bluuebunny/crossref_metadata_2025_split huggingface dataset:
Index of varieties over Henselian fields and Euler characteristic of coherent sheaves
Authors: Esnault Hélène , Levine Marc , Wittenberg Olivier 
Published: June 2015

Let XXbe a smooth proper variety over the quotient field of a Henselian discrete valuation ring with algebraically closed residue field of characteristic pp. We show that for any coherent sheaf EEon XX, the index of XXdivides the Euler–Poincaré characteristicχ(X,E)\chi (X,E)ifp=0p=0orp>dim⁡(X)+1p>\dim (X)+1. If0>p≤dim⁡(X)+10>p\leq \dim (X)+1, the prime-to-pppart of the index of XXdividesχ(X,E)\chi (X,E). Combining this with the Hattori–Stong theorem yields an analogous result concerning the divisibility of the cobordism class of XXby the index of XX.

As a corollary, rationally connected varieties over the maximal unramified extension of app-adic field possess a zero-cycle ofpp-power degree (a zero-cycle of degree 11ifp>dim⁡(X)+1p>\dim (X)+1). Whenp=0p=0, such statements also have implications for the possible multiplicities of singular fibers in degenerations of complex projective varieties.
The New Wandering Rocks
Authors: Watt Stephen 
Published: June 2015

Abstract
This chapter takes its title from an episode in James Joyce’s Ulysses in which Leopold Bloom visits a tawdry book stand seeking salacious titles, most of which are concealed from view. Using this trope of the hidden, a characteristic of the Freudian uncanny, this chapter explores uncanny affinities between—and eruptions of—hidden Irishness and Jewishness in selected works of John Banville, Brendan Behan, Norman Mailer, Harold Pinter, and Howard Jacobson. The chapter also makes the case for a “multidirectional” historical memory that juxtaposes such widespread traumas as the Great Famine and the Holocaust, in the process continuing a long tradition of paralleling Irish and Jewish diasporic experiences. One test case of multidirectional reading is provided by Bernard MacLaverty’s adducing of parallels between the Troubles in Northern Ireland and the Shoah. The chapter and book conclude with a summary of more recent representations of immigrant America by Brian Friel and Gish Jen.
Conclusion
Authors: Adams-Prassl Jeremias 
Published: June 2015

AbstractThe concluding chapter tests whether the reconceptualization has been successful, both in practical terms and by addressing the fundamental tension head-on: the functional strand is strengthened, in particular by the development of a robust theoretical framework. It summarizes the argument presented in preceding chapters, and culminates in several examples of the functional concept of the employer at work in multilateral settings such as triangular agency work and the information and consultation of employees in a corporate group. A final section turns to the broader normative implications of widening the conceptual focus of employment law to include the concept of the employer as counterparty to the contract of employment, and suggests that the functional concept of the employer proposed is an important step towards the restoration of the personal scope of employment law.
Physics
Authors: Glasner Ruth 
Published: June 2015

Abstract
Gersonides seeks to resolve the incompatibility between Ptolemaic astronomy and Aristotelian physics by reworking both sciences. He elaborates his own astronomical system, based on the eccentric and equant hypotheses (avoiding epicycles), and was thus motivated to disassociate the physics of motion from cosmological premises. Gersonides radically revises Aristotle’s concepts of natural motion and natural place. Moreover, critical reading of Aristotle (most notably De caelo II.12 and Physics VIII.10) and inventive thought experiments led him to dismiss Aristotle’s conception of motion as a dynamic balance: he shows that no moving force is necessary to keep a body in motion and argues that in the celestial region a moving body does not encounter resistance. This argument leads him to the further conclusion that no separate intellects are necessary to keep the world moving. The chapter closes with a short summary of Gersonides’ contribution to the history of the principle of inertia.
Cosmology
Authors: Glasner Ruth 
Published: June 2015

Abstract
Two perceptions of celestial animation prevailed in the Middle Ages: [I] each sphere is animated by a soul [I.1], or an innate intellect [I.2], or a separate intellect [I.3]; [II] the entire universe is a single organism. Gersonides refutes [II] through an argument with Ptolemy, who was unable to account for the transmission of the daily and precession motions from the outermost spheres to the planets, and therefore eschewed the problem by introducing the bird metaphor. Gersonides dismisses [I.1] too and undermines [I.3] by showing that the separate intellects—the cornerstone of medieval Aristotelianism—are not needed to keep the world rotating. He cannot, however, dispose of celestial animation altogether. Not having the mathematical means to account for the non-simple equant motion, he compromises on [I.2]: innate intellects whose role is to keep a mental picture of the divine plan of the natural order of the world.
Metaphysics
Authors: Glasner Ruth 
Published: June 2015

Abstract
His empiricist tendency and his interest in the applied mathematical sciences led Gersonides to reconsider the philosophically oriented Platonic-Aristotelian hierarchical conception of the system of the sciences with the intention to upgrade the status of the mathematical sciences, and to expose several shortages of metaphysics. Gersonides approaches this subject in his early biblical commentaries (notably those on the books ascribed to King Solomon) after having abandoned his commentary on the Metaphysics. Relying on the authority of King Solomon, rather than on that of Aristotle, Gersonides comes up with a new notion of science and in particular of divine science.
Astronomy
Authors: Glasner Ruth 
Published: June 2015

Abstract
In his late years Gersonides does not come back to natural science or philosophy. He pursues the biblical commentaries’ project and devotes most of his effort to astronomical observations and computations, seeking to complete and perfect his astronomical models by computing the parameters with precision. To this end he developed a mathematical method of iterations, which he called ‘heuristic reasoning’ (heqesh taḥbuli). He is aware of the fact that observations and computations cannot lead to the certainty that he aspired to achieve in his middle period, when he devised his models using the method of the ‘parts of the contradictory’.
Concluding Remark
Authors: Glasner Ruth 
Published: June 2015

Abstract
The concluding remark comes back to the question raised in the Preface, whether Gersonides should be considered an Aristotelian philosopher. The conclusion is that although he followed Aristotle on a wide range of issues, Gersonides’ overall world picture was non-Aristotelian. His science was more empirical and less bound by metaphysical considerations than the scholastic science of his time. Throughout the book an attempt was made to avoid presenting Gersonides as a forerunner of modern science. The concluding remark addresses this issue briefly. Although mechanical philosophy was a product of the seventeenth century and the adjectives ‘mechanistic’ or ‘mechanical’ were not yet part of the conceptual vocabulary of the fourteenth century, it nonetheless seems that, without naming it, Gersonides strived to advance some aspects of it.
Fast-SL: an efficient algorithm to identify synthetic lethal sets in metabolic networks
Authors: Pratapa Aditya , Balachandran Shankar , Raman Karthik 
Published: June 2015

Abstract
Motivation: Synthetic lethal sets are sets of reactions/genes where only the simultaneous removal of all reactions/genes in the set abolishes growth of an organism. Previous approaches to identify synthetic lethal genes in genome-scale metabolic networks have built on the framework of flux balance analysis (FBA), extending it either to exhaustively analyze all possible combinations of genes or formulate the problem as a bi-level mixed integer linear programming (MILP) problem. We here propose an algorithm, Fast-SL, which surmounts the computational complexity of previous approaches by iteratively reducing the search space for synthetic lethals, resulting in a substantial reduction in running time, even for higher order synthetic lethals.
Results: We performed synthetic reaction and gene lethality analysis, using Fast-SL, for genome-scale metabolic networks of Escherichia coli, Salmonella enterica Typhimurium and Mycobacterium tuberculosis. Fast-SL also rigorously identifies synthetic lethal gene deletions, uncovering synthetic lethal triplets that were not reported previously. We confirm that the triple lethal gene sets obtained for the three organisms have a precise match with the results obtained through exhaustive enumeration of lethals performed on a computer cluster. We also parallelized our algorithm, enabling the identification of synthetic lethal gene quadruplets for all three organisms in under 6 h. Overall, Fast-SL enables an efficient enumeration of higher order synthetic lethals in metabolic networks, which may help uncover previously unknown genetic interactions and combinatorial drug targets.
Availability and implementation: The MATLAB implementation of the algorithm, compatible with COBRA toolbox v2.0, is available at https://github.com/RamanLab/FastSL
Contact: kraman@iitm.ac.in
Supplementary information: Supplementary data are available at Bioinformatics online.
PrediXcan: Trait Mapping Using Human Transcriptome Regulation
Authors: Gamazon Eric R. , Wheeler Heather E. , Shah Kaanan P. , Mozaffari Sahar V. , Aquino-Michaels Keston , Carroll Robert J. , Eyler Anne E. , Denny Joshua C. ,   GTEx Consortium, Nicolae Dan L. , Cox Nancy J. , Im Hae Kyung 
Published: June 2015

ABSTRACTGenome-wide association studies (GWAS) have identified thousands of variants robustly associated with complex traits. However, the biological mechanisms underlying these associations are, in general, not well understood. We propose a gene-based association method called PrediXcan that directly tests the molecular mechanisms through which genetic variation affects phenotype. The approach estimates the component of gene expression determined by an individual’s genetic profile and correlates the “imputed” gene expression with the phenotype under investigation to identify genes involved in the etiology of the phenotype. The genetically regulated gene expression is estimated using whole-genome tissue-dependent prediction models trained with reference transcriptome datasets. PrediXcan enjoys the benefits of gene-based approaches such as reduced multiple testing burden, more comprehensive annotation of gene function compared to that derived from single variants, and a principled approach to the design of follow-up experiments while also integrating knowledge of regulatory function. Since no actual expression data are used in the analysis of GWAS data - onlyin silicoexpression - reverse causality problems are largely avoided. PrediXcan harnesses reference transcriptome data for disease mapping studies. Our results demonstrate that PrediXcan can detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations.
Evolution and coexistence in response to a key innovation in a long-term evolution experiment withEscherichia coli
Authors: Turner Caroline B. , Blount Zachary D. , Mitchell Daniel H. , Lenski Richard E. 
Published: June 2015

AbstractEvolution of a novel function can greatly alter the effects of an organism on its environment. These environmental changes can, in turn, affect the further evolution of that organism and any coexisting organisms. We examine these effects and feedbacks following evolution of a novel function in the long-term evolution experiment (LTEE) withEscherichia coli. A characteristic feature ofE. coliis its inability to consume citrate aerobically. However, that ability evolved in one of the LTEE populations. In this population, citrate-utilizing bacteria (Cit+) coexisted stably with another clade of bacteria that lacked the capacity to utilize citrate (Cit−). This coexistence was shaped by the evolution of a cross-feeding relationship in which Cit+cells released the dicarboxylic acids succinate, fumarate, and malate into the medium, and Cit−cells evolved improved growth on these carbon sources, as did the Cit+cells. Thus, the evolution of citrate consumption led to a flask-based ecosystem that went from a single limiting resource, glucose, to one with five resources either shared or partitioned between two coexisting clades. Our findings show how evolutionary novelties can change environmental conditions, thereby facilitating diversity and altering both the structure of an ecosystem and the evolutionary trajectories of coexisting organisms.Evolution does not produce novelties from scratch. It works on what already exists, either transforming a system to give it new functions or combining several systems to produce a more elaborate one.–Francois Jacob
Detection of virulence‐associated genes characteristic of intestinal Escherichia coli pathotypes, including the enterohemorrhagic/enteroaggregative O104:H4, in bovines from Germany and Spain
Authors: Cabal Adriana , Geue Lutz , Gómez‐Barrero Susana , Barth Stefanie , Bárcena Carmen , Hamm Katharina , Porrero M.Concepción , Valverde Aránzazu , Cantón Rafael , Menge Christian , Gortázar Christian , Domínguez Lucas , Álvarez Julio 
Published: June 2015

AbstractCattle are reservoirs of enterohemorrhagic Escherichia coli; however, their role in the epidemiology of other pathogenic E. coli remains undefined. A new set of quantitative real‐time PCR assays for the direct detection and quantification of nine virulence‐associated genes (VAGs) characteristic of the most important human E. coli pathotypes and four serotype‐related genes (wzxO104, fliCH4, rbfO157, fliCH7) that can be used as a surveillance tool for detection of pathogenic strains was developed. A total of 970 cattle fecal samples were collected in slaughterhouses in Germany and Spain, pooled into 134 samples and analyzed with this tool. stx1, eae and invA were more prevalent in Spanish samples whereas bfpA, stx2, ehxA, elt, est and the rbfO157/fliCH7 combination were observed in similar proportions in both countries. Genes characteristic of the hybrid O104:H4 strain of the 2011 German outbreak (stx2/aggR/wzxO104/fliCH4) were simultaneously detected in six fecal pools from one German abattoir located near the outbreak epicenter. Although no isolate harboring the full stx2/aggR/wzxO104/fliCH4 combination was cultured, sequencing of the aggR positive PCR products revealed 100% homology to the aggR from the outbreak strain. Concomitant detection by this direct approach of VAGs from a novel human pathogenic E. coli strain in cattle samples implies that the E. coli gene pool in these animals can be implicated in de novo formation of such highly‐virulent strains. The application of this set of qPCRs in surveillance studies could be an efficient early‐warning tool for the emergence of zoonotic E. coli in livestock.
Construction of an attenuated Salmonella enterica serovar Paratyphi A vaccine strain harboring defined mutations in htrA and yncD
Authors: Zhu Chunyue , Xiong Kun , Chen Zhijin , Hu Xiaomei , Li Jianhua , Wang Yiran , Rao Xiancai , Cong Yanguang 
Published: June 2015

AbstractThe global epidemic features of enteric fever have changed greatly in recent years. The incidence of enteric fever caused by Salmonella enterica serovar Paratyphi A has progressively increased. In some areas of Asia, infections with S. Paratyphi A have exceeded those with S. Typhi, resulting in S. Paratyphi A becoming the main causative agent of enteric fever. However, two currently licensed typhoid vaccines do not confer adequate cross‐protection against S. Paratyphi A infection. Therefore, development of specific vaccines against enteric fever caused by S. Paratyphi A is urgently needed. In the present study, an attenuated strain was constructed by double deletion of the htrA and yncD genes in a wild‐type strain of S. Paratyphi A and its safety and immunogenicity assessed. In a mouse model, the 50% lethal dose of the double deletion mutant and the wild‐type strain were 3.0 × 108 CFU and 1.9 × 103 CFU, respectively, suggesting that the double deletion resulted in remarkably decreased bacterial virulence. Bacterial colonization of the double deletion mutant in the livers and spleens of infected mice was strikingly less than that of the wild‐type strain. A single nasal administration of the attenuated vaccine candidate elicited high concentrations of anti‐LPS and anti‐flagellin IgG in a mouse model and protected immunized mice against lethal challenge with the wild‐type strain. Thus, our findings suggest that the attenuated vaccine strain is a promising candidate worthy of further evaluation both as a human enteric fever vaccine and as a vaccine delivery vector for heterologous antigens.
Endangered Florida panther population size determined from public reports of motor vehicle collision mortalities
Authors: McClintock Brett T. , Onorato Dave P. , Martin Julien 
Published: June 2015

Summary

Reliably estimating the abundance of rare or elusive animals is notoriously difficult. An archetypical example is the endangered Florida panther, whose conservation status is intrinsically linked to population size, but for which reliable abundance information is lacking across its range. This is due not only to the inherent difficulty of sampling a rare and elusive species over a large geographic area, but also because of restricted scientific access to private land.

Human interactions with wildlife are a regular occurrence, and interactions with non‐scientists constitute an important and underutilized source of information about species distribution and abundance. For example, motor vehicle collisions with Florida panthers are recurrent on the vast network of roads within the public and private lands comprising its range in southern Florida, USA.

Capitalizing on a tendency for the public to report collisions with species of concern to wildlife officials, we describe a novel methodology using public reports along with routine telemetry monitoring data to produce the first statistically defensible population estimates for the Florida panther across its entire breeding range. In essence, our approach uses traffic volume and road density to estimate the probability of motor vehicle collision mortality from telemetered animals and models counts reported by the public accordingly.

Despite low motor vehicle collision mortality probabilities, our methodology achieved abundance estimates of reasonable precision (29% CV) that was similar to that of previous panther studies using conventional approaches on much smaller study areas. While recovery criteria require establishment of three distinct populations of 240 Florida panthers, we found this single population may never have exceeded 150 individuals from 2000 to 2012.

Synthesis and applications. By extracting critical demographic information from underutilized aspects of human–wildlife ecology, our citizen‐based approach can cost less than conventional alternatives and could conceivably be used for long‐term population monitoring of other species over broad geographic areas, for example from reports of avian wind farm collisions, beached whales or marine mammal boat strikes. An additional benefit is that it can be applied to historical data sets of carcass recovery programmes, in our case permitting abundance estimation over a 13‐year period.
Spatial occupancy models for predicting metapopulation dynamics and viability following reintroduction
Authors: Chandler Richard B. , Muths Erin , Sigafus Brent H. , Schwalbe Cecil R. , Jarchow Christopher J. , Hossack Blake R. 
Published: June 2015

SummaryThe reintroduction of a species into its historic range is a critical component of conservation programmes designed to restore extirpated metapopulations. However, many reintroduction efforts fail, and the lack of rigorous monitoring programmes and statistical models have prevented a general understanding of the factors affecting metapopulation viability following reintroduction.Spatially explicit metapopulation theory provides the basis for understanding the dynamics of fragmented populations linked by dispersal, but the theory has rarely been used to guide reintroduction programmes because most spatial metapopulation models require presence–absence data from every site in the network, and they do not allow for observation error such as imperfect detection.We develop a spatial occupancy model that relaxes these restrictive assumptions and allows for inference about metapopulation extinction risk and connectivity. We demonstrate the utility of the model using six years of data on the Chiricahua leopard frogLithobates chiricahuensis, a threatened desert‐breeding amphibian that was reintroduced to a network of sites in Arizona USA in 2003.Our results indicate that the model can generate precise predictions of extinction risk and produce connectivity maps that can guide conservation efforts following reintroduction. In the case ofL. chiricahuensis, many sites were functionally isolated, and 82% of sites were characterized by intermittent water availability and high local extinction probabilities (0·84, 95% CI: 0·64–0·99). However, under the current hydrological conditions and spatial arrangement of sites, the risk of metapopulation extinction is estimated to be <3% over a 50‐year time horizon.Low metapopulation extinction risk appears to result from the high dispersal capability of the species, the high density of sites in the region and the existence of predator‐free permanent wetlands with low local extinction probabilities. Should management be required, extinction risk can be reduced by either increasing the hydroperiod of existing sites or by creating new sites to increase connectivity.Synthesis and applications. This work demonstrates how spatio‐temporal statistical models based on ecological theory can be applied to forecast the outcomes of conservation actions such as reintroduction. Our spatial occupancy model should be particularly useful when management agencies lack the funds to collect intensive individual‐level data.
Real Existing Regionalism: The Region between Talk, Territory and Technology
Authors: Addie Jean‐Paul D. , Keil Roger 
Published: June 2015

AbstractIn this essay, we propose the notion of real existing ‘lived’ regionalism as a rejoinder to the normative and ideological debates around new regionalism. Regional forms have shown little convergence in this age of globalized regionalization. Instead of an ideational construct or set of predictable practices, we argue that regionalism is a contested product of discourses (talk), territorial relationships (territory) and technologies (material and of power). The concept of real existing regionalism confronts the tensions between the discursive constructions and normative interventions characterizing much current regionalist debate and the territorial politics and technologies reflecting, generating and directing new state spatial strategic choices. The essay demonstrates the utility of the real existing regionalism framework through an analysis of the greenbelt, transport planning and post‐ suburbanization in Southern Ontario. We argue that regulatory institutions capture the Toronto region in a mix of rhetorical and technological change that complies with neither preconceived notions of regionalization nor the pessimism of total regional dysfunctionality. Rather, the lived experience of regionalization illuminates the emergent assemblages, multiplicity of everyday flows and ongoing multiscalar negotiations of diverse communities that produce the real existing region.