bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational modelling of wet adhesive mussel foot proteins (Bivalvia): Insights into the evolutionary convolution in diverse perspectives
Authors: Anand P. P. , Vardhanan Y. Shibu 
Published: February 2020

AbstractUnderwater adhesion in mussels (Bivalvia) is an extreme adaptation to achieve robust and firm wet adhesion in the freshwater/brackish/ocean, which biochemically shaped through millions of years. The protein-based adhesion has huge prospective in various fields like industry, medical, etc. Currently, no comprehensive records related to the systematic documentation of structural and functional properties of Mussel foot proteins (Mfps). In this study, we identified the nine species of bivalves in which the complete sequence of at least one adhesive protein is known. The insilico characterization revealed the specific physio-chemical structural and functional characters of each Mfps. The evolutionary analyses of selected bivalves are mainly based on Mfps, Mitogenome, and TimeTree. The outcome of the works has great applications for designing biomimetic materials in future.
Paternal leakage of mitochondrial DNA and maternal inheritance of heteroplasmy in Drosophila hybrids
Authors: Polovina Eirini-Slavka , Parakatselaki Maria-Eleni , Ladoukakis Emmanuel D. 
Published: February 2020

AbstractMitochondrial DNA (mtDNA) is maternally transmitted in animals and therefore, individuals are expected to have a single mtDNA haplotype (homoplasmy). Yet, heteroplasmic individuals have been observed in a large number of animal species. Heteroplasmy may emerge as a result of somatic mtDNA mutations, paternal leakage during fertilization or be inherited from a heteroplasmic mother. Understanding the causes of heteroplasmy could shed light into the evolution of mtDNA inheritance. In this study we examined heteroplasmy in progeny from heterospecific crosses of Drosophila for two consecutive generations. We studied the generation of heteroplasmy from paternal leakage and the maternal transmission of heteroplasmy. Our data reveal non-random patterns in the emergence and transmission of heteroplasmy and suggest that heteroplasmy depends on the family of origin.
Dynamic Tracking Algorithm for Time-Varying Neuronal Network Connectivity using Wide-Field Optical Image Video Sequences
Authors: Renteria Carlos , Liu Yuan-Zhi , Chaney Eric J. , Barkalifa Ronit , Sengupta Parijat , Boppart Stephen A. 
Published: February 2020

AbstractPropagation of signals between neurons and brain regions provides information about the functional properties of neural networks, and thus information transfer. Advances in optical imaging and statistical analyses of acquired optical signals have yielded various metrics for inferring neural connectivity, and hence for mapping signal intercorrelation. However, a single coefficient is traditionally derived to classify the connection strength between two cells, ignoring the fact that neural systems are inherently time-variant systems. To overcome these limitations, we utilized a time-varying Pearson’s correlation coefficient, spike-sorting, wavelet transform, and wavelet coherence of calcium transients from DIV 12–15 hippocampal neurons from GCaMP6s mice after applying various concentrations of glutamate. Results provide a comprehensive overview of resulting firing patterns, network connectivity, signal directionality, and network properties. Together, these metrics provide a more comprehensive and robust method of analyzing transient neural signals, and enable future investigations for tracking the effects of different stimuli on network properties.
Contact Nonlinear Acoustic Diode
Authors: Huang Yao , Wang Xiaoyu , Gong Xun , Wu Haodong , Zhang Dong , Zhang De 
Published: February 2020

AbstractNonlinear implementations of acoustic diodes are inherently nonreciprocal and have received continuous attention from the beginning of the research boom for acoustic diodes. However, all the reported nonlinear schemes usually have the shortcomings such as low transmission ratio, action threshold, lack of stability and cumbersome setups. In the present design, we take advantage of extraordinarily large contact acoustic nonlinearity which is several orders of magnitude stronger than material nonlinearity. It is theoretically found that the spectra of the transmitted wave depend on the contact time. It is proven experimentally that the contact nonlinearity can be tamed by adjusting the driving amplitude, the static stress and the elastic constants of the materials. In order to build a compact acoustic diode, a sub-wavelength filter with a sandwich structure is designed. The total length of the acoustic diode is only three eighths of the incident wavelength. The amplitude-dependent behavior of the device exhibits similarities with electronic diodes. A more than 50% transmission ratio is obtained. A robust, stable, compact, highly efficient and solid-state acoustic diode is realized.
Female mouse tears contain an anti-aggression pheromone
Authors: Cavaliere Rosa Maria , Silvotti Lucia , Percudani Riccardo , Tirindelli Roberto 
Published: February 2020

AbstractTears contain pheromones that trigger specific behavioral responses. In the mouse, male tear fluid is involved in long and short-term effects such as the receptive behavior and pregnancy block in females and the aggression in males. In contrast, pup tears exert an inhibitory effect on male mating behavior, also promoting sexual rejection in females. In the rat, a male lacrimal protein acts as an intraspecific and heterospecific signal enhancing sexual behavior in females and evoking avoidance behavior in mouse. However, behavioral effects of female tears on male behavior have yet to be described. Here, we report that female lacrimal fluid of different mouse strains contains a relatively small and involatile factor that abolishes inter-male aggression switching it into a copulatory behavior. The production of this molecule by the lacrimal glands is not affected by the estrous cycle but it is sensitive to ovariectomy, thus suggesting a control mediated by hormones. Moreover, this lacrimal anti-aggression pheromone modulates the activity of the lateral habenula, a brain area responsible for the valence of the aggressive interactions.
The anti-tumoral potential of the saporin-based uPAR-targeting chimera ATF-SAP
Authors: Zuppone S. , Assalini C. , Minici C. , Bertagnoli S. , Branduardi P. , Degano M. , Fabbrini M. S. , Montorsi F. , Salonia A. , Vago R. 
Published: February 2020

AbstractThe development of personalized therapies represents an urgent need owing to the high rate of cancer recurrence and systemic toxicity of conventional drugs. So far, targeted toxins have shown promising results as potential therapeutic compounds. Specifically, toxins conjugated to antibodies or fused to growth factors/enzymes have been largely demonstrated to selectively address and kill cancer cells. We investigated the anti-tumor potential of a chimeric recombinant fusion protein formed by the Ribosome Inactivating Protein saporin (SAP) and the amino-terminal fragment (ATF) of the urokinase-type plasminogen activator (uPA), whose receptor has been shown to be over-expressed on the surface of aggressive tumors. ATF-SAP was recombinantly produced by the P. pastoris yeast and its activity was assessed on a panel of bladder and breast cancer cell lines. ATF-SAP resulted to be highly active in vitro, as nano-molar concentrations were sufficient to impair viability on tumor cell lines. In contrast to untargeted toxins, the chimeric fusion protein displayed a significantly improved toxic effect in uPAR-expressing cells, demonstrating that the selective activity was due to the presence of the targeting moiety. Fibroblasts were not sensitive to ATF-SAP despite uPAR expression, indicating that cell-specific receptor-mediated internalization pathway(s) might be considered. The in vivo anti-tumor effect of the chimera was shown in a bladder cancer xenograft model. Current findings indicate ATF-SAP as a suitable anti-tumoral therapeutic option to cope with cancer aggressiveness, as a single treatment or in combination with traditional therapeutic approaches, to appropriately address the intra- and inter- tumor heterogeneity.
The earliest farmers of northwest China exploited grain-fed pheasants not chickens
Authors: Barton Loukas , Bingham Brittany , Sankaranarayanan Krithivasan , Monroe Cara , Thomas Ariane , Kemp Brian M. 
Published: February 2020

AbstractThough chickens (Gallus gallus domesticus) are globally ubiquitous today, the timing, location, and manner of their domestication is contentious. Until recently, archaeologists placed the origin of the domestic chicken in northern China, perhaps as early as 8,000 years ago. Such evidence however complicates our understanding of how the chicken was domesticated because its wild progenitor – the red jungle fowl (Gallus gallus) – lives in tropical ecosystems and does not exist in northern China today or in the recent past. Increasingly, multiple lines of evidence suggest that many of the archaeological bird remains underlying this northern origins hypothesis have been misidentified. Here we analyze the mitochondrial DNA of some of the earliest purported chickens from the Dadiwan site in northern China and conclude that they are pheasants (Phasianus colchicus). Curiously, stable isotope values from the same birds reveal that their diet was heavy in agricultural products (namely millet), meaning that they lived adjacent to or among some of the earliest farming communities in East Asia. We suggest that the exploitation of these baited birds was an important adaptation for early farmers in China’s arid north, and that management practices like these likely played a role in the domestication of animals – including the chicken – in similar contexts throughout the region.
Assessing the progression of systemic sclerosis by monitoring the tissue optic axis using PS-OCT
Authors: Adams David C. , Szabari Margit V. , Lagares David , McCrossan Andrew F. , Hariri Lida P. , Tager Andrew M. , Suter Melissa J. 
Published: February 2020

AbstractThe clinical assessment of fibrosis is critical to the diagnosis and management of patients with systemic sclerosis. Current clinical standards for patient assessment is to use skin fibrosis as an indicator of organ involvement, though this approach is highly subjective and relies on manual palpation. The development of a new method for accurately quantifying collagen content may therefore significantly improve the accuracy of the traditional skin score in patients with systemic sclerosis and may additionally aid in the monitoring of anti-fibrotic therapies in clinical practice. Polarization-sensitive optical coherence tomography (PS-OCT) is a high-speed volumetric imaging modality that can be used to assess birefringent tissues including collagen. In this work we demonstrate a novel computational approach using PS-OCT for the assessment of fibrosis. This approach, based on the measured distribution of optic axis values associated with a given volume of collagen orientation, characterizes fibrotic changes independently from the depth of the region of interest in the tissue. This approach has the potential to accurately quantify collagen content and orientation faster and more robustly compared to traditional PS-OCT metrics. We investigate the viability of this approach for assessing the development of fibrosis in a bleomycin induced skin fibrosis mouse model.
Individual variation in the attribution of incentive salience to social cues
Authors: Fitzpatrick Christopher J. , Morrow Jonathan D. 
Published: February 2020

AbstractResearch on the attribution of incentive salience to drug cues has furthered our understanding of drug self-administration in animals and addiction in humans. The influence of social cues on drug-seeking behavior has garnered attention recently, but few studies have investigated how social cues gain incentive-motivational value. In the present study, a Pavlovian conditioned approach (PCA) procedure was used to identify rats that are more (sign-trackers; STs) or less (goal-trackers; GTs) prone to attribute incentive salience to food reward cues. In Experiment 1, a novel procedure employed social ‘peers’ to compare the tendency of STs and GTs to attribute incentive salience to social reward cues as well as form a social-conditioned place preference. In Experiment 2, social behavior of STs and GTs was compared using social interaction and choice tests. Finally, in Experiment 3, levels of plasma oxytocin were measured in STs and GTs seven days after the last PCA training session, because oxytocin is known to modulate the mesolimbic reward system and social behavior. Compared to GTs, STs attributed more incentive salience to social-related cues and exhibited prosocial behaviors (e.g., social-conditioned place preference, increased social interaction, and social novelty-seeking). No group differences were observed in plasma oxytocin levels. Taken together, these experiments demonstrate individual variation in the attribution of incentive salience to both food- and social-related cues, which has important implications for the pathophysiology of addiction.
Pyrocatechol, a component of coffee, suppresses LPS-induced inflammatory responses by inhibiting NF-κB and activating Nrf2
Authors: Funakoshi-Tago Megumi , Nonaka Yusuke , Tago Kenji , Takeda Mika , Ishihara Yuma , Sakai Ami , Matsutaka Mari , Kobata Kenji , Tamura Hiroomi 
Published: February 2020

AbstractCoffee is a complex mixture of many bioactive compounds possessing anti-inflammatory properties. However, the mechanisms by which coffee exerts anti-inflammatory effects remains unclear and the active ingredients have not yet been identified. In this study, we found that coffee extract at more than 2.5%(v/v) significantly inhibited LPS-induced inflammatory responses in RAW264.7 cells and that anti-inflammatory activity of coffee required the roasting process. Interestingly, we identified pyrocatechol, a degradation product derived from chlorogenic acid during roasting, as the active ingredient exhibiting anti-inflammatory activity in coffee. HPLC analysis showed that 124 μM pyrocatechol was included in 100% (v/v) roasted coffee. A treatment with 5%(v/v) coffee extract and more than 2.5 μM pyrocatechol inhibited the LPS-induced activation of NF-κB and also significantly activated Nrf2, which acts as a negative regulator in LPS-induced inflammation. Furthermore, intake of 60% (v/v) coffee extract and 74.4 μM pyrocatechol, which is the concentration equal to contained in 60% (v/v) coffee, markedly inhibited the LPS-induced inflammatory responses in mice. Collectively, these results demonstrated that pyrocatechol, which was formed by the roasting of coffee green beans, is one of the ingredients contributing to the anti-inflammatory activity of coffee.
Comb-locked frequency-swept synthesizer for high precision broadband spectroscopy
Authors: Gotti Riccardo , Puppe Thomas , Mayzlin Yuriy , Robinson-Tait Julian , Wójtewicz Szymon , Gatti Davide , Alsaif Bidoor , Lamperti Marco , Laporta Paolo , Rohde Felix , Wilk Rafal , Leisching Patrick , Kaenders Wilhelm G. , Marangoni Marco 
Published: February 2020

AbstractFrequency combs have made optical metrology accessible to hundreds of laboratories worldwide and they have set new benchmarks in multi-species trace gas sensing for environmental, industrial and medical applications. However, current comb spectrometers privilege either frequency precision and sensitivity through interposition of a cw probe laser with limited tuning range, or spectral coverage and measurement time using the comb itself as an ultra-broadband probe. We overcome this restriction by introducing a comb-locked frequency-swept optical synthesizer that allows a continuous-wave laser to be swept in seconds over spectral ranges of several terahertz while remaining phase locked to an underlying frequency comb. This offers a unique degree of versatility, as the synthesizer can be either repeatedly scanned over a single absorption line to achieve ultimate precision and sensitivity, or swept in seconds over an entire rovibrational band to capture multiple species. The spectrometer enables us to determine line center frequencies with an absolute uncertainty of 30 kHz and at the same time to collect absorption spectra over more than 3 THz with state-of-the-art sensitivity of a few 10−10 cm−1. Beyond precision broadband spectroscopy, the proposed synthesizer is an extremely promising tool to force a breakthrough in terahertz metrology and coherent laser ranging.
MicroRNAs regulate innate immunity against uropathogenic and commensal-like Escherichia coli infections in the surrogate insect model Galleria mellonella
Authors: Mukherjee Krishnendu , Amsel Daniel , Kalsy Miriam , Billion Andre , Dobrindt Ulrich , Vilcinskas Andreas 
Published: February 2020

AbstractUropathogenic Escherichia coli (UPEC) strains cause symptomatic urinary tract infections in humans whereas commensal-like E. coli strains in the urinary bladder cause long-term asymptomatic bacteriuria (ABU). We previously reported that UPEC and ABU strains differentially regulate key DNA methylation and histone acetylation components in the surrogate insect host Galleria mellonella to epigenetically modulate innate immunity-related gene expression, which in turn controls bacterial growth. In this follow-up study, we infected G. mellonella larvae with UPEC strain CFT073 or ABU strain 83972 to identify differences in the expression of microRNAs (miRNAs), a class of non-coding RNAs that regulate gene expression at the post-transcriptional level. Our small RNA sequencing analysis showed that UPEC and ABU infections caused significant changes in the abundance of miRNAs in the larvae, and highlighted the differential expression of 147 conserved miRNAs and 95 novel miRNA candidates. We annotated the G. mellonella genome sequence to investigate the miRNA-regulated expression of genes encoding antimicrobial peptides, signaling proteins, and enzymatic regulators of DNA methylation and histone acetylation in infected larvae. Our results indicate that miRNAs play a role in the epigenetic reprograming of innate immunity in G. mellonella larvae to distinguish between pathogenic and commensal strains of E. coli.
A record of seafloor methane seepage across the last 150 million years
Authors: Oppo D. , De Siena L. , Kemp D. B. 
Published: February 2020

AbstractSeafloor methane seepage is a significant source of carbon in the marine environment. The processes and temporal patterns of seafloor methane seepage over multi-million-year time scales are still poorly understood. The microbial oxidation of methane can store carbon in sediments through precipitation of carbonate minerals, thus providing a record of past methane emission. In this study, we compiled data on methane-derived carbonates to build a proxy time series of methane emission over the last 150 My and statistically compared it with the main hypothesised geological controllers of methane emission. We quantitatively demonstrate that variations in sea level and organic carbon burial are the dominant controls on methane leakage since the Early Cretaceous. Sea level controls methane seepage variations by imposing smooth trends on timescales in the order of tens of My. Organic carbon burial is affected by the same cyclicities, and instantaneously controls methane release because of the geologically rapid generation of biogenic methane. Both the identified fundamental (26–27 My) and higher (12 My) cyclicities relate to global phenomena. Temporal correlation analysis supports the evidence that modern expansion of hypoxic areas and its effect on organic carbon burial may lead to higher seawater methane concentrations over the coming centuries.
Demonstration of electron focusing using electronic lenses in low-dimensional system
Authors: Yan Chengyu , Pepper Michael , See Patrick , Farrer Ian , Ritchie David , Griffiths Jonathan 
Published: February 2020

AbstractWe report an all-electric integrable electron focusing lens in n-type GaAs. It is shown that a pronounced focusing peak takes place when the focal point aligns with an on-chip detector. The intensity and full width half maximum (FWHM) of the focusing peak are associated with the collimation of injected electrons. To demonstrate the reported focusing lens can be a useful tool, we investigate the characteristic of an asymmetrically gate biased quantum point contact with the assistance of a focusing lens. A correlation between the occurrence of conductance anomaly in low conductance regime and increase in FWHM of focusing peak is observed. The correlation is likely due to the electron-electron interaction. The reported electron focusing lens is essential for a more advanced electron optics device.
Linear and nonlinear optical probing of various excitons in 2D inorganic-organic hybrid structures
Authors: Adnan Mohammad , Baumberg Jeremy J. , Vijaya Prakash G 
Published: February 2020

AbstractNonlinear optical properties, such as two-(or multi-) photon absorption (2PA), are of special interest for technologically important applications in fast optical switching, in vivo imaging and so on. Highly intense infrared ultrashort pulses probe deep into samples and reveal several underlying structural perturbations (inter-layer distortions, intra-layer crumpling) and also provide information about new excited states and their relaxation. Naturally self-assembled inorganic-organic multiple quantum wells (IO-MQWs) show utility from room-temperature exciton emission features (binding energies ~200–250 meV). These Mott type excitons are highly sensitive to the self-assembly process, inorganic network distortions, thickness and inter-layer distortions of these soft two-dimensional (2D) and weak van der Waal layered hybrids. We demonstrate strong room-temperature nonlinear excitation intensity dependent two-photon absorption induced exciton photoluminescence (2PA-PL) from these IO-MQWs, excited by infrared femtosecond laser pulses. Strongly confined excitons show distinctly different one- and two-photon excited photoluminescence energies: from free-excitons (2.41 eV) coupled to the perfectly aligned MQWs and from energy down-shifted excitons (2.33 eV) that originate from the locally crumpled layered architecture. High intensity femtosecond induced PL from one-photon absorption (1PA-PL) suggests saturation of absorption and exciton-exciton annihilation, with typical reduction in PL radiative relaxation times from 270 ps to 190 ps upon increasing excitation intensities. From a wide range of IR excitation tuning, the origin of 2PA-PL excitation is suggested to arise from exciton dark states which extend below the bandgap. Observed two-photon absorption coefficients (β ~75 cm/GW) and two-photon excitation cross-sections (η2σ2 ~ 110GM), further support the evidence for 2PA excitation origin. Both 1PA- and 2PA-PL spatial mappings over large areas of single crystal platelets demonstrate the co-existence of both free and deep-level crumpled excitons with some traces of defect-induced trap state emission. We conclude that the two-photon absorption induced PL is highly sensitive to the self-assembly process of few to many mono layers, the crystal packing and deep level defects. This study paves a way to tailor the nonlinear properties of many 2D material classes. Our results thus open new avenues for exploring fundamental phenomena and novel optoelectronic applications using layered inorganic-organic and other metal organic frameworks.