bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased CCL25 and T Helper Cells Expressing CCR9 in the Salivary Glands of Patients With Primary Sjögren's Syndrome: Potential New Axis in Lymphoid Neogenesis
Authors: Blokland Sofie L. M. , Hillen Maarten R. , Kruize Aike A. , Meller Stephan , Homey Bernhard , Smithson Glennda M. , Radstake Timothy R. D. J. , van Roon Joel A. G. 
Published: June 2017

ObjectiveFollicular helper T (Tfh) cells play a critical role in germinal center formation and B cell activation, both of which are hallmarks of primary Sjögren's syndrome (SS). CCR9‐expressing T helper cells have “Tfh‐like” characteristics and their numbers are increased at mucosa‐associated sites in several inflammatory conditions. Because the characteristics of these cells are unique and evaluation has been limited, this study was undertaken to investigate the local and systemic CCL25/CCR9 axis in patients with primary SS.MethodsLevels of CCL25 protein and messenger RNA (mRNA) and CCR9+ T helper cells were evaluated in the labial salivary glands (LSGs) of patients with primary SS and patients with sicca syndrome without a diagnosis of primary SS (non‐SS sicca controls). CCL25 levels were assessed for correlation with parameters of inflammation and clinical features. Circulating CCR9+ and CXCR5+ T helper cells were compared on the basis of phenotypic and functional properties.ResultsCCL25 protein and mRNA levels were elevated in the LSGs of patients with primary SS as compared to non‐SS sicca controls. Increased levels of CCL25 were associated with B cell hyperactivity, autoimmunity, and levels of interleukin‐21 (IL‐21) and soluble IL‐7 receptor α‐chain (IL‐7Rα). Furthermore, the frequency of CCR9‐expressing cells in the LSGs was increased and levels of circulating CCR9+ T helper cells expressing programmed death 1 and inducible T cell costimulator were elevated in patients with primary SS. CCR9+ T helper cells displayed higher expression of IL‐7Rα and secreted higher levels of interferon‐γ, IL‐17, IL‐4, and IL‐21 as compared to CXCR5+ T helper cells, ex vivo and upon triggering with antigen or IL‐7. Both CCR9+ and CXCR5+ T helper cells induced IgG production by B cells more potently than that induced in the cultures with CCR9−CXCR5− T helper cells.ConclusionEnhanced expression of CCL25 in LSGs of patients with primary SS can facilitate attraction of CCR9+ T helper cells, and these cells secrete high levels of proinflammatory cytokines when triggered with antigen or IL‐7. The observed associations with B cell hyperactivity, autoimmunity, and markers of lymphoid neogenesis indicate that the CCL25/CCR9 axis plays a significant role in the immunopathology of primary SS, suggesting that this axis could represent a novel therapeutic target for the disease.
A flexible e‐learning resource promoting the critical reading of scientific papers for science undergraduates
Authors: Letchford Julie , Corradi Hazel , Day Trevor 
Published: June 2017

AbstractAn important aim of undergraduate science education is to develop student skills in reading and evaluating research papers. We have designed, developed, and implemented an on‐line interactive resource entitled “Evaluating Scientific Research literature” (ESRL) aimed at students from the first 2 years of the undergraduate program. In this article, we describe the resource, then use student data collected from questionnaire surveys to evaluate the resource within 2 years of its launch. Our results add to those reported previously and indicate that ESRL can enable students to start evaluating research articles when used during their undergraduate program. We conclude maximal learning is likely to occur when the resource can be embedded in the curriculum such that students have a clearly articulated context for the resource's activities, can see their relevance in relation to assessed assignments and can be encouraged to think deeply about the activities in conversation with one another and/or with staff. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):483–490, 2017.
CHEMOTION: A gesture based chemistry virtual laboratory with leap motion
Authors: Al‐Khalifa Hend S. 
Published: June 2017

AbstractChemistry laboratories are expensive to setup and operate as well as it entails safety issues. However, as technologies develop and new technologies are being produced every day, an advance solution for physical Chemistry laboratories limitation is the use of virtual laboratories. In this paper, we present the design and implementation of a virtual chemistry laboratory system that utilizes gesture computing technology to create an interactive and entertaining laboratory application for pupils. The system is software that works on PCs with the help of Leap motion controller, off‐the‐shelf gesture recognition hardware, to simulate a chemistry laboratory. The system provides number of experiments to perform along with tutorials and quizzes. A preliminary usability evaluation of the system shows the high level of interest from the pupils in using such a system and the positive feedback.
Glycodendrimers as Chondroitin Sulfate Mimetics: Synthesis and Binding to Growth Factor Midkine
Authors: Domínguez‐Rodríguez Pedro , Reina José J. , Gil‐Caballero Sergio , Nieto Pedro M. , de Paz José L. , Rojo Javier 
Published: June 2017

AbstractChondroitin sulfate (CS) is a member of the glycosaminoglycan (GAG) family, a class of polysaccharides implicated in relevant biological functions. The structural complexity of these carbohydrates demands the development of simple glycomimetics as useful tools to study the biological processes in which GAGs are involved. In this work we described the synthesis of the disaccharide unit of the CS‐E (GlcA‐GalNAc(4,6‐di‐OSO3)), in a multivalent presentation. Using a fluorescence polarization competition assay we have demonstrated that a hexavalent dendrimer of this disaccharide interact with midkine, in the low micromolar range. This result highlights the potency of these disaccharide‐displaying multivalent systems as interesting mimetics of longer and synthetically more complex GAG oligosaccharides.
Synthesis and Antigenic Evaluation of Oligosaccharide Mimics of Vi Antigen from Salmonella typhi
Authors: Zhang Gao‐Lan , Yang Lin , Zhu Jingjing , Wei Mengman , Yan Wanjun , Xiong De‐Cai , Ye Xin‐Shan 
Published: June 2017

AbstractSalmonella typhi is responsible for typhoid fever, which is a serious health threat in developing countries. As a virulent factor of Salmonella typhi, the purified Vi polysaccharide (Vi PS) has become an effective vaccine to combat typhoid fever. The chemical synthesis can provide homogeneous and well‐defined molecules for the development of Vi‐based vaccines. However, the synthesis of Vi oligosaccharides in high yields and with exclusive α‐stereoselectivities remains very challenging. In this paper, a series of Vi pseudooligosaccharides, including pseudo tetra‐, hexa‐, and octa‐saccharides were efficiently synthesized. These oligosaccharide analogues were conjugated by carbon chain tether through olefin cross metathesis or by the 1,2,3‐triazole moiety through copper (I)‐catalyzed alkyne–azide cycloaddition reaction (CuAAC). The binding affinities of these oligosaccharide mimics to anti‐Vi antibodies were investigated. These results will be beneficial to the further development of Vi‐based oligosaccharide vaccines.
Multiagent induction chemotherapy followed by chemoradiation is associated with improved survival in locally advanced pancreatic cancer
Authors: Torgeson Anna , Lloyd Shane , Boothe Dustin , Tao Randa , Whisenant Jonathan , Garrido‐Laguna Ignacio , Cannon George M. 
Published: June 2017

BACKGROUNDThe role of chemoradiotherapy (CRT) in locally advanced pancreatic cancer (LAPC) is uncertain after multiple randomized clinical trials have yielded mixed results. The authors used the National Cancer Data Base (NCDB) to determine whether CRT yields a survival benefit compared with chemotherapy alone (CT).METHODSPatients with nonmetastatic LAPC diagnosed during 2004 through 2014 were identified in the NCDB. Patients who received CT were compared with those who received CRT using chi‐square analysis. Univariate and multivariate Cox regression analyses were used to compare demographic, clinical, and treatment characteristics that were predictive of survival. Propensity score matching and shared frailty analysis were done. Subgroup analyses were undertaken to examine patients who underwent pancreatectomy and cohorts of patients who received different CT or CRT regimens.RESULTSIn total, 8689 patients with LAPC were identified. CRT was associated with improved survival (median survival [MS], 13.5 months) compared with CT (MS, 10.6 months) on multivariate analysis (hazard ratio [HR], 0.80; P < .001). Induction chemotherapy before CRT (HR, 0.67; P < .001) and multiagent chemotherapy (HR, 0.72; P < .001) were also identified as independent predictors of survival compared with concurrent CRT and single‐agent CT, respectively. Patients in the CRT group who received multiagent induction chemotherapy had superior MS and pancreatectomy rates (MS, 17.5 months; HR, 0.70; P < .001; pancreatectomy rate, 10%) compared with those who received multiagent CT alone (MS, 12.4 months; pancreatectomy rate, 3.3%). Patients who underwent pancreatectomy experienced improved survival (MS, 22 vs 10.6 months; HR, 0.39; P < .001).CONCLUSIONSIn this NCDB analysis, maximizing systemic chemotherapy before CRT improved survival compared with CT alone in patients with LAPC. Continued analysis of CRT in properly selected patients after maximized systemic therapy is needed. Cancer 2017;123:3816‐24. © 2017 American Cancer Society.
Sustainable Separations of C4‐Hydrocarbons by Using Microporous Materials
Authors: Gehre Mascha , Guo Zhiyong , Rothenberg Gadi , Tanase Stefania 
Published: June 2017

AbstractPetrochemical refineries must separate hydrocarbon mixtures on a large scale for the production of fuels and chemicals. Typically, these hydrocarbons are separated by distillation, which is extremely energy intensive. This high energy cost can be mitigated by developing materials that can enable efficient adsorptive separation. In this critical review, the principles of adsorptive separation are outlined, and then the case for C4 separations by using zeolites and metal–organic frameworks (MOFs) is examined. By analyzing both experimental and theoretical studies, the challenges and opportunities in C4 separation are outlined, with a focus on the separation mechanisms and structure–selectivity correlations. Zeolites are commonly used as adsorbents and, in some cases, can separate C4 mixtures well. The pore sizes of eight‐membered‐ring zeolites, for example, are in the order of the kinetic diameters of C4 isomers. Although zeolites have the advantage of a rigid and highly stable structure, this is often difficult to functionalize. MOFs are attractive candidates for hydrocarbon separation because their pores can be tailored to optimize the adsorbate–adsorbent interactions. MOF‐5 and ZIF‐7 show promising results in separating all C4 isomers, but breakthrough experiments under industrial conditions are needed to confirm these results. Moreover, the flexibility of the MOF structures could hamper their application under industrial conditions. Adsorptive separation is a promising viable alternative and it is likely to play an increasingly important role in tomorrow's refineries.
How can distinct egg polymorphism be maintained in the rufescent prinia (Prinia rufescens)–plaintive cuckoo (Cacomantis merulinus) interaction—a modeling approach
Authors: Liang Wei , Yang Canchao , Takasu Fugo 
Published: June 2017

AbstractIn avian brood parasitism, both the host and the parasite are expected to develop various conflicting adaptations; hosts develop a defense against parasitism, such as an ability to recognize and reject parasitic eggs that look unlike their own, while parasites evolve egg mimicry to counter this host defense. Hosts may further evolve to generate various egg phenotypes that are not mimicked by parasites. Difference in egg phenotype critically affects the successful reproduction of hosts and parasites. Recent studies have shown that clear polymorphism in egg phenotype is observed in several host–parasite interactions, which suggests that egg polymorphism may be a more universal phenomenon than previously thought. We examined the mechanism for maintaining egg polymorphism in the rufescent prinia (Prinia rufescens) that is parasitized by the plaintive cuckoo (Cacomantis merulinus) from a theoretical viewpoint based on a mathematical model. The prinia has four distinct egg phenotypes: immaculate white, immaculate blue, white with spots, and blue with spots. Only two egg phenotypes, white with spots and blue with spots, are found in the cuckoo population. We show that the observed prinia and cuckoo phenotypes cannot be at an equilibrium and that egg polymorphism can be maintained either at stationary equilibrium or with dynamic, frequency oscillations, depending on the mutation rates of the background color and spottiness. Long‐term monitoring of the prinia–cuckoo interaction over a wide geographic range is needed to test the results of the model analyses.
The role of macroinvertebrates for conservation of freshwater systems
Authors: Nieto Carolina , Ovando Ximena M.C. , Loyola Rafael , Izquierdo Andrea , Romero Fátima , Molineri Carlos , Rodríguez José , Rueda Martín Paola , Fernández Hugo , Manzo Verónica , Miranda María José 
Published: June 2017

AbstractFreshwater ecosystems are the most threatened ecosystems worldwide. Argentinian‐protected areas have been established mainly to protect vertebrates and plants in terrestrial ecosystems. In order to create a comprehensive biodiverse conservation plan, it is crucial to integrate both aquatic and terrestrial systems and to include macroinvertebrates. Here, we address this topic by proposing priority areas of conservation including invertebrates, aquatic ecosystems, and their connectivity and land uses. Location: Northwest of Argentina. We modeled the ecological niches of different taxa of macroinvertebrates such as Coleoptera, Ephemeroptera, Hemiptera, Megaloptera, Lepidoptera, Odonata, Plecoptera, Trichoptera, Acari, and Mollusca. Based on these models, we analyzed the contribution of currently established protected areas in the conservation of the aquatic biodiversity and we propose a spatial prioritization taking into account possible conflict regarding different land uses. Our analysis units were the real watersheds, to which were added longitudinal connectivity up and down the rivers. A total of 132 species were modeled in the priority area analyses. The analysis 1 showed that only an insignificant percentage of the macroinvertebrates distribution is within the protected areas in the North West of Argentina. The analyses 2 and 3 recovered similar values of protection for the macroinvertebrate species. The upper part of Bermejo, Salí‐Dulce, San Francisco, and the Upper part of Juramento basins were identified as priority areas of conservation. The aquatic ecosystems need special protection and 10% or even as much as 17% of land conservation is insufficient for species of macroinvertebrates. In turn the protected areas need to combine the aquatic and terrestrial systems and need to include macroinvertebrates as a key group to sustain the biodiversity. In many cases, the land uses are in conflict with the conservation of biodiversity; however, it is possible to apply the connectivity of the watersheds and create multiple‐use modules.
Characterization of measurement errors using structure‐from‐motion and photogrammetry to measure marine habitat structural complexity
Authors: Bryson Mitch , Ferrari Renata , Figueira Will , Pizarro Oscar , Madin Josh , Williams Stefan , Byrne Maria 
Published: June 2017

AbstractHabitat structural complexity is one of the most important factors in determining the makeup of biological communities. Recent advances in structure‐from‐motion and photogrammetry have resulted in a proliferation of 3D digital representations of habitats from which structural complexity can be measured. Little attention has been paid to quantifying the measurement errors associated with these techniques, including the variability of results under different surveying and environmental conditions. Such errors have the potential to confound studies that compare habitat complexity over space and time. This study evaluated the accuracy, precision, and bias in measurements of marine habitat structural complexity derived from structure‐from‐motion and photogrammetric measurements using repeated surveys of artificial reefs (with known structure) as well as natural coral reefs. We quantified measurement errors as a function of survey image coverage, actual surface rugosity, and the morphological community composition of the habitat‐forming organisms (reef corals). Our results indicated that measurements could be biased by up to 7.5% of the total observed ranges of structural complexity based on the environmental conditions present during any particular survey. Positive relationships were found between measurement errors and actual complexity, and the strength of these relationships was increased when coral morphology and abundance were also used as predictors. The numerous advantages of structure‐from‐motion and photogrammetry techniques for quantifying and investigating marine habitats will mean that they are likely to replace traditional measurement techniques (e.g., chain‐and‐tape). To this end, our results have important implications for data collection and the interpretation of measurements when examining changes in habitat complexity using structure‐from‐motion and photogrammetry.
Discrepancies in occupancy and abundance approaches to identifying and protecting habitat for an at‐risk species
Authors: Dibner Reilly R. , Doak Daniel F. , Murphy Melanie 
Published: June 2017

AbstractPredicting how environmental factors affect the distribution of species is a fundamental goal of conservation biology. Conservation biologists rely on species distribution and abundance models to identify key habitat characteristics for species. Occupancy modeling is frequently promoted as a practical alternative to use of abundance in identifying habitat quality. While occupancy and abundance are potentially governed by different limiting factors operating at different scales, few studies have directly compared predictive models for these approaches in the same system. We evaluated how much occupancy and abundance are driven by the same environmental factors for a species of conservation concern, the greater short‐horned lizard (Phrynosoma hernandesi). Occupancy was most strongly dictated by precipitation, temperature, and density of ant mounds. While these factors were also in the best‐supported predictive models for lizard abundance, the magnitude of the effects varied, with the sign of the effect changing for temperature and precipitation. These discrepancies show that while occupancy modeling can be an efficient approach for conservation planning, predictors of occupancy probability should not automatically be equated with predictors of population abundance. Understanding the differences in factors that control occupancy versus abundance can help us to identify habitat requirements and mitigate the loss of threatened species.
High salmon density and low discharge create periodic hypoxia in coastal rivers
Authors: Sergeant Christopher J. , Bellmore J. Ryan , McConnell Casey , Moore Jonathan W. 
Published: June 2017

AbstractDissolved oxygen (DO) is essential to the survival of almost all aquatic organisms. Here, we examine the possibility that abundant Pacific salmon (Oncorhynchus spp.) and low streamflow combine to create hypoxic events in coastal rivers. Using high‐frequency DO time series from two similar watersheds in southeastern Alaska, we summarize DO regimes and the frequency of hypoxia in relationship to salmon density and stream discharge. We also employ a simulation model that links salmon oxygen respiration to DO dynamics and predicts combinations of salmon abundance, discharge, and water temperature that may result in hypoxia. In the Indian River, where DO was monitored hourly during the ice‐free season from 2010 to 2015, DO levels decreased when salmon were present. In 2013, a year with extremely high spawning salmon densities, DO dropped to 1.7 mg/L and 16% saturation, well below lethal limits. In Sawmill Creek, where DO was monitored every six minutes across an upstream–downstream gradient during the 2015 spawning season, DO remained fully saturated upstream of spawning reaches, but declined markedly downstream to 2.9 mg/L and 26% saturation during spawning. Modeled DO dynamics in the Indian River closely tracked field observations. Model sensitivity analysis illustrates that low summertime river discharge is a precursor to salmon‐induced oxygen depletion in our study systems. Our results provide compelling evidence that dense salmon populations and low discharge can trigger hypoxia, even in rivers with relatively cold thermal regimes. Although climate change modeling for southeastern Alaska predicts an increase in annual precipitation, snowfall in the winter and rainfall in the summer are likely to decrease, which would in turn decrease summertime discharge in rain‐ and snow‐fed streams and potentially increase the frequency of hypoxia. Our model template can be adapted by resource managers and watershed stakeholders to create real‐time predictive models of DO trends for individual streams. While preserving thermally suitable stream habitat for cold‐water taxa facing climate change has become a land management priority, managers should also consider that some protected watersheds may still be at risk of increasingly frequent hypoxia due to human impacts such as water diversion and artificially abundant salmon populations caused by hatchery straying.
Review of emerging metabolomic tools and resources: 2015–2016
Authors: Misra Biswapriya B. , Fahrmann Johannes F. , Grapov Dmitry 
Published: June 2017

AbstractData processing and analysis are major bottlenecks in high‐throughput metabolomic experiments. Recent advancements in data acquisition platforms are driving trends toward increasing data size (e.g., petabyte scale) and complexity (multiple omic platforms). Improvements in data analysis software and in silico methods are similarly required to effectively utilize these advancements and link the acquired data with biological interpretations. Herein, we provide an overview of recently developed and freely available metabolomic tools, algorithms, databases, and data analysis frameworks. This overview of popular tools for MS and NMR‐based metabolomics is organized into the following sections: data processing, annotation, analysis, and visualization. The following overview of newly developed tools helps to better inform researchers to support the emergence of metabolomics as an integral tool for the study of biochemistry, systems biology, environmental analysis, health, and personalized medicine.