The Hierarchy-of-Hypotheses Approach: A Synthesis Method for Enhancing Theory Development in Ecology and Evolution.

In the current era of Big Data, existing synthesis tools such as formal meta-analyses are critical means to handle the deluge of information. However, there is a need for complementary tools that help to (a) organize evidence, (b) organize theory, and (c) closely connect evidence to theory. We present the hierarchy-of-hypotheses (HoH) approach to address these issues. In an HoH, hypotheses are conceptually and visually structured in a hierarchically nested way where the lower branches can be directly connected to empirical results. Used for organizing evidence, this tool allows researchers to conceptually connect empirical results derived through diverse approaches and to reveal under which circumstances hypotheses are applicable. Used for organizing theory, it allows researchers to uncover mechanistic components of hypotheses and previously neglected conceptual connections. In the present article, we offer guidance on how to build an HoH, provide examples from population and evolutionary biology and propose terminological clarifications.

Urban Hedgehog Behavioural Responses to Temporary Habitat Disturbance versus Permanent Fragmentation.

Anthropogenic activities can result in both transient and permanent changes in the environment. We studied spatial and temporal behavioural responses of European hedgehogs (Erinaceus europaeus) to a transient (open-air music festival) and a permanent (highly fragmented area) disturbance in the city of Berlin, Germany. Activity, foraging and movement patterns were observed in two distinct areas in 2016 and 2017 using a "Before & After" and "Control & Impact" study design. Confronted with a music festival, hedgehogs substantially changed their movement behaviour and nesting patterns and decreased the rhythmic synchronization (DFC) of their activity patterns with the environment. These findings suggest that a music festival is a substantial stressor influencing the trade-off between foraging and risk avoidance. Hedgehogs in a highly fragmented area used larger home ranges and moved faster than in low-fragmented and low-disturbed areas. They also showed behaviours and high DFCs similar to individuals in low-fragmented, low disturbed environment, suggesting that fragmentation posed a moderate challenge which they could accommodate. The acute but transient disturbance of a music festival, therefore, had more substantial and severe behavioural effects than the permanent disturbance through fragmentation. Our results are relevant for the welfare and conservation measure of urban wildlife and highlight the importance of allowing wildlife to avoid urban music festivals by facilitating avoidance behaviours.

Individual dietary specialization in a generalist predator: A stable isotope analysis of urban and rural red foxes.

Some carnivores are known to survive well in urban habitats, yet the underlying behavioral tactics are poorly understood. One likely explanation for the success in urban habitats might be that carnivores are generalist consumers. However, urban populations of carnivores could as well consist of specialist feeders. Here, we compared the isotopic specialization of red foxes in urban and rural environments, using both a population and an individual level perspective. We measured stable isotope ratios in increments of red fox whiskers and potential food sources. Our results reveal that red foxes have a broad isotopic dietary niche and a large variation in resource use. Despite this large variation, we found significant differences between the variance of the urban and rural population for δ13C as well as δ15N values, suggesting a habitat-specific foraging behavior. Although urban regions are more heterogeneous regarding land cover (based on the Shannon index) than rural regions, the dietary range of urban foxes was smaller compared with that of rural conspecifics. Moreover, the higher δ13C values and lower δ15N values of urban foxes suggest a relatively high input of anthropogenic food sources. The diet of most individuals remained largely constant over a longer period. The low intraindividual variability of urban and rural red foxes suggests a relatively constant proportion of food items consumed by individuals. Urban and rural foxes utilized a small proportion of the potentially available isotopic dietary niche as indicated by the low within-individual variation compared to the between-individual variation. We conclude that generalist fox populations consist of individual food specialists in urban and rural populations at least over those periods covered by our study.

Circadian rhythms enable efficient resource selection in a human-modified landscape.

Animals access resources such as food and shelter, and acquiring these resources has varying risks and benefits, depending on the suitability of the landscape. Some animals change their patterns of resource selection in space and time to optimize the trade-off between risks and benefits. We examine the circadian variation in resource selection of swamp wallabies (Wallabia bicolor) within a human-modified landscape, an environment of varying suitability. We used GPS data from 48 swamp wallabies to compare the use of landscape features such as woodland and scrub, housing estates, farmland, coastal areas, wetlands, waterbodies, and roads to their availability using generalized linear mixed models. We investigated which features were selected by wallabies and determined whether the distance to different landscape features changed, depending on the time of the day. During the day, wallabies were more likely to be found within or near natural landscape features such as woodlands and scrub, wetlands, and coastal vegetation, while avoiding landscape features that may be perceived as more risky (roads, housing, waterbodies, and farmland), but those features were selected more at night. Finally, we mapped our results to predict habitat suitability for swamp wallabies in human-modified landscapes. We showed that wallabies living in a human-modified landscape selected different landscape features during day or night. Changing circadian patterns of resource selection might enhance the persistence of species in landscapes where resources are fragmented and disturbed.

Inflammatory Potential of Four Different Phases of Calcium Pyrophosphate Relies on NF-κB Activation and MAPK Pathways.

Background: Calcium pyrophosphate (CPP) microcrystal deposition is associated with wide clinical phenotypes, including acute and chronic arthritis, that are interleukin 1ß (IL-1ß)-driven. Two CPP microcrystals, namely monoclinic and triclinic CPP dihydrates (m- and t-CPPD), have been identified in human tissues in different proportions according to clinical features. m-CPP tetrahydrate beta (m-CPPTß) and amorphous CPP (a-CPP) phases are considered as m- and t-CPPD crystal precursors in vitro. Objectives: We aimed to decipher the inflammatory properties of the three crystalline phases and one amorphous CPP phase and the intracellular pathways involved. Methods: The four synthesized CPP phases and monosodium urate crystals (MSU, as a control) were used in vitro to stimulate the human monocytic leukemia THP-1 cell line or bone marrow-derived macrophages (BMDM) isolated from WT or NLRP3 KO mice. The gene expression of pro- and anti-inflammatory cytokines was evaluated by quantitative PCR; IL-1ß, IL-6 and IL-8 production by ELISA; and mitogen-activated protein kinase (MAPK) activation by immunoblot analysis. NF-κB activation was determined in THP-1 cells containing a reporter plasmid. In vivo, the inflammatory potential of CPP phases was assessed with the murine air pouch model via cell analysis and production of IL-1ß and CXCL1 in the exudate. The role of NF-κB was determined by a pharmacological approach, both in vivo and in vitro. Results:In vitro, IL-1ß production induced by m- and t-CPPD and m-CPPTß crystals was NLRP3 inflammasome dependent. m-CPPD crystals were the most inflammatory by inducing a faster and higher production and gene expression of IL-1ß, IL-6, and IL-8 than t-CPPD, m-CPPTß and MSU crystals. The a-CPP phase did not show an inflammatory property. Accordingly, m-CPPD crystals led to stronger activation of NF-κB, p38, extracellular signal-regulated kinase 1/2 (ERK1/2) and c-Jun N-terminal kinase (JNK) MAPKs. Inhibition of NF-κB completely abrogated IL-1ß and IL-8 synthesis and secretion induced by all CPP crystals. Also, inhibition of JNK and ERK1/2 MAPKs decreased both IL-1ß secretion and NF-κB activation induced by CPP crystals. In vivo, IL-1ß and CXCL1 production and neutrophil infiltration induced by m-CPPD crystals were greatly decreased by NF-κB inhibitor treatment. Conclusion: Our results suggest that the inflammatory potential of different CPP crystals relies on their ability to activate the MAPK-dependent NF-κB pathway. Studies are ongoing to investigate the underlying mechanisms.

Pushing the limits of sensitivity and resolution for natural abundance 43Ca NMR using ultra-high magnetic field (35.2 T).

Natural abundance 43Ca solid state NMR experiments are reported for the first time at ultra-high magnetic field (35.2 T) on a series of Ca-(pyro)phosphate and Ca-oxalate materials, which are of biological relevance in relation to biomineralization processes and the formation of pathological calcifications. The significant gain in both sensitivity and resolution at 35.2 T leads to unprecedented insight into the structure of both crystalline and amorphous phases.

Wild inside: Urban wild boar select natural, not anthropogenic food resources.

Most wildlife species are urban avoiders, but some became urban utilizers and dwellers successfully living in cities. Often, they are assumed to be attracted into urban areas by easily accessible and highly energetic anthropogenic food sources. We macroscopically analysed stomachs of 247 wild boar (Sus scrofa, hereafter WB) from urban areas of Berlin and from the surrounding rural areas. From the stomach contents we determined as predictors of food quality modulus of fineness (MOF,), percentage of acid insoluble ash (AIA) and macronutrients such as amount of energy and percentage of protein, fat, fibre and starch. We run linear mixed models to test: (1) differences in the proportion of landscape variables, (2) differences of nutrients consumed in urban vs. rural WB and (3) the impact of landscape variables on gathered nutrients. We found only few cases of anthropogenic food in the qualitative macroscopic analysis. We categorized the WB into five stomach content categories but found no significant difference in the frequency of those categories between urban and rural WB. The amount of energy was higher in stomachs of urban WB than in rural WB. The analysis of landscape variables revealed that the energy of urban WB increased with increasing percentage of sealing, while an increased human density resulted in poor food quality for urban and rural WB. Although the percentage of protein decreased in areas with a high percentage of coniferous forests, the food quality increased. High percentage of grassland decreased the percentage of consumed fat and starch and increased the percentage of fibre, while a high percentage of agricultural areas increased the percentage of consumed starch. Anthropogenic food such as garbage might serve as fallback food when access to natural resources is limited. We infer that urban WB forage abundant, natural resources in urban areas. Urban WB might use anthropogenic resources (e.g. garbage) if those are easier to exploit and more abundant than natural resources. This study shows that access to natural resources still is mandatory and drives the amount of protein, starch, fat or fibre in wild boar stomachs in urban as well as rural environments.

Biomineralization of a titanium-modified hydroxyapatite semiconductor on conductive wool fibers.

Metal ions are frequently incorporated into crystalline materials to improve their electrochemical properties and to confer new physicochemical properties. Naturally-occurring phosphate apatite, which is formed geologically and in biomineralization processes, has extensive potential applications and is therefore an attractive functional material. In this study, we generate a novel building block for flexible optoelectronics using bio-inspired methods to deposit a layer of photoactive titanium-modified hydroxyapatite (TiHA) nanoparticles (NPs) on conductive polypyrrole(PPy)-coated wool yarns. The titanium concentration in the reaction solution was varied between 8-50 mol% with respect to the phosphorous, which led to titanate ions replacing phosphate in the hydroxyapatite lattice at levels up to 17 mol%. PPy was separately deposited on wool yarns by oxidative polymerization, using two dopants: (i) anthraquinone-2,6-disulfonic acid to increase the conductivity of the PPy layer and (ii) pyroglutamic acid, to reduce the resistivity of the wool yarns and to promote the heterogeneous nucleation of the TiHA NPs. A specific titanium concentration (25 mol% wrt P) was used to endow the TiHA NPs on the PPy-coated fibers with a desirable band gap value of 3.68 eV, and a specific surface area of 146 m2 g-1. This is the first time that a thin film of a wide-band gap semiconductor has been deposited on natural fibers to create a fiber-based building block that can be used to manufacture flexible electronic devices.

Development of a new family of monolithic calcium (pyro)phosphate glasses by soft chemistry.

UNLABELLED: The development of bioactive phosphate-based glasses is essential in biomaterials science, and especially for bone substitution applications. In this context, the preparation of amorphous calcium-phosphorus hydroxide/oxide monoliths at low temperature is a key challenge for being able to develop novel hybrid materials for these applications. We herein report for the first time the synthesis and physical chemical characterisation of a novel family of pyrophosphate-based glasses (with the formula: {[(Ca(2+))1-x(H(+)/K(+))2x]2[(P2O7(4-))1-y(PO4(3-))4y/3]} n(H2O)), which were prepared by soft chemistry using low temperatures (T<70°C) and water as a solvent. The effect of the initial Ca/Pyrophosphate ratio on the structure and morphology of these pyrophosphate glasses was investigated in detail. Depending on this ratio, a glass (mixed calcium pyro- and orthophosphate) or a glass-ceramic (Ca10K4(P2O7)6·9H2O crystals embedded in the amorphous phase) was obtained. The proportion of the crystalline phase increased with an increase in the Ca/Pyrophosphate ratio in the batch solution. As expected for a glass, the formation of the glassy material was demonstrated not to be thermodynamically but rather kinetically driven, and the washing step was found to be crucial to prevent crystallisation. The stability of the amorphous phase was discussed considering the structural degrees of freedom of pyrophosphate entities, ionic strength of the initial solution and the inhibitory effect of orthophosphate ions. Overall, this new strategy of preparation of monolithic calcium-(pyro)phosphate based glasses using soft chemistry in water is highly promising in view of preparing new functional organic-inorganic hybrids for bone substitution applications. STATEMENT OF SIGNIFICANCE: Phosphate-based glasses have gradually emerged as a potential alternative to silicate bioactive glasses in order to induce different biological mechanisms of degradation. The synthesis of such monolithic glasses at low temperature is a key step to allow new inorganic glass compositions to be reached and hybrid materials to be prepared. Although sol-gel and coacervate methods (respectively orthophosphate and metaphosphate precursors) have already been described to prepare such glasses, the use of toxic solvents and/or the final temperature treatment associated to these processes could limit the use of these materials for biomedical applications and/or the further development of hybrids. It is shown here that pyrophosphate precursors are an alternative strategy to obtain monolithic calcium (pyro)phosphate glasses under soft conditions (water solvent, 70°C).

Crystal structure of monoclinic calcium pyrophosphate dihydrate (m-CPPD) involved in inflammatory reactions and osteoarthritis.

Pure monoclinic calcium pyrophosphate dihydrate (m-CPPD) has been synthesized and characterized by synchrotron powder X-ray diffraction and neutron diffraction. Rietveld refinement of complementary diffraction data has, for the first time, allowed the crystal structure of m-CPPD to be solved. The monoclinic system P2(1)/n was confirmed and unit-cell parameters determined: a = 12.60842 (4), b = 9.24278 (4), c = 6.74885 (2) Å and ß = 104.9916 (3)°. Neutron diffraction data especially have allowed the precise determination of the position of H atoms in the structure. The relationship between the m-CPPD crystal structure and that of the triclinic calcium pyrophosphate dihydrate (t-CPPD) phase as well as other pyrophosphate phases involving other divalent cations are discussed by considering the inflammatory potential of these phases and/or their involvement in different diseases. These original structural data represent a key step in the understanding of the mechanisms of crystal formation involved in different types of arthritis and to improve early detection of calcium pyrophosphate (CPP) phases in vivo.

From crystalline to amorphous calcium pyrophosphates: A solid state Nuclear Magnetic Resonance perspective.

Hydrated calcium pyrophosphates (CPP, Ca2P2O7·nH2O) are a fundamental family of materials among osteoarticular pathologic calcifications. In this contribution, a comprehensive multinuclear NMR (Nuclear Magnetic Resonance) study of four crystalline and two amorphous phases of this family is presented. (1)H, (31)P and (43)Ca MAS (Magic Angle Spinning) NMR spectra were recorded, leading to informative fingerprints characterizing each compound. In particular, different (1)H and (43)Ca solid state NMR signatures were observed for the amorphous phases, depending on the synthetic procedure used. The NMR parameters of the crystalline phases were determined using the GIPAW (Gauge Including Projected Augmented Wave) DFT approach, based on first-principles calculations. In some cases, relaxed structures were found to improve the agreement between experimental and calculated values, demonstrating the importance of proton positions and pyrophosphate local geometry in this particular NMR crystallography approach. Such calculations serve as a basis for the future ab initio modeling of the amorphous CPP phases. STATEMENT OF SIGNIFICANCE: The general concept of NMR crystallography is applied to the detailed study of calcium pyrophosphates (CPP), whether hydrated or not, and whether crystalline or amorphous. CPP are a fundamental family of materials among osteoarticular pathologic calcifications. Their prevalence increases with age, impacting on 17.5% of the population after the age of 80. They are frequently involved or associated with acute articular arthritis such as pseudogout. Current treatments are mainly directed at relieving the symptoms of joint inflammation but not at inhibiting CPP formation nor at dissolving these crystals. The combination of advanced NMR techniques, modeling and DFT based calculation of NMR parameters allows new original insights in the detailed structural description of this important class of biomaterials.

Feeding behavior and aggression in wild Siberut macaques (Macaca siberu) living under low predation risk.

Investigating which factors influence feeding competition is crucial for our understanding of the diversity of social relationships. Socio-ecological models differ in their predictions whether predation risk directly influences feeding competition and which factors exactly predict contest competition. We investigated feeding competition in Siberut macaques (Macaca siberu), a species endemic to Siberut Island (West Sumatra, Indonesia). Siberut macaques experience low predation risk, as major predators (felids, raptors) are absent. They are therefore appropriate subjects to test the prediction that low predation risk reduces feeding competition. To estimate contest potential, we quantified size, spatial distribution and density of food plants, and the availability of alternative resources. We recorded behavior in food patches using a modified focal tree method. Food patches, sorted by decreasing average feeding group size, included large trees (40% of focal plant observations), lianas/strangler (16%), medium trees (9%), small (palm) trees (20%), and rattan (15%). Most food patches were clumped but occurred at low densities relative to the area of average group spread. Thus, availability of alternative food patches was low. Although food patch characteristics indicate high contest potential, the observed aggression rate (0.13 bouts between adults/h) was low relative to other primates. Average feeding group size was small relative to total group size, and feeding group size matched crown volume. Perceived predation risk was low, based on spatial and feeding behavior of juveniles. Together, these results suggest that predation risk may influence feeding competition. Social and temporal factors (patch feeding time), but not ecological factors (fruit abundance in patch and forest, alternative resources) predicted aggression frequency in food patches. Overall, comparative data are still relatively scarce, and researchers should collect more data on group spread, sub-grouping, perceived predation risk, and aggression in food patches before we can draw final conclusions about the role of predation risk for feeding competition.

Structure of the calcium pyrophosphate monohydrate phase (Ca2P2O7·H2O): towards understanding the dehydration process in calcium pyrophosphate hydrates.

Calcium pyrophosphate hydrate (CPP, Ca(2)P(2)O(7) · nH2O) and calcium orthophosphate compounds (including apatite, octacalcium phosphate etc.) are among the most prevalent pathological calcifications in joints. Even though only two dihydrated forms of CPP (CPPD) have been detected in vivo (monoclinic and triclinic CPPD), investigations of other hydrated forms such as tetrahydrated or amorphous CPP are relevant to a further understanding of the physicochemistry of those phases of biological interest. The synthesis of single crystals of calcium pyrophosphate monohydrate (CPPM; Ca(2)P(2)O(7) · H2O) by diffusion in silica gel at ambient temperature and the structural analysis of this phase are reported in this paper. Complementarily, data from synchrotron X-ray diffraction on a CPPM powder sample have been fitted to the crystal parameters. Finally, the relationship between the resolved structure for the CPPM phase and the structure of the tetrahydrated calcium pyrophosphate ß phase (CPPT-ß) is discussed.

Interaction between a bisphosphonate, tiludronate, and biomimetic nanocrystalline apatites.

Bisphosphonates (BPs) are well established as successful antiresorptive agents for the prevention and treatment of bone diseases such as osteoporosis and Paget's disease. The aim of this work was to clarify the reaction mechanisms between a BP molecule, tiludronate, and the nanocrystalline apatite surface. The adsorption of tiludronate on well-characterized synthetic biomimetic nanocrystalline apatites with homogeneous but different compositions and surface characteristics was investigated to determine the effect of the nanocrystalline apatite substrate on the adsorption behavior. The results show that the adsorption of tiludronate on nanocrystalline biomimetic apatite surfaces varies over a large range. The most immature apatitic samples exhibited the highest affinity and the greatest amount adsorbed at saturation. Maturation of the nanocrystals induces a decrease of these values. The amount of phosphate ion released per adsorbed BP molecule varied, depending on the nanocrystalline substrate considered. The adsorption mechanism, although associated with a release of phosphate ions, cannot be considered as a simple ion exchange process involving one or two phosphate ions on the surface. A two-step process is proposed consisting of a surface binding of BP groups to calcium ions associated with a proton release inducing the protonation of surface orthophosphate ions and their eventual solubilization.