bluuebunny/crossref_metadata_2025_split huggingface dataset:
From axiomatics of quantum probability to modelling geological uncertainty and management of intelligent hydrocarbon reservoirs with the theory of open quantum systems
Authors: Lozada Aguilar Miguel Ángel , Khrennikov Andrei , Oleschko Klaudia 
Published: March 2018

As was recently shown by the authors, quantum probability theory can be used for the modelling of the process of decision-making (e.g. probabilistic risk analysis) for macroscopic geophysical structures such ashydrocarbon reservoirs.This approach can be considered as a geophysical realization of Hilbert's programme on axiomatization of statistical models in physics (the famous sixth Hilbert problem). In thisconceptual paper, we continue development of this approach to decision-making under uncertainty which is generated by complexity, variability, heterogeneity, anisotropy, as well as the restrictions to accessibility of subsurface structures. The belief state of a geological expert about the potential of exploring a hydrocarbon reservoir is continuously updated by outputs of measurements, and selection of mathematical models and scales of numerical simulation. These outputs can be treated as signals from theinformation environment E. The dynamics of the belief state can be modelled with the aid of the theory of open quantum systems: a quantum state (representing uncertainty in beliefs) is dynamically modified through coupling withE; stabilization to a steady state determines a decision strategy. In this paper, the process of decision-making about hydrocarbon reservoirs (e.g. ‘explore or not?'; ‘open new well or not?’; ‘contaminated by water or not?’; ‘double or triple porosity medium?’) is modelled by using theGorini–Kossakowski–Sudarshan–Lindbladequation. In our model, this equation describes the evolution of experts' predictions about a geophysical structure. We proceed with theinformation approach to quantum theoryand the subjective interpretation of quantum probabilities (due to quantum Bayesianism).This article is part of the theme issue ‘Hilbert's sixth problem’.
Boltzmann equation and hydrodynamics beyond Navier–Stokes
Authors: Bobylev A. V. 
Published: March 2018

We consider in this paper the problem of derivation and regularization of higher (in Knudsen number) equations of hydrodynamics. The author’s approach based on successive changes of hydrodynamic variables is presented in more detail for the Burnett level. The complete theory is briefly discussed for the linearized Boltzmann equation. It is shown that the best results in this case can be obtained by using the ‘diagonal’ equations of hydrodynamics. Rigorous estimates of accuracy of the Navier–Stokes and Burnett approximations are also presented.
This article is part of the theme issue ‘Hilbert’s sixth problem’.
Scale matters
Authors: Margolin L. G. 
Published: March 2018

The applicability of Navier–Stokes equations is limited to near-equilibrium flows in which the gradients of density, velocity and energy are small. Here I propose an extension of the Chapman–Enskog approximation in which the velocity probability distribution function (PDF) is averaged in the coordinate phase space as well as the velocity phase space. I derive a PDF that depends on the gradients and represents a first-order generalization of local thermodynamic equilibrium. I then integrate this PDF to derive a hydrodynamic model. I discuss the properties of that model and its relation to the discrete equations of computational fluid dynamics.
This article is part of the theme issue ‘Hilbert’s sixth problem’.
Blessing of dimensionality: mathematical foundations of the statistical physics of data
Authors: Gorban A. N. , Tyukin I. Y. 
Published: March 2018

The concentrations of measure phenomena were discovered as the mathematical background to statistical mechanics at the end of the nineteenth/beginning of the twentieth century and have been explored in mathematics ever since. At the beginning of the twenty-first century, it became clear that the proper utilization of these phenomena in machine learning might transform thecurse of dimensionalityinto theblessing of dimensionality. This paper summarizes recently discovered phenomena of measure concentration which drastically simplify some machine learning problems in high dimension, and allow us to correct legacy artificial intelligence systems. The classical concentration of measure theorems state that i.i.d. random points are concentrated in a thin layer near a surface (a sphere or equators of a sphere, an average or median-level set of energy or another Lipschitz function, etc.). The newstochastic separation theoremsdescribe the thin structure of these thin layers: the random points are not only concentrated in a thin layer but are all linearly separable from the rest of the set, even for exponentially large random sets. The linear functionals for separation of points can be selected in the form of the linear Fisher’s discriminant. All artificial intelligence systems make errors. Non-destructive correction requires separation of the situations (samples) with errors from the samples corresponding to correct behaviour by a simple and robust classifier. The stochastic separation theorems provide us with such classifiers and determine a non-iterative (one-shot) procedure for their construction.This article is part of the theme issue ‘Hilbert’s sixth problem’.
Acquisition and loss of secondary metabolite clusters shaped the evolutionary path of three recently emerged phytopathogens of wheat
Authors: Thynne Elisha , Mead Oliver L. , Chooi Yit-Heng , McDonald Megan C. , Solomon Peter S. 
Published: March 2018

SummaryWhite grain disorder is a recently emerged wheat disease in Australia, caused by threeBotryosphaeriaceae spp.;Eutiarosporella darliae, E. pseudodarliae, andE. tritici-australis. The disease cycle of these pathogens and the molecular basis of their interaction with wheat are poorly understood. To address this, we undertook a comparative genomics approach to identify potential pathogenicity factors.Subsequent genome analysis revealed that each of the white grain disorder species harbour modular polyketide synthase genes. To our knowledge, this is the first report of fungi harbouring such genes. Further comparative analysis using the modular polyketide synthase genes discovered their presence in the closely relatedMacrophomina phaseolina. Phylogenetic analysis implicates horizontal acquisition of these genes from a bacterial or a protist species.BothE. darliaeandE. pseudodarliaepossess a secondary metabolite cluster with multiple polyketide/non-ribosomal peptide synthase genes (Hybrid-1, -2, and -3). In contrast, only remnant and partial genes homologous to this cluster were identified at a syntenic locus inE. tritici-australissuggesting loss of this cluster. Homologues ofHybrid-2in other fungi have been proposed to facilitate disease induction in woody plants. Subsequent assays confirmed thatE. darliaeandE. pseudodarliaewere both pathogenic on woody plant hosts, butE. tritici-australiswas not, implicating woody plants as potential host reservoirs for the fungi. We hypothesise that loss of the cluster inE. tritici-australisrepresents a committed lifestyle jump to grasses.Combined, our observations relating to the secondary metabolite potential of the WGDEutiarosporella spp.have contributed novel data to the field by expanding the range of known fungal secondary metabolite genes, and helped develop our understanding of the lifestyle and potential host-range of a recently emerged pathogen of wheat.
The expansion in lymphoid organs of IL-4+BATF+ T follicular helper cells is linked to IgG4 class switchingin vivo
Authors: Maehara Takashi , Mattoo Hamid , Mahajan Vinay S. , Murphy Samuel J.H. , Yuen Grace J. , Ishiguro Noriko , Ohta Miho , Moriyama Masafumi , Saeki Takako , Yamamoto Hidetaka , Yamauchi Masaki , Daccache Joe , Kiyoshima Tamotsu , Nakamura Seiji , Stone John H. , Pillai Shiv 
Published: March 2018

ABSTRACTDistinct TFHsubsets that influence specific class-switching events are assumed to exist, but the accumulation of isotype-specific TFHsubsets in secondary and tertiary lymphoid organs has not been hitherto demonstrated. IL-4 expressing TFHcells are surprisingly sparse in human secondary lymphoid organs. In sharp contrast, in IgG4-related disease (IgG4-RD), a disorder characterized by polarized Ig class switching, most TFHcells in tertiary and secondary lymphoid organs make IL-4. Human IL-4+TFHcells do not express GATA-3 but express nuclear BATF, and the transcriptomes of IL-4 secreting TFHcells differ both from PD1hiTFHcells that do not secrete IL-4 and IL4-secreting non-TFHcells. Unlike IgG4-RD, IL-4+TFHcells are rarely found in tertiary lymphoid organs in Sjögren’s syndrome, a disorder in which IgG4 is not elevated. The proportion of CD4+IL-4+BATF+T cells as well as of CD4+IL-4+CXCR5+T cells in IgG4-RD tissues correlates tightly with tissue IgG4 plasma cell numbers and plasma IgG4 levels in patients but not with the total plasma levels of other isotypes. These data describe a disease-related TFHsub-population in human tertiary and secondary lymphoid organs that is linked to IgG4 class switching.
Paracingulate sulcus morphology and hallucinations in clinical and non-clinical groups
Authors: Garrison Jane R. , Fernyhough Charles , McCarthy-Jones Simon , Simons Jon S. , Sommer Iris E.C. 
Published: March 2018

AbstractHallucinations are a characteristic symptom of psychotic mental health conditions that are also experienced by many individuals without a clinical diagnosis. Research has linked the experience of hallucinations in schizophrenia to differences in the length of the paracingulate sulcus (PCS), a structure in the medial prefrontal cortex of the brain which has previously been associated with the ability to differentiate perceived and imagined information. We investigated whether this notion of a specific morphological basis for hallucinations in the paracingulate cortex extends to individuals without a clinical diagnosis by testing the hypothesis that non-clinical individuals with hallucinations have shorter PCS than non-clinical individuals without hallucinations. Structural MRI scans were examined from three demographically matched groups of individuals: 50 patients with psychotic diagnoses who experienced auditory verbal hallucinations, 50 non-clinical individuals with auditory verbal hallucinations, and 50 healthy control subjects with no life-time history of hallucinations. Measurements of paracingulate sulcal length were compared between the groups and the results verified using automated data-driven gyrification analyses. Patients with hallucinations had shorter PCS than both healthy controls and non-clinical individuals with hallucinations, with no difference between non-clinical individuals with hallucinations and healthy controls. These findings suggest that the association of shorter PCS length with hallucinations is specific to patients with a psychotic disorder. This presents challenges for continuum models of psychosis and suggests possible differences in the mechanisms underlying hallucinations in clinical and non-clinical groups.
Finding reliable phenotypes and detecting artefacts among in vivo and in vitro assays to characterize the refractory transcriptional activator Sxy (TfoX) in Escherichia coli
Authors: Alshabib Ebtihal Y. , Fitzgerald Stephen F. , Chao Tzu-Chiao , Cameron Rhiannon C. , Redfield Rosemary J. , Sinha Sunita , Cameron Andrew D.S. 
Published: March 2018

AbstractThe Sxy (TfoX) protein is required for expression of a distinct subset of the genes regulated by the cAMP receptor protein (CRP) in the model organisms Escherichia coli, Haemophilus influenzae, and Vibrio cholerae. Genetic studies have established that CRP and Sxy co-activate transcription at gene promoters containing DNA binding sites called CRP-S sites. In contrast, CRP acts without Sxy at gene promoters containing canonical CRP-N sites, suggesting that Sxy makes physical contacts with CRP and/or DNA to assist in transcriptional activation at CRP-S promoters. Despite growing interest in Sxy’s activity as a transcription factor, Sxy remains poorly characterized due to a lack of reliable phenotypes in E. coli. Experiments are further hampered by growth inhibition and formation of inclusion bodies when Sxy is overexpressed. In this study we applied diverse phenotypic and molecular assays to test for postulated Sxy functions and interactions. Mutations in conserved regions of Sxy and truncations in the Sxy C-terminus abolish transcriptional activation of a CRP-S promoter, and a 37 amino acid truncation of the C-terminus relieves the growth inhibition normally caused by Sxy overexpression. Sxy was unable to augment weakened CRP interactions to restore carbon metabolism phenotypes. Bandshift analysis and chromatin pull-down assays of Sxy-CRP-DNA interactions yielded intriguing evidence of CRP-Sxy and Sxy-DNA physical interactions. However, despite the careful application of standard protein purification protocols and quality control steps for nickel affinity column purification, protein mass spectrometry revealed the enrichment of additional DNA-binding proteins in nickel column eluates, presenting a probable source of artefactual protein-protein and protein-DNA interaction results. These findings highlight the importance of extensive controls and phenotypic assays for the study of poorly characterized and recalcitrant proteins like Sxy.
Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two sexual species
Authors: Denton Robert D. , Morales Ariadna E. , Gibbs H. Lisle 
Published: March 2018

AbstractQuantifying genetic introgression between sexual species and polyploid lineages traditionally thought to be asexual is an important step in understanding what factors drive the longevity of putatively asexual groups. However, the presence of multiple distinct subgenomes within a single lineage provides a significant logistical challenge to evaluating the origin of genetic variation in most polyploids. Here, we capitalize on three recent innovations—variation generated from ultraconserved elements (UCEs), bioinformatic techniques for assessing variation in polyploids, and model-based methods for evaluating historical gene flow—to measure the extent and tempo of introgression over the evolutionary history of an allopolyploid lineage of all-female salamanders and two ancestral sexual species. We first analyzed variation from more than a thousand UCEs using a reference mapping method developed for polyploids to infer subgenome specific patterns of variation in the all-female lineage. We then used PHRAPL to choose between sets of historical models that reflected different patterns of introgression and divergence between the genomes of the parental species and the same genomes found within the polyploids. Our analyses support a scenario in which the genomes sampled in unisexuals salamanders were present in the lineage ∼3.4 million years ago, followed by an extended period of divergence from their parental species. Recent secondary introgression has occurred at different times between each sexual species and their representative genomes within the unisexuals during the last 500,000 years. Sustained introgression of sexual genomes into the unisexual lineage has been the defining characteristic of their reproductive mode, but this study provides the first evidence that unisexual genomes have also undergone long periods of divergence without introgression. Unlike other unisexual, sperm-dependent taxa in which introgression is rare, the alternating periods of divergence and introgression between unisexual salamanders and their sexual relatives could reveal the scenarios in which the influx of novel genomic material is favored and potentially explain why these salamanders are among the oldest described unisexual animals.
Region Specific Central Arbor Morphologies of Nociceptive Afferents Develop Independently of Their Peripheral Target Innervation
Authors: Olson William , Luo Wenqin 
Published: March 2018

ABSTRACTFunctionally important regions of sensory maps are overrepresented in the sensory pathways and cortex, but the underlying developmental mechanisms are not clear. In the spinal cord dorsal horn (DH), we recently showed that paw innervating Mrgprd+ non-peptidergic nociceptors display distinctive central arbor morphologies that well correlate with increased synapse transmission efficiency and heightened sensitivity of distal limb skin. Given that peripheral and central arbor formation of Mrgprd+ neurons co-occurs around the time of birth, we tested whether peripheral cues from different skin areas and/or postnatal reorganization mechanisms could instruct this somatotopic difference among central arbors. We found that, while terminal outgrowth/refinement occurs during early postnatal development in both the skin and the DH, postnatal refinement of central terminals precedes that of peripheral terminals. Further, we used single-cell ablation of Ret to genetically disrupt epidermal innervation of Mrgprd+ neurons and revealed that the somatotopic difference among their central arbors was unaffected by this manipulation. Finally, we saw that region-specific Mrgprd+ central terminal arbors are present from the earliest postnatal stages, before skin terminals are evident. Together, our data indicate that region-specific organization of Mrgprd+ neuron central arbors develops independently of peripheral target innervation and is present shortly after initial central terminal formation, suggesting that either cell-intrinsic and/or DH local signaling may establish this somatotopic difference.
Farm business financial performance in local foods value chains
Authors: Ahearn Mary Clare , Liang Kathleen , Goetz Stephan 
Published: March 2018

Purpose
The purpose of this paper is to identify the factors associated with farm financial success for those farms known to produce for local supply chains. The analysis considers alternative measures of farm financial performance and considers the role of the local foods supply chain in the choice to market locally.

Design/methodology/approach
The paper uses a two-stage Heckman approach which addresses the possibility of sample selection bias. In the first stage, the choice model to engage in direct marketing is estimated. In the second stage, the authors estimate a model of the financial performance of those in the sample that direct marketed which includes an IMR term calculated from the parameters of the first stage equation. The analysis uses national farm-level data from the Agricultural and Resource Management Survey of the US Department of Agriculture and combines data from 2009 to 2012 to overcome the constraint of small samples.

Findings
Indicators of the development of a local foods supply were positively related to the choice to engage in direct marketing. Factors affecting farm financial performance varied significantly between a short-term and a long-term measure. The results emphasize the importance of considering multiple outcome measures, developing local supply chains and provide implications about beginning farms.

Originality/value
If a local foods system is going to thrive, the farms that market the agricultural products in the local food system must attain a certain level of profitability. The value of the analysis is an improved understanding of the financial performance of farms producing for a small, but growing segment of the food supply chain.
Human vulnerability and robo-advisory
Authors: Beltramini Enrico 
Published: March 2018

Purpose
The purpose of this paper is to introduce the work of Mark Coeckelbergh into the field of management.

Design/methodology/approach
This is a conceptual paper with interviews.

Findings
The author suggests that Coeckelberghs’ considerations of an anthropology of vulnerability have the potential to provide a rich and insightful exploration of the machine-human interface, which is not afforded by many of the current approaches taken in this field. Their development of an anthropology of vulnerability suggests an approach to the machine-human interface that re-frames the machine-human interface in terms of human vulnerability, rather than machine’s performance, and sustains that the machine-human interface can be understood in terms of the transfer of human vulnerability.

Research limitations/implications
This paper reveals some of the possibilities inherent in Coeckelbergh’s theories by providing an analysis of a specific event, the recent introduction of robo-advisors in portfolio management, from a Coeckelberghian perspective and by exploring some of the implications of this type of approach for the machine-human interface.

Originality/value
As far as the author knows, there is no previous paper on this topic.
Maintaining digital collections with declining resources, fewer staff
Authors: Walker Wendy , Keenan Teressa 
Published: March 2018

Purpose
The purpose of this paper is to describe methods for restructuring workflows and efficiently using staff members and volunteers to continue work on multiple, simultaneous digital collections as budgets and resources decline.

Design/methodology/approach
This paper describes one library’s varied approaches to several digital collections supported by literature or volunteers in libraries.

Findings
In the face of continually declining resources and new, time-sensitive priorities and compliance responsibilities, librarians can continue to maintain digital collections by modifying workflows, using the services of volunteers and communicating strategically.

Practical implications
This paper is relevant to librarians, archivists and others who are looking for ways to justify and capitalize on the use of unconventional personnel in digital collections programs.

Originality/value
This paper presents a case of the successful use of volunteers to accomplish digital collections-related tasks in an academic library and provides a communication-based strategy for addressing some of the challenges related to volunteers in academic libraries.