Search

Neutron dark-field imaging (DFI) was used to investigate the microstructure of additive manufactured steels. Several DFI methods were combined to assess the microstructure over more than two orders of magnitude in size. Different degrees of porosity and other building features were found depending on the parameters of the selective laser melting additive manufacturing process. A sample built with processing parameters yielding the lowest porosity was deformed which induced a phase transformation of the austenitic phase (fcc) into the martensitic phase (bcc). In the deformed sample an increased dark-field contrast was observed which can only be explained by accounting for the fcc-bcc phase distribution and the magnetic properties of the martensitic phase. We demonstrate that neutron dark-field imaging is well suited to not only detect build flaws like cracks but quantitatively characterize the microstructure in additive manufactured steels.

Saguinus inustus (Schwarz, 1951) is one of the neotropical primates least studied. The distribution of the species ranges from the north of the Solimões River, between the Negro and Japurá Rivers in Brazil, and Guayabero-Guaviare Rivers in Colombia. Nevertheless, due to the low number of specimens collected from the lower Japurá and lower Negro Rivers areas, the geographic distribution is so far poorly delineated. In this study, field data was composed of sightings and the collection of specimens during a survey of mammal diversity in the Amana Sustainable Development Reserve (ASDR). For this survey, two 40-day expeditions were carried out in 2004. The first one occurred during the flooded season in June and July, and the second was during the peak of the dry season in October. Direct sightings were made through hiking along transects, navigation along water channels with a 30-hp speedboat, and gliding along flooded trails in the forest. New records of S. inustus were made in 11 different localities in ASDR. The study has confirmed the presence of the species in the Amanã area, carrying out the first records of the species in flooded forest habitats.Saguinus inustus (Schwarz, 1951) é um dos primatas neotropicais menos estudados. No Brasil, a espécie ocorre ao norte do Rio Amazonas entre os Rios Negro e Japurá (Caquetá), e Guayabero-Guaviare na Colômbia. No entanto, devido ao pequeno número de espécimes coletados entre o baixo Japurá e o baixo Negro a distribuição geográfica é mal delineada. No presente estudo, os dados de campo são compostos por observações e coletas realizadas durante o levantamento da diversidade de mamíferos da Reserva de Desenvolvimento Sustentável Amanã (RDSA). Para este levantamento, duas expedições de 40 dias foram realizadas em 2004. A primeira ocorreu durante a estação da cheia em junho e julho, e a segunda durante o pico da estação seca em outubro. Observações diretas foram feitas através de deslocamentos a pé em transecções, de lancha 30 hp ao longo de cursos d'água, e de canoas durante a cheia na área de várzea. Novos registros de S. inustus foram realizados em 11 diferentes localidades na RDSA. Este estudo confirmou a presença da espécie em Amanã, realizando os primeiros registros da espécie em florestas alagadas.

Saguinus inustus (Schwarz, 1951) is one of the neotropical primates least studied. The distribution of the species ranges from the north of the Solimões River, between the Negro and Japurá Rivers in Brazil, and Guayabero-Guaviare Rivers in Colombia. Nevertheless, due to the low number of specimens collected from the lower Japurá and lower Negro Rivers areas, the geographic distribution is so far poorly delineated. In this study, field data was composed of sightings and the collection of specimens during a survey of mammal diversity in the Amana Sustainable Development Reserve (ASDR). For this survey, two 40-day expeditions were carried out in 2004. The first one occurred during the flooded season in June and July, and the second was during the peak of the dry season in October. Direct sightings were made through hiking along transects, navigation along water channels with a 30-hp speedboat, and gliding along flooded trails in the forest. New records of S. inustus were made in 11 different localities in ASDR. The study has confirmed the presence of the species in the Amanã area, carrying out the first records of the species in flooded forest habitats.

While neutron imaging is a well-established technique for investigations of inner structures and processes in materials, complex systems, and devices, the utilization of polarized neutron beams to visualize magnetic phenomena has been introduced only about a decade ago. In contrast to neutron scattering studies, where the interaction of the neutron’s magnetic moment with magnetic states of matter has been exploited for a long time, the direct visualization of magnetic fields in neutron imaging is a relatively new field and is still developing. Here, we give an overview of the status and provide approaches to visualizing magnetic fields with polarized neutrons, together with a report on the latest developments in attempting to record neutron tomographies for 3D reconstructions of magnetic vector fields. [ABSTRACT FROM AUTHOR]

Ungulates, large primates and caviomorfs are cited by Amazonian hunters as preferred species. In this research, paca (Cuniculus paca) hunting was investigated in relation to water levels and the lunar cycle. In eight years of monitoring in the Amanã Sustainable Development Reserve, the killing of 625 pacas was registered in five monitored communities. Paca hunting took place mainly at night and the most commonly used method is “spotlighting”. A positive correlation between the number of pacas killed and water level (rs=0.890; p

Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into the bald and black uakari groups, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of bald and black uakari populations. With this work we have explored the effects of the Amazon rainforest's dynamism on wild primates' genetics and increased the representation of platyrrhine genomes, thus opening the door to future research on the complexity and diversity of primate genomics., (© 2024. The Author(s).)

Saimiri cassiquiarensis cassiquiarensis (Cebidae) is a primate subspecies with a wide distribution in the Amazonian region of Brazil, Colombia, and Venezuela. However, the boundaries of its geographic range remain poorly defined. This study presents new occurrence localities for this subspecies and updates its distribution using a compiled data set of 140 occurrence records based on literature, specimens vouchered in scientific collections, and new field data to produce model-based range maps. After cleaning our data set, we updated the subspecies' extent of occurrence, which was used in model calibration. We then modeled the subspecies' range using a maximum entropy algorithm (MaxEnt). The final model was adjusted using a fixed threshold, and we revised this polygon based on known geographic barriers and parapatric congeneric ranges. Our findings indicate that this subspecies is strongly associated with lowland areas, with consistently high daily temperatures. We propose modifications to all range boundaries and estimate that 3% of the area of occupancy (AOO, as defined by IUCN) has already been lost due to deforestation, resulting in a current range of 224,469 km 2 . We also found that 54% of their AOO is currently covered by protected areas (PAs). Based on these results, we consider that this subspecies is currently properly classified as Least Concern, because it occupies an extensive range, which is relatively well covered by PAs, and is currently experiencing low rates of deforestation., (© 2024 Wiley Periodicals LLC.)

Noncoding DNA is central to our understanding of human gene regulation and complex diseases 1,2 , and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome 3-9 . Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA 10 , the relatively short timescales separating primate species 11 , and the previously limited availability of whole-genome sequences 12 . Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals., (© 2023. The Author(s).)

Neutron dark-field imaging is a powerful technique for investigating the microstructural properties of materials through high-resolution full-field mapping of small-angle scattering. However, conventional neutron dark-field imaging utilizing Talbot-Lau interferometers is limited to probing only one scattering direction at a time. Here, we introduce a novel multi-directional neutron dark-field imaging approach that utilizes a single absorption grating with a two-dimensional pattern to simultaneously probe multiple scattering directions. The method is demonstrated to successfully resolve fiber orientations in a carbon compound material as well as the complex morphology of the transformed martensitic phase in additively manufactured stainless steel dogbone samples after mechanical deformation. The latter results reveal a preferential alignment of transformed domains parallel to the load direction, which is verified by EBSD. The measured real-space correlation functions are in good agreement with those extracted from the EBSD map. Our results demonstrate that multi-directional neutron dark-field imaging is overcoming significant limitations of conventional neutron dark-field imaging in assessing complex heterogeneous anisotropic microstructures and providing quantitative structural information on multiple length scales., (© 2023. Springer Nature Limited.)

Polycystic Echinococcosis (PE), a neglected life-threatening zoonotic disease caused by the cestode Echinococcus vogeli, is endemic in the Amazon. Despite being treatable, PE reaches a case fatality rate of around 29% due to late or missed diagnosis. PE is sustained in Pan-Amazonia by a complex sylvatic cycle. The hunting of its infected intermediate hosts (especially the lowland paca Cuniculus paca ) enables the disease to further transmit to humans, when their viscera are improperly handled. In this study, we compiled a unique dataset of host occurrences (~86000 records) and disease infections (~400 cases) covering the entire Pan-Amazonia and employed different modeling and statistical tools to unveil the spatial distribution of PE's key animal hosts. Subsequently, we derived a set of ecological, environmental, climatic, and hunting covariates that potentially act as transmission risk factors and used them as predictors of two independent Maximum Entropy models, one for animal infections and one for human infections. Our findings indicate that temperature stability promotes the sylvatic circulation of the disease. Additionally, we show how El Niño-Southern Oscillation (ENSO) extreme events disrupt hunting patterns throughout Pan-Amazonia, ultimately affecting the probability of spillover. In a scenario where climate extremes are projected to intensify, climate change at regional level appears to be indirectly driving the spillover of E. vogeli . These results hold substantial implications for a wide range of zoonoses acquired at the wildlife-human interface for which transmission is related to the manipulation and consumption of wild meat, underscoring the pressing need for enhanced awareness and intervention strategies.

Objectives: The morphological features of the gastrointestinal tract (GIT) in mammals reflect a species' food niche breadth and dietary adaptations. For many wild mammals, the relationship between the structure of the GIT and diet is still poorly understood, for example, the GIT for frugivorous primates is usually classified as unspecialized and homogeneous. Here, we compare the GIT structure of 13 primate species from the three families of extant platyrrhines (Atelidae, Pitheciidae, and Cebidae) in Amazonia, and discuss possible evolutionary adaptations to different diets and trophic niches., Methods: We measured the length of the esophagus, stomach, small intestine, large intestine, cecum, colon, and rectum of the digestive tracts of 289 primate specimens. We determined the allometric relationships of the different tubular organs with the total length of the GIT as a proxy of specimen body size. Allometric parameters were used to establish the quotients of differentiation of every organ for each primate specimen., Results: There was a high differentiation in structure of the digestive organs among genera. Alouatta specimens clearly separated from the other genera based on dissimilarities in gastric, colonic, and rectal quotients, likely linked to the fermentation of plant contents. In contrast, all cebines (Sapajus, Cebus, and Saimiri) and Cacajao species had similar small intestine quotients, which is expected due to their high rates of animal matter consumed., Conclusions: We show that diverse adaptations in digestive structure exist among frugivorous primates, which in turn reflect different dietary patterns within this group that may enable the geographic coexistence of different primate species., (© 2023 The Authors. American Journal of Biological Anthropology published by Wiley Periodicals LLC.)

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.

Although the Amazon has the greatest diversity of primates, there are still taxonomic uncertainties for many taxa, such as the species of the Saguinus mystax group. The most geographically broadly distributed and phenotypically diverse species in this group is S . mystax , and its phenotypic diversity has been recognized as three subspecies- S . mystax mystax , S . mystax pileatus and S . mystax pluto -with non-overlapping geographic distributions. In this sense, we carried out an extensive field survey in their distribution areas and used a framework of taxonomic hypothesis testing of genomic data combined with an integrative taxonomic decision-making framework to carry out a taxonomic revision of S. mystax . Our tests supported the existence of three lineages/species. The first species corresponds to Saguinus mystax mystax from the left bank of the Juruá River, which was raised to the species level, and we also discovered and described animals from the Juruá-Tefé interfluve previously attributed to S . mystax mystax as a new species. The subspecies S . m . pileatus and S . m . pluto are recognized as a single species, under a new nomenclatural combination. However, given their phenotypic distinction and allopatric distribution, they potentially are a manifestation of an early stage of speciation, and therefore we maintain their subspecific designations., Competing Interests: Tomas Hrbek is an Academic Editor for PeerJ., (© 2023 Lopes et al.)

The study of fetal development allows for evaluating the different strategies adopted by mammal species to maximize neonatal survival. Autonomous locomotion is fundamental for newborns to perform foraging activities and increases newborn survival from predation. In this study, we assess the gestational bone development of 53 collared (CP, Pecari tajacu) and 61 white-lipped (WLP, Tayassu pecari) peccaries, collected through the collaboration of subsistence hunters in the Amazon. The bone mineralization and biometry of the axial and appendicular skeleton were assessed by ultrasound examinations, and the timing of the main bone developmental events was calculated in relation to the total dorsal length (TDL) and the percentage of the total gestational period (GP). The first US signs of mineralization of the axial skeleton in CP and WLP were observed in fetuses with 3.4 cm (42 gestation days, 30% GP CP ) and 5.1 cm (51 gestation days, 32% GP WLP ). The early development of the appendicular skeleton was observed by the synchronic appearance of the mineralized scapula, humerus, radius, ulna, ilium, ischium, femur, tibia, and fibula at 36% GP CP (50 gestation days), and 35% GP WLP (56 gestation days) . The pubis was mineralized in fetuses at 55% GP CP (75 gestation days) and 59% GP WLP (94 gestation days). The mineralization was observed in all autopod bones at 79% GP CP (109 gestation days) and 67% GP WLP (106 gestation days). All primary ossification centers in long bones of thoracic and pelvic limbs were mineralized in advanced fetuses (GP CP and GP WLP ≥75%). The mineralized patella was not observed in advanced fetuses in either species. Secondary ossification centers first appeared at the distal epiphysis of the femur in the CP (99 gestation days, 72% GP CP ) and the distal epiphysis of the radius, femur, and tibia in the WLP (106 gestation days, 67% GP WLP ). Advanced fetuses of CP and WLP presented 60% (15/25) and 68% (17/25) of the total secondary ossification centers observed present in the adult domestic pig, while newborns from the domestic pig presented 52% (13/25). The early intrauterine development of the skeletal system in both peccary species suggests a precocial development strategy, which likely correlates with neonatal ability to escape predators and reduces the dependence on parental care., (© 2022 Anatomical Society.)

Bald uakaris, genus Cacajao, are Amazonian primates currently classified as one species and four subspecies based on the patterns of pelage coloration. In this study, we test if their current taxonomy is represented by the phylogenetic relationship of the main lineages retrieved from molecular data. We included, for the first time, all bald uakari taxa in a mitochondrial (cytochrome b) and genome-wide (ddRAD) phylogenetic analyses. We also examined the pattern of pelage colouration in specimens from zoological collections. Having determined the number of lineages using Maximum Likelihood and the species tree using coalescent analyses, we test their divergence time using a Bayesian approach. While the cytochrome b analysis only recovered two clades, the ddRAD analysis supported the reciprocal monophyly of five lineages of bald uakaris, with all clades including only individuals with distinct and exclusive diagnostic phenotypic characters. We found that species diversification in Cacajao occurred during the last 300 Kya and may have been influenced by the formation of rivers and flooded forests in western Amazonia. We propose that the four bald uakari subspecies currently recognised can be upgraded to species level and we describe the white uakaris from the basin of the Rio Tarauacá as a new species., (Copyright © 2022 Elsevier Inc. All rights reserved.)

This study presents 35 negative serologies for antibodies anti-T. gondii in free-living primates from Central Amazonia. Our results suggest that these populations have not had contact with the parasite and, therefore, do not have antibodies. This was the first study surveying T. gondii in Cacajao, Callicebus, Pithecia, and Saguinus monkeys., (© 2022 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high-quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long-standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys (Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys (Alouatta spp.), uakaris (Cacajao spp.), sakis (Pithecia spp.), and robust capuchins (Sapajus spp.). Our results support a more nuanced, clade-specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines., (© 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Globally, community-based initiatives are effective in protecting ecosystems and the species within them. In this paper, we analyze the emergence and large-scale expansion of a community-based environmental protection system (the Voluntary Environmental Agents Program - VEA Program) in the Brazilian Amazon and identify factors that have determined its success since its inception, 25 years ago. Collective actions to protect the environment in the region have been undertaken by local people for at least 40 years, before their legal regulation in 2001 by the federal government of Brazil, and by the Amazonas state in 2007. The system is based on territorial surveillance and monitoring, and on guidelines for the better use of the territory and its natural resources. Between 1995 and 2020, the VEA Program expanded into the two protected areas where it was first implemented reaching approximately 9 thousand km 2 of area protected by the system. The number of people participating also grew in this period by around 2050%, as did the participation of women, which grew by 5600%. The system was replicated in 37 protected areas in central Amazonia, and currently covers almost 200 thousand km 2 of Amazon rainforest. From our analyses we unveil four main factors that may have allowed the VEA Program to expand and flourish: (a) the communities' previous demand for an effective control system, (b) its legal formalization and regulation, (c) the support from external institutions, and (d) the consolidation of community-based management programs to fund actions. These factors shall be further investigated as to confirm their critical role in the success of the VEA Program. We demonstrate that this community-based environmental protection system has established itself as a legitimate form of social control, and as a mechanism of socio-environmental governance in the areas in which it operates. By allowing more effective protection of territories, it generates consensus amongst users for the adequate management of natural resources, especially in contexts where government's actions are absent or inefficient. We claim that this system can be replicated in various parts of the world., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

In the past decade neutron dark-field contrast imaging has developed from a qualitative tool depicting microstructural inhomogeneities in bulk samples on a macroscopic scale of tens to hundreds of micrometers to a quantitative spatial resolved small-angle scattering instrument. While the direct macroscopic image resolution around tens of micrometers remains untouched microscopic structures have become assessable quantitatively from the nanometer to the micrometer range. Although it was found that magnetic structures provide remarkable contrast we could only recently introduce polarized neutron grating interferometric imaging. Here we present a polarized and polarization analyzed dark-field contrast method for spatially resolved small-angle scattering studies of magnetic microstructures. It is demonstrated how a polarization analyzer added to a polarized neutron grating interferometer does not disturb the interferometric measurements but allows to separate and measure spin-flip and non-spin-flip small-angle scattering and thus also the potential for a distinction of nuclear and different magnetic contributions in the analyzed small-angle scattering.

We have recently shown how a polarized beam in Talbot-Lau interferometric imaging can be used to analyze strong magnetic fields through the spin dependent differential phase effect at field gradients. While in that case an adiabatic spin coupling with the sample field is required, here we investigate a nonadiabatic coupling causing a spatial splitting of the neutron spin states with respect to the external magnetic field. This subsequently leads to no phase contrast signal but a loss of interferometer visibility referred to as dark-field contrast. We demonstrate how the implementation of spin analysis to the Talbot-Lau interferometer setup enables one to recover the differential phase induced to a single spin state. Thus, we show that the dark-field contrast is a measure of the quantum mechanical spin split analogous to the Stern-Gerlach experiment without, however, spatial beam separation. In addition, the spin analyzed dark-field contrast imaging introduced here bears the potential to probe polarization dependent small-angle scattering and thus magnetic microstructures.

Cheracebus is a new genus of New World primate of the family Pitheciidae, subfamily Callicebinae. Until recently, Cheracebus was classified as the torquatus species group of the genus Callicebus. The genus Cheracebus has six species: C. lucifer, C. lugens, C. regulus, C. medemi, C. torquatus, and C. purinus, which are all endemic to the Amazon biome. Before the present study, there had been no conclusive interpretation of the phylogenetic relationships among most of the Cheracebus species. The present study tests the monophyly of the genus and investigates the relationships among the different Cheracebus species, based on DNA sequencing of 16 mitochondrial and nuclear markers. The phylogenetic analyses were based on Maximum Likelihood, Bayesian Inference, and multispecies coalescent approaches. The divergence times and genetic distances between the Cheracebus taxa were also estimated. The analyses confirmed the monophyly of the genus and a well-supported topology, with the following arrangement: ((C. torquatus, C. lugens), (C. lucifer (C. purinus, C. regulus))). A well-differentiated clade was also identified within part of the geographic range of C. lugens, which warrants further investigation to confirm its taxonomic status., (© 2020 Wiley Periodicals LLC.)

Studying the timing of the main events of embryonic and fetal development may clarify the strategies adopted by species to maximize neonatal survival and the consequences of these events for their life history. This study describes bone development during the fetal phase of the lowland paca (Cuniculus paca), comparing it with other precocial or altricial species, and its relationship with the species' adaptive strategies. A total of 102 embryos/fetuses obtained over the course of 17 years through collaboration with local subsistence hunters in the Amazon were analyzed. Measurements of mineralization of the axial and appendicular skeletons were performed by ultrasonography using a 10-18-MHz linear transducer. The chronological order of occurrence of mineralization in relation to the total dorsal length (TDL) was: skull (TDL = 4.1 cm); vertebral bodies (TDL = 4.6 cm); scapula, humerus, radius, ulna, ilium, ischium, femur, tibia, and fibula (TDL = 6.7 cm); ribs (TDL = 7.8 cm); clavicle (TDL = 8.5 cm); metacarpi/metatarsi (TDL = 11 cm); phalanges (TDL = 15 cm); tarsus (TDL = 18 cm); patella (TDL = 23 cm); and carpus (TDL = 27.2 cm). Secondary ossification centers first appeared in the femoral distal epiphysis (TDL = 16.6 cm) and tibial proximal epiphysis (TDL = 18.4 cm). Advanced fetuses (TDL > 30 cm, 97% gestational period) presented mineralization in all primary and most secondary centers. Compared to other species, paca neonates have a well-developed skeletal system at birth, which is important for their independent postnatal locomotion. Our results may contribute to the monitoring of bone development in other wild species, helping us to understand their life history, and serving as parameters for comparisons between precocial and altricial mammals., (© 2020 Anatomical Society.)

The persistent high deforestation rate and fragmentation of the Amazon forests are the main threats to their biodiversity. To anticipate and mitigate these threats, it is important to understand and predict how species respond to the rapidly changing landscape. The short-eared dog Atelocynus microtis is the only Amazon-endemic canid and one of the most understudied wild dogs worldwide. We investigated short-eared dog habitat associations on two spatial scales. First, we used the largest record database ever compiled for short-eared dogs in combination with species distribution models to map species habitat suitability, estimate its distribution range and predict shifts in species distribution in response to predicted deforestation across the entire Amazon (regional scale). Second, we used systematic camera trap surveys and occupancy models to investigate how forest cover and forest fragmentation affect the space use of this species in the Southern Brazilian Amazon (local scale). Species distribution models suggested that the short-eared dog potentially occurs over an extensive and continuous area, through most of the Amazon region south of the Amazon River. However, approximately 30% of the short-eared dog's current distribution is expected to be lost or suffer sharp declines in habitat suitability by 2027 (within three generations) due to forest loss. This proportion might reach 40% of the species distribution in unprotected areas and exceed 60% in some interfluves (i.e. portions of land separated by large rivers) of the Amazon basin. Our local-scale analysis indicated that the presence of forest positively affected short-eared dog space use, while the density of forest edges had a negative effect. Beyond shedding light on the ecology of the short-eared dog and refining its distribution range, our results stress that forest loss poses a serious threat to the conservation of the species in a short time frame. Hence, we propose a re-assessment of the short-eared dog's current IUCN Red List status (Near Threatened) based on findings presented here. Our study exemplifies how data can be integrated across sources and modelling procedures to improve our knowledge of relatively understudied species., Competing Interests: The authors have declared that no competing interests exist., (© 2020 The Authors.)

The switch from hunting wild meat for home consumption to supplying more lucrative city markets in Amazonia can adversely affect some game species. Despite this, information on the amounts of wild meat eaten in Amazonian cities is still limited. We estimated wild meat consumption rates in 5 cities in the State of Amazonas in Brazil through 1046 door-to-door household interviews conducted from 2004 to 2012. With these data, we modeled the relationship between wild meat use and a selection of socioeconomic indices. We then scaled up our model to determine the amounts of wild meat likely to be consumed annually in the 62 urban centers in central Amazonia. A total of 80.3% of all interviewees reported consuming wild meat during an average of 29.3 (CI 11.6) days per year. Most wild meat was reported as bought in local markets (80.1%) or hunted by a family member (14.9%). Twenty-one taxa were cited as consumed, mostly mammals (71.6%), followed by reptiles (23.2%) and then birds (5.2%). The declared frequency of wild meat consumption was positively correlated with the proportion of rural population as well as with the per capita gross domestic product of the municipality (administrative divisions) where the cities were seated. We estimated that as much as 10,691 t of wild meat might be consumed annually in the 62 urban centers within central Amazonia, the equivalent of 6.49 kg per person per year. In monetary terms, this amounts to US$21.72 per person per year or US$35.1 million overall, the latter figure is comparable to fish and timber production in the region. Given this magnitude of wild meat trade in central Amazonia, it is fundamental to integrate this activity into the formal economy and actively develop policies that allow the trade of more resilient taxa and restrict trade in species sensitive to hunting., (© 2019 Society for Conservation Biology.)

Quantitative 2D neutron dark-field-imaging with neutron grating interferometry has been used to characterize structures in the size range below the imaging resolution. We present the first 3D quantitative neutron dark-field imaging experiment. We characterize sub-pixel structure sizes below the imaging resolution in tomography by quantitatively analyzing the change in dark-field contrast with varying neutron wavelength. This proof of principle experiment uses a dedicated reference sample with four different solutions of microspheres, each with a different diameter. The result is a 3D tomogram featuring a real space scattering function in each voxel. The presented experiment is expected to mark the path for future material science research through the individual quantification of small-angle scattering structures in each voxel of a volume of a bulk inhomogeneous sample material.

We demonstrate a simple single grating beam modulation technique, which enables the use of a highly intense neutron beam for differential phase and dark-field contrast imaging and thus spatially resolved structural correlation measurements in full analogy to interferometric methods. In contrast to these interferometric approaches our method is intrinsically achromatic and provides unprecedented flexibility in the choice of experimental parameters. In particular the method enables straight forward application of quantitative dark-field contrast imaging in time-of-flight mode at pulsed neutron sources. Utilizing merely a macroscopic absorption mask unparalleled length scales become accessible. We present results of quantitative dark-field contrast imaging combining microstructural small angle scattering analyses with real space imaging for a variety of materials.

We introduce the application of a symmetric Talbot-Lau neutron grating interferometer which provides a significantly extended autocorrelation length range essential for quantitative dark-field contrast imaging. The highly efficient set-up overcomes the limitation of the conventional Talbot-Lau technique to a severely limited micrometer range as well as the limitation of the other advanced dark-field imaging techniques in the nanometer regime. The novel set-up enables efficient and continuous dark-field contrast imaging providing quantitative small-angle neutron scattering information for structures in a regime from some tens of nanometers to several tens of micrometers. The quantitative analysis enabled in and by such an extended range is demonstrated through application to reference sample systems of the diluted polystyrene particle in aqueous solutions. Here we additionally demonstrate and successfully discuss the correction for incoherent scattering. This correction results to be necessary to achieve meaningful quantitative structural results. Furthermore, we present the measurements, data modelling and analysis of the two distinct kinds of cohesive powders enabled by the novel approach, revealing the significant structural differences of their fractal nature.

The intrinsic magnetic moment of a neutron, combined with its charge neutrality, is a unique property which allows the investigation of magnetic phenomena in matter. Here we present how the utilization of a cold polarized neutron beam in neutron grating interferometry enables the visualization and characterization of magnetic properties on a microscopic scale in macroscopic samples. The measured signal originates from the phase shift induced by the magnetic potential. Our method enables the detection of previously inaccessible magnetic field gradients, in the order of T cm -1 , extending the probed range by an order of magnitude. We visualize and quantify the phase shift induced by a well-defined square shaped uniaxial magnetic field and validate our experimental findings with theoretical calculations based on Hall probe measurements of the magnetic field distribution. This allows us to further extend our studies to investigations of inhomogeneous and anisotropic magnetic field distribution.

The red brocket deer (Mazama americana), a medium-sized Neotropical ungulate, is one of the most hunted mammals in the Amazon. This study analyzes the intrauterine development in the red brocket deer through the description of the external and internal morphology in one embryo and 38 fetuses collected from animals hunted for subsistence in the Amazon. The chronological order of occurrence of external characteristics in relation to the total dorsal length (TDL) was: differentiated genitalia, limbs and eyelid buds (TDL = 3.9 cm), fusioned eyelids, outer ear and hooves (TDL ≥ 9.5 cm), skin (TDL ≥ 20.4 cm), tactile pelage and nasal pigmentation (TDL ≥ 21.5 cm), covering pelage and skin spots (TDL ≥ 31.3 cm), and teeth eruption and opened eyelids (TDL ≥ 34.2 cm). The formula of fetal age was ∛W = 0.072 (t - 42), with a high linear relationship between TDL and gestational age. Multiple linear and non-linear regressions showed strong positive associations between biometric measures and absolute visceral weights with TDL. The relative weight of the tubular gastrointestinal organs, spleen and thymus increased during the fetal development; in contrast, the liver and kidneys' relative weight diminished during the fetal development. Advanced fetuses (≥44.0 cm TDL) had lower proportion of liver and larger tubular gastrointestinal organs within the visceral weight than adults. The chronology of appearance of the main events of the fetal development suggests that the red brocket deer adopt some precocial features, such as the early development of the sensorial function, including the early development of eyelids, outer ear and tactile pelage, the early development of the covering pelage which acts in thermoregulation and the early teeth eruption which allows the early foraging. Nevertheless, the precocial level of the red brocket deer is apparently lower than other species more frequently predated by large felids, such as peccaries and the paca., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Generation length (GL) of a mammal, calculated through the age at sexual maturity, first reproduction and reproductive senescence can be used to assess the capacity of a population of a species to withstand differing amounts of hunting pressure by humans without depletion of animal numbers. Due to the lack of reproductive data for wild mammals, the GL is often difficult to determine for most species. In the present study, the GL parameters were assessed for the wild lowland paca (Cuniculus paca) from a sample of 119 female genitalia obtained during a 15-year hunter participatory program in the Amazon. The probability of female pacas being sexually active, with observable ovarian functionality or pregnancy, increased as both body and genitalia masses increased. The average body mass at puberty was 5.46 kg. Puberty was estimated to occur at 4 months of age, from which there was estimation when age at first parturition would occur 9 months after birth. Additionally, there was no indication that there was a decrease in parturition rate at more advanced ages. The estimated age of first reproduction for pacas was much less than previous estimates, most from assessments of captive animals. In addition, because there was no evidence of reproductive senescence, it is suggested that the average age of mature hunted pacas should be used to determine optimal harvesting rates of pacas by humans. The present study highlights the importance of in situ studies on reproduction of animals in their natural habitat because these will yield more accurate reproductive variable estimates than those obtained from captive animals. It is suggested that similar methods be used to accurately assess reproductive parameters of other tropical species that are hunted by humans., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Structural properties of cohesive powders are dominated by their microstructural composition. Powders with a fractal microstructure show particularly interesting properties during compaction where a microstructural transition and a fractal breakdown happen before compaction and force transport. The study of this phenomenon has been challenging due to its long-range effect and the subsequent necessity to characterize these microstructural changes on a macroscopic scale. For the detailed investigation of the complex nature of powder compaction for various densification states along with the heterogeneous breakdown of the fractal microstructure we applied neutron dark-field imaging in combination with a variety of supporting techniques with various spatial resolutions, field-of-views and information depths. We used scanning electron microscopy to image the surface microstructure in a small field-of-view and X-ray tomography to image density variations in 3D with lower spatial resolution. Non-local spin-echo small-angle neutron scattering results are used to evaluate fitting models later used as input parameters for the neutron dark-field imaging data analysis. Finally, neutron dark-field imaging results in combination with supporting measurements using scanning electron microscopy, X-ray tomography and spin-echo small angle scattering allowed us to comprehensively study the heterogeneous transition from a fractal to a homogeneous microstructure of a cohesive powder in a quantitative manner.

The white-lipped peccary (Tayassu pecari) is an endangered large-sized Neotropical ungulate that is one of the most hunted mammals in the Amazon. Here, we used two embryos and 102 white-lipped peccary fetuses originated from animals hunted for subsistence in the Peruvian and Brazilian Amazon to describe the intrauterine development of external and internal morphology of this Neotropical ungulate. Logistic regressions were used to estimate the probability of occurrence of main external characteristics in relation to the total dorsal length (TDL), while multiple linear and non-linear regressions were conducted to assess the relationship between external and visceral biometry with TDL. External characteristics appeared in the following chronological order: limbs, differentiated genitalia and opened eyelids (≥5.1 cm TDL), fused eyelids (≥6.2 cm TDL), hooves and outer ear (≥7.9 cm TDL), dorsal gland (≥9.4 cm TDL), skin (≥11.5 cm TDL); tactile pelage (≥13.8 cm TDL), covering pelage (≥20.9 cm TDL), tooth eruption (≥26.4 cm TDL) and opened eyelids (≥27.8 cm TDL). The formula of fetal age was ∛W = 0.084 (t - 31.80), with a high linear relationship between TDL and gestational age. All external biometric parameters and absolute volume of visceral organs showed strong positive relationship with TDL. Except for the liver, we found differences in the relative volume of most visceral organs between advanced fetuses (≥34.2 cm TDL) and adults. The most important events during the intrauterine development in the white-lipped peccary show that, in contrast with the domestic pig, it is a highly precocial species producing newborns with a high fetal growth velocity which allows newborns to achieve an early autonomous functionality. Our results are relevant to improve imaging techniques and assist the reproductive and clinical management for the white-lipped peccary both in captivity and in the wild., (Copyright © 2018 Elsevier Inc. All rights reserved.)

The development of neutron imaging from a qualitative inspection tool towards a quantitative technique in materials science has increased the requirements for accuracy significantly. Quantifying the thickness or the density of polycrystalline samples with high accuracy using neutron imaging has two main problems: (i) the scattering from the sample creates artefacts on the image and (ii) there is a lack of specific reference attenuation coefficients. This work presents experimental and simulation results to explain and approach these problems. Firstly, a series of neutron radiography and tomography experiments of iron, copper and vanadium are performed and serve as a reference. These materials were selected because they attenuate neutrons mainly through coherent (Fe and Cu) and incoherent (V) scattering. Secondly, an ad hoc Monte Carlo model was developed, based on beamline, sample and detector parameters, in order to simulate experiments, understand the physics involved and interpret the experimental data. The model, developed in the McStas framework, uses a priori information about the sample geometry and crystalline structure, as well as beamline settings, such as spectrum, geometry and detector type. The validity of the simulations is then verified with experimental results for the two problems that motivated this work: (i) the scattering distribution in transmission imaging and (ii) the calculated attenuation coefficients.

In mammals, the embryonic and fetal development of a species has evolved to maximize neonatal survival. In this study, we use a sample of 132 embryos/fetuses of wild lowland paca (Cuniculus paca), obtained over a period of 15 years through collaborative methods with local hunters in the Amazon to describe the intrauterine development of external and internal morphology of this Neotropical rodent. We also compare the newborn survival strategy in this species with other rodents. The crown-rump length (CRL) ranged between 0.6 and 24.6 cm. External features appeared in the following chronological order: limbs, eyelid buds, fusioned eyelids, genitalia, outer ear, tactile pelage, claws, skin, skin spots, covering pelage, teeth and open eyelids. Fetuses with CRL >19.5 cm presented all external features fully developed. The growth formula of fetal age was calculated as ∛W = 0.082 (t - 37.25), and age was accurately associated with CRL. We described the relationship between CRL and external and internal biometry. The liver declined in proportion within the internal cavity, while the relative volume of tubular gastrointestinal organs increased significantly along the embryo/fetal development. All organs, except the heart and the thymus, had similar relative volumes in advanced fetuses and adults. Our comparison of the intrauterine development in several rodent species indicates that the paca's reproductive strategy is comparable to species that are subject to low natural predation. Given that C. paca is perhaps the most hunted animal in Latin America, sustainable hunting throughout its range must take into account its relative reproductive performance., (Copyright © 2017 Elsevier Inc. All rights reserved.)

We present a framework to estimate the fundamental statistical uncertainty of grating interferometer experiments based on a Monte-Carlo method. Using the framework, we are able to determine the uncertainty of individual measurements as well as suggesting experimental protocols that minimise the statistical uncertainty for given overall exposure times. The method presented here is valid for both X-rays and neutrons and can be generalised for any modulation measurement.

The performance of X-ray and neutron grating interferometers is characterised by their visibility, which is a measure for the maximum achievable contrast. In this study we show how the real grating geometry in a grating interferometer with three gratings impacts the interference and self projection that leads to visibility in the first place. We quantify the individual contributions of wavelength distributions and grating shapes in terms of visibility reduction by determining the absolute as well as relative effect of each contribution. The understanding of the impact of changed geometry and wavelength distributions on the interference of neutrons/X-rays allows us to present the first fully quantitative model of a grating interferometer setup. We demonstrate the capability of the simulation framework by building a model of the neutron grating interferometer at the ICON beamline and directly comparing simulated and measured visibility values. The general nature of the model makes it possible to extend it to any given grating interferometer for both X-rays and neutrons.

Ungulates, large primates and caviomorfs are cited by Amazonian hunters as preferred species. In this research, paca (Cuniculus paca) hunting was investigated in relation to water levels and the lunar cycle. In eight years of monitoring in the Amanã Sustainable Development Reserve, the killing of 625 pacas was registered in five monitored communities. Paca hunting took place mainly at night and the most commonly used method is "spotlighting". A positive correlation between the number of pacas killed and water level (rs=0.890; p<0.0001) was found. At least 37% of the pacas were hunted when moon illumination level was less than 10%, before moonrise or after moonset. In the Boa Esperança community, capture of paca tended to decrease on nights with high moon illumination (rs= -0.663; p=0.067). At the same time, an expressive catch-per-unity-effort decrease was also observed in this community (r2= -0.881; p<0.001), allowing us to predict unsustainable hunting levels for the next decade. The stock of animals in these areas could be continuously replaced if surrounding areas consisted of continuous forests. However, continuous hunting and deforestation force local hunters to travel longer distances to kill prey such as pacas. The confirmation of the relation between paca habits and lunar illumination and water level, a pattern described by local hunters, demonstrates the potential value of participatory research and the possibility of integrating traditional knowledge into scientific knowledge.

The black-faced black spider monkey (Ateles chamek) is endangered because of hunting and habitat loss. There are many gaps in our understanding of its geographic distribution. The Ucayali-Solimões-Amazon fluvial complex is currently recognized as the northern boundary of the species' range, although published reports have indicated that it occurs north of the Rio Solimões. In this study we investigate published records, generate new field records, and assess the current information concerning the northern boundary of this species' range. We conducted the study at the Mamirauá Sustainable Development Reserve in the central Brazilian Amazon, an area of 1,124,000 ha that consists entirely of Amazonian flooded forest (várzea). We collected data on the occurrence of the species from museum specimens and through field surveys, including interviews with local residents, direct observations, and the collection of new museum specimens. We confirmed the presence of A. chamek at 17 locations in the reserve, one of which was an island formed by a river bend cut-off that would have effectively taken any resident spider to the (new) north bank of the Solimões. We therefore conclude that fluvial dynamics were involved in creating the conditions for the dispersal and colonization of the species on the northern bank of the Rio Solimões. The data we present extends the known distribution of the species and increases its representation in protected areas.

The white bald uakari (Cacajao calvus calvus) is among the least studied of the Amazonian primates and is found exclusively in remote areas of the central Amazon. The geographic distribution of this subspecies is still uncertain, and information on current threats and its conservation status is sparse. In this paper, we identify new locations of occurrence and propose range expansion of the Cacajao calvus calvus. Between 2008 and 2010, six field expeditions were undertaken in the middle Solimões region to search for the subspecies and to conduct interviews with local residents regarding its presence. The presence of the white bald uakari was confirmed in the lower courses of the Juruá and lower Jutaí rivers, in addition to areas inside the Mamirauá Reserve, where its presence was expected. Results indicate an expansion and new limits on the geographic range of the subspecies, including its detection in areas in which it had not previously been reported and its exclusion from areas where white bald uakaris were assumed to occur. The new information provided by this study and the remaining shortcomings regarding the distribution of the calvus group point to the urgent need for further research on the geographic distribution and habitat use of this group, especially along the lower courses of the Juruá and Jutaí rivers, which remain little explored.

The histo-blood group ABH antigens were first described in humans. These antigens are only present on erythrocytes from great apes and humans, while in more primitive animals they are found in tissues and body fluids. The ABH antigens are mainly distributed in tissues exposed to the external environment and potentially serve as ligands for pathogens or inhibitors of tissue connections. The objective of this paper was two-fold: (i) to determine the presence of Helicobacter sp. in the gastric mucosa of 16 captive and 24 free-living New World monkeys and (ii) to evaluate the presence of histopathological alterations related to bacterial infection and the associated expression of ABH antigens in the tissue. Stomach tissues from 13 species of monkey were assessed using haematoxylin-eosin and modified Gram staining (Hucker) methods. An immunohistochemical analysis of the tissue revealed the presence of infectious bacteria that were characteristic of the genus Helicobacter sp. The results demonstrate that various species of monkey might be naturally infected with the Helicobacter sp. and that there is an increased susceptibility to infection. This study serves as a comparative analysis of infection between human and non-human primates and indicates the presence of a new species of Helicobacter.

Saguinus inustus (Schwarz, 1951) is one of the neotropical primates least studied. The distribution of the species ranges from the north of the Solimões River, between the Negro and Japurá Rivers in Brazil, and Guayabero-Guaviare Rivers in Colombia. Nevertheless, due to the low number of specimens collected from the lower Japurá and lower Negro Rivers areas, the geographic distribution is so far poorly delineated. In this study, field data was composed of sightings and the collection of specimens during a survey of mammal diversity in the Amana Sustainable Development Reserve (ASDR). For this survey, two 40-day expeditions were carried out in 2004. The first one occurred during the flooded season in June and July, and the second was during the peak of the dry season in October. Direct sightings were made through hiking along transects, navigation along water channels with a 30-hp speedboat, and gliding along flooded trails in the forest. New records of S. inustus were made in 11 different localities in ASDR. The study has confirmed the presence of the species in the Amanã area, carrying out the first records of the species in flooded forest habitats.

1. River system dynamics results in ecological heterogeneities that play a central role in maintaining biodiversity in riverine regions. In central Amazonia, large expanses of forest are seasonally flooded by nutrient-rich water (várzea forests) or by nutrient-poor water (igapó forests). Inundation patterns and the nutrient load of floodwaters are perhaps the most important abiotic factors determining spatial ecological variations in lowland Amazonia, and so they are expected to strongly influence the structuring of animal communities. 2. We examined how inundation patterns and water-nutrient load influence the structure of neotropical assemblages of bats, one of the most diverse vertebrate groups in tropical forests. Bat assemblages were sampled with mist nets in central Brazilian Amazonia, across a mosaic of várzea, igapó, and non-flooding nutrient-poor terra firme forests in the low- and high-water seasons. 3. An ordination analysis clearly separated the assemblages of the three forest types, demonstrating the structural relevance of both flooding and floodwater-nutrient load. Flooded forests had lower species richness because of the absence or rarity of species that make roosts out of leaves of understorey plants, and of those that feed on fruits of shrubs. Gleaning insectivores, also partly dependent on the understorey, were less abundant in flooded forests, but aerial insectivores more abundant, presumably because they benefited from a less cluttered foraging environment. These differences suggest that flooding affects bat assemblages mostly because it reduces the availability of niches associated with understorey vegetation, which tends to be sparser in flooded forests. 4. Nutrient-rich várzea forests had a bat biomass twice that of nutrient-poor igapó and unflooded forests. This difference was not only mostly due to a greater overall abundance of bats, but also attributable to a disproportionate higher abundance of large-bodied bat species. 5. We concluded that both flooding and floodwater-nutrient load are very important in the structuring of lowland Amazonian bat assemblages, with inundation mostly constraining the species composition of the assemblages, and water-nutrient load mostly influencing the abundance of species. The distinctiveness of bat assemblages associated with flooding emphasizes the need to preserve inundated forests, which are under particular pressure in Amazonia.