bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Self‐Assembly of Helical Peptide Building Blocks
Authors: Mondal Sudipta , Gazit Ehud 
Published: February 2016

AbstractThe self‐assembly of peptide building blocks represents a central direction in bionanotechnology. A β‐sheet secondary structure serves as the basis of numerous peptide‐based bionanomaterials owing to their association with several neurodegenerative diseases. Although the α‐helix embodies the most common secondary structure motif in proteins, the utilization of this module as a building block for supramolecular aggregation is much less explored. In this Focus Review, we will discuss the advancement made so far to induce higher level organization in helical peptide building blocks. The primary design strategies involving coiled coil proteins mimetic approaches, incorporation of noncoded and synthetic amino acids and conjugation of peptides to aliphatic alkyl tails will be dealt with in detail. In parallel, we will also outline the self‐assembled materials developed in these progressions. Finally, possible future prospects of such assembly modules will be briefed.
Femtosecond Stimulated Raman Spectroscopy
Authors: Dietze Daniel R. , Mathies Richard A. 
Published: February 2016

AbstractFemtosecond stimulated Raman spectroscopy (FSRS) is an ultrafast nonlinear optical technique that provides vibrational structural information with high temporal (sub‐50 fs) precision and high spectral (10 cm−1) resolution. Since the first full demonstration of its capabilities ≈15 years ago, FSRS has evolved into a mature technique, giving deep insights into chemical and biochemical reaction dynamics that would be inaccessible with any other technique. It is now being routinely applied to virtually all possible photochemical reactions and systems spanning from single molecules in solution to thin films, bulk crystals and macromolecular proteins. This review starts with an historic overview and discusses the theoretical and experimental concepts behind this technology. Emphasis is put on the current state‐of‐the‐art experimental realization and several variations of FSRS that have been developed. The unique capabilities of FSRS are illustrated through a comprehensive presentation of experiments to date followed by prospects.
Do seasonal patterns of rat snake (Pantherophis obsoletus) and black racer (Coluber constrictor) activity predict avian nest predation?
Authors: DeGregorio Brett A. , Weatherhead Patrick J. , Ward Michael P. , Sperry Jinelle H. 
Published: February 2016

AbstractAvian nest success often varies seasonally and because predation is the primary cause of nest failure, seasonal variation in predator activity has been hypothesized to explain seasonal variation in nest success. Despite the fact that nest predator communities are often diverse, recent evidence from studies of snakes that are nest predators has lent some support to the link between snake activity and nest predation. However, the strength of the relationship has varied among studies. Explaining this variation is difficult, because none of these studies directly identified nest predators, the link between predator activity and nest survival was inferred. To address this knowledge gap, we examined seasonal variation in daily survival rates of 463 bird nests (of 17 bird species) and used cameras to document predator identity at 137 nests. We simultaneously quantified seasonal activity patterns of two local snake species (N = 30 individuals) using manual (2136 snake locations) and automated (89,165 movements detected) radiotelemetry. Rat snakes (Pantherophis obsoletus), the dominant snake predator at the site (~28% of observed nest predations), were most active in late May and early June, a pattern reported elsewhere for this species. When analyzing all monitored nests, we found no link between nest predation and seasonal activity of rat snakes. When analyzing only nests with known predator identities (filmed nests), however, we found that rat snakes were more likely to prey on nests during periods when they were moving the greatest distances. Similarly, analyses of all monitored nests indicated that nest survival was not linked to racer activity patterns, but racer‐specific predation (N = 17 nests) of filmed nests was higher when racers were moving the greatest distances. Our results suggest that the activity of predators may be associated with higher predation rates by those predators, but that those effects can be difficult to detect when nest predator communities are diverse and predator identities are not known. Additionally, our results suggest that hand‐tracking of snakes provides a reliable indicator of predator activity that may be more indicative of foraging behavior than movement frequency provided by automated telemetry systems.
Differential responses of cryptic bat species to the urban landscape
Authors: Lintott Paul R. , Barlow Kate , Bunnefeld Nils , Briggs Philip , Gajas Roig Clara , Park Kirsty J. 
Published: February 2016

AbstractUrbanization is a key global driver in the modification of land use and has been linked to population declines even in widespread and relatively common species. Cities comprise a complex assortment of habitat types yet we know relatively little about the effects of their composition and spatial configuration on species distribution. Although many bat species exploit human resources, the majority of species are negatively impacted by urbanization. Here, we use data from the National Bat Monitoring Programme, a long‐running citizen science scheme, to assess how two cryptic European bat species respond to the urban landscape. A total of 124 × 1 km2 sites throughout Britain were surveyed. The landscape surrounding each site was mapped and classified into discrete biotope types (e.g., woodland). Generalized linear models were used to assess differences in the response to the urban environment between the two species, and which landscape factors were associated with the distributions of P. pipistrellus and P. pygmaeus. The relative prevalence of P. pygmaeus compared to P. pipistrellus was greater in urban landscapes with a higher density of rivers and lakes, whereas P. pipistrellus was frequently detected in landscapes comprising a high proportion of green space (e.g., parklands). Although P. pipistrellus is thought to be well adapted to the urban landscape, we found a strong negative response to urbanization at a relatively local scale (1 km), whilst P. pygmaeus was detected more regularly in wooded urban landscapes containing freshwater. These results show differential habitat use at a landscape scale of two morphologically similar species, indicating that cryptic species may respond differently to anthropogenic disturbance. Even species considered relatively common and well adapted to the urban landscape may respond negatively to the built environment highlighting the future challenges involved in maintaining biodiversity within an increasingly urbanized world.
Tolerance to multiple climate stressors: a case study of Douglas‐fir drought and cold hardiness
Authors: Bansal Sheel , Harrington Constance A. , St. Clair John Bradley 
Published: February 2016

Summary

Drought and freeze events are two of the most common forms of climate extremes which result in tree damage or death, and the frequency and intensity of both stressors may increase with climate change. Few studies have examined natural covariation in stress tolerance traits to cope with multiple stressors among wild plant populations.

We assessed the capacity of coastal Douglas‐fir (Pseudotsuga menziesii var. menziesii), an ecologically and economically important species in the northwestern USA, to tolerate both drought and cold stress on 35 populations grown in common gardens. We used principal components analysis to combine drought and cold hardiness trait data into generalized stress hardiness traits to model geographic variation in hardiness as a function of climate across the Douglas‐fir range.

Drought and cold hardiness converged among populations along winter temperature gradients and diverged along summer precipitation gradients. Populations originating in regions with cold winters had relatively high tolerance to both drought and cold stress, which is likely due to overlapping adaptations for coping with winter desiccation. Populations from regions with dry summers had increased drought hardiness but reduced cold hardiness, suggesting a trade‐off in tolerance mechanisms.

Our findings highlight the necessity to look beyond bivariate trait–climate relationships and instead consider multiple traits and climate variables to effectively model and manage for the impacts of climate change on widespread species.
Tackling intraspecific genetic structure in distribution models better reflects species geographical range
Authors: Marcer Arnald , Méndez‐Vigo Belén , Alonso‐Blanco Carlos , Picó F. Xavier 
Published: February 2016

AbstractGenetic diversity provides insight into heterogeneous demographic and adaptive history across organisms’ distribution ranges. For this reason, decomposing single species into genetic units may represent a powerful tool to better understand biogeographical patterns as well as improve predictions of the effects of GCC (global climate change) on biodiversity loss. Using 279 georeferenced Iberian accessions, we used classes of three intraspecific genetic units of the annual plant Arabidopsis thaliana obtained from the genetic analyses of nuclear SNPs (single nucleotide polymorphisms), chloroplast SNPs, and the vernalization requirement for flowering. We used SDM (species distribution models), including climate, vegetation, and soil data, at the whole‐species and genetic‐unit levels. We compared model outputs for present environmental conditions and with a particularly severe GCC scenario. SDM accuracy was high for genetic units with smaller distribution ranges. Kernel density plots identified the environmental variables underpinning potential distribution ranges of genetic units. Combinations of environmental variables accounted for potential distribution ranges of genetic units, which shrank dramatically with GCC at almost all levels. Only two genetic clusters increased their potential distribution ranges with GCC. The application of SDM to intraspecific genetic units provides a detailed picture on the biogeographical patterns of distinct genetic groups based on different genetic criteria. Our approach also allowed us to pinpoint the genetic changes, in terms of genetic background and physiological requirements for flowering, that Iberian A. thaliana may experience with a GCC scenario applying SDM to intraspecific genetic units.
Resource quality affects weapon and testis size and the ability of these traits to respond to selection in the leaf‐footed cactus bug,Narnia femorata
Authors: Sasson Daniel A. , Munoz Patricio R. , Gezan Salvador A. , Miller Christine W. 
Published: February 2016

AbstractThe size of weapons and testes can be central to male reproductive success. Yet, the expression of these traits is often extremely variable. Studies are needed that take a more complete organism perspective, investigating the sources of variation in both traits simultaneously and using developmental conditions that mimic those in nature. In this study, we investigated the components of variation in weapon and testis sizes using the leaf‐footed cactus bug,Narnia femorata(Hemiptera: Coreidae) on three natural developmental diets. We show that the developmental diet has profound effects on both weapon and testis expression and scaling. Intriguingly, males in the medium‐quality diet express large weapons but have relatively tiny testes, suggesting complex allocation decisions. We also find that heritability, evolvability, and additive genetic variation are highest in the high‐quality diet for testis and body mass. This result suggests that these traits may have an enhanced ability to respond to selection during a small window of time each year when this diet is available. Taken together, these results illustrate that normal, seasonal fluctuations in the nutritional environment may play a large role in the expression of sexually selected traits and the ability of these traits to respond to selection.
Population‐level responses of life history traits to flow regime in three common stream fish species
Authors: Bennett Micah G. , Whiles Matt R. , Whitledge Gregory W. 
Published: February 2016

AbstractTrait‐based approaches may improve understanding in ecology by linking environmental variation to fitness‐related characteristics of species. Most trait–environment studies focus on assemblage‐level relationships; yet intraspecific trait variation is important for community, ecosystem, and evolutionary processes, and has substantial implications for these approaches. Assessing population‐level trait–environment relationships could test the generality of trait models whilst assessing intraspecific variation. We evaluated the generality of the trilateral life history model (TLHM opportunistic, periodic, and equilibrium endpoints) for fishes – a well‐studied trait–environment model at the assemblage level – to populations of three stream fishes in the Midwestern United States in relation to flow regime. The TLHM adequately described major trade‐offs in traits amongst populations in all species. Some TLHM flow‐based predictions were confirmed, with periodic traits (high fecundity) favoured at sites with greater flow seasonality and lower flow variability in two species, and equilibrium traits (large eggs) in more stable flow conditions in two species. Size at maturity was also inversely related to variability in one species. However, relationships contradicting the TLHM were also found. Coupled with the explanatory power of the TLHM for populations, supporting relationships suggest that synthesizing habitat template models with demographic life history theory could be valuable. Trait–environment models that are well‐supported at multiple levels of biological organization could improve understanding of the impacts of environmental change on populations and communities and the valuable ecosystem services that they support. Copyright © 2016 John Wiley & Sons, Ltd.
Rainfall‐triggered shallow landslides: infiltration dynamics in a physical hillslope model
Authors: Lora M. , Camporese M. , Troch P. A. , Salandin P. 
Published: February 2016

AbstractIn this study, we investigate the triggering of shallow landslides through the analysis of physical experiments performed in an artificial hillslope. The physical model consists of a reinforced concrete box containing a soil prism with maximum height of 3.5 m, length of 6 m, and width of 2 m. In order to analyse and examine the factors leading to the failure and the triggering modes, the hillslope is equipped with sensors to monitor the pore water pressure and moisture content response to rainfall in a 60 cm thick sand layer overlying a sandy clay soil. Two experiments were performed with different degrees of the sand initial compaction, to investigate the role of porosity on the hydrologic response and the subsequent failure. The experimental results showed that, with initially loose sand, the failure occurred suddenly, without premonitory signs, the soil behaving like a viscous fluid. The collected data showed a rapid increase of the water pressure contextual to the failure of the sand layer. In the second experiment, with initially dense sand, three levels of instability were observed: (i) abundant runoff with limited erosion of the ground surface; (ii) local slip detachments involving a soil thickness of few centimetres; and (iii) a slow advancement of the entire sand layer volume. The hydrologic dynamics observed in the landslide experiments were simulated with numerical solutions of the Richards equation. The results of the simulations agree well with the experiments for the loose sand, while for the dense sand the comparison between experimental and numerical results shows some limitations related to the assumptions of single phase and rigid soil matrix implicit in the Richards equation. Copyright © 2016 John Wiley & Sons, Ltd.
Modelling water, nutrients, and organic carbon in forested catchments: a HYPE application
Authors: Pers Charlotta , Temnerud Johan , Lindström Göran 
Published: February 2016

AbstractBoth monitoring and model simulation are useful for understanding and detecting changes in the environment. To understand and simulate leaching in small forested catchments, it is important to have knowledge of soil processes. Here, we describe recent development of the Hydrological Predictions for the Environment (HYPE) model for forested catchments. HYPE includes an organic carbon (OC) variable in addition to previously published nitrogen (N), phosphorus (P), and water flow models. The aspects addressed in the current study included P concentrations under low‐flow conditions and high concentrations of inorganic N. HYPE was further developed based on nine small forested catchments (0.5–200 ha) in Sweden, which were calibrated separately using local data. The model (excluding the OC variable) was tested on a larger set of forest catchments from the operational HYPE model of Sweden (S‐HYPE). We observed the following: (1) dissolved organic P could make a significant contribution to the total P concentration in a stream during low‐flow periods, (2) the inorganic N concentration simulated in a stream improved when part of the atmospheric N was retained in the soil, (3) the soil flow path formulation was critical for simulating concentration dynamics, and (4) evaluating an additional variable (OC) further elucidated the soil runoff processes in the model. Copyright © 2016 Swedish Meteorological and Hydrological Institute. Hydrological Processes published by John Wiley & Sons, Ltd.
MRI and histopathologic study of a novel cholesterol‐fed rabbit model of xanthogranuloma
Authors: Chen Yuanxin , Hamilton Amanda M. , Parkins Katie M. , Wang Jian‐Xiong , Rogers Kem A. , Zeineh Michael M. , Rutt Brian K. , Ronald John A. 
Published: February 2016

PurposeTo develop a rabbit model of xanthogranuloma based on supplementation of dietary cholesterol. The aim of this study was to analyze the xanthogranulomatous lesions using magnetic resonance imaging (MRI) and histological examination.Materials and MethodsRabbits were fed a low‐level cholesterol (CH) diet (n = 10) or normal chow (n = 5) for 24 months. In vivo brain imaging was performed on a 3T MR system using fast imaging employing steady state acquisition, susceptibility‐weighted imaging, spoiled gradient recalled, T1‐weighted inversion recovery imaging and T1 relaxometry, PD‐weighted and T2‐weighted spin‐echo imaging and T2 relaxometry, iterative decomposition of water and fat with echo asymmetry and least‐squares estimation, ultrashort TE MRI (UTE‐MRI), and
relaxometry. MR images were evaluated using a Likert scale for lesion presence and quantitative analysis of lesion size, ventricular volume, and T1, T2, and
values of lesions was performed. After imaging, brain specimens were examined using histological methods.ResultsIn vivo MRI revealed that 6 of 10 CH‐fed rabbits developed lesions in the choroid plexus. Region‐of‐interest analysis showed that for CH‐fed rabbits the mean lesion volume was 8.5 ± 2.6 mm3 and the volume of the lateral ventricle was significantly increased compared to controls (P < 0.01). The lesions showed significantly shorter mean T2 values (35 ± 12 msec, P < 0.001), longer mean T1 values (1581 ± 146 msec, P < 0.05), and shorter
values (22 ± 13 msec, P < 0.001) compared to adjacent brain structures. The ultrashort
components were visible using UTE‐MRI. Histopathologic evaluation of lesions demonstrated features of human xanthogranuloma.ConclusionRabbits fed a low‐level CH diet develop sizable intraventricular masses that have similar histopathological features as human xanthogranuloma. Multiparametric MRI techniques were able to provide information about the complex composition of these lesions. J. Magn. Reson. Imaging 2016;44:673–682.
Encapsulation of (−)‐epigallocatechin gallate into liposomes and into alginate or chitosan microparticles reinforced with liposomes
Authors: Istenič Katja , Cerc Korošec Romana , Poklar Ulrih Nataša 
Published: February 2016

AbstractBACKGROUND(−)‐Epigallocatechin gallate (EGCG) was encapsulated into liposomes that were further incorporated into alginate and chitosan microparticles. The stability of free and encapsulatedEGCGin all three systems was evaluated at differentpHvalues and in fruit nectar. Furthermore, the interactions betweenEGCGand the compounds of the microparticles were studied using Fourier transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC).RESULTSAll three encapsulation systems showed high encapsulation efficiency (>97%) and sustained release; in 14 days, no more than 15% ofEGCGwas released. The encapsulation systems successfully protectedEGCGagainst degradation at alkalinepH. For non‐encapsulatedEGCG, >70% was degraded after 14 days, while there was no significant degradation of encapsulatedEGCGin these three systems. In fruit nectar, >30% of non‐encapsulatedEGCGwas degraded in 14 days, while only 6% ofEGCGencapsulated into liposomes or chitosan microparticles reinforced with liposomes was degraded at that time. TheDSCandFTIRanalyses showed that the main interactions occurred between the liposomes and theEGCG.CONCLUSIONThis study demonstrates that liposomes as well as alginate and chitosan microparticles reinforced with liposomes have the potential to enhanceEGCGstability in food products during storage. © 2016 Society of Chemical Industry
Advances in genomics for the improvement of quality in coffee
Authors: Tran Hue TM , Lee L Slade , Furtado Agnelo , Smyth Heather , Henry Robert J 
Published: February 2016

AbstractCoffee is an important crop that provides a livelihood to millions of people living in developing countries. Production of genotypes with improved coffee quality attributes is a primary target of coffee genetic improvement programmes. Advances in genomics are providing new tools for analysis of coffee quality at the molecular level. The recent report of a genomic sequence for robusta coffee, Coffea canephora, is a major development. However, a reference genome sequence for the genetically more complex arabica coffee (C. arabica) will also be required to fully define the molecular determinants controlling quality in coffee produced from this high quality coffee species. Genes responsible for control of the levels of the major biochemical components in the coffee bean that are known to be important in determining coffee quality can now be identified by association analysis. However, the narrow genetic base of arabica coffee suggests that genomics analysis of the wild relatives of coffee (Coffea spp.) may be required to find the phenotypic diversity required for effective association genetic analysis. The genomic resources available for the study of coffee quality are described and the potential for the application of next generation sequencing and association genetic analysis to advance coffee quality research are explored. © 2016 Society of Chemical Industry