bluuebunny/crossref_metadata_2025_split huggingface dataset:
A semiconducting layered metal-organic framework magnet
Authors: Yang Chongqing , Dong Renhao , Wang Mao , Petkov Petko St. , Zhang Zhitao , Wang Mingchao , Han Peng , Ballabio Marco , Bräuninger Sascha A. , Liao Zhongquan , Zhang Jichao , Schwotzer Friedrich , Zschech Ehrenfried , Klauss Hans-Henning , Cánovas Enrique , Kaskel Stefan , Bonn Mischa , Zhou Shengqiang , Heine Thomas , Feng Xinliang 
Published: July 2019

AbstractThe realization of ferromagnetism in semiconductors is an attractive avenue for the development of spintronic applications. Here, we report a semiconducting layered metal-organic framework (MOF), namely K3Fe2[(2,3,9,10,16,17,23,24-octahydroxy phthalocyaninato)Fe] (K3Fe2[PcFe-O8]) with spontaneous magnetization. This layered MOF features in-plane full π-d conjugation and exhibits semiconducting behavior with a room temperature carrier mobility of 15 ± 2 cm2 V−1 s−1 as determined by time-resolved Terahertz spectroscopy. Magnetization experiments and 57Fe Mössbauer spectroscopy demonstrate the presence of long-range magnetic correlations in K3Fe2[PcFe-O8] arising from the magnetic coupling between iron centers via delocalized π electrons. The sample exhibits superparamagnetic features due to a distribution of crystal size and possesses magnetic hysteresis up to 350 K. Our work sets the stage for the development of spintronic materials exploiting magnetic MOF semiconductors.
Absence of emergent supersymmetry at superconducting quantum critical points in Dirac and Weyl semimetals
Authors: Zhao Peng-Lu , Liu Guo-Zhu 
Published: July 2019

AbstractSupersymmetry plays a crucial role in superstring theory and high-energy physics, but has never been observed in experiments. Recently, an effective space–time supersymmetry (SUSY) was argued to emerge in the low-energy region by tuning Dirac or Weyl semimetal to approach a superconducting (SC) quantum critical point (QCP), at which the Dirac or Weyl fermion and the bosonic order parameter are both massless. Here, we study under what circumstances can SUSY be realized at a quantum critical point. We demonstrate that the Yukawa-type coupling between the massless fermion and massless boson can dynamically generate an infinite number of non-supersymmetric terms in the effective field theory of the boson. Owing to these terms, no space–time supersymmetry emerges at the SC QCPs. The results provide important constraint on the exploration of emergent SUSY in condensed matter systems.
Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes
Authors: Roux Simon , Krupovic Mart , Daly Rebecca A. , Borges Adair L. , Nayfach Stephen , Schulz Frederik , Sharrar Allison , Matheus Carnevali Paula B. , Cheng Jan-Fang , Ivanova Natalia N. , Bondy-Denomy Joseph , Wrighton Kelly C. , Woyke Tanja , Visel Axel , Kyrpides Nikos C. , Eloe-Fadrosh Emiley A. 
Published: July 2019

AbstractBacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a machine learning approach leveraging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem. Putative inoviruses were also detected in several archaeal genomes, suggesting that, collectively, members of this supergroup infect hosts across the domains Bacteria and Archaea. Finally, we identified an expansive diversity of inovirus-encoded toxin–antitoxin and gene expression modulation systems, alongside evidence of both synergistic (CRISPR evasion) and antagonistic (superinfection exclusion) interactions with co-infecting viruses, which we experimentally validated in a Pseudomonas model. Capturing this previously obscured component of the global virosphere may spark new avenues for microbial manipulation approaches and innovative biotechnological applications.
Transcriptome sequencing, molecular markers, and transcription factor discovery of Platanus acerifolia in the presence of Corythucha ciliata
Authors: Li Fengqi , Wu Chunyan , Gao Mengzhu , Jiao Mengmeng , Qu Cheng , Gonzalez-Uriarte Asier , Luo Chen 
Published: July 2019

AbstractThe London Planetree (Platanus acerifolia) are present throughout the world. The tree is considered a greening plant and is commonly planted in streets, parks, and courtyards. The Sycamore lace bug (Corythucha ciliata) is a serious pest of this tree. To determine the molecular mechanism behind the interaction between the London Planetree and the Sycamore lace bug, we generated a comprehensive RNA-seq dataset (630,835,762 clean reads) for P. acerifolia by sequencing both infected and non-infected leaves of C. ciliata using the Illumina Hiseq 4000 system. We assembled the transcriptomes using the Trinity De Novo assembly followed by annotation. In total, 121,136 unigenes were obtained, and 80,559 unigenes were successfully annotated. From the 121,136 unigenes, we identified 3,010,256 SNPs, 39,097 microsatellites locus, and 1,916 transcription factors. The transcriptomic dataset we present are the first reports of transcriptome information in Platanus species and will be incredibly useful in future studies with P. acerifolia and other Platanus species, especially in the areas of genomics, molecular biology, physiology, and population genetics.
Modeling Zika Virus Transmission Dynamics: Parameter Estimates, Disease Characteristics, and Prevention
Authors: Rahman Munsur , Bekele-Maxwell Kidist , Cates LeAnna L. , Banks H. T. , Vaidya Naveen K. 
Published: July 2019

AbstractBecause of limited data, much remains uncertain about parameters related to transmission dynamics of Zika virus (ZIKV). Estimating a large number of parameters from the limited information in data may not provide useful knowledge about the ZIKV. Here, we developed a method that utilizes a mathematical model of ZIKV dynamics and the complex-step derivative approximation technique to identify parameters that can be estimated from the available data. Applying our method to epidemic data from the ZIKV outbreaks in French Polynesia and Yap Island, we identified the parameters that can be estimated from these island data. Our results suggest that the parameters that can be estimated from a given data set, as well as the estimated values of those parameters, vary from Island to Island. Our method allowed us to estimate some ZIKV-related parameters with reasonable confidence intervals. We also computed the basic reproduction number to be from 2.03 to 3.20 across islands. Furthermore, using our model, we evaluated potential prevention strategies and found that peak prevalence can be reduced to nearly 10% by reducing mosquito-to-human contact by at least 60% or increasing mosquito death by at least a factor of three of the base case. With these preventions, the final outbreak-size is predicted to be negligible, thereby successfully controlling ZIKV epidemics.
Regulation of stomatal opening and histone modification by photoperiod in Arabidopsis thaliana
Authors: Aoki Saya , Toh Shigeo , Nakamichi Norihito , Hayashi Yuki , Wang Yin , Suzuki Takamasa , Tsuji Hiroyuki , Kinoshita Toshinori 
Published: July 2019

AbstractStomatal movements are regulated by many environmental signals, such as light, CO2, temperature, humidity, and drought. Recently, we showed that photoperiodic flowering components have positive effects on light-induced stomatal opening in Arabidopsis thaliana. In this study, we determined that light-induced stomatal opening and increased stomatal conductance were larger in plants grown under long-day (LD) conditions than in those grown under short-day (SD) conditions. Gene expression analyses using purified guard cell protoplasts revealed that FT and SOC1 expression levels were significantly increased under LD conditions. Interestingly, the enhancement of light-induced stomatal opening and increased SOC1 expression in guard cells due to LD conditions persisted for at least 1 week after plants were transferred to SD conditions. We then investigated histone modification using chromatin immunoprecipitation–PCR, and observed increased trimethylation of lysine 4 on histone 3 (H3K4) around SOC1. We also found that LD-dependent enhancement of light-induced stomatal opening and H3K4 trimethylation in SOC1 were suppressed in the ft-2 mutant. These results indicate that photoperiod is an important environmental cue regulating stomatal opening, and that LD conditions enhance light-induced stomatal opening and epigenetic modification (H3K4 trimethylation) around SOC1, a positive regulator of stomatal opening, in an FT-dependent manner. Thus, this study provides novel insights into stomatal responses to photoperiod.
Functional spectroscopic imaging reveals specificity of glutamate response in mouse brain to peripheral sensory stimulation
Authors: Seuwen Aline , Schroeter Aileen , Grandjean Joanes , Schlegel Felix , Rudin Markus 
Published: July 2019

AbstractNon-invasive investigation of physiological changes and metabolic events associated with brain activity in mice constitutes a major challenge. Conventionally, fMRI assesses neuronal activity by evaluating activity-evoked local changes in blood oxygenation levels (BOLD). In isoflurane-anaethetized mice, however, we found that BOLD signal changes during paw stimulation appear to be dominated by arousal responses even when using innocuous stimuli. Widespread responses involving both hemispheres have been observed in response to unilateral stimulation. MRS allows probing metabolic changes associated with neuronal activation and provides a complementary readout to BOLD fMRI for investigating brain activity. In this study we evaluated the sensitivity of a free induction decay (FID) based spectroscopic imaging (MRSI) protocol for the measurement of alterations in glutamate levels elicited by unilateral electrical paw stimulation at different current amplitudes. Coronal MRSI maps of glutamate distribution with 17 × 17 voxels of 1 µl volume have been recorded with a temporal resolution of 12 min. Significant region-specific increases in glutamate levels have been observed in the contralateral but not in the ispiateral S1 somatosensory cortex upon stimulation. The amplitude of glutamate changes increased in a dose-dependent manner with the stimulus amplitude. The study demonstrates feasibility of functional MRSI in mice for studying activity-evoked glutamate changes in a temporo-spatially resolved manner.
Surgical anatomy of the ovine sural nerve for facial nerve regeneration and reconstruction research
Authors: Niimi Yosuke , Fukuda Satoshi , Gilbert Ryan S. , Baljinnyam Tuvshintugs , Niimi Yu , Matsumine Hajime , Liu Keibun , Jacob Sam , Hawkins Hal K. , Cox Robert A. , Herndon David N. , Prough Donald S. , Enkhbaatar Perenlei 
Published: July 2019

AbstractThe lack of a clinically relevant animal models for research in facial nerve reconstruction is challenging. In this study, we investigated the surgical anatomy of the ovine sural nerve as a potential candidate for facial nerve reconstruction, and performed its histological quantitative analysis in comparison to the buccal branch (BB) of the facial nerve using cadaver and anesthetized sheep. The ovine sural nerve descended to the lower leg along the short saphenous vein. The length of the sural nerve was 14.3 ± 0.5 cm. The distance from the posterior edge of the lateral malleolus to the sural nerve was 7.8 ± 1.8 mm. The mean number of myelinated fibers in the sural nerve was significantly lower than that of the BB (2,311 ± 381vs. 5,022 ± 433, respectively. p = 0.003). The number of fascicles in the sural nerve was also significantly lower than in the BB (10.5 ± 1.7 vs. 21.3 ± 2.7, respectively. p = 0.007). The sural nerve was grafted to the BB with end-to-end neurorrhaphy under surgical microscopy in cadaver sheep. The surgical anatomy and the number of fascicles of the ovine sural nerve were similar of those reported in humans. The results suggest that the sural nerve can be successfully used for facial nerve reconstruction research in a clinically relevant ovine model.
Virus Genotype-Dependent Transcriptional Alterations in Lipid Metabolism and Inflammation Pathways in the Hepatitis C Virus-infected Liver
Authors: d’Avigdor W. M. H. , Budzinska M. A. , Lee M. , Lam R. , Kench J. , Stapelberg M. , McLennan S. V. , Farrell G. , George J. , McCaughan G. W. , Tu T. , Shackel N. A. 
Published: July 2019

AbstractDespite advances in antiviral therapy, molecular drivers of Hepatitis C Virus (HCV)-related liver disease remain poorly characterised. Chronic infection with HCV genotypes (1 and 3) differ in presentation of liver steatosis and virological response to therapies, both to interferon and direct acting antivirals. To understand what drives these clinically important differences, liver expression profiles of patients with HCV Genotype 1 or 3 infection (n = 26 and 33), alcoholic liver disease (n = 8), and no liver disease (n = 10) were analysed using transcriptome-wide microarrays. In progressive liver disease, HCV genotype was the major contributor to altered liver gene expression with 2151 genes differentially expressed >1.5-fold between HCV Genotype 1 and 3. In contrast, only 6 genes were altered between the HCV genotypes in advanced liver disease. Induction of lipogenic, lipolytic, and interferon stimulated gene pathways were enriched in Genotype 1 injury whilst a broad range of immune-associated pathways were associated with Genotype 3 injury. The results are consistent with greater lipid turnover in HCV Genotype 1 patients. Moreover, the lower activity in inflammatory pathways associated with HCV genotype 1 is consistent with relative resistance to interferon-based therapy. This data provides a molecular framework to explain the clinical manifestations of HCV-associated liver disease.
Experimental Characterization of the Ultrafast, Tunable and Broadband Optical Kerr Nonlinearity in Graphene
Authors: Thakur Siddharatha , Semnani Behrooz , Safavi-Naeini Safieddin , Majedi Amir Hamed 
Published: July 2019

AbstractGraphene’s giant nonlinear optical response along with its integrability has made it a vaunted material for on-chip photonics. Despite a multitude of studies confirming its strong nonlinearity, there is a lack of reports examining the fundamental processes that govern the response. Addressing this gap in knowledge we analyse the role of experimental parameters by systematically measuring the near-infrared spectral dependence, the sub-picosecond temporal evolution and pulse-width dependence of the effective Kerr coefficient (n2,eff) of graphene in hundreds of femtosecond regime. The spectral dependence measured using the Z-scan technique is corroborated by a density matrix quantum theory formulation to extract a n2,eff ∝ λ2 dependence. The temporal evolution obtained using the time-resolved Z-scan measurement shows the nonlinearity peaking at zero delay time and relaxing on a time-scale of carrier relaxation. The dependence of the n2,eff on pulse duration is obtained by expanding the input pulse using a prism-pair set-up. Our results provide an avenue for controllable tunability of the nonlinear response in graphene, which is limited in silicon photonics.
Thermodynamic study of the effect of ions on the interaction between dengue virus NS3 helicase and single stranded RNA
Authors: Cababie Leila A. , Incicco J. Jeremías , González-Lebrero Rodolfo M. , Roman Ernesto A. , Gebhard Leopoldo G. , Gamarnik Andrea V. , Kaufman Sergio B. 
Published: July 2019

AbstractDengue virus nonstructural protein 3 (NS3) fulfills multiple essential functions during the viral replication and constitutes a prominent drug target. NS3 is composed by a superfamily-2 RNA helicase domain joined to a serine protease domain. Quantitative fluorescence titrations employing a fluorescein-tagged RNA oligonucleotide were used to investigate the effect of salts on the interaction between NS3 and single stranded RNA (ssRNA). We found a strong dependence of the observed equilibrium binding constant, Kobs, with the salt concentration, decreasing at least 7-fold for a 1-fold increase on cation concentration. As a result of the effective neutralization of ~10 phosphate groups, binding of helicase domain of NS3 to ssRNA is accompanied by the release of 5 or 7 monovalent cations from an oligonucleotide or a polynucleotide, respectively and of 3 divalent cations from the same oligonucleotide. Such estimates are not affected by the type of cation, either monovalent (KCl, NaCl and RbCl) or divalent (MgCl2 and CaCl2), nor by the presence of the protease domain or the fluorescein label. Combined effect of mono and divalent cations was well described by a simple equilibrium binding model which allows to predict the values of Kobs at any concentration of cations.
Female Blow Flies As Vertebrate Resource Indicators
Authors: Owings Charity G. , Banerjee Aniruddha , Asher Travis M. D. , Gilhooly William P. , Tuceryan Anais , Huffine Mary , Skaggs Christine L. , Adebowale Iyun M. , Manicke Nicholas E. , Picard Christine J. 
Published: July 2019

AbstractRapid vertebrate diversity evaluation is invaluable for monitoring changing ecosystems worldwide. Wild blow flies naturally recover DNA and chemical signatures from animal carcasses and feces. We demonstrate the power of blow flies as biodiversity monitors through sampling of flies in three environments with varying human influences: Indianapolis, IN and two national parks (the Great Smoky Mountains and Yellowstone). Dissected fly guts underwent vertebrate DNA sequencing (12S and 16S rRNA genes) and fecal metabolite screening. Integrated Nested Laplace Approximation (INLA) was used to determine the most important abiotic factor influencing fly-derived vertebrate richness. In 720 min total sampling time, 28 vertebrate species were identified, with 42% of flies containing vertebrate resources: 23% DNA, 5% feces, and 14% contained both. The species of blow fly used was not important for vertebrate DNA recovery, however the use of female flies versus male flies directly influenced DNA detection. Temperature was statistically relevant across environments in maximizing vertebrate detection (mean = 0.098, sd = 0.048). This method will empower ecologists to test vertebrate community ecology theories previously out of reach due practical challenges associated with traditional sampling.
Macaques preferentially attend to visual patterns with higher fractal dimension contours
Authors: Finn Kelly R. , Crutchfield James P. , Bliss-Moreau Eliza 
Published: July 2019

AbstractAnimals’ sensory systems evolved to efficiently process information from their environmental niches. Niches often include irregular shapes and rough textures (e.g., jagged terrain, canopy outlines) that must be navigated to find food, escape predators, and master other fitness-related challenges. For most primates, vision is the dominant sensory modality and thus, primates have evolved systems for processing complicated visual stimuli. One way to quantify information present in visual stimuli in natural scenes is evaluating their fractal dimension. We hypothesized that sensitivity to complicated geometric forms, indexed by fractal dimension, is an evolutionarily conserved capacity, and tested this capacity in rhesus macaques (Macaca mulatta). Monkeys viewed paired black and white images of simulated self-similar contours that systematically varied in fractal dimension while their attention to the stimuli was measured using noninvasive infrared eye tracking. They fixated more frequently on, dwelled for longer durations on, and had attentional biases towards images that contain boundary contours with higher fractal dimensions. This indicates that, like humans, they discriminate between visual stimuli on the basis of fractal dimension and may prefer viewing informationally rich visual stimuli. Our findings suggest that sensitivity to fractal dimension may be a wider ability of the vertebrate vision system.
Novel strategy for rapid functional in vivo validation of oncogenic drivers in haematological malignancies
Authors: Pieters Tim , T’Sas Sara , Demoen Lisa , Almeida André , Haenebalcke Lieven , Matthijssens Filip , Lemeire Kelly , D’Hont Jinke , Van Rockeghem Frederique , Hochepied Tino , Lintermans Beatrice , Reunes Lindy , Lammens Tim , Berx Geert , Haigh Jody J. , Goossens Steven , Van Vlierberghe Pieter 
Published: July 2019

AbstractIn cancer research, it remains challenging to functionally validate putative novel oncogenic drivers and to establish relevant preclinical models for evaluation of novel therapeutic strategies. Here, we describe an optimized and efficient pipeline for the generation of novel conditional overexpression mouse models in which putative oncogenes, along with an eGFP/Luciferase dual reporter, are expressed from the endogenous ROSA26 (R26) promoter. The efficiency of this approach was demonstrated by the generation and validation of novel R26 knock-in (KI) mice that allow conditional overexpression of Jarid2, Runx2, MN1 and a dominant negative allele of ETV6. As proof of concept, we confirm that MN1 overexpression in the hematopoietic lineage is sufficient to drive myeloid leukemia. In addition, we show that T-cell specific activation of MN1 in combination with loss of Pten increases tumour penetrance and stimulates the formation of Lyl1+ murine T-cell lymphoblastic leukemias or lymphomas (T-ALL/T-LBL). Finally, we demonstrate that these luciferase-positive murine AML and T-ALL/T-LBL cells are transplantable into immunocompromised mice allowing preclinical evaluation of novel anti-leukemic drugs in vivo.
Tracking the Growth of Superparamagnetic Nanoparticles with an In-Situ Magnetic Particle Spectrometer (INSPECT)
Authors: Malhotra Ankit , von Gladiss Anselm , Behrends André , Friedrich Thomas , Neumann Alexander , Buzug Thorsten M. , Lüdtke-Buzug Kerstin 
Published: July 2019

AbstractMagnetic Particle Spectroscopy (MPS) is a measurement technique to determine the magnetic properties of superparamagnetic iron oxide nanoparticles (SPIONs) in an oscillating magnetic field as applied in Magnetic Particle Imaging (MPI). State of the art MPS devices are solely capable of measuring the magnetization response of the SPIONs to an oscillatory magnetic excitation retrospectively, i.e. after the synthesis process. In this contribution, a novel in-situ magnetic particle spectrometer (INSPECT) is presented, which can be used to monitor the entire synthesis process from particle genesis via growth to the stable colloidal suspension of the nanoparticles in real time. The device is suitable for the use in a biochemistry environment. It has a chamber size of 72 mm such that a 100 ml reaction flask can be used for synthesis. For an alkaline-based precipitation, the change of magnetic properties of SPIONs during the nucleation and growth phase of the synthesis is demonstrated. The device is able to record the changes in the amplitude and phase spectra, and, in turn, the hysteresis. Hence, it is a powerful tool for an in-depth understanding of the nanoparticle formation dynamics during the synthesis process.