bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Systems Biology to decipher design principles of a dynamic cell cycle network: the “Maximum Allowable mammalian Trade–Off–Weight” (MAmTOW)
Authors: Barberis Matteo , Verbruggen Paul 
Published: September 2017

AbstractNetwork complexity is required to lend cellular processes flexibility to respond timely to a variety of dynamic signals, while simultaneously warranting robustness to protect cellular integrity against perturbations. The cell cycle serves as a paradigm for such processes; it maintains its frequency and temporal structure (although these may differ among cell types) under the former, but accelerates under the latter. Cell cycle molecules act together in time and in different cellular compartments to execute cell type-specific programs. Strikingly, the timing at which molecular switches occur is controlled by abundance and stoichiometry of multiple proteins within complexes. However, traditional methods that investigate one effector at a time are insufficient to understand how modulation of protein complex dynamics at cell cycle transitions shapes responsiveness, yet preserving robustness. To overcome this shortcoming, we propose a multidisciplinary approach to gain a systems-level understanding of quantitative cell cycle dynamics in mammalian cells from a new perspective. By suggesting advanced experimental technologies and dedicated modeling approaches, we present innovative strategies (i) to measure absolute protein concentration in vivo, and (ii) to determine how protein dosage, e.g., altered protein abundance, and spatial (de)regulation may affect timing and robustness of phase transitions. We describe a method that we name “Maximum Allowable mammalian Trade–Off–Weight” (MAmTOW), which may be realized to determine the upper limit of gene copy numbers in mammalian cells. These aspects, not covered by current systems biology approaches, are essential requirements to generate precise computational models and identify (sub)network-centered nodes underlying a plethora of pathological conditions.
Magnetic field effect in natural cryptochrome explored with model compound
Authors: Paul Shubhajit , Kiryutin Alexey S. , Guo Jinping , Ivanov Konstantin L. , Matysik Jörg , Yurkovskaya Alexandra V. , Wang Xiaojie 
Published: September 2017

AbstractMany animals sense the Earth’s magnetic-field and use it for navigation. It is proposed that a light-dependent quantum effect in cryptochrome proteins, residing in the retina, allows for such an iron-free spin-chemical compass. The photochemical processes, spin-dynamics and its magnetic field dependence in natural cryptochrome are not fully understood by the in vivo and in vitro studies. For a deeper insight into these biophysical mechanisms in cryptochrome, we had introduced a flavin-tryptophan dyad (F10T). Here we present the magnetic field dependence of 1H photo-CIDNP NMR on F10T and a theoretical model for low-field photo-CIDNP of F10T. This model provides mixing mechanism of energy-levels and spin-dynamics at low magnetic fields. Photo-CIDNP has been observed even at Earth’s magnetic field (~0.05 mT). These experiments prove F10T to be an excellent model compound establishing the key mechanism of avian-magnetoreception and provide insight into the optimal behaviour of cryptochrome at Earth’s magnetic field.
Molecular characterization of emaraviruses associated with Pigeonpea sterility mosaic disease
Authors: Kumar Surender , Subbarao BL , Hallan Vipin 
Published: September 2017

AbstractSterility Mosaic Disease (SMD) of pigeonpea (Cajanus cajan (L.) Millspaugh) is a complex disease due to various factors including the presence of a mixed infection. Comparison of dsRNA profile and small RNA (sRNA) deep sequencing analysis of samples from three locations revealed the presence of Pigeonpea sterility mosaic virus-I and II (PPSMV-I and II) from Chevella and only PPSMV-II from Bengaluru and Coimbatore. PPSMV-I genome consisted of four while PPSMV-II encompassed six RNAs. The two viruses have modest sequence homology between their corresponding RNA 1–4 encoding RdRp, glycoprotein precursor, nucleocapsid and movement proteins and the corresponding orthologs of other emaraviruses. However, PPSMV-II is more related to Fig mosaic virus (FMV) than to PPSMV-I. ELISA based detection methodology was standardized to identify these two viruses, uniquely. Mite inoculation of sub-isolate Chevella sometimes resulted in few- to- many pigeonpea plants containing PPSMV-I alone. The study shows that (i) the N-terminal region of RdRp (SRD-1) of both the viruses contain “cap-snatching” endonuclease domain and a 13 AA cap binding site at the C-terminal, essential for viral cap-dependent transcription similar to the members of Bunyaviridae family and (ii) P4 is the movement protein and may belong to ‘30 K superfamily’ of MPs.
Molecular dissection of transcriptional reprogramming of steviol glycosides synthesis in leaf tissue during developmental phase transitions in Stevia rebaudiana Bert
Authors: Singh Gopal , Singh Gagandeep , Singh Pradeep , Parmar Rajni , Paul Navgeet , Vashist Radhika , Swarnkar Mohit Kumar , Kumar Ashok , Singh Sanatsujat , Singh Anil Kumar , Kumar Sanjay , Sharma Ram Kumar 
Published: September 2017

AbstractStevia is a natural source of commercially important steviol glycosides (SGs), which share biosynthesis route with gibberellic acids (GAs) through plastidal MEP and cytosolic MVA pathways. Ontogeny-dependent deviation in SGs biosynthesis is one of the key factor for global cultivation of Stevia, has not been studied at transcriptional level. To dissect underlying molecular mechanism, we followed a global transcriptome sequencing approach and generated more than 100 million reads. Annotation of 41,262 de novo assembled transcripts identified all the genes required for SGs and GAs biosynthesis. Differential gene expression and quantitative analysis of important pathway genes (DXS, HMGR, KA13H) and gene regulators (WRKY, MYB, NAC TFs) indicated developmental phase dependent utilization of metabolic flux between SGs and GAs synthesis. Further, identification of 124 CYPs and 45 UGTs enrich the genomic resources, and their PPI network analysis with SGs/GAs biosynthesis proteins identifies putative candidates involved in metabolic changes, as supported by their developmental phase-dependent expression. These putative targets can expedite molecular breeding and genetic engineering efforts to enhance SGs content, biomass and yield. Futuristically, the generated dataset will be a useful resource for development of functional molecular markers for diversity characterization, genome mapping and evolutionary studies in Stevia.
Use of an Individual-based Model to Control Transmission Pathways of Mycobacterium avium Subsp. paratuberculosis Infection in Cattle Herds
Authors: Al-Mamun M. A. , Smith R. L. , Schukken Y. H. , Gröhn Y. T. 
Published: September 2017

AbstractJohne’s disease (JD) is a chronic enteric disease in cattle caused by Mycobacterium avian subsp. paratuberculosis (MAP). Eradicating JD is a difficult task due to the long incubation period of MAP, inefficient diagnostic tests, and delayed clinical signs. Effective control strategies can help farmers to reduce prevalence, but those most acceptable to farmers combine specific information about lactation performance and testing results, which existing models do not provide. This paper presents an individual-based model of MAP infection dynamics and assesses the relative performance of the applied alternative control strategies. The base dairy herd model included the daily life events of a dairy cow and reflects several current dairy management processes. We then integrated MAP infection dynamics into the model. The model adopted four different test-based control strategies based on risk-based culling decisions and three hygiene scenarios. The model tracked the source of each infection and quantified the efficacy of each control strategy in reducing the risks of different transmission routes. The results suggest that risk-based culling can reduce prevalence compared with no control, but cannot eliminate the infection. Overall, this work provides not only a valuable tool to investigate MAP transmission dynamics but also offers adaptability to model similar infectious diseases.
Scavenged 239Pu, 240Pu, and 241Am from snowfalls in the atmosphere settling on Mt. Zugspitze in 2014, 2015 and 2016
Authors: Gückel Katharina , Shinonaga Taeko , Christl Marcus , Tschiersch Jochen 
Published: September 2017

AbstractConcentrations of 239Pu, 240Pu, and 241Am, and atomic ratio of 240Pu/239Pu in freshly fallen snow on Mt. Zugspitze collected in 2014, 2015 and 2016 were determined by accelerator mass spectrometry (AMS). For the sub-femtogram (10−15 g) - level of Pu and Am analysis, a chemical separation procedure combined with AMS was improved and an excellent overall efficiency of about 10−4 was achieved. The concentration of 239Pu ranges from 75 ± 13 ag/kg to 2823 ± 84 ag/kg, of 240Pu from 20.6 ± 5.2 to 601 ± 21 ag/kg, and of 241Am was found in the range of 16.7 ± 5.0–218.8 ± 8.9 ag/kg. Atomic ratios of 240Pu/239Pu for most samples are comparable to the fallout in middle Europe. One exceptional sample shows a higher Pu concentration. High airborne dust concentration, wind directions, high Cs concentrations and the activity ratio of 239+240Pu/137Cs lead to the conclusion that the sample was influenced by Pu in Saharan dust transported to Mt. Zugspitze.
Inhibiting P. fluorescens biofilms with fluoropolymer-embedded silver nanoparticles: an in-situ spectroscopic study
Authors: Sportelli M. C. , Tütüncü E. , Picca R. A. , Valentini M. , Valentini A. , Kranz C. , Mizaikoff B. , Barth H. , Cioffi N. 
Published: September 2017

AbstractSurface colonization by microorganisms leads to the formation of biofilms, i.e. aggregates of bacteria embedded within a matrix of extracellular polymeric substance. This promotes adhesion to the surface and protects bacterial community, providing an antimicrobial-resistant environment. The inhibition of biofilm growth is a crucial issue for preventing bacterial infections. Inorganic nanoparticle/Teflon-like (CFx) composites deposited via ion beam sputtering demonstrated very efficient antimicrobial activity. In this study, we developed Ag-CFx thin films with tuneable metal loadings and exceptional in-plane morphological and chemical homogeneity. Ag-CFx antimicrobial activity was studied via mid-infrared attenuated total reflection spectroscopy utilizing specifically adapted multi-reflection waveguides. Biofilm was sampled by carefully depositing the Ag-CFx film on IR inactive regions of the waveguide. Real-time infrared spectroscopy was used to monitor Pseudomonas fluorescens biofilm growth inhibition induced by the bioactive silver ions released from the nanoantimicrobial coating. Few hours of Ag-CFx action were sufficient to affect significantly biofilm growth. These findings were corroborated by atomic force microscopy (AFM) studies on living bacteria exposed to the same nanoantimicrobial. Morphological analyses showed a severe bacterial stress, leading to membrane leakage/collapse or to extended cell lysis as a function of incubation time.
Aligning cellulose nanofibril dispersions for tougher fibers
Authors: Mohammadi Pezhman , Toivonen Matti S. , Ikkala Olli , Wagermaier Wolfgang , Linder Markus B. 
Published: September 2017

AbstractNanocomposite materials made from cellulose show a great potential as future high-performance and sustainable materials. We show how high aspect ratio cellulose nanofibrils can be efficiently aligned in extrusion to fibers, leading to increased modulus of toughness (area under the stress-strain curve), Young’s modulus, and yield strength by increasing the extrusion capillary length, decreasing its diameter, and increasing the flow rate. The materials showed significant property combinations, manifesting as high modulus of toughness (~28–31 MJ/m3) vs. high stiffness (~19–20 GPa), and vs. high yield strength (~130–150 MPa). Wide angle X-ray scattering confirmed that the enhanced mechanical properties directly correlated with increased alignment. The achieved moduli of toughness are approximately double or more when compared to values reported in the literature for corresponding strength and stiffness. Our results highlight a possibly general pathway that can be integrated to gel-spinning process, suggesting the hypothesis that that high stiffness, strength and toughness can be achieved simultaneously, if the alignment is induced while the CNF are in the free-flowing state during the extrusion step by shear at relatively low concentration and in pure water, after which they can be coagulated.
Upregulation of CISD2 augments ROS homeostasis and contributes to tumorigenesis and poor prognosis of lung adenocarcinoma
Authors: Li Shih-Miao , Chen Chung-Hsing , Chen Ya-Wen , Yen Yi-Chen , Fang Wen-Tsen , Tsai Fang-Yu , Chang Junn-Liang , Shen Ying-Ying , Huang Shiu-Feng , Chuu Chih-Pin , Chang I-Shou , Hsiung Chao A. , Jiang Shih Sheng 
Published: September 2017

AbstractCISD2 is a redox-sensitive gene critical for normal development and mitochondrial integrity. CISD2 was known to have aberrant expression in several types of human cancers. However, its relation with lung cancer is still not clear. In this study we found CISD2 mRNA was significantly upregulated in lung adenocarcinoma (ADC) samples, compared with their adjacent normal counterparts, and was correlated with tumor stage, grade, and prognosis based on analysis of clinical specimens-derived expression data in public domain and our validation assay. Cell based assay indicated that CISD2 expression regulated accumulation of reactive oxygen species (ROS), polarization of mitochondrial membrane potential, as well as cell viability, apoptosis, invasiveness, and tumorigenicity. In addition, CISD2 expression was found significantly correlated with stress response/redox signaling genes such as EGR1 and GPX3, while such correlations were also found valid in many public domain data. Taken together, upregulation of CISD2 is involved in an increased antioxidant capacity in response to elevated ROS levels during the formation and progression of lung ADC. The molecular mechanism underlying how CISD2 regulates ROS homeostasis and augments malignancy of lung cancer warrants further investigations.
Restoring tides to reduce methane emissions in impounded wetlands: A new and potent Blue Carbon climate change intervention
Authors: Kroeger Kevin D. , Crooks Stephen , Moseman-Valtierra Serena , Tang Jianwu 
Published: September 2017

AbstractCoastal wetlands are sites of rapid carbon (C) sequestration and contain large soil C stocks. Thus, there is increasing interest in those ecosystems as sites for anthropogenic greenhouse gas emission offset projects (sometimes referred to as “Blue Carbon”), through preservation of existing C stocks or creation of new wetlands to increase future sequestration. Here we show that in the globally-widespread occurrence of diked, impounded, drained and tidally-restricted salt marshes, substantial methane (CH4) and CO2emission reductions can be achieved through restoration of disconnected saline tidal flows. Modeled climatic forcing indicates that tidal restoration to reduce emissions has a much greater impact per unit area than wetland creation or conservation to enhance sequestration. Given that GHG emissions in tidally-restricted, degraded wetlands are caused by human activity, they are anthropogenic emissions, and reducing them will have an effect on climate that is equivalent to reduced emission of an equal quantity of fossil fuel GHG. Thus, as a landuse-based climate change intervention, reducing CH4emissions is an entirely distinct concept from biological C sequestration projects to enhance C storage in forest or wetland biomass or soil, and will not suffer from the non-permanence risk that stored C will be returned to the atmosphere.
Decline of long-range temporal correlations in the human brain during sustained wakefulness
Authors: Meisel Christian , Bailey Kimberlyn , Achermann Peter , Plenz Dietmar 
Published: September 2017

AbstractSleep is crucial for daytime functioning, cognitive performance and general well-being. These aspects of daily life are known to be impaired after extended wake, yet, the underlying neuronal correlates have been difficult to identify. Accumulating evidence suggests that normal functioning of the brain is characterized by long-range temporal correlations (LRTCs) in cortex, which are supportive for decision-making and working memory tasks. Here we assess LRTCs in resting state human EEG data during a 40-hour sleep deprivation experiment by evaluating the decay in autocorrelation and the scaling exponent of the detrended fluctuation analysis from EEG amplitude fluctuations. We find with both measures that LRTCs decline as sleep deprivation progresses. This decline becomes evident when taking changes in signal power into appropriate consideration. In contrast, the presence of strong signal power increases in some frequency bands over the course of sleep deprivation may falsely indicate LRTC changes that do not reflect the underlying long-range temporal correlation structure. Our results demonstrate the importance of sleep to maintain LRTCs in the human brain. In complex networks, LRTCs naturally emerge in the vicinity of a critical state. The observation of declining LRTCs during wake thus provides additional support for our hypothesis that sleep reorganizes cortical networks towards critical dynamics for optimal functioning.
Spiraling Light with Magnetic Metamaterial Quarter-Wave Turbines
Authors: Zeng Jinwei , Luk Ting S. , Gao Jie , Yang Xiaodong 
Published: September 2017

AbstractMiniaturized quarter-wave plate devices empower spin to orbital angular momentum conversion and vector polarization formation, which serve as bridges connecting conventional optical beam and structured light. Enabling the manipulability of additional dimensions as the complex polarization and phase of light, quarter-wave plate devices are essential for exploring a plethora of applications based on orbital angular momentum or vector polarization, such as optical sensing, holography, and communication. Here we propose and demonstrate the magnetic metamaterial quarter-wave turbines at visible wavelength to produce radially and azimuthally polarized vector vortices from circularly polarized incident beam. The magnetic metamaterials function excellently as quarter-wave plates at single wavelength and maintain the quarter-wave phase retardation in broadband, while the turbine blades consist of multiple polar sections, each of which contains homogeneously oriented magnetic metamaterial gratings near azimuthal or radial directions to effectively convert circular polarization to linear polarization and induce phase shift under Pancharatnum-Berry’s phase principle. The perspective concept of multiple polar sections of magnetic metamaterials can extend to other analogous designs in the strongly coupled nanostructures to accomplish many types of light phase-polarization manipulation and structured light conversion in the desired manner.
Deformation mechanics of non-planar topologically interlocked assemblies with structural hierarchy and varying geometry
Authors: Djumas Lee , Simon George P. , Estrin Yuri , Molotnikov Andrey 
Published: September 2017

AbstractStructural hierarchy is known to enhance the performance of many of Nature’s materials. In this work, we apply the idea of hierarchical structure to topologically interlocked assemblies, obtained from measurements under point loading, undertaken on identical discrete block ensembles with matching non-planar surfaces. It was demonstrated that imposing a hierarchical structure adds to the load bearing capacity of topological interlocking assemblies. The deformation mechanics of these structures was also examined numerically by finite element analysis. Multiple mechanisms of surface contact, such as slip and tilt of the building blocks, were hypothesised to control the mechanical response of topological interlocking assemblies studied. This was confirmed using as a model a newly designed interlocking block, where slip was suppressed, which produced a gain in peak loading. Our study highlights the possibility of tailoring the mechanical response of topological interlocking assemblies using geometrical features of both the element geometry and the contact surface profile.
A generic method to synthesise graphitic carbon coated nanoparticles in large scale and their derivative polymer nanocomposites
Authors: Wang Nannan , Yang Zhuxian , Xu Fang , Thummavichai Kunyapat , Chen Hongmei , Xia Yongde , Zhu Yanqiu 
Published: September 2017

AbstractA versatile Rotary Chemical Vapour Deposition (RCVD) technique for the in-situ synthesis of large scale carbon-coated non-magnetic metal oxide nanoparticles (NPs) is presented, and a controllable coating thickness varying between 1–5 nm has been achieved. The technique has significantly up-scaled the traditional chemical vapour deposition (CVD) production for NPs from mg level to 10 s of grams per batch, with the potential for continuous manufacturing. The resulting smooth and uniform C-coatings sheathing the inner core metal oxide NPs are made of well-crystallised graphitic layers, as confirmed by electron microscopy imaging, electron dispersive spectrum elemental line scan, X-ray powder diffractions and Raman spectroscopy. Using nylon 12 as an example matrix, we further demonstrate that the inclusion of C-coated composite NPs into the matrix improves the thermal conductivity, from 0.205 W∙m−1∙K−1 for neat nylon 12 to 0.305 W∙m−1∙K−1 for a 4 wt% C-coated ZnO composite, in addition to a 27% improvement in tensile strength at 2 wt% addition.
Intact animacy perception during chase detection in ASD
Authors: Vanmarcke Steven , van de Cruys Sander , Moors Pieter , Wagemans Johan 
Published: September 2017

AbstractWe explored the strength of implicit social inferences in adolescents with and without Autism Spectrum Disorder (ASD) using a chasing paradigm in which participants judged the absence/presence of a chase within a display of four seemingly randomly moving dots. While two of these dots always moved randomly, the two others could fulfill the role of being either the chasing (wolf) or chased (sheep) dot. In the chase-present (but not the chase-absent) trials the wolf displayed chasing behavior defined by the degree to which the dot reliably moved towards the sheep (chasing subtlety). Previous research indicated that chasing subtlety strongly influenced chase detection in typically developing (TD) adults. We intended to replicate and extend this finding to adolescents with and without ASD, while also adding either a social or a non-social cue to the displays. Our results confirmed the importance of chasing subtlety and indicated that adding social, but not non-social, information further improved chase detection performance. Interestingly, the performance of adolescents with ASD was less dependent on chasing subtlety than that of their TD counterparts. Nonetheless, adolescents with and without ASD did not differ in their use of the added social (or non-social) cue.