bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single molecule secondary structure determination of proteins through infrared absorption nanospectroscopy
Authors: Ruggeri Francesco Simone , Mannini Benedetta , Schmid Roman , Vendruscolo Michele , Knowles Tuomas P. J. 
Published: June 2020

AbstractThe chemical and structural properties of biomolecules determine their interactions, and thus their functions, in a wide variety of biochemical processes. Innovative imaging methods have been developed to characterise biomolecular structures down to the angstrom level. However, acquiring vibrational absorption spectra at the single molecule level, a benchmark for bulk sample characterization, has remained elusive. Here, we introduce off-resonance, low power and short pulse infrared nanospectroscopy (ORS-nanoIR) to allow the acquisition of infrared absorption spectra and chemical maps at the single molecule level, at high throughput on a second timescale and with a high signal-to-noise ratio (~10–20). This high sensitivity enables the accurate determination of the secondary structure of single protein molecules with over a million-fold lower mass than conventional bulk vibrational spectroscopy. These results pave the way to probe directly the chemical and structural properties of individual biomolecules, as well as their interactions, in a broad range of chemical and biological systems.
A cancer drug atlas enables synergistic targeting of independent drug vulnerabilities
Authors: Narayan Ravi S. , Molenaar Piet , Teng Jian , Cornelissen Fleur M. G. , Roelofs Irene , Menezes Renee , Dik Rogier , Lagerweij Tonny , Broersma Yoran , Petersen Naomi , Marin Soto Jhon Alexander , Brands Eelke , van Kuiken Philip , Lecca Maria C. , Lenos Kristiaan J. , In ‘t Veld Sjors G. J. G. , van Wieringen Wessel , Lang Frederick F. , Sulman Erik , Verhaak Roel , Baumert Brigitta G. , Stalpers Lucas J. A. , Vermeulen Louis , Watts Colin , Bailey David , Slotman Ben J. , Versteeg Rogier , Noske David , Sminia Peter , Tannous Bakhos A. , Wurdinger Tom , Koster Jan , Westerman Bart A. 
Published: June 2020

AbstractPersonalized cancer treatments using combinations of drugs with a synergistic effect is attractive but proves to be highly challenging. Here we present an approach to uncover the efficacy of drug combinations based on the analysis of mono-drug effects. For this we used dose-response data from pharmacogenomic encyclopedias and represent these as a drug atlas. The drug atlas represents the relations between drug effects and allows to identify independent processes for which the tumor might be particularly vulnerable when attacked by two drugs. Our approach enables the prediction of combination-therapy which can be linked to tumor-driving mutations. By using this strategy, we can uncover potential effective drug combinations on a pan-cancer scale. Predicted synergies are provided and have been validated in glioblastoma, breast cancer, melanoma and leukemia mouse-models, resulting in therapeutic synergy in 75% of the tested models. This indicates that we can accurately predict effective drug combinations with translational value.
Simultaneous EEG-fMRI during a neurofeedback task, a brain imaging dataset for multimodal data integration
Authors: Lioi Giulia , Cury Claire , Perronnet Lorraine , Mano Marsel , Bannier Elise , Lécuyer Anatole , Barillot Christian 
Published: June 2020

AbstractCombining EEG and fMRI allows for integration of fine spatial and accurate temporal resolution yet presents numerous challenges, noticeably if performed in real-time to implement a Neurofeedback (NF) loop. Here we describe a multimodal dataset of EEG and fMRI acquired simultaneously during a motor imagery NF task, supplemented with MRI structural data. The study involved 30 healthy volunteers undergoing five training sessions. We showed the potential and merit of simultaneous EEG-fMRI NF in previous work. Here we illustrate the type of information that can be extracted from this dataset and show its potential use. This represents one of the first simultaneous recording of EEG and fMRI for NF and here we present the first open access bi-modal NF dataset integrating EEG and fMRI. We believe that it will be a valuable tool to (1) advance and test methodologies for multi-modal data integration, (2) improve the quality of NF provided, (3) improve methodologies for de-noising EEG acquired under MRI and (4) investigate the neuromarkers of motor-imagery using multi-modal information.
Aerial surveys of waterbirds in Australia
Authors: Kingsford Richard T. , Porter John L. , Brandis Kate J. , Ryall Sharon 
Published: June 2020

AbstractTracking long-term environmental change is important, particularly for freshwater ecosystems, often with high rates of decline. Waterbirds are key indicators of freshwater ecosystem change, with groups reflecting food availability (e.g. piscivores and fish). We store waterbird (species abundance, numbers of nests and broods) and wetland area data from aerial surveys of waterbirds across Australia, mostly at the species’ level (∼100 species) from three aerial survey programs: Eastern Australian Waterbird Survey, National Survey and Murray-Darling Basin wetlands. Across eastern Australia, we survey up to 2,000 wetlands annually (October, since 1983), along 10 survey bands (30 km wide), east to west across about one third of Australia. In 2008, we surveyed 4,858 wetlands across Australia and each year (since 2010) we survey the major wetlands in the Murray-Darling Basin. These data inform regulation of hunting seasons in Victoria and South Australia, Game bird culling in NSW, State of the Environment Reporting, environmental assessments, river and wetland management, the status of individual species and identification of high conservation sites.
Autologous fecal transplantation from a lean state potentiates caloric restriction effects on body weight and adiposity in obese mice
Authors: Pérez-Matute Patricia , Íñiguez María , de Toro María , Recio-Fernández Emma , Oteo José A. 
Published: June 2020

AbstractAutologous fecal transplantation (FT-A) emerges as a promising strategy to modulate gut microbiota with minimal side effects since individual´s own feces are transplanted. With the premise of improving obesity and its associated disorders, we investigated if fecal microbiota transplantation (FMT), heterologous and autologous, potentiates the effects of a moderate caloric restriction (CR) in high-fat diet (HFD)-induced obese mice. Mice were randomized into control, HFD, CR (12 weeks on HFD and 6 weeks under CR), FT-H (similar to CR and FMT carried out with feces from controls, weeks 17 & 18), and FT-A (administration of their own feces before developing obesity at weeks 17 & 18). Our study demonstrated that FMT, and, especially, FT-A potentiates the effects of a moderate CR on weight loss and adiposity in the short term, by decreasing feed efficiency and increasing adipose tissue lipolysis. Although FT-A produced a significant increase in bacterial richness/diversity, FMT did not significantly modify gut microbiota composition compared to the CR at phyla and bacteria genera levels, and only significant increases in Bifidobacterium and Blautia genera were observed. These results could suggest that other mechanisms different from bacterial microbiota engraftment participates in these beneficial effects. Thus, FT-A represents a very positive synergetic approach for obese patients that do not respond well to moderate restrictive diets.
Focussing Protons from a Kilojoule Laser for Intense Beam Heating using Proximal Target Structures
Authors: McGuffey C. , Kim J. , Wei M. S. , Nilson P. M. , Chen S. N. , Fuchs J. , Fitzsimmons P. , Foord M. E. , Mariscal D. , McLean H. S. , Patel P. K. , Stephens R. B. , Beg F. N. 
Published: June 2020

AbstractProton beams driven by chirped pulse amplified lasers have multi-picosecond duration and can isochorically and volumetrically heat material samples, potentially providing an approach for creating samples of warm dense matter with conditions not present on Earth. Envisioned on a larger scale, they could heat fusion fuel to achieve ignition. We have shown in an experiment that a kilojoule-class, multi-picosecond short pulse laser is particularly effective for heating materials. The proton beam can be focussed via target design to achieve exceptionally high flux, important for the applications mentioned. The laser irradiated spherically curved diamond-like-carbon targets with intensity 4 × 1018 W/cm2, producing proton beams with 3 MeV slope temperature. A Cu witness foil was positioned behind the curved target, and the gap between was either empty or spanned with a structure. With a structured target, the total emission of Cu Kα fluorescence was increased 18 fold and the emission profile was consistent with a tightly focussed beam. Transverse proton radiography probed the target with ps order temporal and 10 μm spatial resolution, revealing the fast-acting focussing electric field. Complementary particle-in-cell simulations show how the structures funnel protons to the tight focus. The beam of protons and neutralizing electrons induce the bright Kα emission observed and heat the Cu to 100 eV.
Shedding of Brucella melitensis happens through milk macrophages in the murine model of infection
Authors: Jansen Wiebke , Demars Aurore , Nicaise Charles , Godfroid Jacques , de Bolle Xavier , Reboul Angéline , Al Dahouk Sascha 
Published: June 2020

AbstractAlthough shedding of zoonotic brucellae in milk has been demonstrated in natural hosts, these data are still missing for the standard murine infection model. We therefore analysed shedding kinetics and the niche of B. melitensis in murine milk. Pregnant Balb/cByJ mice were intraperitoneally infected with 105 CFU of the 16 M reference strain, a 16 M mCherry mutant or a human isolate. Milk was collected over the course of lactation, and subjected to culture and immunofluorescence assays. Bacteria were also quantified in spleen and mammary glands of maternal mice and in spleen of the litter. The shedding of the three strains did not differ significantly (p = 0.301), ranging from log10 1.5 to 4.04 CFU/ml. A total of 73% of the mice excreted B. melitensis into the milk with peak values at mid-lactation; up to 30 bacteria/cell were found in macrophages and neutrophils. While the bacterial counts in the spleen of lactating females confirmed a well-established infection, only 50% of the pups harboured brucellae in their spleen, including the spleen of an uninfected pup fed by an infected foster mother. In conclusion, the murine model of infection may contribute to a better understanding of the zoonotic transmission of brucellosis.
Learned Representation of Implied Serial Order in Posterior Parietal Cortex
Authors: Munoz Fabian , Jensen Greg , Kennedy Benjamin C. , Alkan Yelda , Terrace Herbert S. , Ferrera Vincent P. 
Published: June 2020

AbstractMonkeys can learn the implied ranking of pairs of images drawn from an ordered set, despite never seeing all of the images simultaneously and without explicit spatial or temporal cues. We recorded the activity of posterior parietal cortex (including lateral intraparietal area LIP) neurons while monkeys learned 7-item transitive inference (TI) lists with 2 items presented on each trial. Behavior and neuronal activity were significantly influenced by the ordinal relationship of the stimulus pairs, specifically symbolic distance (the difference in rank) and joint rank (the sum of the ranks). Symbolic distance strongly predicted decision accuracy and learning rate. An effect of joint rank on performance was found nested within the symbolic distance effect. Across the population of neurons, there was significant modulation of firing correlated with the relative ranks of the two stimuli presented on each trial. Neurons exhibited selectivity for stimulus rank during learning, but not before or after. The observed behavior is poorly explained by associative or reward mechanisms, and appears more consistent with a mental workspace model in which implied serial order is mapped within a spatial framework. The neural data suggest that posterior parietal cortex supports serial learning by representing information about the ordinal relationship of the stimuli presented during a given trial.
Sex differences in dendritic spine density and morphology in auditory and visual cortices in adolescence and adulthood
Authors: Parker Emily M. , Kindja Nathan L. , Cheetham Claire E. J. , Sweet Robert A. 
Published: June 2020

AbstractDendritic spines are small protrusions on dendrites that endow neurons with the ability to receive and transform synaptic input. Dendritic spine number and morphology are altered as a consequence of synaptic plasticity and circuit refinement during adolescence. Dendritic spine density (DSD) is significantly different based on sex in subcortical brain regions associated with the generation of sex-specific behaviors. It is largely unknown if sex differences in DSD exist in auditory and visual brain regions and if there are sex-specific changes in DSD in these regions that occur during adolescent development. We analyzed dendritic spines in 4-week-old (P28) and 12-week-old (P84) male and female mice and found that DSD is lower in female mice due in part to fewer short stubby, long stubby and short mushroom spines. We found striking layer-specific patterns including a significant age by layer interaction and significantly decreased DSD in layer 4 from P28 to P84. Together these data support the possibility of developmental sex differences in DSD in visual and auditory regions and provide evidence of layer-specific refinement of DSD over adolescent brain development.
Structural characterization of SnO nanoparticles synthesized by the hydrothermal and microwave routes
Authors: Dias J. S. , Batista F. R. M. , Bacani R. , Triboni E. R. 
Published: June 2020

AbstractSnO particles were synthesized by an alkali-assisted hydrothermal and microwave methods. The aqueous-based reactions were carried out at pH ~ 8, under inert atmosphere (Ar). The reactions were taken under different times, and a full XRD structural analysis was made to evaluate the conversion from the Sn6O4(OH)4 intermediate to SnO particles. Williamson-Hall analysis showed that the size and strain of the SnO particles were time and route treatment dependent. Microwave heating yielded a single tetragonal SnO phase after 1 h of thermal treatment, and TEM images revealed spherical-shaped SnO nanoparticles with an average size of 9(1) nm. While by the hydrothermal treatment single SnO phase was obtained only after 4 hours, yielding non-uniform and elongated particles with sub-micrometric size. A dissolution-recrystallization process was taken into account as the mechanism for SnO particles formation, in which hydroxylated complexes, Sn2(OH)6−2, then condense to form the oxide. The time-shorting reaction provided by the microwave-assisted synthesis may be attributed to better heat distribution.
Clinical analysis in immunocompetent and immunocompromised patients with pulmonary cryptococcosis in western China
Authors: Qu Junyan , Zhang Xiaoli , Lu Yang , Liu Xijiao , Lv Xiaoju 
Published: June 2020

AbstractCryptococcosis is a systemic infection and it may occur in immunocompromised and immunocompetent hosts. In order to better understand the clinical characteristics of patients with PC in different immune status, we retrospectively investigated the clinical, radiological, and treatment profiles of immunocompetent and immunocompromised patients with PC during a 10-year period (2008–2017). As a result, out of 136 patients, 94 (69.1%) were immunocompromised hosts. For the PC patients without CNS involvement, higher percentage of immunocompetent patients (39.5%, 15/38) had asymptomatic presentation than immunocompromised patients (6.3%, 3/48) (P < 0.05). Multiple pulmonary nodules (72.7%, 56/77), ground-glass attenuation/interstitial changes (94.4%, 17/18) and cavitation (88.6%, 31/35) were significantly frequent in immunocompromised patients (P < 0.05). A total of 47 patients were misdiagnosed as tuberculosis or tumors based on CT signs. PC was likely to be misdiagnosed as tuberculosis in immunocompromised patients (88.2%, 15/17), and tumor was more likely to be considered in immunocompetent patients (43.3%, 13/30). Immunocompetent patients accounted for 80% (24/30) of patients with definite diagnosis on surgical lung biopsy. Fluconazole monotherapy can achieve good clinical outcome in most PC patients without central nervous system (CNS) involvement (91.5%, 54/59). After 3 months of treatment, 92.7% (38/41) patients have improved imaging findings. In conclusion, PC has diverse imaging manifestations and it is easily misdiagnosed. Lobectomy should be carefully selected in immunocompetent patients with a single lung lesion. Fluconazole monotherapy is preferred for PC patients without CNS involvement.
Patterns and Rates of Plastid rps12 Gene Evolution Inferred in a Phylogenetic Context using Plastomic Data of Ferns
Authors: Liu Shanshan , Wang Zhen , Wang Hui , Su Yingjuan , Wang Ting 
Published: June 2020

AbstractThe trans-splicing rps12 gene of fern plastomes (plastid genomes) exhibits a unique structure owing to its variations in intragenic exon location and intron content, and thus, it provides an excellent model system for examining the effect of plastid gene structure on rates and patterns of molecular evolution. In this study, 16 complete fern plastome sequences were newly generated via the Illumina HiSeq sequencing platform. We reconstructed the phylogeny of ferns and inferred the patterns and rates of plastid rps12 gene evolution in a phylogenetic context by combining these plastome data with those of previously published fern species. We uncovered the diversity of fern plastome evolution by characterizing the structures of these genomes and obtained a highly supported phylogenetic framework for ferns. Furthermore, our results revealed molecular evolutionary patterns that were completely different from the patterns revealed in previous studies. There were significant differences in the patterns and rates of nucleotide substitutions in both intron-containing and intron-less rps12 alleles. Rate heterogeneity between single-copy (SC) and inverted repeat (IR) exons was evident. Unexpectedly, however, IR exons exhibited significantly higher synonymous substitution rates (dS) than SC exons, a pattern that contrasts the regional effect responsible for decreased rates of nucleotide substitutions in IRs. Our results reveal that structural changes in plastid genes have important effects on evolutionary rates, and we propose possible mechanisms to explain the variations in the nucleotide substitution rates of this unusual gene.
Prediction of advanced fibrosis in non-alcoholic fatty liver disease using gut microbiota-based approaches compared with simple non-invasive tools
Authors: Lang Sonja , Farowski Fedja , Martin Anna , Wisplinghoff Hilmar , Vehreschild Maria J. G. T. , Krawczyk Marcin , Nowag Angela , Kretzschmar Anne , Scholz Claus , Kasper Philipp , Roderburg Christoph , Lammert Frank , Goeser Tobias , Steffen Hans-Michael , Demir Münevver 
Published: June 2020

AbstractLiver fibrosis is the major determinant of liver related complications in patients with non-alcoholic fatty liver disease (NAFLD). A gut microbiota signature has been explored to predict advanced fibrosis in NAFLD patients. The aim of this study was to validate and compare the diagnostic performance of gut microbiota-based approaches to simple non-invasive tools for the prediction of advanced fibrosis in NAFLD. 16S rRNA gene sequencing was performed in a cohort of 83 biopsy-proven NAFLD patients and 13 patients with non-invasively diagnosed NAFLD-cirrhosis. Random Forest models based on clinical data and sequencing results were compared with transient elastography, the NAFLD fibrosis score (NFS) and FIB-4 index. A Random Forest model containing clinical features and bacterial taxa achieved an area under the curve (AUC) of 0.87 which was only marginally superior to a model without microbiota features (AUC 0.85). The model that aimed to validate a published algorithm achieved an AUC of 0.71. AUC’s for NFS and FIB-4 index were 0.86 and 0.85. Transient elastography performed best with an AUC of 0.93. Gut microbiota signatures might help to predict advanced fibrosis in NAFLD. However, transient elastography achieved the best diagnostic performance for the detection of NAFLD patients at risk for disease progression.
Reduced Graphene Oxide-Silver Nanoparticles for Optical Pulse Generation in Ytterbium- and Erbium-Doped Fiber Lasers
Authors: Ahmad Harith , Albaqawi Hissah Saedoon , Yusoff Norazriena , Reduan Siti Aisyah , Yi Chong Wu 
Published: June 2020

AbstractThis work has demonstrated the potential of a reduced graphene oxide silver/polyvinyl alcohol (rGO-Ag/PVA) film as a saturable absorber (SA) in ytterbium and erbium based Q-switched optical fiber lasers. The facile hydrothermal method was used to synthesize the nanocomposite between rGO and Ag nanoparticles. This was followed by a simple solution method to form the rGO-Ag film using PVA as the host polymer. From nonlinear absorption characterization, the rGO-Ag/PVA SA was determined to have a modulation depth of 30%, a nonsaturable loss of 70%, and a saturable intensity of 0.63 kW/cm2. Stable self-starting Q-switched pulses were obtained at the threshold pump power of 72.76 mW and 18.63 mW in the ytterbium-doped (YDFL) and erbium-doped fiber laser (EDFL) cavities respectively. The center operating wavelengths were observed at 1044.4 nm and 1560 nm for the two cavities. The shortest pulse width and maximum repetition rate of the YDFL and EDFL were 1.10 µs and 62.10 kHz and 1.38 µs and 76.63 kHz respectively. This work has demonstrated that the rGO-Ag/PVA film is suitable as an SA for pulse generation in the 1.0 and 1.5 μm regions and would have many potential photonics applications.
Active control on topological immunity of elastic wave metamaterials
Authors: Li Guan-Hua , Ma Tian-Xue , Wang Yi-Ze , Wang Yue-Sheng 
Published: June 2020

AbstractThe topology concept in the condensed physics and acoustics is introduced into the elastic wave metamaterial plate, which can show the topological property of the flexural wave. The elastic wave metamaterial plate consists of the hexagonal array which is connected by the piezoelectric shunting circuits. The Dirac point is found by adjusting the size of the unit cell and numerical simulations are illustrated to show the topological immunity. Then the closing and breaking of the Dirac point can be generated by the negative capacitance circuits. These investigations denote that the topological immunity can be achieved for flexural wave in mechanical metamaterial plate. The experiments with the active control action are finally carried out to support the numerical design.