bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing Combinability of Phylogenomic Data using Bayes Factors
Authors: Neupane Suman , Fučíková Karolina , Lewis Louise A. , Kuo Lynn , Chen Ming-Hui , Lewis Paul O. 
Published: January 2018

ABSTRACTWith the rapid reduction in sequencing costs of high-throughput genomic data, it has become commonplace to use hundreds of genes/sites to infer phylogeny of any study system. While sampling large number of genes has given us a tremendous opportunity to uncover previously unknown relationships and improve phylogenetic resolution, it also presents us with new challenges when the phylogenetic signal is confused by differences in the evolutionary histories of sampled genes. Given the addition of accurate marginal likelihood estimation methods into popular Bayesian software programs, it is natural to consider using the Bayes Factor (BF) to compare different partition models in which genes within any given partition subset share both tree topology and edge lengths. We explore using marginal likelihood to assess data subset combinability when data subsets have varying levels of phylogenetic discordance due to deep coalescence events among genes (simulated within a species tree), and compare the results with our recently-described phylogenetic informational dissonance index (D) estimated for each data set. BF effectively detects phylogenetic incongruence, and provides a way to assess the statistical significance of D values. We discuss methods for calibrating BFs, and use calibrated BFs to assess data combinability using an empirical data set comprising 56 plastid genes from green algae order Volvocales.
Gene flow and Andean uplift shape the diversification ofGasteracantha cancriformis(Araneae: Araneidae) in Northern South America
Authors: Salgado-Roa Fabian C. , Pardo-Diaz Carolina , Paulis Eloisa Lasso De , Arias Carlos F. , Solferini Vera Nisaka , Salazar Camilo 
Published: January 2018

ABSTRACTAimThe Andean uplift has played a major role shaping the current Neotropical biodiversity. However, in arthropods other than butterflies, little is known about how this geographic barrier has impacted species historical diversification. Here we examined the phylogeography of the widespread and color polymorphic spiderGasteracantha cancriformisto: (i) evaluate the effect of the northern Andean uplift on its divergence and, (ii) assess whether its diversification occurred in the presence of gene flow.LocationNorthern Andes and BrazilMethodsWe inferred phylogenetic relationships and divergence times inG. cancriformisusing mitochondrial and nuclear data from 105 individuals in northern South America. Genetic diversity, divergence and population structure were quantified. We also compared multiple demographic scenarios for this species using a model-based approach (PHRAPL) to establish divergence with or without gene flow. Finally, we evaluated the association between genetic variation and color polymorphism.ResultsBoth nuclear and mitochondrial data supported two well-differentiated clades, which correspond to populations occurring in opposite sides of the Eastern cordillera of the Colombian Andes. The splitting between these clades occurred in the early Pleistocene, around 2.13 million years ago (95% HPD = 0.98–3.93).Despite this vicariant event, there is shared genetic variation between the clades, which is better explained by a scenario of historical divergence in the face of gene flow. Color polymorphism was randomly scattered in both clades and is not statistically associated with the genetic variation studied here.Main ConclusionsThe final uplift of Eastern cordillera of the Colombian Andes was identified as the major force that shaped the diversification ofG. cancriformisin Northern South America, resulting in acis- andtrans-Andean phylogeographic structure for the species. The divergence in the face of gene flow betweencis- andtrans-Andean populations found for this spider has been likely facilitated by the presence of low-elevation passes across the Eastern Colombian cordillera. Our work constitutes the first example where the Andean uplift coupled with gene flow influenced the evolutionary history of an arachnid lineage.
Metagenomics reveals diet-specific specialization of bacterial communities in fungus gardens of grass- and dicot-cutter ants
Authors: Khadempour Lily , Fan Huan , Keefover-Ring Ken , Carlos Camila , Nagamoto Nilson S. , Dam Miranda A. , Pupo Monica T. , Currie Cameron R. 
Published: January 2018

AbstractLeaf-cutter ants in the genusAttaare dominant herbivores in the Neotropics. While most species ofAttacut dicots to incorporate into their fungus gardens, some species specialize on grasses. Here we examine the bacterial community associated with the fungus gardens of grass- and dicot-cutter ants to examine how changes in substrate input affect the bacterial community. We sequenced the metagenomes of 12Attafungus gardens, across four species of ants, with a total of 5.316 Gbp of sequence data. We show significant differences in the fungus garden bacterial community composition between dicot- and grass-cutter ants, with grass-cutter ants having lower diversity. Reflecting this difference in community composition, the bacterial functional profiles between the fungus gardens are significantly different. Specifically, grass-cutter ant fungus garden metagenomes are particularly enriched for genes responsible for amino acid, siderophore, and terpenoid biosynthesis while dicot-cutter ant fungus gardens metagenomes are enriched in genes involved in membrane transport. These differences in bacterial community composition and functional capacity show that different substrate inputs matter for fungus garden bacteria, and sheds light on the potential role of bacteria in mediating the ants’ transition to the use of a novel substrate.
Branch angle responses to photosynthesis are partially dependent on TILLER ANGLE CONTROL 1
Authors: Guseman Jessica M. , Dardick Christopher 
Published: January 2018

ABSTRACTLight serves as an important environmental cue in regulating plant architecture. Previous work had demonstrated that both photoreceptor-mediated signaling and photosynthesis play a role in determining the orientation of plant organs. TILLER ANGLE CONTROL 1 (TAC1) was recently shown to function in setting the orientation of lateral branches in diverse plant species, but the degree to which it plays a role in light-mediated phenotypes is unknown. Here, we demonstrated that TAC1 expression was light dependent, as expression was lost under dark or far-red growth conditions, but did not display any clear diurnal rhythm. Loss of TAC1 in the dark was gradual, and experiments with photoreceptor mutants indicated this was not dependent upon Red/Far-Red or Blue light signaling, but partially required the signaling integrator CONSTITUTIVE PHOTOMORPHGENESIS 1 (COP1). Over-expression of TAC1 partially prevented the narrowing of branch angles in the dark or under Far-Red light. Treatment with the carotenoid biosynthesis inhibitor Norflurazon or the PSII inhibitor DCMU led to loss of TAC1 expression similar to dark or far-red conditions, but surprisingly expression increased in response to the PSI inhibitor Paraquat. Our results indicate that TAC1 plays an important role in modulating plant architecture in response to photosynthetic signals.HIGHLIGHTBranch angles narrow in darkness or under far-red light. This response is partially mediated by TAC1 which responds to photosynthetic signals, providing a key link between photosynthesis and plant architecture.
Quantitative analysis of synaptic pathology and neuroinflammation: an initial study in a female rhesus monkey model of the “synaptic” phase of Alzheimer’s disease
Authors: Beckman Danielle , Donis-Cox Kristine , Ott Sean , Roberts Mary , Novik Lisa , Janssen William G. , Bliss-Moreau Eliza , Rudebeck Peter H. , Baxter Mark G. , Morrison John H. 
Published: January 2018

AbstractBackgroundSoluble oligomers of the Aβ peptide (AβOs) are toxins that target and disrupt synapses. Generation of AβOs has been recently recognized as a probable initiating event in Alzheimer’s disease (AD), leading to cognitive impairment. There is a translational gap in AD studies, with promising drugs developed based on work in rodent models failing in AD patients in clinical trials. Additionally, although women have a two-fold greater lifetime risk of developing AD compared to men, females have not been a focus of preclinical studies. Thus, we sought to develop a model of AβO toxicity in female rhesus monkeys, to take advantage of the more highly differentiated cortical structure in this species as well as the similarities in the endocrine system between rhesus monkeys and humans.MethodsRepeated intracerebroventricular (i.c.v) injections of AβOs were performed in adult female rhesus monkeys. Controls were unoperated aged matched monkeys. High-resolution confocal microscopy and morphometric analysis of Alexa 568 (A568) filled neurons were used to evaluate synaptic, neuronal, and glial markers in the dorsolateral prefrontal cortex (dlPFC) and hippocampus after AβO injections. Cerebrospinal fluid (CSF) and brain tissue were also collected and analyzed for biomarkers of AD pathology, including: phosphorylated Tau protein (pTau), total Tau, Aβ1-42, Aβ1-40 and TNF-α levels.ResultsHere, we report that AβO injection into the lateral ventricle of the brain induces loss of 37% of thin spines in targeted dlPFC neurons, an area highly vulnerable in AD and aging. Further, AβOs associate with the synaptic marker PSD95, inducing loss of more than 60% of local excitatory synapses. AβOs induce a robust neuroinflammatory response in the hippocampus, far from the injection site, with numerous activated ameboid microglia and TNF-α release. Finally, AβOs increased CSF levels of Aβ1-42, pTau Ser396 and pTau Ser199, but not Aβ1-40 or total Tau.ConclusionsThese initial findings from detailed quantitative analysis of effects of AβO administration on synapses in a female nonhuman primate model are a very promising step toward understanding the mechanism of early AD pathogenesis in the primate brain, and may help develop an effective disease-modifying therapy of high relevance to women’s health.
Fall prevention strategy in an emergency department
Authors: Muray Mwali , Bélanger Charles H. , Razmak Jamil 
Published: January 2018

Purpose
The purpose of this paper is to document the need for implementing a fall prevention strategy in an emergency department (ED). The paper also spells out the research process that led to approving an assessment tool for use in hospital outpatient services.

Design/methodology/approach
The fall risk assessment tool was based on the Morse Fall Scale. Gender mix and age above 65 and 80 years were assessed on six risk assessment variables using χ2 analyses. A logistic regression analysis and model were used to test predictor strength and relationships among variables.

Findings
In total, 5,371 (56.5 percent) geriatric outpatients were deemed to be at fall risk during the study. Women have a higher falls incidence in young and old age categories. Being on medications for patients above 80 years exposed both genders to equal fall risks. Regression analysis explained 73-98 percent of the variance in the six-variable tool.

Originality/value
Canadian quality and safe healthcare accreditation standards require that hospital staff develop and adhere to fall prevention policies. Anticipated physiological falls can be prevented by healthcare interventions, particularly with older people known to bear higher risk factors. An aging population is increasing healthcare volumes and medical challenges. Precautionary measures for patients with a vulnerable cognitive and physical status are essential for quality care.
Integrating resilience in a supply chain planning model
Authors: Das Kanchan 
Published: January 2018

PurposeThe purpose of this paper is to create a resilient supply chain (SC) plan to contain disruptions and risks in the overall operations of a business.Design/methodology/approachThe study integrates resilience considerations in a business planning model that formulates resilience performance (RP) of SC functions in terms of flexibility, reliability, and similar system factors. It evaluates the RP of SC plans and determines their vulnerability considering required and planned resources. The model estimates the possible effects of disasters on vulnerable functions using a scenario-based analysis and plans containment options. It also includes decision options for deploying resources to achieve the expected levels of resilience by preventing potential vulnerabilities. The model takes optimum decision in a what-if approach by comparing performance of the existing business plan, with options for containing the vulnerabilities inherent in not considering potential risks when planning to fulfill market demand, and the performance of a resilient plan that includes decision options to prevent vulnerabilities where possible and mitigate them otherwise.FindingsIt is possible, for example, to evaluate RP of SC plans, identify vulnerable functions, and decide optimum option to create resilient business system.Research limitations/implicationsThe present study takes a generic approach and creates bases to explore its application in any industry-based case.Originality/valueThe research introduces formulations for RPs and vulnerability indices that can be included in a planning model to create a resilient SC.
Multiplayer online role-playing as information retrieval and system use: an ethnographic study
Authors: Harviainen J. Tuomas , Rapp Amon 
Published: January 2018

PurposeThe purpose of this paper is to expand the research of games as information systems. It illustrates how significant parts of massively multiplayer online role-playing function like information retrieval from a library database system.Design/methodology/approachBy combining ideas from earlier contributions on the topics of game environments as information systems, the paper explores how gameplay connects to information retrieval, restricted content access, and information system structure. The paper then proceeds to examine this idea through an ethnographic study conducted inWorld of Warcraftduring 2012-2016.FindingsBy discussing how multiplayer digital game play is a form of information retrieval, the paper shows that players enjoy the well-restricted access to information that is a constitutive element of gameplay. Examining controlled access, procedural literacies and emphatic keywords, the paper finds that content relevances and system use may be influenced by hedonic concerns rather than task efficiency.Originality/valueThe study of retrieval issues related to gaming enriches our knowledge on inferences in retrieval. It shows that people may prefer that their access to information be limited, in order to make system use more interesting.
A task completion framework to support single-interaction IR research
Authors: van der Vegt Anton , Zuccon Guido , Koopman Bevan , Bruza Peter 
Published: January 2018

PurposeA conceptual model describes important factors within a system and how they relate to one another. They are important because they help to identify system changes that can yield the greatest improvement. Within information retrieval (IR), most research is directed towards multi-document retrieval and a multi-interaction IR user scenario. There are few, if any, IR conceptual models supporting minimal or single-interaction IR (siIR) user scenarios, however the need for siIR systems is growing rapidly. The purpose of this paper is to take the first step towards constructing a task-oriented conceptual model and experimental framework to support siIR research.Design/methodology/approachA first principles approach is employed to develop a task-oriented conceptual model, called bridging information retrieval (BIR). This model is contrasted with the concept of relevance, a central factor within IR research.FindingsBIR introduces the central concept of bridging information (BI) as the objective of IR systems. BI is the additional information a user requires to complete a task, beyond their innate knowledge. The relationship between BI and relevance is determined.Research limitations/implicationsThe theoretical basis of BIR is derived axiomatically; however the resulting system evaluation model is speculative.Practical implicationsThe proposed operational framework offers researchers a systematic approach to designing and evaluating siIR systems.Originality/valueThis work contributes a novel task-oriented IR conceptual model and evaluation framework, both centred around the concept of BI for siIR. It also contributes a novel search task classification method.
Oral lichenoid reaction showing multiple ulcers associated with anti‐programmed death cell receptor‐1 treatment: A report of two cases and published work review
Authors: Obara Koya , Masuzawa Mamiko , Amoh Yasuyuki 
Published: January 2018

AbstractAnti‐programmed cell death receptor‐1 (PD‐1) antibodies represent an effective treatment opinion for advanced melanoma and non‐small‐cell lung cancer, as well as other cancerous entities. Immune checkpoint inhibitors such as anti‐PD‐1 antibody result in a unique side‐effect profile, commonly described as immune‐related adverse events (irAE). These irAE affect the skin, gastrointestinal tract, liver, endocrine system and other organ systems. We report two cases of oral lichenoid reaction showing multiple ulcers associated with nivolumab treatment. Both patients presented with multiple ulcers covered with fibrinous plaque over the entire oral mucosa, lips and tongue. Histopathological examination of ulceration showed epithelial necrosis and subepidermal clefts with dense band‐like layers of lymphohistiocytic infiltrate within the upper dermis. Nivolumab was interrupted in both cases. Case 1 responded well to topical corticosteroids. Case 2 required oral corticosteroids, however, nivolumab could be restarted without recurrence of oral ulcers. We provide a comprehensive review of reported cases of lichenoid reaction showing multiple oral ulcers associated with anti‐PD‐1 therapy to date. Early recognition and management may improve treatment, avoid discontinuation of life‐saving therapy and maintain quality of life in these patients.
Epidermal aspects of type VII collagen: Implications for dystrophic epidermolysis bullosa and epidermolysis bullosa acquisita
Authors: Watanabe Mika , Natsuga Ken , Shinkuma Satoru , Shimizu Hiroshi 
Published: January 2018

AbstractType VII collagen (COL7), a major component of anchoring fibrils in the epidermal basement membrane zone, has been characterized as a defective protein in dystrophic epidermolysis bullosa and as an autoantigen in epidermolysis bullosa acquisita. Although COL7 is produced and secreted by both epidermal keratinocytes and dermal fibroblasts, the role of COL7 with regard to the epidermis is rarely discussed. This review focuses on COL7 physiology and pathology as it pertains to epidermal keratinocytes. We summarize the current knowledge of COL7 production and trafficking, its involvement in keratinocyte dynamics, and epidermal carcinogenesis in COL7 deficiency and propose possible solutions to unsolved issues in this field.
Characterization of skin blister fluids from children with Epstein–Barr virus‐associated lymphoproliferative disease
Authors: Wada Taizo , Toma Tomoko , Miyazawa Hanae , Koizumi Eiko , Shirahashi Tetsujiro , Matsuda Yusuke , Yachie Akihiro 
Published: January 2018

AbstractEpstein–Barr virus (EBV)‐associated T‐ or natural killer (NK)‐cell lymphoproliferative disease (LPD) is a heterogeneous group of disorders characterized by chronic proliferation of EBV‐infected lymphocytes. Patients may present with severe skin manifestations, including hypersensitivity to mosquito bites (HMB) and hydroa vacciniforme (HV)‐like eruption, which are characterized by blister formation and necrotic ulceration. Skin biopsy specimens show inflammatory reactions comprising EBV‐infected lymphocytes. However, blister fluids have not been fully assessed in patients with this disease. Blister fluids were collected from three patients with EBV‐associated LPD: two with HMB and one with HV. Immunophenotyping of blister lymphocytes and measurement of tumor necrosis factor (TNF)‐α in blister fluids were performed. The patients with HMB and HV exhibited markedly increased percentages of NK and γδ T cells, respectively, in both peripheral blood and blister fluids. These NK and γδ T cells strongly expressed the activation marker human leukocyte antigen‐DR and were considered to be cellular targets of EBV infections. TNF‐α was highly elevated in all blister fluids. Severe local skin reactions of EBV‐associated LPD may be associated with infiltrating EBV‐infected lymphocytes and a high TNF‐α concentration in blister fluids.
Geo‐climatic factors drive diatom community distribution in tropical South American freshwaters
Authors: Benito Xavier , Fritz Sherilyn C. , Steinitz‐Kannan Miriam , Tapia Pedro M. , Kelly Meredith A. , Lowell Thomas V. 
Published: January 2018

AbstractPatterns that maintain and generate biodiversity of macro‐organisms in the Neotropics are widely discussed in the scientific literature, yet the spatial ecology of micro‐organisms is largely unknown. The unique character of the tropical Andes and adjacent Amazon lowlands generates a wide gradient of environmental conditions to advance our understanding of what drives community assembly and diversity processes.We analysed the distribution patterns of benthic diatoms (unicellular siliceous algae) as a model group of microbial passive dispersers, including predictors that describe limnological and geo‐climatic gradients for a total of 113 waterbodies (0–28°S and 58–80°W), including lakes and streams. Complementary multivariate statistical analyses were performed to correlate (1) community composition and (2) diatom species richness with environmental and spatial factors to infer niche‐based and dispersal‐based assembly processes, respectively.Results showed that two gradients structured both diatom assemblages and waterbodies, namely climate and landscape configuration. Variance partitioning revealed that broadscale spatial variables (distance‐based Moran's Eigenvectors) outperformed the two environmental components (limnological and geo‐climatic), suggesting dispersal‐assembled communities. However, diatom assemblages were structured by geo‐climatic (regional) factors in certain lakes in the northern and central Andes, although their effects were partially manifested via local variables after the geographical distances were factored out. In a similar way, climatic and topographic structuring homogenized lake and stream communities within ecoregions, as indicated by the strong overlap between the two community types and the weak correlation between biota and limnological variables. Notably, a significant increase in diatom species richness was related to increased water connectivity, interpreted to indicate that a decrease in the remoteness of the system increase species number.Synthesis. We emphasize the strength of macroecological gradients (landscape configuration and climatic factors) in affecting both diatom diversity and community composition in the South American tropics. In this context, our results and the commonalities of ecoregion patterning with groups of macro‐organisms (vegetation) suggest the need to integrate microbial ecology into a macroecology framework to unravel mechanisms behind diversity gradients.