bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taxonomic and functional diversity change is scale dependent
Authors: Jarzyna Marta A. , Jetz Walter 
Published: June 2018

AbstractEstimates of recent biodiversity change remain inconsistent, debated, and infrequently assessed for their functional implications. Here, we report that spatial scale and type of biodiversity measurement influence evidence of temporal biodiversity change. We show a pervasive scale dependence of temporal trends in taxonomic (TD) and functional (FD) diversity for an ~50-year record of avian assemblages from North American Breeding Bird Survey and a record of global extinctions. Average TD and FD increased at all but the global scale. Change in TD exceeded change in FD toward large scales, signaling functional resilience. Assemblage temporal dissimilarity and turnover (replacement of species or functions) declined, while nestedness (tendency of assemblages to be subsets of one another) increased with scale. Patterns of FD change varied strongly among diet and foraging guilds. We suggest that monitoring, policy, and conservation require a scale-explicit framework to account for the pervasive effect that scale has on perceived biodiversity change.
Understanding crystallization pathways leading to manganese oxide polymorph formation
Authors: Chen Bor-Rong , Sun Wenhao , Kitchaev Daniil A. , Mangum John S. , Thampy Vivek , Garten Lauren M. , Ginley David S. , Gorman Brian P. , Stone Kevin H. , Ceder Gerbrand , Toney Michael F. , Schelhas Laura T. 
Published: June 2018

AbstractHydrothermal synthesis is challenging in metal oxide systems with diverse polymorphism, as reaction products are often sensitive to subtle variations in synthesis parameters. This sensitivity is rooted in the non-equilibrium nature of low-temperature crystallization, where competition between different metastable phases can lead to complex multistage crystallization pathways. Here, we propose an ab initio framework to predict how particle size and solution composition influence polymorph stability during nucleation and growth. We validate this framework using in situ X-ray scattering, by monitoring how the hydrothermal synthesis of MnO2 proceeds through different crystallization pathways under varying solution potassium ion concentrations ([K+] = 0, 0.2, and 0.33 M). We find that our computed size-dependent phase diagrams qualitatively capture which metastable polymorphs appear, the order of their appearance, and their relative lifetimes. Our combined computational and experimental approach offers a rational and systematic paradigm for the aqueous synthesis of target metal oxides.
Oridonin is a covalent NLRP3 inhibitor with strong anti-inflammasome activity
Authors: He Hongbin , Jiang Hua , Chen Yun , Ye Jin , Wang Aoli , Wang Chao , Liu Qingsong , Liang Gaolin , Deng Xianming , Jiang Wei , Zhou Rongbin 
Published: June 2018

AbstractOridonin (Ori) is the major active ingredient of the traditional Chinese medicinal herb Rabdosia rubescens and has anti-inflammatory activity, but the target of Ori remains unknown. NLRP3 is a central component of NLRP3 inflammasome and has been involved in a wide variety of chronic inflammation-driven human diseases. Here, we show that Ori is a specific and covalent inhibitor for NLRP3 inflammasome. Ori forms a covalent bond with the cysteine 279 of NLRP3 in NACHT domain to block the interaction between NLRP3 and NEK7, thereby inhibiting NLRP3 inflammasome assembly and activation. Importantly, Ori has both preventive or therapeutic effects on mouse models of peritonitis, gouty arthritis and type 2 diabetes, via inhibition of NLRP3 activation. Our results thus identify NLRP3 as the direct target of Ori for mediating Ori’s anti-inflammatory activity. Ori could serve as a lead for developing new therapeutics against NLRP3-driven diseases.
Auditory cortical activity drives feedback-dependent vocal control in marmosets
Authors: Eliades Steven J. , Tsunada Joji 
Published: June 2018

AbstractVocal communication is a sensory-motor process requiring auditory self-monitoring to correct errors and to ensure accurate vocal production. When presented with altered speech feedback, humans rapidly change their speech to compensate. Although previous evidence has demonstrated suppression of auditory cortex during both speech and animal vocalization, the specific role of auditory cortex in such feedback-dependent control is unknown. Here we show the relationship between neural activity in the auditory cortex and feedback-dependent vocal control in marmoset monkeys. We demonstrate that marmosets, like humans, exhibit feedback control of vocal acoustics. We further show that feedback-sensitive activity of auditory cortex neurons predict such compensatory vocal changes. Finally, we demonstrate that electrical microstimulation of auditory cortex rapidly evokes similar changes in vocal production. These results are evidence for a causal role of auditory cortex in vocal self-monitoring and feedback-dependent control, and have implications for understanding human speech motor control.
Clustering huge protein sequence sets in linear time
Authors: Steinegger Martin , Söding Johannes 
Published: June 2018

AbstractMetagenomic datasets contain billions of protein sequences that could greatly enhance large-scale functional annotation and structure prediction. Utilizing this enormous resource would require reducing its redundancy by similarity clustering. However, clustering hundreds of millions of sequences is impractical using current algorithms because their runtimes scale as the input set sizeNtimes the number of clustersK, which is typically of similar order asN, resulting in runtimes that increase almost quadratically withN. We developed Linclust, the first clustering algorithm whose runtime scales asN, independent ofK. It can also cluster datasets several times larger than the available main memory. We cluster 1.6 billion metagenomic sequence fragments in 10 h on a single server to 50% sequence identity, >1000 times faster than has been possible before. Linclust will help to unlock the great wealth contained in metagenomic and genomic sequence databases.
A moisture function of soil heterotrophic respiration that incorporates microscale processes
Authors: Yan Zhifeng , Bond-Lamberty Ben , Todd-Brown Katherine E. , Bailey Vanessa L. , Li SiLiang , Liu CongQiang , Liu Chongxuan 
Published: June 2018

AbstractSoil heterotrophic respiration (HR) is an important source of soil-to-atmosphere CO2 flux, but its response to changes in soil water content (θ) is poorly understood. Earth system models commonly use empirical moisture functions to describe the HR–θ relationship, introducing significant uncertainty in predicting CO2 flux from soils. Generalized, mechanistic models that address this uncertainty are thus urgently needed. Here we derive, test, and calibrate a novel moisture function, fm, that encapsulates primary physicochemical and biological processes controlling soil HR. We validated fm using simulation results and published experimental data, and established the quantitative relationships between parameters of fm and measurable soil properties, which enables fm to predict the HR–θ relationships for different soils across spatial scales. The fm function predicted comparable HR–θ relationships with laboratory and field measurements, and may reduce the uncertainty in predicting the response of soil organic carbon stocks to climate change compared with the empirical moisture functions currently used in Earth system models.
Vapor sublimation and deposition to build porous particles and composites
Authors: Tung Hsing-Ying , Guan Zhen-Yu , Liu Ting-Yu , Chen Hsien-Yeh 
Published: June 2018

AbstractThe vapor deposition of polymers on regular stationary substrates is widely known to form uniform thin films. Here we report porous polymer particles with sizes controllable down to the nanometer scale can be produced using a fabrication process based on chemical vapor deposition (CVD) on a dynamic substrate, i.e., sublimating ice particles. The results indicate that the vapor deposition of a polymer is directed by the sublimation process; instead of forming a thin film polymer, the deposited polymers replicated the size and shape of the ice particle. Defined size and porosity of the polymer particles are controllable with respect to varying the processing time. Extendable applications are shown to install multiple functional sites on the particles in one step and to localize metals/oxides forming composite particles. In addition, one fabrication cycle requires approximately 60 min to complete, and potential scaling up the production of the porous particles is manageable.
The relationship of early recurrence of atrial fibrillation and the 3-month integrity of the ablation lesion set
Authors: Mujović Nebojša , Marinković Milan , Marković Nebojša , Vučićević Vera , Lip Gregory Y. H. , Bunch T. Jared , Potpara Tatjana S. 
Published: June 2018

AbstractEarly recurrence of atrial fibrillation (ERAF) after catheter-ablation (CA) can be a transient phenomenon due to inflammation, or a harbinger of late AF recurrence due to CA lesion (re)conduction. We studied the relationship between ERAF and the 3-month CA lesions integrity. Forty one consecutive AF patients who underwent a pulmonary vein isolation (PVI), roof line (RL) and mitral isthmus line (MIL) CA were enrolled. At 3 months all patients underwent invasive assessment of the lesion set integrity irrespective of ERAF. The PVI, RL and MIL ablation was successful in 100.0%, 95.1% and 82.9% patients, respectively. At the 3-month remapping, a gap in PVI-lesion(s), RL or MIL was identified in 61.0%, 31.7% and 36.6% patients, respectively. Patients with (n = 17, 41.5%) compared to those without ERAF (n = 24) had a significantly higher rate of any PV-reconnection (88.2% vs. 41.7%), the right PV(s)-reconnection (82.5% vs. 29.2%) and the RL gap (52.9% vs. 16.7%), as well as a higher number of reconnected right PVI-segments, all p < 0.05. On multivariate analysis, only the number of reconnected right PVI-segments was associated with ERAF (OR 4.26, p = 0.004). The ERAF following PVI + RL + MIL ablation was significantly related to 3-month PV-reconnections and the presence of RL gaps.
Mapping of brain tissue hematocrit in glioma and acute stroke using a dual autoradiography approach
Authors: Broisat A. , Lemasson B. , Ahmadi M. , Collomb N. , Bacot S. , Soubies A. , Fagret D. , Rémy C. , Ghezzi C. , Barbier E. L. 
Published: June 2018

AbstractHematocrit (Hct) determines the ability of blood to carry oxygen. While changes in systemic Hct are known to impact stroke or tumor control, changes in local (tissue) Hct (tHct) induced by these diseases have however received little attention. In this study, we evaluate tHct in acute stroke and in glioma models using a new approach to map tHct across the brain, a dual isotope autoradiography, based on injections of 125I-labeled albumin and 99mTc-lalbeled red blood cells in the same animal. For validation purpose, tHct was mapped in the rat brain (i) under physiological conditions, (ii) following erythropoietin injection, and (iii) following hemodilution. Then, tHct was then mapped in stroke (middle cerebral artery occlusion) and tumor models (9LGS and C6). The mean tHct values observed in healthy brains (tHct = 29 ± 1.3%), were modified as expected by erythropoietin (tHct = 36.7 ± 2.6%) and hemodilution (tHct = 24.2 ± 2.4%). Using the proposed method, we observed a local reduction, spatially heterogeneous, in tHct following acute stroke (tHct = 19.5 ± 2.5%) and in both glioma models (9LGS: tHct = 18.5 ± 2.3%, C6: tHct = 16.1 ± 1.2%). This reduction and this heterogeneity in tHct observed in stroke and glioma raises methodological issues in perfusion imaging techniques where tHct is generally overlooked and could impact therapeutic strategies.
Complex ecological interactions of Staphylococcus aureus in tampons during menstruation
Authors: Jacquemond Isaline , Muggeo Anaëlle , Lamblin Gery , Tristan Anne , Gillet Yves , Bolze Pierre Adrien , Bes Michèle , Gustave Claude Alexandre , Rasigade Jean-Philippe , Golfier François , Ferry Tristan , Dubost Audrey , Abrouk Danis , Barreto Samuel , Prigent-Combaret Claire , Thioulouse Jean , Lina Gérard , Muller Daniel 
Published: June 2018

AbstractMenstrual toxic shock syndrome (mTSS) is a severe disease that occurs in healthy women vaginally colonized by Staphylococcus aureus producing toxic shock toxin 1 and who use tampons. The aim of the present study was to determine the impact of the composition of vaginal microbial communities on tampon colonisation by S. aureus during menses. We analysed the microbiota in menstrual fluids extracted from tampons from 108 healthy women and 7 mTSS cases. Using culture, S. aureus was detected in menstrual fluids of 40% of healthy volunteers and 100% of mTSS patients. Between class analysis of culturomic and 16S rRNA gene metabarcoding data indicated that the composition of the tampons’ microbiota differs according to the presence or absence of S. aureus and identify discriminating genera. However, the bacterial communities of tampon fluid positive for S. aureus did not cluster together. No difference in tampon microbiome richness, diversity, and ecological distance was observed between tampon vaginal fluids with or without S. aureus, and between healthy donors carrying S. aureus and mTSS patients. Our results show that the vagina is a major niche of. S. aureus in tampon users and the composition of the tampon microbiota control its virulence though more complex interactions than simple inhibition by lactic acid-producing bacterial species.
Light Emitting Diodes based Photoacoustic Imaging and Potential Clinical Applications
Authors: Zhu Yunhao , Xu Guan , Yuan Jie , Jo Janggun , Gandikota Girish , Demirci Hakan , Agano Toshitaka , Sato Naoto , Shigeta Yusuke , Wang Xueding 
Published: June 2018

AbstractUsing low cost and small size light emitting diodes (LED) as the alternative illumination source for photoacoustic (PA) imaging has many advantages, and can largely benefit the clinical translation of the emerging PA imaging technology. Here, we present our development of LED-based PA imaging integrated with B-mode ultrasound. To overcome the challenge of achieving sufficient signal-to-noise ratio by the LED light that is orders of magnitude weaker than lasers, extensive signal averaging over hundreds of pulses is performed. Facilitated by the fast response of the LED and the high-speed driving as well as the high pulse repetition rate up to 16 kHz, B-mode PA images superimposed on gray-scale ultrasound of a biological sample can be achieved in real-time with frame rate up to 500 Hz. The LED-based PA imaging could be a promising tool for several clinical applications, such as assessment of peripheral microvascular function and dynamic changes, diagnosis of inflammatory arthritis, and detection of head and neck cancer.
Enhancing bulk defect-mediated absorption in silicon waveguides by doping compensation technique
Authors: Zhang Qiang , Yu Hui , Qi Tian , Fu Zhilei , Jiang Xiaoqing , Yang Jianyi 
Published: June 2018

AbstractSilicon waveguide photodiodes (SiWG PD) based on the bulk defect-mediated absorption (BDA) of sub-bandgap photons are suitable to realize in-line optical power monitors for silicon photonic integrated circuits. Deep-level states to enable the BDA can be induced by exploiting the ion implantation steps that are used to embed PN junctions for carrier-depletion-based modulators. This manner usually exhibits limited responsivities since relevant processing conditions are optimized for the modulation rather than the BDA. In this letter, we solve this issue with the doping compensation technique. This technique overlaps P-type and N-type implantation windows at the waveguide core. The responsivity is enhanced due to the increased density of lattice defects and the reduced density of free carriers in the compensated silicon. Influences of the dimension of the dopant compensation region on responsivity and operation speed are investigated. As the width of this region increases from 0 μm to 0.4 μm, the responsivity at −5 V is improved from 2 mA/W to 17.5 mA/W. This level is comparable to BDA based SiWG PDs relying on dedicated ion bombardments. On the other hand, a bit-error-rate test at 10 Gb/s suggests that the device with 0.2-μm-wide compensation region exhibits the highest sensitivity.
Surface reconstruction in gold nanowires
Authors: Suzuki Yasuchika , Kizuka Tokushi 
Published: June 2018

AbstractSurface reconstructions are caused by structural stabilization resulting from the modulation of surface atomic positions. Studies on surface reconstruction have been conducted for substantially large surfaces, rather than at the size of reconstructed surface unit cells. Hence, well-known surface reconstruction manners may not be applicable for the surfaces of nanometer-sized isolated crystals, such as nanoclusters, nanowires and nanotubes. This is because they have high surface area-to-interior volume ratios exceeding several tens of percent, and their surface structures significantly affect the stabilization of their entire structures. In this study, we demonstrate the inherent surface reconstruction of gold nanowires via nanosecond-pulsed electromigration with the application of tensile stresses. The results lead to evolutions in basic studies relating to surface reconstruction and nanostructures and in applications of nanowires, for which stabilization is essential when they are used in extremely miniaturized integrated circuits for next-generation electronics.
Molecular mechanisms of tannin accumulation in Rhus galls and genes involved in plant-insect interactions
Authors: Chen Hang , Liu Juan , Cui Kai , Lu Qin , Wang Chao , Wu Haixia , Yang Zixiang , Ding Weifeng , Shao Shuxia , Wang Haiying , Ling Xiaofei , King-Jones Kirst , Chen Xiaoming 
Published: June 2018

AbstractFor galling aphids and their hosts, tannins are crucial for plant-insect interactions and for protecting the host plant from herbivory. Due to their peculiar chemical characteristics, tannins from plant galls have been used for medical and chemical purposes for more than 2000 years. In this study, hydrolyzable tannin concentrations in galls increased from gall initiation (38.34% on June 21) to maturation (74.79% on August 8), then decreased gradually thereafter (58.83% on October 12). We identified a total of 81 genes (named as GTS1-81) with putative roles in gallotannin biosynthesis and 22 genes (TS1-22) in condensed tannin biosynthesis. We determined the expression profiles of these genes by real-time PCR over the course of gall development. Multiple genes encoding 1-beta-D-glucosyl transferases were identified, which may play a vital role in gallotannin accumulation in plant galls. This study is the first attempt to examine the molecular basis for the regulation of tannin accumulation in insect gallnuts. The differentially expressed genes we identified may play important roles in both tannin biosynthesis and plant-insect interactions.
Whole genome sequencing reveals widespread distribution of typhoidal toxin genes and VirB/D4 plasmids in bovine-associated nontyphoidal Salmonella
Authors: Delgado-Suárez Enrique Jesús , Selem-Mojica Nelly , Ortiz-López Rocío , Gebreyes Wondwossen A. , Allard Marc W. , Barona-Gómez Francisco , Rubio-Lozano María Salud 
Published: June 2018

AbstractNontyphoidal Salmonella (NTS) is a common pathogen in food-producing animals and a public health concern worldwide. Various NTS serovars may be present in apparently healthy animals. This could result in carcass contamination during the slaughter process leading to human exposure. While most genomic research has focused on Salmonella pathogenesis, little is known on the factors associated with subclinical infections and environmental persistence. We report here the widespread distribution of typhoidal toxin genes (i. e. the cdtB islet, hlyE, taiA), among NTS strains from a beef slaughter operation (n = 39) and from epidemiologically unconnected ground beef (n = 20). These genes were present in 76% of the strains, regardless of serovar, isolation source or geographical location. Moreover, strains that predominated in the slaughterhouse carry plasmid-borne type IV secretion systems (T4SS), which have been linked to persistent infections in numerous pathogens. Population genomics supports clonal dissemination of NTS along the food production chain, highlighting its role as reservoir of genetic variability in the environment. Overall, the study provides a thorough characterization of serovar diversity and genomic features of beef-associated NTS in Mexico. Furthermore, it reveals how common genetic factors could partially explain the emergence and persistence of certain NTS serovars in the beef industry.
S100B immunization triggers NFκB and complement activation in an autoimmune glaucoma model
Authors: Reinehr Sabrina , Reinhard Jacqueline , Gandej Marcel , Gottschalk Ivo , Stute Gesa , Faissner Andreas , Dick H. Burkhard , Joachim Stephanie C. 
Published: June 2018

AbstractIn glaucoma, latest studies revealed an involvement of the complement system with and without an elevated intraocular pressure. In the experimental autoimmune glaucoma model, immunization with antigens, such as S100B, lead to retinal ganglion cell (RGC) loss and optic nerve degeneration after 28 days. Here, we investigated the timeline of progression of the complement system, toll-like-receptor 4 (TLR4), and the transcription factor nucleus factor-kappa B (NFκB). Therefore, rats were immunized with S100B protein (S100) and analyzed at 3, 7, and 14 days. RGC numbers were comparable at all points in time, whereas a destruction of S100 optic nerves was noted at 14 days. A significant increase of mannose binding lectin (MBL) was observed in S100 retinas at 3 days. Subsequently, significantly more MBL+cells were seen in S100 optic nerves at 7 and 14 days. Accordingly, C3 was upregulated in S100 retinas at 14 days. An increase of interleukin-1 beta was noted in S100 aqueous humor samples at 7 days. In this study, activation of complement system via the lectin pathway was obvious. However, no TLR4 alterations were noted in S100 retinas and optic nerves. Interestingly, a significant NFκB increase was observed in S100 retinas at 7 and 14 days. We assume that NFκB activation might be triggered via MBL leading to glaucomatous damage.
Morphological, genomic and transcriptomic responses of
Klebsiella pneumoniae to the last-line antibiotic
colistin
Authors: Cain Amy K. , Boinett Christine J. , Barquist Lars , Dordel Janina , Fookes Maria , Mayho Matthew , Ellington Matthew J. , Goulding David , Pickard Derek , Wick Ryan R. , Holt Kathryn E. , Parkhill Julian , Thomson Nicholas R. 
Published: June 2018

AbstractColistin remains one of the few antibiotics effective against
multi-drug resistant (MDR) hospital pathogens, such as Klebsiella pneumoniae. Yet resistance to this last-line drug is
rapidly increasing. Characterized mechanisms of colR in
K. pneumoniae are largely due to chromosomal mutations in two-component
regulators, although a plasmid-mediated colR mechanism
has recently been uncovered. However, the effects of intrinsic colistin resistance
are yet to be characterized on a whole-genome level. Here, we used a genomics-based
approach to understand the mechanisms of adaptive colR
acquisition in K. pneumoniae. In controlled directed-evolution experiments we observed
two distinct paths to colistin resistance acquisition. Whole genome sequencing
identified mutations in two colistin resistance genes: in the known
colR regulator phoQ
which became fixed in the population and resulted in a single amino acid change, and
unstable minority variants in the recently described two-component sensor crrB. Through RNAseq and microscopy, we reveal the broad
range of effects that colistin exposure has on the cell. This study is the first to
use genomics to identify a population of minority variants with mutations in a
colR gene in K.
pneumoniae.