bluuebunny/crossref_metadata_2025_split huggingface dataset:
Logistics at holy sites.
Authors: Trono A. 
Published: January 2017

Abstract

After briefly analysing the characteristics of visitors to holy places, this chapter explores the identity and role of large and small operators, both secular and religious, in the organization of pilgrimages and the management of certain holy places in the Western world. The chapter analyses how these operators manage tourist flows at their sites, ensuring availability of infrastructure, transport, communication, facilities and private businesses, including tour operators and hotel providers. It also considers the benefits and the limits of the work they do, as well as the risks and opportunities that 'modern' pilgrimage offers the host regions, with reference to some European places of pilgrimage.
The impact of the Islamic State of Iraq and Syria's campaign on Yezidi religious structures and pilgrimage practices.
Authors: Al-Marashi I. 
Published: January 2017

Abstract

This chapter discusses how the Islamic State of Iraq and Syria (ISIS), through the expulsion of Iraqi Christian Chaldean and 'heterodox' Yezidi and Sabean communities, and the destruction of their religious churches, temples and practices, seeks to create a homogenous neo-Salafi space by 'religious cleansing' of persons and physical structures. The chapter considers the ramifications of such a campaign and how it stretches beyond the local. Eliminating these religious sites severs the opportunity for religious pilgrimage for these minority diaspora and destroys the only spiritual link these exiled, refugee communities possess to their ancestral lands.
Inferential Learning of Serial Order of Perceptual Categories by Rhesus Monkeys (Macaca mulatta)
Authors: Tanner Natalie , Jensen Greg , Ferrera Vincent P. , Terrace Herbert S. 
Published: January 2017

AbstractCategory learning in animals is typically trained explicitly, in most instances by varying the exemplars of a single category in a matching-to-sample task. Here, we show that rhesus macaques can learn categories by a transitive inference paradigm in which novel exemplars of five categories were presented throughout each training session. Instead of requiring decisions about a constant set of repetitively presented stimuli, we studied the macaque’s ability to determine the relative order of multiple exemplars of particular stimuli that were rarely repeated. Ordinal decisions generalized both to novel stimuli and, as a consequence, to novel pairings. Thus, we showed that rhesus monkeys could learn to categorize on the basis of implied ordinal position, and that they could then make inferences about category order. Our results challenge the plausibility of association models of category learning and broaden the scope of the transitive inference paradigm.Significance StatementThe cognitive abilities of non-human animals are of enduring interest to scientists and the general public because they blur the dividing line between human and non-human intelligence. Categorization and sequence learning are highly abstract cognitive abilities each in their own right. This study is the first to provide evidence that visual categories can be ordered serially by macaque monkeys using a behavioral paradigm that provides no explicit feedback about category or serial order. These results strongly challenge accounts of learning based on stimulus-outcome associations.
A Logic-Based Dynamic Modeling Approach to Explicate the Evolution of the Central Dogma of Molecular Biology
Authors: Jafari Mohieddin , Ansari-Pour Naser , Azimzadeh Sadegh , Mirzaie Mehdi 
Published: January 2017

AbstractIt is nearly half a century past the age of the introduction of the Central Dogma (CD) of molecular biology. This biological axiom has been developed and currently appears to be all the more complex. In this study, we modified CD by adding further species to the CD information flow and mathematically expressed CD within a dynamic framework by using Boolean network based on its present-day and 1965 editions. We show that the enhancement of the Dogma not only now entails a higher level of complexity, but it also shows a higher level of robustness, thus far more consistent with the nature of biological systems. Using this mathematical modeling approach, we put forward a logic-based expression of our conceptual view of molecular biology. Finally, we show that such biological concepts can be converted into dynamic mathematical models using a logic-based approach and thus may be useful as a framework for improving static conceptual models in biology.
Ultra-fast Identity by Descent Detection in Biobank-Scale Cohorts using Positional Burrows–Wheeler Transform
Authors: Naseri Ardalan , Liu Xiaoming , Zhang Shaojie , Zhi Degui 
Published: January 2017

AbstractWith the availability of genotyping data of very large samples, there is an increasing need for tools that can efficiently identify genetic relationships among all individuals in the sample. One fundamental measure of genetic relationship of a pair of individuals isidentity by descent(IBD), chromosomal segments that are shared among two individuals due to common ancestry. However, the efficient identification of IBD segments among a large number of genotyped individuals is a challenging computational problem. Most existing methods are not feasible for even thousands of individuals because they are based on pairwise comparisons of all individuals and thus scale up quadratically with sample size. Some methods, such as GERMLINE, use fast dictionary lookup of short seed sequence matches to achieve a near-linear time efficiency. However, the number of short seed matches often scales up super-linearly in real population data.In this paper we describe a new approach for IBD detection. We take advantage of an efficient population genotype index, Positional BWT (PBWT), by Richard Durbin. PBWT achieves linear time query of perfectly identical subsequences among all samples. However, the original PBWT is not tolerant to genotyping errors which often interrupt long IBD segments into short fragments. We introduce a randomized strategy by running PBWTs over random projections of the original sequences. To boost the detection power we run PBWT multiple times and merge the identified IBD segments through interval tree algorithms. Given a target IBD segment length, RaPID adjust parameters to optimize detection power and accuracy.Simulation results proved that our tool (RaPID) achieves almost linear scaling up to sample size and is orders of magnitude faster than GERMLINE. At the same time, RaPID maintains a detection power and accuracy comparable to existing mainstream algorithms, GERMLINE and IBDseq. Running multiple times with various target detection lengths over the 1000 Genomes Project data, RaPID can detect population events at different time scales. With our tool, it is feasible to identify IBDs among hundreds of thousands to millions of individuals, a sample size that will become reality in a few years.
Unifying Population and Landscape Ecology with Spatial Capture-recapture
Authors: Royle J. Andrew , Fuller Angela K. , Sutherland Christopher 
Published: January 2017

AbstractSpatial heterogeneity in the environment induces variation in population demographic rates and dispersal patterns, which result in spatio-temporal variation in density and gene flow. Unfortunately, applying theory to learn about the role of spatial structure on populations has been hindered by the lack of mechanistic spatial models and inability to make precise observations of population structure. Spatial capture-recapture (SCR) represents an individual-based analytic framework for overcoming this fundamental obstacle that has limited the utility of ecological theory. SCR methods make explicit use of spatial encounter information on individuals in order to model density and other spatial aspects of animal population structure, and have been widely adopted in the last decade. We review the historical context and emerging developments in SCR models that enable the integration of explicit ecological hypotheses about landscape connectivity, movement, resource selection, and spatial variation in density, directly with individual encounter history data obtained by new technologies (e.g., camera trapping, non-invasive DNA sampling). We describe ways in which SCR methods stand to revolutionize the study of animal population ecology.
Cryo-Electron Microscopy Structure of theMacrobrachium rosenbergiiNodavirus Capsid at 7 Angstroms Resolution
Authors: Ho Kok Lian , Kueh Chare Li , Beh Poay Ling , Tan Wen Siang , Bhella David 
Published: January 2017

AbstractWhite tail disease in the giant freshwater prawnMacrobrachium rosenbergiicauses significant economic losses in shrimp farms and hatcheries and poses a threat to food-security in many developing countries. Outbreaks ofMacrobrachium rosenbergiinodavirus (MrNV), the causative agent of white tail disease (WTD) are associated with up to 100% mortality rates. Recombinant expression of the capsid protein ofMrNV in insect cells leads to the production of VLPs closely resembling the native virus. We have investigated the structure ofMrNV VLPs by cryogenic electron microscopy, determining a structure of the viral capsid at 7 angstroms resolution. Our data show thatMrNV VLPs package nucleic acids in a manner reminiscent of other known nodavirus structures. The structure of the capsid however shows striking differences from insect and fish infecting nodaviruses, which have been shown to assemble trimer-clustered T=3 icosahedral virus particles.MrNV particles have pronounceddimericblade-shaped spikes extending up to 6 nm from the outer surface of the capsid shell. Our structural analysis supports the assertion thatMrNV along with the related virus of marine shrimpPenaeus vannameinodavirus (PvNV) may represent a new genus of theNodaviridae.Author summaryMacrobrachium rosenbergiinodavirus (MrNV) is the causative agent of white tail disease (WTD) which leads to 100% mortality in shrimp-farms growing giant freshwater prawn (M. rosenbergii).MrNV is therefore a significant threat to food security and causes severe economic losses in developing countries such as Malaysia, Indonesia, Pakistan, Thailand and India. Here we have used electron microscopy to study the three-dimensional structure ofMrNV, revealing that the viral capsid – the protein shell that encloses the viral genome, protecting it and transporting it from one host to the next – is differently organised to capsids produced by other viruses in the nodavirus family. The virus was found to have large blade-like spikes on its outer surface that are likely important in the early stages of infection, when the virus attaches to and enters a host cell.
States and traits of neural irregularity in the age-varying human brain
Authors: Waschke Leonhard , Wöestmann Malte , Obleser Jonas 
Published: January 2017

AbstractSensory representations of the physical world and thus human percepts are susceptible to fluctuations in brain state or “neural irregularity”. Furthermore, aging brains display altered levels of irregularity. We here show that a single, within-trial information-theoretic measure (weighted permutation entropy) captures neural irregularity in the human electroencephalogram as a proxy for both, trait-like differences between individuals of varying age, and state-like fluctuations that bias perceptual decisions. First, the overall level of neural irregularity increased with participants‘ age, paralleled by a decrease in variability over time, likely indexing age-related disintegration on structural and functional levels of brain activity. Second, states of higher neural irregularity were associated with optimized sensory encoding and a subsequently increased probability of choosing the first of two physically identical stimuli. In sum, neural irregularity not only characterizes behaviorally relevant brain states, but also can identify trait-like changes that come with age.
Remodeling Pathway Control of Oxidative Phosphorylation by Temperature in the Heart
Authors: Lemieux Hélène , Blier Pierre U. , Gnaiger Erich 
Published: January 2017

AbstractThe capacity of mitochondrial oxidative phosphorylation (OXPHOS) and fuel substrate supply are key determinants of cardiac muscle performance. Although temperature exerts a strong effect on energy metabolism, until recently numerous respiratory studies of mammalian mitochondria have been carried out below physiological temperature, with substrates supporting submaximal respiratory capacity. We measured mitochondrial respiration as a function of temperature in permeabilized fibers from the left ventricle of the mouse heart. At 37 °C, OXPHOS capacity with electron entry through either Complex I or Complex II into the Q-junction was about half of respiratory capacity with the corresponding physiological substrate combination reconstituting tricarboxylic acid cycle function with convergent electron flow through the NADH&succinate (NS) pathway. When separating the component core mitochondrial pathways, the relative contribution of the NADH pathway increased with a decrease of temperature from 37 to 25 ºC. The additive effect of convergent electron flow has profound consequences for optimization of mitochondrial respiratory control. The apparent excess capacity of cytochromecoxidase (CIV) was 0.7 above convergent NS-pathway capacity, but would be overestimated nearly 2-fold with respect to respiration restricted by provision of NADH-linked substrates only. The apparent excess capacity of CIV increased sharply at 4 °C, caused by a strong temperature dependence of and OXPHOS limitation by NADH-linked dehydrogenases. This mechanism of mitochondrial respiratory control in the hypothermic mammalian heart is comparable to the pattern in ectotherm species, pointing towards NADH-linked mt-matrix dehydrogenases and the phosphorylation system rather than electron transfer complexes as the primary drivers of thermal sensitivity at low temperature and likely modulators of temperature adaptation and acclimatization. Delineating the link between stress and remodeling of OXPHOS is critically important for improving our understanding of metabolic perturbations in disease evolution and cardiac protection. Temperature is not a trivial experimental parameter to consider when addressing these questions.
LRSim: a Linked Reads Simulator generating insights for better genome partitioning
Authors: Luo Ruibang , Sedlazeck Fritz J. , Darby Charlotte A. , Kelly Stephen M. , Schatz Michael C. 
Published: January 2017

AbstractMotivationLinked reads are a form of DNA sequencing commercialized by 10X Genomics that uses highly multiplexed barcoding within microdroplets to tag short reads to progenitor molecules. The linked reads, spanning tens to hundreds of kilobases, offer an alternative to long-read sequencing forde novoassembly, haplotype phasing and other applications. However, there is no available simulator, making it difficult to measure their capability or develop new informatics tools.ResultsOur analysis of 13 real linked read datasets revealed their characteristics of barcodes, molecules and partitions. Based on this, we introduce LRSim that simulates linked reads by emulating the library preparation and sequencing process with fine control of 1) the number of simulated variants; 2) the linked-read characteristics; and 3) the Illumina reads profile. We conclude from the phasing and genome assembly of multiple datasets, recommendations on coverage, fragment length, and partitioning when sequencing human and non-human genome.AvailabilityLRSIM is under MIT license and is freely available athttps://github.com/aquaskyline/LRSIMContactrluo5@jhu.edu
Mapping load-bearing in the mammalian spindle reveals local kinetochore-fiber anchorage that provides mechanical isolation and redundancy
Authors: Williard Elting Mary , Prakash Manu , Udy Dylan B. , Dumont Sophie 
Published: January 2017

SummaryActive forces generated at kinetochores move chromosomes, and the dynamic spindle must robustly anchor kinetochore-fibers (k-fibers) to bear this load. We know that the mammalian spindle body can bear the load of chromosome movement far from poles, but do not know where and how – physically and molecularly – this load is distributed across the spindle. In part, this is because perturbing and reading out spindle mechanics in live cells is difficult. Yet, answering this question is key to understanding how the spindle generates and responds to force, and performs its diverse mechanical functions. Here, we map load-bearing across the mammalian spindle in space-time, and dissect local anchorage mechanics and mechanism. To do so, we laser ablate single k-fibers at different spindle locations, and in different molecular backgrounds, and quantify at high time resolution the immediate relaxation of chromosomes, k-fibers, and microtubule speckles. We find that load redistribution is locally confined in all directions: along the first 3-4 μm from kinetochores, scaling with k-fiber length, and laterally within ~2 μm of k-fiber sides, without neighboring k-fibers sharing load. A phenomenological model constrains the mechanistic underpinnings of these data: it suggests that dense, transient crosslinks to the spindle along k-fibers bear the load of chromosome movement, but that these connections do not limit the timescale of spindle reorganization. The microtubule crosslinker NuMA is needed for the local load-bearing observed, while Eg5 and PRC1 are not, suggesting specialization in mechanical function and a novel function for NuMA throughout the spindle body. Together, the data and model suggest that widespread NuMA-mediated crosslinks locally bear load, providing mechanical isolation and redundancy while allowing spindle fluidity. These features are well-suited to support robust chromosome segregation.
Mixed-model multi-manned assembly line balancing problem: a mathematical model and a simulated annealing approach
Authors: Roshani Abdolreza , Ghazi Nezami Farnaz 
Published: January 2017

Purpose
This paper aims to study a generalized type of mixed-model assembly line with multi-manned workstations where multiple workers simultaneously perform different tasks on the same product. This special kind of assembly line is usually utilized to assemble different models of large products, such as buses and trucks, on the same production line.

Design/methodology/approach
To solve the mixed-model multi-manned assembly line balancing problem optimally, a new mixed-integer-programming (MIP) model is presented. The proposed MIP model is nondeterministic polynomial-time (NP)-hard, and as a result, a simulated annealing (SA) algorithm is developed to find the optimal or near-optimal solution in a small amount of computation time.

Findings
The performance of the proposed algorithm is examined for several test problems in terms of solution quality and running time. The experimental results show that the proposed algorithm has a satisfactory performance from computational time efficiency and solution accuracy.

Originality/value
This research is the very first study that minimizes the number of workers and workstations simultaneously, with a higher priority set for the number of workers, in a mixed-model multi-manned assembly line setting using a novel MIP model and an SA algorithm.
Space claim analysis for addressing maintenance of key components in complex products
Authors: Moscheto Andre Diogo , Cziulik Carlos , Junior Simão Marcon , Sulevis Marcos 
Published: January 2017

Purpose
The purpose of this paper is to provide a new approach involving guidelines and supporting techniques that guarantees all needed space for appropriate product maintenance.

Design/methodology/approach
The approach is based on two major areas: field survey to understand how maintainability parameter is applied and converge theory and practice into a systematic space claim method using computer-aided design (CAD) systems to assure proper maintenance procedures at design stages.

Findings
Case studies from a truck industry conducted following the proposed approach contrast the savings that can be achieved by using a proper space claim for aftermarket needs against an unsuitable level of participation by maintenance personnel during the design development.

Research limitations/implications
This approach is highly dependent on maintenance experts with suitable skills on CAD systems.

Practical implications
Products developed according to the approach envisaged can result in following aspects: lower repair time, better maintenance procedures on key components, easier preventive maintenance, less need for special tools, more ergonomic design, better communication between design and service engineers, simplicity and less complex training.

Social implications
Further research on maintainability will provide new information on how to apply this parameter on product development process (PDP), so design teams can better understand and address this relevant issue. The proposed method has been introduced in the PDP of a major multinational automotive company.

Originality/value
A new process is presented, considering the protection of needed spaces for maintenance procedures throughout the PDP, diverging to other studies that only propose analysis addressing maintainability at singular point in time during the product development. In just one case study presented, savings of US$1.3m were achieved by applying this space claim approach.
Investigations for improving the surface finish of FDM based ABS replicas by chemical vapor smoothing process: a case study
Authors: Singh Jaspreet , Singh Rupinder , Singh Harwinder 
Published: January 2017

Purpose
This research work aims to make an effort to investigate the effect of fused deposition modelling (FDM) process parameters on the surface finish of acrylonitrile butadiene styrene (ABS) replicas (as pre-processing stage), followed by chemical vapor smoothing (CVS) process (as a post-processing stage) as a case study.

Design/methodology/approach
The Taguchi L18 orthogonal array has been used for optimizing process parameters of FDM and CVS processes.

Findings
This study highlights that orientation and part density, and the interaction between these two have a significant effect on the surface finish at the pre-processing stage of FDM. However, after post-processing with CVS, there is hardly any influence of pre-processing FDM parameters.

Originality/value
The study highlights that for improving the productivity of the FDM process, the parametric optimization of process may be made on the basis of production cost and time in place of surface finish of ABS replicas. The results obtained have been verified by performing the confirmation experiments.
Enhancing theory development in the domain of relationship marketing: how to avoid the danger of getting stuck in the middle
Authors: Brodie Roderick J. 
Published: January 2017

Purpose
This study aims to explore how relationship marketing can sustain the position as a major domain for academic research and avoid premature stagnation.

Design/methodology/approach
The paper outlines a process in which theory informs empirical research and practice, and at the same time, where practice informs empirical research and theory. This requires giving attention to the process of theorizing itself, rather than treating theory as an outcome. To facilitate this outcome, mid-range theorizing needs to be embedded in the processes.

Findings
The application of mid-range theorizing processes is illustrated. Examples are provided to show how a broader “transcending” relational network perspective informs empirical research, and to illustrate how marketing practice can be used to inform empirical research and theoretical knowledge.

Originality/value
New thinking is provided about enhancing theory development to ensure relationship marketing remains a major domain for research.