bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fluorescence In Situ Hybridization for Glycine max Metaphase Chromosomes
Authors: Findley Seth D. , Birchler James A. , Stacey Gary 
Published: March 2017

AbstractThis article presents protocols for fluorescence in situ hybridization (FISH) in the cultivated soybean, Glycine max. The protocols represent soybean‐optimized versions developed for maize. We describe the use of two different probes types: genomic‐repeat‐based fluorescently‐tagged oligonucleotides and bacterial artificial chromosomes (BACs). The two probe types can be used either individually or together, depending on the experimental questions. The article also includes starting points for executing FISH in additional legume species. © 2017 by John Wiley & Sons, Inc.
Quantitative phase imaging for cell culture quality control
Authors: Kastl Lena , Isbach Michael , Dirksen Dieter , Schnekenburger Jürgen , Kemper Björn 
Published: March 2017

AbstractThe potential of quantitative phase imaging (QPI) with digital holographic microscopy (DHM) for quantification of cell culture quality was explored. Label‐free QPI of detached single cells in suspension was performed by Michelson interferometer‐based self‐interference DHM. Two pancreatic tumor cell lines were chosen as cellular model and analyzed for refractive index, volume, and dry mass under varying culture conditions. Firstly, adequate cell numbers for reliable statistics were identified. Then, to characterize the performance and reproducibility of the method, we compared results from independently repeated measurements and quantified the cellular response to osmolality changes of the cell culture medium. Finally, it was demonstrated that the evaluation of QPI images allows the extraction of absolute cell parameters which are related to cell layer confluence states. In summary, the results show that QPI enables label‐free imaging cytometry, which provides novel complementary integral biophysical data sets for sophisticated quantification of cell culture quality with minimized sample preparation. © 2017 International Society for Advancement of Cytometry
Wild, connected, and diverse: building a more resilient system of protected areas
Authors: Belote R. Travis , Dietz Matthew S. , Jenkins Clinton N. , McKinley Peter S. , Irwin G. Hugh , Fullman Timothy J. , Leppi Jason C. , Aplet Gregory H. 
Published: March 2017

AbstractCurrent systems of conservation reserves may be insufficient to sustain biodiversity in the face of climate change and habitat losses. Consequently, calls have been made to protect Earth's remaining wildlands and complete the system of protected areas by establishing conservation reserves that (1) better represent ecosystems, (2) increase connectivity to facilitate biota movement in response to stressors including climate change, and (3) promote species persistence within intact landscapes. Using geospatial data, we conducted an assessment for expanding protected areas within the contiguous United States to include the least human‐modified wildlands, establish a connected network, and better represent ecosystem diversity and hotspots of biodiversity. Our composite map highlights areas of high value to achieve these goals in the western United States, where existing protected areas and lands with high ecological integrity are concentrated. We also identified important areas in the East rich in species and containing ecosystems that are poorly represented in the existing protected area system. Expanding protection to these priority areas is ultimately expected to create a more resilient system for protecting the nation's biological heritage. This expectation should be subject to rigorous testing prior to implementation, and regional monitoring will ensure areas and actions are adjusted over time.
Linking river flow regimes to riparian plant guilds: a community‐wide modeling approach
Authors: Lytle David A. , Merritt David M. , Tonkin Jonathan D. , Olden Julian D. , Reynolds Lindsay V. 
Published: March 2017

AbstractModeling riparian plant dynamics along rivers is complicated by the fact that plants have different edaphic and hydrologic requirements at different life stages. With intensifying human demands for water and continued human alteration of rivers, there is a growing need for predicting responses of vegetation to flow alteration, including responses related to climate change and river flow management. We developed a coupled structured population model that combines stage‐specific responses of plant guilds with specific attributes of river hydrologic regime. The model uses information on the vital rates of guilds as they relate to different hydrologic conditions (flood, drought, and baseflow), but deliberately omits biotic interactions from the structure (interaction neutral). Our intent was to (1) consolidate key vital rates concerning plant population dynamics and to incorporate these data into a quantitative framework, (2) determine whether complex plant stand dynamics, including biotic interactions, can be predicted from basic vital rates and river hydrology, and (3) project how altered flow regimes might affect riparian communities. We illustrated the approach using five flow‐response guilds that encompass much of the river floodplain community: hydroriparian tree, xeroriparian shrub, hydroriparian shrub, mesoriparian meadow, and desert shrub. We also developed novel network‐based tools for predicting community‐wide effects of climate‐driven shifts and deliberately altered flow regimes. The model recovered known patterns of hydroriparian tree vs. xeroriparian shrub dominance, including the relative proportion of these two guilds as a function of river flow modification. By simulating flow alteration scenarios ranging from increased drought to shifts in flood timing, the model predicted that mature hydroriparian forest should be most abundant near the observed natural flow regime. Multiguild sensitivity analysis identified substantial network connectivity (many connected nodes) and biotic linkage (strong pairwise connections between nodes) under natural flow regime conditions. Both connectivity and linkage were substantially reduced under drought and other flow‐alteration scenarios, suggesting that community structure is destabilized under such conditions. This structured population modeling approach provides a useful tool for understanding the community‐wide effects of altered flow regimes due to climate change and management actions that influence river flow regime.
Integrating ecological theories and traits in process‐based modeling of macroinvertebrate community dynamics in streams
Authors: Mondy Cédric P. , Schuwirth Nele 
Published: March 2017

AbstractPredicting the composition and dynamics of communities is a challenging but useful task to efficiently support ecosystem management. Community ecology has developed a number of promising theories, including food webs, metabolic theory, ecological stoichiometry, and environmental filtering. Their joint implementation in a mechanistic modeling framework should help us to bring community ecology to a new level by improving its predictive abilities. One of the challenges lies in the proper consideration of model uncertainty. In this paper, we contribute to this challenging task by modeling the temporal dynamics of macroinvertebrate communities in a stream subjected to hydropeaking in Switzerland. To this end, we extended the mechanistic model Streambugs regarding flood‐induced drift processes and the use of trait information to define performance filters. Model predictions without any calibration were in the right order of magnitude but did not reflect the dynamics of most of the invertebrate taxa well. Bayesian inference drastically improved the model fit. It revealed that a large share of total model output uncertainty can be attributed to observation errors, which exceeded model parameter uncertainty. Observed and simulated community‐aggregated traits helped to identify and understand model deficits. The combination of different ecological theories and trait information in a single mechanistic modeling framework combined with Bayesian inference can thus help to predict responses of communities to environmental changes, which can support ecosystem management.
Aggregative and feeding thresholds of sympatric rorqual whales within a fjord system
Authors: Keen Eric M. 
Published: March 2017

AbstractRorqual whales (f. Balaenopteridae) supposedly respond to increases in prey supply according to both aggregative and feeding thresholds. With the former, they gather in areas above a minimum prey density set by their basal metabolic needs. With the latter, feeding occurs only above a prey density set by the energetic cost of lunge feeding. To compare prey preferences and the two threshold types in sympatric rorquals, I conducted systematic transect surveys and behavioral observations of humpback whales (Megaptera novaeangliae) and fin whales (Balaenoptera physalus) in a British Columbia fjord system. While multiple prey features were found to influence whale aggregation and feeding, both threshold types were observed in each species' response to krill volume. Humpback response to prey features was less predictable and influenced by more factors than that of fin whales, which appeared to be exclusively euphausivorous and interested in the deepest high‐volume krill patches within the deepest channels. Compared with fin whales, humpbacks found higher‐volume krill patches and had higher aggregative thresholds, but had lower feeding thresholds. Findings aligned overall with the expectations that aggregative behavior is responsive to local prey supply, while feeding thresholds are governed by less mutable energetic constraints imposed by body size and feeding mode. Both aggregative and feeding threshold responses appeared to be a function of local conditions: As total krill‐like backscatter increased, feeding thresholds stabilized (became more nonlinear and more nonrandom), while aggregative thresholds destabilized. All results emphasized the importance of incorporating observations of feeding effort in studies of prey preference and habitat use.
Shrub encroachment in Arctic tundra: Betula nana effects on above‐ and belowground litter decomposition
Authors: McLaren Jennie R. , Buckeridge Kate M. , van de Weg Martine J. , Shaver Gaius R. , Schimel Joshua P. , Gough Laura 
Published: March 2017

AbstractRapid arctic vegetation change as a result of global warming includes an increase in the cover and biomass of deciduous shrubs. Increases in shrub abundance will result in a proportional increase of shrub litter in the litter community, potentially affecting carbon turnover rates in arctic ecosystems. We investigated the effects of leaf and root litter of a deciduous shrub, Betula nana, on decomposition, by examining species‐specific decomposition patterns, as well as effects of Betula litter on the decomposition of other species. We conducted a 2‐yr decomposition experiment in moist acidic tundra in northern Alaska, where we decomposed three tundra species (Vaccinium vitis‐idaea, Rhododendron palustre, and Eriophorum vaginatum) alone and in combination with Betula litter. Decomposition patterns for leaf and root litter were determined using three different measures of decomposition (mass loss, respiration, extracellular enzyme activity). We report faster decomposition of Betula leaf litter compared to other species, with support for species differences coming from all three measures of decomposition. Mixing effects were less consistent among the measures, with negative mixing effects shown only for mass loss. In contrast, there were few species differences or mixing effects for root decomposition. Overall, we attribute longer‐term litter mass loss patterns to patterns created by early decomposition processes in the first winter. We note numerous differences for species patterns between leaf and root decomposition, indicating that conclusions from leaf litter experiments should not be extrapolated to below‐ground decomposition. The high decomposition rates of Betula leaf litter aboveground, and relatively similar decomposition rates of multiple species below, suggest a potential for increases in turnover in the fast‐decomposing carbon pool of leaves and fine roots as the dominance of deciduous shrubs in the Arctic increases, but this outcome may be tempered by negative litter mixing effects during the early stages of encroachment.
Body mass index and distribution of body fat can influence sensory detection and pain sensitivity
Authors: Tashani O. A , Astita R. , Sharp D. , Johnson M. I 
Published: March 2017

AbstractBackgroundThe aim of this study was to investigate the influence of body fat percentage and its distribution on sensory detection and pain sensitivity responses to experimentally induced noxious stimuli in otherwise pain‐free individuals.MethodsSeventy‐two participants were divided into three equal groups according to their body mass index (BMI: normal, overweight and obese). Percentage body fat was estimated using a four‐site skinfold method. Measurements of cold pressor pain threshold, tolerance and intensity; contact thermal sensory detection and heat pain threshold and tolerance (TSA‐II – NeuroSensory Analyzer, Medoc); and blunt pressure pain threshold (algometer, Somedic SenseLab AB) were taken at the waist and thenar eminence.ResultsMean ± SD pressure pain threshold of the obese group (620.72 ± 423.81 kPa) was significantly lower than normal (1154.70 ± 847.18 kPa) and overweight (1285.14 ± 998.89 kPa) groups. Repeated measures ANOVA found significant effects for site for cold detection threshold (F1,68 = 8.3, p = 0.005) and warm detection threshold (F1,68 = 38.69, p = 0.001) with waist having lower sensory detection thresholds than thenar eminence. For heat pain threshold, there were significant effects for site (F1,68 = 4.868, p = 0.031) which was lower for waist compared with thenar eminence (mean difference = 0.89 °C).ConclusionObese individuals were more sensitive than non‐obese individuals to pressure pain but not to thermal pain. Body sites may vary in their response to different types and intensities of stimuli. The inconsistency of findings within and between research studies should catalyse further research in this field.SignificanceThis study provided evidence that body mass index and distribution of body fat can influence sensory detection and pain sensitivity. Obese individuals were more sensitive than normal range body mass index individuals to pressure pain but not to thermal pain. Pain response varied according to subcutaneous body fat at different body sites. These findings strengthen arguments that weight loss should be a significant aspect of a pain management programme for obese pain patients.
Decreased functional connectivity within a language subnetwork in benign epilepsy with centrotemporal spikes
Authors: McGinnity Colm J. , Smith Anna B. , Yaakub Siti N. , Weidenbach Gerbase Sofia , Gammerman Anya , Tyson Adam L. , Bell Tiffany K. , Elmasri Marwa , Barker Gareth J. , Richardson Mark P. , Pal Deb K. 
Published: March 2017

SummaryObjectiveBenign epilepsy with centrotemporal spikes (BECTS, also known as Rolandic epilepsy) is a common epilepsy syndrome that is associated with literacy and language impairments. The neural mechanisms of the syndrome are not known. The primary objective of this study was to test the hypothesis that functional connectivity within the language network is decreased in children with BECTS. We also tested the hypothesis that siblings of children with BECTS have similar abnormalities.MethodsEcho planar magnetic resonance (MR) imaging data were acquired from 25 children with BECTS, 12 siblings, and 20 healthy controls, at rest. After preprocessing with particular attention to intrascan motion, the mean signal was extracted from each of 90 regions of interest. Sparse, undirected graphs were constructed from adjacency matrices consisting of Spearman's rank correlation coefficients. Global and nodal graph metrics and subnetwork and pairwise connectivity were compared between groups.ResultsThere were no significant differences in graph metrics between groups. Children with BECTS had decreased functional connectivity relative to controls within a four‐node subnetwork, which consisted of the left inferior frontal gyrus, the left superior frontal gyrus, the left supramarginal gyrus, and the right inferior parietal lobe (p = 0.04). A similar but nonsignificant decrease was also observed for the siblings. The BECTS groups had significant increases in connectivity within a five‐node, five‐edge frontal subnetwork.SignificanceThe results provide further evidence of decreased functional connectivity between key mediators of speech processing, language, and reading in children with BECTS. We hypothesize that these decreases reflect delayed lateralization of the language network and contribute to specific cognitive impairments.
Understanding mass fluvial erosion along a bank profile: using PEEP technology for quantifying retreat lengths and identifying event timing
Authors: Papanicolaou A. N. Thanos , Wilson Christopher G. , Tsakiris Achilles G. , Sutarto Tommy E. , Bertrand Fabienne , Rinaldi Massimo , Dey Subhasish , Langendoen Eddy 
Published: March 2017

AbstractThis study provides fundamental examination of mass fluvial erosion along a stream bank by identifying event timing, quantifying retreat lengths, and providing ranges of incipient shear stress for hydraulically driven erosion. Mass fluvial erosion is defined here as the detachment of thin soil layers or conglomerates from the bank face under higher hydraulic shear stresses relative to surface fluvial erosion, or the entrainment of individual grains or aggregates under lower hydraulic shear stresses.We explore the relationship between the two regimes in a representative, US Midwestern stream with semi‐cohesive bank soils, namely Clear Creek, IA. Photo‐Electronic Erosion Pins (PEEPs) provide, for the first time, in situ measurements of mass fluvial erosion retreat lengths during a season. The PEEPs were installed at identical locations where surface fluvial erosion measurements exist for identifying the transition point between the two regimes. This transition is postulated to occur when the applied shear stress surpasses a second threshold, namely the critical shear stress for mass fluvial erosion.We hypothesize that the regimes are intricately related and surface fluvial erosion can facilitate mass fluvial erosion. Selective entrainment of unbound/exposed, mostly silt‐sized particles at low shear stresses over sand‐sized sediment can armor the bank surface, limiting the removal of the underlying soil. The armoring here is enhanced by cementation from the presence of optimal levels of sand and clay. Select studies show that fluvial erosion strength can increase several‐fold when appropriate amounts of sand and clay are mixed and cement together. Hence, soil layers or conglomerates are entrained with higher flows.The critical shear stress for mass fluvial erosion was found to be an order of magnitude higher than that of surface fluvial erosion, and proceeded with higher (approximately 2–4 times) erodibility. The results were well represented by a mechanistic detachment model that captures the two regimes. Copyright © 2017 John Wiley & Sons, Ltd.
New cooperative mechanisms for software defined networks based on hybrid switches
Authors: Alvarez‐Horcajo Joaquin , Martinez‐Yelmo Isaias , Rojas Elisa , Carral Juan A. , Lopez‐Pajares Diego 
Published: March 2017

AbstractSoftware defined networking (SDN) aims to provide simplified network design, operation, and management using a decoupled control plane. However, its centralized control and global network knowledge present scalability and reliability issues, which makes SDN deployment very challenging. In this paper, we propose and evaluate a hybrid switch with partial delegation of basic bridging and new cooperative mechanisms between controller and switches. This delegation offloads the SDN controllers while maintaining the capability to install forwarding rules on the switches. In this way, we take full advantage of hybrid switches in addition to using them as backwards compatible equipment, which interoperates with traditional switches.We validate this proposal by implementing a hybrid OpenFlow switch on an open source software switch as a proof of concept. Scalability and path setup delay are improved with respect to traditional centralized SDN solutions, because of the reduction in controller load and, in turn, because of the reduced traffic between switches and controller. Our cooperative mechanisms focus on recovering failures, obtaining the best performance of all approaches on higher loads, and providing a good trade‐off between controller based and traditional distributed approaches.
Uplink resource allocation in multiuser multicarrier cognitive radio networks under power amplifier nonlinearity
Authors: Baghani Mina , Mohammadi Abbas , Majidi Mahdi , Valkama Mikko 
Published: March 2017

AbstractIn this paper, the nonlinear distortion effects of power amplifiers are studied, in particular from uplink subcarrier and power allocation perspectives in multiuser multicarrier cognitive networks. The out‐of‐band emissions of a nonlinear power amplifier create interference to the other users. The target is then to maximize the achievable uplink rate in a multiuser multicarrier cognitive network where a cognitive user should not introduce interference to the other users more than a specified threshold level, called interference power constraint. This task is formulated as a convex optimization problem with interference power constraints. Obtaining a closed‐form solution for this problem is, however, not feasible due to its nonlinear nature. Accordingly, the problem is solved numerically, and extensive simulations are conducted to obtain performance results. The obtained results are also compared with a more simple heuristic approach. The results show that the proposed scheme provides a maximum rate while at the same time also guaranteeing that the interference levels are lower than the specified interference power constraint. The results also indicate that the maximum rate can be closely approximated by using the assisted or optimization‐directed heuristic approach.
AHNS series: Do you know your guidelines? Management of head and neck cancer in the era of human papillomavirus: Educating our patients on human papillomavirus
Authors: Guo Theresa , Goldenberg David , Fakhry Carole 
Published: March 2017

ABSTRACTHuman papillomavirus (HPV) has changed the face of head and neck cancer over the past 2 decades. No longer is this solely a disease of older patients with a history of heavy tobacco and alcohol use. Patients with HPV‐related head and neck cancers tend to be younger, healthier, and have an improved prognosis, compared with those with HPV‐negative tumors. As more patients are diagnosed with HPV‐related head and neck cancer, physicians have important topics to consider. These include prevalence, transmission, and natural history of HPV, the role of screening, vaccines, and HPV testing in head and neck cancer. This article continues a series developed by the American Head and Neck Society's Education Committee entitled “Do you know your guidelines?” and is intended to provide guidance for navigating common questions and concerns patients may have about HPV infection and HPV‐related head and neck cancer. © 2017 Wiley Periodicals, Inc. Head Neck 39: 833–839, 2017