bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Real‐Time Image‐Based Approach to Distinguish and Discriminate Apoptosis from Necrosis
Authors: Lekshmi Asha , Varadarajan Shankara Narayanan , Lupitha Santhik Subhasingh , Nair Mydhily , Chandrasekharan Aneesh , Santhoshkumar T.R. 
Published: February 2018

AbstractRecent cell biology studies reveal that a cell can die through multiple pathways via distinct signaling mechanisms. Among these, apoptosis and necrosis are two distinct cell death pathways, and their detection and discrimination is vital in the drug discovery process and in understanding diverse biological processes. Although sensitive assays for apoptosis and necrosis are available, it is extremely difficult to adapt any of these methods to discriminate apoptosis‐inducing stimuli from necrosis‐inducing stimuli because of the acquisition of secondary necrosis by apoptotic cells when they are not phagocytosed. Essentially, any assay for discriminating apoptosis and necrosis needs to be carried out in real‐time kinetic mode. Caspase 3 or 7 activation is observed in the majority of apoptotic cell death. Similarly, the absence of caspase 3/7 activation and cell membrane leakage are the two prominent indicators for necrotic cell death or necroptosis. The programmed form of necrosis, called pyroptosis, is also accompanied by membrane leakage and most often associated with activation of specific caspases such as caspase 1, 4, or 11, but not through caspase 3/7 activation. Here, a robust and sensitive real‐time method is described to distinguish and discriminate apoptosis from necrosis. The assay utilizes stable integration of a genetically encoded fluorescence resonance energy transfer (FRET) probe for caspase 3/7 activation and the mitochondrion‐targeted DsRed to identify necrotic cells. Caspase activation is determined by cleavage of the FRET probe; loss of soluble FRET probe with retention of mitochondrial red fluorescence indicates necrosis. This unit describes an important protocol for the generation of sensor cells expressing both probes, followed by detailed analysis of apoptosis and necrosis by microscopy imaging, confocal imaging, high‐throughput imaging, and flow cytometry. © 2018 by John Wiley & Sons, Inc.
Preparation of Human Primary Colon Tissue‐Derived Organoid Using Air Liquid Interface Culture
Authors: Usui Tatsuya , Sakurai Masashi , Umata Koji , Yamawaki Hideyuki , Ohama Takashi , Sato Koichi 
Published: February 2018

AbstractIn vitro analysis of intestinal epithelium has been hindered by a lack of suitable culture systems useful for gastrointestinal research. To overcome the problem, an air liquid interface (ALI) method using a collagen gel was established to culture three‐dimensional primary cells containing both primary epithelial and mesenchymal components from mouse gastrointestinal tissues. ALI organoids accurately recapitulate organ structures, multilineage differentiation, and physiology. Since ALI organoids from human tissues have not been produced, we modified the previous protocol for mouse ALI organoid culture to establish the culture system of ALI organoids from normal and tumor colorectal tissues of human patients. The current unit presents a protocol for preparation of the ALI organoid culture from normal and tumor colorectal tissues of human patients. ALI organoid culture from human tissues might be useful for examining not only resistance to chemotherapy in a tumor microenvironment but also toxic effects on organoids. © 2018 by John Wiley & Sons, Inc.
Evaluation of Marijuana Compounds on Neuroimmune Endpoints in Experimental Autoimmune Encephalomyelitis
Authors: Kaplan Barbara L. F. 
Published: February 2018

AbstractCannabinoid compounds refer to a group of more than 60 plant‐derived compounds in Cannabis sativa, more commonly known as marijuana. Exposure to marijuana and cannabinoid compounds has been increasing due to increased societal acceptance for both recreational and possible medical use. Cannabinoid compounds suppress immune function, and while this could compromise one's ability to fight infections, immune suppression is the desired effect for therapies for autoimmune diseases. It is critical, therefore, to understand the effects and mechanisms by which cannabinoid compounds alter immune function, especially immune responses induced in autoimmune disease. Therefore, this unit will describe induction and assessment of the experimental autoimmune encephalomyelitis (EAE) model of multiple sclerosis (MS), and its potential alteration by cannabinoid compounds. The unit includes three approaches to induce EAE, two of which provide correlations to two forms of MS, and the third specifically addresses the role of autoreactive T cells in EAE. © 2018 by John Wiley & Sons, Inc.
Development of an In Vitro Method to Estimate the Sensitization Induction Level of Contact Allergens
Authors: Galbiati Valentina , Gibbs Sue , Roggen Erwin , Corsini Emanuela 
Published: February 2018

AbstractRecently, an in vitro procedure, which combines the epidermal equivalent potency assay with assessment of IL‐18 to provide a single test for identification and classification of skin sensitizers, was developed and validated. This unit will describe a simple in vitro method for estimation of the expected sensitization induction level interpolating in vitro EC50 and IL‐18 SI2 values to predict LLNA EC3 and/or human NOEL from standards curves generated using reference contact allergens, based on the use of Reconstituted human Epidermis (RhE).© 2018 by John Wiley & Sons, Inc.
2‐(N‐Methylbenzyl)pyridine: A Potential Liquid Organic Hydrogen Carrier with Fast H2 Release and Stable Activity in Consecutive Cycles
Authors: Oh Jinho , Jeong Kwanyong , Kim Tae Wan , Kwon Hyunguk , Han Jeong Woo , Park Ji Hoon , Suh Young‐Woong 
Published: February 2018

AbstractInvited for this month's cover is the group of Prof. Young‐Woong Suh at Hanyang University, in collaboration with Dr. Ji Hoon Park at Korea Research Institute of Chemical Technology and Prof. Jeong Woo Han at Pohang at University of Science and Technology. The Cover image is a representation of the H2 economy based on production, storage, and utilization for fuel cell electric vehicles, using our developed liquid organic hydrogen carrier (LOHC) material 2‐(N‐methylbenzyl)pyridine. The Communication itself is available at 10.1002/cssc.201702256.
Fine root responses to temporal nutrient heterogeneity and competition in seedlings of two tree species with different rooting strategies
Authors: Wang Peng , Shu Meng , Mou Pu , Weiner Jacob 
Published: February 2018

AbstractThere is little direct evidence for effects of soil heterogeneity and root plasticity on the competitive interactions among plants. In this study, we experimentally examined the impacts of temporal nutrient heterogeneity on root growth and interactions between two plant species with very different rooting strategies:Liquidambar styraciflua(sweet gum), which shows high root plasticity in response to soil nutrient heterogeneity, andPinus taeda(loblolly pine), a species with less plastic roots. Seedlings of the two species were grown in sandboxes in inter‐ and intraspecific combinations. Nutrients were applied in a patch either in a stable (slow‐release) or in a variable (pulse) manner. Plant aboveground biomass, fine root mass, root allocation between nutrient patch and outside the patch, and root vertical distribution were measured.L. styracifluagrew more aboveground (40% and 27% in stable and variable nutrient treatment, respectively) and fine roots (41% and 8% in stable and variable nutrient treatment, respectively) when competing withP. taedathan when competing with a conspecific individual, but the growth ofP. taedawas not changed by competition fromL. styraciflua. Temporal variation in patch nutrient level had little effect on the species’ competitive interactions. The more flexibleL. styracifluachanged its vertical distribution of fine roots in response to competition fromP. taeda, growing more roots in deeper soil layers compared to its roots in conspecific competition, leading to niche differentiation between the species, while the fine root distribution ofP. taedaremained unchanged across all treatments.Synthesis.L. styracifluashowed greater flexibility in root growth by changing its root vertical distribution and occupying space of not occupied byP. taeda. This flexibility gaveL. styracifluaan advantage in interspecific competition.
Persistence and space preemption explain species‐specific founder effects on the organization of marine sessile communities
Authors: Vieira Edson A. , Flores Augusto A. V. , Dias Gustavo M. 
Published: February 2018

AbstractCommunity assembly may not follow predictable successional stages, with a large fraction of the species pool constituted by potential pioneering species and successful founders defined through lottery. In such systems, priority effects may be relevant in the determination of trajectories of developing communities and hence diversity and assemblage structure at later advanced states. In order to assess how different founder species may trigger variable community trajectories and structures, we conducted an experimental study using subtidal sessile assemblages as model. We manipulated the identity of functionally different founders and initial colony size (a proxy of the time lag before the arrival of later species), and followed trajectories. We did not observe any effects of colony size on response variables, suggesting that priority effects take place even when the time lag between the establishment of pioneering species and late colonizers is very short. Late community structure at experimental panels that started either with the colonial ascidian Botrylloides nigrum, or the arborescent bryozoan Bugula neritina, was similar to control panels allowed natural assembling. In spite of high potential for fast space domination, and hence negative priority effects, B. nigrum suffered high mortality and did not persist throughout succession. Bugula neritina provided complex physical microhabitats through conspecific clustering that have enhanced larval settlement of late species arrivals, but no apparent facilitation was observed. Differently, panels founded by the encrusting bryozoan Schizoporella errata led to different and less diverse communities compared to naturally assembled panels, evidencing strong negative priority effects through higher persistence and space preemption. Schizoporella errata founder colonies inhibited further conspecific settlement, which may greatly relax intraspecific competition, allowing resource allocation to colony growth and space domination, thus reducing the chances for the establishment of other species.
What drives biological nitrogen fixation in high arctic tundra: Moisture or temperature?
Authors: Rousk Kathrin , Sorensen Pernille Laerkedal , Michelsen Anders 
Published: February 2018

AbstractBiological nitrogen (N2) fixation is one of the main sources of available N for pristine ecosystems such as subarctic and arctic tundra. Although this has been acknowledged more than a decade ago, few attempts have been undertaken to identify the foremost driver of N2 fixation in the high Arctic. Here, we report results from in situ measurements of N2 fixation throughout the main growing period (June–August) in high arctic tundra, Greenland, in climate change treatments, shading and warming, and control. Nitrogen fixation was also measured in cores that received additional water prior to the measurements. The climate change field treatments did not lead to significant changes in any measured parameters; however, N2 fixation was promoted by adding water, and moisture was the most important factor influencing N2 fixation in all climate change field treatments. Maximum N2 fixation rates were measured below 14°C soil temperature, which is much lower than the theoretical and previously reported temperature optimum for the nitrogenase enzyme. Diazotroph (N2 fixing bacteria) communities are adapted to low temperatures in high arctic settings, and increased temperature in a future climate may lead to decreased N2 fixation rates, or to a shift in diazotroph communities.
Influence of different discourses on the outcomes of development policies and projects: Insights from water project implementation in Nepal
Authors: Haapala Juho , Keskinen Marko 
Published: February 2018

AbstractThis study develops a systematic, participatory research method to study the impacts of different discourses on the outcomes of development policies and projects. The method visualizes relationships between key project discourses, enabling comparisons to be made between stated and actual discourses, and recognition of mutual synergies or inconsistencies among the discourses. Case study analysis of a rural water resources management project in Nepal demonstrates the ways in which individual responses from project specialists, combined together, lead to distinct hierarchical groups and clusters of discourses that reflect the day‐to‐day ways in which policies and projects are implemented. The paper discusses the ways in which project and organizational management could utilize the analysis in project planning, team formation, monitoring and supervision to meet external policy requirements, fit with local realities, and improve policy and project outcomes.
Comparing apples and oranges and pears and kumquats: The misuse of index systems for processing histopathology data in fish toxicological bioassays
Authors: Wolf Jeffrey C. 
Published: February 2018

Abstract

Histopathology index systems involve the application of weighted scores to various diagnostic findings for the purpose of calculating overall organ and/or whole-animal health measurements. Such systems were originally developed as tools for monitoring the general health of fish populations. More recently, index systems have been applied to hypothesis-based toxicological studies, the goal of which is to investigate whether a cause-and-effect relationship exists between exposure to a particular test substance or environmental contaminant and morphologic effects in fish tissues. However, the application of index systems in that context is problematic for various reasons: a dependency on untested assumptions of toxicological importance for different types of histopathologic findings; organ scores that combine mechanistically unrelated and potentially contradictory diagnoses; calculations that include excessive numbers of findings, some of which may be incidental to the study outcome; failure to incorporate additional relevant results into the data interpretation, such as clinical observations, macroscopic findings, organ/body weights, clinical pathology data, and the results of hormonal or other biochemical assays; the inappropriate mathematical manipulation of ordinal categorical data (e.g., severity scores and “importance factors”); and a tendency of these systems to amplify, mask, and divert attention from methodological weaknesses and inaccurate diagnoses. The purpose of the present article is to demonstrate why the use of index systems is a misguided approach for handling histopathology data in studies of potential fish toxicants. Environ Toxicol Chem 2018;37:1688–1695. © 2018 SETAC
Estimating incident ultraviolet radiation exposure in the northern Gulf of Mexico during the Deepwater Horizon oil spill
Authors: Nielsen Kristin M. , Lay Claire R. , Alloy Matthew M. , Gielazyn Michel L. , Morris Jeffrey M. , Forth Heather P. , Takeshita Ryan , Travers Constance L. , Oris James T. , Roberts Aaron P. 
Published: February 2018

Abstract

Millions of barrels of oil were released into the Gulf of Mexico following the 2010 explosion of the Deepwater Horizon oil rig. Polycyclic aromatic hydrocarbons (PAHs) are toxic components of crude oil, which may become more toxic in the presence of ultraviolet (UV) radiation, a phenomenon known as photo-induced toxicity. The Deepwater Horizon spill impacted offshore and estuarine sites, where biota may be co-exposed to UV and PAHs. Penetration of UV into the water column is affected by site-specific factors. Therefore, measurements and/or estimations of UV are necessary when one is assessing the risk to biota posed by photo-induced toxicity. We describe how estimates of incident UV were determined for the area impacted by the Deepwater Horizon oil spill, using monitoring data from radiometers near the spill, in conjunction with reference spectra characterizing the composition of solar radiation. Furthermore, we provide UV attenuation coefficients for both near- and offshore sites in the Gulf of Mexico. These estimates are specific to the time and location of the spill, and fall within the range of intensities utilized during photo-induced toxicity tests performed in support of the Deepwater Horizon Natural Resource Damage Assessment (NRDA). These data further validate the methodologies and findings of phototoxicity tests included in the Deepwater Horizon NRDA, while underscoring the importance of considering UV exposure when assessing possible risks following oil spills. Environ Toxicol Chem 2018;37:1679–1687. © 2018 SETAC
Enhanced Flocculation of Oil Sands Mature Fine Tailings Using Hydrophobically Modified Polyacrylamide Copolymers
Authors: Hripko Rhys , Vajihinejad Vahid , LopesMotta Fernanda , Soares João B. P. 
Published: February 2018

AbstractHydrophobically modified acrylamide copolymers dewater oil sands tailings more effectively than anionic polyacrylamide, but the root causes for this enhanced performance have not been investigated systematically. Polyacrylamide‐poly(ethylene oxide methyl ether methacrylate) copolymers with different comonomer compositions, hydrophobic chain lengths, and molecular weights to map out these effects systematically are synthetized. Through a statistical design of experiments, it is found out that all three variables above significantly affected flocculation performance and that certain combinations achieve optimal results. The effect of centrifugation on the flocculation and dewatering performance of these polymers is also investigated.
Engaging Farmers in a Research Project. Lessons Learned from Implementing the Community of Practice Concept in Innovation Platforms in Irrigated Schemes in Tunisia, Mozambique and Ethiopia
Authors: Dolinska Aleksandra , Oates Naomi , Ludi Eva , Habtu Solomon , Rougier Jean‐Emmanuel , Sanchez‐Reparaz Maite , Mosello Beatrice , Yazew Eyasu , Kifle Muluberhan , Fissehaye Degol , Aregay Gebremeskel , Tamele Higino Fabiao , Barberá Gonzalo G. , d'Aquino Patrick 
Published: February 2018

AbstractThe role of smallholder farmers in multi‐stakeholder innovation platforms and thus in the innovation process that these platforms facilitate is typically limited. The EAU4Food project, aimed at increasing food production in irrigation schemes in Africa through improved farming strategies, used a platform design inspired by the community of practice (CoP) concept, which opened up space for farmers' interactive learning and enabled their active participation in the innovation process. In this article we present examples of how this approach has been implemented in Ethiopia, Mozambique and Tunisia. We analyse the level of farmers' participation that was achieved at different stages of the implementation process, namely: deciding how to set up the CoP, identifying innovation needs and conducting the experiment. Among different strategies deployed by EAU4Food researchers, working with dialogue groups, engaging farmers in data interpretation and passing the responsibility over elements of the research process to farmers, proved to be the most effective in strengthening farmers' involvement. The use of a simulation game to test innovations also showed promising results and should be explored further. The attitude of researchers proved to be an important factor in achieving a high level of farmers' engagement in the project. Copyright © 2020 John Wiley & Sons, Ltd.
Effect of Fertigation Frequency and Duration on Yield and Water Productivity of Wheat: Field and Modelling Study Using the Saltmed Model
Authors: Abdelraouf R.E. , Ragab R. 
Published: February 2018

AbstractThis study investigated the impact of fertigation frequency and fertigation time on wheat production. The field experiment included nine treatments over two seasons, 2014/2015 and 2015/2016. The same amount of water and nitrogen fertilizer was given for all treatments, either over 1 day, divided over 2 days or over 3 days. Three fertigation times (FT, period of injecting fertilizers in irrigation water) as a fraction of the irrigation period were also applied. In FT strategies, nitrogen is given either during the same period of the irrigation from the start to the end, at the last three‐quarters of the irrigation period or at the second half of the irrigation period, IT [FT = IT, FT = 0.75IT and FT = 0.5IT]. The observed and simulated nitrogen uptake and grain nitrogen content showed an increasing trend when fertigation frequencies increased and fertigation time decreased.The field and modelling results indicated that increasing fertigation frequencies and decreasing fertigation time have benefits particularly for sandy soils, including higher yields and less pollution. In conclusion, the use of the fertigation frequency of 3 days and fertilizer injection in the second half of the irrigation period is a good fertigation strategy for sandy soils. Copyright © 2018 John Wiley & Sons, Ltd.
Vibrio cholerae cytolysin: Multiple facets of the membrane interaction mechanism of a β‐barrel pore‐forming toxin
Authors: Kathuria Reema , Chattopadhyay Kausik 
Published: February 2018

AbstractVibrio cholerae cytolysin (VCC) is a membrane‐damaging protein toxin with potent cytolytic/cytotoxic activity against wide range of eukaryotic cells. VCC is a β‐barrel pore‐forming toxin (β‐PFT), and it inflicts damage to the target cell membranes by forming transmembrane heptameric β‐barrel pores. To exert pore‐forming activity, VCC must bind to the cell membranes in an efficient manner. Efficient interaction with the cell membranes is an essential pre‐requisite to trigger subsequent structural/conformational and organizational changes in the toxin molecules leading toward formation of the transmembrane oligomeric β‐barrel pores. Based on the large numbers of studies investigating the mode of action of VCC, it is now evident that VCC is capable of using multiple distinct mechanisms to recognize and bind to the membrane components and cell surface molecules. In this review article, we present an overview of our current understanding regarding the membrane interaction mechanisms of VCC, and their functional implications for the pore‐forming activity of the toxin. © 2018 IUBMB Life, 70(4):260–266, 2018
Building Literacy Partnerships Across District and Institutional Boundaries
Authors: Ronan Briana , Bauer Julee , Iunker Laurie , Sanford Jesse , Berry Michelle 
Published: February 2018

AbstractOften coauthored by university‐ and school‐based educators, preservice teachers, and youths, this department column considers how literacies are best developed through context‐crossing partnerships among university, school, and community constituents.
IFN-γ orchestrates tumor elimination, tumor dormancy, tumor escape, and progression
Authors: Aqbi Hussein F , Wallace Matthew , Sappal Samay , Payne Kyle K , Manjili Masoud H 
Published: February 2018

Abstract
Tumor immunoediting consisting of three phases of elimination, equilibrium or dormancy, and escape has been supported by preclinical and clinical data. A comprehensive understanding of the molecular mechanisms by which antitumor immune responses regulate these three phases are important for developing highly tailored immunotherapeutics that can control cancer. To this end, IFN-γ produced by Th1 cells, cytotoxic T cells, NK cells, and NKT cells is a pleiotropic cytokine that is involved in all three phases of tumor immunoediting, as well as during inflammation-mediated tumorigenesis processes. This essay presents a review of literature and suggests that overcoming tumor escape is feasible by driving tumor cells into a state of quiescent but not indolent dormancy in order for IFN-γ-producing tumor-specific T cells to prevent tumor relapse.