bluuebunny/crossref_metadata_2025 huggingface dataset:
Nutrient-Colimited Trichodesmium as a Nitrogen Source or Sink in a Future Ocean
Authors: Walworth Nathan G. , Fu Fei-Xue , Lee Michael D. , Cai Xiaoni , Saito Mak A. , Webb Eric A. , Hutchins David A.
Published: November 2017

Nitrogen-fixing (N2) cyanobacteria provide bioavailable nitrogen to vast ocean regions but are in turn limited by iron (Fe) and/or phosphorus (P), which may force them to employ alternative nitrogen acquisition strategies. The adaptive responses of nitrogen fixers to global-change drivers under nutrient-limited conditions could profoundly alter the current ocean nitrogen and carbon cycles. Here, we show that the globally important N2fixerTrichodesmiumfundamentally shifts nitrogen metabolism toward organic-nitrogen scavenging following long-term high-CO2adaptation under iron and/or phosphorus (co)limitation. Global shifts in transcripts and proteins under high-CO2/Fe-limited and/or P-limited conditions include decreases in the N2-fixing nitrogenase enzyme, coupled with major increases in enzymes that oxidize trimethylamine (TMA). TMA is an abundant, biogeochemically important organic nitrogen compound that supports rapidTrichodesmiumgrowth while inhibiting N2fixation. In a future high-CO2ocean, this whole-cell energetic reallocation toward organic nitrogen scavenging and away from N2fixation may reduce new-nitrogen inputs byTrichodesmiumwhile simultaneously depleting the scarce fixed-nitrogen supplies of nitrogen-limited open-ocean ecosystems.

IMPORTANCETrichodesmiumis among the most biogeochemically significant microorganisms in the ocean, since it supplies up to 50% of the new nitrogen supporting open-ocean food webs. We usedTrichodesmiumcultures adapted to high-CO2conditions for 7 years, followed by additional exposure to iron and/or phosphorus (co)limitation. We show that “future ocean” conditions of high CO2and concurrent nutrient limitation(s) fundamentally shift nitrogen metabolism away from nitrogen fixation and instead toward upregulation of organic nitrogen-scavenging pathways. We show that the responses ofTrichodesmiumto projected future ocean conditions include decreases in the nitrogen-fixing nitrogenase enzymes coupled with major increases in enzymes that oxidize the abundant organic nitrogen source trimethylamine (TMA). Such a shift toward organic nitrogen uptake and away from nitrogen fixation may substantially reduce new-nitrogen inputs byTrichodesmiumto the rest of the microbial community in the future high-CO2ocean, with potential global implications for ocean carbon and nitrogen cycling.
Prevalence and sociodemographic correlates of cervicovaginal human papillomavirus (HPV) carriage in a cross-sectional, multiethnic, community-based female Asian population
Authors: Khoo Su Pei , Bhoo-Pathy Nirmala , Yap Siew Hwei , Anwar Shafii Mohd Khairul , Hairizan Nasir Nazrilla , Belinson Jerome , Subramaniam ShriDevi , Goh Pik Pin , Zeng Ming , Tan Hong Dong , Gravitt Patti , Woo Yin Ling
Published: November 2017

Objectives

Cervical cancer is a largely preventable disease, and the strategic implementation of a cervical cancer prevention programme is partly dependent on the impact of human papillomavirus (HPV) infection interpreted within the context of the country’s sociodemographic attributes. The objective of this study is to determine the prevalence of cervicovaginal HPV infection among a healthy, community-based, multiethnic Malaysian population. The HPV prevalence was subsequently correlated to the individual’s sociodemographics and sexual/reproductive history. Of significance, the observed prevalence captured was in a birth cohort not included in the national school-based HPV vaccination programme.

Methods

This was a cross-sectional study where 1293 healthy women aged between 18 and 60 years were recruited via convenience sampling from five community-based clinics in Selangor, Malaysia. Cervicovaginal self-samples were obtained and DNA was extracted for HPV detection and genotyping. A comprehensive questionnaire was administered to determine the sociodemographics and behavioural patterns of participants.

Results

The median age at enrolment was 37 years old (IQR: 30–47). In total, 86/1190 (7.2%) of the samples collected were positive for HPV infection, with the highest HPV prevalence (11.9%) detected in the subgroup of 18–24 years old. The top three most prevalent HPV genotypes were HPV 16, 52 and 58. The independent risk factors associated with higher rates of HPV infection included Indian ethnicity, widowed status and women with partners who are away from home for long periods and/or has another sexual partner.

Conclusions

The overall prevalence of HPV infection in this Malaysian multiethnic population was 7.2%, with 6.5% being high-risk genotypes. The top three most common high-risk HPV types were HPV 16, 52 and 58. This information is important for the planning of primary (HPV vaccination) and secondary (screening) cervical cancer prevention programmes in Malaysia.
Tobacco control in California compared with the rest of the USA: trends in adult per capita cigarette consumption
Authors: Pierce John P , Shi Yuyan , Hendrickson Erik M , White Martha M , Noble Madison L , Kealey Sheila , Strong David R , Trinidad Dennis R , Hartman Anne M , Messer Karen
Published: November 2017

Background

In the 1990s, California led the USA in state-level tobacco control strategies. However, after 2000, California lost ground on cigarette taxes, although it maintained higher levels of smoke-free homes among smokers.

Methods

Trends in per capita cigarette consumption were assessed through taxed sales data and from self-report in repeated national cross-sectional surveys. Linear regressions identified changes in trends after year 2000 separately for California and the rest of the USA. Using data from each state, a linear regression tested the association between different tobacco control strategies and per capita consumption. Change in self-reported per capita consumption was partitioned into contributions associated with initiation, quitting and reduction in cigarette consumption level.

Results

Both taxed cigarette sales and per capita consumption declined rapidly in the USA from 1985 to 2015. Declines were particularly fast in California before 2000 but slowed thereafter. In 2014, per capita consumption in California was 29.4 packs/adult/year, but 90% higher in the rest of the USA. Modelling state-level data, every $1 increase in cigarette taxes reduced consumption by 4.8 (95% CI 2.9 to 6.8) packs/adult/year. Every 5% increase in the proportion of smokers with smoke-free homes reduced consumption by 8.0 (95% CI 7.0 to 8.9) packs/adult/year. The different patterns in California and the rest of the USA are at least partially explained by these two variables. The slow down in per capita consumption in California can be attributed to changes in initiation, quitting and especially smokers reducing their consumption level.

Conclusions

Tobacco control strategies need to be continually updated to maintain momentum towards a smoke-free society.
Exposure of high-light-grown cultures of Chlorella vulgaris to darkness inhibits the relaxation of excitation pressure: uncoupling of the redox state of the photosynthetic electron transport chain and phenotypic plasticity
Authors: Hollis Lauren , Hüner Norman P.A.
Published: November 2017

Chlorella vulgaris acclimated to high light (HL) conditions exhibited a pale-green phenotype characterized by reduced chlorophyll and light harvesting polypeptide abundance compared with the dark green phenotype of the control, low-light-grown (LL) cultures. We hypothesized that if chloroplast redox status was the sole regulator of phenotype, exposure to darkness should cause reversion of the HL to LL phenotype. Surprisingly, HL cells transferred to darkness or dim light failed to green. Thus, phenotypic reversion is light-dependent with an optimal photon flux density (PFD) of 110 μmol photons·m−2·s−1. HL cells shifted to this PFD exhibited increased chlorophyll and light harvesting polypeptide abundance, which were inhibited by 2,5-dibromo-3-methyl-6-isopropyl-benzoquinone but not by 3-(3′,4′-dichlorophenyl)-1,1-dimethylurea. We conclude that photoacclimation of HL-grown cells to LL is governed by the redox state of the intersystem photosynthetic electron transport chain (PETC) at this PFD. At lower light levels, cells maintained the HL phenotype, despite an oxidized status of the PETC. Because 110 μmol photons·m−2·s−1 was the optimal PFD for protochlorophyllide oxidoreductase accumulation, we suggest that stabilization of light-harvesting polypeptides by chlorophyll binding may also govern photoacclimation in C. vulgaris. The possible role of the metabolic balance between respiration and photosynthesis is also discussed.
Identification of native and invasive subspecies of common reed (Phragmites australis) in Alberta, Canada, by RNase-H-dependent PCR
Authors: Zuzak Krista , Yang Yalong , Kimmel Nicole , Harding Michael , Feindel David , Feng Jie
Published: November 2017

Colonies of the invasive subspecies of common reed (Phragmites australis (Cav.) Trin. ex Steud) were found in Alberta in 2016. To facilitate the rapid subspecies identification necessary to support management of this invasive subspecies, a simple and time-saving protocol was developed to differentiate the invasive from the native subspecies. This protocol was based on the RNase-H-dependent PCR (rhPCR) technique, which utilizes the DNA polymorphism found in two chloroplast DNA regions. Compared with the widely used restriction fragment length polymorphism (RFLP) protocol, the rhPCR had the same level of accuracy for subspecies identification, but is simpler and less time-consuming. Using both the rhPCR and RFLP techniques, 27 samples of P. australis derived from 21 colonies in nine Alberta counties were tested to determine their subspecies identity. Fourteen colonies were identified as invasive subspecies, and seven were native subspecies. Based on these preliminary data, we concluded that the invasive subspecies has established across Alberta, and now may be more common than the native subspecies. In addition, RFLP results confirmed that the rhPCR was accurate and could be used independently to identify P. australis subspecies in future studies.
Development of an economically sustainable and balanced tactical forest management plan: a case study in Quebec
Authors: Mobtaker Azadeh , Ouhimmou Mustapha , Rönnqvist Mikael , Paquet Marc
Published: November 2017

In Canada, most of the forests are publicly owned and forest products companies depend on timber licenses issued by the provincial governments for their wood supplies. According to the Sustainable Forest Development Act effective in the province of Quebec since April 2013, the government is responsible for harvest area selection and timber allocation to companies. This is a complex tactical planning decision with important impacts on downstream economic activities. Moreover, to avoid high grading of forest resources and to determine a sustainable tactical plan that ensures a stable level of availability, quality, and cost of supply over several years, it is necessary to take these criteria into consideration simultaneously during the planning process. We propose a mixed-integer nonlinear goal-programming formulation while employing Nadir theory as a reliable scaling technique to model this multi-objective planning problem. The model is solved by a linearization approach for a real case in the province of Quebec. The proposed solution method enables us to obtain good-quality solutions for relatively large cases. Results show that the proposed model outperforms conventional cost-minimization planning strategy by ensuring a more balanced use of wood supply and costs for all stakeholders over a longer period.
On the one-loop calculations with Reggeized quarks
Authors: Nefedov Maxim , Saleev Vladimir
Published: November 2017

The technique of one-loop calculations for the processes involving Reggeized quarks is described in the framework of gauge invariant effective field theory for the Multi-Regge limit of QCD, which has been introduced by Lipatov and Vyazovsky. The rapidity divergences, associated with the terms enhanced by log(s), appear in the loop corrections in this formalism. The covariant procedure of regularization of rapidity divergences, preserving the gauge invariance of effective action is described. As an example application, the one-loop correction to the propagator of Reggeized quark and [Formula: see text]-scattering vertex are computed. Obtained results are used to construct the Regge limit of one-loop [Formula: see text] amplitude. The cancellation of rapidity divergences and consistency of the EFT prediction with the full QCD result is demonstrated. The rapidity renormalization group within the EFT is discussed.
Advances in the study of the mechanochemical coupling of kinesin
Authors: Li Ming , Ou-Yang Zhong-Can , Shu Yao-Gen
Published: November 2017

Kinesin is a two-headed linear motor for intracellular transport. It can walk a long distance in a hand-over-hand manner along the track before detaching (i.e., high processivity), and it consumes one ATP molecule for each step (i.e., tight mechanochemical coupling). The mechanisms of the coordination of its two heads and the mechanochemical coupling are the central issues of numerous researches. A few advances have been made in recent decades, thanks to the development of single-molecule technologies and molecular dynamics simulations. In this paper, we review some progress of the studies on the kinematics, energetics, coordination mechanism, mechanochemical mechanism of kinesin. We also present a personal perspective on the future studies of kinesin.
Molecular dynamics simulation of the coalescence and melting process of Au and Cu nano-clusters
Authors: Chen Gang , Wang Chuan Jie , Zhang Peng
Published: November 2017

Molecular dynamic (MD) method is used to study the coalescence and fusing process of Au and Cu nanoclusters. The results show that shear deformation, surface and interface diffusion play important role in different stages of all simulation procedure. In most cases, shear deformation produces the twin boundary or/and stacking fault in particles by particle rotation and slide. The angle between the {111} of Au and Cu particles decrease with increasing temperature, which promotes the formation of the stable interface. Furthermore, the coalescence point and melting temperature increase as cluster diameter increases. For the other cases, there are no particle rotation and slide phenomenon in the elevating temperature process because the stable interface can be formed by forming twin boundaries once two particles contact.
Analysis of inter-country input–output table based on bibliographic coupling network: How industrial sectors on the GVC compete for production resources
Authors: Guan Jun , Xu Xiaoyu , Xing Lizhi
Published: November 2017

The input–output table is comprehensive and detailed in describing national economic systems with abundance of economic relationships depicting information of supply and demand among industrial sectors. This paper focuses on how to quantify the degree of competition on the global value chain (GVC) from the perspective of econophysics. Global Industrial Strongest Relevant Network models are established by extracting the strongest and most immediate industrial relevance in the global economic system with inter-country input–output (ICIO) tables and then have them transformed into Global Industrial Resource Competition Network models to analyze the competitive relationships based on bibliographic coupling approach. Three indicators well suited for the weighted and undirected networks with self-loops are introduced here, including unit weight for competitive power, disparity in the weight for competitive amplitude and weighted clustering coefficient for competitive intensity. Finally, these models and indicators were further applied empirically to analyze the function of industrial sectors on the basis of the latest World Input–Output Database (WIOD) in order to reveal inter-sector competitive status during the economic globalization.
Co-doped phosphorene: Enhanced sensitivity of CO gas sensing
Authors: Lei S. Y. , Luan S. , Yu H.
Published: November 2017

First-principle calculation was carried out to systematically investigate carbon monoxide (CO) adsorption on pristine and cobalt (Co)-doped phosphorenes (Co-bP). Whether or not CO is adsorped, pristine phosphorene is a direct-band-gap semiconductor. However, the bandgap of Co-bP experiences direct-to-indirect transition after CO molecule adsorption, which will affect optical absorption considerably, implying that Co doping can enhance the sensitivity of phosphorene as a CO gas sensor. Moreover, Co doping can improve an adsorption energy of CO to 1.31 eV, as compared with pristine phosphorene (0.12 eV), also indicating that Co-bP is energetically favorable for CO gas sensing.
Weyl fermions in a family of Gödel-type geometries with a topological defect
Authors: Garcia G. Q. , Oliveira J. R. de S. , Furtado C.
Published: November 2017

In this paper, we study Weyl fermions in a family of Gödel-type geometries in Einstein general relativity. We also consider that these solutions are embedded in a topological defect background. We solve the Weyl equation and find the energy eigenvalues and eigenspinors for all three cases of Gödel-type geometries where a topological defect is passing through them. We show that the presence of a topological defect in these geometries contributes to the modification of the spectrum of energy. The energy zero modes for all three cases of the Gödel geometries are discussed.
Information entropy and dark energy evolution
Authors: Capozziello Salvatore , Luongo Orlando
Published: November 2017

Here, the information entropy is investigated in the context of early and late cosmology under the hypothesis that distinct phases of universe evolution are entangled between them. The approach is based on the entangled state ansatz, representing a coarse-grained definition of primordial dark temperature associated to an effective entangled energy density. The dark temperature definition comes from assuming either Von Neumann or linear entropy as sources of cosmological thermodynamics. We interpret the involved information entropies by means of probabilities of forming structures during cosmic evolution. Following this recipe, we propose that quantum entropy is simply associated to the thermodynamical entropy and we investigate the consequences of our approach using the adiabatic sound speed. As byproducts, we analyze two phases of universe evolution: the late and early stages. To do so, we first recover that dark energy reduces to a pure cosmological constant, as zero-order entanglement contribution, and second that inflation is well-described by means of an effective potential. In both cases, we infer numerical limits which are compatible with current observations.
Multistate scalar field dark matter and its correlation with galactic properties
Authors: Hernández-Almada A. , García-Aspeitia Miguel A.
Published: November 2017

In this paper, we search for the correlations between the intrinsic properties of galaxies and the Bose–Einstein condensate (BEC) under the scheme of a scalar field dark matter (SFDM) at the temperature of condensation greater than zero. According to this paradigm the BEC is distributed in several states. Based on the galactic rotation curves collected in SPARC dataset, we observe that the SFDM parameters present a weak correlation with the most of the galaxy properties, having only a correlation with those related to neutral hydrogen emissions. In addition, we found evidence to the support of self-interaction between the different BEC states proposing that, in future studies, the crossed terms in SFDM equations must be considered. Finally, we find a null correlation with galaxy distances giving support to the nonhierarchy of SFDM formation.
PATHWAYS TO A DRUG: A MIXED METHODS ANALYSIS OF EMERGENCE
Authors: SUOMINEN ARHO , DEDEHAYIR OZGUR
Published: November 2017

Despite the calls for a broader methodological base, the technology management and the forecasting literature remain short of studies synthesising quantitative and qualitative methods. This paper addresses this gap by employing a mixed method approach to study the case of Taxol, a revolutionary drug developed to fight ovarian and breast cancer. The paper shows in detail how a data mining-based network model can be synthesised with qualitatively created event narrative to understand the development of a technology and its ecosystem. As a result, the paper shows an npartite network of Taxol drug ecosystem containing over 4,000 nodes and 11,000 edges. The network enables decision makers to understand the process, interaction of actors and lock-in mechanism in the process of technological development.
RESPONSIBLE INNOVATION IN HEALTHCARE — THE CASE OF HEALTH INFORMATION TV
Authors: BESSANT JOHN , ALEXANDER ALLEN , WYNNE DANIELLE , TRIFILOVA ANNA
Published: November 2017

The paper explores the application of responsible innovation (RI) principles in the design and implementation of innovation in the context of digitally-enabled healthcare. In particular, we are interested in the scope for bringing in RI considerations at various stages in the innovation process and in the relevant tools and frameworks which might facilitate this. Using the particular example of a detailed longitudinal case of the development and diffusion (with subsequent modification and “re-innovation”) of a digital health information platform, we identify a number of key points at which the innovation concept “pivoted” to reflect new information, some of which resulted from a wider level of inclusion (one of the core RI principles). The paper explores the role played by structured frameworks (such as the “Business Model Canvas”) in the development of other digital healthcare innovations at an early stage.
On flexible and robust parameter assignment for periodic real-time components
Authors: Nasri Mitra
Published: November 2017

In order to increase the flexibility of design process, we consider a component-based system in which some components may be changed, repaired, or upgraded. We assume that the worst-case execution time (WCET) of each task that is implemented by a component is known. Our first goal is to find the smallest set of periods that make the task set schedulable by EDF or by RM. We call these periods
safe periods
because then any period assignment which is larger than the safe periods will be schedulable. Having safe periods, system designer will be able to use any optimization criteria of his choice to assign periods of the tasks without a need to incorporate the response time analysis techniques, which are usually NP-Hard problems, into his optimization constraints. Instead, the schedulability constraint will be reduced to verifying that the assigned periods are larger than the safe periods. Our solution for safe periods for the RM, is based on finding the smallest set of harmonic periods with utilization 1. Here we use our recently developed polynomial-time approximation algorithm with bounded error of 2 for finding these safe periods for RM.

As the second part of our contribution, we consider the robustness property. First we explain how to find safe periods such that a certain level of robustness (based on potential changes of each component) is guaranteed. Doing this, if one of the components changes in the future, other components can still run using their previous periods, and hence, we isolate the effect of future changes from parameters of the other components. Finally, we obtain the robustness factor as a function of the available spare capacity of the system, i.e., the unused utilization. We determine to what extend the WCET of any of the components can be increased without violating the safe periods.
Runtime compositional analysis of track-based traffic control systems
Authors: Bagheri Maryam , Khamespanah Ehsan , Sirjani Marjan , Movaghar Ali , Lee Edward A.
Published: November 2017

In this paper we address the development of dependable self-adaptive systems focusing on the specific domain of track-based traffic control systems where timing issues are critical.
Composable routing in mobile mesh networks
Authors: Oliveira Luis , Almeida Luis
Published: November 2017

Small teams of cooperating robots have been shown to be useful in a myriad of applications, with robots communicating with one another in real-time, be it multimedia, motion control or position information. Their mobility leads to a dynamic network mesh topology through which communications have to be routed, interfering in intricate patterns that vary with time, with the number of active robots in the team, and with their relative positions. In this short paper we advocate that routing for small teams of cooperating robots benefits from global synchronization and immediate forwarding, supporting composability of communications in the time domain by isolating the paths of each flow in separate time slots.
A compositional approach for modeling and timing analysis of wireless sensor and actuator networks
Authors: Sirjani Marjan , Khamespanah Ehsan , Mechitov Kirill , Agha Gul
Published: November 2017

Wireless sensor and actuator networks (WSAN) are created through the integration of multiple nodes which acquire data and perform reaction based on them. In a general overview, sensor nodes of WSANs are responsible for data acquisition and sending them to a central node. The central node stores all the received data and performs reactions. Timing verification of WSAN applications to ensure schedulability of tasks is a challenge, and is generally performed by worst-case analysis. This process is error-prone and inherently conservative. On the other hand, using model checking for analyzing WSAN applications results in state space explosion even for middle-sized configurations. The reason is the necessity of considering the interleaving of the large number of sensors in WSANs. In this paper, we show how to build an actor-based model of WSAN applications, starting from sensor node-level and moving towards the full system, and we show how this compositional modeling improves analysability and modifiability. Realtime extension of actor model is appropriate for modeling WSAN applications where we have many concurrent and asynchronous processes, and interdependent realtime deadlines. We demonstrate the approach using a case study of a distributed realtime data acquisition system for high-frequency sensing, where Timed Rebeca is used for modeling. We use model checking to check the intra/inter-sensor node schedulability.
Real-time network function virtualization with timing interfaces
Authors: Phan Linh Thi Xuan
Published: November 2017

More and more infrastructure is becoming virtualized. Recently this trend has begun to include network functions - such as firewalls, WAN optimizers, and intrusion prevention systems - that have traditionally been implemented as middleboxes using dedicated hardware. This trend towards network function virtualization (NFV) offers a variety of potential benefits that resemble those of cloud computing, including consolidation, easier management, higher efficiency, and better scalability. However, current cloud technology is not a perfect match for NFV workloads: since the infrastructure is shared, the time it takes for a packet to pass through a particular function is no longer predictable, and can in fact vary considerably. This is causing headaches for operators, who can no longer treat network functions as "bumps in the wire" and must now consider a complex web of possible interactions and cross-talk when operating or diagnosing their systems.

In this position paper, we propose a compositional approach towards building a scalable NFV platform that can provide latency and throughput guarantees using timing interfaces. We discuss our preliminary results that leverage and extend recent advances on timing interfaces and compositional theory from the real-time systems domain to the NFV setting, and we highlight open challenges and potential directions towards real-time NFV.
Transcriptional Regulation in Archaea: From Individual Genes to Global Regulatory Networks
Authors: Martinez-Pastor Mar , Tonner Peter D. , Darnell Cynthia L. , Schmid Amy K.
Published: November 2017

Archaea are major contributors to biogeochemical cycles, possess unique metabolic capabilities, and resist extreme stress. To regulate the expression of genes encoding these unique programs, archaeal cells use gene regulatory networks (GRNs) composed of transcription factor proteins and their target genes. Recent developments in genetics, genomics, and computational methods used with archaeal model organisms have enabled the mapping and prediction of global GRN structures. Experimental tests of these predictions have revealed the dynamical function of GRNs in response to environmental variation. Here, we review recent progress made in this area, from investigating the mechanisms of transcriptional regulation of individual genes to small-scale subnetworks and genome-wide global networks. At each level, archaeal GRNs consist of a hybrid of bacterial, eukaryotic, and uniquely archaeal mechanisms. We discuss this theme from the perspective of the role of individual transcription factors in genome-wide regulation, how these proteins interact to compile GRN topological structures, and how these topologies lead to emergent, high-level GRN functions. We conclude by discussing how systems biology approaches are a fruitful avenue for addressing remaining challenges, such as discovering gene function and the evolution of GRNs.
Conditional Degrons for Controlling Protein Expression at the Protein Level
Authors: Natsume Toyoaki , Kanemaki Masato T.
Published: November 2017

The conditional depletion of a protein of interest (POI) is useful not only for loss-of-function studies, but also for the modulation of biological pathways. Technologies that work at the level of DNA, mRNA, and protein are available for temporal protein depletion. Compared with technologies targeting the pretranslation steps, direct protein depletion (or protein knockdown approaches) is advantageous in terms of specificity, reversibility, and time required for depletion, which can be achieved by fusing a POI with a protein domain called a degron that induces rapid proteolysis of the fusion protein. Conditional degrons can be activated or inhibited by temperature, small molecules, light, or the expression of another protein. The conditional degron-based technologies currently available are described and discussed.
Nucleases Acting at Stalled Forks: How to Reboot the Replication Program with a Few Shortcuts
Authors: Pasero Philippe , Vindigni Alessandro
Published: November 2017

In a lifetime, a human being synthesizes approximately 2×1016 meters of DNA, a distance that corresponds to 130,000 times the distance between the Earth and the Sun. This daunting task is executed by thousands of replication forks, which progress along the chromosomes and frequently stall when they encounter DNA lesions, unusual DNA structures, RNA polymerases, or tightly-bound protein complexes. To complete DNA synthesis before the onset of mitosis, eukaryotic cells have evolved complex mechanisms to process and restart arrested forks through the coordinated action of multiple nucleases, topoisomerases, and helicases. In this review, we discuss recent advances in understanding the role and regulation of nucleases acting at stalled forks with a focus on the nucleolytic degradation of nascent DNA, a process commonly referred to as fork resection. We also discuss the effects of deregulated fork resection on genomic instability and on the unscheduled activation of the interferon response under replication stress conditions.
A l1 Norm Based Image Prior Combination in Multiframe Superresolution
Authors: Min Lei , Yang Ping , Dong Lizhi , Liu Wenjin , Wang Shuai , Xu Bing , Liu Yong
Published: November 2017

We address the multiframe superresolution problem using the variational Bayesian method in this paper. In the variational Bayesian framework, the prior is crucial in transferring the ill‐posed reconstruction problem to a well‐posed one. We propose a prior combination method based on filter bank and l1 norm. Multiple filters are used in our prior model, and the corresponding combination coefficient vector can be estimated by the characteristics of the filtered image and noise. Furthermore, the local adaptive coefficients of every filter are more effective in removing noise and preserving image edges. Extensive experiments demonstrate the advantages of the proposed method.
Effects of Hole Perpendicularity Error on Mechanical Performance of Single-Lap Double-Bolt Composite Joints
Authors: Liu Xueshu , Yang Yuxing , Wang Yiqi , Bao Yongjie , Gao Hang
Published: November 2017

Static tensile experiments and numerical simulations were carried out to study effects of hole perpendicularity error on mechanical performance of single-lap double-bolt composite joints. Hole tilting angle, varying from 1 to 4 degrees, and hole tilting direction to account for anisotropic properties of composite material were investigated. Progressive damage model (PDM) based on Chang-Lessard type criterion with an extension by Olmedo was created, which involved seven failure modes and made material properties be a direct function of predefined field variables. The model was implemented in ABAQUS/Standard using a UMAT subroutine. Good agreement was found when comparing numerical simulation results with experimental outcomes. In addition, the results demonstrate that, with increasing of hole tilting angle, damage is prone to arise and the load path of the composite bolted joints alters with changing of hole tilting direction, which result in severe stress concentration around the edge of hole and joint failure in advance.
Effectiveness of Fibrin Sealant Patch in Reducing Drain Volume after Pelvic Lymph Node Dissection in Women with Gynecologic Malignancy
Authors: Kim Hwa Cheong , Choi Chahien , Kim Woo Young
Published: November 2017

Background. The goal of this study was to evaluate the effectiveness of fibrin sealant in decreasing postoperative lymphatic drainage in women after pelvic lymphadenectomy and/or para-aortic lymphadenectomy during gynecologic cancer surgery. Methods. This study is a retrospective case-control study. Forty-five patients who underwent staging surgery were enrolled. Twenty-seven patients were in the fibrin sealant group (group A) and 18 in the control group (group B). The two groups were compared for the total volume of drain, hospital stay, harvested lymph node, and incidence of asymptomatic lymphocele. Lymphocele formation was evaluated by computed tomography (CT) on 3 months after surgery. Results. There were no significant differences in patient demographics between group A and B with respect to age, BMI, and harvested lymph nodes. Patients who received fibrin sealants had reduced total volume of drainage from postoperative days 2 to 5 compared to the control group (group A versus group B: 994.819±745.85 ml versus 1847.89±1241.41 ml; P=0.015). However no differences were observed in hospital stay (P=0.282), duration of drain (P=0.207), and incidence of asymptomatic lymphocele at 3 months (P=0.126). Conclusion. The results of this study indicate that the application of fibrin sealants after pelvic and/or para-aortic lymphadenectomy may reduce lymphatic drainage in gynecologic malignancy.
Privacy-Preserving Outsourced Auditing Scheme for Dynamic Data Storage in Cloud
Authors: Tu Tengfei , Rao Lu , Zhang Hua , Wen Qiaoyan , Xiao Jia
Published: November 2017

As information technology develops, cloud storage has been widely accepted for keeping volumes of data. Remote data auditing scheme enables cloud user to confirm the integrity of her outsourced file via the auditing against cloud storage, without downloading the file from cloud. In view of the significant computational cost caused by the auditing process, outsourced auditing model is proposed to make user outsource the heavy auditing task to third party auditor (TPA). Although the first outsourced auditing scheme can protect against the malicious TPA, this scheme enables TPA to have read access right over user’s outsourced data, which is a potential risk for user data privacy. In this paper, we introduce the notion of User Focus for outsourced auditing, which emphasizes the idea that lets user dominate her own data. Based on User Focus, our proposed scheme not only can prevent user’s data from leaking to TPA without depending on data encryption but also can avoid the use of additional independent random source that is very difficult to meet in practice. We also describe how to make our scheme support dynamic updates. According to the security analysis and experimental evaluations, our proposed scheme is provably secure and significantly efficient.
Digital Implementation of an Improved LTE Stream Cipher Snow-3G Based on Hyperchaotic PRNG
Authors: Madani Mahdi , Benkhaddra Ilyas , Tanougast Camel , Chitroub Salim , Sieler Loic
Published: November 2017

SNOW-3G is a stream cipher used by the 3GPP standards as the core part of the confidentiality and integrity algorithms for UMTS and LTE networks. This paper proposes an enhancement of the regular SNOW-3G ciphering algorithm based on HC-PRNG. The proposed cipher scheme is based on hyperchaotic generator which is used as an additional layer to the SNOW-3G architecture to improve the randomness of its output keystream. The objective of this work is to achieve a high security strength of the regular SNOW-3G algorithm while maintaining its standardized properties. The originality of this new scheme is that it provides a good trade-off between good randomness properties, performance, and hardware resources. Numerical simulations, hardware digital implementation, and experimental results using Xilinx FPGA Virtex technology have demonstrated the feasibility and the efficiency of our secure solution while promising technique can be applied to secure the new generation mobile standards. Thorough analysis of statistical randomness is carried out demonstrating the improved statistical randomness properties of the new scheme compared to the standard SNOW-3G, while preserving its resistance against cryptanalytic attacks.
LeptospiraSeroprevalence in Domestic Dogs and Cats on the Caribbean Island of Saint Kitts
Authors: Pratt Nicola , Conan Anne , Rajeev Sreekumari
Published: November 2017

Leptospirosis is an important bacterial zoonotic disease that affects humans and many animal species. Knowledge of prevalence ofLeptospirain a given geographic region supports the implementation of effective control/prevention programmes and thus reduces the transmission risks. This study providesLeptospiraseroprevalence and serovar distribution in dogs and cats on the Caribbean island of Saint Kitts. Convenient serum samples from domestic dogs (n=101) and cats (n=50) were tested by the microscopic agglutination test (MAT) using 21Leptospiraserovars belonging to 17 serogroups. Seroprevalence was recorded at 73.2% in dogs (95% confidence interval CI: 62.5–80.1%). Agglutinating antibodies toLeptospirawere present against 13 of the 21 serovars tested by MAT. The highest seroprevalence was observed for serovar Autumnalis (56.4%) followed by Icterohaemorrhagiae (27.7%), Canicola (17.8%), Djasiman (14.9%), Bratislava (11.9%), Pyrogenes (11.9%), and Pomona (7.9%). A very low seroprevalence (4%, 95% CI: 0.5–14%) was observed in cats. This data confirms that dogs in Saint Kitts have a high-level exposure to a diverse set ofLeptospiraserovars.
Automatic CDR Estimation for Early Glaucoma Diagnosis
Authors: Fernandez-Granero M. A. , Sarmiento A. , Sanchez-Morillo D. , Jiménez S. , Alemany P. , Fondón I.
Published: November 2017

Glaucoma is a degenerative disease that constitutes the second cause of blindness in developed countries. Although it cannot be cured, its progression can be prevented through early diagnosis. In this paper, we propose a new algorithm for automatic glaucoma diagnosis based on retinal colour images. We focus on capturing the inherent colour changes of optic disc (OD) and cup borders by computing several colour derivatives in CIE L∗a∗b∗ colour space with CIE94 colour distance. In addition, we consider spatial information retaining these colour derivatives and the original CIE L∗a∗b∗ values of the pixel and adding other characteristics such as its distance to the OD centre. The proposed strategy is robust due to a simple structure that does not need neither initial segmentation nor removal of the vascular tree or detection of vessel bends. The method has been extensively validated with two datasets (one public and one private), each one comprising 60 images of high variability of appearances. Achieved class-wise-averaged accuracy of 95.02% and 81.19% demonstrates that this automated approach could support physicians in the diagnosis of glaucoma in its early stage, and therefore, it could be seen as an opportunity for developing low-cost solutions for mass screening programs.
Coprophagia in an 8-Year-Old Hospitalized Patient: A Case Report and Review of the Literature
Authors: Bacewicz Aleksandra , Martin Katherine
Published: November 2017

Consult-liaison psychiatrists often encounter difficult clinical scenarios. We present a pediatric case of presumptive coprophagia. After a negative medical work-up, the pediatrics team asked psychiatry to assist them in managing this relatively rare disorder in the hospital setting. Little is known about the etiology and treatment of coprophagia in the pediatric population. Using the case as a catalyst, we discuss what is known about this disorder as well as treatment strategies in the hospital setting.
Modulation of Acupuncture on Cell Apoptosis and Autophagy
Authors: Luo Dan , Chen Rui , Liang Feng-xia
Published: November 2017

Acupuncture has been historically practiced to treat medical disorders by mechanically stimulating specific acupoints. Despite its well‐documented efficacy, its biological basis largely remains elusive. Recent studies suggested that cell apoptosis and autophagy might play key roles in acupuncture therapy. Therefore, we searched PubMed, Embase, Web of Science, and China National Knowledge Infrastructure (CNKI), aiming to find the potential relationship between acupuncture and cell apoptosis and autophagy. To provide readers with objective evidence, some problems regarding the design method, acupoints selection, acupuncture intervention measure, and related diseases existing in 40 related researches were shown in this review. These findings demonstrated that acupuncture has a potential role in modulating cell apoptosis and autophagy in animal models, suggesting it as a candidate mechanism in acupuncture therapy to maintain physiologic homeostasis.
Utility of Single-Cell Genomics in Diagnostic Evaluation of Prostate Cancer
Authors: Alexander Joan , Kendall Jude , McIndoo Jean , Rodgers Linda , Aboukhalil Robert , Levy Dan , Stepansky Asya , Sun Guoli , Chobardjiev Lubomir , Riggs Michael , Cox Hilary , Hakker Inessa , Nowak Dawid G. , Laze Juliana , Llukani Elton , Srivastava Abhishek , Gruschow Siobhan , Yadav Shalini S. , Robinson Brian , Atwal Gurinder , Trotman Lloyd C. , Lepor Herbert , Hicks James , Wigler Michael , Krasnitz Alexander
Published: November 2017

A distinction between indolent and aggressive disease is a major challenge in diagnostics of prostate cancer. As genetic heterogeneity and complexity may influence clinical outcome, we have initiated studies on single tumor cell genomics. In this study, we demonstrate that sparse DNA sequencing of single-cell nuclei from prostate core biopsies is a rich source of quantitative parameters for evaluating neoplastic growth and aggressiveness. These include the presence of clonal populations, the phylogenetic structure of those populations, the degree of the complexity of copy-number changes in those populations, and measures of the proportion of cells with clonal copy-number signatures. The parameters all showed good correlation to the measure of prostatic malignancy, the Gleason score, derived from individual prostate biopsy tissue cores. Remarkably, a more accurate histopathologic measure of malignancy, the surgical Gleason score, agrees better with these genomic parameters of diagnostic biopsy than it does with the diagnostic Gleason score and related measures of diagnostic histopathology. This is highly relevant because primary treatment decisions are dependent upon the biopsy and not the surgical specimen. Thus, single-cell analysis has the potential to augment traditional core histopathology, improving both the objectivity and accuracy of risk assessment and inform treatment decisions.

Significance: Genomic analysis of multiple individual cells harvested from prostate biopsies provides an indepth view of cell populations comprising a prostate neoplasm, yielding novel genomic measures with the potential to improve the accuracy of diagnosis and prognosis in prostate cancer. Cancer Res; 78(2); 348–58. ©2017 AACR.
Distinct TP63 Isoform-Driven Transcriptional Signatures Predict Tumor Progression and Clinical Outcomes
Authors: Abbas Hussein A. , Bui Ngoc Hoang Bao , Rajapakshe Kimal , Wong Justin , Gunaratne Preethi , Tsai Kenneth Y. , Coarfa Cristian , Flores Elsa R.
Published: November 2017

TP63 is required to maintain stem cell pluripotency and suppresses the metastatic potential of cancer cells through multiple mechanisms. These functions are differentially regulated by individual isoforms, necessitating a deeper understanding of how the distinct transcriptional programs controlled by these isoforms affect cancer progression and outcomes. In this study, we conducted a pan-cancer analysis of The Cancer Genome Atlas to identify transcriptional networks regulated by TAp63 and ΔNp63 using transcriptomes derived from epidermal cells of TAp63−/− and ΔNp63−/− mice. Analysis of 17 cancer developmental and 27 cancer progression signatures revealed a consistent tumor suppressive pattern for TAp63. In contrast, we identified pleiotropic roles for ΔNp63 in tumor development and found that its regulation of Lef1 was crucial for its oncogenic role. ΔNp63 performed a distinctive role as suppressor of tumor progression by cooperating with TAp63 to modulate key biological pathways, principally cell-cycle regulation, extracellular matrix remodeling, epithelial-to-mesenchymal transition, and the enrichment of pluripotent stem cells. Importantly, these TAp63 and ΔNp63 signatures prognosticated progression and survival, even within specific stages, in bladder and renal carcinomas as well as low-grade gliomas. These data describe a novel approach for understanding transcriptional activities of TP63 isoforms across a large number of cancer types, potentially enabling identification of patient subsets most likely to benefit from therapies predicated on manipulating specific TP63 isoforms.

Significance: Transcriptomic analyses of patient samples and murine knockout models highlight the prognostic role of several critical mechanisms of tumor suppression that are regulated by TP63. Cancer Res; 78(2); 451–62. ©2017 AACR.