This collection is where we will collate faculty and staff collections listed alphabetically by surname.

Displaying 1 - 10 of 2645
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Cyclical nursing patterns in wild orangutans

Description

Nursing behavior is notoriously difficult to study in arboreal primates, particularly when offspring suckle inconspicuously in nests. Orangutans have the most prolonged nursing period of any mammal, with the cessation

Nursing behavior is notoriously difficult to study in arboreal primates, particularly when offspring suckle inconspicuously in nests. Orangutans have the most prolonged nursing period of any mammal, with the cessation of suckling (weaning) estimated to occur at 6 to 8 years of age in the wild. Milk consumption is hypothesized to be relatively constant over this period, but direct evidence is limited. We previously demonstrated that trace element analysis of bioavailable elements from milk, such as barium, provides accurate estimates of early-life diet transitions and developmental stress when coupled with growth lines in the teeth of humans and nonhuman primates. We provide the first detailed nursing histories of wild, unprovisioned orangutans (Pongo abelii and Pongo pygmaeus) using chemical and histological analyses. Laser ablation inductively coupled plasma mass spectrometry was used to determine barium distributions across the teeth of four wild-shot individuals aged from postnatal biological rhythms. Barium levels rose during the first year of life in all individuals and began to decline shortly after, consistent with behavioral observations of intensive nursing followed by solid food supplementation. Subsequent barium levels show large sustained fluctuations on an approximately annual basis. These patterns appear to be due to cycles of varying milk consumption, continuing until death in an 8.8-year-old Sumatran individual. A female Bornean orangutan ceased suckling at 8.1 years of age. These individuals exceed the maximum weaning age reported for any nonhuman primate. Orangutan nursing may reflect cycles of infant demand that relate to fluctuating resource availability.

Contributors

Agent

Created

Date Created
2017-05-17

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Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand

Description

The Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal

The Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combining the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs.

Contributors

Agent

Created

Date Created
2017-05-17

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Conversing with a devil’s advocate: Interpersonal coordination in deception and disagreement

Description

This study investigates the presence of dynamical patterns of interpersonal coordination in extended deceptive conversations across multimodal channels of behavior. Using a novel "devil’s advocate" paradigm, we experimentally elicited deception

This study investigates the presence of dynamical patterns of interpersonal coordination in extended deceptive conversations across multimodal channels of behavior. Using a novel "devil’s advocate" paradigm, we experimentally elicited deception and truth across topics in which conversational partners either agreed or disagreed, and where one partner was surreptitiously asked to argue an opinion opposite of what he or she really believed. We focus on interpersonal coordination as an emergent behavioral signal that captures interdependencies between conversational partners, both as the coupling of head movements over the span of milliseconds, measured via a windowed lagged cross correlation (WLCC) technique, and more global temporal dependencies across speech rate, using cross recurrence quantification analysis (CRQA). Moreover, we considered how interpersonal coordination might be shaped by strategic, adaptive conversational goals associated with deception. We found that deceptive conversations displayed more structured speech rate and higher head movement coordination, the latter with a peak in deceptive disagreement conversations. Together the results allow us to posit an adaptive account, whereby interpersonal coordination is not beholden to any single functional explanation, but can strategically adapt to diverse conversational demands.

Contributors

Agent

Created

Date Created
2017-06-02

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Communication and Inference of Intended Movement Direction during Human–Human Physical Interaction

Description

Of particular interest to the neuroscience and robotics communities is the understanding of how two humans could physically collaborate to perform motor tasks such as holding a tool or moving

Of particular interest to the neuroscience and robotics communities is the understanding of how two humans could physically collaborate to perform motor tasks such as holding a tool or moving it across locations. When two humans physically interact with each other, sensory consequences and motor outcomes are not entirely predictable as they also depend on the other agent’s actions. The sensory mechanisms involved in physical interactions are not well understood. The present study was designed (1) to quantify human–human physical interactions where one agent (“follower”) has to infer the intended or imagined—but not executed—direction of motion of another agent (“leader”) and (2) to reveal the underlying strategies used by the dyad. This study also aimed at verifying the extent to which visual feedback (VF) is necessary for communicating intended movement direction. We found that the control of leader on the relationship between force and motion was a critical factor in conveying his/her intended movement direction to the follower regardless of VF of the grasped handle or the arms. Interestingly, the dyad’s ability to communicate and infer movement direction with significant accuracy improved (>83%) after a relatively short amount of practice. These results indicate that the relationship between force and motion (interpreting as arm impedance modulation) may represent an important means for communicating intended movement direction between biological agents, as indicated by the modulation of this relationship to intended direction. Ongoing work is investigating the application of the present findings to optimize communication of high-level movement goals during physical interactions between biological and non-biological agents.

Created

Date Created
2017-04-13

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Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome

Description

Plastids are supported by a wide range of proteins encoded within the nucleus and imported from the cytoplasm. These plastid-targeted proteins may originate from the endosymbiont, the host, or other

Plastids are supported by a wide range of proteins encoded within the nucleus and imported from the cytoplasm. These plastid-targeted proteins may originate from the endosymbiont, the host, or other sources entirely. Here, we identify and characterise 770 plastid-targeted proteins that are conserved across the ochrophytes, a major group of algae including diatoms, pelagophytes and kelps, that possess plastids derived from red algae. We show that the ancestral ochrophyte plastid proteome was an evolutionary chimera, with 25% of its phylogenetically tractable nucleus-encoded proteins deriving from green algae. We additionally show that functional mixing of host and plastid proteomes, such as through dual-targeting, is an ancestral feature of plastid evolution. Finally, we detect a clear phylogenetic signal from one ochrophyte subgroup, the lineage containing pelagophytes and dictyochophytes, in plastid-targeted proteins from another major algal lineage, the haptophytes. This may represent a possible serial endosymbiosis event deep in eukaryotic evolutionary history.

Contributors

Agent

Created

Date Created
2017-05-12

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Chemosensory sensitivity reflects reproductive status in the ant Harpegnathos saltator

Description

Insects communicate with pheromones using sensitive antennal sensilla. Although trace amounts of pheromones can be detected by many insects, context-dependent increased costs of high sensitivity might lead to plasticity in

Insects communicate with pheromones using sensitive antennal sensilla. Although trace amounts of pheromones can be detected by many insects, context-dependent increased costs of high sensitivity might lead to plasticity in sensillum responsiveness. We have functionally characterized basiconic sensilla of the ant Harpegnathos saltator for responses to general odors in comparison to cuticular hydrocarbons which can act as fertility signals emitted by the principal reproductive(s) of a colony to inhibit reproduction by worker colony members. When released from inhibition workers may become reproductive gamergates. We observed plasticity in olfactory sensitivity after transition to reproductive status with significant reductions in electrophysiological responses to several long-chained cuticular hydrocarbons. Although gamergates lived on average five times longer than non-reproductive workers, the shift to reproductive status rather than age differences matched the pattern of changes in olfactory sensitivity. Decreasing sensillum responsiveness to cuticular hydrocarbons could potentially reduce mutually inhibitory or self-inhibitory effects on gamergate reproduction.

Contributors

Agent

Created

Date Created
2017-06-16

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The Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species

Description

Agassiz’s desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for

Agassiz’s desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.

Contributors

Agent

Created

Date Created
2017-05-31

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Gang truce for violence prevention, El Salvador

Description

Objective To estimate the effects on homicide rates of the gang truce that was brokered in El Salvador in 2012.
Methods Mathematical models based on municipal-level census, crime and gang-intelligence

Objective To estimate the effects on homicide rates of the gang truce that was brokered in El Salvador in 2012.
Methods Mathematical models based on municipal-level census, crime and gang-intelligence data were used to estimate the effect of the truce on homicide rates. One model estimated the overall effect after accounting for the linear trend and seasonality in the homicide rate. In a moderated-effect model, we investigated the relationship between the truce effect and the numbers of MS13 (Mara Salvatrucha 13) and Eighteenth-Street gang members imprisoned per 100 000 population. We then ran each of these two models with additional control variables. We compared values before the truce – 1 January 2010 to 29 February 2012 – with those after the truce – 1 March 2012 to 31 December 2013.
Findings The overall-effect models with and without additional control variables indicated a homicide rate after the truce that was significantly lower than the value before the truce, giving rate ratios of 0.55 (95% confidence interval, CI: 0.49–0.63) and 0.61 (95% CI: 0.54–0.69), respectively. For any given municipality, the effectiveness of the truce appeared to increase as the number of MS13 gang members imprisoned per 100 000 population increased. We did not observe the same significant relationship for imprisoned Eighteenth-Street gang members.
Conclusion In the 22 months following the establishment of a national gang truce, the homicide rate was about 40% lower than in the preceding 26 months. The truce’s impact appeared particularly strong in municipalities with relatively high numbers of imprisoned MS13 gang members per 100 000 population.

Contributors

Agent

Created

Date Created
2016-06-01

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Principles of cooperation across systems: from human sharing to multicellularity and cancer

Description

From cells to societies, several general principles arise again and again that facilitate cooperation and suppress conflict. In this study, I describe three general principles of cooperation and how they

From cells to societies, several general principles arise again and again that facilitate cooperation and suppress conflict. In this study, I describe three general principles of cooperation and how they operate across systems including human sharing, cooperation in animal and insect societies and the massively large-scale cooperation that occurs in our multicellular bodies. The first principle is that of Walk Away: that cooperation is enhanced when individuals can leave uncooperative partners. The second principle is that resource sharing is often based on the need of the recipient (i.e., need-based transfers) rather than on strict account-keeping. And the last principle is that effective scaling up of cooperation requires increasingly sophisticated and costly cheater suppression mechanisms. By comparing how these principles operate across systems, we can better understand the constraints on cooperation. This can facilitate the discovery of novel ways to enhance cooperation and suppress cheating in its many forms, from social exploitation to cancer.

Created

Date Created
2015-10-17

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Predicted rarity-weighted richness, a new tool to prioritize sites for species representation

Description

Lack of biodiversity data is a major impediment to prioritizing sites for species representation. Because comprehensive species data are not available in any planning area, planners often use surrogates (such

Lack of biodiversity data is a major impediment to prioritizing sites for species representation. Because comprehensive species data are not available in any planning area, planners often use surrogates (such as vegetation communities, or mapped occurrences of a well-inventoried taxon) to prioritize sites. We propose and demonstrate the effectiveness of predicted rarity-weighted richness (PRWR) as a surrogate in situations where species inventories may be available for a portion of the planning area. Use of PRWR as a surrogate involves several steps. First, rarity-weighted richness (RWR) is calculated from species inventories for a q% subset of sites. Then random forest models are used to model RWR as a function of freely available environmental variables for that q% subset. This function is then used to calculate PRWR for all sites (including those for which no species inventories are available), and PRWR is used to prioritize all sites. We tested PRWR on plant and bird datasets, using the species accumulation index to measure efficiency of PRWR. Sites with the highest PRWR represented species with median efficiency of 56% (range 32%–77% across six datasets) when q = 20%, and with median efficiency of 39% (range 20%–63%) when q = 10%. An efficiency of 56% means that selecting sites in order of PRWR rank was 56% as effective as having full knowledge of species distributions in PRWR's ability to improve on the number of species represented in the same number of randomly selected sites. Our results suggest that PRWR may be able to help prioritize sites to represent species if a planner has species inventories for 10%–20% of the sites in the planning area.

Contributors

Agent

Created

Date Created
2016-10-27