bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial and Temporal Quantification of Community Resilience: Gotham City under Attack
Authors: Mahmoud Hussam , Chulahwat Akshat 
Published: November 2017

AbstractMitigating the impact of disasters on communities requires not only a deep understanding of the essential features of infrastructure, social, and economical components that make a community resilient; but also the development of mathematical models that can seamlessly integrate these features. This article lays the foundation for an integrative model that captures interaction between these components. The underlying fundamentals of the proposed model hinges on the principle of a damped harmonic oscillator by assuming the behavior of a community in response to a hazard is equivalent to the response of a vibrating mass of finite stiffness and damping. We implemented the dynamic model by developing a novel finite element formulation capable of quantifying resilience both temporally and spatially. We then used the developed model to devise a suitable hazard‐agnostic definition of community resilience. This was realized through a set of demonstration and logical verification tests conducted on Gotham City, the fictional city of the infamous character, Batman. It was observed that the model can be used to identify sensitive and vulnerable areas in a community, provide a spatial and temporal quantification of community resilience, and accommodate various types of hazards such as physical disruptions, economic downtimes, and even social disorders.
Clostridium butyricum exerts a neuroprotective effect in a mouse model of traumatic brain injury via the gut‐brain axis
Authors: Li H. , Sun J. , Du J. , Wang F. , Fang R. , Yu C. , Xiong J. , Chen W. , Lu Z. , Liu J. 
Published: November 2017

AbstractBackgroundTraumatic brain injury (TBI) is a common occurrence following gastrointestinal dysfunction. Recently, more and more attentions are being focused on gut microbiota in brain and behavior. Glucagon‐like peptide‐1 (GLP‐1) is considered as a mediator that links the gut‐brain axis. The aim of this study was to explore the neuroprotective effects of Clostridium butyricum (Cb) on brain damage in a mouse model of TBI.MethodsMale C57BL/6 mice were subjected to a model of TBI‐induced by weight‐drop impact head injury and were treated intragastrically with Cb. The cognitive deficits, brain water content, neuronal death, and blood‐brain barrier (BBB) permeability were evaluated. The expression of tight junction (TJ) proteins, Bcl‐2, Bax, GLP‐1 receptor (GLP‐1R), and phosphorylation of Akt (p‐Akt) in the brain were also measured. Moreover, the intestinal barrier permeability, the expression of TJ protein and GLP‐1, and IL‐6 level in the intestine were detected.ResultsCb treatment significantly improved neurological dysfunction, brain edema, neurodegeneration, and BBB impairment. Meanwhile, Cb treatment also significantly increased the expression of TJ proteins (occludin and zonula occluden‐1), p‐Akt and Bcl‐2, but decreased expression of Bax. Moreover, Cb treatment exhibited more prominent effects on decreasing the levels of plasma d‐lactate and colonic IL‐6, upregulating expression of Occludin, and protecting intestinal barrier integrity. Furthermore, Cb‐treated mice showed increased the secretion of intestinal GLP‐1 and upregulated expression of cerebral GLP‐1R.ConclusionsOur findings demonstrated the neuroprotective effect of Cb in TBI mice and the involved mechanisms were partially attributed to the elevating GLP‐1 secretion through the gut‐brain axis.
Comparison of multiple regression analysis using dummy variables and a NARX network model: an example of a heavy metal adsorption process
Authors: Bingöl Deniz , Xiyili Haibibu , Elevli Sermin , Kılıç Erdal , Çetintaş Seda 
Published: November 2017

AbstractIn the present study, the adsorption characteristics of coal fly ash obtained from the Kangal Power Plant, Turkey and activated fly ash in the planetary ball mill were investigated to remove the heavy metal ions from aqueous solutions. The adsorption capacity was compared for the first time using a multiple regression analysis with dummy variables and a non‐linear auto regressive exogenous (NARX) network model. An equation was obtained for all types of adsorbents or heavy metals using the regression of qe on the dummy variables. The predictive ability of NARX was found to be better than that of multiple regression using dummy variables. These models can also be successfully implemented on the experimental data to evaluate the adsorption process. In addition, fly ash is a low cost alternative since it is a more economical and environmentally friendly adsorbent and it is abundant in both nature and from waste material from industry.
Development and Validation of a Real-Time PCR Assay for Rapid Detection of Candida auris from Surveillance Samples
Authors: Leach L. , Zhu Y. , Chaturvedi S. 
Published: November 2017

ABSTRACT

Candida auris
is an emerging multidrug-resistant yeast causing invasive health care-associated infection with high mortality worldwide. Rapid identification of
C. auris
is of primary importance for the implementation of public health measures to control the spread of infection. To achieve these goals, we developed and validated a TaqMan-based real-time PCR assay targeting the internal transcribed spacer 2 (
ITS
2) region of the ribosomal gene. The assay was highly specific, reproducible, and sensitive, with the detection limit of 1
C. auris
CFU/PCR. The performance of the
C. auris
real-time PCR assay was evaluated by using 623 surveillance samples, including 365 patient swabs and 258 environmental sponges. Real-time PCR yielded positive results from 49 swab and 58 sponge samples, with 89% and 100% clinical sensitivity with regard to their respective culture-positive results. The real-time PCR also detected
C. auris
DNA from 1% and 12% of swab and sponge samples with culture-negative results, indicating the presence of dead or culture-impaired
C. auris
. The real-time PCR yielded results within 4 h of sample processing, compared to 4 to 14 days for culture, reducing turnaround time significantly. The new real-time PCR assay allows for accurate and rapid screening of
C. auris
and can increase effective control and prevention of this emerging multidrug-resistant fungal pathogen in health care facilities.
Type III Interferon Restriction by Porcine Epidemic Diarrhea Virus and the Role of Viral Protein nsp1 in IRF1 Signaling
Authors: Zhang Qingzhan , Ke Hanzhong , Blikslager Anthony , Fujita Takashi , Yoo Dongwan 
Published: November 2017

ABSTRACT
Type III interferons (IFNs) play a vital role in maintaining the antiviral state of the mucosal epithelial surface in the gut, and in turn, enteric viruses may have evolved to evade the type III IFN responses during infection. To study the possible immune evasion of the type III IFN response by porcine epidemic diarrhea virus (PEDV), a line of porcine intestinal epithelial cells was developed as a cell model for PEDV replication. IFN-λ1 and IFN-λ3 inhibited PEDV replication, indicating the anti-PEDV activity of type III IFNs. Of the 21 PEDV proteins, nsp1, nsp3, nsp5, nsp8, nsp14, nsp15, nsp16, open reading frame 3 (ORF3), E, M, and N were found to suppress type III IFN activities, and IRF1 (interferon regulatory factor 1) signaling mediated the suppression. PEDV specifically inhibited IRF1 nuclear translocation. The peroxisome is the innate antiviral signaling platform for the activation of IRF1-mediated IFN-λ production, and the numbers of peroxisomes were found to be decreased in PEDV-infected cells. PEDV nsp1 blocked the nuclear translocation of IRF1 and reduced the number of peroxisomes to suppress IRF1-mediated type III IFNs. Mutational studies showed that the conserved residues of nsp1 were crucial for IRF1-mediated IFN-λ suppression. Our study for the first time provides evidence that the porcine enteric virus PEDV downregulates and evades IRF1-mediated type III IFN responses by reducing the number of peroxisomes.

IMPORTANCE
Porcine epidemic diarrhea virus (PEDV) is a highly contagious enteric coronavirus that emerged in swine in the United States and has caused severe economic losses. PEDV targets intestinal epithelial cells in the gut, and intestinal epithelial cells selectively induce and respond to the production of type III interferons (IFNs). However, little is known about the modulation of the type III IFN response by PEDV in intestinal epithelial cells. In this study, we established a porcine intestinal epithelial cell model for PEDV replication. We found that PEDV inhibited IRF1-mediated type III IFN production by decreasing the number of peroxisomes in porcine intestinal epithelial cells. We also demonstrated that the conserved residues in the PEDV nsp1 protein were crucial for IFN suppression. This study for the first time shows PEDV evasion of the type III IFN response in intestinal epithelial cells, and it provides valuable information on host cell-virus interactions not only for PEDV but also for other enteric viral infections in swine.
Exosomes Mediate Intercellular Transmission of Porcine Reproductive and Respiratory Syndrome Virus
Authors: Wang Ting , Fang Liurong , Zhao Fuwei , Wang Dang , Xiao Shaobo 
Published: November 2017

ABSTRACT

Exosomes are small membrane-enclosed vesicles produced by various cells and actively released into the extracellular space. They participate in intercellular communication and transfer of biologically active proteins, lipids, and nucleic acids. Accumulating evidence suggests that exosomes derived from cells infected by some viruses selectively encapsulate viral proteins, genetic materials, or even virions to mediate cell-to-cell communication and/or virus transmission. Porcine reproductive and respiratory syndrome virus (PRRSV) is an
Arterivirus
that has been devastating the global swine industry since the late 1980s. Recent studies have shown that major proteins secreted from PRRSV-infected cells are exosomal proteins and that the serum-derived exosomes from PRRSV-infected pigs contain viral proteins. However, the role of exosomes in PRRSV infection remains unclear. In this study, purified exosomes isolated from PRRSV-infected cells were shown with reverse transcription-PCR and mass spectrometry to contain viral genomic RNA and partial viral proteins. Furthermore, exosomes from PRRSV-infected cells established productive infection in both PRRSV-susceptible and -nonsusceptible cells. More importantly, exosome-mediated infection was not completely blocked by PRRSV-specific neutralizing antibodies. In summary, this study demonstrated that exosomes can mediate PRRSV transmission and are even resistant to antibody neutralization, identifying a potential immune evasion mechanism utilized by PRRSV.

IMPORTANCE
Exosomes have recently been characterized as bioactive vesicles that function to promote intercellular communication. The exosomes from virally infected cells containing altered compositions confer numerous novel functionalities. A study of the secretome of cells infected with PRRSV indicated that the exosomal pathway is strongly activated by PRRSV infection. Here, we demonstrate that PRRSV can utilize host exosomes to infect naive healthy cells. Furthermore, exosome-mediated viral transmission is largely resistant to PRRSV-specific neutralizing antibodies. Our study provides novel insights into an alternative mechanism of PRRSV transmission that can compromise the host's anti-PRRSV immune response.
Microbial Community Structure and Arsenic Biogeochemistry in Two Arsenic-Impacted Aquifers in Bangladesh
Authors: Gnanaprakasam Edwin T. , Lloyd Jonathan R. , Boothman Christopher , Ahmed Kazi Matin , Choudhury Imtiaz , Bostick Benjamin C. , van Geen Alexander , Mailloux Brian J. 
Published: November 2017

ABSTRACT
Long-term exposure to trace levels of arsenic (As) in shallow groundwater used for drinking and irrigation puts millions of people at risk of chronic disease. Although microbial processes are implicated in mobilizing arsenic from aquifer sediments into groundwater, the precise mechanism remains ambiguous. The goal of this work was to target, for the first time, a comprehensive suite of state-of-the-art molecular techniques in order to better constrain the relationship between indigenous microbial communities and the iron and arsenic mineral phases present in sediments at two well-characterized arsenic-impacted aquifers in Bangladesh. At both sites, arsenate [As(V)] was the major species of As present in sediments at depths with low aqueous As concentrations, while most sediment As was arsenite [As(III)] at depths with elevated aqueous As concentrations. This is consistent with a role for the microbial As(V) reduction in mobilizing arsenic. 16S rRNA gene analysis indicates that the arsenic-rich sediments were colonized by diverse bacterial communities implicated in both dissimilatory Fe(III) and As(V) reduction, while the correlation analyses involved phylogenetic groups not normally associated with As mobilization. Findings suggest that direct As redox transformations are central to arsenic fate and transport and that there is a residual reactive pool of both As(V) and Fe(III) in deeper sediments that could be released by microbial respiration in response to hydrologic perturbation, such as increased groundwater pumping that introduces reactive organic carbon to depth.

IMPORTANCE
The consumption of arsenic in waters collected from tube wells threatens the lives of millions worldwide and is particularly acute in the floodplains and deltas of southern Asia. The cause of arsenic mobilization from natural sediments within these aquifers to groundwater is complex, with recent studies suggesting that sediment-dwelling microorganisms may be the cause. In the absence of oxygen at depth, specialist bacteria are thought able to use metals within the sediments to support their metabolism. Via these processes, arsenic-contaminated iron minerals are transformed, resulting in the release of arsenic into the aquifer waters. Focusing on a field site in Bangladesh, a comprehensive, multidisciplinary study using state-of-the-art geological and microbiological techniques has helped better understand the microbes that are present naturally in a high-arsenic aquifer and how they may transform the chemistry of the sediment to potentially lethal effect.
Forward Genetics Approach Reveals Host Genotype-Dependent Importance of Accessory Chromosomes in the Fungal Wheat Pathogen
Zymoseptoria tritici
Authors: Habig Michael , Quade Jakob , Stukenbrock Eva Holtgrewe 
Published: November 2017

ABSTRACT

The fungal wheat pathogen
Zymoseptoria tritici
possesses a large complement of accessory chromosomes showing presence/absence polymorphism among isolates. These chromosomes encode hundreds of genes; however, their functional role and why the chromosomes have been maintained over long evolutionary times are so far not known. In this study, we addressed the functional relevance of eight accessory chromosomes in reference isolate IPO323. We induced chromosome losses by inhibiting the β-tubulin assembly during mitosis using carbendazim and generated several independent isogenic strains, each lacking one of the accessory chromosomes. We confirmed chromosome losses by electrophoretic karyotyping and whole-genome sequencing. To assess the importance of the individual chromosomes during host infection, we performed
in planta
assays comparing disease development results in wild-type and chromosome mutant strains. Loss of the accessory chromosomes 14, 16, 18, 19, and 21 resulted in increased virulence on wheat cultivar Runal but not on cultivars Obelisk, Titlis, and Riband. Moreover, some accessory chromosomes affected the switch from biotrophy to necrotrophy as strains lacking accessory chromosomes 14, 18, 19, and 21 showed a significantly earlier onset of necrosis than the wild type on the Runal cultivar. In general, we observed that the timing of the lifestyle switch affects the fitness of
Z. tritici
. Taking the results together, this study was the first to use a forward-genetics approach to demonstrate a cultivar-dependent functional relevance of the accessory chromosomes of
Z. tritici
during host infection.

IMPORTANCE
Zymoseptoria tritici
is a prominent fungal pathogen of wheat of worldwide distribution. This fungus shows a remarkable genome organization, with a large number of chromosomes that are present in only some isolates and therefore considered to be “accessory” chromosomes. To date, the function of these accessory chromosomes in
Z. tritici
has been unknown, although their maintenance in the species over evolutionary times suggests a functional relevance. Here we deleted whole accessory chromosomes to test the effect of these chromosomes on host specificity and virulence of the fungus. We show for the first time that some accessory chromosomes of
Z. tritici
affect the fitness of the fungus during host infection in a cultivar-dependent manner. These results show that the accessory chromosomes encode host-specific virulence determinants having a negative effect on fitness. Understanding the population dynamic of the accessory chromosomes and the molecular interaction of pathogen and plant traits is crucial to improve wheat-breeding strategies.
Classical and quantum dynamics of higher-derivative systems
Authors: Smilga Andrei 
Published: November 2017

A brief review of the physics of systems including higher derivatives in the Lagrangian is given. All such systems involve ghosts, i.e. the spectrum of the Hamiltonian is not bounded from below and the vacuum ground state is absent. Usually, this leads to collapse and loss of unitarity. In certain special cases, this does not happen, however, ghosts are benign. We speculate that the Theory of Everything is a higher-derivative field theory, characterized by the presence of such benign ghosts and defined in a higher-dimensional bulk. Our Universe then represents a classical solution in this theory, having the form of a 3-brane embedded in the bulk.
CROWDING AND LIGHT LIMITATION AFFECT PHYTOPLANKTON COMPETITION FOR NITROGEN
Authors: KHONTHAPAGDEE SUBHORN , PILYUGIN SERGEI S. 
Published: November 2017

We consider a chemostat model of phytoplankton competing for nitrogen taking into account effects of both intra- and interspecific crowding and the light limitation. We consider crowding as an additive density-dependent mortality rate. Crowding effects may be classified into intra- and interspecific crowding depending on whether the additional mortality is caused by the same or alternate species. We analyze the existence and local and global stability of single species and coexistence equilibria using the linearization and stability method of Lyapunov. We present a numerical example illustrating the fact that the crowding effects may lead to the bistable coexistence of two phytoplankton species. We demonstrate that the crowding effects and the light limitation affect the outcome of exploitative competition for a single resource and promote coexistence. We also show that while the crowding has a stabilizing effect on phytoplankton community, the light limitation may destabilize the system and produce sustained oscillations.
Tafoni and honeycomb structures as indicators of ascending fluid flow and hypogene karstification
Authors: Klimchouk Alexander 
Published: November 2017

Abstract
Tafoni and honeycombs remain some of the most enigmatic and puzzling geomorphological phenomena. Their globally widespread occurrence across a wide range of lithologies and environmental conditions suggests that their formation is determined by a factor that overarches variations in these conditions and weathering processes. Based on a study of tafoni and honeycombs in the Crimean Piedmont, this paper demonstrates that the primary factor in their formation is the pre-exposure alteration of rocks along fractures and karst conduits as a result of fluid–rock interactions. Such alteration is commonly induced by ascending flow and is related to hypogene karstification. The morphological expression of cavernous features through removal of the alterite can occur under subsurface conditions, but is more frequent on exposure to atmospheric weathering. The local or regional characteristics of a weathering system are irrelevant or of only secondary importance in determining the localization and morphology of cavernous features. New features do not form on rock surfaces where the alteration zone was totally denuded or never present. The proposed model resolves major issues inherent to previous interpretations of cavernous features. It has general applicability and important implications for geodynamic and palaeohydrogeological reconstructions. Typical tafoni and honeycombs may indicate past events of ascending flow and the potential presence of hypogene karst systems.
Modeling the Subclonal Evolution of Cancer Cell Populations
Authors: Chowell Diego , Napier James , Gupta Rohan , Anderson Karen S. , Maley Carlo C. , Sayres Melissa A. Wilson 
Published: November 2017

Abstract
Increasing evidence shows that tumor clonal architectures are often the consequence of a complex branching process, yet little is known about the expected dynamics and extent to which these divergent subclonal expansions occur. Here, we develop and implement more than 88,000 instances of a stochastic evolutionary model simulating genetic drift and neoplastic progression. Under different combinations of population genetic parameter values, including those estimated for colorectal cancer and glioblastoma multiforme, the distribution of sizes of subclones carrying driver mutations had a heavy right tail at the time of tumor detection, with only 1 to 4 dominant clones present at ≥10% frequency. In contrast, the vast majority of subclones were present at &lt;10% frequency, many of which had higher fitness than currently dominant clones. The number of dominant clones (≥10% frequency) in a tumor correlated strongly with the number of subclones (&lt;10% of the tumor). Overall, these subclones were frequently below current standard detection thresholds, frequently harbored treatment-resistant mutations, and were more common in slow-growing tumors.
Significance: The model presented in this paper addresses tumor heterogeneity by framing expectations for the number of resistant subclones in a tumor, with implications for future studies of the evolution of therapeutic resistance. Cancer Res; 78(3); 830–9. ©2017 AACR.
The E3 Ligase RING1 Targets p53 for Degradation and Promotes Cancer Cell Proliferation and Survival
Authors: Shen Jiajia , Li Pengyu , Shao Xuejing , Yang Yang , Liu Xiujun , Feng Min , Yu Qiang , Hu Ronggui , Wang Zhen 
Published: November 2017

Abstract
As a component of the transcriptional repression complex 1 (PRC1), the ring finger protein RING1 participates in the epigenetic regulation in cancer. However, the contributions of RING1 to cancer etiology or development are unknown. In this study, we report that RING1 is a critical negative regulator of p53 homeostasis in human hepatocellular and colorectal carcinomas. RING1 acts as an E3 ubiquitin (Ub) ligase to directly interact with and ubiquitinate p53, resulting in its proteasome-dependent degradation. The RING domain of RING1 was required for its E3 Ub ligase activity. RING1 depletion inhibited the proliferation and survival of the p53 wild-type cancer cells by inducing cell-cycle arrest, apoptosis, and senescence, with only modest effects on p53-deficient cells. Its growth inhibitory effect was partially rescued by p53 silencing, suggesting an important role for the RING1–p53 complex in human cancer. In clinical specimens of hepatocellular carcinoma, RING1 upregulation was evident in association with poor clinical outcomes. Collectively, our results elucidate a novel PRC1-independent function of RING1 and provide a mechanistic rationale for its candidacy as a new prognostic marker and/or therapeutic target in human cancer.
Significance: These results elucidate a novel PRC1-independent function of RING1 and provide a mechanistic rationale for its candidacy as a new prognostic marker and/or therapeutic target in human cancer. Cancer Res; 78(2); 359–71. ©2017 AACR.