards group Infrared Precipitation with Stations (CHIRPS) dataset builds on previous approaches to ‘smart’ interpolation techniques and high resolution, long period of record precipitation estimates based on infrared Cold Cloud Duration (CCD) observations. The algorithm i) is built around a 0.05° climatology that incorporates satellite information to represent sparsely gauged locations, ii) incorporates daily, pentadal, and monthly 1981-present 0.05° CCD-based precipitation estimates, iii) blends station data to produce a preliminary information product with a latency of about 2 days and a final product with an average latency of about 3 weeks, and iv) uses a novel blending procedure incorporating the spatial correlation structure of CCD-estimates to assign interpolation weights. We present the CHIRPS algorithm, global and regional validation results, and show how CHIRPS can be used to quantify the hydrologic impacts of decreasing precipitation and rising air temperatures in the Greater Horn of Africa. Using the Variable Infiltration Capacity model, we show that CHIRPS can support effective hydrologic forecasts and trend analyses in southeastern Ethiopia.
Multi-omic profiles of human non-alcoholic fatty liver disease tissue highlight heterogenic phenotypes
Authors: Wruck Wasco , Kashofer Karl , Rehman Samrina , Daskalaki Andriani , Berg Daniela , Gralka Ewa , Jozefczuk Justyna , Drews Katharina , Pandey Vikash , Regenbrecht Christian , Wierling Christoph , Turano Paola , Korf Ulrike , Zatloukal Kurt , Lehrach Hans , Westerhoff Hans V. , Adjaye James 
Published: December 2015

AbstractNon-alcoholic fatty liver disease (NAFLD) is a consequence of sedentary life style and high fat diets with an estimated prevalence of about 30% in western countries. It is associated with insulin resistance, obesity, glucose intolerance and drug toxicity. Additionally, polymorphisms within, e.g., APOC3, PNPLA3, NCAN, TM6SF2 and PPP1R3B, correlate with NAFLD. Several studies have already investigated later stages of the disease. This study explores the early steatosis stage of NAFLD with the aim of identifying molecular mechanisms underlying the etiology of NAFLD. We analyzed liver biopsies and serum samples from patients with high- and low-grade steatosis (also pre-disease states) employing transcriptomics, ELISA-based serum protein analyses and metabolomics. Here, we provide a detailed description of the various related datasets produced in the course of this study. These datasets may help other researchers find new clues for the etiology of NAFLD and the mechanisms underlying its progression to more severe disease states.
Long-term monitoring dataset of fish assemblages impinged at nuclear power plants in northern Taiwan
Authors: Chen Hungyen , Liao Yun-Chih , Chen Ching-Yi , Tsai Jeng-I , Chen Lee-Sea , Shao Kwang-Tsao 
Published: December 2015

AbstractThe long-term species diversity patterns in marine fish communities are garnering increasing attention from ecologists and conservation biologists. However, current databases on quantitative abundance information lack consistent long-term time series, which are particularly important in exploring the possible underlying mechanism of community changes and evaluating the effectiveness of biodiversity conservation measures. Here we describe an impinged fish assemblage dataset containing 1, 283, 707 individuals from 439 taxa. Once a month over 19 years (1987–1990 and 2000–2014), we systematically collected the fish killed by impingement upon cooling water intake screens at two nuclear power plants on the northern coast of Taiwan. Because impingement surveys have low sampling errors and can be carried out over many years, they serve as an ideal sampling tool for monitoring how fish diversity and community structure vary over an extended period of time.
Hair-bundle proteomes of avian and mammalian inner-ear utricles
Authors: Wilmarth Phillip A. , Krey Jocelyn F. , Shin Jung-Bum , Choi Dongseok , David Larry L. , Barr-Gillespie Peter G. 
Published: December 2015

AbstractExamination of multiple proteomics datasets within or between species increases the reliability of protein identification. We report here proteomes of inner-ear hair bundles from three species (chick, mouse, and rat), which were collected on LTQ or LTQ Velos ion-trap mass spectrometers; the constituent proteins were quantified using MS2 intensities, which are the summed intensities of all peptide fragmentation spectra matched to a protein. The data are available via ProteomeXchange with identifiers PXD002410 (chick LTQ), PXD002414 (chick Velos), PXD002415 (mouse Velos), and PXD002416 (rat LTQ). The two chick bundle datasets compared favourably to a third, already-described chick bundle dataset, which was quantified using MS1 peak intensities, the summed intensities of peptides identified by high-resolution mass spectrometry (PXD000104; updated analysis in PXD002445). The mouse bundle dataset described here was comparable to a different mouse bundle dataset quantified using MS1 intensities (PXD002167). These six datasets will be useful for identifying the core proteome of vestibular hair bundles.
A global planktic foraminifer census data set for the Pliocene ocean
Authors: Dowsett Harry , Robinson Marci , Foley Kevin 
Published: December 2015

AbstractThis article presents data derived by the USGS Pliocene Research, Interpretation and Synoptic Mapping (PRISM) Project. PRISM has generated planktic foraminifer census data from core sites and outcrops around the globe since 1988. These data form the basis of a number of paleoceanographic reconstructions focused on the mid-Piacenzian Warm Period (3.264 to 3.025 million years ago). Data are presented as counts of individuals within 64 taxonomic categories for each locality. We describe sample acquisition and processing, age dating, taxonomy and archival storage of material. These data provide a unique, stratigraphically focused opportunity to assess the effects of global warming on marine plankton.
New hope for the survival of the Amur leopard in China
Authors: Jiang Guangshun , Qi Jinzhe , Wang Guiming , Shi Quanhua , Darman Yury , Hebblewhite Mark , Miquelle Dale G. , Li Zhilin , Zhang Xue , Gu Jiayin , Chang Youde , Zhang Minghai , Ma Jianzhang 
Published: December 2015

AbstractNatural range loss limits the population growth of Asian big cats and may determine their survival. Over the past decade, we collected occurrence data of the critically endangered Amur leopard worldwide and developed a distribution model of the leopard’s historical range in northeastern China over the past decade. We were interested to explore how much current range area exists, learn what factors limit their spatial distribution, determine the population size and estimate the extent of potential habitat. Our results identify 48,252 km2 of current range and 21,173.7 km2 of suitable habitat patches and these patches may support 195.1 individuals. We found that prey presence drives leopard distribution, that leopard density exhibits a negative response to tiger occurrence and that the largest habitat patch connects with 5,200 km2of Russian current range. These insights provide a deeper understanding of the means by which endangered predators might be saved and survival prospects for the Amur leopard not only in China, but also through imperative conservation cooperation internationally.
Ceramides And Stress Signalling Intersect With Autophagic Defects In Neurodegenerative Drosophila blue cheese (bchs) Mutants
Authors: Hebbar Sarita , Sahoo Ishtapran , Matysik Artur , Argudo Garcia Irene , Osborne Kathleen Amy , Papan Cyrus , Torta Federico , Narayanaswamy Pradeep , Fun Xiu Hui , Wenk Markus R , Shevchenko Andrej , Schwudke Dominik , Kraut Rachel 
Published: December 2015

AbstractSphingolipid metabolites are involved in the regulation of autophagy, a degradative recycling process that is required to prevent neuronal degeneration. Drosophilablue cheesemutants neurodegenerate due to perturbations in autophagic flux and consequent accumulation of ubiquitinated aggregates. Here, we demonstrate thatblue cheesemutant brains exhibit an elevation in total ceramide levels; surprisingly, however, degeneration is ameliorated when the pool of available ceramides is further increased and exacerbated when ceramide levels are decreased by altering sphingolipid catabolism or blockingde novosynthesis. Exogenous ceramide is seen to accumulate in autophagosomes, which are fewer in number and show less efficient clearance inblue cheesemutant neurons. Sphingolipid metabolism is also shifted away from salvage towardde novopathways, while pro-growth Akt and MAP pathways are down-regulated and ER stress is increased. All these defects are reversed under genetic rescue conditions that increase ceramide generation from salvage pathways. This constellation of effects suggests a possible mechanism whereby the observed deficit in a potentially ceramide-releasing autophagic pathway impedes survival signaling and exacerbates neuronal death.
TLR4 drives the pathogenesis of acquired cholesteatoma by promoting local inflammation and bone destruction
Authors: Si Yu , Chen Yu Bin , Chen Sui Jun , Zheng Yi Qing , Liu Xiang , Liu Yi , Jiang Huai Li , Xu Guo , Li Zhuo Hao , Huang Qiu Hong , Xiong Hao , Zhang Zhi Gang 
Published: December 2015

AbstractAcquired cholesteatoma is a chronic inflammatory disease characterized by both hyperkeratinized squamous epithelial overgrowth and bone destruction. Toll-like receptor (TLR) activation and subsequent inflammatory cytokine production are closely associated with inflammatory bone disease. However, the expression and function of TLRs in cholesteatoma remain unclear.We observed inflammatory cell infiltration of the matrix and prematrix of human acquired cholesteatoma, as well as dramatically increased expression of TLR4 and the pro-inflammatory cytokines TNF-α and IL-1β. TLR2 exhibited an up-regulation that was not statistically significant. TLR4 expression in human acquired cholesteatoma correlated with disease severity; the number of TLR4-positive cells increased with an increased degree of cholesteatoma, invasion, bone destruction and hearing loss. Moreover, TLR4 deficiency was protective against experimental acquired cholesteatoma-driven bone destruction and hearing loss, as it reduced local TNF-α and IL-1β expression and impaired osteoclast formation by decreasing expression of the osteoclast effectors receptor activator of nuclear factor (NF)-κB ligand (RANKL) and tartrate-resistant acid phosphatase (TRAP). TLR2 deficiency did not relieve disease severity, inflammatory responses, or osteoclast formation. Moreover, neither TLR2 nor TLR4 deficiency had an effect on antimicrobial peptides, inducible iNOS,BD-2 expression or bacterial clearance. Therefore, TLR4 may promote cholesteatoma-induced bone destruction and deafness by enhancing inflammatory responses and osteoclastogenesis.
Monitoring Network Confirms Land Use Change is a Substantial Component of the Forest Carbon Sink in the eastern United States
Authors: Woodall C. W. , Walters B. F. , Coulston J. W. , D’Amato A. W. , Domke G. M. , Russell M. B. , Sowers P. A. 
Published: December 2015

AbstractQuantifying forest carbon (C) stocks and stock change within a matrix of land use (LU) and LU change is a central component of large-scale forest C monitoring and reporting practices prescribed by the Intergovernmental Panel on Climate Change (IPCC). Using a region–wide, repeated forest inventory, forest C stocks and stock change by pool were examined by LU categories. In eastern US forests, LU change is a substantial component of C sink strength (~37% of forest sink strength) only secondary to that of C accumulation in forests remaining forest where their comingling with other LUs does not substantially reduce sink strength. The strongest sinks of forest C were study areas not completely dominated by forests, even when there was some loss of forest to agriculture/settlement/other LUs. Long-term LU planning exercises and policy development that seeks to maintain and/or enhance regional C sinks should explicitly recognize the importance of maximizing non-forest to forest LU changes and not overlook management and conservation of forests located in landscapes not currently dominated by forests.
Detection of gene communities in multi-networks reveals cancer drivers
Authors: Cantini Laura , Medico Enzo , Fortunato Santo , Caselle Michele 
Published: December 2015

AbstractWe propose a new multi-network-based strategy to integrate different layers of genomic information and use them in a coordinate way to identify driving cancer genes. The multi-networks that we consider combine transcription factor co-targeting, microRNA co-targeting, protein-protein interaction and gene co-expression networks. The rationale behind this choice is that gene co-expression and protein-protein interactions require a tight coregulation of the partners and that such a fine tuned regulation can be obtained only combining both the transcriptional and post-transcriptional layers of regulation. To extract the relevant biological information from the multi-network we studied its partition into communities. To this end we applied a consensus clustering algorithm based on state of art community detection methods. Even if our procedure is valid in principle for any pathology in this work we concentrate on gastric, lung, pancreas and colorectal cancer and identified from the enrichment analysis of the multi-network communities a set of candidate driver cancer genes. Some of them were already known oncogenes while a few are new. The combination of the different layers of information allowed us to extract from the multi-network indications on the regulatory pattern and functional role of both the already known and the new candidate driver genes.
The Potential of High Resolution Magnetic Resonance Microscopy in the Pathologic Analysis of Resected Breast and Lymph Tissue
Authors: Dashevsky Brittany Z. , D'Alfonso Timothy , Sutton Elizabeth J. , Giambrone Ashley , Aronowitz Eric , Morris Elizabeth A. , Juluru Krishna , Ballon Douglas J. 
Published: December 2015

AbstractPathologic evaluation of breast specimens requires a fixation and staining procedure of at least 12 hours duration, delaying diagnosis and post-operative planning. Here we introduce an MRI technique with a custom-designed radiofrequency resonator for imaging breast and lymph tissue with sufficient spatial resolution and speed to guide pathologic interpretation and offer value in clinical decision making. In this study, we demonstrate the ability to image breast and lymphatic tissue using 7.0 Tesla MRI, achieving a spatial resolution of 59 × 59 × 94 μm3 with a signal-to-noise ratio of 15–20, in an imaging time of 56 to 70 minutes. These are the first MR images to reveal characteristic pathologic features of both benign and malignant breast and lymph tissue, some of which were discernible by blinded pathologists who had no prior training in high resolution MRI interpretation.
A highly efficient CMOS nanoplasmonic crystal enhanced slow-wave thermal emitter improves infrared gas-sensing devices
Authors: Pusch Andreas , De Luca Andrea , Oh Sang S. , Wuestner Sebastian , Roschuk Tyler , Chen Yiguo , Boual Sophie , Ali Zeeshan , Phillips Chris C. , Hong Minghui , Maier Stefan A. , Udrea Florin , Hopper Richard H. , Hess Ortwin 
Published: December 2015

AbstractThe application of plasmonics to thermal emitters is generally assisted by absorptive losses in the metal because Kirchhoff’s law prescribes that only good absorbers make good thermal emitters. Based on a designed plasmonic crystal and exploiting a slow-wave lattice resonance and spontaneous thermal plasmon emission, we engineer a tungsten-based thermal emitter, fabricated in an industrial CMOS process and demonstrate its markedly improved practical use in a prototype non-dispersive infrared (NDIR) gas-sensing device. We show that the emission intensity of the thermal emitter at the CO2 absorption wavelength is enhanced almost 4-fold compared to a standard non-plasmonic emitter, which enables a proportionate increase in the signal-to-noise ratio of the CO2 gas sensor.
Developmental exposure to Ethinylestradiol affects transgenerationally sexual behavior and neuroendocrine networks in male mice
Authors: Derouiche Lyes , Keller Matthieu , Duittoz Anne Hélène , Pillon Delphine 
Published: December 2015

AbstractReproductive behavior and physiology in adulthood are controlled by hypothalamic sexually dimorphic neuronal networks which are organized under hormonal control during development. These organizing effects may be disturbed by endocrine disrupting chemicals (EDCs). To determine whether developmental exposure to Ethinylestradiol (EE2) may alter reproductive parameters in adult male mice and their progeny, Swiss mice (F1 generation) were exposed from prenatal to peripubertal periods to EE2 (0.1–1 μg/kg/d). Sexual behavior and reproductive physiology were evaluated on F1 males and their F2, F3 and F4 progeny. EE2-exposed F1 males and their F2 to F4 progeny exhibited EE2 dose-dependent increased sexual behavior, with reduced latencies of first mount and intromission and higher frequencies of intromissions with a receptive female. The EE2 1 μg/kg/d exposed animals and their progeny had more calbindin immunoreactive cells in the medial preoptic area, known to be involved in the control of male sexual behavior in rodents. Despite neuroanatomical modifications in the Gonadotropin-Releasing Hormone neuron population of F1 males exposed to both doses of EE2, no major deleterious effects on reproductive physiology were detected. Therefore EE2 exposure during development may induce a hypermasculinization of the brain, illustrating how widespread exposure of animals and humans to EDCs can impact health and behaviors.
Fine-tuned SRF activity controls asymmetrical neuronal outgrowth: implications for cortical migration, neural tissue lamination and circuit assembly
Authors: Scandaglia Marilyn , Benito Eva , Morenilla-Palao Cruz , Fiorenza Anna , del Blanco Beatriz , Coca Yaiza , Herrera Eloísa , Barco Angel 
Published: December 2015

AbstractThe stimulus-regulated transcription factor Serum Response Factor (SRF) plays an important role in diverse neurodevelopmental processes related to structural plasticity and motile functions, although its precise mechanism of action has not yet been established. To further define the role of SRF in neural development and distinguish between cell-autonomous and non cell-autonomous effects, we bidirectionally manipulated SRF activity through gene transduction assays that allow the visualization of individual neurons and their comparison with neighboring control cells. In vitro assays showed that SRF promotes survival and filopodia formation and is required for normal asymmetric neurite outgrowth, indicating that its activation favors dendrite enlargement versus branching. In turn, in vivo experiments demonstrated that SRF-dependent regulation of neuronal morphology has important consequences in the developing cortex and retina, affecting neuronal migration, dendritic and axonal arborization and cell positioning in these laminated tissues. Overall, our results show that the controlled and timely activation of SRF is essential for the coordinated growth of neuronal processes, suggesting that this event regulates the switch between neuronal growth and branching during developmental processes.
Integration of CdSe/CdSexTe1−x Type-II Heterojunction Nanorods into Hierarchically Porous TiO2 Electrode for Efficient Solar Energy Conversion
Authors: Lee Sangheon , Flanagan Joseph C. , Kang Joonhyeon , Kim Jinhyun , Shim Moonsub , Park Byungwoo 
Published: December 2015

AbstractSemiconductor sensitized solar cells, a promising candidate for next-generation photovoltaics, have seen notable progress using 0-D quantum dots as light harvesting materials. Integration of higher-dimensional nanostructures and their multi-composition variants into sensitized solar cells is, however, still not fully investigated despite their unique features potentially beneficial for improving performance. Herein, CdSe/CdSexTe1−x type-II heterojunction nanorods are utilized as novel light harvesters for sensitized solar cells for the first time. The CdSe/CdSexTe1−x heterojunction-nanorod sensitized solar cell exhibits ~33% improvement in the power conversion efficiency compared to its single-component counterpart, resulting from superior optoelectronic properties of the type-II heterostructure and 1-octanethiol ligands aiding facile electron extraction at the heterojunction nanorod-TiO2 interface. Additional ~31% enhancement in power conversion efficiency is achieved by introducing percolation channels of large pores in the mesoporous TiO2 electrode, which allow 1-D sensitizers to infiltrate the entire depth of electrode. These strategies combined together lead to 3.02% power conversion efficiency, which is one of the highest values among sensitized solar cells utilizing 1-D nanostructures as sensitizer materials.