bluuebunny/crossref_metadata_2025 huggingface dataset:
The Tupac Amaru Rebellion
Authors: Walker Charles
Published: July 2016

The Tupac Amaru Rebellion raged across the Andes from 1780 to 1783. Centered in southern Peru, from Cuzco to Lake Titicaca, it also allied with the Katarista uprisings in Upper Peru (Bolivia). In addition, revolts inspired by Tupac Amaru took place in what became Argentina, Chile, and Colombia. José Gabriel Condorcanqui was a kuraka or ethnic intermediary in three small towns sixty miles south of Cuzco and a merchant who worked the Cuzco to Potosí circuit. Well educated and bilingual (Spanish and Quechua), he claimed lineage from the Incas, thus the Tupac Amaru (e.g., Tupa or Túpac, Amaro) name. His wife, Micaela Bastidas, was an important commander in the uprising, overseeing the rebel base in Pampamarca and logistics. The rebellion began in November 1780 when Tupac Amaru seized and executed a local authority, the corregidor Antonio Arriaga. Tupac Amaru organized his indigenous followers and attacked other corregidors, ransacked haciendas, and razed the hated obrajes, or textile mills. He claimed to be fighting in the name of the King of Spain. He and Micaela sought a multiethnic and multiclass alliance, recruiting not only Indians but also mestizos, blacks, Creoles, and “good” Spaniards. Tupac Amaru returned from the Lake Titicaca in late 1780 to lay siege to the city of Cuzco, Peru’s second-largest city and still considered the by many to be the “Inca capital.” Although he surrounded Cuzco with tens of thousands of troops, the rebels could not take the city. The royalists received important reinforcements from Lima in early January. After three months of intense fighting, they captured Tupac Amaru, Micaela Bastidas, and much of their inner circle in April 1781, executing them in a gruesome public ritual in Cuzco’s central plaza on 17 May. Led by Tupac Amaru’s cousin, Diego Cristóbal Tupac Amaru, their son Mariano, and another relative, the rebellion continued for two years, centered in the area around Lake Titicaca. The rebellion became more of a caste or total war as neither side took prisoners. The exhausted rebel leaders signed an armistice in early 1783, but hardline royalists broke the treaty and executed Diego Cristóbal in even more horrific fashion than Tupac Amaru and Micaela Bastidas. Tupac Amaru became a hero in Peru. He became even more famous in 1968 when General Velasco Alvarado’s military regime made Tupac Amaru its icon. The Tupamaro (Uruguay) and MRTA (Peru) guerrilla groups as well as the rapper Tupac Amaru Shakur are named after him.
Information Structure
Authors: Zimmermann Malte
Published: July 2016

The term information structure refers to the interface between the structure and meaning of linguistic utterances, on the one hand, and the interlocutors’ mental representations of information, discourse referents, and the overall universe of discourse, on the other. It is at this interfacing level of mental representation that linguistic rules and constraints on structure-building, interpretation, and processing interact with general cognitive processes involved in belief formation, such as memory, attention, pragmatic reasoning, and general inference processes. Information structure plays a crucial role in embedding linguistic utterances in ever-changing communicative settings and contexts, and it does so by imposing structure on the ways in which the information conveyed by an utterance is linguistically expressed. Information structure is responsible for an efficient information transfer between interlocutors, where information transfer consists in the updating of the interlocutors’ mental models of the world, and in the establishment of mutually shared knowledge bases (common grounds) through the exchange of linguistic utterances. A central observation is that linguistically coded information is structured in a specific way, such that it fits the context of the utterance and the knowledge states of the discourse participants. The information structure of linguistic utterances is typically reflected in their grammatical form. Linguistic marking of information structure facilitates information update and the actualization of belief states. For this reason, information structure, in the general sense, is often characterized in terms of information packaging or content management. In a more narrow sense, information structure refers to the concrete structural realization of information structure categories in linguistic utterances. The information structure categories themselves are taken to be universal, whereas their formal reflexes in the grammatical systems of natural languages are subject to cross-linguistic variation. The categories of information structure are organized along several independent but interacting dimensions, namely focus-background, topic-comment, and given-new. Some scholars assume an additional category of contrast, whereas others treat contrast as a pragmatic epiphenomenon, which is dependent on focus. Under certain conditions, information structure can directly affect the semantic interpretation of clauses. This is observed with focus-sensitive elements, which change the truth-conditions of sentences or trigger additional presuppositions. A further interpretive effect is often found with noncanonical sentence structures, which typically express a marked state of affairs from the perspective of information structure, and which frequently give rise to conversational implicatures. Finally, the interfacing nature of information structure between language and cognition makes it an important research topic in psycholinguistics, neurolinguistics, language acquisition, and historical linguistics.
On the independent loci assumption in phylogenomic studies
Authors: Jennings W. Bryan
Published: July 2016

Studies using multi-locus coalescent methods to infer species trees or historical demographic parameters usually require the assumption that the gene tree for each locus (or SNP) is genealogically independent from the gene trees of other sampled loci. In practice, however, researchers have used two different criteria to delimit independent loci in phylogenomic studies. The first criterion, which directly addresses the condition of genealogical independence of sampled loci, considers the long-term effects of homologous recombination and effective population size on linkage between two loci. In contrast, the second criterion, which only considers the single-generation effects of recombination in the meioses of individuals, identifies sampled loci as being independent of each other if they undergo Mendelian independent assortment. Methods that use these criteria to estimate the number of independent loci per genome as well as intra-chromosomal “distance thresholds” that can be used to delimit independent loci in phylogenomic datasets are reviewed. To compare the efficacy of each criterion, they are applied to two species (an invertebrate and vertebrate) for which relevant genetic and genomic data are available. Although the independent assortment criterion is relatively easy to apply, the results of this study show that it is overly conservative and therefore its use would unfairly restrict the sizes of phylogenomic datasets. It is therefore recommended that researchers only refer togenealogicallyindependent loci when discussing the independent loci assumption in phylogenomics and avoid using terms that may conflate this assumption with independent assortment. Moreover, whenever feasible, researchers should use methods for delimiting putatively independent loci that take into account both homologous recombination and effective population size (i.e., long-term effective recombination).
Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation
Authors: Vandenbon Alexis , Kumagai Yutaro , Suzuki Yutaka , Nakai Kenta
Published: July 2016

Background

The importance of transcription factors (TFs) and epigenetic modifications in the control of gene expression is widely accepted. However, causal relationships between changes in TF binding, histone modifications, and gene expression during the response to extracellular stimuli are not well understood. Here, we analyzed the ordering of these events on a genome-wide scale in dendritic cells (DCs) in response to lipopolysaccharide (LPS) stimulation.

Results

Using a ChIP-seq time series dataset, we found that the LPS-induced accumulation of different histone modifications follow clearly distinct patterns. Increases in H3K4me3 appear to coincide with transcriptional activation. In contrast, H3K9K14ac accumulates early after stimulation, and H3K36me3 at later time points. Integrative analysis with TF binding data revealed potential links between TF activation and dynamics in histone modifications. Especially, LPS-induced increases in H3K9K14ac and H3K4me3 were associated with binding by STAT1/2, and were severely impaired inStat1-/-cells.

Conclusions

While the timing of short-term changes of some histone modifications coincides with changes in transcriptional activity, this is not the case for others. In the latter case, dynamics in modifications more likely reflect strict regulation by stimulus-induced TFs, and their interactions with chromatin modifiers.
Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations
Authors: Brammeld Jonathan S. , Petljak Mia , Martincorena Inigo , Williams Steven P. , Garcia Alonso Luz , Dalmases Alba , Bellosillo Beatriz , Robles-Espinoza Carla Daniela , Price Stacey , Barthorpe Syd , Tarpey Patrick , Alifrangis Constantine , Bignell Graham , Vidal Joana , Young Jamie , Stebbings Lucy , Beal Kathryn , Stratton Michael R , Saez-Rodriguez Julio , Garnett Mathew , Montagut Clara , Iorio Francesco , McDermott Ultan
Published: July 2016

Drug resistance is an almost inevitable consequence of cancer therapy and ultimately proves fatal for the majority of patients. In many cases this is the consequence of specific gene mutations that have the potential to be targeted to re-sensitize the tumor. The ability to uniformly saturate the genome with point mutations without chromosome or nucleotide sequence context bias would open the door to identify all putative drug resistance mutations in cancer models. Here we describe such a method for elucidating drug resistance mechanisms using genome-wide chemical mutagenesis allied to next-generation sequencing. We show that chemically mutagenizing the genome of cancer cells dramatically increases the number of drug-resistant clones and allows the detection of both known and novel drug resistance mutations. We have developed an efficient computational process that allows for the rapid identification of involved pathways and druggable targets. Such a priori knowledge would greatly empower serial monitoring strategies for drug resistance in the clinic as well as the development of trials for drug resistant patients.
Cytomegalovirus Antigenic Mimicry of Human Alloreactive Peptides: A Potential Trigger for Graft versus Host Disease
Authors: Hall Charles , Koparde Vishal , Jameson-Lee Max , Elnasseh Abdelrhman , Scalora Allison , Kobulnicky Jared , Serrano Myrna , Roberts Catherine , Buck Gregory , Neale Micheal , Nixon Daniel , Toor Amir
Published: July 2016

The association between human cytomegalovirus (hCMV) reactivation and the development of graft-versus-host-disease (GVHD) has been observed in stem cell transplantation (SCT). Seventy seven SCT donor-recipient pairs (DRP) (HLA matched unrelated donor (MUD), n=50; matched related donor (MRD), n=27) underwent whole exome sequencing to identify single nucleotide polymorphisms (SNPs) generating alloreactive peptide libraries for each DRP (9-mer peptide-HLA complexes); Human CMV CROSS (Cross-Reactive Open Source Sequence) Database was compiled from NCBI; HLA class I binding affinity for each DRPs HLA was calculated by NetMHCpan 2.8 and hCMV-derived 9-mers algorithmically compared to the alloreactive peptide-HLA complex libraries. Short consecutive (≥6) amino acid (AA) sequence homology matching hCMV to recipient peptides was considered for HLA-bound-peptide (IC50<500nM) cross reactivity. Of the 70,686 hCMV 9-mers contained within the hCMV CROSS database, 29,658.8 ± 9038.5 were found to match MRD DRP alloreactive peptides and 52,910.2 ± 16121.8 matched MUD DRP peptides (Student’s T-test, p<0.001).In silicoanalysis revealed multiple high affinity, immunogenic CMV-Human peptide matches (IC50<500 nM) expressed in GVHD-affected tissue-specific manner (proteins expressed at ≥10 RPKM). hCMV+GVHD was found in 18 patients, 13 developing hCMV viremia before GVHD onset with a subset analysis of 7 instances of hCMV viremia prior to acute GVHD onset (n=3), chronic GVHD (n=2) and acute + chronic GVHD (n=2) indicating cross reactive peptide expression within affected organs. We propose that based on our analysis and preliminary clinical correlations that hCMV immune cross-reactivity may cause antigenic mimicry of human alloreactive peptides triggering GVHD.
Genome Editing With Targeted Deaminases
Authors: Yang Luhan , Briggs Adrian W. , Chew Wei Leong , Mali Prashant , Guell Marc , Aach John , Goodman Daniel Bryan , Cox David , Kan Yinan , Lesha Emal , Soundararajan Venkataramanan , Zhang Feng , Church George
Published: July 2016

Precise genetic modifications are essential for biomedical research and gene therapy. Yet, traditional homology-directed genome editing is limited by the requirements for DNA cleavage, donor DNA template and the endogenous DNA break-repair machinery. Here we present programmable cytidine deaminases that enable site-specific cytidine to thymidine (C-to-T) genomic edits without the need for DNA cleavage. Our targeted deaminases are efficient and specific inEscherichia coli, converting a genomic C-to-T with 13% efficiency and 95% accuracy. Edited cells do not harbor unintended genomic abnormalities. These novel enzymes also function in human cells, leading to a site-specific C-to-T transition in 2.5% of cells with reduced toxicity compared with zinc-finger nucleases. Targeted deaminases therefore represent a platform for safer and effective genome editing in prokaryotes and eukaryotes, especially in systems where DSBs are toxic, such as human stem cells and repetitive elements targeting.
Sensitivity in binding free energies due to protein reorganization
Authors: Lim Nathan M. , Wang Lingle , Abel Robert , Mobley David L.
Published: July 2016

Tremendous recent improvements in computer hardware, coupled with advances in sampling techniques and force fields, are now allowing protein-ligand binding free energy calculations to be routinely used to aid pharmaceutical drug discovery projects. However, despite these recent innovations, there are still needs for further improvement in sampling algorithms to more adequately sample protein motion relevant to protein-ligand binding. Here, we report our work identifying and studying such clear and remaining needs in the apolar cavity of T4 Lysozyme L99A. In this study, we model recent experimental results that show the progressive opening of the binding pocket in response to a series of homologous ligands.1Even while using enhanced sampling techniques, we demonstrate that the predicted relative binding free energies (RBFE) are sensitive to the initial protein conformational state. Particularly, we highlight the importance of sufficient sampling of protein conformational changes and demonstrate how inclusion of three key protein residues in the ‘hot’ region of the FEP/REST simulation improves the sampling and resolves this sensitivity.
Loss of l(3)mbt leads to acquisition of the ping-pong cycle in Drosophila ovarian somatic cells
Authors: Sumiyoshi Tetsutaro , Sato Kaoru , Yamamoto Hitomi , Iwasaki Yuka W. , Siomi Haruhiko , Siomi Mikiko C.
Published: July 2016

In Drosophila germ cells, PIWI-interacting RNAs (piRNAs) are amplified through a PIWI slicer-dependent feed-forward loop termed the ping-pong cycle, yielding secondary piRNAs. However, the detailed mechanism remains poorly understood, largely because an ex vivo model system amenable to biochemical analyses has not been available. Here, we show that CRISPR-mediated loss of function of lethal (3) malignant brain tumor [l(3)mbt] leads to ectopic activation of the germ-specific ping-pong cycle in ovarian somatic cells. Perinuclear foci resembling nuage, the ping-pong center, appeared following l(3)mbt mutation. This activation of the ping-pong machinery in cultured cells will greatly facilitate elucidation of the mechanism underlying secondary piRNA biogenesis in Drosophila.
Molecular basis for oncohistone H3 recognition by SETD2 methyltransferase
Authors: Yang Shuang , Zheng Xiangdong , Lu Chao , Li Guo-Min , Allis C. David , Li Haitao
Published: July 2016

High-frequency point mutations of genes encoding histones have been identified recently as novel drivers in a number of tumors. Specifically, the H3K36M/I mutations were shown to be oncogenic in chondroblastomas and undifferentiated sarcomas by inhibiting H3K36 methyltransferases, including SETD2. Here we report the crystal structures of the SETD2 catalytic domain bound to H3K36M or H3K36I peptides with SAH (S-adenosylhomocysteine). In the complex structure, the catalytic domain adopts an open conformation, with the K36M/I peptide snuggly positioned in a newly formed substrate channel. Our structural and biochemical data reveal the molecular basis underying oncohistone recognition by and inhibition of SETD2.
Oncogenic transformation of Drosophila somatic cells induces a functional piRNA pathway
Authors: Fagegaltier Delphine , Falciatori Ilaria , Czech Benjamin , Castel Stephane , Perrimon Norbert , Simcox Amanda , Hannon Gregory J.
Published: July 2016

Germline genes often become re-expressed in soma-derived human cancers as “cancer/testis antigens” (CTAs), and piRNA (PIWI-interacting RNA) pathway proteins are found among CTAs. However, whether and how the piRNA pathway contributes to oncogenesis in human neoplasms remain poorly understood. We found that oncogenic Ras combined with loss of the Hippo tumor suppressor pathway reactivates a primary piRNA pathway in Drosophila somatic cells coincident with oncogenic transformation. In these cells, Piwi becomes loaded with piRNAs derived from annotated generative loci, which are normally restricted to either the germline or the somatic follicle cells. Negating the pathway leads to increases in the expression of a wide variety of transposons and also altered expression of some protein-coding genes. This correlates with a reduction in the proliferation of the transformed cells in culture, suggesting that, at least in this context, the piRNA pathway may play a functional role in cancer.
Oversatiation negatively affects evaluation of goal-relevant (but not goal-irrelevant) advertised brands
Authors: Karremans Johan C. , Kacha Mathieu , Herrmann Jean-Luc , Vermeulen Christophe , Corneille Olivier
Published: July 2016

Purpose

The purpose of the present paper is to examine the effects of overconsumption on consumer evaluations of advertised brands. While the determinants and health consequences of overconsumption have received considerable attention, the authors suggest that there are important marketing and advertising implications. Specifically, based on goal theory, the authors examined whether the aversive state of oversatiation is associated with more negative evaluations of advertised brands of the overconsumed product.

Design/methodology/approach

In three studies, oversatiation was measured or experimentally induced by having participants drink (too) much mineral water. Subsequently, participants watched advertisement of mineral water brands and control brands. Evaluations of the brands, buying intentions and estimates of future purchases of the advertised brands were measured.

Findings

Oversatiation negatively affected evaluations, buying intentions and estimates of future purchases of advertised mineral water brands. Importantly, a state of oversatiation did not affect evaluation of advertised brands not relevant to the overfulfilled goal.

Originality/value

Overconsumption of food and drinks can have detrimental health effects and results in large costs to society. While its health implications have received abundant scientific attention, little attention has been paid to the psychological consequences of the state of being oversatiated. Here, the authors show that the state of oversatiation (which might, for example, be very common during watching television commercials) can lead to particularly negative evaluations of advertised brands. As such, these findings have important marketing implications.
Public participation in decision-making on the coverage of new antivirals for hepatitis C
Authors: Kieslich Katharina , Ahn Jeonghoon , Badano Gabriele , Chalkidou Kalipso , Cubillos Leonardo , Hauegen Renata Curi , Henshall Chris , Krubiner Carleigh B , Littlejohns Peter , Lu Lanting , Pearson Steven D , Rid Annette , Whitty Jennifer A , Wilson James
Published: July 2016

Purpose

– New hepatitis C medicines such as sofosbuvir underline the need to balance considerations of innovation, clinical evidence, budget impact and equity in health priority-setting. The purpose of this paper is to examine the role of public participation in addressing these considerations.

Design/methodology/approach

– The paper employs a comparative case study approach. It explores the experience of four countries – Brazil, England, South Korea and the USA – in making coverage decisions about the antiviral sofosbuvir and involving the public and patients in these decision-making processes.

Findings

– Issues emerging from public participation ac tivities include the role of the universal right to health in Brazil, the balance between innovation and budget impact in England, the effect of unethical medical practices on public perception in South Korea and the legitimacy of priority-setting processes in the USA. Providing policymakers are receptive to these issues, public participation activities may be re-conceptualized as processes that illuminate policy problems relevant to a particular context, thereby promoting an agenda-setting role for the public.

Originality/value

– The paper offers an empirical analysis of public involvement in the case of sofosbuvir, where the relevant considerations that bear on priority-setting decisions have been particularly stark. The perspectives that emerge suggest that public participation contributes to raising attention to issues that need to be addressed by policymakers. Public participation activities can thus contribute to setting policy agendas, even if that is not their explicit purpose. However, the actualization of this contribution is contingent on the receptiveness of policymakers.
Between consensus and contestation
Authors: Weale Albert
Published: July 2016

Purpose

– Noting that discussions of public participation and priority setting typically presuppose certain political theories of democracy, the purpose of this paper is to discuss two theories: the consensual and the agonistic. The distinction is illuminating when considering the difference between institutionalized public participation and contestatory participation.

Design/methodology/approach

– The approach is a theoretical reconstruction of two ways of thinking about public participation in relation to priority setting in health care, drawing on the work of Habermas, a deliberative theorist, and Mouffe, a theorist of agonism.

Findings

– The different theoretical approaches can be associated with different ways of understanding priority setting. In particular, agonistic democratic theory would understand priority setting as system of inclusions and exclusions rather than the determination of a consensus of social values, which is the typical deliberative way of thinking about the issues.

Originality/value

– The paper shows the value of drawing out explicitly the tacit assumptions of practices of political participation in order to reveal their scope and limitations. It suggests that making such theoretical presuppositions explicit has value for health services management in recognizing these implicit choices.
Alliance portfolio capability
Authors: Lichtenthaler Ulrich
Published: July 2016

Purpose

– The purpose of this paper is to develop a conceptual framework and propositions on a capability-based view that examine the role of a firm’s primary type of alliances, i.e., exploration or exploitation, in the determinants and impact of alliance portfolio capability.

Design/methodology/approach

– This is a conceptual research paper, which builds on prior conceptual and empirical management research.

Findings

– Regarding determinants, capability-based arguments indicate that firms with an emphasis on exploration alliances have higher levels of alliance portfolio capability. However, a focus on exploration alliances aggravates the development of alliance portfolio capability through alliance experience and a dedicated alliance function. Regarding impact, alliance portfolio capability may positively affect a firm’s alliance, innovation, and financial performance. While alliance portfolio capability is assumed to have an equally positive effect on alliance performance for all types of alliance portfolios, a relative focus on exploration alliances is expected to limit the positive effects of alliance portfolio capability on innovation and subsequent financial performance.

Originality/value

– These new conceptual arguments help to reconcile inconsistent earlier findings, and they deepen the understanding of interfirm differences in alliance portfolio capability and performance.
Decision-making processes in football clubs associated with an external advisory programme
Authors: Egli Benjamin Thomas , Schlesinger Torsten , Splinter Mariëlle , Nagel Siegfried
Published: July 2016

Purpose

The purpose of this paper is to foster a better understanding of how decision-making processes work in sport clubs and to develop appropriate advisory concepts or management tools in order to successfully realize structural changes in sport clubs. This paper examines the decision-making processes associated with an external advisory programme. Based on the assumption of bounded rationality, the garbage can model is used to grasp these decision-making processes theoretically and to access them empirically.

Design/methodology/approach

Based on a case study framework, an in-depth analysis of the decision-making and implementation processes involved in an advisory programme was performed in ten selected football clubs. Guided interviews were conducted on the basis of the four streams of the garbage can model. The interviews were analysed with qualitative content analysis.

Findings

Results show that three types of club can be distinguished in terms of their implementation processes: low implementation of the external input; partial implementation of the external input; and rigorous implementation of the external input. In addition, the analysis shows that the participants in the advisory programme are the key actors in both the decision-making process and the implementation.

Originality/value

The paper provides insights into the practicability of advisory programmes for sport clubs and the transfer to the clubs’ practical decision-making routines. Additionally, it shows how sport clubs deal with (external) advisory impulses, and which different decision-making practices underlie these processes.
Football clubs’ profitability after the Financial Fair Play regulation: evidence from Italy
Authors: Nicoliello Mario , Zampatti Davide
Published: July 2016

Purpose

In 2009, the Union of European Football Associations approved the Financial Fair Play (FFP) regulations. These regulations refer to the requirements of transparency and financial conditions for football clubs participating in European competitions. The purpose of this paper is to combine the managerial and the economic points-of-view in order to understand if Italian football clubs are ready to comply with the new FFP rules.

Design/methodology/approach

In the analysis, the authors focus on the main Italian football league, Serie A. Using business model analysis, the authors determine what the main profit determinants of football associations are, through panel data for 15 clubs from 2011-2013. The authors then try to match the statistical and managerial approach.

Findings

The results show that the key contributing factors to profits are on the costs side. In particular, the most relevant expenses are player wages. The core revenue for clubs comes from the net profit from player trading, while other income, such as TV rights, commercial and match-day proceeds, have no statistical significance for profit formation.

Research limitations/implications

The main limitation of the analysis is that the survey regarded only on Italian Championship. So it is deeply influenced by the competitive structure of the Italian league that is different from that of other European leagues. Therefore, the authors think that the future developments of this work could be the examination of another European Championship, for example, English Premier League, and the compared analysis of Italian league and other European one.

Practical implications

There is a close-link between costs and profitability, and especially between expenditure on players and the ability to close the financial year with a profit. Clubs must address the issue of player wages in order to follow a path of economic recovery towards profitability.

Originality/value

In the work the authors put together managerial point of view and economical one, in order to understand how FFP can impact on profitability of football clubs. The authors use an empirical econometrics model to test the hypothesis about business model of Italian Clubs.
The remaining cases of the Kramer–Tunnell conjecture
Authors: Česnavičius Kęstutis , Imai Naoki
Published: July 2016

For an elliptic curve $E$ over a local field $K$ and a separable quadratic extension of $K$, motivated by connections to the Birch and Swinnerton-Dyer conjecture, Kramer and Tunnell have conjectured a formula for computing the local root number of the base change of $E$ to the quadratic extension in terms of a certain norm index. The formula is known in all cases except some where $K$ is of characteristic $2$, and we complete its proof by reducing the positive characteristic case to characteristic $0$. For this reduction, we exploit the principle that local fields of characteristic $p$ can be approximated by finite extensions of $\mathbb{Q}_{p}$: we find an elliptic curve $E^{\prime }$ defined over a $p$-adic field such that all the terms in the Kramer–Tunnell formula for $E^{\prime }$ are equal to those for $E$.
The integrated network model of pipeline, sea and road distribution of petroleum product
Authors: Öztürkoğlu Ömer , Lawal Oyewale
Published: July 2016

Nigeria ranks high among the community of oil producers both in the world. It is, therefore, paradoxical that Nigeria, with such profile in Organization of Petroleum Exporting Countries (OPEC) statistics finds it difficult to optimize its supply distribution while spending so much money on transportation and distribution. This paper thus reviews the petroleum product supply and distribution systems in the country. Thus, we develop a single period, single product deterministic mathematical model to effectively distribute the product to the end user through the most effective channel to the interest of the economy of the country. In our model, we first consider a perfect condition in the petroleum industry irrespective of the production crises and conflicts like pipeline vandalism, communal instability. We then consider different scnearios that presumes several breakdown cases in pipeline connection to anaylze the survivability of the network of petroleum distribution.
Sales plan generation problem on TV broadcasting
Authors: Cosgun Özlem , Gultas İlkay
Published: July 2016

Major advertisers and/or advertisement agencies purchase hundreds of slots during a given broadcast period. Deterministic optimization approaches have been well developed for the problem of meeting client requests. The challenging task for the academic research currently is to address optimization problem under uncertainty. This paper is concerned with the sales plan generation problem when the audience levels of advertisement slots are random variables with known probability distributions. There are several constraints the TV networks must meet including client budget, product category and demographic information, plan weighting by week, program mix requirements, and the lengths of advertisement slots desired by the client. We formulate the problem as a chance constrained goal program and we demonstrate that it provides a robust solution with a user specified level of reliability.
New complex exact travelling wave solutions for the generalized-Zakharov equation with complex structures
Authors: Baskonus Haci Mehmet , Bulut Hasan
Published: July 2016

In this paper, we apply the sine-Gordon expansion method which is one of the powerful methods to the generalized-Zakharov equation with complex structure. This algorithm yields new complex hyperbolic function solutions to the generalized-Zakharov equation with complex structure. Wolfram Mathematica 9 has been used throughout the paper for plotting two- and three-dimensional surface of travelling wave solutions obtained.
Enhanced Coarse-Graining of Thermoplastic Polyurethane Elastomer for Multiscale Modeling
Authors: Uddin Md Salah , Ju Jaehyung
Published: July 2016

The objective of this work is to develop a multiscale modeling tool of copolymers with long chains. We propose an enhanced coarse-graining method of thermoplastic polyurethane (TPU) with three beads. The proposed coarse-graining provides an accurate molecular modeling tool to keep the molecular interaction together with computational efficiency. The coarse-grained model with three beads is further improved with pressure-correction of the force-field. The improved coarse-grained model holds similar properties of a bulk model of TPU—varying density with temperature, a close density value of TPU at 1 atm, and the phase separation. Equating potential energy densities of the coarse-grained model to the strain energy functions of the continuum model at volumetric and isochoric deformation modes, bulk and shear moduli of TPU are directly obtained and used to estimate Young's modulus and Poisson's ratio. The molecular simulation with the coarse-grained model of TPU demonstrates its much greater bulk modulus than the shear modulus, which is typically observed in elastomers. Modifying the coarse-grained model of TPU with hard and soft segments, we successfully demonstrated the material design of bulk modulus and Poisson's ratio by varying hard and soft segments at the molecular level. The proposed coarse-graining tool will pave a new way to explore the multiscale modeling of copolymers with long chains and can be directly applied to the multiscale modeling of other thermoplastic elastomers (TPE).
Effects of Blade Pitch, Rotor Yaw, and Wind–Wave Misalignment on a Large Offshore Wind Turbine Dynamics in Western Gulf of Mexico Shallow Water in 100-Year Return Hurricane
Authors: Yin Ling Ling , Lo King Him , Wang Su Su
Published: July 2016

To determine the optimal park configuration of a large offshore turbine in a hurricane, a study is conducted on effects of blade pitch and rotor yaw, and wind–wave misalignment, in a 100-year return hurricane on a 13.2-MW large offshore wind turbine (OWT) in western Gulf of Mexico (GOM) shallow water. The OWT structure considered includes a rotor with three 100-m long blades and a monotower support structure. Maximum loads on the wind turbine are determined with blade pitch and rotor yaw, with and without wind–wave misalignment in the 100-year return hurricane. The results show that effects of blade pitch and rotor yaw on turbine structural dynamics are significant, whereas the effect of wind–wave misalignment is small in the context of structural design in strength. The study provides deep insight to wind turbine dynamics and its structural design in the extreme hurricane.
Draft Genome Sequence of the
Mycobacterium tuberculosis
Complex Pathogen
M. mungi
, Identified in a Banded Mongoose (
Mungos mungo
) in Northern Botswana
Authors: Alexander Kathleen A. , Larsen Michelle H. , Robbe-Austerman Suelee , Stuber Tod P. , Camp Patrick M.
Published: July 2016

Mycobacterium mungi
, a
Mycobacterium tuberculosis
complex pathogen, has emerged in banded mongoose in northern Botswana and Northwest Zimbabwe. The pathogen is transmitted through infected secretions used in olfactory communication behavior (K. A. Alexander, C. E. Sanderson, M. H. Larsen, S. Robbe-Austerman, M. C. Williams, and M. V. Palmer, mBio 7(3):e00281-16, 2016,
http://dx.doi.org/10.1128/mBio.00281-16
). We announce here the draft genome sequence of this emerging pathogen
.
Draft Genome Sequence of the Emerging Bivalve Pathogen
Vibrio tubiashii
subsp.
europaeus
Authors: Spinard Edward J. , Dubert Javier , Nelson David R. , Gomez-Chiarri Marta , Barja Juan L.
Published: July 2016

Vibrio tubiashii
subsp.
europaeus
is a bivalve pathogen isolated during episodes of mortality affecting larval cultures in different shellfish hatcheries. Here, we announce the draft genome sequence of the type strain PP-638 and describe potential virulence factors, which may provide insight into the mechanism of pathogenicity.
Draft Genome Sequence of an
Oceanobacillus
sp. Strain Isolated from Soil in a Burial Crypt
Authors: Martínez-Ballesteros Ilargi , Arizaga Ylenia , Bikandi Joseba , Garaizar Javier , Ganau Giulia , Paglietti Bianca , Murgia Manuela , Deligios Massimo , Rubino Salvatore
Published: July 2016

We present the draft genome of an
Oceanobacillus
sp. strain isolated from spores found in soil samples from a burial crypt of the Cathedral of Sant'Antonio Abate in Castelsardo, Italy. The data obtained indicated the closest relation of the strain with
Oceanobacillus caeni
.
Complete Genome Sequence of an Avian Paramyxovirus Representative of Putative New Serotype 13
Authors: Goraichuk Iryna , Sharma Poonam , Stegniy Borys , Muzyka Denys , Pantin-Jackwood Mary J. , Gerilovych Anton , Solodiankin Olexii , Bolotin Vitaliy , Miller Patti J. , Dimitrov Kiril M. , Afonso Claudio L.
Published: July 2016

Here, we report the complete genome sequence of a virus of a putative new serotype of avian paramyxovirus (APMV). The virus was isolated from a white-fronted goose in Ukraine in 2011 and designated white-fronted goose/Ukraine/Askania-Nova/48-15-02/2011. The genomic characterization of the isolate suggests that it represents the novel avian paramyxovirus group APMV 13.
Draft Genome Sequence of
Ustilago trichophora
RK089, a Promising Malic Acid Producer
Authors: Zambanini Thiemo , Buescher Joerg M. , Meurer Guido , Wierckx Nick , Blank Lars M.
Published: July 2016

The basidiomycetous smut fungus
Ustilago trichophora
 RK089 produces malate from glycerol.
De novo
genome sequencing revealed a 20.7-Mbp genome (301 gap-closed contigs, 246 scaffolds). A comparison to the genome of
Ustilago maydis
 521 revealed all essential genes for malate production from glycerol contributing to metabolic engineering for improving malate production.
Human Rhinovirus B and C Genomes from Rural Coastal Kenya
Authors: Agoti Charles N. , Kiyuka Patience K. , Kamau Everlyn , Munywoki Patrick K. , Bett Anne , van der Hoek Lia , Kellam Paul , Nokes D. James , Cotten Matthew
Published: July 2016

Primer-independent agnostic deep sequencing was used to generate three human rhinovirus (HRV) B genomes and one HRV C genome from samples collected in a household respiratory survey in rural coastal Kenya. The study provides the first rhinovirus genomes from Kenya and will help improve the sensitivity of local molecular diagnostics.
Outpatient management of selected young febrile infants without antibiotics
Authors: Mintegi Santiago , Gomez Borja , Martinez-Virumbrales Lidia , Morientes Oihane , Benito Javier
Published: July 2016

Objective

To analyse the outpatient management of selected febrile infants younger than 90 days without systematic lumbar puncture and antibiotics.

Methods

A prospective registry-based cohort study including all the infants ≤90 days with fever without a source (FWS) who were evaluated in a paediatric emergency department (ED) over a 7-year period (September 2007–August 2014). We analysed the outcome of those infants with low-risk criteria for serious bacterial infection (SBI) managed as outpatients without antibiotics and without undergoing a lumbar puncture. Low-risk criteria: Well appearing, older than 21 days of age, no leucocyturia, absolute neutrophil count ≤10 000, serum C reactive protein ≤20 mg/L, procalcitonin <0.5 ng/mL and no clinical deterioration during the stay in the ED (always <24 hours).

Results

1472 infants with FWS attended the ED. Of these, 676 were classified to be at low risk for SBI without performing a lumbar puncture. After staying <24 hours in the short-stay unit of the ED, 586 (86.6%) were managed as outpatients without antibiotics. Two patients were diagnosed with SBI: one occult bacteraemia and one bacterial gastroenteritis. Both were afebrile when evaluated again and did well. No patient returned to the ED due to clinical deterioration. Fifty-one infants (8.7%) returned to the ED mainly due to persistence of fever or irritability. None was diagnosed with definite SBI or non-bacterial meningitis.

Conclusions

Outpatient management without antibiotics and systematic lumbar puncture is appropriate for selected febrile infants younger than 3 months of age with close follow-up.
Paraneoplastic neuropsychiatric syndrome presenting as delirium
Authors: Roldan Urgoiti Gloria , Sinnarajah Aynharan , Hussain Seema , Hao Desiree
Published: July 2016

Delirium in patients with cancer is associated with poor outcomes, but reversible causes need to be ruled out. We report the case of a 59-year-old woman who was presented with behavioural and cognitive changes over 2 weeks. She was non-verbal and combative, requiring involuntary admission and declaration of incompetence to make healthcare treatment decisions. Infectious and metabolic investigations and initial brain imaging were unremarkable. She was diagnosed with limited-stage small cell lung cancer and a paraneoplastic neuropsychiatric syndrome. Owing to the patient's delirium, chemotherapy delivery required pharmacological and physical restraints. After 2 cycles of chemotherapy, she could participate in the decision process and was discharged home. She completed radical chemo-radiotherapy and has remained free of disease progression for 18 months. Paraneoplastic neuropsychiatric syndromes, although rare, are potentially treatable and need to be excluded as a cause of delirium.
Lymphocytic oesophagitis, eosinophilic oesophagitis and compound lymphocytic–eosinophilic oesophagitis I: histological and immunohistochemical findings
Authors: Rubio C A , Ichiya T , Schmidt P T
Published: July 2016

Aims

To report four histological–immunohistochemical oesophagitis phenotypes.

Methods

Oesophageal biopsies from 311 patients were stained with H&E and with CD3, a T cell marker. Additional immunohistochemical stains (n=413) were performed in 77 cases.

Results

Four histological–immunohistochemical oesophagitis phenotypes were recorded: lymphocytic oesophagitis (LyE, ≥40 CD3+ lymphocytes/HPF in CD3 immunostain), eosinophilic oesophagitis (EoE, ≥15 eosinophils/HPF in H&E stain), lymphocytic infiltration (≤39 CD3+/HPF) and compound lymphocytic oesophagitis–eosinophilic oesophagitis (Co LyE-EoE). At index biopsy, 28.3% (n=88) had LyE, 21.2% (n=66) EoE, 10.6% (n=33) Co LyE-EoE and 39.9% (n=124) lymphocytic infiltration. A persistent oesophagitis phenotype was found in 42.5% (37/87) in the first follow-up biopsy, in 34.4% (21/61) in the second follow-up biopsy and in 48.1% (26/54) in the third follow-up biopsy. Using βF1 immunostain, two different surface T cell receptors were detected in LyE and Co Lye-EoE: one having ≥40 βF1+/HPF (βF1+ high) and the other having <39 βF1+/HPF (βF1+ low).

Conclusions

Based on the literature regarding the significance of intraepithelial lymphocytes (IELs) in the initiation of EoE, we submit that the IEL phenotypes in LyE might differ from those found in EoE as they were unable to elicit the same eosinophilic response. Recent studies disclosed that group 2 innate lymphocytes (ILC2s), enriched in EoE, remain undetected in CD3 immunostain as they lack surface markers for T, B, natural killer (NK) or NK T cells. If ILC2s also participate in the lymphocytic infiltration of EoE, then the frequency of cases with Co LyE-EoE here reported might have been much higher. The four oesophagitis phenotypes described are easy to recognise, provided that the dual staining procedure (H&E-CD3) is implemented.
Towards a Medicine of the Invisible: bioethics and relationship in “The Little Prince”
Authors: Colucci Massimiliano , Pegoraro Renzo
Published: July 2016

The Little Princeis one of the most famous fables. In this paper, we attempt to look at three bioethical issues through the Little Prince's eyes: the end-of-life context, the patient–physician relationship and prevention/precaution. The fable gives us the basis for a perspective we have called ‘Medicine of the Invisible’, which is value-focused. The Little Prince suggests that we seek the invisible—the “thing that is important”, the “matters of consequence”, even on a gnoseological and epistemological level—as a new type of ‘clinical data’ which may help to make healthcare more ethical and effective. However, this invisible is attainable only within a relationship, in which the physician needs to be tamed by the patient and the patient needs to be tamed by the physician—each one becoming responsible for the other, each one becoming himself through the dialogue with the other. Responsibility is also projected towards the future, against those threats to life that are still unseen and unknown: owning a part of the world entails the ethical imperative to act, in order to safeguard life. But, without a relationship—saturated with lived time, shared experiences, and individual's uniqueness—no meaning and no value can be given. For this reason, the Medicine of the Invisible reminds bioethics that “the thing that is important is the thing that is not seen”.
Republished: Rapid delayed growth of ruptured supraclinoid blister aneurysm after successful flow diverting stent treatment
Authors: Lang Stefan Thomas , Assis Zarina , Wong John H , Morrish William , Mitha Alim P
Published: July 2016

A 62-year-old woman presented with a subarachnoid hemorrhage secondary to a ruptured right supraclinoid internal carotid artery blister aneurysm. She was treated in an emergent fashion with two flow diverting pipeline embolization devices (PED) deployed in a telescoping fashion. CT angiography performed for unrelated reasons at 7 months showed successful treatment of the aneurysm without evidence of residual aneurysm. However, a follow-up digital subtraction angiogram performed at 9 months showed a large aneurysm in a modified position compared with the original aneurysm. This is the first case of rapid regrowth of a supraclinoid blister aneurysm after successful treatment with a PED, and demonstrates the need for close follow-up for similar aneurysms treated with this novel device.
A new hesperornithiform (Aves) specimen from the Late Cretaceous Canadian High Arctic with comments on high-latitude hesperornithiform diet
Authors: Wilson Laura E. , Chin Karen , Cumbaa Stephen L.
Published: July 2016

Here we describe a new hesperornithiform specimen from the Upper Cretaceous Kanguk Formation of Devon Island, Nunavut, Canada. This specimen (NUVF 286) is referred to cf. Hesperornis sp. based on size and shape of femora and teeth preserved with other skeletal elements. Previous osteohistologic analyses indicate a subadult ontogenetic stage at the time of death. This new cf. Hesperornis specimen includes the first teeth associated with a high-latitude hesperornithiform, allowing for comments on the trophic behavior of these birds. Paleoecological reconstructions based on current knowledge of polar assemblages and comparisons to modern birds suggest that high-latitude hesperornithiform birds may have had more varied diets than previously assumed.