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opencc-by-nc-sa-4.0Dec 2018View details →

Macaca mulatta and Macaca fascicularis anatomical and functional MRI data

The ION dataset includes anatomical, field map, and fMRI data from 8 monkeys: 4 Macaca mulatta and 4 Macaca fascicularis. The data is provided both as a directory structure compressed as <code>all_the_data.zip</code>, and as individual files. The correspondence between the directory structure and the individual files is contained in the file <code>tree.json</code>. The bash command <code>source unflatten.sh</code> can be used to convert the individual files into the original directory structure. Scanner Specifications <ul> <li>Siemens Tim Trio 3T whole-body scanner with or without head-only gradient insert (Siemens AC88)</li> <li>8-channel phased-array transceiver coils</li> <li>Optimization of the magnetic field prior to data acquisition: Manual shimming</li> </ul> Sample Description <ul> <li>Sample size: 8</li> <li>Age distribution: 3.80-5.99 years</li> <li>Weight distribution: 5.0-10.2 kg</li> <li>Sex distribution: 7 male, 1 female</li> </ul> Click <a href="http://fcon_1000.projects.nitrc.org/indi/PRIME/files/ion.csv">here</a> for the full sample description (.csv download) Scan Procedures and Parameters Ethics approval: All experimental procedures for nonhuman primate research were approved by the Institutional Animal Care and Use Committee in the Institute of Neuroscience and by the Biomedical Research Ethics Committee, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and conformed to National Institutes of Health guidelines for the humane care and use of laboratory animals. Animal care and housing: Animals were housed in single cage Any applicable training: none Scanning preparations Anesthesia procedures: Anesthesia of the animals was inducted with an intramuscular injection of a cocktail of dexmedetomidine (18 - 30 µg/kg) and midazolam (0.2 - 0.3 mg/kg), supplemented with atropine sulfate (0.05 mg/kg). After intubation, anesthesia was maintained using the lowest possible concentration of isoflurane gas via a MRI-compatible ventilator. Time between anesthesia and scanning: Scanning lasted about 1.5 hours after induction. Head fixation: Custom-built MRI-compatible stereotaxic frame Position in scanner and procedure used: Sphinx position Contrast agent: none During scanning Physiological monitoring: Physiological parameters including blood oxygenation, ECG, rectal temperature, respiration rate and end-tidal CO2 were monitored. Oxygen saturation was kept over 95%. Additional procedures: Animals were ventilated by a MRI-compatible ventilator. Body temperature was kept constant using hot water blanket. Scan sequences <ul> <li>Resting-state: <ul> <li>Gradient-echo EPI</li> <li>TR: 2000ms</li> <li>TE: 29ms</li> <li>Flip angle: 77°</li> <li>Field of view: 96 x 96 mm</li> <li>In plane resolution: 1.5 x 1.5 mm</li> <li>Slices number: 32</li> <li>Slice thickness: 2.5mm</li> <li>GRAPPA factor: 2</li> <li>Measurements: 200</li> <li>Slice direction: Coronal slice</li> </ul> </li> <li>Structural: <ul> <li>T1 MPRAGE Sequence</li> <li>Voxel resolution: 0.5 x 0.5 x 0.5 mm</li> <li>TE: 3.12ms</li> <li>TR: 2500ms</li> <li>TI: 1100ms</li> <li>Flip angle: 9°</li> <li>Slice direction: 44 sagittal slices</li> <li>Number of averages: 2</li> </ul> </li> <li>Additional: <ul> <li>Field map: a pair of gradient echo images</li> <li>TE1: 4.22ms</li> <li>TE2: 6.68ms</li> <li>Orientation and resolution: same as resting-state images</li> <li>Intended for EPI distortion correction</li> </ul> </li> </ul> Publications <ul> <li>Lv, Q., Yang, L., Li, G., Wang, Z., Shen, Z., Yu, W., Jiang, Q., Hou, B., Pu, J., Hu, H., & Wang, Z. (2016). Large-Scale Persistent Network Reconfiguration Induced by Ketamine in Anesthetized Monkeys: Relevance to Mood Disorders. Biological Psychiatry, 79(9), 765–775. <a href="https://doi.org/10.1016/j.biopsych.2015.02.028">https://doi.org/10.1016/j.biopsych.2015.02.028</a></li> </ul> Personnel Zheng Wang1 1Institute of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China Acknowledgements The authors thank Drs. Lawrence Wald, Ravi Menon, John Gore, Franz Schmitt, Renate Jerecic, Thomas Benner, Kecheng Liu, Ignacio Vallines, and Hui Liu for their generous help and contribution to the construction of our custom-tuned gradient-insert (AC88) 3T MRI facility for nonhuman primate subjects. Funding <ul> <li>Hundred Talent Program of Chinese Academy of Sciences (Technology) (Zheng Wang)</li> <li>Chinese 973 Program (2011CBA00400)</li> <li>The “Strategic Priority Research Program (B) of the Chinese Academy of Sciences (XDB02030004)</li> <li>The Outstanding Youth Grant (Hailan Hu)</li> </ul> Detailed information can be found at <a href="http://fcon_1000.projects.nitrc.org/indi/PRIME/ion.html">http://fcon_1000.projects.nitrc.org/indi/PRIME/ion.html</a>. Citation  <ul> <li>Wang, Z. (2019). Macaca mulatta and Macaca fascicularis anatomical and functional MRI data [Data set]. Zenodo. <a href="https://doi.org/10.5281/ZENODO.3402112">https://doi.org/10.5281/ZENODO.3402112</a>.</li> <li>Milham, M. P., Ai, L., Koo, B., Xu, T., Amiez, C., Balezeau, F., … Schroeder, C. E. (2018). An Open Resource for Non-human Primate Imaging. Neuron, 100(1), 61–74.e2. <a href="https://doi.org/10.1016/j.neuron.2018.08.039">https://doi.org/10.1016/j.neuron.2018.08.039</a>.</li> </ul>

Fig. 6 in Gastro-intestinal parasites of urban rhesus macaques (Macaca mulatta) in the Kathmandu Valley, Nepal

Fig. 6. The prevalence of parasites is examined in relation to a) location and b) season. Multicolor triangles and circles in the plots represent individual data points (triangles) and centroid of each specific grouping factor (circle).

Fig. 3 in Gastro-intestinal parasites of urban rhesus macaques (Macaca mulatta) in the Kathmandu Valley, Nepal

Fig. 3. Photomicrographs of various GI parasites of the rhesus macaques at 400×: Trophozoite of E. histolytica (A), Cyst of E. histolytica (B), Cyst of E. coli (C), Cyst of Iodomoeba butschlii (D), Cyst of Giardia spp. (E), Trophozoite of Balantioides coli (F), Cyst of Balantioides coli (G), Egg of Trichuris spp. (H), Egg of Strongyloides spp. (I), Larva of Strongyloides spp. (J), Egg of Hookworm (K), Egg of Trichostrongylus spp. (L), Egg of Ascarid spp. (M), Egg of Physaloptera spp. (N), Egg of Toxocara spp.(O), Egg of Toxocara spp. (P), Egg of Strongyle spp. (Q), Egg of Strongyle spp.(R), Oocyst of Cryptosporidium spp. (S), Unknown spp. 1 (T).

Fig. 1 in Gastro-intestinal parasites of urban rhesus macaques (Macaca mulatta) in the Kathmandu Valley, Nepal

Fig. 1. Map showing the four fecal collection sites of the urban rhesus macaques in the Kathmandu Valley.

opencc-by-4.0Aug 2022View details →

Fig. 3 in Prevalence and new genotypes of Enterocytozoon bieneusi in wild rhesus macaque (Macaca mulatta) in China: A zoonotic concern

Fig. 3. Sequence variation in the ITS region of the rRNA gene of Enterocytozoon bieneusi isolates from rhesus macaque. The ITS sequences of 5 known genotypes (D, PL9, CAF4, EbpC, and SCC-2) and 8 novel genotypes (Mul6 to 13) identified in this study, were aligned with each other. The dots and transverse lines indicate base identities and deletions, respectively, relative to the ITS sequence of genotype D.

opencc-by-4.0Aug 2022View details →

Fig. 2. Phylogenetic relationship among the Enterocytozoon bieneusi groups. The relationship between the E in Prevalence and new genotypes of Enterocytozoon bieneusi in wild rhesus macaque (Macaca mulatta) in China: A zoonotic concern

Fig. 2. Phylogenetic relationship among the Enterocytozoon bieneusi groups. The relationship between the E. bieneusi genotypes identified in this study and other known genotypes deposited in GenBank was inferred by neighbor-joining analysis of ITS sequences based on genetic distance using the Kimura-2-parameter model. The numbers on the branches represent percent bootstrapping values from 1000 replicates, with more than 50% shown in the tree. Each sequence is identified by its accession number, genotype designation, and host origin. Genotypes marked with black dot are identified in this study.

opencc-by-4.0Aug 2023View details →

Results of the differential gene expression analysis in SIV infection in Chlorocebus sabaeus and Macaca mulatta

Results of differential gene expression analysis in SIV infection in Chlorocebus sabaeus and Macaca mulatta. From the transcriptome data repository MACE (http://mace.ihes.fr)

opencc-zeroNov 2023View details →

Data from: Hair and plasma cortisol throughout the first three years of development in infant rhesus macaques, Macaca mulatta

Cortisol expression has been demonstrated to have variation across development in rhesus macaques (Macaca mulatta). There exists contradictory evidence for the nature of this change, and age at which it occurs, across biological sample types. Consequently, we lack a cohesive understanding for cortisol concentrations across the development of a major human health translational model. We examined hair cortisol concentrations over the first three years of life for 49 mother-reared infant macaques from mixed-sex outdoor units at the California National Primate Research Center. For 48 of these subjects at infancy, one year, and two years, we obtained plasma cortisol samples for: response to a stressor, adjustment to prolonged stress, and response to dexamethasone injection. Hair cortisol concentrations decreased dramatically between three and ten months, followed by relative stability up to the final sampling event at around 34 months of age. Plasma cortisol showed within-year consistency, and consistency between infancy and year one. We document variability in the infant plasma cortisol samples, especially in percent change between samples one and two. Our plasma cortisol results indicate that infants possess the physiological capacity to effectively inhibit the release of cortisol when stimulated, as effectively as later responses in juveniles. Age-related changes in hair cortisol parallel findings indicating a large decline in the weeks following postparturation.

opencc-zeroJan 2024View details →

Data from: Social stability via management of natal males in captive rhesus macaques (Macaca mulatta)

Keystone individuals are expected to disproportionately contribute to group stability. For instance, rhesus macaques (Macaca mulatta) who police conflict contribute towards stability. Not all individuals' motivations align with mechanisms of group stability. In wild systems, males typically disperse at maturity and attempt to ascend via contest competition. In a captive system, dispersal is not naturally enabled – individuals attempt to ascend in their natal groups, which can be enabled by matrilineal kin potentially destabilizing group dynamics. We relocated select high-ranking natal males from five groups and assessed group stability before and after. We quantified hierarchical metrics at the individual and group level. After removal, we found significantly higher aggression against the established hierarchy (reversals), indicative of opportunistic attempts to change the hierarchy. Mixed-sex social signaling became more hierarchical, but the strength of this effect varied. Stable structure was not uniformly reached across the groups and alpha males did not all benefit. Indiscriminate natal male removal is an unreliable solution to group instability. Careful assessment of how natal males are embedded within their group is necessary to balance individual and group welfare.

opencc-zeroApr 2022View details →

Data from: Sensitivity to line-of sight in tolerant versus despotic macaques (Macaca sylvanus and Macaca mulatta)

Complex social life is considered important to the evolution of cognition in primates. One key aspect of primate social interactions concerns the degree of competition that individuals face in their social group. To examine how social tolerance versus competition shapes social cognition, we experimentally assessed capacities for flexible gaze-following in more tolerant Barbary macaques (Macaca sylvanus) and compared to previous data from despotic rhesus macaques (Macaca mulatta). Monkeys experienced one of two possible conditions. In the barrier condition, they observed an actor look upwards into an overheard barrier, so they could not directly see the target of the actor's gaze without reorienting. In the no barrier condition, they observed an actor look upwards without a barrier blocking her line-of-sight, so they could observe the target of the actor's gaze by also looking upwards. Both species (N = 58 Barbary macaques, 64 rhesus macaques) could flexibly modulate their gaze responses to account for the demonstrator's line of sight, looking up more often when no barrier was present, and this flexible modulation declined with age in both species. However, neither species preferentially approached to look inside the barrier when their view of the target location was obscured, although rhesus macaques approached more overall. This pattern suggests that both tolerant and despotic macaques exhibit similar capacities to track other's line of sight and do not preferentially reorient their bodies to observe what an actor looks at in this situation. This contrasts with other work indicating that competitive primates are especially adept at some aspects of theory of mind. Thus, it is important to understand both the similarities and differences in the social–cognitive abilities of primates with different social styles.

opencc-zeroOct 2022View details →

Greater variability in rhesus macaque (Macaca mulatta) endocranial volume among males than females

The greater male variability (GMV) hypothesis proposes that traits are more variable among males than females, and is supported by numerous empirical studies. Interestingly, GMV is also observed for human brain size and internal brain structure, a pattern which may have implications for sex-biased neurological and psychiatric conditions. A better understanding of neuroanatomical variability in nonhuman primates may illuminate whether certain species are appropriate models for these conditions. Here, we tested for sex differences in the variability of endocranial volume (ECV, a proxy for brain size) in a sample 542 rhesus macaques (Macaca mulatta) from a large pedigreed free-ranging population. We also examined the components of phenotypic variance (additive genetic and residual variance) to tease apart the potential drivers of sex differences in variability. Our results suggest that males exhibit more variable ECVs, and that this pattern reflects either balancing/disruptive selection on male behaviour (associated with alternative male mating strategies) or sex chromosome effects (associated with mosaic patterns of X chromosome gene expression in females), rather than extended neurodevelopment among males. This represents evidence of GMV for brain size in a nonhuman primate species and highlights the potential of rhesus macaques as a model for sex-biased brain-based disorders.

opencc-zeroJul 2024View details →

Data from: Individual differences in sociocognitive traits in semi-free-ranging rhesus monkeys (Macaca mulatta)

Characterizing individual differences in cognition is crucial for understanding the evolution of cognition as well as to test the biological consequences of different cognitive traits. Here, we harnessed the strengths of a uniquely large, naturally-living primate population at the Cayo Santiago Biological Field Station to characterized individual differences in rhesus monkey performance across two social cognitive tasks. A total of n = 204 semi-free-ranging adult rhesus monkeys participated in a data collection procedure, where we aimed to test individuals on both tasks at two time-points that were one year apart. In the socioemotional responses task, we assessed monkeys' attention to conspecific photographs with neutral versus negative emotional expressions. We found that monkeys showed overall declines in interest in conspecific photographs with age, but relative increases in attention to threat stimuli specifically, and further that these responses exhibited long-term stability across repeated testing. In the gaze following task we assessed monkeys' propensity to co-orient with an experimenter. Here, we found no evidence for age-related change in responses, and responses showed only limited repeatability over time. Finally, we found some evidence for common individual variation for performance across the tasks: monkeys that showed greater interest in conspecific photographs were more likely to follow a human's gaze. These results show how studies of comparative cognitive development and aging can provide insights into the evolution of cognition, and identify core primate social cognitive traits that may be related across and within individuals.

Fig. 2 in Gastro-intestinal parasites of urban rhesus macaques (Macaca mulatta) in the Kathmandu Valley, Nepal

Fig. 2. Prevalence of gastro-intestinal parasites in the rhesus macaques of Kathmandu Valley.

Fig. 4 in Gastro-intestinal parasites of urban rhesus macaques (Macaca mulatta) in the Kathmandu Valley, Nepal

Fig. 4. Location-wise richness of parasitic infection in rhesus macaques of the Kathmandu Valley.

Fig. 5 in Gastro-intestinal parasites of urban rhesus macaques (Macaca mulatta) in the Kathmandu Valley, Nepal

Fig. 5. Species Richness of GI parasite infection in rhesus macaques of the Kathmandu Valley.

opencc-by-4.0Aug 2022View details →

Fig. 1 in Prevalence and new genotypes of Enterocytozoon bieneusi in wild rhesus macaque (Macaca mulatta) in China: A zoonotic concern

Fig. 1. Specific locations at which specimens were collected in this study.

publicJan 2024View details →

Repeatability of measures of biobehavioral organization over two years in captive infant rhesus macaques, Macaca mulatta

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publicMay 2025View details →

Vocal membranes lower the phonation threshold pressure in rhesus macaques (Macaca mulatta)

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publicOct 2022View details →

Greater variability in rhesus macaque (Macaca mulatta) endocranial volume among males than females

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