bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of In-Depth Degradation of Artificially Aged Triterpenoid Paint Varnishes Using Nonlinear Microscopy Techniques
Authors: Filippidis George , Mari Meropi , Kelegkouri Lambrini , Philippidis Aggelos , Selimis Aleksandros , Melessanaki Kristallia , Sygletou Maria , Fotakis Costas 
Published: November 2014

AbstractThe present work investigates the applicability of nonlinear imaging microscopy for the precise assessment of degradation of the outer protective layers of painted artworks as a function of depth due to aging. Two fresh and artificially aged triterpenoid varnishes, dammar and mastic, were tested. Nonlinear imaging techniques have been employed as a new diagnostic tool for determination of the exact thickness of the affected region due to artificial aging of the natural varnishes. The measured thicknesses differ from the calculated mean penetration depths of the samples. These nondestructive, high resolution modalities are valuable analytical tools for aging studies and they have the potential to provide unique in-depth information. Single photon laser induced fluorescence measurements and Raman spectroscopy were used for the integrated investigation and analysis of aging effects in varnishes.
Towards a comprehensive model of Earth's disk-integrated Stokes vector
Authors: García Muñoz A. 
Published: November 2014

AbstractA significant body of work on simulating the remote appearance of Earth-like exoplanets has been done over the last decade. The research is driven by the prospect of characterizing habitable planets beyond the Solar System in the near future. In this work, I present a method to produce the disk-integrated signature of planets that are described in their three-dimensional complexity, i.e. with both horizontal and vertical variations in the optical properties of their envelopes. The approach is based on Pre-conditioned Backward Monte Carlo integration of the vector Radiative Transport Equation and yields the full Stokes vector for outgoing reflected radiation. The method is demonstrated through selected examples inspired by published work at wavelengths from the visible to the near infrared and terrestrial prescriptions of both cloud and surface albedo maps. I explore the performance of the method in terms of computational time and accuracy. A clear strength of this approach is that its computational cost does not appear to be significantly affected by non-uniformities in the planet optical properties. Earth's simulated appearance is strongly dependent on wavelength; both brightness and polarization undergo diurnal variations arising from changes in the planet cover, but polarization yields a better insight into variations with phase angle. There is partial cancellation of the polarized signal from the northern and southern hemispheres so that the outgoing polarization vector lies preferentially either in the plane parallel or perpendicular to the planet scattering plane, also for non-uniform cloud and albedo properties and various levels of absorption within the atmosphere. The evaluation of circular polarization is challenging; a number of one-photon experiments of 109 or more is needed to resolve hemispherically integrated degrees of circular polarization of a few times 10−5. Last, I introduce brightness curves of Earth obtained with one of the Messenger cameras at three wavelengths (0.48, 0.56 and 0.63 μm) during a flyby in 2005. The light curves show distinct structure associated with the varying aspect of the Earth's visible disk (phases of 98–107°) as the planet undergoes a full 24 h rotation; the structure is reasonably well reproduced with model simulations.
AXIOMS FOR FINITE COLLAPSE MODELS OF ARITHMETIC
Authors: TEDDER ANDREW 
Published: November 2014

AbstractThe collapse models of arithmetic are inconsistent, nontrivial models obtained from ℕ and set out in the Logic of Paradox (LP). They are given a general treatment by Priest (Priest, 2000). Finite collapse models are decidable, and thus axiomatizable, because finite. LP, however, is ill-suited to normal axiomatic reasoning, as it invalidates Modus Ponens, and almost all other usual conditional inferences. I set out a logic, A3, first given by Avron (Avron, 1991), and give a first order axiom system for the finite collapse models. I present some standard arithmetical axioms in addition to a cyclic axiom and prove that these axioms are sound and complete for the cyclic models, reporting a similar result for the heap models. The state of the situation for the each of the kinds of infinite collapse model is, however, left an open question.
Evidence for henipavirus spillover into human populations in Africa
Authors: Pernet Olivier , Schneider Bradley S. , Beaty Shannon M. , LeBreton Matthew , Yun Tatyana E. , Park Arnold , Zachariah Trevor T. , Bowden Thomas A. , Hitchens Peta , Ramirez Christina M. , Daszak Peter , Mazet Jonna , Freiberg Alexander N. , Wolfe Nathan D. , Lee Benhur 
Published: November 2014

AbstractZoonotic transmission of lethal henipaviruses (HNVs) from their natural fruit bat reservoirs to humans has only been reported in Australia and South/Southeast Asia. However, a recent study discovered numerous HNV clades in African bat samples. To determine the potential for HNV spillover events among humans in Africa, here we examine well-curated sets of bat (Eidolon helvum, n=44) and human (n=497) serum samples from Cameroon for Nipah virus (NiV) cross-neutralizing antibodies (NiV-X-Nabs). Using a vesicular stomatitis virus (VSV)-based pseudoparticle seroneutralization assay, we detect NiV-X-Nabs in 48% and 3–4% of the bat and human samples, respectively. Seropositive human samples are found almost exclusively in individuals who reported butchering bats for bushmeat. Seropositive human sera also neutralize Hendra virus and Gh-M74a (an African HNV) pseudoparticles, as well as live NiV. Butchering bat meat and living in areas undergoing deforestation are the most significant risk factors associated with seropositivity. Evidence for HNV spillover events warrants increased surveillance efforts.
The DUSP–Ubl domain of USP4 enhances its catalytic efficiency by promoting ubiquitin exchange
Authors: Clerici Marcello , Luna-Vargas Mark P. A. , Faesen Alex C. , Sixma Titia K. 
Published: November 2014

AbstractUbiquitin-specific protease USP4 is emerging as an important regulator of cellular pathways, including the TGF-β response, NF-κB signalling and splicing, with possible roles in cancer. Here we show that USP4 has its catalytic triad arranged in a productive conformation. Nevertheless, it requires its N-terminal DUSP–Ubl domain to achieve full catalytic turnover. Pre-steady-state kinetics measurements reveal that USP4 catalytic domain activity is strongly inhibited by slow dissociation of ubiquitin after substrate hydrolysis. The DUSP–Ubl domain is able to enhance ubiquitin dissociation, hence promoting efficient turnover. In a mechanism that requires all USP4 domains, binding of the DUSP–Ubl domain promotes a change of a switching loop near the active site. This ‘allosteric regulation of product discharge’ provides a novel way of regulating deubiquitinating enzymes that may have relevance for other enzyme classes.
MNKs act as a regulatory switch for eIF4E1 and eIF4E3 driven mRNA translation in DLBCL
Authors: Landon Ari L. , Muniandy Parameswary A. , Shetty Amol C. , Lehrmann Elin , Volpon Laurent , Houng Simone , Zhang Yongqing , Dai Bojie , Peroutka Raymond , Mazan-Mamczarz Krystyna , Steinhardt James , Mahurkar Anup , Becker Kevin G. , Borden Katherine L. , Gartenhaus Ronald B. 
Published: November 2014

AbstractThe phosphorylation of eIF4E1 at serine 209 by MNK1 or MNK2 has been shown to initiate oncogenic mRNA translation, a process that favours cancer development and maintenance. Here, we interrogate the MNK-eIF4E axis in diffuse large B-cell lymphoma (DLBCL) and show a distinct distribution of MNK1 and MNK2 in germinal centre B-cell (GCB) and activated B-cell (ABC) DLBCL. Despite displaying a differential distribution in GCB and ABC, both MNKs functionally complement each other to sustain cell survival. MNK inhibition ablates eIF4E1 phosphorylation and concurrently enhances eIF4E3 expression. Loss of MNK protein itself downregulates total eIF4E1 protein level by reducing eIF4E1 mRNA polysomal loading without affecting total mRNA level or stability. Enhanced eIF4E3 expression marginally suppresses eIF4E1-driven translation but exhibits a unique translatome that unveils a novel role for eIF4E3 in translation initiation. We propose that MNKs can modulate oncogenic translation by regulating eIF4E1-eIF4E3 levels and activity in DLBCL.
Structure and function of a spectrin-like regulator of bacterial cytokinesis
Authors: Cleverley Robert M. , Barrett Jeffrey R. , Baslé Arnaud , Bui Nhat Khai , Hewitt Lorraine , Solovyova Alexandra , Xu Zhi-Qiang , Daniel Richard A. , Dixon Nicholas E. , Harry Elizabeth J. , Oakley Aaron J. , Vollmer Waldemar , Lewis Richard J. 
Published: November 2014

AbstractBacterial cell division is facilitated by a molecular machine—the divisome—that assembles at mid-cell in dividing cells. The formation of the cytokinetic Z-ring by the tubulin homologue FtsZ is regulated by several factors, including the divisome component EzrA. Here we describe the structure of the 60-kDa cytoplasmic domain of EzrA, which comprises five linear repeats of an unusual triple helical bundle. The EzrA structure is bent into a semicircle, providing the protein with the potential to interact at both N- and C-termini with adjacent membrane-bound divisome components. We also identify at least two binding sites for FtsZ on EzrA and map regions of EzrA that are responsible for regulating FtsZ assembly. The individual repeats, and their linear organization, are homologous to the spectrin proteins that connect actin filaments to the membrane in eukaryotes, and we thus propose that EzrA is the founding member of the bacterial spectrin family.
Period doubling induced by thermal noise amplification in genetic circuits
Authors: Ruocco G. , Fratalocchi A. 
Published: November 2014

AbstractRhythms of life are dictated by oscillations, which take place in a wide rage of biological scales. In bacteria, for example, oscillations have been proven to control many fundamental processes, ranging from gene expression to cell divisions. In genetic circuits, oscillations originate from elemental block such as autorepressors and toggle switches, which produce robust and noise-free cycles with well defined frequency. In some circumstances, the oscillation period of biological functions may double, thus generating bistable behaviors whose ultimate origin is at the basis of intense investigations. Motivated by brain studies, we here study an “elemental” genetic circuit, where a simple nonlinear process interacts with a noisy environment. In the proposed system, nonlinearity naturally arises from the mechanism of cooperative stability, which regulates the concentration of a protein produced during a transcription process. In this elemental model, bistability results from the coherent amplification of environmental fluctuations due to a stochastic resonance of nonlinear origin. This suggests that the period doubling observed in many biological functions might result from the intrinsic interplay between nonlinearity and thermal noise.
Nonstationary Precipitation Intensity-Duration-Frequency Curves for Infrastructure Design in a Changing Climate
Authors: Cheng Linyin , AghaKouchak Amir 
Published: November 2014

AbstractExtreme climatic events are growing more severe and frequent, calling into question how prepared our infrastructure is to deal with these changes. Current infrastructure design is primarily based on precipitation Intensity-Duration-Frequency (IDF) curves with the so-called stationary assumption, meaning extremes will not vary significantly over time. However, climate change is expected to alter climatic extremes, a concept termed nonstationarity. Here we show that given nonstationarity, current IDF curves can substantially underestimate precipitation extremes and thus, they may not be suitable for infrastructure design in a changing climate. We show that a stationary climate assumption may lead to underestimation of extreme precipitation by as much as 60%, which increases the flood risk and failure risk in infrastructure systems. We then present a generalized framework for estimating nonstationary IDF curves and their uncertainties using Bayesian inference. The methodology can potentially be integrated in future design concepts.
Potential microRNA-mediated oncogenic intercellular communication revealed by pan-cancer analysis
Authors: Li Yue , Zhang Zhaolei 
Published: November 2014

AbstractCarcinogenesis consists of oncogenesis and metastasis and intriguingly microRNAs (miRNAs) are involved in both processes. Although aberrant miRNA activities are prevalent in diverse tumor types, the exact mechanisms for how they regulate cancerous processes are not always clear. To this end, we performed a large-scale pan-cancer analysis via a novel probabilistic approach to infer recurrent miRNA-target interactions implicated in 12 cancer types using data from The Cancer Genome Atlas. We discovered ~20,000 recurrent miRNA regulations, which are enriched for cancer-related miRNAs/genes. Notably, miRNA 200 family (miR-200/141/429) is among the most prominent miRNA regulators, which is known to be involved in metastasis. Importantly, the recurrent miRNA regulatory network is not only enriched for cancer pathways but also for extracellular matrix (ECM) organization and ECM-receptor interactions. The results suggest an intriguing cancer mechanism involving miRNA-mediated cell-to-cell communication, which possibly involves delivery of tumorigenic miRNA messengers to adjacent cells via exosomes. Finally, survival analysis revealed 414 recurrent-prognostic associations, where both gene and miRNA involved in each interaction conferred significant prognostic power in one or more cancer types. Together, our comprehensive pan-cancer analysis provided not only biological insights into metastasis but also brought to bear the clinical relevance of the proposed recurrent miRNA-gene associations.
Comprehensive study on a 2 × 2 full‐rate and linear decoding complexity space–time block code
Authors: Hosseini Seyyed Saleh , Talebi Siamak , Abouei Jamshid 
Published: November 2014

This paper presents a comprehensive study on the Full‐Rate and Linear‐Receiver (FRLR) STBC proposed as a newly coding scheme with the low decoding complexity for a 2×2 MIMO system. It is shown that the FRLR code suffers from the lack of the non‐vanishing determinant (NVD) property that is a key parameter in designing a full‐rate STBC with a good performance in higher data rates, across QAM constellation. To overcome this drawback, we show that the existence of the NVD feature for the FRLR code depends on the type of the modulation. In particular, it is analytically proved that the FRLR code fulfills the NVD property across the PAM constellation but not for the QAM scheme. Simulation results show that, at a BER equal to 10−4, utilising the PAM modulation for the FRLR‐STBC, provides about 2 dB gain over a use of the QAM when the bandwidth efficiency is 6b/s/Hz. In addition, for the PAM constellation, the FRLR code significantly outperforms some existing full‐rate STBCs. Finally, we utilise the moment generating function approach to derive an exact closed‐form expression for the average error probability of the FRLR code with the BPSK modulation.
Adapting to catastrophic water scarcity in agriculture through social networking and inter-generational occupational transitioning
Authors: Ranjan Ram 
Published: November 2014

Abstract
Increasing frequency of drought threatens the long-term viability of agriculture in many regions of the world. Some farmers will exit the agricultural industry abruptly, but for many, the path out of agriculture is prolonged and involves several generations within a household. This paper presents a model of dynamic inter-generational preferences and occupational choices to explore possible transition paths out of agriculture. Differing preferences across generations within a farming household are incorporated through a dynamically-evolving utility function, which influences the time paths of optimal investments in human, social and natural capital. A dwindling natural resource base, such as groundwater, requires increasing reliance on urban livelihoods. However, inter-generational differences in preferences for rural versus urban lifestyles, modelled as different weights in the household's utility function, may determine whether this occupational transition can be attained.
Trade Liberalization versus Climate Change Policy for Reducing Greenhouse Gas Emissions in Agriculture: Some Insights from Norway
Authors: Blandford David , Gaasland Ivar , Vårdal Erling 
Published: November 2014

AbstractUsing a mathematical programming model of Norwegian agriculture, we explore interconnections between trade liberalization and reductions in greenhouse gas (GHG) emissions. We show that the Doha Round proposals for a new agreement on agriculture through the World Trade Organization would not generate significant reductions in emissions. Further trade liberalization would reduce emissions by cutting agricultural production but would not change production methods. Imposing a carbon tax would lead both to a reduction in output and the extensification of production. In contrast, if farmers are allowed to claim a credit for carbon sequestration the effect is to intensify agricultural production.
Fitting state–space models to seal populations with scarce data
Authors: Øigård Tor Arne , Skaug Hans J. 
Published: November 2014

Abstract
We estimate temporal variation in fecundity, the reproduction rate, for Barents Sea and Greenland Sea harp seals using a state–space approach. A stochastic process model for fecundity is integrated with an age-structured population dynamics model and fit to available data for these two harp seal populations. Owing to scarceness of data, it is necessary to “borrow strength” from the Northwest Atlantic harp seal population in form of prior distributions on autocorrelation and variance in fecundity. Comparison is made to a simpler deterministic population dynamics model. The state–space model is more flexible and is able to account for the variations in the data. For Barents Sea harp seals, the state–space model gives a higher estimate of current population size but also a much higher associated uncertainty. In the Greenland Sea, the differences between the stochastic and deterministic models are much smaller.
Iron Supplementation Until 6 Months Protects Marginally Low‐Birth‐Weight Infants From Iron Deficiency During Their First Year of Life
Authors: Berglund Staffan K. , Westrup Björn , Domellöf Magnus 
Published: November 2014

ABSTRACTObjectives:Low‐birth‐weight (LBW) infants (<2500 g) have an increased risk of iron deficiency (ID) during their first 6 months of life. The optimal dose and duration of iron supplementation to LBW infants are, however, unknown. The objective of the present study was to investigate the long‐term effect on iron status and growth in marginally LBW (2000–2500 g) infants, of iron supplements given until 6 months of life.Methods:In a randomized controlled trial, 285 healthy marginally LBW infants received 0, 1, or 2 mg · kg−1 · day−1 of iron supplements from 6 weeks to 6 months of age. At 12 months and 3.5 years of life we measured length, weight, head circumference, and indicators of iron status (hemoglobin, ferritin, mean corpuscular volume, and transferrin saturation) and assessed the prevalence of iron depletion, functional ID, and ID anemia.Results:At 12 months of age, there was a significant difference in ferritin between the groups (P = 0.006). Furthermore, there was a significant difference in the prevalence of iron depletion (23.7%, 10.6%, and 6.8%, respectively, in the placebo, 1‐mg, and 2‐mg groups, P = 0.009) and similar nonsignificant trends for functional ID and ID anemia. At 3.5 years of life there were no significant differences in iron status and the mean prevalence of iron depletion was 3.2%. Anthropometric data were not affected by the intervention.Conclusions:Iron supplements with 2 mg · kg−1 · day−1 until 6 months of life effectively reduces the risk of ID during the first 12 months of life and is an effective intervention for preventing early ID in marginally LBW infants.
Cost‐Effectiveness Analysis of Zinc Supplementation for Treatment of Acute Diarrhea in Children Younger Than 5 Years in Colombia
Authors: Mejía Aurelio , Atehortúa Sara , Flórez Iván D. , Sierra Javier M. , Mejia María E. , Ramírez Carolina 
Published: November 2014

ABSTRACTObjective:The objective of this study was to determine the cost‐effectiveness of zinc supplementation for the treatment of acute diarrhea (AD) in children younger than 5 years in Colombia.Methods:The cost‐effectiveness analysis was performed from the perspective of the Colombian health system. The standard treatment with the addition of zinc was compared with the standard treatment without zinc in children younger than 5 years. The time horizon was 1 month. Effectiveness was extracted from a systematic review of literature. The specific data for Colombia were taken from local databases and observational studies. To determine the costs, a typical case was constructed by reviewing guidelines and medical records and validated by experts. To evaluate the resources consumed, Colombian tariff manuals were used. Costs were stated in Colombian pesos (COP) and US dollar (USD) for 2010. Deterministic sensitivity analysis was performed to evaluate the impact of changes in cost and effectiveness of the strategies on the results from the model.Results:The results from the model indicate that zinc supplementation is a dominant strategy; it is less costly and more effective than standard treatment without zinc (reduction of $15,210 COP [8.14 USD] per child). The results are sensitive to changes in the probability of hospitalization and of persistent diarrhea.Conclusions:Zinc for the treatment of AD is a highly cost‐effective strategy and is recommended for inclusion in the benefit plan of the Colombian health system. This intervention is more cost‐effective in children with a higher risk of persistent diarrhea and hospitalization.
Polymerase ζ activity is linked to replication timing in humans: evidence from mutational signatures
Authors: Seplyarskiy Vladimir B. , Bazykin Georgii A. , Soldatov Ruslan A. 
Published: November 2014

AbstractReplication timing is an important determinant of germline mutation patterns, with a higher rate of point mutations in late replicating regions. Mechanisms underlying this association remain elusive. One of the suggested explanations is the activity of error-prone DNA polymerases in late-replicating regions. Polymerase ζ (pol ζ), an essential error-prone polymerase biased towards transversions, also has a tendency to produce dinucleotide mutations (DNMs), complex mutational events that simultaneously affect two adjacent nucleotides. Experimental studies have shown that pol ζ is strongly biased towards GC->AA/TT DNMs. Using primate divergence data, we show that the GC->AA/TT pol ζ mutational signature is the most frequent among DNMs, and its rate exceeds the mean rate of other DNM types by a factor of ~10. Unlike the overall rate of DNMs, the pol ζ signature drastically increases with the replication time in the human genome. Finally, the pol ζ signature is enriched in transcribed regions, and there is a strong prevalence of GC->TT over GC->AA DNMs on the non-template strand, indicating association with transcription. A recurrently occurring GC->TT DNM in HRAS gene causes the Costello syndrome; we find a 2-fold increase in the mutation rate, and a 2-fold decrease in the transition/transversion ratio, at distances of up to 1 kb from the DNM, suggesting a link between the Costello syndrome and pol ζ activity. This study uncovers the genomic preferences of pol ζ, shedding light on a novel cause of mutational heterogeneity along the genome.