bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reward cues readily direct monkeys’ auditory performance resulting in broad auditory cortex modulation and interaction with sites along cholinergic and dopaminergic pathways
Authors: Wikman Patrik , Rinne Teemu , Petkov Christopher I. 
Published: February 2019

AbstractIn natural settings, the prospect of reward often influences the focus of our attention, but how cognitive and motivational systems influence sensory cortex is not well understood. Also, challenges in training nonhuman animals on cognitive tasks complicate cross-species comparisons and interpreting results on the neurobiological bases of cognition. Incentivized attention tasks could expedite training and evaluate the impact of attention on sensory cortex. Here we develop an Incentivized Attention Paradigm (IAP) and use it to show that macaque monkeys readily learn to use auditory or visual reward cues, drastically influencing their performance within a simple auditory task. Next, this paradigm was used with functional neuroimaging to measure activation modulation in the monkey auditory cortex. The results show modulation of extensive auditory cortical regions throughout primary and non-primary regions, which although a hallmark of attentional modulation in human auditory cortex, has not been studied or observed as broadly in prior data from nonhuman animals. Psycho-physiological interactions were identified between the observed auditory cortex effects and regions including basal forebrain sites along acetylcholinergic and dopaminergic pathways. The findings reveal the impact and regional interactions in the primate brain during an incentivized attention engaging auditory task.
Gold-Nanocluster-Assisted Nanotransfer Printing Method for Metasurface Hologram Fabrication
Authors: Hwang Soon Hyoung , Cho Jaebum , Jeon Sohee , Kang Hyeok-Jung , Zhao Zhi-Jun , Park Sungjae , Lee Yohan , Lee Jonghyun , Kim Mugeon , Hahn Joonku , Lee Byoungho , Jeong Jun Ho , Kim Hwi , Youn Jae Ryoun 
Published: February 2019

AbstractGiven the development of nano/microscale patterning techniques, efforts are being made to use them for fabricating metasurfaces. In particular, by using abrupt phase discontinuities, it is possible to generate holographic images from two-dimensional nanoscale-patterned metasurfaces. However, the fabrication of metasurface holograms is hindered by the high costs and long fabrication time involved, because the process requires expensive equipment such as that for electron-beam lithography. Therefore, it is difficult to realize metasurface holograms in a fast and repetitive manner. In this study, we propose a method for fabricating metasurface holograms based on the nanotransfer printing of the desired nanoscale patterns, which is assisted by Au nanoclusters, while controlling the bonding energy based on the shape of the deposited Au layer. Robust covalent bonds are formed between the Si of the adhesive used and the O of the SiO2 layer in order to transfer the deposited Au onto the transparent substrate quickly. It was found that the fabricated metasurface hologram coincides with the one designed by computer-generated holography. The proposed method should lead to a significant breakthrough in the fabrication of holograms based on different types of metasurfaces at a low cost in a fast, repetitive manner with various metals.
Inferring Temporal Information from a Snapshot of a Dynamic Network
Authors: Sreedharan Jithin K. , Magner Abram , Grama Ananth , Szpankowski Wojciech 
Published: February 2019

AbstractThe problem of reverse-engineering the evolution of a dynamic network, known broadly as network archaeology, is one of profound importance in diverse application domains. In analysis of infection spread, it reveals the spatial and temporal processes underlying infection. In analysis of biomolecular interaction networks (e.g., protein interaction networks), it reveals early molecules that are known to be differentially implicated in diseases. In economic networks, it reveals flow of capital and associated actors. Beyond these recognized applications, it provides analytical substrates for novel studies – for instance, on the structural and functional evolution of the human brain connectome. In this paper, we model, formulate, and rigorously analyze the problem of inferring the arrival order of nodes in a dynamic network from a single snapshot. We derive limits on solutions to the problem, present methods that approach this limit, and demonstrate the methods on a range of applications, from inferring the evolution of the human brain connectome to conventional citation and social networks, where ground truth is known.
Comparison Between Performances of In2O3 and In2TiO5-Based EIS Biosensors Using Post Plasma CF4 Treatment Applied in Glucose and Urea Sensing
Authors: Lin Chun Fu , Kao Chyuan Haur , Lin Chan Yu , Liu Chia Shao , Liu Yi Wen 
Published: February 2019

AbstractIn this study, the effect of post-deposition tetrafluoromethane (CF4) plasma treatment on the physical and electrical characteristics of an In2TiO5 based electrolyte-insulator-semiconductor (EIS) sensor was investigated. Post-deposition CF4 plasma treatment typically improved the crystalline structure and repaired dangling bonds at the grain boundaries. We used the newly fabricated device to detect several ions, such as sodium and potassium, which are essential for many biological processes. The as-deposited and CF4 plasma treated In2TiO5 sensing window with an EIS structure was also able to detect the pH of a solution, different alkali ions (Na+ and K+), glucose, and urea. The sensing membrane after a 60-sec CF4 plasma treatment displayed improved biosensing characteristics, such as higher sensitivity (59.64 mV/pH), better drift rate, and a smaller hysteresis voltage of approximately 0.424 mV/h. The In2TiO5 sensing membrane treated with CF4 plasma is a promising material for use in EIS biosensing applications.
Insights into the karyotype and genome evolution of haplogyne spiders indicate a polyploid origin of lineage with holokinetic chromosomes
Authors: Král Jiří , Forman Martin , Kořínková Tereza , Lerma Azucena C. Reyes , Haddad Charles R. , Musilová Jana , Řezáč Milan , Herrera Ivalú M. Ávila , Thakur Shefali , Dippenaar-Schoeman Ansie S. , Marec František , Horová Lucie , Bureš Petr 
Published: February 2019

AbstractSpiders are an ancient and extremely diverse animal order. They show a considerable diversity of genome sizes, karyotypes and sex chromosomes, which makes them promising models to analyse the evolution of these traits. Our study is focused on the evolution of the genome and chromosomes in haplogyne spiders with holokinetic chromosomes. Although holokinetic chromosomes in spiders were discovered a long time ago, information on their distribution and evolution in these arthropods is very limited. Here we show that holokinetic chromosomes are an autapomorphy of the superfamily Dysderoidea. According to our hypothesis, the karyotype of ancestral Dysderoidea comprised three autosome pairs and a single X chromosome. The subsequent evolution has frequently included inverted meiosis of the sex chromosome and an increase of 2n. We demonstrate that caponiids, a sister clade to Dysderoidea, have enormous genomes and high diploid and sex chromosome numbers. This pattern suggests a polyploid event in the ancestors of caponiids. Holokinetic chromosomes could have arisen by subsequent multiple chromosome fusions and a considerable reduction of the genome size. We propose that spider sex chromosomes probably do not pose a major barrier to polyploidy due to specific mechanisms that promote the integration of sex chromosome copies into the genome.
Evaluating a scale of excessive mind wandering among males and females with and without attention-deficit/hyperactivity disorder from a population sample
Authors: Mowlem Florence D. , Agnew-Blais Jessica , Pingault Jean-Baptiste , Asherson Philip 
Published: February 2019

AbstractRecent studies highlight the role of excessive mind wandering in attention-deficit/hyperactivity disorder (ADHD) and its association with impairment. We believe assessing mind wandering could be especially relevant to individuals, including many females, who present with less externalising manifestations of ADHD. Using a new measure based on ADHD patient reports, the Mind Excessively Wandering Scale (MEWS), we previously found adults with ADHD had elevated levels of mind wandering that contributed to impairment independently of core ADHD symptoms. Using data from an online general population survey, the current study assessed the factor-structure, reliability, validity and measurement invariance of the MEWS. We also investigated sex differences in mind wandering, as well as ADHD symptoms, impairment and wellbeing in those with and without ADHD. The MEWS had a unidimensional structure, was invariant across sex, age and ADHD status, and accounted for unique variance in impairment and wellbeing beyond core ADHD symptoms. Among those with ADHD, we found no evidence for sex differences in mind wandering and among those without ADHD males had higher scores. We also found similar levels of hyperactivity/impulsivity, emotional lability, and impairment in males and females with ADHD, but males reported greater inattention and lower wellbeing. Results suggest the MEWS is a reliable and valid instrument measuring the same construct across sex, age and ADHD status, which could aid diagnosis and monitoring of outcomes.
Genotoxic stress increases cytoplasmic mitochondrial DNA editing by human APOBEC3 mutator enzymes at a single cell level
Authors: Mussil Bianka , Suspène Rodolphe , Caval Vincent , Durandy Anne , Wain-Hobson Simon , Vartanian Jean-Pierre 
Published: February 2019

AbstractHuman cells are stressed by numerous mechanisms that can lead to leakage of mitochondrial DNA (mtDNA) to the cytoplasm and ultimately apoptosis. This agonist DNA constitutes a danger to the cell and is counteracted by cytoplasmic DNases and APOBEC3 cytidine deamination of DNA. To investigate APOBEC3 editing of leaked mtDNA to the cytoplasm, we performed a PCR analysis of APOBEC3 edited cytoplasmic mtDNA (cymtDNA) at the single cell level for primary CD4+ T cells and the established P2 EBV blast cell line. Up to 17% of primary CD4+ T cells showed signs of APOBEC3 edited cymtDNA with ~50% of all mtDNA sequences showing signs of APOBEC3 editing – between 1500–5000 molecules. Although the P2 cell line showed a much lower frequency of stressed cells, the number of edited mtDNA molecules in such cells was of the same order. Addition of the genotoxic molecules, etoposide or actinomycin D increased the number of cells showing APOBEC3 edited cymtDNA to around 40%. These findings reveal a very dynamic image of the mitochondrial network, which changes considerably under stress. APOBEC3 deaminases are involved in the catabolism of mitochondrial DNA to circumvent chronic immune stimulation triggered by released mitochondrial DNA from damaged cells.
Insights from distribution dynamics inform strategies to conserve a dhole Cuon alpinus metapopulation in India
Authors: Srivathsa Arjun , Karanth K. Ullas , Kumar N. Samba , Oli Madan K. 
Published: February 2019

AbstractMost large carnivore populations currently occur in heterogeneous landscapes, with source populations embedded in a matrix of human-dominated habitats. Understanding changes in distribution of endangered carnivores is critical for prioritizing and implementing conservation strategies. We examined distribution and dynamics of a dhole Cuon alpinus metapopulation, first in 2007 and subsequently in 2015, based on indirect sign surveys across 37, 000sq. km of India’s Western Ghats. Predicted dhole occupancy declined from 0.62 (95% CI: 0.58–0.66) in 2007 to 0.54 (95% CI: 0.50–0.58) in 2015. Occupancy was associated with abundance of primary prey species and anthropogenic disturbance. Local extinction appeared to be influenced by forest cover loss, and offset by protected reserves; colonization was influenced by occupancy in neighbouring sites. Perturbation analysis indicated that occupancy was more sensitive to local extinction within reserves and to colonization in sites abutting reserves. The Western Ghats could serve as a stronghold for the endangered dhole, provided future colonizations are facilitated through habitat consolidation beyond reserve boundaries, and local extinctions are prevented by increasing protection efforts within select reserves. We advocate for wildlife managers to adopt a landscape-based approach and periodic monitoring to ensure persistence of the dhole metapopulation in Western Ghats, and in other critical conservation regions across the species’ geographic range.
Optimal estimation of entanglement and discord in two-qubit states
Authors: Virzì Salvatore , Rebufello Enrico , Avella Alessio , Piacentini Fabrizio , Gramegna Marco , Ruo Berchera Ivano , Degiovanni Ivo Pietro , Genovese Marco 
Published: February 2019

AbstractRecently, the fast development of quantum technologies led to the need for tools allowing the characterization of quantum resources. In particular, the ability to estimate non-classical aspects, e.g. entanglement and quantum discord, in two-qubit systems, is relevant to optimise the performance of quantum information processes. Here we present an experiment in which the amount of entanglement and discord are measured exploiting different estimators. Among them, some will prove to be optimal, i.e., able to reach the ultimate precision bound allowed by quantum mechanics. These estimation techniques have been tested with a specific family of states ranging from nearly pure Bell states to completely mixed states. This work represents a significant step towards the development of reliable metrological tools for quantum technologies.
An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria
Authors: Wei Yulong , Silke Jordan R. , Xia Xuhua 
Published: February 2019

AbstractThe degree to which codon usage can be explained by tRNA abundance in bacterial species is often inadequate, partly because differential tRNA abundance is often approximated by tRNA copy numbers. To better understand the coevolution between tRNA abundance and codon usage, we provide a better estimate of tRNA abundance by profiling tRNA mapped reads (tRNA tpm) using publicly available RNA Sequencing data. To emphasize the feasibility of our approach, we demonstrate that tRNA tpm is consistent with tRNA abundances derived from RNA fingerprinting experiments in Escherichia coli, Bacillus subtilis, and Salmonella enterica. Furthermore, we do not observe an appreciable reduction in tRNA sequencing efficiency due to post-transcriptional methylations in the seven bacteria studied. To determine optimal codons, we calculate codon usage in highly and lowly expressed genes determined by protein per transcript. We found that tRNA tpm is sensitive to identify more translationally optimal codons than gene copy number and early tRNA fingerprinting abundances. Additionally, tRNA tpm improves the predictive power of tRNA adaptation index over codon preference. Our results suggest that dependence of codon usage on tRNA availability is not always associated with species growth-rate. Conversely, tRNA availability is better optimized to codon usage in fast-growing than slow-growing species.
Hyper-acidic fusion minipeptides escort the intrinsic antioxidative ability of the pattern recognition receptor CRP in non-animal organisms
Authors: Zhang Mengru , Liu Yanjuan , Liu Zhibin , Wang Jianmei , Gong Ming , Ge Hu , Li Xufeng , Yang Yi , Zou Zhurong 
Published: February 2019

AbstractC-reactive protein (CRP) is widely used as a biomarker of inflammation. It plays important roles in innate immunity response as a member of pattern recognition receptors, by binding oxidation-specific epitopes including some intermediates of lipid oxidative chain reaction. The inferred antioxidative ability of CRP was ever demonstrated by only fewin vitroevidences, and needs to be clarified especiallyin vivo. Herein, we expressed human CRP in three representative non-animal organisms (Escherichia coli,Saccharomyces cerevisiae, and tobacco) inherently lacking the milieu for CRP signalling, and found CRP did possess an intrinsic antioxidative ability. Heterologous CRP could confer increased oxidative resistance in its recombinantE.coliand yeast cells and transgenic tobaccos. We also revealed a positive correlation between the antioxidative effect of CRP and its solubility. Only soluble CRP could exhibit distinct antioxidative activity, while the CRP aggregates might be instead toxic (probably pro-oxidative) to cells. Moreover, fusion with hyper-acidic minipeptides could remarkably improve CRP solubility, and meanwhile guarantee or enhance CRP antioxidative ability. These results not only provide a new insight for understanding the etiology of CRP-involved inflammations and diseases, and also endorse a potential of CRP biotechnological applications in developing new pharmaceutical therapies and improving plant oxidative resistance.
Key Role of the Ocean Western Boundary currents in shaping the Northern Hemisphere climate
Authors: Omrani Nour-Eddine , Ogawa Fumiaki , Nakamura Hisashi , Keenlyside Noel , Lubis Sandro W. , Matthes Katja 
Published: February 2019

AbstractThe individual impact of North Atlantic and Pacific Ocean Western Boundary Currents (OWBCs) on the tropospheric circulation has recently been studied in depth. However, their simultaneous role in shaping the hemisphere-scale wintertime troposphere/stratosphere-coupled circulation and its variability have not been considered. Through semi-idealized Atmospheric General-Circulation-Model experiments, we show that the North Atlantic and Pacific OWBCs jointly maintain and shape the wintertime hemispheric circulation and its leading mode of variability Northern Annular Mode (NAM). The OWBCs energize baroclinic waves that reinforce quasi-annular hemispheric structure in the tropospheric eddy-driven jetstreams and NAM variability. Without the OWBCs, the wintertime NAM variability is much weaker and its impact on the continental and maritime surface climate is largely insignificant. Atmospheric energy redistribution caused by the OWBCs acts to damp the near-surface atmospheric baroclinicity and compensates the associated oceanic meridional energy transport. Furthermore, the OWBCs substantially weaken the wintertime stratospheric polar vortex by enhancing the upward planetary wave propagation, and thereby affecting both stratospheric and tropospheric NAM-annularity. Whereas the overall impact of the extra-tropical OWBCs on the stratosphere results mainly from the Pacific, the impact on the troposphere results from both the Pacific and Atlantic OWBCs.
Analysis of the Antigenic Properties of Membrane Proteins of Mycobacterium tuberculosis
Authors: Li Haifeng , Liu Liguo , Zhang Wei-jia , Zhang Xiaobing , Zheng Jianhua , Li Li , Zhu Xiuyun , Yang Qianting , Zhang Mingxia , Liu Haiying , Chen Xinchun , Jin Qi 
Published: February 2019

AbstractTuberculosis (TB) is a continuing major threat to global health and a leading cause of death, particularly in developing countries. In this study, we aimed to identify a specific and sensitive diagnostic biomarker and develop a vaccine to prevent this disease. We investigated membrane proteins to reveal biomarkers in serum and peripheral blood mononuclear cells (PBMCs) obtained from TB patients. We employed Western blotting to evaluate serological immunoglobulin G levels, and Enzyme Linked Immunospot (ELISpot) to assess the antigen-specific cellular interferon-γ secretion from PBMCs after membrane protein stimulation. A total of 219 membrane proteins were identified, 52 exhibited at a higher levels than the 38-kDa prositive control. Of these 18 exhibited reacted ratios above 1, especially Rv1111c (427–981), with a ratios at 3.38. Accuracy and sensitivity were markedly higher for the top two antigen candidates, Rv0232 and Rv1115, after two rounds of ELISpot tests than ESAT-6 in the commercial kit (42.15 and 43.62%, respectively). These two proteins were administered to mice to detect whether they acted as effective antigens in vivo. These data provide a comprehensive view of the membranes involved in humoural and cellular immune responses that may be used as biomarkers for TB and candidates for a vaccine.
Ribosome profiling analysis of eEF3-depleted Saccharomyces cerevisiae
Authors: Kasari Villu , Margus Tõnu , Atkinson Gemma C. , Johansson Marcus J. O. , Hauryliuk Vasili 
Published: February 2019

AbstractIn addition to the standard set of translation factors common in eukaryotic organisms, protein synthesis in the yeast Saccharomyces cerevisiae requires an ABCF ATPase factor eEF3, eukaryotic Elongation Factor 3. eEF3 is an E-site binder that was originally identified as an essential factor involved in the elongation stage of protein synthesis. Recent biochemical experiments suggest an additional function of eEF3 in ribosome recycling. We have characterised the global effects of eEF3 depletion on translation using ribosome profiling. Depletion of eEF3 results in decreased ribosome density at the stop codon, indicating that ribosome recycling does not become rate limiting when eEF3 levels are low. Consistent with a defect in translation elongation, eEF3 depletion causes a moderate redistribution of ribosomes towards the 5′ part of the open reading frames. We observed no E-site codon- or amino acid-specific ribosome stalling upon eEF3 depletion, supporting its role as a general elongation factor. Surprisingly, depletion of eEF3 leads to a relative decrease in P-site proline stalling, which we hypothesise is a secondary effect of generally decreased translation and/or decreased competition for the E-site with eIF5A.
Rapalog resistance is associated with mesenchymal-type changes in Tsc2-null cells
Authors: Valianou Matthildi , Filippidou Natalia , Johnson Daniel L. , Vogel Peter , Zhang Erik Y. , Liu Xiaolei , Lu Yiyang , Yu Jane J. , Bissler John J. , Astrinidis Aristotelis 
Published: February 2019

AbstractTuberous Sclerosis Complex (TSC) and Lymphangioleiomyomatosis (LAM) are caused by inactivating mutations in TSC1 or TSC2, leading to mTORC1 hyperactivation. The mTORC1 inhibitors rapamycin and analogs (rapalogs) are approved for treating of TSC and LAM. Due to their cytostatic and not cytocidal action, discontinuation of treatment leads to tumor regrowth and decline in pulmonary function. Therefore, life-long rapalog treatment is proposed for the control of TSC and LAM lesions, which increases the chances for the development of acquired drug resistance. Understanding the signaling perturbations leading to rapalog resistance is critical for the development of better therapeutic strategies. We developed the first Tsc2-null rapamycin-resistant cell line, ELT3-245, which is highly tumorigenic in mice, and refractory to rapamycin treatment. In vitro ELT3-245 cells exhibit enhanced anchorage-independent cell survival, resistance to anoikis, and loss of epithelial markers. A key alteration in ELT3-245 is increased β-catenin signaling. We propose that a subset of cells in TSC and LAM lesions have additional signaling aberrations, thus possess the potential to become resistant to rapalogs. Alternatively, when challenged with rapalogs TSC-null cells are reprogrammed to express mesenchymal-like markers. These signaling changes could be further exploited to induce clinically-relevant long-term remissions.