bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes
Authors: Conte Matthew A. , Joshi Rajesh , Moore Emily C. , Nandamuri Sri Pratima , Gammerdinger William J. , Roberts Reade B. , Carleton Karen L. , Lien Sigbjørn , Kocher Thomas D. 
Published: August 2018

AbstractBackgroundAfrican cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to understand the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages.ResultsWe re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We developed a newde novogenome assembly of the Lake Malawi cichlid,Metriaclima zebra, using high-coverage PacBio sequencing, and anchored contigs to linkage groups (LGs) using four different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes.Large intra-chromosomal structural differences (~2-28Mbp) among species are common, while inter-chromosomal differences are rare (< 10Mbp total). Placement of the centromeres within chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11 and LG20 are associated with reductions in recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids.M. zebrahas a larger number of recent transposable element (TE) insertions compared toO. niloticus, suggesting that several TE families have a higher rate of insertion in the haplochromine cichlid lineage.ConclusionThis study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.
Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions
Authors: Richelle Anne , Chiang Austin W.T. , Kuo Chih-Chung , Lewis Nathan E. 
Published: August 2018

AbstractGenome-scale metabolic models provide a valuable context for analyzing data from diverse high-throughput experimental techniques. Models can quantify the activities of diverse pathways and cellular functions. Since some metabolic reactions are only catalyzed in specific environments, several algorithms exist that build context-specific models. However, these methods make differing assumptions that influence the content and associated predictive capacity of resulting models, such that model content varies more due to methods used than cell types. Here we overcome this problem with a novel framework for inferring the metabolic functions of a cell before model construction. For this, we curated a list of metabolic tasks and developed a framework to infer the activity of these functionalities from transcriptomic data. We protected the data-inferred tasks during the implementation of diverse context-specific model extraction algorithms for 44 cancer cell lines. We show that the protection of data-inferred metabolic tasks decreases the variability of models across extraction methods. Furthermore, resulting models better capture the actual biological variability across cell lines. This study highlights the potential of using biological knowledge, inferred from omics data, to obtain a better consensus between existing extraction algorithms. It further provides guidelines for the development of the next-generation of data contextualization methods.
Characterization of cis-prenyltransferase complexes in guayule (Parthenium argentatum), an alternative natural rubber-producing plant
Authors: Lakusta Adam M. , Kwon Moonhyuk , Kwon Eun-Joo , Stonebloom Solomon , Scheller Henrik V. , Ro Dae-Kyun 
Published: August 2018

AbstractGuayule (Parthenium argentatum) is a perennial shrub in the Asteraceae family and synthesizes a high quality, hypoallergenic cis-1,4-polyisoprene (or natural rubber; NR). Despite its potential to be an alternative NR supplier, the enzymes for cis-polyisoprene biosynthesis have not been comprehensively studied in guayule. Recently, implications of the protein complex involving cis-prenyltransferases (CPTs) and CPT-binding proteins (CBPs) in NR biosynthesis were shown in lettuce and dandelion, but such protein complexes have yet to be examined in guayule. Here we identified four guayule genes – three PaCPTs (PaCPT1-3) and one PaCBP, whose protein products form PaCPT/PaCBP complexes. Co-expression of both PaCBP and each of the PaCPTs could complemented the dolichol (a short cis-polyisoprene)-deficient yeast, whereas the individual expressions could not. Microsomes from the PaCPT/PaCBP-expressing yeast efficiently incorporated 14C-isopentenyl diphosphate into dehydrodolichyl diphosphates. Furthermore, co-immunoprecipitation and split-ubiquitin yeast 2-hybrid assays using PaCPTs and PaCBP confirmed the formation of protein complexes. Of the three PaCPTs, transcriptomics analysis indicated that the protein complex formed by PaCPT3 and PaCBP is likely to be the key component in guayule NR biosynthesis. The comprehensive analyses of these PaCPTs and PaCBP here provide the foundational knowledge to generate a high NR-yielding guayule.
Non-coding Class Switch Recombination-related transcription in human normal and pathological immune responses
Authors: Kuri-Magaña Helena , Collado-Torres Leonardo , Jaffe Andrew E. , Valdovinos-Torres Humberto , Ovilla-Muñoz Marbella , Téllez-Sosa Juan M , Bonifaz Alfonzo Laura C , Martinez-Barnetche Jesùs 
Published: August 2018

AbstractBackgroundAntibody class switch recombination (CSR) to IgG, IgA or IgE is a hallmark of adaptive immunity, allowing antibody function diversification beyond IgM. CSR involves a deletion of the IgM/IgD constant region genes placing a new acceptor Constant (CH) gene, downstream of the VDJH exon. CSR depends on non-coding (CSRnc) transcription of donor Iμ and acceptor IH exons, located 5’ upstream of each CH coding gene. Although our knowledge of the role of CSRnc transcription has advanced greatly, its extension and importance in healthy and diseased humans is scarce.MethodsWe analyzed CSRnc transcription in 70,603 publicly available RNA-seq samples, including GTEx, TCGA and the Sequence Read Archive (SRA) using recount2, an online resource consisting of normalized RNA-seq gene and exon counts, as well as coverage BigWig files that can be programmatically accessed through R. CSRnc transcription was validated with a qRT-PCR assay for Iμ, Iγ3 and Iγ1 in humans in response to vaccination.ResultsWe mapped IH transcription for the human IgH locus, including the less understood IGHD gene. CSRnc transcription was restricted to B cells and is widely distributed in normal adult tissues, but predominant in blood, spleen, MALT-containing tissues, visceral adipose tissue and some so-called “immune privileged” tissues. However, significant Iγ4 expression was found even in non-lymphoid fetal tissues. CSRnc expression in cancer tissues mimicked the expression of their normal counterparts, with notable pattern changes in some common cancer subsets. CSRnc transcription in tumors appears to result from tumor infiltration by B cells, since CSRnc transcription was not detected in corresponding tumor-derived immortal cell lines. Additionally, significantly increased I5 transcription in ileal mucosa in Crohn’s disease with ulceration was found.ConclusionsCSRnc transcription occurs in multiple anatomical locations beyond classical secondary lymphoid organs, representing a potentially useful marker of effector B cell responses in normal and pathological immune responses. The pattern of IH exon expression may reveal clues of the local immune response (i.e. cytokine milieu) in health and disease. This is a great example of how the public recount2 data can be used to further our understanding of transcription, including regions outside the known transcriptome.
A Cell Proliferation and Inflammatory Signature is Induced by Lawsonia intracellularis Infection in Swine
Authors: Leite Fernando L. , Abrahante Juan E. , Vasquez Erika , Vannucci Fabio , Gebhart Connie J. , Winkelman Nathan , Mueller Adam , Torrison Jerry , Rambo Zachary , Isaacson Richard E. 
Published: August 2018

AbstractLawsonia intracellularis causes porcine proliferative enteropathy. This is an enteric disease characterized by thickening of the wall of the ileum that leads to decreased growth and diarrhea of animals. In this study, we investigated the host response to L. intracellularis infection by performing transcriptomic and pathway analysis of intestinal tissue in groups of infected and non-infected animals at 14, 21 and 28 days post challenge. At the peak of infection, when animals developed most severe lesions, infected animals expressed higher levels of several genes involved in cellular proliferation and inflammation including matrix metalloproteinase-7 (MMP7), transglutaminase-2 (TGM2) and Oncostatin M (OSM). Histomorphology also revealed general features of intestinal inflammation. This study identified important pathways associated with the host response in developing and resolving lesions due to L. intracellularis infection.ImportanceLawsonia intracellularis is among the most important enteric pathogens of swine and it can also infect other mammalian species. Much is still unknown regarding its pathogenesis and the host response, especially at the site of infection. In this study we uncovered several novel genes and pathways associated with infection. These differentially expressed genes, in addition to histological changes in infected tissue, revealed striking similarities between L. intracellularis infection and cellular proliferation mechanisms described in some cancers and inflammatory diseases of the gastrointestinal tract. This research sheds important light into the pathogenesis of L. intracellularis and the host response associated with the lesions caused by infection.
Mechanical properties of the stigmatic cell wall mediate pollen tube path in Arabidopsis
Authors: Riglet Lucie , Rozier Frédérique , Kodera Chie , Fobis-Loisy Isabelle , Gaude Thierry 
Published: August 2018

ABSTRACTSuccessful fertilization in angiosperms depends on the proper trajectory of pollen tubes through the pistil tissues to reach the ovules. Pollen tubes first grow within the cell wall of the papilla cells, applying pressure to the cell. Mechanical forces are known to play a major role in plant cell shape by controlling the orientation of cortical microtubules (CMTs), which in turn mediate deposition of cellulose microfibrils (CMFs). Here, by combining cell imaging and genetic approaches, we show that isotropic reorientation of CMTs and CMFs in aged andkatanin1-5(ktn1-5) papilla cells is accompanied by a tendency of pollen tubes to coil around the papillae. Furthermore, we uncover that aged andktn1-5papilla cells have a softer cell wall and provide less resistance to pollen tube growth. Our results reveal an unexpected role for KTN1 in pollen tube guidance by ensuring mechanical anisotropy of the papilla cell wall.
The small and large ribosomal subunits depend on each other for stability and accumulation
Authors: Gregory Brian , Rahman Nusrat , Bommakanti Ananth , Shamsuzzaman Md , Thapa Mamata , Lescure Alana , Zengel Janice M. , Lindahl Lasse 
Published: August 2018

AbstractThe 1:1 balance between the numbers of large and small ribosomal subunits can be disturbed by mutations that inhibit the assembly of one of the subunits. We have investigated if the cell has mechanisms to counteract an imbalance of subunits. We show that accumulation of 40S subunits stops after abrogating 60S assembly. In contrast, cessation of the 40S pathways does not prevent 60S accumulation, but does, however, lead to fragmentation of the 25S rRNA in 60S subunits. Even though 40S subunits do not accumulate in the absence of 60S assembly, 40S assembly continues, indicating that excess 40S is degraded after assembly. Thus, the cell expends substantial resources in a futile attempt to increase the number of functional 80S ribosomes. We propose that a mechanism for preventing the accumulation of 40S subunits in excess over 60S subunits may have evolved to prevent mRNAs from being tied up in 40S-mRNA translation initiation complexes that cannot be turned into productive translation complexes because of the deficit of 60S subunits.
Megaprojects – symbolic and sublime: an ontological review
Authors: Syn Thant , Ramaprasad Arkalgud 
Published: August 2018

PurposeMegaprojects are symbolic milestones of human history. Most megaprojects are one-of-a-kind endeavors to which traditional project management principles are neither applicable nor suitable, rendering the holistic study of megaprojects especially difficult. There is no systemic framework that can help systematically assess and guide megaprojects and megaproject research. In the absence of such a framework there is a significant risk of bias in planning the projects and the topics researched. The purpose of this paper is to present an ontological framework of megaprojects and discuss how it can help analyze individual megaprojects and synthesize the corpus of megaproject research.Design/methodology/approachAn ontology framework of megaproject is developed by deconstructing the symbolism and purpose of megaprojects into respective dimensions and their categories. The ontological framework is then used to map the extent literature on megaproject to identify the dominant themes and gaps in the state-of-the-research.FindingsThe megaproject research has predominantly focused on select stakeholders (builders, governments, and communities), translation stages (implementation and conceptualization), and sublime (mostly economic). Other aspects of megaprojects have received little or no attention.Originality/valueThe paper presents an ontological framework to holistically capture the symbolism and sublime of megaprojects. The framework is complete, expansive, and grounded, yet simple, parsimonious, and innovative. It is a tool for decision makers more than a formal ontology readable by machines.
“Power to the workers”
Authors: Leyer Michael , Richter Alexander , Steinhüser Melanie 
Published: August 2018

PurposeThe purpose of this paper is to reveal how information and communication technology (ICT) can empower shop floor workers in collaborative manufacturing environments.Design/methodology/approachThe authors gather data from a mobile maintenance department of a steel manufacturing company and apply the method of a scenario-based design. The authors use data from interviews, observations and company documents to create problem and activity scenarios. The authors also demonstrate the development of a worker-centric digital design in multiple demonstration and evaluation cycles.FindingsThe authors find that ICT can be used to ensure that empowerment is not only a concept, but can sustainably empower daily operations.Research limitations/implicationsThe authors contribute to theory by showing how structural empowerment can be used as a guiding theoretical lens to design ICT for shop floor workers in collaborative manufacturing work environments. These implications are limited to findings from a single case study.Practical implicationsThe results provide an overview of different empowerment dimensions, namely, the access to information, resources, support and opportunities, that can support employees in collaborative manufacturing environments.Originality/valueThis paper is first in suggesting a framework of how ICT designs can be used to empower shop floor workers in collaborative manufacturing environments.
Risk management and firm performance: the moderating role of supplier integration
Authors: Shou Yongyi , Hu Wenjin , Kang Mingu , Li Ying , Park Young Won 
Published: August 2018

PurposeThe purpose of this paper is to scrutinize the performance effects of supply chain risk management (SCRM). Besides financial performance, two aspects of operational performance are examined: operational efficiency and flexibility. Moreover, the authors explore the moderating role of supplier integration in the relationship between SCRM and operational performance.Design/methodology/approachA survey-based methodology was adopted. Based on the data from an international survey, this study applied the structural equation modeling and latent moderated structural equations approach to test the hypotheses.FindingsThe results indicate that SCRM positively influences both operational efficiency and flexibility, and has an indirect effect on financial performance. In addition, supplier integration enhances the impact of SCRM on operational flexibility, but does not moderate the relationship between SCRM and operational efficiency.Originality/valueThis study extends the existing literature by providing a comprehensive analysis of the performance effects of SCRM. It also provides managerial insights on both risk management and supplier integration.
Analyzing operating and support costs for Air Force aircraft
Authors: Hewitson Scott C. , Ritschel Jonathan D. , White Edward , Brown Gregory 
Published: August 2018

Purpose
Recent legislation resulted in an elevation of operating and support (O&S) costs’ relative importance for decision-making in Department of Defense programs. However, a lack of research in O&S hinders a cost analyst’s abilities to provide accurate sustainment estimates. Thus, the purpose of this paper is to investigate when Air Force aircraft O&S costs stabilize and to what degree. Next, a parametric O&S model is developed to predict median O&S costs for use as a new tool for cost analyst practitioners.

Design/methodology/approach
Utilizing the Air Force total ownership cost database, 44 programs consisting of 765 observations from 1996 to 2016 are analyzed. First, stability is examined in three areas: total O&S costs, the six O&S cost element structures and by aircraft type. Next, stepwise regression is used to predict median O&S costs per total active inventory (CPTAI) and identify influential variables.

Findings
Stability results vary by category but generally are found to occur approximately five years from initial operating capability. The regression model explains 89.01 per cent of the variance in the data set when predicting median O&S CPTAI. Aircraft type, location of lead logistics center and unit cost are the three largest contributing factors.

Originality/value
Results from this research provide insight to cost analysts on when to start using actual O&S costs as a baseline for estimates in lieu of analogous cost program data and also derives a new parametric O&S estimating tool designed as a cross-check to current estimating methodologies.
A consumer behavioural approach to food waste
Authors: Aktas Emel , Sahin Hafize , Topaloglu Zeynep , Oledinma Akunna , Huda Abul Kalam Samsul , Irani Zahir , Sharif Amir M. , van’t Wout Tamara , Kamrava Mehran 
Published: August 2018

Purpose
Food waste occurs in every stage of the supply chain, but the value-added lost to waste is the highest when consumers waste food. The purpose of this paper is to understand the food waste behaviour of consumers to support policies for minimising food waste.

Design/methodology/approach
Using the theory of planned behaviour (TPB) as a theoretical lens, the authors design a questionnaire that incorporates contextual factors to explain food waste behaviour. The authors test two models: base (four constructs of TPB) and extended (four constructs of TPB plus six contextual factors). The authors build partial least squares structural equation models to test the hypotheses.

Findings
The data confirm significant relationships between food waste and contextual factors such as motives, financial attitudes, planning routines, food surplus, social relationships and Ramadan.

Research limitations/implications
The data comes from an agriculturally resource-constrained country: Qatar.

Practical implications
Food waste originating from various causes means more food should flow through the supply chains to reach consumers’ homes. Contextual factors identified in this work increase the explanatory power of the base model by 75 per cent.

Social implications
Changing eating habits during certain periods of the year and food surplus have a strong impact on food waste behaviour.

Originality/value
A country is considered to be food secure if it can provide its citizens with stable access to sufficient, safe and nutritious food. The findings and conclusions inform and impact upon the development of food waste and food security policies.
Fire increases drought vulnerability of Quercus alba juveniles by altering forest microclimate and nitrogen availability
Authors: Refsland Tyler , Fraterrigo Jennifer 
Published: August 2018

Abstract

Shifts in rainfall patterns due to climate change are expected to increase drought stress and mortality in forests. Natural and anthropogenic fire regimes are also changing, highlighting the need to understand the interactive effects of fire and drought on tree ecophysiological response and growth.

Using rainout shelters, we imposed summer drought on natural and planted populations of Quercus alba juveniles located in periodically burned and unburned sites in Shawnee National Forest, IL, USA. A subset of planted juveniles was clipped to simulate topkill. We measured predawn leaf water potential (Ψpd), leaf gas exchange (Amax, gmax) and relative growth rate (RGR) across treatments to test two hypotheses: (H1) Fire reduces juvenile drought stress by improving water relations through increased root‐to‐shoot ratios after topkill, or (H2) fire exacerbates juvenile drought stress by promoting a warmer, drier microclimate or amplifying drought‐induced nitrogen (N) limitation.

Burned stands had higher vapour pressure deficits and 13% lower soil inorganic N availability than unburned stands. Rainout shelters reduced soil moisture (0–45 cm) by 10%–24% relative to ambient conditions. Consistent with H2, small, natural resprouts in burned stands experienced greater drought stress than unburned juveniles, with a 7% decrease in leaf nitrogen content (LNC), a 21%–29% reduction in Amax and gmax and a 41% reduction in RGR under drought. Drought effects on unburned juveniles, in contrast, were limited to a 5% reduction in LNC and a neutral to positive effect on leaf gas exchange and RGR. Large natural juveniles were largely unaffected by drought. Recent resprouts (i.e., clipped, planted juveniles) experienced less drought stress than unclipped juveniles, providing partial support for H1.

Collectively, these results suggest that resprouting after fire can temporarily improve leaf water relations until root‐to‐shoot ratios re‐equilibrate. In contrast, fire can exacerbate drought‐driven declines in the growth of small juveniles by both promoting a warmer, drier microclimate and intensifying N limitation. Our results suggest that despite the high drought tolerance of Quercus spp., fire‐driven changes to local microclimate and resource conditions could limit tree recruitment under future scenarios of rainfall variability.

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